Array 1 57-738 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHOJ01000027.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51303 N51303_contig_27, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 57 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 160 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 221 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 282 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 343 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 404 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 465 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 526 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 587 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 648 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 709 29 96.6 0 A............................ | A [735] ========== ====== ====== ====== ============================= ========================================================================== ================== 11 29 99.4 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCCGCGCCAGCGGGGATAAACCGAAACGGTAGTGTTTTAAAACCGTTTCGAGGTGCG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 5.94 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.28, 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 [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [41.7-48.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 97918-98615 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHOJ01000029.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51303 N51303_contig_29, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 97918 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 97979 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 98040 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 98101 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 98162 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 98223 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 98284 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 98345 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 98406 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 98467 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 98528 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 98589 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 12 29 99.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : | # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-0.0]%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], // Array 1 699-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHOJ01000057.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51303 N51303_contig_57, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 698 28 96.6 32 -............................ CCAGCTTACGCTATTTACGACGTTATTGAGCA 638 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 577 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 516 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 454 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 393 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 332 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 271 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 210 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 149 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 88 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 12 29 97.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # Questionable array : NO Score: 5.80 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 5:0, 6:0.25, 7:0.01, 8:1, 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 : 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 [-8.90,-10.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [2-3] 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: R [0,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 822-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHOJ01000061.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51303 N51303_contig_61, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 821 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 760 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 699 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 638 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 577 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 515 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 454 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 393 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 332 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 271 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 210 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 149 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 88 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 14 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : C # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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: R [2-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 17226-16954 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHOJ01000061.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51303 N51303_contig_61, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 17225 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 17164 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 17103 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 17042 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 16981 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 5 29 95.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ACGC # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:0.80, 5:0, 6:0.25, 7:0.01, 8:0.8, 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 [4,6] 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 [-14.00,-14.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [6-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-1.7]%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], //