Array 1 446-50 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFP01000067.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N44709 N44709_contig_67, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 445 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 384 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 323 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 262 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 201 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 139 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 78 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 7 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GCGTCACTACCGAGACCGAGACCGAGACCGAGAGTGTTCCCCGCGCCAGC # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.00,-13.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [26.7-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 30573-29585 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFP01000083.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N44709 N44709_contig_83, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 30572 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 30511 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 30450 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 30389 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 30328 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 30266 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 30163 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 30102 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 30041 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 29980 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 29919 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 29858 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 29797 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 29736 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 29675 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 29614 29 96.6 0 A............................ | A [29587] ========== ====== ====== ====== ============================= ========================================================================== ================== 16 29 99.6 35 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGCCAGCGGGGATAAACCGACGCCCCGAATGTGTTTGCCTCGCCCGCTGC # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.05 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.18, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.00,-13.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-26.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-270 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFP01000146.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N44709 N44709_contig_148, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 61 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 122 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 183 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 244 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 5 29 97.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # Questionable array : NO Score: 5.84 # Score Detail : 1:0, 2:3, 3:0, 4:0.86, 5:0, 6:0.25, 7:0.01, 8:0.8, 9:0.92, # 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] 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 [5.24,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 50-1297 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFP01000130.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N44709 N44709_contig_130, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 50 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 111 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 172 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 233 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 294 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 355 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 416 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 477 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 538 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 599 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 660 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 721 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 782 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 844 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 905 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 966 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1027 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1088 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1149 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1210 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1271 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 21 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGCCGGCATCAGCGCCGATCCGTTCATAGTGCCCG # Right flank : | # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [1-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [28.3-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //