Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: NW_018398320.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1620.0, whole genome shotgun sequence Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 4084 ACGTcount: A:0.29, C:0.10, G:0.10, T:0.32 Warning! 763 characters in sequence are not A, C, G, or T Found at i:736 original size:173 final size:171 Alignment explanation
Indices: 471--1289 Score: 638 Period size: 170 Copynumber: 4.9 Consensus size: 171 461 TGCTTTATAG * * 471 TTTTTTATATTTTTGGTTAAAATATATTATAATTGAATGTCTATCTCTGAAAATGTGAAGCAAAA 1 TTTTTTATATTTTTGATTAAAATATATTATAATTGAATGTCTATCTCTGGAAATGTGAAGCAAAA * * * * * * 536 GTCATTCATT-GTGGAGAAAAGTTCATTTATAGTTACTTATACCTTCGAAAGCATTATTACTCGC 66 GCCATCCATTGGT-GTGAAAAGTTCATTTATAGTCACTCATACCTTCGAAAGCATTACTACTCGC * ********** 600 TTTAAATGACTTTATAATNNNNNNNNNNATTTTAAGTTGAAT 130 TTTAAATAACTTTATAATCTTAGAATTGATTTTAAGTTGAAT * * * 642 TTTTTTATATTTTTGATTTAAATATATATTATAATTGAATGTCTATCTTTGGCAACGTGAAGCAA 1 TTTTTTATATTTTTGA-TTAAA-ATATATTATAATTGAATGTCTATCTCTGGAAATGTGAAGCAA * ** * ** * 707 CAA-CCATCCGTTGGTGTGAAAAGTTCATTTATAGTCACTCATGGCTTCAAAATTATTACTGCTC 64 -AAGCCATCCATTGGTGTGAAAAGTTCATTTATAGTCACTCATACCTTCGAAAGCATTACTACTC * 771 GCTTTAAATAATTTTATAATCTTAGAATTGATTTTAAGTTGAAT 128 GCTTTAAATAACTTTATAATCTTAGAATTGATTTTAAGTTGAAT * * * * * * 815 ATTTTTACATTTTTGA-TGAAATATATTATAATTGAATGTCTATCTCAGGAAATATGAAACAAAA 1 TTTTTTATATTTTTGATTAAAATATATTATAATTGAATGTCTATCTCTGGAAATGTGAAGCAAAA *** * * * 879 GCCATCCATTGAAATGAAAAGTTCATTTATAGTCACTCATACTTTTGAAAGCATTACTACTCACT 66 GCCATCCATTGGTGTGAAAAGTTCATTTATAGTCACTCATACCTTCGAAAGCATTACTACTCGCT ** * * * * * 944 TTAAATAGTTTTATAATCTCA-TATTCATTTTAAGTAGAAC 131 TTAAATAACTTTATAATCTTAGAATTGATTTTAAGTTGAAT * * * ** 984 TTTTTTATATTTTT-AGTTAAAACATATTATAATTGAATGTCTATCT-TGAGAACTATGAATAAA 1 TTTTTTATATTTTTGA-TTAAAATATATTATAATTGAATGTCTATCTCTG-GAAATGTGAAGCAA * *** * * * 1047 AAGCCATTCATTGGAAAGAAAAG-TCTATGTATAGTCACTCA-AGCCTTCGAAAGCCTTA--A-A 64 AAGCCATCCATTGGTGTGAAAAGTTC-ATTTATAGTCACTCATA-CCTTCGAAAGCATTACTACT * * * * * 1107 CG------AT---TTTATAATCTCATAGTTGA-TTTAAATTAAAT 127 CGCTTTAAATAACTTTATAATCTTAGAATTGATTTTAAGTTGAAT * * * * * * * * 1142 TGTTTTAAATTTTTAATTAAAATATATTATAATT-AATGTTTATCTCTGAAAACGTGAAACGAAA 1 TTTTTTATATTTTTGATTAAAATATATTATAATTGAATGTCTATCTCTGGAAATGTGAAGCAAAA * ** * * ** * * * 1206 GTCATTTATTGGAGAGAAAAGTTCATTTATAGTCACTCATGTCTTCGAAAGCATTATTGCTCACT 66 GCCATCCATTGGTGTGAAAAGTTCATTTATAGTCACTCATACCTTCGAAAGCATTACTACTCGCT * * 1271 TTAAATGATTTTATAATCT 131 TTAAATAACTTTATAATCT 1290 CNNNNNNNNN Statistics Matches: 518, Mismatches: 103, Indels: 56 0.77 0.15 0.08 Matches are distributed among these distances: 157 64 0.12 158 53 0.10 159 4 0.01 160 1 0.00 161 2 0.00 166 2 0.00 167 1 0.00 168 2 0.00 169 43 0.08 170 190 0.37 171 18 0.03 172 5 0.01 173 129 0.25 174 4 0.01 ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40 Consensus pattern (171 bp): TTTTTTATATTTTTGATTAAAATATATTATAATTGAATGTCTATCTCTGGAAATGTGAAGCAAAA GCCATCCATTGGTGTGAAAAGTTCATTTATAGTCACTCATACCTTCGAAAGCATTACTACTCGCT TTAAATAACTTTATAATCTTAGAATTGATTTTAAGTTGAAT Found at i:904 original size:170 final size:167 Alignment explanation
Indices: 471--1654 Score: 547 Period size: 170 Copynumber: 7.0 Consensus size: 167 461 TGCTTTATAG * * * * 471 TTTTTTATATTTTTGGTTAAAATATATTATAATTGAATGTCTATCTCTGAAAATGTGAAGCAAAA 1 TTTTTTATATTTTT-GATAAAATATATTATAATTGAATGTCTATCT-TGGAAATATGAAACAAAA * * ** * * * * * * 536 GTCATTCATTGTGGA-GAAAAGTTCATTTATAGTTACTTATACCTTCGAAAGCATTATTACTCGC 64 GCCATCCATTG-AAATGAAAAGTTCATTTATAGTCACTCATACTTTCAAAAGCATTACTACTCAC * * ********* 600 TTTAAATGACTTTATAATNNNNNNNNNNATTTTAAGTTGAA 128 TTTAAATAATTTTATAAT-CTCAAATTCATTTTAAGTTGAA * ** * 641 TTTTTTTATATTTTTGATTTAAATATATATTATAATTGAATGTCTATCTTTGGCAACGTGAAGCA 1 -TTTTTTATATTTTTGA--TAAA-ATATATTATAATTGAATGTCTATC-TTGGAAATATGAAACA * *** * ** * 706 ACAA-CCATCCGTTGGTGTGAAAAGTTCATTTATAGTCACTCATGGC-TTCAAAATTATTACTGC 61 A-AAGCCATCCATTGAAATGAAAAGTTCATTTATAGTCACTCAT-ACTTTCAAAAGCATTACTAC * * * 769 TCGCTTTAAATAATTTTATAATCTTAGAATTGATTTTAAGTTGAA 124 TCACTTTAAATAATTTTATAATCTCA-AATTCATTTTAAGTTGAA * * * 814 TATTTTTACATTTTTGATGAAATATATTATAATTGAATGTCTATCTCAGGAAATATGAAACAAAA 1 T-TTTTTATATTTTTGATAAAATATATTATAATTGAATGTCTATCT-TGGAAATATGAAACAAAA ** 879 GCCATCCATTGAAATGAAAAGTTCATTTATAGTCACTCATACTTTTGAAAGCATTACTACTCACT 64 GCCATCCATTGAAATGAAAAGTTCATTTATAGTCACTCATACTTTCAAAAGCATTACTACTCACT * * * 944 TTAAATAGTTTTATAATCTCATATTCATTTTAAGTAGAA 129 TTAAATAATTTTATAATCTCAAATTCATTTTAAGTTGAA * * * 983 CTTTTTTATATTTTTAGTTAAAACATATTATAATTGAATGTCTATCTTGAGAACTATGAATA-AA 1 -TTTTTTATATTTTT-GATAAAATATATTATAATTGAATGTCTATCTTG-GAAATATGAA-ACAA * * * 1047 AAGCCATTCATTGGAAA-GAAAAG-TCTATGTATAGTCACTCA-AGCCTTC----G-A--A--A- 62 AAGCCATCCATT-GAAATGAAAAGTTC-ATTTATAGTCACTCATA-CTTTCAAAAGCATTACTAC * ** * * * * 1099 GC-C-TTAAACGATTTTATAATCTCATAGTTGA-TTTAAATTAAA 124 TCACTTTAAATAATTTTATAATCTCA-AATTCATTTTAAGTTGAA * * * * ** * 1141 TTGTTTTAAATTTTTAATTAAAATATATTATAATT-AATGTTTATCTCTGAAAACGTGAAACGAA 1 TT-TTTTATATTTTTGA-TAAAATATATTATAATTGAATGTCTATCT-TGGAAATATGAAACAAA * ** * * * * * 1205 AGTCATTTATTGGAGA-GAAAAGTTCATTTATAGTCACTCAT-GTCTTCGAAAGCATTATTGCTC 63 AGCCATCCATT-GAAATGAAAAGTTCATTTATAGTCACTCATACT-TTCAAAAGCATTACTACTC * ********* 1268 ACTTTAAATGATTTTATAATCTCNNNNNNNNNNTTAAGTTGAA 126 ACTTTAAATAATTTTATAATCTC-AAATTCATTTTAAGTTGAA * * * * * * * ** * 1311 TTTTTTTACATTTTTTTGTTAAAACAGATTATGATTGAATGTCTACCTCGAGAACCATGAAAAAA 1 -TTTTTT--ATATTTTTGATAAAATATATTATAATTGAATGTCTATCTTG-GAAATATG-AAACA ** * * * * * * * * * 1376 AAAATCTTTCATTGGCAA-GAAAAGTCCATCTATAGTCACCCA-AGCCTT--AAAGCCTTATTAC 61 AAAGCCATCCATT-GAAATGAAAAGTTCATTTATAGTCACTCATA-CTTTCAAAAGCATTACTAC * * * * * * * 1437 TTACTTTAAATGATTTTCTAATCTCATTATTGATTTTAAATTAAAA 124 TCACTTTAAATAATTTTATAATCTCA-AATTCATTTTAAGTT-GAA * * * * * * ** * 1483 TTTTTTATGTTGTTGATTAAAGTAGATTATAATTGAATGTTTGTCTCAAGAAACATGAAGA-AAA 1 TTTTTTATATTTTTGA-TAAAATATATTATAATTGAATGTCTATCT-TGGAAATATGAA-ACAAA ** * * * * * 1547 AGCCATCTGTTGAAGA-GAAAAGTCCATTTATAGTCGCTTATGCCTTT-AAAAGCATTATTACTC 63 AGCCATCCATTGAA-ATGAAAAGTTCATTTATAGTCACTCAT-ACTTTCAAAAGCATTACTACTC ** * * * * 1610 ACTTTAAATGGTTTCATAATGTTATAATTGATTTTAAGTTGAA 126 ACTTTAAATAATTTTATAATCTCA-AATTCATTTTAAGTTGAA 1653 TT 1 TT 1655 GTTTNNNNNN Statistics Matches: 780, Mismatches: 175, Indels: 117 0.73 0.16 0.11 Matches are distributed among these distances: 156 1 0.00 157 56 0.07 158 57 0.07 159 4 0.01 160 1 0.00 161 2 0.00 162 1 0.00 163 1 0.00 164 1 0.00 165 1 0.00 166 1 0.00 167 1 0.00 168 3 0.00 169 92 0.12 170 230 0.29 171 131 0.17 172 28 0.04 173 165 0.21 174 4 0.01 ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40 Consensus pattern (167 bp): TTTTTTATATTTTTGATAAAATATATTATAATTGAATGTCTATCTTGGAAATATGAAACAAAAGC CATCCATTGAAATGAAAAGTTCATTTATAGTCACTCATACTTTCAAAAGCATTACTACTCACTTT AAATAATTTTATAATCTCAAATTCATTTTAAGTTGAA Found at i:1274 original size:327 final size:329 Alignment explanation
Indices: 781--1629 Score: 747 Period size: 327 Copynumber: 2.5 Consensus size: 329 771 GCTTTAAATA * * * * * * 781 ATTTTATAATCTTAGAATTGATTTTAAGTTGAATATTTTTACATTTTTGATGAAATATATTATAA 1 ATTTTATAATCTCAGAATTGATTTTAAATTAAATATTTTTAAATTTTTAATAAAATATATTATAA * * 846 TTGAATGTCTATCTCAGGAAATATGAAACAAAAGCCATCCATTGAAATGAAAAGTTCATTTATAG 66 TTGAATGTCTATCTCAGAAAACATGAAACAAAAGCCATCCATTGAAATGAAAAGTTCATTTATAG * 911 TCACTCATACTTTTGAAAGCATTACTACTCACTTTAAAT-AGTTTTATAATCTC-ATATTCATTT 131 TCACTCATACTTTCGAAAGCATTACTACTCACTTTAAATGA-TTTTATAATCTCAATATTCATTT * * * * * 974 TAAGTAGAACTTTTTTATA-TTTTTAGTTAAAACATATTATAATTGAATGTCTATCTTGAGAACT 195 TAAGTAGAACTTTTTTACATTTTTTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAACC * * * * * 1038 ATG-AATAAAAAGCCATTCATTGGAAAGAAAAGTCTATGTATAGTCACTCAAGCCTTCGAAAGCC 260 ATGAAAAAAAAAACCATTCATTGGAAAGAAAAGTCCATCTATAGTCACCCAAGCCTT--AAAGCC 1102 TTAAACG 323 TTAAACG * * 1109 ATTTTATAATCTCATAGTTGA-TTTAAATTAAAT-TGTTTTAAATTTTTAATTAAAATATATTAT 1 ATTTTATAATCTCAGAATTGATTTTAAATTAAATAT-TTTTAAATTTTTAA-TAAAATATATTAT * * * * * ** * 1172 AATT-AATGTTTATCTCTGAAAACGTGAAACGAAAGTCATTTATTGGAGA-GAAAAGTTCATTTA 64 AATTGAATGTCTATCTCAGAAAACATGAAACAAAAGCCATCCATT-GAAATGAAAAGTTCATTTA * * * ******** 1235 TAGTCACTCAT-GTCTTCGAAAGCATTATTGCTCACTTTAAATGATTTTATAATCTCNNNNNNNN 128 TAGTCACTCATACT-TTCGAAAGCATTACTACTCACTTTAAATGATTTTATAATCTCAATATTCA ** * * * * 1299 NNTTAAGTTGAATTTTTTTACATTTTTTTGTTAAAACAGATTATGATTGAATGTCTACCTCGAGA 192 TTTTAAGTAGAACTTTTTTACATTTTTTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA * * * 1364 ACCATGAAAAAAAAAATCTTTCATTGGCAAGAAAAGTCCATCTATAGTCACCCAAGCCTTAAAGC 257 ACCATGAAAAAAAAAACCATTCATTGGAAAGAAAAGTCCATCTATAGTCACCCAAGCCTTAAAGC 1429 CTTATTACTTACTTTAAATG 322 CTTA--A---AC-------G * ** * * * * 1449 ATTTTCTAATCTCATTATTGATTTTAAATTAAA-ATTTTT-TATGTTGTTGATTAAAGTAGATTA 1 ATTTTATAATCTCAGAATTGATTTTAAATTAAATATTTTTAAAT-TT-TT-AATAAAATATATTA * * ** * 1512 TAATTGAATGTTTGTCTCA-AGAAACATGAAGA-AAAAGCCATCTGTTGAAGA-GAAAAGTCCAT 63 TAATTGAATGTCTATCTCAGA-AAACATGAA-ACAAAAGCCATCCATTGAA-ATGAAAAGTTCAT * * * * * * * 1574 TTATAGTCGCTTATGCCTTT-AAAAGCATTATTACTCACTTTAAATGGTTTCATAAT 125 TTATAGTCACTCAT-ACTTTCGAAAGCATTACTACTCACTTTAAATGATTTTATAAT 1630 GTTATAATTG Statistics Matches: 419, Mismatches: 71, Indels: 48 0.78 0.13 0.09 Matches are distributed among these distances: 326 2 0.00 327 115 0.27 328 64 0.15 329 42 0.10 330 46 0.11 333 2 0.00 339 2 0.00 340 25 0.06 341 32 0.08 342 85 0.20 343 3 0.01 344 1 0.00 ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39 Consensus pattern (329 bp): ATTTTATAATCTCAGAATTGATTTTAAATTAAATATTTTTAAATTTTTAATAAAATATATTATAA TTGAATGTCTATCTCAGAAAACATGAAACAAAAGCCATCCATTGAAATGAAAAGTTCATTTATAG TCACTCATACTTTCGAAAGCATTACTACTCACTTTAAATGATTTTATAATCTCAATATTCATTTT AAGTAGAACTTTTTTACATTTTTTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAACCA TGAAAAAAAAAACCATTCATTGGAAAGAAAAGTCCATCTATAGTCACCCAAGCCTTAAAGCCTTA AACG Found at i:2030 original size:171 final size:168 Alignment explanation
Indices: 1727--2420 Score: 639 Period size: 171 Copynumber: 4.1 Consensus size: 168 1717 NNNNNNGAAG ** * * * * 1727 CAAAAGCCACCCATTGGCAAGAAAAGTCCATTTATAGTCACTCAAGCCTTTGAAAGTCATATTAG 1 CAAAAGCCATTCATT-GCAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGTCTTATTAC * * * * * 1792 TCGGTTTAAACAGTTTTATATTCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTG-GTT 65 TCGCTTTAAATAGTTTTATAATCTCATAATTGATTTCAAGTTGAA-TTTTTTATA-TTTTGAGTT * * 1856 AAAAGAGATAATATTTGAATGTCTACCTTAGGAAACATGAA 128 AAAATAGATTATATTTGAATGTCTACCTTAGGAAACATGAA * 1897 CAGAAAGCCATTCATTGTCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCT-CAAGTCTTATT 1 CA-AAAGCCATTCATTG-CAAGAAAAGTCCATTTATAGTCACCCATGCCTT-TGAAAGTCTTATT * * * * * 1961 ACTCACTTTAAATGGTTTTGTAATCTCTTAATTAATTTCAAGTTGAATTTTTCTATATTTTGAGT 63 ACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTCAAGTTGAATTTTT-TATATTTTGAGT * * * * * 2026 TAAAATAGATTATATTTAAATCTTTTCCTTCA-GAAATATGAA 127 TAAAATAGATTATATTTGAATGTCTACCTT-AGGAAACATGAA * * ** * * 2068 GAAAGAGTCATTCATTGACAA-ATAAACCCCATTTATAGTCGCCCATG-CTTTCGAAAGTCTTGT 1 CAAA-AGCCATTCATTG-CAAGA-AAAGTCCATTTATAGTCACCCATGCCTTT-GAAAGTCTTAT * * * 2131 TACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTCAAGTTGAATTTTTATATATTTTTAG 62 TACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTCAAGTTGAATTTTT-TATATTTTGAG * * * * * 2196 TGAAAATATATTATAGTTGAATGTCTATCTTAGGAAACGTGAA 126 TTAAAATAGATTATATTTGAATGTCTACCTTAGGAAACATGAA * * * * ** * 2239 GCAAAAGACA-TCAATTAG-AGAGCAAAGTTCATTTATATTCACTTATGCCTTTGAAAGTATTAT 1 -CAAAAGCCATTC-ATT-GCA-AGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGTCTTAT * * * * * 2302 TACTCGTTTTAAATAGTTTTATAATCACATAATTGATTTTAAGTTAAAATTTTTTATATTTTTTA 62 TACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTCAAGTT-GAATTTTTTATA-TTTTGA * * * * * ** 2367 -TTAAAATATATTATAATTGAATGTCTATCTTGGGCAATGTGAA 125 GTTAAAATAGATTATATTTGAATGTCTACCTTAGGAAACATGAA 2410 GCAAAAGCCAT 1 -CAAAAGCCAT 2421 CCNNNNNNNN Statistics Matches: 431, Mismatches: 73, Indels: 38 0.80 0.13 0.07 Matches are distributed among these distances: 169 1 0.00 170 23 0.05 171 384 0.89 172 23 0.05 ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39 Consensus pattern (168 bp): CAAAAGCCATTCATTGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGTCTTATTACT CGCTTTAAATAGTTTTATAATCTCATAATTGATTTCAAGTTGAATTTTTTATATTTTGAGTTAAA ATAGATTATATTTGAATGTCTACCTTAGGAAACATGAA Found at i:2839 original size:171 final size:170 Alignment explanation
Indices: 2622--3043 Score: 420 Period size: 170 Copynumber: 2.5 Consensus size: 170 2612 NNNNNNNNCA * * * * * 2622 CTTTAAATGGTTTTATAATCTCATAGTTAATTTTAAATTAAATTTTTTTATATGTTTGATTAAAA 1 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAGATTGAATTTTTTTACATGTTTGATTAAAA * * * * * 2687 CAGATTATAATTGAATGTCTACCCCTAAGAATATAAAGAAAAAGCCATTCATTGATAAGAAAAGT 66 CAGATTATAATTGAATGTATACCCCAAAAAACATAAAGAAAAAG-CATTCATTAATAAGAAAAGT * * 2752 CCATTTATA-GTCACCCATACTCTT-GAAAACCTTATTACAT-G 130 CCATTTATAGGT-ACCAATAC-CTTCGAAAACCTTATCAC-TCG * * * ********** 2793 CTTTAAATGGTTTTATAGTCTCATAATCGATTTTAGGTTGAATTTTTTTACNNNNNNNNNNAAAA 1 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAGATTGAATTTTTTTACATGTTTGATTAAAA * * * * * * 2858 CAAATTATAATTAAATGTATGCCTCAAAAAACGTGAAGAAAAAGCATTCATTAATAAGAAAAGTC 66 CAGATTATAATTGAATGTATACCCCAAAAAACATAAAGAAAAAGCATTCATTAATAAGAAAAGTC * * * 2923 CATTTATAGGTACTAATACCTTCGAAAGCGTTATCACTCG 131 CATTTATAGGTACCAATACCTTCGAAAACCTTATCACTCG * * * * 2963 CTTTAAATGGCTTTATAATCTCATAATTGATTTTAGAATG-ATTTTTTTACATTTTTTTATTAAA 1 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAGATTGAATTTTTTTACA-TGTTTGATTAAA * 3027 ATAGATTATAATTGAAT 65 ACAGATTATAATTGAAT 3044 ATTTGCCTTG Statistics Matches: 195, Mismatches: 52, Indels: 9 0.76 0.20 0.04 Matches are distributed among these distances: 169 14 0.07 170 98 0.50 171 83 0.43 ACGTcount: A:0.37, C:0.12, G:0.11, T:0.38 Consensus pattern (170 bp): CTTTAAATGGTTTTATAATCTCATAATTGATTTTAGATTGAATTTTTTTACATGTTTGATTAAAA CAGATTATAATTGAATGTATACCCCAAAAAACATAAAGAAAAAGCATTCATTAATAAGAAAAGTC CATTTATAGGTACCAATACCTTCGAAAACCTTATCACTCG Done.