Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397823.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1125.0, 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: 18843
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.22

Warning! 7530 characters in sequence are not A, C, G, or T


Found at i:550 original size:172 final size:169

Alignment explanation

Indices: 9--554 Score: 486 Period size: 172 Copynumber: 3.2 Consensus size: 169 1 AATTTAAT * * * * 9 TTAAAATCAATTATGAGATTATAAAATCATTTAAACCGAGTAATAAAGCTGTCGAA-AGAATGCG 1 TTAAAATCAATTATGAGATTATAAAACCATTTAAACCGAGTAATAAGGCTTTCGAAGA-AATGAG * * * * * * * * 73 TGACTAAAAATAGATTTTTCTTCTCAATGAATAGCTTTTCCTATATCTTTCATAAGGCAGACT-T 65 TGACTATAAATGGACTTTT-TTCTCAATGAATAGCTTTTTCTACATATTTCACAAGGCA-AGTAT 137 TCAATTATAGTCTGTTTTAAAGAAAAATGTAAAAAAAATTCAAC 128 TCAATTATAGTCTGTTTTAAA-AAAAATGT-AAAAAAATTCAAC * * ********** * * 181 TTAAAATAAATTATGAGATTATAAAACTATTTAANNNNNNNNNNAAGGCTTTTGAAGGAATGAGT 1 TTAAAATCAATTATGAGATTATAAAACCATTTAAACCGAGTAATAAGGCTTTCGAAGAAATGAGT * * * * * 246 GACTATAAATGGACTTTTCTTCTCAATGAATAGTTTTTTTTACATATTTCTCAAGG-TAGACATT 66 GACTATAAATGGACTTTT-TTCTCAATGAATAGCTTTTTCTACATATTTCACAAGGCAAG-TATT * * 310 CAATTATAGTCTGTTTTAGCAAAAAATGTAAAAAAAGTCAAC 129 CAATTATAGTCTGTTTTA-AAAAAAATGTAAAAAAATTCAAC * ********** * 352 TTAAAATTAANNNNNNNNNNATAAAACCATTTAAACCGAGTAATAAGGCTTTCGAAGAAATGGGT 1 TTAAAATCAATTATGAGATTATAAAACCATTTAAACCGAGTAATAAGGCTTTCGAAGAAATGAGT * * * * * 417 GGCTATAAATGGACTTTTTATCACAATGAACTGGCTTTTTCTACATGTTTCCCAAGGCAAGTATT 66 GACTATAAATGGACTTTTT-TCTCAATGAA-TAGCTTTTTCTACATATTTCACAAGGCAAGTATT * * * 482 CAATTATATTCTGTTTTAATAAAACATGTAAAAAAATTTAAC 129 CAATTATAGTCTGTTTTAA-AAAAAATGTAAAAAAATTCAAC * 524 TTAAAATCAATTATCAGATTATAAAACCATT 1 TTAAAATCAATTATGAGATTATAAAACCATT 555 AAAAGTGGGN Statistics Matches: 283, Mismatches: 83, Indels: 16 0.74 0.22 0.04 Matches are distributed among these distances: 170 2 0.01 171 78 0.28 172 200 0.71 173 3 0.01 ACGTcount: A:0.39, C:0.12, G:0.12, T:0.34 Consensus pattern (169 bp): TTAAAATCAATTATGAGATTATAAAACCATTTAAACCGAGTAATAAGGCTTTCGAAGAAATGAGT GACTATAAATGGACTTTTTTCTCAATGAATAGCTTTTTCTACATATTTCACAAGGCAAGTATTCA ATTATAGTCTGTTTTAAAAAAAATGTAAAAAAATTCAAC Found at i:1427 original size:171 final size:171 Alignment explanation

Indices: 1115--1500 Score: 427 Period size: 171 Copynumber: 2.3 Consensus size: 171 1105 NNNNNNNNNN * * 1115 TATAGTCTGTTTTAATAAAAAATATAAAATAATTCAACTTAAAATCAATTATTAAATTACAAAAC 1 TATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAAATTACAAAAC * 1180 TATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATCGGTGAATCGAAATGGACTTTTCCTATCAAT 66 TATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATCGGTGAATAGAAATGGACTTTTCCTATCAAT * 1245 AAATACTTGTTTCTTCATGTTTCTCGACGCAAACATTCAAT 131 AAATACTTGTTTCTTCACGTTTCTCGACGCAAACATTCAAT * * * 1286 TATAGTCTGTTTTAACAAAAAATATAAAACAATTCAACTTGAAATCAATTA-TAAGATTATAAAA 1 TATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAA-ATTACAAAA ********** * * * * * 1350 CTATTTAANNNNNNNNNNAAGCCTTTTGAAGGAATCGGTGACTATAAAT-GATTTTTTCTTGTCA 65 CTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATCGGTGAATAGAAATGGA-CTTTTCCTATCA * * * * * * * * 1414 CTGAATGCTTGTTTCTTTACGTTTCTCGAGGTAGAGATTCAAT 129 ATAAATACTTGTTTCTTCACGTTTCTCGACGCAAACATTCAAT * * * 1457 TACAGTATGTTTTAATC-AAAAATCTAAAAAAATTCAACTTAAAA 1 TATAGTCTGTTTTAA-CAAAAAATATAAAAAAATTCAACTTAAAA 1501 NNNNNNNNNN Statistics Matches: 178, Mismatches: 34, Indels: 6 0.82 0.16 0.03 Matches are distributed among these distances: 170 5 0.03 171 172 0.97 172 1 0.01 ACGTcount: A:0.39, C:0.13, G:0.11, T:0.35 Consensus pattern (171 bp): TATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATTAAATTACAAAAC TATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATCGGTGAATAGAAATGGACTTTTCCTATCAAT AAATACTTGTTTCTTCACGTTTCTCGACGCAAACATTCAAT Found at i:6339 original size:171 final size:171 Alignment explanation

Indices: 5476--6520 Score: 697 Period size: 171 Copynumber: 6.2 Consensus size: 171 5466 NNNNNNNNNN * 5476 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAG-CTTTTGAAAGAAATG 1 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTCG-AAGAAATG * * * * 5540 GGTGACTCTAAATGGACTTTTCTTGTCAATTAATGGATTTTT-TCACACGTTTCTCGAGATAGAC 65 GGTGACTCTAAATGGACTTTTCTTCTCAATAAATAGCTTTTTCT-ACACGTTTCTCGAGATAGAC * 5604 ATTCAATTATTGTCTGTTTTATAGAAAAATAG-AAAAAAATTCA 129 ATTCAATTATTGTCTGTTTTAAAGAAAAAT-GTAAAAAAATTCA ********* ** 5647 ACTTAAAATCAATTAT-A-ANNNNNNNNNNTCATTTAAACCGAGTAATAAAG-CTTTCGAA-AGA 1 ACTTAAAATCAATTATGAGA-TTATAAAACT-ATTTAAAGTGAGTAAT-AAGCCTTTCGAAGA-A * ** * * * * ** 5708 ATTGGTGACTAAAAATAGATTTTTCTTCTCAATAAATAGCTTTTTCTATACCTTTCGT-GAGGCA 62 ATGGGTGACTCTAAATGGACTTTTCTTCTCAATAAATAGCTTTTTCTACACGTTTC-TCGAGATA * * * 5772 GACTTTCAATTATGGTCTATTTT-------AA--TAAAAAAATTCA 126 GACATTCAATTATTGTCTGTTTTAAAGAAAAATGTAAAAAAATTCA * * * * 5809 ACTTAGAATCAATTATGAGATTATAAAACTATTGAAAGTGAGTAATAAGCCTTT-TAAGGAATGG 1 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTCGAAGAAATGG * ********** 5873 GTGACT-TGAAATGGACTTTTCTTCTCAATCAATAGCTTTTTCTACACGTNNNNNNNNNNAGACA 66 GTGACTCT-AAATGGACTTTTCTTCTCAATAAATAGCTTTTTCTACACGTTTCTCGAGATAGACA * * * 5937 TTCAATTATTGTCCGTTTTAAAGAAAAATCTTAAAAAATTCA 130 TTCAATTATTGTCTGTTTTAAAGAAAAATGTAAAAAAATTCA * * * * 5979 ACTTAAAATTAATTATGAGATTATAAAA-TCATTTAGA-TCGAGTGATAAGGCTTTCGAA-AGAA 1 ACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGT-GAGTAATAAGCCTTTCGAAGA-AA ********** * * * * * ** 6041 TGGGTNNNNNNNNNNGAATTTTTCTTCTCAATAAATGGCTTTTTCTATAAC-TTTAGT-GAGGCA 63 TGGGTGACTCTAAATGGACTTTTCTTCTCAATAAATAGCTTTTTCTA-CACGTTT-CTCGAGATA * * * * * 6104 GGCTTTCAATTATAGTCTGTTTTAAAGAAAAATATAAAAAAACTCA 126 GACATTCAATTATTGTCTGTTTTAAAGAAAAATGTAAAAAAATTCA ********** * 6150 ACNNNNNNNNNNTTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTGGAAGAAATGG 1 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTCGAAGAAATGG * * * * * 6215 GTGACTCTAAATGGACTTTTCTTGTCAATTAATAGATTTTTTTACATGTTTCTCGAGATAGACAT 66 GTGACTCTAAATGGACTTTTCTTCTCAATAAATAGCTTTTTCTACACGTTTCTCGAGATAGACAT * * 6280 TCAATTATTGTCTGTTTTAACA-AAAAATGTGAAAAAATTTA 131 TCAATTATTGTCTGTTTTAA-AGAAAAATGTAAAAAAATTCA ************* * * * * 6321 ACTTAAAATCAATTATGAGATTNNNNNNNNNNNNNAAGCGAGTAATATGCCTTTTGAAGGAATGG 1 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTCGAAGAAATGG * * * * * 6386 GTGACTCTAAATGAACTTTTCTTGC-CTATCAATAGCTTTTTCTACACATTTCTC-ATGATAAAC 66 GTGACTCTAAATGGACTTTTCTT-CTCAATAAATAGCTTTTTCTACACGTTTCTCGA-GATAGAC 6449 ATTCAATTATTGTCTGTTTTAAAGAAAAATG-AAACAAAATTCA 129 ATTCAATTATTGTCTGTTTTAAAGAAAAATGTAAA-AAAATTCA * 6492 ATTTAAAAATCAATTATGAGATTATAAAA 1 ACTT-AAAATCAATTATGAGATTATAAAA 6521 TCATTTANNN Statistics Matches: 644, Mismatches: 190, Indels: 79 0.71 0.21 0.09 Matches are distributed among these distances: 161 71 0.11 162 43 0.07 163 2 0.00 164 3 0.00 168 2 0.00 169 3 0.00 170 64 0.10 171 422 0.66 172 34 0.05 ACGTcount: A:0.36, C:0.11, G:0.13, T:0.34 Consensus pattern (171 bp): ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTTCGAAGAAATGG GTGACTCTAAATGGACTTTTCTTCTCAATAAATAGCTTTTTCTACACGTTTCTCGAGATAGACAT TCAATTATTGTCTGTTTTAAAGAAAAATGTAAAAAAATTCA Found at i:8439 original size:342 final size:341 Alignment explanation

Indices: 7862--8554 Score: 855 Period size: 342 Copynumber: 2.0 Consensus size: 341 7852 GAGGTAGGTT * * * 7862 TTCAATTATTATCTGTTTTAAAGAAAAATATAAAAAAATTCAACTTAAAGTCAATTATAAGAATA 1 TTCAATTATTATCTATTTTAAAGAAAAATATAAAAAAATTCAAATTAAAATCAATTATAAGAATA * * ** * 7927 TAAAACTATTTAAAGCGAGTGATATGGCTTTTGAAGGAATGAGTGACCATAAATGAACTTTTCTT 66 TAAAACTATTTAAACCGAGTAATAAAGCTTTTGAAAGAATGAGTGACCATAAATGAACTTTTCTT * 7992 CTCAATGAATGGCTTTTTTGGCTTGTTTCTCGAGCCAAGCATTCAATTATAGTCTGTTTTAACAA 131 CTCAATGAATGGCTTTTTT-GCTTCTTTCTCGAGCCAAGCATTCAATTATAGTCTGTTTTAACAA * * * * 8057 AAAATGTTAAAAAATTCAACTTAAAGTCAATTATGAGATTATCAAACTATTTAAAGCGAGTAATA 195 AAAATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA * * * 8122 TACCTTTTT-AAGGAATGGGTGACTCTAAATGGACTTTTCTTGTCTATCAATAGCTT-TTTCTAC 260 -ACCTTTTTGAAGGAATGGGTAACTCTAAATGGACTTTTCTTATCAATCAAT-GCTTGTTTCTAC * 8185 ACATTTCTTAAGATAGATA 323 ACATTTCTTAAGATAGACA * * * * * 8204 TTTAATTATTATCTATTTTAAAGAAAAATGTAACAAAATTCAAATTAAAATCAATTATGAGATTA 1 TTCAATTATTATCTATTTTAAAGAAAAATATAAAAAAATTCAAATTAAAATCAATTATAAGAATA * * * * 8269 TAAAA-TCATTTAAACCGAGTAATAAAGCTTTTGAAAGAATGGGTGGCTA-AATATGGACTTTTC 66 TAAAACT-ATTTAAACCGAGTAATAAAGCTTTTGAAAGAATGAGTGACCATAA-ATGAACTTTTC * * * * * 8332 TTCTCAATGAATGGC-TTTTT-CTATACCTTTCAT-GTGGCAGGCTTTCAATTATTGTCTGTTTT 129 TTCTCAATGAATGGCTTTTTTGCT-T--CTTTC-TCGAGCCAAGCATTCAATTATAGTCTGTTTT * 8394 AA-AGAAAAATATAAAAAAATTCAACTTCAAA-TCAATTATGAGATTATAAAACCATTTAAAGTG 190 AACA-AAAAATATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACCATTTAAAGCG * * * * * * 8457 ATTAATAAGCTTTTTGAAGGAATGTGTAACTCTAAATGGACTTTTTTTATCAATGAATTCTTGTT 253 AGTAATAACCTTTTTGAAGGAATGGGTAACTCTAAATGGACTTTTCTTATCAATCAATGCTTGTT * * * 8522 TCTTCACGTTTCTTAAGGTAGACA 318 TCTACACATTTCTTAAGATAGACA 8546 TTCAATTAT 1 TTCAATTAT 8555 AGTATGTTTT Statistics Matches: 299, Mismatches: 42, Indels: 20 0.83 0.12 0.06 Matches are distributed among these distances: 339 2 0.01 340 1 0.00 341 19 0.06 342 273 0.91 343 4 0.01 ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38 Consensus pattern (341 bp): TTCAATTATTATCTATTTTAAAGAAAAATATAAAAAAATTCAAATTAAAATCAATTATAAGAATA TAAAACTATTTAAACCGAGTAATAAAGCTTTTGAAAGAATGAGTGACCATAAATGAACTTTTCTT CTCAATGAATGGCTTTTTTGCTTCTTTCTCGAGCCAAGCATTCAATTATAGTCTGTTTTAACAAA AAATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA CCTTTTTGAAGGAATGGGTAACTCTAAATGGACTTTTCTTATCAATCAATGCTTGTTTCTACACA TTTCTTAAGATAGACA Found at i:8552 original size:171 final size:170 Alignment explanation

Indices: 7814--8566 Score: 750 Period size: 171 Copynumber: 4.4 Consensus size: 170 7804 NNAAATGAAT * * * * *** * 7814 TTTTCTTCTCAATGAATGGCTTTTTCTATACCTTTCATGAGGTAGGTTTTCAATTATTATCTGTT 1 TTTTCTTCTCAATGAATGGCTTTTTCT-TACGTTTCTTAAGGCAGACATTCAATTATTGTCTGTT * * * 7879 TTAAAGAAAAATATAAAAAAATTCAACTTAAAGTCAATTATAAGAATATAAAACTATTTAAAGCG 65 TTAAAGAAAAATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCG * * * * 7944 AGTGATATGGCTTTTGAAGGAATGAGTGAC-CATAAATGAAC 130 AGTAATATAGCTTTTGAAGGAATGGGTGACTC-TAAATGGAC ** * * 7985 TTTTCTTCTCAATGAATGGCTTTTTTGGCTT--GTTTCTCGAGCCA-AGCATTCAATTATAGTCT 1 TTTTCTTCTCAATGAATGGC-TTTTT--CTTACGTTTCTTAAGGCAGA-CATTCAATTATTGTCT * * * * 8047 GTTTTAACA-AAAAATGTTAAAAAATTCAACTTAAAGTCAATTATGAGATTATCAAACTATTTAA 62 GTTTTAA-AGAAAAATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAA * * 8111 AGCGAGTAATATACCTTTTTAAGGAATGGGTGACTCTAAATGGAC 126 AGCGAGTAATATAGCTTTTGAAGGAATGGGTGACTCTAAATGGAC * * * * * * ** * * * * 8156 TTTTCTTGTCTATCAATAGCTTTTTCTACACATTTCTTAAGATAGATATTTAATTATTATCTATT 1 TTTTCTTCTCAATGAATGGCTTTTTCT-TACGTTTCTTAAGGCAGACATTCAATTATTGTCTGTT * * * * * * 8221 TTAAAGAAAAATGTAACAAAATTCAAATTAAAATCAATTATGAGATTATAAAATCATTTAAACCG 65 TTAAAGAAAAATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCG * * * * 8286 AGTAATAAAGCTTTTGAAAGAATGGGTGGCT-AAATATGGAC 130 AGTAATATAGCTTTTGAAGGAATGGGTGACTCTAA-ATGGAC * * ** * * 8327 TTTTCTTCTCAATGAATGGCTTTTTCTATACCTTTCATGTGGCAGGCTTTCAATTATTGTCTGTT 1 TTTTCTTCTCAATGAATGGCTTTTTCT-TACGTTTCTTAAGGCAGACATTCAATTATTGTCTGTT * 8392 TTAAAGAAAAATATAAAAAAATTCAACTTCAAA-TCAATTATGAGATTATAAAACCATTTAAAGT 65 TTAAAGAAAAATATAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACCATTTAAAGC * * * 8456 GATTAATA-AGCTTTTTGAAGGAATGTGTAACTCTAAATGGAC 129 GAGTAATATAGC-TTTTGAAGGAATGGGTGACTCTAAATGGAC * * * * * * 8498 TTTTTTTATCAATGAAT-TCTTGTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTATGT 1 TTTTCTTCTCAATGAATGGCTT-TTTCTT-ACGTTTCTTAAGGCAGACATTCAATTATTGTCTGT 8562 TTTAA 64 TTTAA 8567 TTANNNNNNN Statistics Matches: 474, Mismatches: 91, Indels: 34 0.79 0.15 0.06 Matches are distributed among these distances: 168 2 0.00 170 15 0.03 171 441 0.93 172 13 0.03 173 1 0.00 174 2 0.00 ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38 Consensus pattern (170 bp): TTTTCTTCTCAATGAATGGCTTTTTCTTACGTTTCTTAAGGCAGACATTCAATTATTGTCTGTTT TAAAGAAAAATATAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACCATTTAAAGCGA GTAATATAGCTTTTGAAGGAATGGGTGACTCTAAATGGAC Found at i:17031 original size:171 final size:171 Alignment explanation

Indices: 16666--17057 Score: 403 Period size: 171 Copynumber: 2.3 Consensus size: 171 16656 NNNNNNNNAT * * * * * * 16666 TGAATGTTTACCTCGAGAAACATGAAGAAACAAGCTTTCATTGACAAAAAAAAGCCCATTTAAAG 1 TGAATGTCTACCTAGAGAAACGTGAAGAAACAAGCATTCATTGA-GAAAAAAAGCCCATTCAAAG * 16731 TCACCCATTCCTTCAAAAAGCTTATTACTCGCTTTGAATGGGTTTATAACCTCATAATTGATTTT 65 TCACCCATTCCTTCAAAAAGCTTATTACTCACTTTGAATGGGTTTATAACCTCATAATTGATTTT * * * * * 16796 AAGTTGAATTTTTTTATATTGTTGATTAAAACTTACTGTAAT 130 AAGTTAAATTATTTTATATTGTTGATTAAAACTGACTATAAG * * * * * * 16838 TGAATGTTTATCTCGAGAAACGTGAAGAAACAAGCATTCATTGAGAAGAAAAGTCCATTCAGAGT 1 TGAATGTCTACCTAGAGAAACGTGAAGAAACAAGCATTCATTGAGAAAAAAAGCCCATTCAAAGT * ********** * * 16903 CACCCATTCTTTCAAAAAGCTTATTACTCACTTNNNNNNNNNNTATAATCTCGTAATTGATTTTA 66 CACCCATTCCTTCAAAAAGCTTATTACTCACTTTGAATGGGTTTATAACCTCATAATTGATTTTA * * * 16968 AGTTAAATTATTTTATATTTTTTATTCAAA-TAGACTATAAG 131 AGTTAAATTATTTTATATTGTTGATTAAAACT-GACTATAAG * * 17009 TGATTGTCTACCTAGGGAAACGT-ATAGAAA-AAGCTATTCATTGAGAAAA 1 TGAATGTCTACCTAGAGAAACGTGA-AGAAACAAGC-ATTCATTGAGAAAA 17058 NNNNNNNNNN Statistics Matches: 181, Mismatches: 36, Indels: 7 0.81 0.16 0.03 Matches are distributed among these distances: 170 6 0.03 171 134 0.74 172 41 0.23 ACGTcount: A:0.36, C:0.14, G:0.13, T:0.34 Consensus pattern (171 bp): TGAATGTCTACCTAGAGAAACGTGAAGAAACAAGCATTCATTGAGAAAAAAAGCCCATTCAAAGT CACCCATTCCTTCAAAAAGCTTATTACTCACTTTGAATGGGTTTATAACCTCATAATTGATTTTA AGTTAAATTATTTTATATTGTTGATTAAAACTGACTATAAG Done.