Array 1 107863-106081 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINJ01000022.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46841 N46841_contig_22, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 107862 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 107801 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 107740 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 107679 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 107618 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 107556 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 107495 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 107434 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 107373 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 107312 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 107251 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 107190 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 107129 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 107068 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 107007 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 106946 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 106885 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 106824 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 106762 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 106659 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 106598 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 106537 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 106476 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 106415 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 106354 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 106293 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 106232 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 106171 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 106110 29 96.6 0 A............................ | A [106083] ========== ====== ====== ====== ============================= ========================================================================== ================== 29 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.09, 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 [50.0-73.3]%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 1 50-503 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINJ01000077.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46841 N46841_contig_77, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 50 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 111 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 172 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 233 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 294 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 355 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 416 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 477 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 8 29 98.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGGCGAGGTCAATAAAAAATGGTGTGGCTTTACCG # Right flank : | # 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [40.0-0.0]%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], // Array 1 56-204 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINJ01000078.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46841 N46841_contig_78, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 56 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 117 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 179 26 89.7 0 ..........................--- | ========== ====== ====== ====== ============================= ================================= ================== 3 29 96.6 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCCGCGCCAGCAGGGATAAATCGAAACGAAAGAGGCTATGCGGTTGTTTATCGGTG # Right flank : C # Questionable array : NO Score: 5.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.02, 8:0.4, 9:0.69, # 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 [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [43.3-0.0]%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], // Array 1 1-208 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINJ01000079.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46841 N46841_contig_79, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 61 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 122 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 183 26 89.7 0 ..........................--- | ========== ====== ====== ====== ============================= ================================ ================== 4 29 94.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # Questionable array : NO Score: 5.29 # Score Detail : 1:0, 2:3, 3:0, 4:0.74, 5:0, 6:0.25, 7:0.01, 8:0.6, 9:0.69, # 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 [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 210-59 **** Predicted by CRISPRDetect 2.4 *** >NZ_LINJ01000080.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46841 N46841_contig_80, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 209 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 148 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 87 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCGGGGATAAACCGAATTATTTCTGTGGCTGGGGTTTCGATTCGA # Right flank : GCCAGCTTACGCTATTTACGACGTTATTGAGCAGTGTTCCCCGCGCCAGCAGGGATAAA # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [46.7-40.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //