Array 1 1-926 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHED01000085.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43469 N43469_contig_85, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 1 28 96.6 32 -............................ GTCGTTCATCAGGCACTACCGGCACTTTCTGG 61 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 122 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 183 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 245 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 348 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 409 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 470 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 531 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 592 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 653 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 714 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 775 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 836 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 897 29 96.6 0 A............................ | A [923] ========== ====== ====== ====== ============================= ========================================================================== ================== 15 29 99.3 35 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.02 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:-0.19, 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: NA [0.0-0.0]%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 9-218 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHED01000129.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43469 N43469_contig_130, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 9 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 70 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 131 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 192 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 4 29 97.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GATAAAGAG # 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 [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [10.0-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-577 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHED01000141.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43469 N43469_contig_142, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 61 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 122 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 183 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 244 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 305 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 366 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 427 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 488 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 549 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 10 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTGACGGTGACGTCAGTGCCGAAGGCGAAATAGTGTTCCCCGCGCCAGC # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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: R [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-31.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.68 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-211 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHED01000142.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N43469 N43469_contig_143, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ CCAGCTTACGCTATTTACGACGTTATTGAGCA 61 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 122 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 183 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 4 29 97.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGCGTGTTCCCCGCGCCAGC # 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: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-36.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.68 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //