Array 1 1-455 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWLV01000220.1 Salmonella enterica subsp. enterica serovar Gallinarum strain NCTC 10532 NODE_220_length_484_cov_1.98319_ID_5124, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ CTGATATCGCCTCGTTAATTTCTTTTACAGCT 61 29 100.0 32 ............................. AATTAAATGAAATACGACAGCGCACGTTAAAA 122 29 96.6 32 ............................A TCCAGTCGGCGATGTTAAACAGTGACGCGACC 183 29 100.0 32 ............................. GTTGCCGGGATATGGCGGAGAATTATATATCG 244 29 100.0 32 ............................. CAGAAAGCGGTCATCACCTCCGTAATTGGTGT 305 29 100.0 32 ............................. AAATCGACCGAAAATTCGGACAGTACAACGTC 366 29 96.6 32 .................C........... TCCAGTGTTTATTTTAGACTCGCAACAATTAA 427 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 8 29 98.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : CAGAAAGCGGTCATCACCTCCGTAATTGG # 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: R [2-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-23.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.68 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 373-39 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWLV01000301.1 Salmonella enterica subsp. enterica serovar Gallinarum strain NCTC 10532 NODE_303_length_407_cov_0.628571_ID_5282, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 372 29 96.6 32 ..............G.............. CAATTGACGAGCCTTCCATATAGGACGCCCGC 311 29 100.0 32 ............................. GCATATGGAGAATACATTTACTCAGTGAATAT 250 29 100.0 32 ............................. AATATTTCTGGCGCCAGGTGCATTCCGTCGCA 189 29 100.0 32 ............................. TTCTCTGGAATTATATTTTGTTCCGCACGTTC 128 29 96.6 32 .................T........... TCATTCAGCGAACGCAGGAGAACCAGCCGCCG 67 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 98.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCGTCGCTGTTAACCGCTCTCGCACTGCGTCAGG # Right flank : GTTCGGGAATTTATTCAGCCAGACGACAGCCGAGTGTTC # 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: F [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [31.7-20.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.68,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 207686-207535 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWLV01000002.1 Salmonella enterica subsp. enterica serovar Gallinarum strain NCTC 10532 NODE_2_length_633261_cov_38.6158_ID_4678, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 207685 29 100.0 32 ............................. CAGGGCAAATTCATCCGCCGCTGATCACTGGT 207624 29 100.0 32 ............................. GACGCTTACATCTCACCGAGAGATTTTGAGGC 207563 29 93.1 0 ...........................AC | ========== ====== ====== ====== ============================= ================================ ================== 3 29 97.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATGATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATAATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGTACTACATCGCGGCTACGGCGCTCAATTCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTC # Questionable array : NO Score: 5.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 5:0, 6:0.25, 7:0.02, 8:0.4, 9:0.69, # 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: NA [5,5] 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 [-14.20,-15.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-73.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.55 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 224478-223839 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWLV01000002.1 Salmonella enterica subsp. enterica serovar Gallinarum strain NCTC 10532 NODE_2_length_633261_cov_38.6158_ID_4678, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 224477 29 96.6 32 ...........................T. AGGATTTCGCCGCGCTGTTGGCCTCCAGATTC 224416 29 96.6 32 ...........................T. CCGTGCCTGTCCAGGACAAATTGCCGATTATT 224355 29 96.6 32 ...........................T. CTGCCGGTCTGTGCTGTTGTCGTCAATAATCA 224294 29 96.6 32 ............................C AATTTAGGGGCCGGAACTCCGGGAAAGGCAGC 224233 29 100.0 33 ............................. CAAACACCAAGCTCTTCCGCCGCGCGTTCCTGA 224171 29 100.0 32 ............................. TTGCTCTCATTAAAGGGGTTTCCATGTTTGAT 224110 29 100.0 32 ............................. CCATAAGAGCATCCCCGCCATCCGGAGGGGAA 224049 29 100.0 32 ............................. AAAAAAATGCGATCGGTACTCAACCCGGCCAC 223988 29 100.0 32 ............................. CGGTCGCAGCCTGGCCTGTTGCCGTAGAATCG 223927 29 96.6 32 .........T................... TGCGCCAACGACTGGAATTTTTGCGTGTAGCC 223866 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 11 29 96.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAAGCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCGCGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGCGCTGATAAAAAGTAGTTTATAAACAATGACATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGGTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGGAGGCTTTTCTACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGATTAAGCCTGTTAGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCTCTGCCGATTGG # Questionable array : NO Score: 5.90 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.79, # 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 : GTGTTCCCCGCGCCAGCGGGGATAAACTG # 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 [6-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-66.7]%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], // Array 1 1003-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWLV01000088.1 Salmonella enterica subsp. enterica serovar Gallinarum strain NCTC 10532 NODE_88_length_1002_cov_1.55886_ID_4864, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1002 27 89.7 32 --...............C........... TCCAGTGTTTATTTTAGACTCGCAACAATTAA 943 29 100.0 32 ............................. CACGTTTCCTGCCTAATAAATGGATGATGTCG 882 29 100.0 32 ............................. CTCCAGGCGGCCCCGACATATAGCGCTCATGC 821 29 100.0 32 ............................. CAGGTCACTAAAATTTGTAGGGTTATCCACAG 760 29 100.0 32 ............................. GCCTTAGAAGATGACGACCTGATTTCAATTGA 699 29 100.0 32 ............................. TAAATTTTCAAAACCAGCTTGTGATGGTTATA 638 29 100.0 32 ............................. GGGATTTTGGATCGCCCGGTGATAGAGAATTA 577 29 100.0 32 ............................. CGGTTCCATTGACCCGCGCTGCGGGCTGTCCT 516 29 100.0 32 ............................. CACGTTTCCTGCCTAATAAATGGATGATGTCG 455 29 100.0 32 ............................. GACAGTGCCCTGCTGTTGGGCGGTGTCAGCAC 394 29 100.0 32 ............................. CGTGGAACTTTATCCGCACAGATTTCCTGCGC 333 29 100.0 32 ............................. GACGCAGGGGTTACTGATGAACTGAAAAAGCA 272 29 100.0 32 ............................. CAGCGGGAGGAAATTAACAGCCTGAAATCAGG 211 29 100.0 32 ............................. GGAAACGCATATGAGCACACAAACAACCGGCA 150 29 100.0 32 ............................. TACCGTTAACCAGCTCAATAAAAACCAGGTGA 89 29 100.0 33 ............................. GTTGCCAGCGCAATTCCGTGAACACCCACAATT 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 17 29 99.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # 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: F [1-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //