Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019909.1 Corchorus olitorius cultivar O-4 contig19942, 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: 19664
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:113 original size:44 final size:43
Alignment explanation
Indices: 64--187 Score: 203
Period size: 44 Copynumber: 2.8 Consensus size: 43
54 CATAAGGAGA
* *
64 AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
107 AGATGCCCCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
*
151 AATTGCCCCTGTGTTATATATGTGTTTGGGGACTTTT
1 AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTTT
188 TGGTTATTGG
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
43 2 0.03
44 74 0.97
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (43 bp):
AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
Found at i:1203 original size:219 final size:219
Alignment explanation
Indices: 824--1257 Score: 751
Period size: 219 Copynumber: 2.0 Consensus size: 219
814 AATTAATGAT
*
824 TGGGCAACTTATTTTAATTTTTAAACTTGATAATAATACTTTTATTAGTTTATATTATAAAATTG
1 TGGGCAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTATTAGTTTATATTATAAAATTG
* *
889 AAATGGGTCCAGAACTATCAAAATGTCTCCAATTTTTTAAAATTAAAATGGTAAAAATAAAATAT
66 AAATGGGTCCAGAACTATCAAAAAGTCTCCAATTTTTTAAAATTAAAATGGGAAAAATAAAATAT
* * * *
954 TTGTAAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTTAGCAGAATAATTGTAAAAGTTTA
131 TTATAAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTTAACAAAATAACTGTAAAAGTTTA
* *
1019 TTTCTAACAAAAAATTGTAAGATA
196 TTTATAACAAAAAACTGTAAGATA
*
1043 TGGGCAACTTATTTTAACTTTTAAACTTGATAATAATGCTTTTATTAGTTTATATTATAAAATTG
1 TGGGCAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTATTAGTTTATATTATAAAATTG
* *
1108 AAATTGTTCCAGAACTATCAAAAAGTCTCCAATTTTTTAAAATTAAAATGGGAAAAATAAAATAT
66 AAATGGGTCCAGAACTATCAAAAAGTCTCCAATTTTTTAAAATTAAAATGGGAAAAATAAAATAT
*
1173 TTATAAAAATATTTAATTTAATTAAATAAAAATAGAGTTTTTAACAAAATAACTGTAAAAGTTTA
131 TTATAAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTTAACAAAATAACTGTAAAAGTTTA
1238 TTTATAACAAAAAACTGTAA
196 TTTATAACAAAAAACTGTAA
1258 AATTTAAACA
Statistics
Matches: 202, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
219 202 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (219 bp):
TGGGCAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTATTAGTTTATATTATAAAATTG
AAATGGGTCCAGAACTATCAAAAAGTCTCCAATTTTTTAAAATTAAAATGGGAAAAATAAAATAT
TTATAAAAATATTGAATTTAATTAAATAAAAATAGAGTTTTTAACAAAATAACTGTAAAAGTTTA
TTTATAACAAAAAACTGTAAGATA
Found at i:1232 original size:28 final size:26
Alignment explanation
Indices: 1201--1260 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
1191 TAATTAAATA
*
1201 AAAATAGAGTTTTTAACAAAATAACTGT
1 AAAATAGA-TTTATAACAAAA-AACTGT
**
1229 AAAAGTTTATTTATAACAAAAAACTGT
1 AAAA-TAGATTTATAACAAAAAACTGT
1256 AAAAT
1 AAAAT
1261 TTAAACAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 10 0.36
28 15 0.54
29 2 0.07
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.32
Consensus pattern (26 bp):
AAAATAGATTTATAACAAAAAACTGT
Found at i:1426 original size:22 final size:22
Alignment explanation
Indices: 1398--1444 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1388 TTTTTAGTTG
*
1398 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
1420 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
1442 AGT
1 AGT
1445 TATGAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:1530 original size:93 final size:93
Alignment explanation
Indices: 1321--1505 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 93
1311 ACTTTTTAAT
* * * * *
1321 TAAATTAGTAATATCGTAAAAATAAAATAGGTTTAAGGATATTAGATTTAATTAAATAAGAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTTTAAGGATATTAGATATAATTAAATAAAAATAG
*
1386 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
*
1414 TAAAATAGTAAAATGGTAAAAATAAAATA-GTTATGAGGATATTAGATATAATTAAATAAAAATA
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTT-TAAGGATATTAGATATAATTAAATAAAAATA
1478 GAGTTTTTAGTTGACTAAAACTATAAAA
65 GAGTTTTTAGTTGACTAAAACTATAAAA
1506 ATTTAAAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 3 0.04
93 81 0.96
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTTTAAGGATATTAGATATAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:1583 original size:31 final size:30
Alignment explanation
Indices: 1544--1601 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
1534 TTGAAAAATA
*
1544 AAGGTATAATAGATGATTCAAAAGTTTAAT
1 AAGGTATAATAGACGATTCAAAAGTTTAAT
1574 AAGGATATAATAGACGATTCAAAAGTTT
1 AAGG-TATAATAGACGATTCAAAAGTTT
1602 TACAAAACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.31
Consensus pattern (30 bp):
AAGGTATAATAGACGATTCAAAAGTTTAAT
Found at i:9692 original size:19 final size:19
Alignment explanation
Indices: 9668--9729 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
9658 CCTAGCTCCA
9668 TTTAGTAATTTAGTTGCAC
1 TTTAGTAATTTAGTTGCAC
* * ***
9687 TTTAGTCATATAGCTTAGGGTT
1 TTTAGTAATTTAG-TT--GCAC
9709 TTTAGTAATTTAGTTGCAC
1 TTTAGTAATTTAGTTGCAC
9728 TT
1 TT
9730 CATGGCCTAG
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 2 0.07
22 12 0.40
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (19 bp):
TTTAGTAATTTAGTTGCAC
Found at i:13348 original size:16 final size:16
Alignment explanation
Indices: 13325--13362 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13315 ATCTAGAGAT
13325 AGAAAAAGATCAAAATC
1 AGAAAAAGA-CAAAATC
*
13342 A-AAAAAGAGAAAATC
1 AGAAAAAGACAAAATC
13357 AGAAAA
1 AGAAAA
13363 TAAAAAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 11 0.58
17 1 0.05
ACGTcount: A:0.71, C:0.08, G:0.13, T:0.08
Consensus pattern (16 bp):
AGAAAAAGACAAAATC
Done.