Array 1 163366-161907 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWQS01000014.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM4298::STM0928 BCW_7516_1__paired__contig_14, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= =========================================================================== ================== 163365 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 163304 29 69.0 75 ....................NNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNCGCCAGCGGGGATAAACCGCAACCAGGCTGGATCGTAACTCCTATCCCCTC 163200 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 163138 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 163077 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 163016 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 162955 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 162894 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 162833 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 162772 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 162711 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 162650 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 162589 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 162528 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 162467 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 162405 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 162302 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 162241 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 162180 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 162119 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 162058 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 161997 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 161936 29 96.6 0 A............................ | A [161909] ========== ====== ====== ====== ============================= =========================================================================== ================== 23 29 98.2 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.92 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 5:0, 6:0.25, 7:-0.24, 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: R [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.00,-13.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [3-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 181479-179498 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWQS01000014.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM4298::STM0928 BCW_7516_1__paired__contig_14, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 181478 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 181417 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 181356 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 181295 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 181234 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 181173 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 181112 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 181051 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 180990 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 180929 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 180868 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 180807 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 180746 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 180685 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 180624 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 180563 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 180502 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 180441 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 180380 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 180319 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 180258 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 180197 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 180136 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 180075 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 180013 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 179952 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 179891 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 179830 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 179769 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 179708 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 179647 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 179586 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 179525 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 33 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGAGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # 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: R [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.00,-13.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [10-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //