Array 1 273-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHEP01000115.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43822 N43822_contig_124, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 272 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 210 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 149 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 88 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 5 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCCGCGCCAGCGGGGATAAACCGAAAATGCAGGTGGGGTAACGAATGCGAGATT # Right flank : C # 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: 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 [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-38.3]%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 2-639 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHEP01000111.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43822 N43822_contig_112, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 2 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 63 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 124 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 186 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 247 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 308 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 369 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 430 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 491 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 552 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 613 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 11 29 97.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AG # Right flank : | # Questionable array : NO Score: 5.91 # Score Detail : 1:0, 2:3, 3:0, 4:0.86, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.79, # 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 [3-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [1.7-0.0]%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 1 163419-162309 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHEP01000020.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43822 N43822_contig_20, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 163418 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 163357 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 163296 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 163235 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 163174 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 163113 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 163052 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 162990 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 162887 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 162826 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 162765 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 162704 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 162643 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 162582 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 162521 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 162460 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 162399 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 162338 29 96.6 0 A............................ | A [162311] ========== ====== ====== ====== ============================= ========================================================================== ================== 18 29 99.4 35 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCAGCGGGGATAAACCGTTACGTGTTTATTCATCTGTTGCATTAGATT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.07 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.15, 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 [3-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [50.0-46.7]%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 1 333-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHEP01000081.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43822 N43822_contig_81, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 332 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 271 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 210 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 149 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 88 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 6 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGAACAGGAACAGGAAAAAAAAGATTTGTCCGG # Right flank : C # 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 [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-43.3]%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], //