Array 1 162-2126 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDJQ01000110.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM19, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 162 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 223 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 284 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 345 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 406 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 467 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 528 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 590 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 651 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 712 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 773 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 834 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 895 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 956 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 1017 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1078 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1139 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 1200 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 1261 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1322 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1383 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1445 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 1548 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1609 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1670 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1731 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1792 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1853 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1914 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1975 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 2036 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 2097 29 96.6 0 A............................ | A [2123] ========== ====== ====== ====== ============================= ========================================================================== ================== 32 29 99.6 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.15 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 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 : 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 [1-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-48.3]%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 31-1340 **** Predicted by CRISPRDetect 2.4 *** >NZ_CDJQ01000317.1 Salmonella enterica subsp. enterica serovar Typhimurium strain STM19, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 31 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 92 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 153 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 214 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 275 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 336 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 397 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 458 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 519 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 580 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 641 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 702 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 763 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 825 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 886 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 947 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1008 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1069 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1130 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1191 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1252 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1313 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 22 29 98.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTAGTTTATAAACAATTATATCCGTTTAGTG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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 [0-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [38.3-63.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //