Array 1 1-577 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCIL01000202.1 Salmonella enterica subsp. enterica serovar Newport strain SE93 NEWPORT_S5_trimmed_contig_223, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 29 100.0 32 ............................. TTGATTTACCCGCCACTTATTCCCCATTGCAT 62 29 96.6 32 ..........................T.. GGACTATCAAACCATCTATGATGCCAATTTTA 123 29 100.0 32 ............................. CGCGGGGCTGGTATTCGATACAGACCCGGCTA 184 29 100.0 32 ............................. GGAATAAAAATGAATTTGAGTCAACTCTATAA 245 29 100.0 32 ............................. CGTTAGGCTGCGGTTGGGCACCGAAGAAAAAA 306 29 100.0 32 ............................. ATTATCCCGGAAATCGTGATCAACTACGCAGG 367 29 100.0 32 ............................. ATTGTTATTGCGGTAACGGATAATTTATCATT 428 29 100.0 32 ............................. CCTGGCGATCGCATTTGGGTGCGGGAAACATT 489 29 100.0 32 ............................. CCGAATATGGTGATAATGTTGCACCTTCGCTC 550 28 93.1 0 .......................-....T | ========== ====== ====== ====== ============================= ================================ ================== 10 29 99.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TAATCCAGACAAAAAAACTGGCCAATTACCCGTATCCCAATTTATTATCGATTTCATTGTAATCCCCCTGCTACAGGAAAAAGATGACACAGATAGAATATCTGGACTACCTCTGCTATTGGGGGAAAACTGATAAATCAACAAAAAACATAATCTGTAATTATCATTTACTGGCATACCATTGCCTGGACGTTGCTGCATGCGGGAAATACATAATAAAAAACAATATATTCAATTCATGTAATATATTAAAGGAATGTAATATCTCAGGTACAAATGCAGAAAACTGGATAATCTGGTTTCTTACCAGCCACGATATCGGAAAATTCGCCAGAGGATTTCAAAAATACGCCGAATTCCCAGACTCTCCCTTAGTCTCTCCCATTAGCGGTGTTTCCGCATTTGAGAGACATGATTCCTTAGGCTTCTATTTATGGGGTAAATTATTTGAAGCGTGGAGTTCAGGCAGTAATGAAATTATCGCAGGTATTGAACCAGAA # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 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 [1-2] 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 1-884 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCIL01000074.1 Salmonella enterica subsp. enterica serovar Newport strain SE93 NEWPORT_S5_trimmed_contig_78, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 29 100.0 32 ............................. CCAATAACCGACGAGGGCAAACGCCGTGCGCG 62 29 100.0 32 ............................. AGGACTGAGGGAATAGGGACCGTAATTGTAAA 123 29 100.0 32 ............................. ACAATGTTGCGTCTAATTCTCATTAATTAAAA 184 29 100.0 32 ............................. CAGACGAAAATCAGCCCGCATATTCCGACACA 245 29 100.0 32 ............................. AACAGTGGTTTTAGGTTGTCGGTGCTGATCCC 306 29 100.0 32 ............................. ATTAAACAACAGGATTTTGCAATTACTGTTGG 367 29 100.0 32 ............................. CAGACGGCAGCAGCGTGAAACACGTCAGTATT 428 29 100.0 32 ............................. TCAGCTGTTCCATACTCACCCCCTGTGCAATC 489 29 100.0 32 ............................. GCGATGTATGCCGCGACGATCGAGAGCGAACT 550 29 100.0 32 ............................. CAGCAGATGAAAAATATTTACAGATTGGTAAA 611 29 100.0 32 ............................. AAAAAATCCCGCTGACAATATTTTGCCACCTC 672 29 100.0 32 ............................. CCGGAAAACTATCTCTATCGCAGGCTGGATAT 733 29 100.0 32 ............................. TTCCAAAGGTACTCCCATATCTCCAGCCAACG 794 29 100.0 32 ............................. TAAGTTACGCCAGTGCGGGCGTGTTGCTCATC 855 29 100.0 0 ............................. | A [882] ========== ====== ====== ====== ============================= ================================ ================== 15 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 [0-1] 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 8505-7380 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCIL01000171.1 Salmonella enterica subsp. enterica serovar Newport strain SE93 NEWPORT_S5_trimmed_contig_188, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 8504 29 100.0 32 ............................. CAGTGCGGCAGCGCGCAATCGAGACACGCCAT 8443 29 100.0 32 ............................. CACAAAACGCCAGTGGCATGGTACAACCCGTA 8382 29 100.0 32 ............................. GCGTGACCATGTTTAACTCTAAATCAGGCCGT 8321 29 96.6 32 ........A.................... TCATGCTTTCGACTAAATACTACCGCGACAAC 8260 29 100.0 32 ............................. AAAATAACAACATTATCAGTGTGAAAAGTCTC 8199 29 100.0 32 ............................. AGATATGAAAAACGTAAAAATTTACACCGCCA 8138 29 100.0 32 ............................. CAATAGGACAGCCATTCGAGCGCCCAGAGTTT 8077 29 100.0 32 ............................. GTCAGTATGCACTGCTTGATAAAGTCAGGCCA 8016 29 100.0 32 ............................. AACTAACGTCTATAGCTAAATGTAGAGAAAAC 7955 29 100.0 32 ............................. CAGTTTGGAGTCAATGTTATTTCTTCAGGTCA 7894 29 100.0 32 ............................. TCTCGCTGGTTGCTCCAACTCCTGATATGCCG 7833 29 100.0 32 ............................. TAAAAATCTTCTTTCATATAACCGTAAGGGTT 7772 29 100.0 32 ............................. AGGGTTTTGTCACCTCAACGGTCGGGAGTGCA 7711 29 100.0 32 ............................. GTGCAACAGTTTCTTACCGCAAGCAGTTTGAA 7650 29 100.0 32 ............................. ATCATCGGGATTCATTTTGTTGTCCGGGTGGC 7589 29 100.0 32 ............................. CGGTGCTCTATGTCTAAAAATAAAAGCGGTTC 7528 29 93.1 32 ........T...................C AGCACAATCATTATTAGATGAACTTTCATCAA 7467 28 96.6 32 .............-............... GGGATCGCGCTGGCGGTCGCATCCGTTGCCGT 7407 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 19 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGGC # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 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 [8-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-0.0]%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], //