Array 1 59-454 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKNJ010000010.1 Salmonella enterica subsp. enterica strain 78A Scaffold10, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 59 29 96.6 32 .............T............... GACCACGACTGGAGTGATCAGATCGGTGTGGT 120 29 96.6 32 .............T............... CGAGCGGTACAACTCCAGCATTAATCCCCACC 181 29 96.6 32 .............T............... GACGCGTCTTTTCCACAGCAGGACTCTAAATC 242 29 100.0 32 ............................. TACGCCAGAGGAATGGCTTTCAGTGTTTTGGT 303 29 100.0 32 ............................. GAGCGGCTAAACGATGAATTAACCAGGGAGCG 364 29 100.0 32 ............................. TCGCACAACGCCTGGATATCCGCCCATCGGCC 425 29 96.6 0 ............T................ | A [452] ========== ====== ====== ====== ============================= ================================ ================== 7 29 98.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTTGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.01 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.85, # 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # 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 [70.0-48.3]%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 59-1254 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKNJ010000118.1 Salmonella enterica subsp. enterica strain 78A Scaffold118, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ====================================== ================== 59 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 120 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 181 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 242 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 303 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 364 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 426 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 487 29 100.0 38 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGACCGAGA 554 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 615 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 676 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 737 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 798 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 859 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 920 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 981 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 1042 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1103 29 100.0 32 ............................. CCACGTTCGGCGATGGTGGCCCCATCGGTCCA 1164 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1226 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ====================================== ================== 20 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTG # Right flank : AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCG # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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: R [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-36.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 866-44 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKNJ010000140.1 Salmonella enterica subsp. enterica strain 78A Scaffold140, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 865 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 804 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 743 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 682 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 621 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 559 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 498 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 437 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 376 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 315 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 254 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 193 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 132 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 71 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 14 29 97.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAAC # Questionable array : NO Score: 6.11 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 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 [6-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [45.0-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.92 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 314958-315717 **** Predicted by CRISPRDetect 2.4 *** >NZ_JADKNJ010000003.1 Salmonella enterica subsp. enterica strain 78A Scaffold3, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 314958 29 100.0 32 ............................. AACTGAAACCAGGCCAGGTGATATTTATCAAA 315019 29 100.0 32 ............................. CATACCCTGTAGTTTCAATTTCCGCAGGTGGG 315080 29 100.0 32 ............................. AGCGCGGAATGATTTTTAACGCTGAGATGGTG 315141 29 100.0 32 ............................. TACCGCGACACCGTCAACGACAGCAACCACTT 315202 29 100.0 32 ............................. CAGGTCACTAAAATTTGTAGGGTTATCCACAG 315263 29 100.0 32 ............................. GCGCAATTGCAGTTTGACGCGGTGCTGTCATT 315324 29 100.0 32 ............................. TGTCTTAACTCCATTGCTGAGTCGATTGTGAA 315385 29 100.0 32 ............................. CACACAGAACGCCAGTTATAATCATCGGTGCT 315446 29 100.0 32 ............................. TCGTTTGTGGCGTCAGTAATACTATTATCGGT 315507 29 96.6 32 .............T............... TTTTTAAATCCGGACAGACCCTGTAACGGATC 315568 29 100.0 32 ............................. ATCCGACTGTATGCCCAGCAGAACGAGGGCGC 315629 29 96.6 32 .............T............... CACGAGTGGCAAATTGATTTCGACGAAAAACC 315690 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 13 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACGGACGGCCTGCCGATGCCGTCTGTGACTTATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCGGATAAATTTTTCCATAGCGATGCATGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTAGTGCTGATAAAAAGTAGTTTATAAACAATGATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGATCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGACCCCTGCCGATTGG # 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: 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 [0-7] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%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], //