Array 1 52-263 **** Predicted by CRISPRDetect 2.4 *** >NZ_JRGR01000093.1 Salmonella enterica subsp. enterica serovar Typhimurium strain S15 contig_93, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 52 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 113 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 174 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 235 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 4 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGCCAGCGGGGATAAACCGTGGATTATCTGTATTTTACGGAAGTGGGCGCGG # Right flank : AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGCGTGTTCCCCGCGCCAGCGGGGATAA # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 : 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [38.3-45.0]%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 1-213 **** Predicted by CRISPRDetect 2.4 *** >NZ_JRGR01000126.1 Salmonella enterica subsp. enterica serovar Typhimurium strain S15 contig_127, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 63 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 124 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 185 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 4 29 100.0 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : CCGCTGACGCACTGGATCAACCTGACGCAACGGTGTTCCCCGCGCCAGCGGGGATAA # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 : 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [0.0-33.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-518 **** Predicted by CRISPRDetect 2.4 *** >NZ_JRGR01000044.1 Salmonella enterica subsp. enterica serovar Typhimurium strain S15 contig_44, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 62 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 123 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 184 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 245 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 306 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 367 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 428 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 489 29 100.0 0 ............................. | A [516] ========== ====== ====== ====== ============================= ================================ ================== 9 29 99.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.24 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 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: NA [0.0-0.0]%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 1 331-58 **** Predicted by CRISPRDetect 2.4 *** >NZ_JRGR01000012.1 Salmonella enterica subsp. enterica serovar Typhimurium strain S15 contig_12, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 330 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 269 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 208 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 147 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 86 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 5 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GAAAATGCAGGTGGGGTAACGAATGCGAGATTGGTGTTCCCCGCGCCAGCGGGGATAA # Questionable array : NO Score: 6.02 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 [4,5] 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: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [41.7-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 17955-16462 **** Predicted by CRISPRDetect 2.4 *** >NZ_JRGR01000012.1 Salmonella enterica subsp. enterica serovar Typhimurium strain S15 contig_12, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 17954 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 17893 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 17832 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 17771 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 17710 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 17649 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 17588 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 17527 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 17466 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 17405 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 17344 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 17283 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 17222 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 17161 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 17100 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 17039 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 16977 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 16916 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 16855 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 16794 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 16733 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 16672 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 16611 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 16550 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 16489 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 25 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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 [9-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%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], //