Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400171.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_339.0, 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: 8744
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.28

Warning! 1975 characters in sequence are not A, C, G, or T


Found at i:928 original size:171 final size:169

Alignment explanation

Indices: 638--1072 Score: 563 Period size: 171 Copynumber: 2.5 Consensus size: 169 628 NNNNNNNNTC * * * * 638 TCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATG-TAAAAACATTTAACTTAAAATG 1 TCAAGGTAGACATT-AATTATAGTCTGTTTTAA-CTAAAATGTTAAAAA-ATTCAACTTAAAATC * * * 702 AATTATGGGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAGAGAATGGGTGACTACAA 63 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTAAGAGAATGGGTGACTACAA * * 767 ATATACTTTTCTTGCCAATGAAT-CTCTTTTTCTTCATGTTTCT 128 ATAGACTTTTCTTGCCAATGAATGCT-TTTTTCTTCATATTT-T * * * 810 T-AAGGTAGACAGTTAATTATAGTCTTTTTTAACTAAGAATGTTAAAAAATACAACTTCAAATCA 1 TCAAGGTAGACA-TTAATTATAGTCTGTTTTAACTAA-AATGTTAAAAAATTCAACTTAAAATCA * * 874 GTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTTAAG-GAATGGGTGACTATAA 64 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCC-TTTTAAGAGAATGGGTGACTACAA * * 938 ATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATATTTT 128 ATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATATTTT * * * * 980 TCAAGTTAGACAATTAATTATTGTCTGTTTTAACTAAAACTGTGAAAAAATTCAAGTTAAAATCA 1 TCAAGGTAGAC-ATTAATTATAGTCTGTTTTAACTAAAA-TGTTAAAAAATTCAACTTAAAATCA * 1045 ATTATGAGATTATAAAATCATTTAAAGC 64 ATTATGAGATTATAAAACCATTTAAAGC 1073 AAGNNNNNNN Statistics Matches: 230, Mismatches: 25, Indels: 17 0.85 0.09 0.06 Matches are distributed among these distances: 170 7 0.03 171 205 0.89 172 18 0.08 ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37 Consensus pattern (169 bp): TCAAGGTAGACATTAATTATAGTCTGTTTTAACTAAAATGTTAAAAAATTCAACTTAAAATCAAT TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTAAGAGAATGGGTGACTACAAATA GACTTTTCTTGCCAATGAATGCTTTTTTCTTCATATTTT Found at i:1717 original size:171 final size:171 Alignment explanation

Indices: 1388--1760 Score: 390 Period size: 171 Copynumber: 2.2 Consensus size: 171 1378 NNNNNNNNNN ** * * * * * 1388 AAAAAAATTCAATTTAAAATCAATTATAAGATTATAAAACTATTTAAAGCGAGTGATAAGGTTTT 1 AAAAAAATTCAGCTTAAAATCAATTTTGAGATTATAAAACTATTTAAAACGAGTAATAAGGCTTT * * 1453 TAAAAGAACGGGTGACTATAAATATACTTTTCTTATCAAGGAACGGCTTTTTCTACAAGTTTCCT 66 TAAAAGAACGGGTGACTATAAATAGACTTTTCTTATCAAGGAACGCCTTTTTCTACAAGTTTCCT * * * * ** 1518 AAGTCAAGCATTTAATTATAGCCTGTTTTAATGAAAAATGA 131 AAGTCAAGCATTCAAATACAACCTGTTTTAACCAAAAATGA * * 1559 AAAAAAATTCAGCTTAAAATCAATTTTGAGATTATAAGACTATTTAAAATGAGTAATAAGGCTTT 1 AAAAAAATTCAGCTTAAAATCAATTTTGAGATTATAAAACTATTTAAAACGAGTAATAAGGCTTT * * * * * * * * * * * 1624 TGAAGGAATGGGTGACTATAAATGGATTTTTTTTGTCAATGAATC-CCTTTTTCTTCACGTTTCT 66 TAAAAGAACGGGTGACTATAAATAGACTTTTCTTATCAAGGAA-CGCCTTTTTCTACAAGTTTCC * * * * * 1688 TGAG-CTAGACATTCAAATACAATCTGTTTTAACCAATAATGT 130 TAAGTCAAG-CATTCAAATACAACCTGTTTTAACCAAAAATGA * * * 1730 TAAAAAATTGAGCCTAAAATCAATTTTGAGA 1 AAAAAAATTCAGCTTAAAATCAATTTTGAGA 1761 AATAAGGCTT Statistics Matches: 164, Mismatches: 36, Indels: 4 0.80 0.18 0.02 Matches are distributed among these distances: 170 3 0.02 171 160 0.98 172 1 0.01 ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35 Consensus pattern (171 bp): AAAAAAATTCAGCTTAAAATCAATTTTGAGATTATAAAACTATTTAAAACGAGTAATAAGGCTTT TAAAAGAACGGGTGACTATAAATAGACTTTTCTTATCAAGGAACGCCTTTTTCTACAAGTTTCCT AAGTCAAGCATTCAAATACAACCTGTTTTAACCAAAAATGA Found at i:2093 original size:171 final size:169 Alignment explanation

Indices: 1761--2325 Score: 491 Period size: 171 Copynumber: 3.3 Consensus size: 169 1751 AATTTTGAGA * * * * * * 1761 AATAAGGCTTTTGAAGGAATAGAAGACAATAAA-GGACTTTTCTTGCCAATAAATTCTTTTTTCT 1 AATAAGGCTTTTGAAGGAATGGAAGACTATAAATAGACTTTT-TTACCAATGAATGCTTTTTTCT ** * * * * ** 1825 TTACATTTCTCC-AG-TAGATATTCAATTATAGCCTAT-TTG-AACCAAAAATAAAAAAAATTCA 65 ACACATTTC-CCAAGATAAACAATCAATTATAG--TATGTTGTAAGCAAAAATGTAAAAAATTCA * * ** * 1886 A-TTAAAAATTAATTATCAGATTATAAAATAATTTAAAACGAGT 127 ACTT-AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGT * * 1929 AATAAGGCTTTTGAAGGAATGGAAAACTATAAATAGACTTTTTTTCTCAATGAATGAC-TTTTTC 1 AATAAGGCTTTTGAAGGAATGGAAGACTATAAATAGACTTTTTTAC-CAATGAATG-CTTTTTTC * * ** * * * 1993 TACACGTTTCCCTAGATAGGCAATCAATTATAGTATGTTGTACTG-AAAAGTGTTAAAAAATTAA 64 TACACATTTCCCAAGATAAACAATCAATTATAGTATGTTGTA-AGCAAAAATG-TAAAAAATTCA * 2057 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGT 127 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGT * * * * * * 2100 AATAAGGCTTTTGAAGGAATAGAAGACCATAAATAAAATTTTCTACCGAATGAATGCTTTTTTTT 1 AATAAGGCTTTTGAAGGAATGGAAGACTATAAATAGACTTTTTTACC-AATGAATGCTTTTTTCT * * ** * * * * * 2165 TCATATTTTTCAAGGTAAACATTCTATTATAGTCTGTTTTAAGCAAAAATGTAAACAAATTCAAC 65 ACACATTTCCCAAGATAAACAATCAATTATAGTATGTTGTAAGCAAAAATGTAAA-AAATTCAAC 2230 TTAAAATCAATTATG-GCATTATAAAACCATTTAAAGCGAGT 129 TTAAAATCAATTATGAG-ATTATAAAACCATTTAAAGCGAGT * * * ** * * 2271 AGTGAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT 1 AATAAGGCTTTTGAAGGAATGGAAGACTATAAATAGACTTTT-TTACCAATGAAT 2326 CCCNNNNNNN Statistics Matches: 319, Mismatches: 62, Indels: 29 0.78 0.15 0.07 Matches are distributed among these distances: 168 38 0.12 169 32 0.10 170 29 0.09 171 215 0.67 172 5 0.02 ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35 Consensus pattern (169 bp): AATAAGGCTTTTGAAGGAATGGAAGACTATAAATAGACTTTTTTACCAATGAATGCTTTTTTCTA CACATTTCCCAAGATAAACAATCAATTATAGTATGTTGTAAGCAAAAATGTAAAAAATTCAACTT AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGT Found at i:3406 original size:171 final size:171 Alignment explanation

Indices: 3090--4781 Score: 1657 Period size: 171 Copynumber: 9.9 Consensus size: 171 3080 NNNNNNNNNN * * * ** 3090 TAAAGAAATTCAACTTAAAATCAATTATAAGATTATAAAATCATTTAAAGCTTGTAATAAGGCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * * * * * * ** 3155 TTGAGGGAATGGGTGACTATAAGTAGAGTTTTCTTACCAATTAATGCTTTTTTCTGCATGTTT-T 66 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCT * * * 3219 TAGAGGCAGGCATTCAATTATAGTCTATTTTAACCAAAAATG 131 TA-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG * * 3261 TAAAAAAATTTAACTTAAAATCAATTATGGGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * * * * * * 3326 TTGAGGGAATAGGTGACTACAAATATACTTTTCTTGCCAATGAATCCCTTTTTCTTCACATTTCT 66 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCT 3391 TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG 131 TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG * * * * 3432 T-AAAAAATTGCAACTTAAAATCAGTTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGCCT 1 TAAAAAAATT-CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT * * ** * * 3496 TTTTAAGGAATGGGTGACTATAAACAGACTTTTCTTGTCAATGAATACTTTTTTCTTCACATTT- 65 TTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTC * * * * * 3560 TTCAAGGTAGACAATCAATCATTGTCTGTTTTAACTAAAAATT 130 TT-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG * * * * * 3603 TGAAAAAATTCAAGTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAGTAATTAGGCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * * * * 3668 TTGAAGGAATGGGTGACTGTAAAT-GAACTTTTCTT-CTGAATTAATGGCTTTTTC--CACATGT 66 TTGAAGGAATGGGTGACTATAAATAG-ACTTTTCTTAC-CAATGAATGCCTTTTTCTTCACA--T * * * * * ** 3729 TTCTTGAGGTAGGCATTTC-ATTATATTCTATTTGAATGAAAAATG 127 TTCTTAAGGTAGACA-TTCAATTATAGTCTGTTTTAACCAAAAATG * * * * * * 3774 TAAAAAAATTCGACTTAAAATTAATTATAAGATTACAAAACCATTTAAAGCGAGTGATAAGGGTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * * * * * * 3839 TTAAAAGAATGGGTGACTATAAATAGACTTTTCTTAACAATGAATGGC-TTTTCTACACGTTT-T 66 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCT ** ** * 3902 CTAA-GTCA-AGCATTCAATTATAACCTGTTTTAATGAAAAATTT 131 -TAAGGT-AGA-CATTCAATTATAGTCTGTTTTAACCAAAAA-TG * * * * * * 3945 TAAAAAAATTCAGCTTAAAATCAATTTTGAGATTATGAGACTATTTAAAGCGAGTAATAAGCCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * * * * * 4010 TTGAAGGAATGGATGGCTA-AAGAT-GATTTTTCTTGA-AAATGAATGCATTTTTCTTCACATTT 66 TTGAAGGAATGGGTGACTATAA-ATAGACTTTTCTT-ACCAATGAATGCCTTTTTCTTCACATTT * * * * 4072 CTCAAGGTAGGCATTTAATTATAGTCTGTTTTAACTAAAAAT- 129 CTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG * * * * * * 4114 AAAAAAAATTCAACTTAAAATTAATTATCAGATTATAAAACAATTTACAGCGAGTAATAAAGCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT *** ** 4179 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGCC-TTTTCAAAATGTTTC 66 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTAC-CAATGAATGCCTTTTTCTTCACATTT- * * * * * 4242 CCT-AGGTAGACAATCAATTATAGTATGTTGT-ACTGAAAAATG 129 CTTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-CAAAAATG * * * * 4284 TTAAAAAATTAAACTTGAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * ** * * * * * 4349 TTGAAGGAATAGAAGACAATAAATGGAATTTTC-TACCGAATGAATGCTTTTTTCTTCATATTTC 66 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACC-AATGAATGCCTTTTTCTTCACATTTC * ** * 4413 TCTCAAGGTAGACATTCAATTATAGTTTGTACTAACCAAAAATA 130 T-T-AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG * * * 4457 TAAAAAAATTCAACTTAAAATCAATTATGGGAATATAAAACCATTTAAAGCGAATAATAAGGCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * * * * * * ** 4522 TTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCTAATAAATCCCTTTTTCTTCATGTTTC- 66 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCT * * * * * * * 4586 TAGAGCTAGAC-TTGAATTACAATCTATTTTAACCAATAATA 131 TA-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG * * * * * * 4627 TAAAACAATTGAACCTAAAATCAATTTTGAGAATATAAAACCATTTAAAGAGAGTAATAAGGCTT 1 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT * ** * * * * ** 4692 TTGAAGGAATAGAAGACTATAAATGGACTTCTCTTACCAATAAATGCTTTTTTCTTCATGTTTCT 66 TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCT * 4757 CAAGGTAGACATTCAATTATAGTCT 131 TAAGGTAGACATTCAATTATAGTCT 4782 NNNNNNNNNN Statistics Matches: 1254, Mismatches: 224, Indels: 86 0.80 0.14 0.05 Matches are distributed among these distances: 168 2 0.00 169 123 0.10 170 323 0.26 171 641 0.51 172 22 0.02 173 139 0.11 174 4 0.00 ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35 Consensus pattern (171 bp): TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT TTGAAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCT TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATG Found at i:5424 original size:170 final size:169 Alignment explanation

Indices: 5020--5428 Score: 441 Period size: 169 Copynumber: 2.4 Consensus size: 169 5010 NNNNNNNNNC * * 5020 CCATTCCCTC-AAAAGCCTTATTACTCACTTTAAATTA-TTTTATAATCTGATAATTAATTTTAA 1 CCATTCCC-CAAAAAGCCTTATTACTCACTTTAAA-TAGTTTTATAATCTCATAATTGATTTTAA ** 5083 GTTGAATTTTTTTTATTTTTGATTAAAACAGACTATAATTGAATGCCTATCTTAAGAAACATGAA 64 GTTGAATTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGCCTATCTTAAGAAACATGAA * * 5148 GGAAAAAGCATTCCTTGGTAAGAAAGTCTATTTATAGTCAT 129 GGAAAAAGCATTCCTTGGCAAGAAAGTCTATTTATAATCAT ** * * * * * 5189 CCATTCCTTAAAAAGGCTTATTACTCATTTTAAATGGTTTTATAATATCATAACTGATTTTAAGT 1 CCATTCCCCAAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGT * *********** * 5254 TGCATTTTTTACATTTTT-AGTTAAAACAGACTATAATTGAATGTNNNNNNNNNNAAACGTGAA- 66 TGAATTTTTTACATTTTTGA-TTAAAACAGACTATAATTGAATGCCTATCTTAAGAAACATGAAG * * * * 5317 GAAAAAGAGATTCTTTGGCAAGAAAAGTTTATTTGTAATCA- 130 GAAAAAG-CATTCCTTGGCAAG-AAAGTCTATTTATAATCAT * * 5358 CCTATTCCCCAAAAAGCCATATTACTCACTTTAAATAGTTTTATAATCCCATAATTGATTTTAAG 1 CC-ATTCCCCAAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAG 5423 TTGAAT 65 TTGAAT 5429 GTNNNNNNNN Statistics Matches: 194, Mismatches: 40, Indels: 11 0.79 0.16 0.04 Matches are distributed among these distances: 168 9 0.05 169 112 0.58 170 73 0.38 ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38 Consensus pattern (169 bp): CCATTCCCCAAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGT TGAATTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGCCTATCTTAAGAAACATGAAGG AAAAAGCATTCCTTGGCAAGAAAGTCTATTTATAATCAT Found at i:6324 original size:42 final size:42 Alignment explanation

Indices: 6265--6349 Score: 170 Period size: 42 Copynumber: 2.0 Consensus size: 42 6255 ATATTTCTAG 6265 AGCTAGACATTCAATTACAATCTGTTTTAACCAATAATATAA 1 AGCTAGACATTCAATTACAATCTGTTTTAACCAATAATATAA 6307 AGCTAGACATTCAATTACAATCTGTTTTAACCAATAATATAA 1 AGCTAGACATTCAATTACAATCTGTTTTAACCAATAATATAA 6349 A 1 A 6350 ACAATTGAAC Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 42 43 1.00 ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33 Consensus pattern (42 bp): AGCTAGACATTCAATTACAATCTGTTTTAACCAATAATATAA Found at i:7065 original size:171 final size:171 Alignment explanation

Indices: 6857--7179 Score: 468 Period size: 171 Copynumber: 1.9 Consensus size: 171 6847 NNNNNNNNAT * * 6857 GTAAAAAAATTCAACTTGAAATCAATTATGAGATTATAAAATCATTTAAAGCTAGTAATAAGGCT 1 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCT * * * * * * 6922 TTTGAGGGAATGGGTGACTATAAATAGAGTTTTCTTACAAATTAATGCT-TTTTTCTTTATGTTT 66 TTTGAGGGAATAGGTGACTACAAATAGACTTTTCTTACAAATGAAT-CTCTTTTTCTTAACGTTT * 6986 CTAGAGGCAGGCATTCAATTATATTCCATTTTAGCCAAAAAA 130 CTAGAGGCAGACATTCAATTATATTCCATTTTAGCCAAAAAA * * * * 7028 GTAAAAAAATTCAACTTAAAATGAATTATGGGATTATAAAATTATTTAAAGCGAGTAATAATGCT 1 GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCT * * * 7093 TTTGAGGGAATAGGTGACTACAAATATACTTTTCTTGCCAATGAATCTCTTTTTCTTAACGTTTC 66 TTTGAGGGAATAGGTGACTACAAATAGACTTTTCTTACAAATGAATCTCTTTTTCTTAACGTTTC * * 7158 TTGAGGTAGACATTCAATTATA 131 TAGAGGCAGACATTCAATTATA 7180 GNNNNNNNNN Statistics Matches: 133, Mismatches: 18, Indels: 2 0.87 0.12 0.01 Matches are distributed among these distances: 170 2 0.02 171 131 0.98 ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37 Consensus pattern (171 bp): GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCT TTTGAGGGAATAGGTGACTACAAATAGACTTTTCTTACAAATGAATCTCTTTTTCTTAACGTTTC TAGAGGCAGACATTCAATTATATTCCATTTTAGCCAAAAAA Done.