Array 1 1647-49 **** Predicted by CRISPRDetect 2.4 *** >NZ_NAAM01000028.1 Salmonella enterica subsp. enterica serovar Typhimurium strain R9_3275_R1 NODE_2_length_336407_cov_0.96461_ID_3, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1646 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 1585 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1524 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 1463 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 1402 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 1341 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 1280 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 1218 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 1157 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 1096 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 1035 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 974 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 913 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 852 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 791 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 730 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 669 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 608 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 547 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 486 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 424 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 363 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [322] 321 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 260 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 199 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 138 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 77 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 27 29 98.5 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GAACGAATTGAGACTATTAGAGATTATTCGCCTGTGTTCCCCGCGCCAG # Questionable array : NO Score: 6.13 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:-0.05, 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 [10-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [41.7-71.7]%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 19271-17778 **** Predicted by CRISPRDetect 2.4 *** >NZ_NAAM01000028.1 Salmonella enterica subsp. enterica serovar Typhimurium strain R9_3275_R1 NODE_2_length_336407_cov_0.96461_ID_3, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 19270 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 19209 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 19148 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 19087 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 19026 29 100.0 32 ............................. CGTCAGCTCGGTATTGAGGCCGGGGACCGCCC 18965 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 18904 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 18843 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 18782 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 18721 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 18660 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 18599 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 18538 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 18477 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 18416 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 18355 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 18293 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 18232 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 18171 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 18110 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 18049 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 17988 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 17927 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 17866 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 17805 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 25 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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 [9-1] 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], // Array 1 52-325 **** Predicted by CRISPRDetect 2.4 *** >NZ_NAAM01000057.1 Salmonella enterica subsp. enterica serovar Typhimurium strain R9_3275_R1 NODE_15_length_106462_cov_0.947736_ID_29, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 52 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 113 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 174 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 235 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 296 29 96.6 0 A............................ | A [322] ========== ====== ====== ====== ============================= ================================ ================== 5 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGCCAGCGGGGATAAACCGAACGAATTGAGACTATTAGAGATTATTCGCCTG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:0.01, 8:0.8, 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [45.0-48.3]%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], //