Array 1 1019331-1021250 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014982.2 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1810 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1019331 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 1019392 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 1019453 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 1019514 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 1019575 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 1019636 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 1019697 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 1019758 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 1019819 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 1019880 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 1019941 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 1020002 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 1020063 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 1020124 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 1020185 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1020246 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1020307 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1020368 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 1020429 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 1020490 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 1020551 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1020612 29 100.0 32 ............................. CCCCGATAGAGACGCTTCTGTAGTCACTGGCA 1020673 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1020735 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1020796 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 1020857 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1020918 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1020979 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1021040 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1021101 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1021162 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1021223 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 32 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # 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 1037383-1038797 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014982.2 Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1810 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 1037383 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1037444 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 1037505 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 1037566 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 1037627 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 1037688 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 1037749 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 1037810 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 1037871 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 1037932 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 1037993 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 1038054 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 1038116 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 1038219 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1038280 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1038341 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1038402 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1038463 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1038524 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1038585 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1038646 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1038707 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1038768 29 96.6 0 A............................ | A [1038794] ========== ====== ====== ====== ============================= ========================================================================== ================== 23 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.11, 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 [1-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-48.3]%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], //