Array 1 507-51 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAOHZ010000059.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CNR1776 CNR1776_S11_L001_R1_001_(paired)_contig_59, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 506 28 96.6 33 -............................ CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 445 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 384 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 323 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 262 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 201 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 140 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 79 29 96.6 0 ............................T | ========== ====== ====== ====== ============================= ================================= ================== 8 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TGAGGCGTACAGGCTGTTAGATGAGAAATTACCGTGTTCCCCGCGCCAGCG # 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: NA [1-1] Score: 0/0.41 # AT richness analysis in flanks prediction: F [35.0-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 137418-136552 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAOHZ010000030.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CNR1776 CNR1776_S11_L001_R1_001_(paired)_contig_30, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 137417 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 137356 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 137295 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 137233 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 137130 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 137069 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 137008 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 136947 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 136886 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 136825 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 136764 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 136703 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 136642 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 136581 29 96.6 0 A............................ | A [136554] ========== ====== ====== ====== ============================= ========================================================================== ================== 14 29 99.5 35 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCCGCGCCAGCGGGGATAAACCGGTCGTTCATCAGGCACTACCGGCACTTTCTG # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.01 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.21, 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 [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-33.3]%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 1 357-23 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAOHZ010000034.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CNR1776 CNR1776_S11_L001_R1_001_(paired)_contig_34, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 356 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 295 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 234 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 173 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 112 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 51 29 93.1 0 ....C...............A........ | ========== ====== ====== ====== ============================= ================================ ================== 6 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GCCATTATTCAACCCTCCAGGCT # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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 [2-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [18.3-71.7]%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 17737-16488 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAOHZ010000034.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CNR1776 CNR1776_S11_L001_R1_001_(paired)_contig_34, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 17736 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 17675 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 17614 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 17553 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 17492 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 17431 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 17370 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 17309 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 17248 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 17187 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 17126 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 17065 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 17004 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 16942 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 16881 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 16820 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 16759 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 16698 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 16637 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 16576 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 16515 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 21 29 97.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGCCGGCATCAGCGCCGATCCGTTCATAGTGCC # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # 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 [9-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-28.3]%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], //