Array 1 3022718-3020736 **** Predicted by CRISPRDetect 2.4 *** >NZ_PCMH01000004.1 Salmonella enterica subsp. enterica serovar Derby strain 2014LSAL01311 2014LSAL01311_4, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 3022717 29 100.0 32 ............................. TTGAGGTTTGCGTTGAGCCTGTTCAGCATCAC 3022656 29 96.6 32 ............................C GCTGACTCTGCGGCGGATCTTCTCAACCAGTC 3022595 29 100.0 32 ............................. CCTAGAAAAGTTTGTTTAGGCAATCAAGCCCC 3022534 29 100.0 32 ............................. GTGTTAATTAATGAGTTTATTCCGTTTTAACA 3022473 29 100.0 32 ............................. AAATTTGGTTGACAGTAAAAGAGTGTGTCGGT 3022412 29 100.0 32 ............................. TCGGCTCGAGCACTTGCGACAACAAACACACG 3022351 29 100.0 32 ............................. GCGTTGAACTTGATATTCTCTACACCGATGCA 3022290 29 96.6 32 ..C.......................... ATATGAGGCAGCTCGCTGGCGGCTGGGATGGT 3022229 29 100.0 32 ............................. CCGTTTTTTTCCCACAGTTTGCCACCGAGACG 3022168 29 100.0 32 ............................. TTAAGTCGCTCTTTGTACGCTACACCGGAGGC 3022107 29 100.0 32 ............................. AAATATCCAGAGCTGGGCTTGAGGCTGACGGT 3022046 29 100.0 32 ............................. TAATTGACATACATTCACCATATTAAGGAAGA 3021985 29 100.0 32 ............................. CCATGCGCGGCGGCGCTTGCCCAGCTCAGAAA 3021924 29 100.0 32 ............................. GTAGTCTTCATATGCAGCGACATCATTGCCGA 3021863 29 100.0 32 ............................. GTCATTTTCTTGTTAATGGCGCTTGCATTAAC 3021802 29 100.0 32 ............................. CTGTGTGGTCTGTGCATAACGGTGTAACAGAG 3021741 29 100.0 32 ............................. AAAAATAGTCCTGAACGATAGCCCGCGCGGTC 3021680 29 100.0 32 ............................. CAGGAGTGGCTGGAGACTGTCGTCAAGCCTGA 3021619 29 100.0 32 ............................. GACCTATCAGCCTAATTTCCGGGGCAAGAGCT 3021558 29 100.0 32 ............................. ATTACGGGATAATAGTTTTGGTAATGGGTTGC 3021497 29 100.0 32 ............................. CCGCCAATATAAAGAACACTTTTATTTAAATA 3021436 29 100.0 32 ............................. GCGTTTATTTTTGATTTGTTATTTGGACGTTA 3021375 29 100.0 32 ............................. TTCCGGTCCTGCCCACTATTCGACAAAATCAG 3021314 29 100.0 32 ............................. GCTGATATCCGCCTGATTGGTGATCTGCGTCG 3021253 29 100.0 32 ............................. AATCCACATCCTGTTTAGCTCCATATAGCCCC 3021192 29 100.0 32 ............................. CCGAATTTCTCCGCGAACGCCCACCAGTCGCG 3021131 29 100.0 32 ............................. AGTTCGCCAGCGGTGCCCGCGATCTGGAGCTG 3021070 29 100.0 32 ............................. TCGCTTATCTTGAAATCGTCATCGGTCAGACC 3021009 29 100.0 32 ............................. GATCATCACCCAGGCATTTTCTGGAATATGAA 3020948 29 100.0 32 ............................. AATCCCGATGATCATGAATATTTCTGGCGCCA 3020887 29 100.0 32 ............................. GCAGAAACAGAAACCGGATATGAGCCATCCAT 3020826 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 3020765 29 96.6 0 A............................ | A [3020738] ========== ====== ====== ====== ============================= ================================ ================== 33 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCCCCTCAGCCTGCGTCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTCAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # 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: 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 [2-2] 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 3040654-3038976 **** Predicted by CRISPRDetect 2.4 *** >NZ_PCMH01000004.1 Salmonella enterica subsp. enterica serovar Derby strain 2014LSAL01311 2014LSAL01311_4, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 3040653 29 100.0 32 ............................. AGCGCCGATCCGGTGGTGTCCAACACAACGAA 3040592 29 100.0 32 ............................. GCTTCTGATTGCATTAGCTCCAAATCAGTACC 3040531 29 100.0 32 ............................. GCGTCAGGCGTGGTGGCCGTGATTACGGACGA 3040470 29 100.0 32 ............................. GCGTGCGCCGGGATATTGCGCCGCGCCGAGAA 3040409 29 100.0 32 ............................. GGCTAACCCATGAACACTATTACCAAATTCAC 3040348 29 100.0 32 ............................. GTTGCCGCCCTTACTGCGCGAGGCGTTGGAAC 3040287 29 100.0 32 ............................. GAGGGGCCGTCTGCCGCATATCAAACGCTATC 3040226 29 100.0 32 ............................. CAACACGAAAGAAAAAATACTCAATATTATTG 3040165 29 100.0 32 ............................. AAAATCATCATGGCCAGCGCTGGCGCGCTCGC 3040104 29 100.0 32 ............................. AATGATTATATCGATCGACCAATCGATGAGCA 3040043 29 100.0 32 ............................. TCGGTGAGACAAATCATTCCAGATTGATCAAC 3039982 29 100.0 32 ............................. AATTTAAACAGTAATTTAAAATTGTTAGCGTC 3039921 29 100.0 33 ............................. GCAACGGCGGCGCGGCATTCTGCGGTGCAAATA 3039859 29 100.0 32 ............................. GATTCCAGCGCGCCAAAATCAGGAGATTCCGT 3039798 29 100.0 32 ............................. CCCCCGGCATTCGGCTATGCCTATTCATATGT 3039737 29 100.0 32 ............................. TGGTCACTACCGTCTATCTCTTCCGGATACAC 3039676 29 100.0 32 ............................. CTTGCAGCCGAATACGGTATAGAGTGGGACGG 3039615 29 100.0 33 ............................. GCCTGTCCTGCGTCAGCGTTACCAGCTTCATGC 3039553 29 100.0 32 ............................. AAATTCAATTACGACTCGCTGCCTGACGGGGT 3039492 29 100.0 32 ............................. ATTTTGAGCGGACGGGAGCTGGCCGAATGACC 3039431 29 100.0 33 ............................. CGGTTTTTACTTTTGCTGCATTCCGCCTCCCGG 3039369 29 100.0 32 ............................. TCCTGGCAGGAATACAAACTTGTGATGCTGCG 3039308 29 96.6 32 .............T............... ACCGCAGGCGCAGCGGCAATATTCTGGTTCAA 3039247 29 96.6 32 .............T............... TCGTTTCTGGGAGCGGGTCTTTCCAGTATTGC 3039186 29 96.6 32 ...........C................. CAGGGGAAGAGGTTCCGGCCCAGCAGTTCTAT 3039125 29 100.0 32 ............................. CTGCTGGGTCGTGTTTGACTCAACGCTCCCCA 3039064 29 100.0 32 ............................. ATTTTAGAATTACGCATTGAGCCGATGATGTA 3039003 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 28 29 99.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTCGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # 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: 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], //