Array 1 1033598-1035211 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014969.1 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1033598 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 1033659 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 1033720 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 1033781 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 1033842 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 1033903 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 1033964 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 1034025 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 1034086 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 1034147 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 1034208 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 1034269 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 1034330 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 1034391 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 1034452 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 1034513 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 1034574 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1034635 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1034696 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1034757 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 1034818 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 1034879 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 1034940 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1035001 29 96.6 32 ........A.................... CAGGTTATGCGCAAAAATTAATTCATATTATA 1035062 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1035123 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1035184 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 27 29 98.7 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 [0-9] 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 1051344-1051983 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014969.1 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1051344 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1051405 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1051466 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1051527 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1051588 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1051649 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1051710 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1051771 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1051832 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1051893 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1051954 29 96.6 0 A............................ | A [1051980] ========== ====== ====== ====== ============================= ================================ ================== 11 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.23 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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 [0-3] 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], //