Array 1 88334-88972 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYRZ01000024.1 Salmonella enterica strain CVM 43808 43808_contig_24, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 88334 29 100.0 33 ............................. TCGTACACCAGCGCTTTACCGGAGTGTCCGTGC 88396 29 100.0 32 ............................. ATCAAATATCAGATAACCCCCGTCGGCAAACC 88457 29 100.0 32 ............................. ATCACATTCCTGAAAAATGACTCCCTTAGCGA 88518 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 88579 29 100.0 32 ............................. TCCAGCATTGACGCGAACCCTGCGCCGCTGGC 88640 29 100.0 32 ............................. GCTGAAATATTGCTATTTCCGAAGGGGCTGAT 88701 29 100.0 32 ............................. TCCCGCCTGAACAAAATCGACCACGTTATTAA 88762 29 100.0 32 ............................. GCTCCCGCGGGCGCTCCTGTTGGCCAGCATCA 88823 29 100.0 32 ............................. CGTCCAATACGAGCTGAGTGCGCACGCCCTTA 88884 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 88945 28 96.6 0 ............................- | ========== ====== ====== ====== ============================= ================================= ================== 11 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCGCGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAACAGTTTATAAACAACAATATACGTTTAGT # Right flank : | # 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: 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 [70.0-0.0]%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 150084-148431 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYRZ01000033.1 Salmonella enterica strain CVM 43808 43808_contig_33, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 150083 29 100.0 32 ............................. GCCCAATTGCCGGCGACGGTTTCCATGTCAGC 150022 29 100.0 32 ............................. TGGCGAAACAGGCCAGAGAACGCGAATTGCAG 149961 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 149900 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAA 149839 29 100.0 32 ............................. TTGGCATGGCTGGCGACGTAGCGAACAAAATC 149778 29 100.0 32 ............................. CATAAATTACTCGATGCGTACCTGTGAAATCT 149717 29 100.0 32 ............................. ATACAGTAGCAAAATAAAAAGGCCGCGTGAGC 149656 29 100.0 32 ............................. CAATGCCGTTTTGCCCGAGTTTTCACCGCCGT 149595 29 100.0 32 ............................. CTCTATTGCCGGGGGTCGAGATGGCCGCCTGC 149534 29 100.0 32 ............................. GTGATCCGCGCCTATGACGCAATGGTAACGAC 149473 29 96.6 32 ............................T GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 149412 29 100.0 32 ............................. CAGGAGACGGCCAGCCGCACCGGTGGCGGTGC 149351 29 100.0 32 ............................. GGCGTTTTATTCGACCTGAAAAAATGGATCGT 149290 29 96.6 32 .............T............... ACATCTCGCGGACAATAGCGATTTCCACCGTC 149229 29 96.6 32 .............T............... CGTTTCGTTCATTTATTTAGTTTCCTGTTTCG 149168 29 93.1 29 .............T..............C CTTGTTAAATACAGGCGGCGGCGGGGTTG 149110 29 96.6 32 .............T............... AACGGCGACGGGATCGTTTTTTGTGGCGAAAA 149049 29 96.6 32 .............T............... CAGGATTGGATTAATGAAGACGGGTACGAAAT 148988 29 96.6 32 .............T............... AGATTGCAGAATTATATTTCACGCTGGCAGCA 148927 29 96.6 32 .............T............... CTGTTGTTATGCGTTGGATCGTAATAGTTAAC 148866 29 96.6 32 .............T............... CTTGGCAGGGCTGCGCCGCAATGGCAGCAACA 148805 29 96.6 32 .............T............... GTCTTATAAATTGGGCTGATAGTGCCGCTGAT 148744 29 100.0 32 ............................. TACCTGCCGGGACTGGAGTGCAGGTAACCCCA 148683 29 100.0 11 ............................. CGGCCAGCCAT Deletion [148644] 148643 29 72.4 32 T.AAA.AG...TG................ ACAGGGTATATGAGCTTATACGTCATGAACCA 148582 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 148521 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 148460 29 93.1 0 A...........T................ | A [148433] ========== ====== ====== ====== ============================= ================================ ================== 28 29 97.4 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.87, 5:0, 6:0.25, 7:-0.06, 8:1, 9:0.93, # 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # 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 [11-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-0.0]%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], // Array 1 16364-16574 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYRZ01000040.1 Salmonella enterica strain CVM 43808 43808_contig_40, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 16364 29 100.0 32 ............................. GCGGAATACCACTATATAAAGCCCCTCAACCC 16425 29 100.0 32 ............................. ATTTTTACAAAAACTGGCCCCCTGAATTCATC 16486 29 100.0 32 ............................. TTGATTTTAATGGCGGGCGAATTGTATTTAAC 16547 28 96.6 0 ............................- | ========== ====== ====== ====== ============================= ================================ ================== 4 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : | # Questionable array : NO Score: 5.82 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 [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 [71.7-0.0]%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 1-261 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYRZ01000064.1 Salmonella enterica strain CVM 43808 43808_contig_65, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 18 62.1 32 -----------.................. TAAAACCGGTGCTGGATTTTGATGAAGACGAA 51 29 100.0 32 ............................. CCATTCAACATCGCACTTAAGAACTTGTGCCA 112 29 100.0 32 ............................. CGATATTTATCCAGACTGTCGGACAGGGTGGT 173 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 234 28 96.6 0 ............................- | ========== ====== ====== ====== ============================= ================================ ================== 5 29 91.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # Questionable array : NO Score: 5.65 # Score Detail : 1:0, 2:3, 3:0, 4:0.59, 5:0, 6:0.25, 7:0.01, 8:0.8, 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: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 395-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYRZ01000066.1 Salmonella enterica strain CVM 43808 43808_contig_68, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 394 29 100.0 32 ............................. GAAACAGAGATCGCGTCCGATAATGCCGACAT 333 29 100.0 32 ............................. AGAATATTCAACTCCAGCGGGAAAAAGACGCA 272 29 100.0 32 ............................. AACTTTCATCAAACTGGATCGAAGGGCCACTT 211 29 100.0 32 ............................. CCGGTTTTAGCTCGCTGGAAACCTCGCTTTTG 150 29 100.0 32 ............................. ACGCCGAGGGTGAATATTTAGACCGGGACGCA 89 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 28 28 96.6 0 ............................- | ========== ====== ====== ====== ============================= ================================ ================== 7 29 99.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGGCGTGGATTGATTCTGATCGCCGTGGGCGGG # Right flank : C # 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 [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-28.3]%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], //