Array 1 86-1084 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000016.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ================================== =========================================================== ================== 86 34 100.0 39 .................................. GCGCGAATTGTCCCTCACGTGCTTTCATCCACGCCACAA 159 34 100.0 38 .................................. GCTCGGCCAGAGCCGCCGCCCAGCTGGCCGCCGACCAG 231 34 79.4 59 ...........................NNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGTAGCAATCACACAGAGACTTTGCAAGC 324 34 100.0 38 .................................. GCCAGGCTTCGATCCAGGCATCCCAGATCGTCGGGCAG 396 34 100.0 39 .................................. GCCGTCATCAACCCTGCCGACTACCAGTCGATCCGTCTG 469 34 82.4 39 ............................NNNNNN NNNNTAGGACTCGATCCCCCTCCATGCGTGACGCGTTAC 542 34 82.4 39 ............................NNNNNN NNNNTGGCTCGTGATCGCGCTATCACTACCGGCGCCTAT 615 34 100.0 38 .................................. GCCGCGCCACGTGGCAGGTGGTCGGCACTGATTGGAAG 687 34 82.4 37 ............................NNNNNN NNNNACGTGATGGTGGCATTCGCGTGGATCGCCTGCG 758 34 100.0 38 .................................. GCGGGGTCCAGACGGCACCGACGGGCTCCACGAGCAGG 830 34 100.0 39 .................................. GCGATGGGGCTGGCCATCATTCTGCACCGTTTATGACAC 903 34 82.4 41 ............................NNNNNN NNNNGTCGGCGCGCTTCGGCCTGGTGCTGCCTCTGCGGGTG 978 34 100.0 39 .................................. GCTCGGCATGATGCCAGCGCCGATTATCGTGAGCGTATT 1051 34 85.3 0 .............................NNNNN | ========== ====== ====== ====== ================================== =========================================================== ================== 14 34 92.5 40 ATTGCCCCTCCTTCTGGAGGGGCCCTTCATTGAG # Left flank : CCATGTTGCTTCGACGCCTTGACATCGCCGGGCCCTTCATTGAGGCGGACGCGGGTTGCACCTGCTGGGGCTCCCGGTGGAGACGA # Right flank : NNNNNNAAGCCGGCGGCGAGCCATGGTTCGTGCTAACTGATATTGCCCCTCCTTCTGGTGGGCCTACCCTGGTTTTTCGGACACCTGATGTGGCGGGGCCTGGTGGCCCGAGAGTGTGGCGGATGCTGGTCCGTAGTCGAACCAGGATCCGCCACCACCTCAGCGGGACCACATCTGACCGGGCTCCAGGGGCCCCGACCGGGCCCGGAGTCGCTACTTCAGCTCTGCCGCCCGTTGCGAGGCGGTGGAGGCCGAGTCGGTGGGGATGCCGGGAGTCGTGGGGCGTGCGGAGCAGTTCACCTGCGCCCCGGGGTTCGTGATCGCTCTCGTGCAGATCTGCGAGGGCGTACCGGGCGGTCCGTGGCCGGATGTGGGAGTGATCGTTTCAGTAGCGGGCCCGGCTGCTGGGGTCGTGAACCGCAGGGAGCCGGGACGGTTGCCGAACTGGACACCGATTCGGTGGGCATGCCCATGGTGTCGATGGCTACCGCTCTTTTGGA # Questionable array : NO Score: 5.79 # Score Detail : 1:0, 2:3, 3:0, 4:0.62, 5:0, 6:0.25, 7:-0.08, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : ATTGCCCCTCCTTCTGGAGGGGCCCTTCATTGAG # Alternate repeat : ATTGCCCCTCCTTCTGGAGGGGCCCTTCNNNNNN # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [4,10] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: F [-12.30,-11.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [7-17] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [26.7-36.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.78,0.64 Confidence: LOW] # Array family : NA // Array 2 3180-2852 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000016.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ======================================= ================== 3179 36 100.0 39 .................................... GAGTGGAATCAAACCAAAATGGTGTTCACCAACGGAAGC 3104 36 97.2 38 .............G...................... TTTGCCAGATAGATGGACGTGCCCGGCGCCCACGACGA 3030 36 100.0 37 .................................... CCGAGAAGGCTGCGACGGTGGCACGGTCTACAGCTCC 2957 36 97.2 34 .............G...................... TCTTGCTCATCATTGCTGACGTCATCATCCATAA 2887 36 69.4 0 .............G.........TG..CCTAC.CTG | ========== ====== ====== ====== ==================================== ======================================= ================== 5 36 92.8 37 GCCTCAATGAAGGTCCCCTCCAGAAGGAGGGGCAAT # Left flank : NNNNNGAAGGGCCCCTCCAGAAGGAGGGGCAATGCGGTCGTGACGACAACCGGGAAGCCCCACAGGTTGCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAATCCGCGTCCCGGGTCGAACCCCTCGGCCCGCTCATCTTGCCTCAATGAAGGGCCCCTCCAGAAGGAGGAGCAATCTTTGCCGCTGTCTGGCTCACGCTCAGCCCGAGCTCACGCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAATACGGCAACCGTCCCTCGCCGAGCCGGGGCCTTGGTNNNNNNNNNNCCTTCTGGAGGGGCCCTTCATTGAGGCGCGTTCGCGAAGGCGATCGTCTCCAGCAGCCCTTGATTGCCCCTCCTTCTGGAGGGGCCCTTCATTGAGGCTCCTTGCACTCCACGACGAGCCTCCCCCGCATANNNNNNNNNNGAAGGGCCCCTCCAGAAGGAGGGGCAATTCCCGGCAAGGATCTGGCCACCCACCTCACCCCAA # Right flank : GTTTTTCGGACACCTGATGTGGCGGGGCCTGGTGGCCCTGCCCAGTTGCTCGGACTCGTCGCGGGTGGGAAGGATGCCGGCAACTCGAAACTCGAGAAGGCGGGATCCCATGAGACCGGCGCCGGCTTCCCCGTTACCTGGCGCACTGACACCGATCACCAGGGCTTCTGAGCCTCGGACGAGTTCAGGGCACTCGACATACCCCAACGACATACCCCAACTCGATCTGTCGGCCAGACAGTGCATGATGTTCAGAGAAGTCCGACCGAAGGGATCCTCACCCATGCCCAATCCCGTACACGACATCGACGCAGGCGGCCAGCCGATGGATAAGTATGACGCTCGAGTATGGAAGTCGCTGAACGAGTTCTGGGAGAAGAAGAGTGATCCCCAGACCCTGACGAACCGAGCCGCCGCGGCGCTTCAGCACGGCGGTGCAGCTGTCGAAGGAGCCGCCAAGAAGGCCACCGGCGCCATCCCTGAGATGGTGAAACAGCCGA # Questionable array : NO Score: 5.79 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:0.01, 8:0.6, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GCCTCAATGAAGGTCCCCTCCAGAAGGAGGGGCAAT # Alternate repeat : GCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAAT # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [5,10] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: F [-12.30,-11.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [48.3-33.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.64,0.78 Confidence: LOW] # Array family : NA // Array 3 3429-3611 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000016.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ====================================== ================== 3429 36 100.0 38 .................................... GTGAGCTCGGGCTGAGCGTGAGCCAGACAGCGGCAAAG 3503 36 97.2 37 .....T.............................. AAGATGAGCGGGCCGAGGGGTTCGACCCGGGACGCGG 3576 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== ====================================== ================== 3 36 99.1 38 ATTGCCCCTCCTTCTGGAGGGGCCCTTCATTGAGGC # Left flank : CTCCTTCTGGAGGGGCCCTTCATTGAGGCGGAGCTGTAGACCGTGCCACCGTCGCAGCCTTCTCGGATTGCCCCTCCTTCTGGAGGGGACCTTCATTGAGGCTCGTCGTGGGCGCCGGGCACGTCCATCTATCTGGCAAAATTGCCCCTCCTTCTGGAGGGGCCCTTCATTGAGGCGCTTCCGTTGGTGAACACCATTTTGGTTTGATTCCACTCATTGCCCCTCCTTCTGGAGGGGACCTTCATTGAGGCTTGGGGTGAGGTGGGTGGCCAGATCCTTGCCGGGAATTGCCCCTCCTTCTGGAGGGGCCCTTCNNNNNNNNNNTATGCGGGGGAGGCTCGTCGTGGAGTGCAAGGAGCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAATCAAGGGCTGCTGGAGACGATCGCCTTCGCGAACGCGCCTCAATGAAGGGCCCCTCCAGAAGGNNNNNNNNNNACCAAGGCCCCGGCTCGGCGAGGGACGGTTGCCGT # Right flank : CAACCTGTGGGGCTTCCCGGTTGTCGTCACGACCGCATTGCCCCTCCTTCTGGAGGGGCCCTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGCGCCAGCTCTCGGAGACGATGGCGCCTTGACGTGGCGTTGCCCCTCTCCCCGGGCGAAGCCCTCCACCCGTTCAACGTCCCGAAACTCACGGAACTCCCGCCGGCGCCGAGAGCTAGACTCGCCATGAGAAGGTGGGAGGTAGGGCAGACGCCCAGCTGACCCACCTTCCCTTTTTCGCACCCCCGGTGGCGCCAAGAGCCACCGATTCCGTCCAACCGCCCACCCTCTCGTCCACCCGCGCGAGGACCCGTCACCCCGATCAGCGCTCACTGACAAGGCCACGTGGCCGCGCACGAGCCCTAGGCGTTTCCGGACCTGACAGTCGCCATGACAAGGCGTT # Questionable array : NO Score: 5.31 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 5:0, 6:0.25, 7:0.02, 8:0.4, 9:0.69, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : ATTGCCCCTCCTTCTGGAGGGGCCCTTCATTGAGGC # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [4,10] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: F [-12.30,-11.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [21.7-33.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.78,0.64 Confidence: LOW] # Array family : NA // Array 1 737-1300 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000017.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== =========================================================== ================== 737 36 100.0 33 .................................... ATTCTGGGCCCTAGCAAGAGAAACCAAATACTT 806 36 100.0 37 .................................... ATCGGCAATTGCACACCGAACATGGTTGTGATGGCGA 879 36 100.0 36 .................................... CATCCCCGTCGCGGAGCCGTCACCGGCCATCTCGTA 951 36 100.0 38 .................................... ACCCGCAAAGGGTCCCGTTGTCCCGGGTTCGGGGTTGG 1025 36 80.6 36 .............................NNNNNNN NNNTGCCGGTGGGATGCGGTCAGGGTCGGATTGGGC 1097 36 100.0 37 .................................... TTGAGACCGCATCCGCATCGTGACCCGGACCCAGACC 1170 36 77.8 59 ............................NNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNAAGCAGGCTTGCTATGATGAACAGGGCCTCAGCCA 1265 36 100.0 0 .................................... | ========== ====== ====== ====== ==================================== =========================================================== ================== 8 36 94.8 40 GCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAAT # Left flank : NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCGCTGCAAGAGGGTGGAGGGTCCGCCACCCTATGCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAATATTGTGCCTGAAACCGGAATCTATGCGGTGTTCGCGCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAATCACAGCGGAGGATTCTGCGCAATGCCACCGGAGCCGCCTCAATGAAGGGCCCCTCCAGAAGGNNNNNNNNNNTCGCCATTGTCGTCGTGGCATTTGATTGATCGCCGCCTCAATGAAGGGCCCCTCCAGAANNNNNNNNNNATGTCTGTAGCCGCTATGGCTAAGATGTATGGCCTCAATGAAGGGCCCCTCCAGAAGGNNNNNNNNNNAGGCCGGCGCCATGTCTGCTCCTGGTGGAGATGCCCGCCTCAATGAAGGGCCCCTCCAGAAGGNNNNNNNNNNAGGCTGTTCGCCCGGACGACGGTACTGACTTCT # Right flank : TGGCGGGCGTGGGAACAGGGCTCCCACTAGGCATTATACCGGCCGCCTGCGAGCGGTGCTGAAGAAGGATGGCTCGCGCGTGGAGGATTGATGACCCCTTCAGCGCAATCTGCTTGTGACAAGGGGAAACATCACGCGAGCGGCTCCGCGTGACAACCGGGCCGCAGAGCCGCTGGTCGTCAGATGATGATGCTGCGTCCGCCGCTCTGGTACCTCTGACCGCCCAACCAGGTGATGCGTTGGGCGTCTGCCGACGTGGACATGCCCAGGTCGCAGATCACCACCGAGTCCTCATCAATATCCATCGCGTCGGTGAGATCGTGGCGTAGCACCAGCAGGTGTGACGGCGGACAATCAACCATGAATACGCTGTACTGCACACGCTCCCCGTAGCCCTTCAGTACCGTGGCCAACCTGGTGCGACGACGGTCATCGGGCACGTCGTAGGCGATCAGAAAGCAATGGGAATCTCGTCGGCTCATCTGACCGTCATTCCTATA # Questionable array : NO Score: 5.82 # Score Detail : 1:0, 2:3, 3:0, 4:0.74, 5:0, 6:0.25, 7:-0.17, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GCCTCAATGAAGGGCCCCTCCAGAAGGAGGGGCAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: F [10,4] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: R [-11.00,-12.30] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-15] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [30.0-30.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.78,0.37 Confidence: MEDIUM] # Array family : NA // Array 2 33503-35299 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000017.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= =================================================== ================== 33503 29 100.0 33 ............................. CAGTGCAGTCCGTCTCCACCGAGGCCGACGACA 33565 29 100.0 32 ............................. GACGCCACCGACGTCGCTGGGAGCCTCCAGAA 33626 29 93.1 38 ...........................NN NNNNNNNNAAGATCCCCGCCGGCGCGACCACATCATCC 33693 29 96.6 39 ............................N NNNNNNNNNTGCGGTGATGCCGATCAGCTCGTGGTCGGC 33761 29 100.0 31 ............................. ATCGTTGGCCCCACCGGCTGGGCGTCGCACA 33821 29 96.6 33 ............................G TCGAACTGGTCCTTGGTGCGGGTTGCCGTGTTG 33883 29 96.6 32 ............................G GACGACGACATTGAATTCTTTCAGGATGGCTA 33944 29 100.0 32 ............................. GAAACGGAGCCAGCACGTGATCGCCGAAGTCG 34005 29 100.0 32 ............................. TGACATCACATAGCGAGGCATGATGACGCCCC 34066 29 96.6 32 ............................G ATCCTCGGCACGGCACTGATCGATCAGCTGTC 34127 29 100.0 32 ............................. ACGATGAGCAGCAGCGCAGTCCAGTACATTGA 34188 29 93.1 51 ...........................NN NNNNNNNNNNNNNNNNNNNNNNNGGTCCACGATTGATCATCTCGACCATCA 34268 29 96.6 32 ............................T GATCACCATCGCGGCCAGAATCGTCCGCACGG 34329 29 100.0 32 ............................. GATTTCGACGGCGATCTCGGTGTTCATCGTGG 34390 29 100.0 32 ............................. CTGGGAGCCGGTCATCTCCCAATCGTGCTGCA 34451 29 96.6 32 ............................T GCACCACCACAACCGAAGGAGAATGACCATGA 34512 29 100.0 33 ............................. GTGGGAGGTGGCCTCGGCGATCGGTGTGCTGGT 34574 29 93.1 36 ...........................NN NNNNNNNNTTCGCCGGGATGCTCGGCCAGCCGGAAA 34639 29 100.0 32 ............................. CGGGGATGATCTTGCCGAGCGTGCCGACCATC 34700 29 96.6 32 ............................T GGTGCTTTGCTGCCCACCGCGCAGCATTGCCC 34761 29 100.0 32 ............................. ACAGGAAGGGATGTGCACCATGACACTCATGT 34822 29 96.6 49 ............................N NNNNNNNNNNNNNNNNNNTTGCTGGCTCCGTGGGTGTCGGTGATGGGCC 34900 29 96.6 32 ............................T TGGGGCGACGTGGAGAAGCGTGCCGATTCGGA 34961 29 100.0 32 ............................. CTTGGACAGCCCGGTGACATGTCCGGACGGGA 35022 29 93.1 39 ...........................NN NNNNNNNNAGGAGCCGAAGACGCTCGGGGCGCCGTTGAA 35090 29 96.6 32 ............................G AGTTTGATGGCGGTGTTGGACACGATGCCGAC 35151 29 96.6 32 ............................T GCCCTGCCCCGCATCCTTCACCGCCTGAACGG 35212 29 100.0 32 ............................. AGAATTGCAATGCTGCAAACCCCGATAGCCCG 35273 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= =================================================== ================== 29 29 97.5 34 GTTCTCCCCGCATACGCGGGGGTGATCCC # Left flank : GGCTCACCGATGACGACTCCGACCATGAGTGGGACATTGTCGAGCTTTGGGATGACAAGGACGGGGTCGTGCCGGGTGGCCGGTCATGGAGTGAACAGCCATGATGGTGTTGGTGCTCACTGCCTGCCCGGCCGGTTTGCGCGGGTTCGTGACGCGGTGGCTGCTGGAGATCAGCCCGGGAGTTTTTGTGGGCAAAGTCTCTGCGCGGGTGCGTGAAGCCATTTGGGCGCGGGTTGAGGACCTCTGCCAGGACGGACGAGCAATTCTGGTGCACACGGCGCGGAACGAGCAGGGCTTTGACTTCAAAGTACATAGGCACGATTGGGAAGTTGTTGATCTGGAGGGCCTCAAACTGATGCGTCGCCCCAGAACCCCGGATCGTGCGTCCAGTGGCATGCGCTCCGGATGGAGCAACGCTGCCAAGCGACGACGGTGGGGTCGCTGACTCGGAACGTCCTCGTATCGGCCTTGAGCGCCAGTAACATGCGTAGTCAGGAAGT # Right flank : | # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.88, 5:0, 6:0.25, 7:-0.01, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTCTCCCCGCATACGCGGGGGTGATCCC # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [3,6] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCATACGCGGGGATGATCCC with 96% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.00,-12.30] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [1-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [43.3-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.55,0.37 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-1092 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000032.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================== ================== 1 29 96.6 32 ............................T GGTGGGATCTGAGCCTCGACCACACCGCCGAG 62 29 93.1 38 ...........................NN NNNNNNNNACGTCGTCGCCCGGAAGATGCGCGAGGAAG 129 29 100.0 32 ............................. GGGGCCCCGCCGGCGCTCAGATAGGCAACCGA 190 29 100.0 32 ............................. ACCGAGCTCACCTACCAGAGGATCCTGTAATG 251 29 96.6 33 ............................G CTTCCGCCGCCCTTGACTCTGCGCCCAGCCAAC 313 29 100.0 32 ............................. CACCCGACGTCACCGGGGAGGTTGTCCAGGAA 374 29 93.1 37 ...........................NN NNNNNNNNGTCCTACCCCGAGCACCGGTATGAAACAT 440 29 96.6 32 ............................T AAAGGTTGCACACGTAGACAGGATCAGGAAGA 501 29 96.6 32 ............................T GCACGGAATCAATCGACGGCCTTGTCTAATTC 562 29 96.6 32 ............................G ACCAAGTATAATGCCGCCCACATGCCTATGAG 623 29 96.6 32 ............................G ATGGGGAATGTGGCGTTGTTGTCCTCGTCCAC 684 29 93.1 38 ...........................NN NNNNNNNNGCCCGATCGCCTACCGCGTCACCGAGTATG 751 29 100.0 32 ............................. GGCGACCTTATTCTTATCACATGGGACGGATA 812 29 96.6 40 ............................N NNNNNNNNNTACATCTGTCACGCGGGTTCCGTACGCCTGA 881 29 96.6 32 ............................G TGGGCACCCGAGCAGGTCACGCTCCCGCTGGC 942 29 100.0 32 ............................. CAGTGGCGCTGCCCAGCAAGCGGGCCTCGATC 1003 29 100.0 32 ............................. TGCACCGCCCCTGTCGCGATCGCCGGGACCGC 1064 29 96.6 0 ............................G | ========== ====== ====== ====== ============================= ======================================== ================== 18 29 97.1 34 GTTCTCCCCGCATACGCGGGGGTGATCCC # Left flank : | # Right flank : GNNNNNNNNNNCCATTCACGTCGTCGCACCATTGTGCAAGAGGATCACCCCCGCGTATGCGGGGAGAACTGACCAAACAAATCAGATTCGCCATACATCTTAGGATCACCCCCGCGTATGCGGGGAGAANNNNNNNNNNGGAGGCGATCGTCGCACCCTCGGGGGTCTCGGTTCTCCCCGCATACGCGGGGGTGATCNNNNNNNNNNTCTCCGAGCTGCCCGGGGGTGACATCACCAGGATCACCCCCGCGTATGCGGGGAGAACCAGATGCACCTGATGTTCCGGCGACGATCATCACAGGATCACCCCCGCGTATGCGGGGAGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN # Questionable array : NO Score: 6.05 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.94, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTCTCCCCGCATACGCGGGGGTGATCCC # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [3,6] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCATACGCGGGGATGATCCC with 96% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.00,-12.30] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [1-1] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.87,0.37 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 2206-1838 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000032.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================================= ================== 2205 29 93.1 32 N...........................C ATGCCGTCCTTGTTCTTCAATGCCACGACAAT 2144 29 100.0 32 ............................. TCATCGAATCCGCTGCGGCCTTCACCGACGCT 2083 29 96.6 37 ............................G GTGGCTTGCTCGGTCCGGTCGGATGCCGANNNNNNNN 2017 29 93.1 61 NN........................... GCAACTGGCCTGCGGTCGTGTCGGCGGCACGGCGNNNNNNNNNNNNNNNNNNNNNNNNNNN 1927 29 96.6 32 N............................ TGTACTCAAGATGCTATTAGATTTGGTGATGG 1866 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ============================================================= ================== 6 29 96.6 39 GTTCTCCCCGCATACGCGGGGGTGATCCT # Left flank : GGGGGTGATCCGATTACTTTAGGCGTGACGGGTATGACGGGTTTGTTCTCCCCGCATACGCGGGGGTGATCCCGCCGTGGTCCCTTCCAGGGCCCCAAAAACANNNNNNNNNNGTTCTCCCCGCATACGCGGGGGTGATCCTCGTGGCGTTAGGCATCTCGAAAGCCGTCGANNNNNNNNNNATCACCCCCGCGTATGCGGGGAGAACACCGGCCTTGTGGCTGGCGGCTACGTGCGGGAGGGATCACCCCCGCGTATGCGGGGAGAACGGGGACGAGCGCGGTCGCCTGCGCAACCTTGGCNNNNNNNNNNATCACCCCCGCGTATGCGGGGAGAACATGTGTGGCACATCGGCAGCGTCGGCACCGAACGGATCACCCCCGCGTATGCGGGGAGAACGATTCGCCGCCGGCTTCGACGCGGGGTTGGTGGGGATCACCCCCGCGTATGCGGGGAGAACCCCTGGTGGCTGATGTGCTCGACCCCGACACNNNNNNNNN # Right flank : CCTTCAGCGAACCATTCTTGCTGTTCTCCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCTCCCCGCATACGCGGGGGTGATCCGACACCACACACCCCACCAGCCCCGCAGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCTCCCCGCATACGCGGGGGTGATCCTGTGATGATCGTCGCCGGAACATCAGGTGCATCTGGTTCTCCCCGCATACGCGG # Questionable array : NO Score: 5.76 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:-0.32, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTCTCCCCGCATACGCGGGGGTGATCCT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: F [6,3] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCATACGCGGGGATGATCCC with 96% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-9.00,-9.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [25.0-26.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.37,4.87 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 3 2246-2465 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000032.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================== ================== 2246 29 100.0 32 ............................. CACCAACCCCGCGTCGAAGCCGGCGGCGAATC 2307 29 96.6 32 ............................G TTCGGTGCCGACGCTGCCGATGTGCCACACAT 2368 29 89.7 40 ..........................NNN NNNNNNNGCCAAGGTTGCGCAGGCGACCGCGCTCGTCCCC 2437 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ======================================== ================== 4 29 96.6 35 GTTCTCCCCGCATACGCGGGGGTGATCCC # Left flank : NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGGAGAACAGCAAGAATGGTTCGCTGAAGGAGGATCACCCCCGCGTATGCGGGGAGAACCCATCACCAAATCTAATAGCATCTTGAGTACAAGGATCACCCCCGCGTATGCGGGGAGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCCGTGCCGCCGACACGACCGCAGGCCAGTTGCAGGATCACCCCCGCGTATGCGGGGAGANNNNNNNNNNTCGGCATCCGACCGGACCGAGCAAGCCACCGGATCACCCCCGCGTATGCGGGGAGAACAGCGTCGGTGAAGGCCGCAGCGGATTCGATGAAGGATCACCCCCGCGTATGCGGGGAGAACATTGTCGTGGCATTGAAGAACAAGGACGGCATGGGATCACCCCCGCGTATGCGGGGAGAANNNNNNNNNNGTGTCGGGGTCGAGCACATCAGCCACCAGGG # Right flank : CTCCCGCACGTAGCCGCCAGCCACAAGGCCGGTGTTCTCCCCGCATACGCGGGGGTGATNNNNNNNNNNTCGACGGCTTTCGAGATGCCTAACGCCACGAGGATCACCCCCGCGTATGCGGGGAGAACNNNNNNNNNNTGTTTTTGGGGCCCTGGAAGGGACCACGGCGGGATCACCCCCGCGTATGCGGGGAGAACAAACCCGTCATACCCGTCACGCCTAAAGTAATCGGATCACCCCCGCGTATGCGGGGAGAACTGCGGTGAGTGCGGCAAGGACCTCGGGAGTCAGGGATCACCCCCGCGTATGCGGGGAGAACACCGCCCTGCCCACCATCGCCTCCGCGCGCGTTCGGATCACCCCCGCGTATGCGGGGAGAACTGCGCCGGTGGGTGCGTGCCGTGGCCGCTTTCGGGATCACCCCCGCGTATGCGGGGAGAACCTCTCCAAGGCTGTTCGACCAGACGGGACCGACGGATCACCCCCGCGTATGCGGGGAG # Questionable array : NO Score: 5.69 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.01, 8:0.6, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTCTCCCCGCATACGCGGGGGTGATCCC # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [3,6] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCATACGCGGGGATGATCCC with 96% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.00,-12.30] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [26.7-30.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.28,0.37 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 4 3456-2564 **** Predicted by CRISPRDetect 2.4 *** >NZ_CCYY01000032.1 Propionibacterium freudenreichii strain CIRM-BIA 134, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ======================================== ================== 3455 29 96.6 32 ............................G GCCGCGTTTGAACTGACTTTTCAGGGGGCGAC 3394 29 100.0 32 ............................. GGAATCAGAGAAACACCGATAGCCACACCGAT 3333 29 96.6 32 ............................T ACACCGCGCTGCGGCGTGTGTCTTCTTTGCCG 3272 29 96.6 32 ............................T CCGTTGCACCCATCGACGGAGCAGGCAAGAAC 3211 29 100.0 32 ............................. GGCAGCGGCCCTCTGGGCGGACATTGACAGCA 3150 29 96.6 32 ............................T GTCCGAATGGACCAGGGGCGACTGGGACGCCG 3089 29 100.0 32 ............................. ACGGGCATGACGGTGGTGCTGGCCCCGGCAGT 3028 29 100.0 32 ............................. CCCACACCGGCCACCGACGGCAATGCCGCGCT 2967 29 96.6 32 ............................G TCGGTCCCGTCTGGTCGAACAGCCTTGGAGAG 2906 29 100.0 32 ............................. GAAAGCGGCCACGGCACGCACCCACCGGCGCA 2845 29 96.6 33 ............................G AACGCGCGCGGAGGCGATGGTGGGCAGGGCGGT 2783 29 100.0 32 ............................. TGACTCCCGAGGTCCTTGCCGCACTCACCGCA 2722 29 96.6 32 ............................G ATTACTTTAGGCGTGACGGGTATGACGGGTTT 2661 29 100.0 40 ............................. GCCGTGGTCCCTTCCAGGGCCCCAAAAACANNNNNNNNNN 2592 29 96.6 0 ............................T | ========== ====== ====== ====== ============================= ======================================== ================== 15 29 98.2 33 GTTCTCCCCGCATACGCGGGGGTGATCCC # Left flank : CGCTTCGACGCGAAGAAGGCCGCCGCTTTTTCCAGGAACTCGTTGTCCATCCGCAGCTGCGAGTTCTCACGCCGGAGCCGTTTCAGCTCGGCCCGCTCGTCATCGCTCAACAAATCACCAGCAGCTGTCTCTTTCTGCGCACGCACCCATTTGCCCAGCAACTGCTCACCAAGTCCCAATTCCTTCGCGACGTCCGCGATCGTGCGACCAGACGTCAGCACCAGCCTCGCGGCCTCGTGGCGGTACTCCGCAGCGAACTTCCGCCGCCTCCGCGGCACCTGCTCCGGATCCACACCCATGACAACACCTTCCCGCACGACCCACCGGCCATGCCACATCAGGTGTCCGAAAAAACAGGGTAACCCCACCCCCGCGTATGCGGGGAGAACATCCCCGACATTCGCGCCCACCTGAATCAANNNNNNNNNNCGTGCGCTACACCCTCATCTGGGAAGAGCCGGTGATCCATCCCCAGGAACATCCCCGCCACCGATGATCAC # Right flank : CGTGGCGTTAGGCATCTCGAAAGCCGTCGANNNNNNNNNNATCACCCCCGCGTATGCGGGGAGAACACCGGCCTTGTGGCTGGCGGCTACGTGCGGGAGGGATCACCCCCGCGTATGCGGGGAGAACGGGGACGAGCGCGGTCGCCTGCGCAACCTTGGCNNNNNNNNNNATCACCCCCGCGTATGCGGGGAGAACATGTGTGGCACATCGGCAGCGTCGGCACCGAACGGATCACCCCCGCGTATGCGGGGAGAACGATTCGCCGCCGGCTTCGACGCGGGGTTGGTGGGGATCACCCCCGCGTATGCGGGGAGAACCCCTGGTGGCTGATGTGCTCGACCCCGACACNNNNNNNNNNTTCTCCCCGCATACGCGGGGGTGATCCCATGCCGTCCTTGTTCTTCAATGCCACGACAATGTTCTCCCCGCATACGCGGGGGTGATCCTTCATCGAATCCGCTGCGGCCTTCACCGACGCTGTTCTCCCCGCATACGCGGG # Questionable array : NO Score: 5.93 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.76, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7: exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTCTCCCCGCATACGCGGGGGTGATCCC # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: F [6,3] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCATACGCGGGGATGATCCC with 96% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.30,-13.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [31.7-38.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.37,4.87 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //