Array 1 420356-421572 **** Predicted by CRISPRDetect 2.4 *** >NZ_APGX01000065.1 Salmonella enterica subsp. enterica serovar Newport str. VA_R100808502 SEEN8502_2, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 420356 29 100.0 32 ............................. TTGCGTATTTCGATTGTCTGGACATTTCGTAC 420417 29 100.0 32 ............................. GCAGAATATGATTTATATAGAACCAATGAACT 420478 29 100.0 32 ............................. CCGGCGTGTGTTGTTGAGGATCAGTCTGGAGA 420539 29 100.0 32 ............................. CGGGCCATGTTCTTTTCCCTCTAAAAAATCCG 420600 29 96.6 32 ............................C GTTGCTCAAAAAACTGAACGAGGGTAACTACC 420661 29 100.0 32 ............................. ATTGTGTTGTCGCCGCTAGTGGCTTGGGTTAA 420722 29 100.0 32 ............................. AATATCCACTTAAACACAACCATTATTCGCTA 420783 29 100.0 0 ............................. - Deletion [420812] 420812 29 93.1 32 ..T...A...................... CCGGCATCAGCGCCGATCCGTTCATAGTGCCC C [420816] 420874 29 100.0 32 ............................. GTCCGTCAGGTTGGATCGGATGGCATTCCGGT 420935 29 100.0 32 ............................. CTTTCATTGCGCAGGGTATGCAGTCGGTTTCC 420996 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 421057 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 421118 29 100.0 32 ............................. ACGTTTTAACAGGGTAATATTTACTTAATTAT 421179 29 100.0 32 ............................. GTTACTTTATTATCTCTCGCATAGACCCGGCA 421240 29 100.0 32 ............................. GTTACTTTATTATCTCTCGCATAGACCCGGCA 421301 29 100.0 32 ............................. CGGTCATTTTAAAGAATCCCGTTAAACAACAC 421362 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 421423 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 421484 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 421545 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 437820-438642 **** Predicted by CRISPRDetect 2.4 *** >NZ_APGX01000065.1 Salmonella enterica subsp. enterica serovar Newport str. VA_R100808502 SEEN8502_2, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 437820 29 100.0 32 ............................. CCAGCCTGTAGCGTGGGGGCGTTGGGTAGCCT 437881 29 100.0 32 ............................. CATCTTTTACGCATGTTGATGTGCGTTCAAAT 437942 29 100.0 32 ............................. AAATCGTCAATAAAATTATTGGCGCGCCATCC 438003 29 100.0 32 ............................. ATAATTTGCTGAACTACGTCCGTATTGAGCTG 438064 29 100.0 32 ............................. TGGCCGGAGCCTAAAGACGGGGAGCCGCGTTT 438125 29 100.0 32 ............................. GGGGGTGATAACCGCCTCGCTGAACGCTACGC 438186 29 100.0 32 ............................. AGTGAAAAATTGCGGTTCGTCCTCCTCATCGT 438247 29 100.0 32 ............................. ACTAACGAAAGATTAAACCAGCGCATTGAGTT 438308 29 100.0 32 ............................. CATTCGCTCAATAGCGGCCCGCGTGGCGGTGA 438369 29 100.0 32 ............................. GGGATTATGTCCTCTAAAGACTGGCTAATCAC 438430 29 100.0 32 ............................. CGCGCCCTGCGTGATTTTGAAAATCTGGTGGA 438491 29 96.6 32 .........................G... TTGAATACGTCGCGATACCAGTCACTCCGGAA 438552 29 93.1 32 ..C..........T............... AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 438613 29 93.1 0 A...........T................ | A [438639] ========== ====== ====== ====== ============================= ================================ ================== 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], //