Array 1 195995-194703 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHID01000031.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46824 N46824_contig_31, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 195994 28 96.6 32 -............................ TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 195934 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 195873 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 195812 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 195751 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 195690 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 195629 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 195568 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 195507 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 195446 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 195384 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 195281 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 195220 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 195159 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 195098 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 195037 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 194976 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 194915 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 194854 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 194793 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 194732 29 96.6 0 A............................ | A [194705] ========== ====== ====== ====== ============================= ========================================================================== ================== 21 29 99.4 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.09 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.13, 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 [3-2] 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 1 211-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHID01000069.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46824 N46824_contig_69, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 210 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 149 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 88 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 4 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : C # Questionable array : NO Score: 5.77 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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: 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 16921-16343 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHID01000069.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46824 N46824_contig_69, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 16920 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 16858 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 16797 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 16736 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 16675 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 16614 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 16553 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 16492 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 16431 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 16370 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 10 29 96.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCAGCGGGGATAAACCGCCCCGATAGCGACGCTTCTGTAGTCACTGGC # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.01 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.92, # 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 [6-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-31.7]%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], // Array 1 1-210 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHID01000078.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46824 N46824_contig_78, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 96.6 33 -............................ CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 62 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 123 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 184 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 4 29 97.4 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # Questionable array : NO Score: 5.73 # Score Detail : 1:0, 2:3, 3:0, 4:0.87, 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 [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # 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 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 210-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHID01000087.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46824 N46824_contig_89, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 209 28 96.6 32 -............................ TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 149 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 88 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 4 29 95.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # Questionable array : NO Score: 5.34 # Score Detail : 1:0, 2:3, 3:0, 4:0.79, 5:0, 6:0.25, 7:0.01, 8:0.6, 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: 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 [-8.90,-10.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [2-0] 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 [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 263-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHID01000085.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46824 N46824_contig_85, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================================================================= ================== 262 29 100.0 93 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATTGTGTTCCCCGCGCTAGCGGGGATAAACCGATGCCGGAACGCTGATGGCGTTTGACATGAGC 140 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 79 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 18 18 62.1 0 ..................----------- | ========== ====== ====== ====== ============================= ============================================================================================= ================== 4 29 90.5 53 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGCAGATCCTCAACGGTCAGGCTGTTTAGTTCC # Right flank : G # Questionable array : NO Score: 3.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.53, 5:0, 6:0.25, 7:-2.24, 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 [3,1] 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 [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [0.0-36.7]%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], //