Array 1 97965-99945 **** Predicted by CRISPRDetect 2.4 *** >NZ_MZYS01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM3112 BCW_8427_1__paired__contig_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 97965 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 98026 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 98087 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 98148 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 98209 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 98270 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 98331 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 98392 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 98453 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 98514 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 98575 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 98636 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 98697 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 98758 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 98819 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 98880 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 98941 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 99002 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 99063 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 99124 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 99185 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 99246 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 99307 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 99368 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 99430 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 99491 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 99552 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 99613 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 99674 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 99735 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 99796 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 99857 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 99918 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 33 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGAGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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 [0-12] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 116269-117562 **** Predicted by CRISPRDetect 2.4 *** >NZ_MZYS01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM3112 BCW_8427_1__paired__contig_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 116269 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 116331 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 116392 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 116453 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 116514 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 116575 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 116636 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 116697 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 116758 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 116819 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 116880 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 116941 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 117002 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 117064 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 117167 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 117228 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 117289 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 117350 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 117411 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 117472 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 117533 29 96.6 0 A............................ | A [117559] ========== ====== ====== ====== ============================= ========================================================================== ================== 21 29 99.5 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTGTGTTCCCCGCGCCAGCGGGGATAAACCGTGAGCAACGACAGTAAATAATTTTTCGTGCTGGTGTTCCCCGCGCCAGCGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCCAGCGGGGATAAACCGCAACCAGGCTGGATCGTAACTCCTATCCCCTC # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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: 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 [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [33.3-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //