Array 1 420042-421197 **** Predicted by CRISPRDetect 2.4 *** >NZ_QWJK01000003.1 Salmonella enterica strain CFSAN048117 CFSAN048117__contig_3, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 420042 29 100.0 32 ............................. TTGCGTATTTCGATTGTCTGGACATTTCGTAC 420103 29 100.0 32 ............................. GCAGAATATGATTTATATAGAACCAATGAACT 420164 29 100.0 32 ............................. CCGGCGTGTGTTGTTGAGGATCAGTCTGGAGA 420225 29 100.0 32 ............................. CGGGCCATGTTCTTTTCCCTCTAAAAAATCCG 420286 29 96.6 32 ............................C GTTGCTCAAAAAACTGAACGAGGGTAACTACC 420347 29 100.0 32 ............................. ATTGTGTTGTCGCCGCTAGTGGCTTGGGTTAA 420408 29 100.0 32 ............................. AATATCCACTTAAACACAACCATTATTCGCTA 420469 29 100.0 0 ............................. - Deletion [420498] 420498 29 93.1 32 ..T...A...................... CCGGCATCAGCGCCGATCCGTTCATAGTGCCC C [420502] 420560 29 100.0 32 ............................. GTCCGTCAGGTTGGATCGGATGGCATTCCGGT 420621 29 100.0 32 ............................. CTTTCATTGCGCAGGGTATGCAGTCGGTTTCC 420682 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 420743 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 420804 29 100.0 32 ............................. ACGTTTTAACAGGGTAATATTTACTTAATTAT 420865 29 100.0 32 ............................. GTTACTTTATTATCTCTCGCATAGACCCGGCA 420926 29 100.0 32 ............................. CGGTCATTTTAAAGAATCCCGTTAAACAACAC 420987 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 421048 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 421109 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 421170 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 20 29 98.5 30 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGG # Questionable array : NO Score: 6.04 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:-0.14, 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 [1-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%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 2 437445-438267 **** Predicted by CRISPRDetect 2.4 *** >NZ_QWJK01000003.1 Salmonella enterica strain CFSAN048117 CFSAN048117__contig_3, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 437445 29 100.0 32 ............................. CCAGCCTGTAGCGTGGGGGCGTTGGGTAGCCT 437506 29 100.0 32 ............................. CATCTTTTACGCATGTTGATGTGCGTTCAAAT 437567 29 100.0 32 ............................. AAATCGTCAATAAAATTATTGGCGCGCCATCC 437628 29 100.0 32 ............................. ATAATTTGCTGAACTACGTCCGTATTGAGCTG 437689 29 100.0 32 ............................. TGGCCGGAGCCTAAAGACGGGGAGCCGCGTTT 437750 29 100.0 32 ............................. GGGGGTGATAACCGCCTCGCTGAACGCTACGC 437811 29 100.0 32 ............................. AGTGAAAAATTGCGGTTCGTCCTCCTCATCGT 437872 29 100.0 32 ............................. ACTAACGAAAGATTAAACCAGCGCATTGAGTT 437933 29 100.0 32 ............................. CATTCGCTCAATAGCGGCCCGCGTGGCGGTGA 437994 29 100.0 32 ............................. GGGATTATGTCCTCTAAAGACTGGCTAATCAC 438055 29 100.0 32 ............................. CGCGCCCTGCGTGATTTTGAAAATCTGGTGGA 438116 29 96.6 32 .........................G... TTGAATACGTCGCGATACCAGTCACTCCGGAA 438177 29 93.1 32 ..C..........T............... AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 438238 29 93.1 0 A...........T................ | A [438264] ========== ====== ====== ====== ============================= ================================ ================== 14 29 98.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATTTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATCCG # 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 [0-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-48.3]%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], //