Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402935.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5981.0, 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, 665
Length: 1109
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Found at i:536 original size:131 final size:131
Alignment explanation
Indices: 384--847 Score: 351
Period size: 131 Copynumber: 3.6 Consensus size: 131
374 ATTAGAAAAT
* * * * *
384 TAGTTAGAAAATTGAAGAAAAAAA-TGTTATCGAAAATTGAAGTTGATAAACTACTCAAACAAGT
1 TAGTTAGAAAATT-AAAAAAAAAAGTATTGTCAAAAATTGAAGTTAATAAACTACTCAAACAAGT
*
448 TTGAGGTGTGATATACTATTTTTAAAGATAATTTCCACCAAAAACTTAAGAGAAAACTCTTCTTG
65 TTGAGGTGTGATATACTATTTTTAAAGATAATTTCCAACAAAAACTTAAGAGAAAACTCTTCTTG
513 AA
130 AA
* * * * *
515 TAGTTAGAAAATTAAAAAAAAAGGTGTTGTCAAAAATTGAAGCTAATAAACTACGGC--TCAA--
1 TAGTTAGAAAATTAAAAAAAAAAGTATTGTCAAAAATTGAAGTTAATAAACTAC-TCAAACAAGT
* * * * * * * * * * * *
576 CTAAAGT-TGATAT--TGA----TAAA-CT-A-TTCAAAC-AAATCTGAGGTGTGATACGCTGT-
65 TTGAGGTGTGATATACT-ATTTTTAAAGATAATTTCCAACAAAAACTTAAGAG-AAAACTCT-TC
*
629 TAGAAAA
127 TTG--AA
* * * *
636 TTAGTTAAAAAATT--GAAAAAATGTATTGTCAAAAATTGAAGTTGATAAACTACTCAAACAAGT
1 -TAGTTAGAAAATTAAAAAAAAAAGTATTGTCAAAAATTGAAGTTAATAAACTACTCAAACAAGT
* * * * *
699 TTGAGGTGTAATACACTATTTTGAAAGATAATTT-CATTCAAAATA-TTGAGAGAAAACTCTTCT
65 TTGAGGTGTGATATACTATTTTTAAAGATAATTTCCA-ACAAAA-ACTTAAGAGAAAACTCTTCT
762 TGAA
128 TGAA
* * *
766 TAGTTAGAAAATTAAAAGAAAAAGTATTGTCGAAAATTGAAGTTAAAAAACTACTCAAACAAGTT
1 TAGTTAGAAAATTAAAAAAAAAAGTATTGTCAAAAATTGAAGTTAATAAACTACTCAAACAAGTT
831 TGCA-GTGTGATATACTA
66 TG-AGGTGTGATATACTA
848 AGTGTTGTTG
Statistics
Matches: 247, Mismatches: 57, Indels: 58
0.68 0.16 0.16
Matches are distributed among these distances:
118 8 0.03
119 13 0.05
120 36 0.15
121 6 0.02
122 16 0.06
123 4 0.02
124 4 0.02
125 2 0.01
126 2 0.01
127 6 0.02
128 4 0.02
129 15 0.06
130 14 0.06
131 99 0.40
132 12 0.05
133 6 0.02
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (131 bp):
TAGTTAGAAAATTAAAAAAAAAAGTATTGTCAAAAATTGAAGTTAATAAACTACTCAAACAAGTT
TGAGGTGTGATATACTATTTTTAAAGATAATTTCCAACAAAAACTTAAGAGAAAACTCTTCTTGA
A
Found at i:657 original size:21 final size:23
Alignment explanation
Indices: 632--675 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
622 ACGCTGTTAG
632 AAAAT-TAGT-TAAAAAATTGAA
1 AAAATGTAGTGTAAAAAATTGAA
* *
653 AAAATGTATTGTCAAAAATTGAA
1 AAAATGTAGTGTAAAAAATTGAA
676 GTTGATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (23 bp):
AAAATGTAGTGTAAAAAATTGAA
Found at i:780 original size:251 final size:253
Alignment explanation
Indices: 335--819 Score: 719
Period size: 251 Copynumber: 1.9 Consensus size: 253
325 TCAACCGAAG
* * *
335 TTGATAAACTACTCAAACAAATTTGAGGTGCGATACATTATTAGAAAATTAGTTAGAAAATTGAA
1 TTGATAAACTACTCAAACAAATCTGAGGTGCGATACACTATTAGAAAATTAGTTAAAAAATTGAA
* * * *
400 GAAAAAAATGTTATCGAAAATTGAAGTTGATAAACTACTCAAACAAGTTTGAGGTGTGATATACT
66 GAAAAAAATATTATCAAAAATTGAAGTTGATAAACTACTCAAACAAGTTTGAGGTGTAATACACT
*
465 ATTTTTAAAGATAATTTCCACCAAAAACTTAAGAGAAAACTCTTCTTGAATAGTTAGAAAATTAA
131 ATTTTGAAAGATAATTTCCACCAAAAACTTAAGAGAAAACTCTTCTTGAATAGTTAGAAAATTAA
* *
530 AA-AAAAAGGTGTTGTCAAAAATTGAAGCTAATAAACTACGGCTCAACTAAAGTTGATA
196 AAGAAAAA-GTATTGTCAAAAATTGAAGCTAAAAAACTACGGCTCAACTAAAGTTGATA
* * * *
588 TTGATAAACTATTCAAACAAATCTGAGGTGTGATACGCTGTTAGAAAATTAGTTAAAAAATTG-A
1 TTGATAAACTACTCAAACAAATCTGAGGTGCGATACACTATTAGAAAATTAGTTAAAAAATTGAA
** *
652 -AAAAATGTATTGTCAAAAATTGAAGTTGATAAACTACTCAAACAAGTTTGAGGTGTAATACACT
66 GAAAAAAATATTATCAAAAATTGAAGTTGATAAACTACTCAAACAAGTTTGAGGTGTAATACACT
* *
716 ATTTTGAAAGATAATTT-CATTCAAAATA-TTGAGAGAAAACTCTTCTTGAATAGTTAGAAAATT
131 ATTTTGAAAGATAATTTCCA-CCAAAA-ACTTAAGAGAAAACTCTTCTTGAATAGTTAGAAAATT
* *
779 AAAAGAAAAAGTATTGTCGAAAATTGAAGTTAAAAAACTAC
194 AAAAGAAAAAGTATTGTCAAAAATTGAAGCTAAAAAACTAC
820 TCAAACAAGT
Statistics
Matches: 208, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
250 2 0.01
251 143 0.69
252 7 0.03
253 56 0.27
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (253 bp):
TTGATAAACTACTCAAACAAATCTGAGGTGCGATACACTATTAGAAAATTAGTTAAAAAATTGAA
GAAAAAAATATTATCAAAAATTGAAGTTGATAAACTACTCAAACAAGTTTGAGGTGTAATACACT
ATTTTGAAAGATAATTTCCACCAAAAACTTAAGAGAAAACTCTTCTTGAATAGTTAGAAAATTAA
AAGAAAAAGTATTGTCAAAAATTGAAGCTAAAAAACTACGGCTCAACTAAAGTTGATA
Done.