Array 1 252132-249661 **** Predicted by CRISPRDetect 2.4 *** >NZ_QUTS01000001.1 Salmonella enterica strain CFSAN071937 CFSAN071937_1, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 252131 29 100.0 32 ............................. GCAATTTCCGATATGCGACTTGGGACACCAAT 252070 29 100.0 32 ............................. ACACCGACTCATCCGTTGTTACTCCTGGTATT 252009 29 100.0 32 ............................. CGCTACGCCCTGCCCGGTCTCGGTCTCGGTCT 251948 29 100.0 32 ............................. CACATCGGGAGCCTCAATCAACCCGGCACGGA 251887 29 100.0 32 ............................. AGTTCGATATCCCTTAACGGTACTGCCGTCCT 251826 29 100.0 32 ............................. CCTCACGCAATTGAGCCTCTTTCTCGACACGC 251765 29 100.0 32 ............................. GGCCAGTTCAACAAACACCACGACGCGGGAAT 251704 29 100.0 32 ............................. TTCATCACCGTCAGCAAGCTGCGATCCGAAAT 251643 29 100.0 32 ............................. CCAGCTTGCCGATATCAACGACCTATACCTGT 251582 29 100.0 32 ............................. GTTAAAATTTGGGAGGATCGCCCGGGACTCCC 251521 29 100.0 32 ............................. GGACCATTGAAACGGCGCTGACATCAGATGTT 251460 29 100.0 32 ............................. TACCGAACGGCTCAAAGTATGTTCCAATTGAC 251399 29 100.0 32 ............................. GTTGAAACCAGCATTCCTTATGCTGTGCTGCC 251338 29 100.0 32 ............................. GAGATTTTTCTTGTCCCGCCACACCAGCGGCT 251277 29 100.0 32 ............................. TGCATCATCTGATTCGTACGATACGGCAGGGT 251216 29 100.0 32 ............................. GGCTGACAAACGAGCAGGTTGAATTTGTCCTG 251155 29 100.0 32 ............................. CATGGTCTGTACCGCCTGCATTTCTGCATTGT 251094 29 100.0 32 ............................. GGCCGCACCGCTGGCGATCACGATTAATCAGC 251033 29 100.0 32 ............................. CGCCTCGCAAAACTGGTCGGGGTTTTTCCCCA 250972 29 100.0 32 ............................. TTCGTGTTCTAACAGCAGATCGCTGATACGGC 250911 29 100.0 32 ............................. CCAGTAATGAAACGCTGGCAACATTGACGAGC 250850 29 100.0 32 ............................. CGCAGACGGCGCAATTGGATTCGGTGATCGGG 250789 29 100.0 32 ............................. TGCTCGAGCCGACATTGATCCCGCAAAAATAC 250728 29 100.0 32 ............................. GGATGCCGATAGCGGTCAGTAATGAAAATGGC 250667 29 100.0 32 ............................. AAGATCCTGTCTCTTTTGTGCGGAGCGCCGAC 250606 29 100.0 32 ............................. TTCGTTTGATCTCCACTCACAACGGTATTGAA 250545 29 100.0 33 ............................. GACAATTAGTTCCGACAGACGCCGGTATTAAAT 250483 29 96.6 32 ............T................ CCCACGCGCGGCCGCACTGGCCTCGCGGATAA 250422 29 100.0 32 ............................. TCCGGGCCGCCGCTACCACCACTCAGCGGCGT 250361 29 100.0 32 ............................. CCTAATGGTGATGGGGCGTTTAATCTTATCTC 250300 29 100.0 32 ............................. TGGTTTAATAGTATCGGGCAGCATTTTACCGA 250239 29 100.0 32 ............................. ATCTCAATTAGTCCGTTTCCGGTTGAATCAAT 250178 29 96.6 32 ...C......................... GGGTGTACCACGGCATGATGACGGCCAGCCAT 250117 29 100.0 32 ............................. ATTGACAACAGTCTGCTTACCCGAGCTGCTCC 250056 29 100.0 32 ............................. TCCTGTCGGCGGTACGGTGGACATCCCGCAGG 249995 29 96.6 32 .........A................... CCAGTCAGCCACTGTTCTTTGCCGTACCTTTC 249934 29 100.0 32 ............................. GGGTTATAACCGGGATACCATCCGCTCCAACC 249873 29 100.0 32 ............................. CGCCACGTTTTTTGCATTTTATTGGCATCATC 249812 29 100.0 32 ............................. GGCAACTGGGCGATCATCTGGGCGCTGTTTAT 249751 29 100.0 32 ............................. GTGCTCCAGTGGGCTGCTAAGGGGCTTGGTGG 249690 29 100.0 0 ............................. | A [249663] ========== ====== ====== ====== ============================= ================================= ================== 41 29 99.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : TTTCCCCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # 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: 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 [4-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [48.3-70.0]%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 271675-268677 **** Predicted by CRISPRDetect 2.4 *** >NZ_QUTS01000001.1 Salmonella enterica strain CFSAN071937 CFSAN071937_1, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 271674 29 100.0 32 ............................. CACATTTCCTCAGTGTGCTTCAGAGGGTGGTA 271613 29 100.0 32 ............................. CCGATATCAAAAAAGCGTTTAAACGCCTTGCC 271552 29 96.6 32 ............................T TCCTGCGCTTTGGCCAGTTTGGAACCCGCCGC 271491 29 100.0 32 ............................. GCACAATTTGTGCTTTTGCAATTCACTTTGAA 271430 29 100.0 32 ............................. TGATCACAGAACTGACCGGGTACACCATACCT 271369 29 100.0 32 ............................. TAACGCCGTTCTGCATACGCTCTACCGCGCGC 271308 29 100.0 32 ............................. GGGAATGTATGGATTTAGAAGAAGAGCTGGCA 271247 29 100.0 32 ............................. GGGTATTACGGCGACACAGCGCTTGTTGTCTA 271186 29 100.0 32 ............................. TTAACAAATGTTTTTAAAACGCTTATAACAAA 271125 29 100.0 32 ............................. GGGGCGGCAATGGTGGTCAGGGTGATGGCGGC 271064 29 100.0 32 ............................. TTTAAAAATTTATCTCGATAAATCCAACGATG 271003 29 100.0 32 ............................. AATGATCGTATTTTTCGCTACGTCGCACAAAT 270942 29 100.0 32 ............................. CCCGTTATTTGTAGTTAACGGGCACGTAGTGG 270881 29 100.0 32 ............................. ATCGGGCAGCTCAACGCGGCTATGAAAATCAC 270820 29 100.0 32 ............................. TTGATCGCCGTGGCGGTGAGATTAGAAACGCG 270759 29 100.0 32 ............................. CTGCCAAACTTCTGACAATCCCGGACAGCATC 270698 29 100.0 32 ............................. CGAGTCTGGAAATTGAGGACACCGAAACCGGC 270637 29 100.0 32 ............................. TGCTGGTGGGCGGTACGCCGTGCCAGGCGTTC 270576 29 96.6 32 ............................T TATCCTTACCCTCAACGGCGCAGGCCGATCTC 270515 29 100.0 32 ............................. CGATCTGGTGAGCGCATCGGTTCGGGAGAGTG 270454 29 100.0 32 ............................. GATTGTTCAGATTGGGAATTTGACCAACGCCC 270393 29 69.0 11 ................TAAT..CGT.T.C GTGAACCAGTT TT [270372] Deletion [270354] 270351 29 100.0 32 ............................. GGGAATATCGTTAAAGTGGTTTACCACAATAT 270290 29 100.0 32 ............................. GCGCTCAGGGCCGCCTTGCTGCGGGCACTCAT 270229 29 100.0 32 ............................. GACGTGATCAAACAATTTGGCCGCCCGGAACA 270168 29 100.0 32 ............................. CGATCAAGCGAATGCGTCGGCTGGAGCATCGC 270107 29 100.0 32 ............................. GTTTTCGCGGCCGCGAGATTGTTCTTGCCGAC 270046 29 100.0 32 ............................. TACCGTTTTTACTCCCCCGCATTTGGTTACAC 269985 29 100.0 32 ............................. CAGGAGCAAGCACAAACATAGAGCAAATTAAA 269924 29 100.0 32 ............................. CCAGTGCATTCGAACTCATGGAACGGTGCTAA 269863 29 100.0 32 ............................. GCGCACCGCTTTAGAGTGCCAGGCATAGGCAA 269802 29 100.0 32 ............................. ACACAATACGTATCAGTAAAGACACAAATTGT 269741 29 100.0 32 ............................. CGCATTACCGGGAAAACCTGGGAAGAGACGAT 269680 29 100.0 32 ............................. TCTTGTTTGTTTCTGATTCTTTTTCTGAATGA 269619 29 100.0 32 ............................. AGTCAGAAGAGGACTCATTAGTATCACTCTCA 269558 29 100.0 32 ............................. AATAAACAGCGTCGTAAATGGATCGAGGAAAT 269497 29 100.0 32 ............................. CATCTCTCTATATGCAGCGCCAGCCAGCGCAA 269436 29 100.0 32 ............................. CTTTCCTTGCGTCAATTTTGAGGGAGATTGAT 269375 29 100.0 32 ............................. ATCCCGCGCTCTATTAAAATCTTTGATTGCGT 269314 29 100.0 32 ............................. GTAATGTGCGCCGCGCCGGTGATATCTACTTT 269253 29 96.6 32 .....T....................... CCATTGCTGACAGGCAGTGATTTCAATGTGTC 269192 29 100.0 32 ............................. GTCATGAATGGCCTCATAAAAACGATGTTGGT 269131 29 100.0 32 ............................. TGTTCGCGCTAAATAATGCAGTAGGCCGCGCT 269070 29 100.0 32 ............................. CCAGAAATTTAAATGGCTATTCCTGGCTGTAG 269009 29 100.0 32 ............................. GCGCAATTGCAGTTTGACGCGGTGCTGTCATT 268948 29 100.0 32 ............................. TCGTTTGTGGCGTCAGTAATACTATTATCGGT 268887 29 96.6 32 .............T............... TTTTTAAATCCGGACAGACCCTGTAACGGATC 268826 29 100.0 32 ............................. ATCCGACTGTATGCCCAGCAGAACGAGGGCGC 268765 29 96.6 32 .............T............... CACGAGTGGCAAATTGATTTCGACGAAAAACC 268704 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 50 29 98.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGCTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGGGCTGGAGCGGATAAATCGTTGAAGGCCAGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 5:0, 6:0.25, 7:-0.03, 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 [8-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%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], //