Array 1 52-873 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQI01000360.1 Salmonella enterica subsp. enterica serovar Mississippi strain BCW_4007 NODE_360_length_923_cov_1.18333, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 52 29 100.0 32 ............................. GTTGGGTAACTGAATATGTTTCTAATAATAAT 113 29 100.0 32 ............................. AGAAGCGGGTGCGTATGCCGGCAGCAAAAATC 174 29 100.0 32 ............................. ATGTCCGTAATCATTTTGGTCAGCCAGTATCA 235 29 100.0 32 ............................. TTTCAGGCAATTTTTTCCGGCAACGGAACGAA 296 29 100.0 32 ............................. CCACATTGAAATGCTCGAGGACGCCGCAGACC 357 29 100.0 32 ............................. GCCGAATGCAAAACCCCCGCAAACAGCAGCAA 418 29 100.0 32 ............................. TTTTATGTATGTATCTTTCAATATCAAAATAT 479 29 100.0 32 ............................. AATTCCCGACCCCATCAGCAACATTAACTCCG 540 29 100.0 32 ............................. ATTAACCCTCAAATGTGGTTATTTGCGCAGGC 601 29 100.0 32 ............................. ATAGATTCTCTTAAATCATTCATTAATTTAAA 662 29 100.0 32 ............................. CTGAATTGCTGCATCCAGGCGATCCGACCATG 723 29 100.0 32 ............................. GATTAGTTTTACTGTAAGCCTTGTATGAATCT 784 29 100.0 32 ............................. CCCCATATGGTATGGGGCCAGAGTAATCAGGT 845 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 14 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGCCAGCGGGGATAAACCGTGTGGCTTATATGAAATTTCCTATTAACATGTG # Right flank : ATGCTGGATCAGCCACCACAACCATTTACCGGGTGTTCCCCGCGCCAGCG # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [48.3-31.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 247-1066 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQI01000351.1 Salmonella enterica subsp. enterica serovar Mississippi strain BCW_4007 NODE_351_length_1072_cov_1.3367, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 247 29 100.0 32 ............................. CTACAGGATCTAATTTTGATGGATCGGCATAC 308 29 100.0 32 ............................. ATAGAGGATATAGACTATAATTTAGTTGTTAA 369 29 100.0 32 ............................. CAGGTGCTTGGGATGGATGAAGTTGACGGGAT 430 29 100.0 32 ............................. CGATCGGGGAAGCGCTCCGGGTCAGCAAATCA 491 29 100.0 32 ............................. GCCGGGACCGCCGAGTCAGCGATCACGGTGAC 552 29 100.0 32 ............................. TTCATTGCGAGATTCAACAAATCGCTCCGGGT 613 29 100.0 32 ............................. CCTGCCGGAAACGTTTTTGACGCAACAACGGT 674 29 100.0 32 ............................. TAACGGTGTGTGGGTCGGAGATGCCTCTGATG 735 29 100.0 32 ............................. TTTATTATTTACGGCAGGGGCTAAGAGTACCA 796 29 96.6 32 ............................C ATAATTTCATTATATACAGTATCTCCCGATAC 857 29 100.0 32 ............................. ATAATAAAACTTTCATGATACCACCTAATCAT 918 29 100.0 32 ............................. GTGGTACAATCGGAGGTGAAGGGGGTGTAAAA 979 29 100.0 32 ............................. GATTAATATATGGCAGATACAATCGTTATTCC 1040 27 86.2 0 ......................--G.T.. | ========== ====== ====== ====== ============================= ================================ ================== 14 29 98.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAATAGTTTATAAACAATGATATACGTTTAGTG # Right flank : GAAGAG # 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: F [0-7] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-3.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 48-380 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQI01000385.1 Salmonella enterica subsp. enterica serovar Mississippi strain BCW_4007 NODE_385_length_380_cov_1.59596, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 48 29 100.0 32 ............................. TGAATAATATTACTCCCTTTTAAGGGAGTTGG 109 29 100.0 32 ............................. TGCTTCTTCTGGATTTTCTTTAGGTTTCTCAT 170 29 100.0 32 ............................. TGACTGTATCAGCCGCAGCAAACGCACACTCC 231 29 100.0 32 ............................. TTGCCAACCCACAGCAGTCCGTCAGTAAAATC 292 29 100.0 32 ............................. GTTATTCTCAAAACACCGCTACGCCGGGGTGA 353 28 96.6 0 ............................- | ========== ====== ====== ====== ============================= ================================ ================== 6 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AGCGGGGATAAACCGGGTGTAATAATAATTGGGATAAATTCGTAAGTG # Right flank : | # 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: 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: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [48.3-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 42-619 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQI01000375.1 Salmonella enterica subsp. enterica serovar Mississippi strain BCW_4007 NODE_375_length_637_cov_1.13177, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 42 29 100.0 32 ............................. CGACCAGGAGCTGCTCACGGAGAGCTCGCTGG 103 29 100.0 32 ............................. CTATCATTAATAGATAATGTAATAGAGGCTAA 164 29 100.0 32 ............................. TGATTGAGCTACATTATAAACGAATGATGAAT 225 29 100.0 32 ............................. AACTGCAATTATTTATAGTAAATTATCCAGAA 286 29 100.0 32 ............................. AATTTGCTCTCACGCCTGGCGACCCGTCTCGA 347 29 100.0 32 ............................. TAATAGAGGCTAATATGTTTAAACATAAATTA 408 29 100.0 32 ............................. CCAGTACCAATTGTCAAATAACCGCATTTAGC 469 29 100.0 32 ............................. ACGGGGGCGTCATCCTCAACAGTGCAGGCGAT 530 29 100.0 32 ............................. CCGGGGCCGCTTACGTGCTGATCCTGACGCTC 591 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 10 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GATAAACCGGTAAATCAACTACTAATAGATTTTTATTAGTAG # Right flank : ATGGACGAGAGAGAGCGG # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [51.7-11.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 207-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQI01000397.1 Salmonella enterica subsp. enterica serovar Mississippi strain BCW_4007 NODE_397_length_241_cov_0.803797, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 206 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 145 29 100.0 32 ............................. GGGTACCGGACAGGCCGATCACCTTTGTCTGC 84 29 100.0 32 ............................. GTGAACATGATGCCTGGAGCACTATTTACAGT 23 23 79.3 0 .......................------ | ========== ====== ====== ====== ============================= ================================ ================== 4 29 94.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCGGGGATAAAGGGGACAAAGGCGATCAGGGTGT # Right flank : T # Questionable array : NO Score: 5.60 # Score Detail : 1:0, 2:3, 3:0, 4:0.74, 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 : 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 [4,2] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATGAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-3.00,-3.20] Score: 0/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [0.0-25.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.37,4.77 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 49-260 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQI01000391.1 Salmonella enterica subsp. enterica serovar Mississippi strain BCW_4007 NODE_391_length_303_cov_1.32273, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 49 29 100.0 32 ............................. ATGGACGAGAGAGAGCGGAAACATCATGTTGA 110 29 100.0 32 ............................. TGTGATCTGATCGCCTCTGGCGTCACTGTACG 171 29 100.0 32 ............................. GAGTATAGTTCTATGGGCCTGGAAAAACAGAA 232 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 4 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TCTTCCGATCTAACCGGAGTATAGTTCTATGGGCCTGGAAAAACAGAAG # Right flank : GCAACCAAAAAGGCCGCGAAATCGCAGCGAGATCGGAAGAGCG # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 : 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 [6,4] 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 [-14.90,-14.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [43.3-30.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 9308-7876 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXQI01000157.1 Salmonella enterica subsp. enterica serovar Mississippi strain BCW_4007 NODE_157_length_9314_cov_1.74908, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 9307 29 100.0 32 ............................. CGGTACCGAAAAAGAGTCCGTATTAAACGCAA 9246 29 100.0 32 ............................. AATGCAGTTTCACGCACACCTCGCCGGCAACG 9185 29 100.0 32 ............................. AACTCGCCAAATGGGAAGCGCGCGTTGAGAGC 9124 29 100.0 32 ............................. CCAATGGAGAGGACGCGCAAAAAACTTCTCGT 9063 29 100.0 32 ............................. TTCCGTCCGGGCTGTCTGCGCCAATCGTAATC 9002 29 100.0 32 ............................. TTCGATTACAGTAAAATTTATGTTTATTCAAT 8941 29 100.0 32 ............................. AGAAGATATTAAACCCCATATAAACCCCACTC 8880 29 100.0 32 ............................. TGTGCCCGCTGACAATACCGTGGGTGTAGGCC 8819 29 100.0 32 ............................. GGCCGTATGGCTGCGCTACTGGATGAATTGAT 8758 29 100.0 32 ............................. ATCGCCTTAACTAAGTGCTCCGCTTCTGGTAG 8697 29 100.0 30 ............................. ATATGAGTGAAAATAACAATTCATATTTGA 8638 29 100.0 32 ............................. ATACATTCCTTACTCCTCGCACATTCACGAAT 8577 29 100.0 32 ............................. GAGCTGTATACAAACGGGAATATTCCGCTATT 8516 29 100.0 32 ............................. GTAATTACCGCACAGCGCATGATTTTAGTACG 8455 29 100.0 32 ............................. CCACAGCGCGAAAGAGGTCTATTCCTGGCTGT 8394 29 100.0 33 ............................. CTACAATGTCAAAATGATGCCAGTTATCCTGGT 8332 29 100.0 32 ............................. AAAGAAGAAAATACAATGCTTGTAATGATGAA 8271 29 100.0 32 ............................. GTTTTTTCTCAGCGGCTGGCAGACCTGATCGC 8210 29 100.0 32 ............................. CGAGAAATGAGTGCCATTTAAACCCCGCCCGT 8149 29 100.0 32 ............................. TGCCGACGATACCCTGCAAAATCTGCGGCGGT 8088 29 100.0 32 ............................. TTCGCCGTCGTGAAAGCGGGTGAGCATTCCAG 8027 29 100.0 32 ............................. GCTGATAGCCAACCTGTAAGTGATCGTGATGA 7966 29 100.0 32 ............................. CTTTCTTCAGACATTTCTCCAACCCGGCAACC 7905 29 100.0 0 ............................. | A [7878] ========== ====== ====== ====== ============================= ================================= ================== 24 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ACTGAG # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGTACTACATCGCGGCTACGGCGCTCAATTCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-6.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //