Array 1 987888-989868 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014971.2 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 987888 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 987949 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 988010 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 988071 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 988132 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 988193 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 988254 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 988315 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 988376 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 988437 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 988498 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 988559 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 988620 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 988681 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 988742 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 988803 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 988864 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 988925 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 988986 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 989047 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 989108 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 989169 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 989230 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 989291 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 989353 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 989414 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 989475 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 989536 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 989597 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 989658 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 989719 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 989780 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 989841 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 33 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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 1006001-1007483 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014971.2 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 1006001 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1006062 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 1006123 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 1006184 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 1006245 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 1006307 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 1006368 29 100.0 38 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGACCGAGA 1006435 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 1006496 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 1006557 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 1006618 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 1006679 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 1006740 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 1006801 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 1006862 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1006923 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1006985 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 1007088 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1007149 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1007210 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1007271 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1007332 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1007393 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1007454 29 96.6 0 A............................ | A [1007480] ========== ====== ====== ====== ============================= ========================================================================== ================== 24 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 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], //