Array 1 989423-991586 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014981.1 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1880 isolate ST13123 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 989423 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 989484 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 989545 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 989606 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 989667 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 989728 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 989789 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 989850 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 989911 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 989972 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 990033 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 990094 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 990155 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 990216 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 990277 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 990338 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 990399 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 990460 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 990521 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 990582 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 990643 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 990704 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 990765 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 990826 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 990887 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 990948 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 991009 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 991071 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 991132 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 991193 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 991254 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 991315 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 991376 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 991437 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 991498 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 991559 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 36 29 98.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.20 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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 [0-12] 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], // Array 2 1007719-1008523 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014981.1 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1880 isolate ST13123 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1007719 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1007780 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 1007841 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1007902 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1007963 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1008025 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 1008086 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [1008128] 1008128 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1008189 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1008250 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1008311 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1008372 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1008433 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1008494 29 96.6 0 A............................ | A [1008520] ========== ====== ====== ====== ============================= ================================= ================== 14 29 97.0 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 5:0, 6:0.25, 7:-0.11, 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: 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], //