Array 1 2955974-2954846 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025448.1 Salmonella enterica subsp. enterica serovar Agona strain USDA-ARS-USMARC-76336 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 2955973 29 100.0 32 ............................. GAGGCGCTGGCCGCGCTGGCCGCAGAAAAATT 2955912 29 100.0 32 ............................. GTAGCCTTCAGACACTTTAGCCAGGTTCCCTA 2955851 29 100.0 32 ............................. AGCGAAAAAAAAGACGACGAACTCGTCACAAC 2955790 29 100.0 32 ............................. CGCACCTGCCGGGACATGACCCTGCCGGAGCT 2955729 29 100.0 32 ............................. GTCATTTTCTTGTTAATGGCGCTTGCATTAAC 2955668 29 100.0 32 ............................. CTGTGTGGTCTGTGCATAACGGTGTAACAGAG 2955607 29 100.0 32 ............................. CTGGGAAGATTGGGCGCTTTCAATATCTTCCA 2955546 29 100.0 32 ............................. AAAAATAGTCCTGAACGATAGCCCGCGCGGTC 2955485 29 100.0 32 ............................. CAGGAGTGGCTGGAGACTGTCGTCAAGCCTGA 2955424 29 100.0 32 ............................. TTTTATAACGACACTAAAACCCGCCAGTTATA 2955363 29 100.0 32 ............................. ATTTTAACGGCAAGGTCGACAGGAGATACCAC 2955302 29 100.0 32 ............................. GATCATCACCCAGGCATTTTCTGGAATATGAA 2955241 29 100.0 32 ............................. AATCCCGATGATCATGAATATTTCTGGCGCCA 2955180 29 100.0 32 ............................. GCTAAAACGGCGCTTGAGAACAGTATCAATAT 2955119 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 2955058 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 2954997 29 100.0 32 ............................. GCAGAAACAGAAACCGGATATGAGCCATCCAT 2954936 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 2954875 29 93.1 0 A...........T................ | A [2954848] ========== ====== ====== ====== ============================= ================================ ================== 19 29 99.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTGAACCCCCTCAGCCTGCGTCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCTTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACACGTTGCTGGTATCCGTCTTTTTTACCCAGGTTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.23 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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: R [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.00,-13.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [4-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.92 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 2972776-2972260 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025448.1 Salmonella enterica subsp. enterica serovar Agona strain USDA-ARS-USMARC-76336 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 2972775 29 100.0 32 ............................. GCGACTGGCTGGTCAGCACGCCGTTAGTCGCC 2972714 29 100.0 32 ............................. AAATTGTCTGATAGATTGGCAAAAGCGATGGA 2972653 29 100.0 32 ............................. GCATCCCGGACAACAGGATCATCCCATTTATT 2972592 29 100.0 32 ............................. CCAACTGGCCTAAAGCAAATCCCGGCTTAGGC 2972531 29 100.0 32 ............................. GTTAAGGGGGAGTGAGATGCAGATAAAAACGA 2972470 29 100.0 32 ............................. TTTCCAAAAATCACGTCACCCGTTGTGATCTG 2972409 29 100.0 32 ............................. AAGGTTAGCGTTGTCATTGATCTGGTCGGCAA 2972348 29 96.6 32 ............T................ AGCGGCTAAACCTGCCGGTTATCGCTGAGCAG 2972287 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 9 29 97.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.15 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 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: R [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-12.00,-13.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [6-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //