Array 1 2955945-2954817 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025446.1 Salmonella enterica subsp. enterica serovar Agona strain USDA-ARS-USMARC-76333 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 2955944 29 100.0 32 ............................. GAGGCGCTGGCCGCGCTGGCCGCAGAAAAATT 2955883 29 100.0 32 ............................. GTAGCCTTCAGACACTTTAGCCAGGTTCCCTA 2955822 29 100.0 32 ............................. AGCGAAAAAAAAGACGACGAACTCGTCACAAC 2955761 29 100.0 32 ............................. CGCACCTGCCGGGACATGACCCTGCCGGAGCT 2955700 29 100.0 32 ............................. GTCATTTTCTTGTTAATGGCGCTTGCATTAAC 2955639 29 100.0 32 ............................. CTGTGTGGTCTGTGCATAACGGTGTAACAGAG 2955578 29 100.0 32 ............................. CTGGGAAGATTGGGCGCTTTCAATATCTTCCA 2955517 29 100.0 32 ............................. AAAAATAGTCCTGAACGATAGCCCGCGCGGTC 2955456 29 100.0 32 ............................. CAGGAGTGGCTGGAGACTGTCGTCAAGCCTGA 2955395 29 100.0 32 ............................. TTTTATAACGACACTAAAACCCGCCAGTTATA 2955334 29 100.0 32 ............................. ATTTTAACGGCAAGGTCGACAGGAGATACCAC 2955273 29 100.0 32 ............................. GATCATCACCCAGGCATTTTCTGGAATATGAA 2955212 29 100.0 32 ............................. AATCCCGATGATCATGAATATTTCTGGCGCCA 2955151 29 100.0 32 ............................. GCTAAAACGGCGCTTGAGAACAGTATCAATAT 2955090 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 2955029 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 2954968 29 100.0 32 ............................. GCAGAAACAGAAACCGGATATGAGCCATCCAT 2954907 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 2954846 29 93.1 0 A...........T................ | A [2954819] ========== ====== ====== ====== ============================= ================================ ================== 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 2972747-2972231 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP025446.1 Salmonella enterica subsp. enterica serovar Agona strain USDA-ARS-USMARC-76333 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 2972746 29 100.0 32 ............................. GCGACTGGCTGGTCAGCACGCCGTTAGTCGCC 2972685 29 100.0 32 ............................. AAATTGTCTGATAGATTGGCAAAAGCGATGGA 2972624 29 100.0 32 ............................. GCATCCCGGACAACAGGATCATCCCATTTATT 2972563 29 100.0 32 ............................. CCAACTGGCCTAAAGCAAATCCCGGCTTAGGC 2972502 29 100.0 32 ............................. GTTAAGGGGGAGTGAGATGCAGATAAAAACGA 2972441 29 100.0 32 ............................. TTTCCAAAAATCACGTCACCCGTTGTGATCTG 2972380 29 100.0 32 ............................. AAGGTTAGCGTTGTCATTGATCTGGTCGGCAA 2972319 29 96.6 32 ............T................ AGCGGCTAAACCTGCCGGTTATCGCTGAGCAG 2972258 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], //