Array 1 422411-424024 **** Predicted by CRISPRDetect 2.4 *** >NZ_CQGS01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain CH1 isolate CH1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 422411 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 422472 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 422533 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 422594 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 422655 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 422716 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 422777 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 422838 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 422899 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 422960 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 423021 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 423082 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 423143 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 423204 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 423265 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 423326 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 423387 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 423448 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 423509 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 423570 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 423631 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 423692 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 423753 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 423814 29 96.6 32 ........A.................... CAGGTTATGCGCAAAAATTAATTCATATTATA 423875 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 423936 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 423997 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 440157-440796 **** Predicted by CRISPRDetect 2.4 *** >NZ_CQGS01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain CH1 isolate CH1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 440157 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 440218 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 440279 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 440340 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 440401 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 440462 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 440523 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 440584 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 440645 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 440706 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 440767 29 96.6 0 A............................ | A [440793] ========== ====== ====== ====== ============================= ================================ ================== 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], //