Array 1 44820-45671 **** Predicted by CRISPRDetect 2.4 *** >NZ_SDJD01000039.1 Salmonella enterica strain CFSAN074577 CFSAN074577_R1_contig_39, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 44820 29 100.0 32 ............................. TTGCGTATTTCGATTGTCTGGACATTTCGTAC 44881 29 100.0 32 ............................. GCAGAATATGATTTATATAGAACCAATGAACT 44942 29 100.0 32 ............................. CCGGCGTGTGTTGTTGAGGATCAGTCTGGAGA 45003 29 100.0 32 ............................. CGGGCCATGTTCTTTTCCCTCTAAAAAATCCG 45064 29 96.6 32 ............................C GTTGCTCAAAAAACTGAACGAGGGTAACTACC 45125 29 100.0 32 ............................. ATTGTGTTGTCGCCGCTAGTGGCTTGGGTTAA 45186 29 100.0 32 ............................. AATATCCACTTAAACACAACCATTATTCGCTA 45247 29 100.0 0 ............................. - Deletion [45276] 45276 29 93.1 32 ..T...A...................... CCGGCATCAGCGCCGATCCGTTCATAGTGCCC C [45280] 45338 29 100.0 32 ............................. GTCCGTCAGGTTGGATCGGATGGCATTCCGGT 45399 29 100.0 32 ............................. CTTTCATTGCGCAGGGTATGCAGTCGGTTTCC 45460 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 45521 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 45582 29 100.0 32 ............................. ACGTTTTAACAGGGTAATATTTACTTAATTAT 45643 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 15 29 99.3 30 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTACTTTATTATCTCTCGCATAGACCCGGCAGTGTTCCCCGCGCCAGCGGGGATAA # Questionable array : NO Score: 6.01 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:-0.20, 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 [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-43.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 50-260 **** Predicted by CRISPRDetect 2.4 *** >NZ_SDJD01000052.1 Salmonella enterica strain CFSAN074577 CFSAN074577_R1_contig_52, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 50 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 111 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 172 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 233 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 4 29 94.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGCGGTCATTTTAAAGAATCCCGTTAAACAACACG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGG # Questionable array : NO Score: 5.61 # Score Detail : 1:0, 2:3, 3:0, 4:0.75, 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: F [1-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [43.3-63.3]%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 2 16508-17330 **** Predicted by CRISPRDetect 2.4 *** >NZ_SDJD01000052.1 Salmonella enterica strain CFSAN074577 CFSAN074577_R1_contig_52, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 16508 29 100.0 32 ............................. CCAGCCTGTAGCGTGGGGGCGTTGGGTAGCCT 16569 29 100.0 32 ............................. CATCTTTTACGCATGTTGATGTGCGTTCAAAT 16630 29 100.0 32 ............................. AAATCGTCAATAAAATTATTGGCGCGCCATCC 16691 29 100.0 32 ............................. ATAATTTGCTGAACTACGTCCGTATTGAGCTG 16752 29 100.0 32 ............................. TGGCCGGAGCCTAAAGACGGGGAGCCGCGTTT 16813 29 100.0 32 ............................. GGGGGTGATAACCGCCTCGCTGAACGCTACGC 16874 29 100.0 32 ............................. AGTGAAAAATTGCGGTTCGTCCTCCTCATCGT 16935 29 100.0 32 ............................. ACTAACGAAAGATTAAACCAGCGCATTGAGTT 16996 29 100.0 32 ............................. CATTCGCTCAATAGCGGCCCGCGTGGCGGTGA 17057 29 100.0 32 ............................. GGGATTATGTCCTCTAAAGACTGGCTAATCAC 17118 29 100.0 32 ............................. CGCGCCCTGCGTGATTTTGAAAATCTGGTGGA 17179 29 96.6 32 .........................G... TTGAATACGTCGCGATACCAGTCACTCCGGAA 17240 29 93.1 32 ..C..........T............... AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 17301 29 93.1 0 A...........T................ | A [17327] ========== ====== ====== ====== ============================= ================================ ================== 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], //