Array 1 88199-90179 **** Predicted by CRISPRDetect 2.4 *** >NZ_MZNJ01000016.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO_STM3538 BCW_7502_1__paired__contig_16, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 88199 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 88260 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 88321 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 88382 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 88443 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 88504 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 88565 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 88626 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 88687 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 88748 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 88809 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 88870 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 88931 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 88992 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 89053 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 89114 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 89175 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 89236 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 89297 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 89358 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 89419 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 89480 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 89541 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 89602 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 89664 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 89725 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 89786 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 89847 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 89908 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 89969 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 90030 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 90091 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 90152 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 33 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGAGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # 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 106498-107791 **** Predicted by CRISPRDetect 2.4 *** >NZ_MZNJ01000016.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO_STM3538 BCW_7502_1__paired__contig_16, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 106498 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 106560 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 106621 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 106682 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 106743 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 106804 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 106865 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 106926 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 106987 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 107048 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 107109 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 107170 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 107231 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 107293 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 107396 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 107457 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 107518 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 107579 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 107640 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 107701 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 107762 29 96.6 0 A............................ | A [107788] ========== ====== ====== ====== ============================= ========================================================================== ================== 21 29 99.5 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTGTGTTCCCCGCGCCAGCGGGGATAAACCGTGAGCAACGACAGTAAATAATTTTTCGTGCTGGTGTTCCCCGCGCCAGCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCCAGCGGGGATAAACCGCAACCAGGCTGGATCGTAACTCCTATCCCCTC # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.09 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.13, 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: R [33.3-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //