Array 1 1-272 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHIQ01000128.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46844 N46844_contig_128, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 61 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 122 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 183 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 244 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 5 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : CGTCGCGGAAAATTTCGCATTGACGATAAAGAGTGTTCCCCGCG # Questionable array : NO Score: 6.02 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-35.0]%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], // Array 1 50-503 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHIQ01000130.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46844 N46844_contig_130, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 50 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 111 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 172 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 233 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 294 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 355 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 416 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 477 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 8 29 97.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGCAGATCCTCAACGGTCAGGCTGTTTAGTTCCTG # Right flank : | # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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 [1-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [36.7-0.0]%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 51-507 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHIQ01000129.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46844 N46844_contig_129, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 51 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 113 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 174 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 235 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 296 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 357 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 418 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 479 29 96.6 0 .................A........... | ========== ====== ====== ====== ============================= ================================= ================== 8 29 97.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCAGCGGGGATAAACCGCCCCGATAGCGACGCTTCTGTAGTCACTGGCAG # Right flank : GACGAGTTCTGGAAATGGTTAGCTGATAAAGAGTGTTCCCCGCG # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.98, # 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 [2-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [31.7-36.7]%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 1-209 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHIQ01000139.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46844 N46844_contig_139, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 61 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 122 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 183 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 4 29 97.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # Questionable array : NO Score: 5.73 # Score Detail : 1:0, 2:3, 3:0, 4:0.87, 5:0, 6:0.25, 7:0.01, 8:0.6, 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 [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # 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 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 190309-189444 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHIQ01000023.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46844 N46844_contig_23, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 190308 28 96.6 32 -............................ ATATTCGCCGCTTTCCATTTACCGAACGTAAC 190248 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 190187 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 190125 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 190022 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 189961 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 189900 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 189839 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 189778 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 189717 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 189656 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 189595 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 189534 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 189473 29 96.6 0 A............................ | A [189446] ========== ====== ====== ====== ============================= ========================================================================== ================== 14 29 99.3 35 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.00 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:-0.21, 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: F [50.0-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //