Array 1 470480-472093 **** Predicted by CRISPRDetect 2.4 *** >NZ_QRCO01000002.1 Salmonella enterica subsp. enterica serovar Alachua strain 98/15 NODE_2_length_704824_cov_36.4881, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 470480 29 96.6 32 ............................A TTACCGTATGACAAGCGGGTAAAAAAAAGCCC 470541 29 100.0 32 ............................. AAAACATGCATATGGGCTGGTAACGGCTTTGT 470602 29 100.0 32 ............................. TCGTGACCATGAATAATGACGTCATCACCGCG 470663 29 100.0 32 ............................. TGCACATTATTTCAGGGCGAAATCTCGTCCGC 470724 29 100.0 32 ............................. ATGCTGGCGCATCATGTAAAATCGCGTGCCAA 470785 29 100.0 32 ............................. TCGGTTATTGAGGACGTCACCGACGACGCACT 470846 29 100.0 32 ............................. ACATTGAACCTCCTCAATAGGGCAGGTCGTTC 470907 29 100.0 32 ............................. GAACGACGACCAGATTAACGCCGGTCTGGAAA 470968 29 100.0 32 ............................. GCTCAAAACTCGGATGGTATAGGCGTGGCGCA 471029 29 100.0 32 ............................. GCGCGGCATAACAGCACGGGCACGCCGCCAGG 471090 29 96.6 32 .................A........... ATAAATTATCGGGAAATCATAATCAGCGCCGC 471151 29 100.0 32 ............................. TCGAGTTCTGGCATGTCAGACTGACGTATCGC 471212 29 100.0 32 ............................. CCATTTTTGATCATCTCCTCCAGCCTGCTGAG 471273 29 96.6 32 .............T............... GCGCAGTATCAGGGAACGGCCGTTATTACGGT 471334 29 100.0 32 ............................. GCAATGGCAAGTAGTTCTCAGATGAAAGTCAG 471395 29 100.0 32 ............................. CCAACGGACGAGATCCTGGACTGCGACGGGCT 471456 29 100.0 32 ............................. GAAAGATTCACATTTAAAACTAGTGATTTTTC 471517 29 100.0 32 ............................. CGGGCGTTAACGTCCGAAGAGGTTCGCGAAAC 471578 29 100.0 32 ............................. TCTGGTGATTTGAAAGACTGGCACGCAGAGGA 471639 29 100.0 32 ............................. AAGATACAAAAAAGTACACGTAAAGTGCACGT 471700 29 100.0 32 ............................. CCATAAGAGCATCCCCGCCATCCGGAGGGGAA 471761 29 100.0 32 ............................. AAAAAAATGCGATCGGTACTCAACCCGGCCAC 471822 29 100.0 32 ............................. TGGGACATTCTCGCTAGTCACGGTCATGTCAT 471883 29 100.0 32 ............................. TGGTCGCAGCCTGGCCTGTTGCCGTAGAATCG 471944 29 96.6 32 .........T................... AGTTACTGATGCAGACTGCGGATCTTAATCGG 472005 29 100.0 32 ............................. TGCGCCAACGACTGGAATTTTTGCGTGTAGCC 472066 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 27 29 98.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCTCTATCAATTTTACGGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGGGCTGGAGCGGATAAATCGTTGAAGGCTAGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTCGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCATGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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 [1-6] 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 488352-489175 **** Predicted by CRISPRDetect 2.4 *** >NZ_QRCO01000002.1 Salmonella enterica subsp. enterica serovar Alachua strain 98/15 NODE_2_length_704824_cov_36.4881, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 488352 29 100.0 32 ............................. ACGAGTCGCAGGAGGGCGAAACCATATTATCC 488413 29 100.0 32 ............................. ACCCATATCAACGCACCGAAATTACGGACGGC 488474 29 100.0 32 ............................. ACGACTGAATTAAAACCATACGGCGGCTCATA 488535 29 100.0 32 ............................. ACGGGGAGTCAGTCACATCCATTGAGGATGCG 488596 29 100.0 32 ............................. CCTCCAGGATACCCCCACCGATGAAGGTGGGG 488657 29 100.0 32 ............................. CAGTATTTCGGTATGGCTAGCCACAGCGCGAA 488718 29 100.0 32 ............................. AAATCATTCATCATCGCGATAGCGATCGAATC 488779 29 100.0 32 ............................. GCGTTGGCGTCGCCCAACACCATCGCCGGGGC 488840 29 100.0 32 ............................. AATGCTTTGGCAAAATCAATTCCCCCAATTGA 488901 29 100.0 32 ............................. TCCGGGCGTACAGATATCATGAGTTCTGACGA 488962 29 100.0 32 ............................. GTGCTCCAGTGGGCTGCTAAGGGGCTTGGTGG 489023 29 100.0 33 ............................. GCCTCAAGGTCATGCAGGTGAATGTCCCCAGAC 489085 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 489146 29 96.6 0 A............................ | A [489172] ========== ====== ====== ====== ============================= ================================= ================== 14 29 99.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGCTACCGCCAGCGATACCAGAACCTGAATCCCTGGGGGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTGGAGATTCGTGCCGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCTTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGTATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGCGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-50.0]%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], //