Array 1 989421-990913 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014977.1 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1896 isolate ST03-F34 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 989421 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 989482 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 989543 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 989604 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 989665 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 989726 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 989787 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 989848 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 989909 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 989970 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 990031 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 990092 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 990153 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 990214 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 990275 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 990336 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 990398 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 990459 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 990520 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 990581 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 990642 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 990703 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 990764 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 990825 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 990886 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 25 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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 [0-10] 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 1007045-1008887 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014977.1 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1896 isolate ST03-F34 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 1007045 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 1007106 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1007167 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 1007228 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 1007289 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 1007350 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 1007411 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 1007473 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 1007534 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 1007595 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 1007656 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 1007717 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 1007778 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 1007839 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 1007900 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1007961 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 1008022 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1008083 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1008144 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1008206 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 1008309 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1008370 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1008431 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1008492 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1008553 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1008614 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1008675 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1008736 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1008797 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1008858 29 96.6 0 A............................ | A [1008884] ========== ====== ====== ====== ============================= ========================================================================== ================== 30 29 99.5 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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], //