Array 1 5127-5397 **** Predicted by CRISPRDetect 2.4 *** >NZ_LNCZ01000045.1 Salmonella enterica subsp. enterica serovar Derby strain 2013LSAL02374 contig_14, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================ =================================== ================== 5127 28 100.0 35 ............................ TGGTCAACTGTTGGTTACCTGCGACCGACAGCGTC 5190 28 100.0 32 ............................ GCACCAGTTGGTTGCCTGATAGCGTCAGCAAC 5250 28 89.3 32 .CC...............A......... TGGTCAGTTGATTATCTGATACCGACAGCACC 5310 28 100.0 32 ............................ TGGTCAGTTGGTTACCTGCTACAGTAAGCACC 5370 28 82.1 0 .CC.......A.....G..T........ | ========== ====== ====== ====== ============================ =================================== ================== 5 28 94.3 33 TGTAGTCCTGCCGGCAACGGCGGCAGGC # Left flank : TCATCTGGTGCAGAGCAAGTGTGACCCGATCCTGGCAGCTTGCTGTTGCCTCTGTTGCCATGGCAAAGGTTTTTGCTCTCAGCGCCTCATCTTCAGCCAGTTGTACCAGCCAGGACGATATCTGTGCCTTAAACCCCGCGTCCTTCATGAAGTTTTCCGTCTCACTCAGTCTGTCCAGGAAGAGGCTGAAGGCAGCAGCGTTATCTTCCTGTCCGAACATATGCCATCTGTCTGCAGGAGCCGGTTCGCCCTCCCGGGCAGGCACCAGCCAGCCAGCGGCCGCCAGGTGCAGTGCCCGGGCTTCCCGGGGGGCTGAGGCTCCCGCCATATCGAATAGTATCCTGGGGCCTGAATAGCCTGGCGCGCTGGTGATCTCCCGCAGCGCCTGCAGAGTGCGTTCAGACAGAGGATTGCCTTCCAGATTTACGCTTGCCTCTGAAGACAGACCCGTGATGCTTTCCGGCAGGCTGGTCAGTTGGTTATTGCGGGCATACAACCGT # Right flank : CTAGTCAGATAATTATTATGAGGAATAACTAATGTTGTTATATGCGTTGGTAAACAGTCTGGTAAGGCGGTAAGGCCTGACTCTCCCACATTAAGCTCTCGACTGCCGTTATTCAGGCAAGTACATATTCTCTGTACCGTCGCAGCACGACCGCGTAACTCTTCTGCTGGCGCAGCCCTCTTCCATTCTGACCAGACAGCATCATACGCTGCTGGTGTCTGTGGAGCCGCCGGATCAGGAAGGGGGGATACCTGGAGTGTCCCGGATGCCCCTTCCGCATGTTCTGTACATTCCTCTCCCTGTTCTATGTCCATGGTGAAGCGATATGTTTCATTGTGCCCCTGGCAATTCACGGTATAGTTCCCGGCGTCATCAAGGGTGACCGACAATATCTCCTGGTTGTCTGCATCCAGGATACAGAAGTGGCTTTCCCCGTGGCGGCCGGAGTGAATGCTTTCCTCGTATCCGGCATACGCGAGCATCCTGAGCTGTTCAAATCT # Questionable array : NO Score: 2.57 # Score Detail : 1:0, 2:0, 3:0, 4:0.71, 5:0, 6:0.25, 7:0.01, 8:0.6, 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 : TGTAGTCCTGCCGGCAACGGCGGCAGGC # 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: NA [4,4] Score: 0.37/0.37 # Reference repeat match prediction: NA # Secondary Structural analysis prediction: F [-10.20,-7.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [43.3-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.78,0.27 Confidence: MEDIUM] # Array family : NA // Array 1 29944-28205 **** Predicted by CRISPRDetect 2.4 *** >NZ_LNCZ01000068.1 Salmonella enterica subsp. enterica serovar Derby strain 2013LSAL02374 contig_35, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 29943 29 100.0 32 ............................. CGAATATATATGATATCGAATAACGAAGCAAA 29882 29 100.0 33 ............................. CGCCTGATCCCGGTACTCCAGAGTATTTCCAGT 29820 29 100.0 32 ............................. TCTAACACTCAAAGGTGGAATGACAGAGCCTT 29759 29 100.0 32 ............................. TTTGCCACGCACCGCAAACAGGCAGTCTTCAC 29698 29 100.0 32 ............................. CACGCCGCCATCACTGACAGCACAAAAACAAA 29637 29 100.0 32 ............................. GATGAGTACATGGAAAGCTTTAAGCAAAAGTT 29576 29 100.0 32 ............................. GCGATAGCTGTTTTCATAACGTGATCTCCAAT 29515 29 100.0 32 ............................. GGGTAAAAAACTATACGATCCGCGCTTAGGGG 29454 29 100.0 32 ............................. GGACAATTTGTGCTTTTGCAATTCACTTTGAA 29393 29 100.0 32 ............................. TTTGTATTTAAACAATAAGGCGAATTATGAAA 29332 29 100.0 32 ............................. GTTCCACAGGACGTTGAGAACGGCTTTATACA 29271 29 100.0 32 ............................. AGACGATGGCGGAGGCGCAGAAATCTAACCTG 29210 29 100.0 32 ............................. CTGATTGACATGACGTCCGGCGACGACTGGAA 29149 29 100.0 32 ............................. GTCTATAACCGTCGCCTCACGACTCGGCATGT 29088 29 100.0 32 ............................. CGCCCGGAATCAGCGCCGTCTATTGAGGGGTT 29027 29 100.0 32 ............................. AACGATATCACCGTACTGGCGAAAACGCTGCG 28966 29 100.0 32 ............................. CCCGATAATTCTATATCGGGCATTGATTACTG 28905 29 100.0 32 ............................. ACTGGCAGCACATAACCGGTTCGGACGCAGCC 28844 29 100.0 32 ............................. GCTGCGTTCAACAACGGGGAAATGCCGGAGAA 28783 29 100.0 32 ............................. GAGAGGCCGACTCAGCAACCAAAAAAGGGAAG 28722 29 100.0 32 ............................. AACGCGCAGCGCAGCAAAAAGCCGAGCTGGAG 28661 29 96.6 32 .............T............... CTGTTAACAGGGGGAATGCTGAAGCAGCGAAA 28600 29 96.6 32 .............T............... CGTGACTACTGCAACTTAAATCACGACGAAAT 28539 29 96.6 32 .............T............... TCTCTGCCGCTACCGCGCTGGACTGCGCCGCC 28478 29 100.0 32 ............................. AGTAATCAACTCAATGCGCTCACAACGCAATG 28417 29 100.0 32 ............................. CCAGATCGCGCAAATCGCTGCGAGTATTCAGG 28356 29 96.6 32 ............T................ TCCACGTCGCCCGCCATCAGGTTCGCCAGCTC 28295 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 28234 29 93.1 0 A...........T................ | A [28207] ========== ====== ====== ====== ============================= ================================= ================== 29 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTAGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTAGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAATAAAAAAGGGCTTTTAGAACAAATACATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGAACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 [51.7-70.0]%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 47222-46584 **** Predicted by CRISPRDetect 2.4 *** >NZ_LNCZ01000068.1 Salmonella enterica subsp. enterica serovar Derby strain 2013LSAL02374 contig_35, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 47221 29 100.0 32 ............................. ACAACGCCGGGCCGGGGCGGGGGGCGGAAGCT 47160 29 100.0 32 ............................. CCGCATCATTACTGACCTGAACGCCCCGCAAG 47099 29 100.0 32 ............................. CCTGACAATTTGAAATACTCCGCTGAAATGAT 47038 29 100.0 32 ............................. TCAACGGCCTGCCGGGTAAATCGGTTCACGTG 46977 29 100.0 32 ............................. TTGACGAGCGGTGATGTGTGCCGGAGTGGATA 46916 29 100.0 32 ............................. TGATATGAGGCAAACGGCAGGTTACGCGCCAG 46855 29 100.0 32 ............................. AACATCGTCGCCAGGCGTTTTTGCATGTCGTC 46794 29 100.0 32 ............................. CCTCGCCGTCATTCGACATTACGTTCACTCAC 46733 29 100.0 32 ............................. TAACCATCGTGACGTGTGAAGTTGCCGCCCAG 46672 29 100.0 32 ............................. ATTTTAGAATTACGCATTGAGCCGATGATGTA 46611 28 79.3 0 ...........C...A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 11 29 98.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATTGCCTGATGCTCTATCAATTTTACGGACGGCCTGCCGATGCCGTCTGTGACTTATCCATTACCTTGCATTGTTTATTTTCTCTATGCGAATTTCGATGAGTGTATAAAAGCGCGGATAAATTTTTCCATAGCGATGCATGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTAGTGCTGATAAAAAGTGGTTTATAAACAATGACATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGGAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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 [63.3-68.3]%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], //