Array 1 276956-275418 **** Predicted by CRISPRDetect 2.4 *** >NZ_AHUZ01000007.1 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2-4_delta.ramA::kan SEETLT21_16, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 276955 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 276894 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 276833 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 276772 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 276711 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 276649 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 276588 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 276527 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 276466 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 276405 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 276344 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 276283 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 276222 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 276161 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 276100 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 276039 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 275978 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 275916 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 275813 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 275752 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 275691 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 275630 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 275569 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 275508 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 275447 29 96.6 0 A............................ | A [275420] ========== ====== ====== ====== ============================= ========================================================================== ================== 25 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.13 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.10, 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 [3-0] 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 [0,5.92 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 295072-293088 **** Predicted by CRISPRDetect 2.4 *** >NZ_AHUZ01000007.1 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2-4_delta.ramA::kan SEETLT21_16, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 295071 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 295010 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 294949 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 294888 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 294827 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 294766 29 100.0 33 ............................. GCTCATTAAATAACTATATAACCCCCCGGACTC 294704 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 294643 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 294582 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT G [294561] 294520 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 294459 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 294398 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 294337 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 294276 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 294215 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 294154 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 294093 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 294032 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 293971 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 293910 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 293849 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 293788 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 293727 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 293666 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC C [293657] 293603 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 293542 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 293481 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 293420 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 293359 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 293298 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 293237 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 293176 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 293115 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 [11-1] 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], //