Array 1 317170-318385 **** Predicted by CRISPRDetect 2.4 *** >NZ_AUQR01000001.1 Salmonella enterica subsp. enterica serovar Newport str. #11-2 isolate Levine 11-2 SEEN0112_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 317170 29 100.0 32 ............................. TTGCGTATTTCGATTGTCTGGACATTTCGTAC 317231 29 100.0 32 ............................. GCAGAATATGATTTATATAGAACCAATGAACT 317292 29 100.0 32 ............................. CCGGCGTGTGTTGTTGAGGATCAGTCTGGAGA 317353 29 100.0 32 ............................. CGGGCCATGTTCTTTTCCCTCTAAAAAATCCG 317414 29 96.6 32 ............................C GTTGCTCAAAAAACTGAACGAGGGTAACTACC 317475 29 100.0 32 ............................. ATTGTGTTGTCGCCGCTAGTGGCTTGGGTTAA 317536 29 100.0 32 ............................. AATATCCACTTAAACACAACCATTATTCGCTA 317597 29 100.0 0 ............................. - Deletion [317626] 317626 29 93.1 32 ..T...A...................... CCGGCATCAGCGCCGATCCGTTCATAGTGCCC C [317630] 317688 29 100.0 32 ............................. GTCCGTCAGGTTGGATCGGATGGCATTCCGGT 317749 29 100.0 32 ............................. CTTTCATTGCGCAGGGTATGCAGTCGGTTTCC 317810 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 317871 29 100.0 31 ............................. AACAGGAACAGGAAAAAAAGATTTGTCCGGT 317931 29 100.0 32 ............................. ACGTTTTAACAGGGTAATATTTACTTAATTAT 317992 29 100.0 32 ............................. GTTACTTTATTATCTCTCGCATAGACCCGGCA 318053 29 100.0 32 ............................. GTTACTTTATTATCTCTCGCATAGACCCGGCA 318114 29 100.0 32 ............................. CGGTCATTTTAAAGAATCCCGTTAAACAACAC 318175 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 318236 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 318297 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 318358 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 21 29 98.5 30 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGG # Questionable array : NO Score: 6.05 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:-0.13, 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 334633-335455 **** Predicted by CRISPRDetect 2.4 *** >NZ_AUQR01000001.1 Salmonella enterica subsp. enterica serovar Newport str. #11-2 isolate Levine 11-2 SEEN0112_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 334633 29 100.0 32 ............................. CCAGCCTGTAGCGTGGGGGCGTTGGGTAGCCT 334694 29 100.0 32 ............................. CATCTTTTACGCATGTTGATGTGCGTTCAAAT 334755 29 100.0 32 ............................. AAATCGTCAATAAAATTATTGGCGCGCCATCC 334816 29 100.0 32 ............................. ATAATTTGCTGAACTACGTCCGTATTGAGCTG 334877 29 100.0 32 ............................. TGGCCGGAGCCTAAAGACGGGGAGCCGCGTTT 334938 29 100.0 32 ............................. GGGGGTGATAACCGCCTCGCTGAACGCTACGC 334999 29 100.0 32 ............................. AGTGAAAAATTGCGGTTCGTCCTCCTCATCGT 335060 29 100.0 32 ............................. ACTAACGAAAGATTAAACCAGCGCATTGAGTT 335121 29 100.0 32 ............................. CATTCGCTCAATAGCGGCCCGCGTGGCGGTGA 335182 29 100.0 32 ............................. GGGATTATGTCCTCTAAAGACTGGCTAATCAC 335243 29 100.0 32 ............................. CGCGCCCTGCGTGATTTTGAAAATCTGGTGGA 335304 29 96.6 32 .........................G... TTGAATACGTCGCGATACCAGTCACTCCGGAA 335365 29 93.1 32 ..C..........T............... AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 335426 29 93.1 0 A...........T................ | A [335452] ========== ====== ====== ====== ============================= ================================ ================== 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], //