Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014016.1 Corchorus olitorius cultivar O-4 contig14049, 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: 7957
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Found at i:975 original size:28 final size:28
Alignment explanation
Indices: 908--984 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
898 GCGTGGACTT
908 AAAATGACCAAAATGCCCCT-GAATATG
1 AAAATGACCAAAATGCCCCTAGAATATG
* * * *
935 CAAATGACTAAAATGCCCCTAGATTTTG
1 AAAATGACCAAAATGCCCCTAGAATATG
963 AAAATGACCAAAATGCCCCTAG
1 AAAATGACCAAAATGCCCCTAG
985 GTGATCATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 18 0.42
28 25 0.58
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAGAATATG
Found at i:1298 original size:23 final size:23
Alignment explanation
Indices: 1272--1348 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
1262 AAAAAGGACC
1272 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
* ** * *
1295 GTCTACCAATTCAAT-CTTAGAAGGACC
1 GTCTTCCGCTT--ATCCTTTG-A--ACT
1322 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
1345 GTCT
1 GTCT
1349 ACCAATTCAA
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
23 14 0.37
24 4 0.11
25 6 0.16
26 4 0.11
27 10 0.26
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACT
Found at i:1339 original size:50 final size:50
Alignment explanation
Indices: 1222--1461 Score: 408
Period size: 50 Copynumber: 4.8 Consensus size: 50
1212 GAATGGATCA
* * *
1222 TCTTCGGCTTATCCCTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCG
1 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT-AAAAGGACCG
*
1273 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAGAAGGACCG
1 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCG
1323 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCG
1 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCG
*
1373 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCA
1 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCG
* *
1423 TCTTCCGCTTATCCTTTGAATTGTCTTCCAATTCAATCT
1 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
1462 CGAGAAAACC
Statistics
Matches: 181, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 144 0.80
51 37 0.20
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.36
Consensus pattern (50 bp):
TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCG
Found at i:1835 original size:64 final size:64
Alignment explanation
Indices: 1676--2045 Score: 456
Period size: 64 Copynumber: 5.8 Consensus size: 64
1666 TAAATAGCCG
* * * * * * * * *
1676 TCTTCTGGTGTGCTTTTTAACAAGATCGTCTTCCGACCGACTTTTGAAAA-TTTTAAGAATCCA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCA
*
1739 TCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCA
* * * *
1803 TCTTCTGGTGTACTTTTTGAGAAGATCATCTTCCGATCAACTTCTGAAAACTGTTGAGAAAACA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCA
* * * * * *
1867 TCTTCTGGTGTAGTTCTTGACAAGATCATCTTCTGATCAATTTCTGAAAACTATTGGGAAACCA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCA
* * * * ** *
1931 TCTTCTGGTGTGCTTTTTGACAAGATCGTCTTTCGATCAACTT-AGAAATTTTTTTTGAGAAACC
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAA--ACTGTTGAGAAACC
1995 A
64 A
*
1996 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAA
1 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAA
2046 TTCTTTCTAG
Statistics
Matches: 262, Mismatches: 41, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
63 47 0.18
64 161 0.61
65 50 0.19
66 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (64 bp):
TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCA
Found at i:1905 original size:128 final size:126
Alignment explanation
Indices: 1676--2045 Score: 506
Period size: 128 Copynumber: 2.9 Consensus size: 126
1666 TAAATAGCCG
* * * * *
1676 TCTTCTGGTGTGCTTTTTAACAAGATCGTCTTCCGACCGACTTTTGAAAATTTTAAGAATCCATC
1 TCTTCTGGTGTGCTTTTTGACAAGATCGTCTTCCGATCAAC-TTTGAAAATTTTGAGAAACCATC
*
1741 TTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCA
65 TTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAACCA
* * * * *
1803 TCTTCTGGTGTACTTTTTGAGAAGATCATCTTCCGATCAACTTCTGAAAACTGTTGAGAAAACAT
1 TCTTCTGGTGTGCTTTTTGACAAGATCGTCTTCCGATCAACTT-TGAAAA-TTTTGAGAAACCAT
* * * *
1868 CTTCTGGTGTAGTTCTTGACAAGATCATCTTCTGATCAATTTCTGAAAACTATTGGGAAACCA
64 CTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAACCA
* * *
1931 TCTTCTGGTGTGCTTTTTGACAAGATCGTCTTTCGATCAACTTAGAAATTTTTTTTGAGAAACCA
1 TCTTCTGGTGTGCTTTTTGACAAGATCGTCTTCCGATCAACTTTGAAA---ATTTTGAGAAACCA
* *
1996 TCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAA
63 TCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAA
2046 TTCTTTCTAG
Statistics
Matches: 210, Mismatches: 28, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
126 2 0.01
127 45 0.21
128 107 0.51
129 56 0.27
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (126 bp):
TCTTCTGGTGTGCTTTTTGACAAGATCGTCTTCCGATCAACTTTGAAAATTTTGAGAAACCATCT
TCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTATTGAGAAACCA
Found at i:2262 original size:121 final size:122
Alignment explanation
Indices: 2017--2311 Score: 441
Period size: 121 Copynumber: 2.4 Consensus size: 122
2007 ACTTCTTGAC
* * *
2017 AAGATCGTCTTCCGATCAAC-TCCTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTGTC
1 AAGATTGTCTTCCAATCAACAT-TTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTGTC
* *
2081 TTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCGGGGTTCCCCTTAAT
65 TTCCAATCAACATTTGAAAATCCTTTCTAACAAACCGTCTTCCAGGGTTCCCCTTAAT
* *
2139 AAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTTCGATG-TATTGTCT
1 AAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTGTCT
* * * *
2203 TCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCAGTGTTCTCCTTCAT
66 TCCAATCAACATTTGAAAATCCTTTCTAACAAACCGTCTTCCAGGGTTCCCCTTAAT
* * *
2260 AAGATTGTCTTCCAATCAGCATTTGAAATTTCTTTCTATCAAACCGTCTTCC
1 AAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCC
2312 AGTGTATTCC
Statistics
Matches: 157, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
121 106 0.68
122 50 0.32
123 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (122 bp):
AAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTGTCT
TCCAATCAACATTTGAAAATCCTTTCTAACAAACCGTCTTCCAGGGTTCCCCTTAAT
Found at i:2304 original size:67 final size:67
Alignment explanation
Indices: 2196--2386 Score: 287
Period size: 67 Copynumber: 2.9 Consensus size: 67
2186 CTTTCGATGT
*
2196 ATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCAGTGTTCTCCTTCATA
1 ATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCAGTGTTCTCCTTAATA
2261 AG
66 AG
* * *
2263 ATTGTCTTCCAATCAGCATTTGAAATTTCTTTCTATCAAACCGTCTTCCAGTGTAT-TCCTTAAT
1 ATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCAGTGT-TCTCCTTAAT
*
2327 GAG
65 AAG
* *
2330 ATTGCCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCC-GATGTTCT
1 ATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCAG-TGTTCT
2387 TTTAAAATTC
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
66 2 0.02
67 109 0.97
68 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (67 bp):
ATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCAGTGTTCTCCTTAATA
AG
Found at i:4199 original size:12 final size:11
Alignment explanation
Indices: 4182--4229 Score: 78
Period size: 12 Copynumber: 4.2 Consensus size: 11
4172 TTAATTCACT
4182 TTTGATTTGAA
1 TTTGATTTGAA
4193 CTTTGATTTGAA
1 -TTTGATTTGAA
4205 TTTTGATTTGAA
1 -TTTGATTTGAA
4217 TTTGATTTGAA
1 TTTGATTTGAA
4228 TT
1 TT
4230 ACTTAACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
11 13 0.37
12 22 0.63
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (11 bp):
TTTGATTTGAA
Found at i:4209 original size:7 final size:6
Alignment explanation
Indices: 4182--4229 Score: 50
Period size: 5 Copynumber: 8.3 Consensus size: 6
4172 TTAATTCACT
4182 TTTG-A TTTGAA CTTTG-A TTTGAA TTTTG-A TTTGAA TTTG-A TTTGAA
1 TTTGAA TTTGAA -TTTGAA TTTGAA -TTTGAA TTTGAA TTTGAA TTTGAA
4228 TT
1 TT
4230 ACTTAACGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
5 17 0.46
6 12 0.32
7 8 0.22
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (6 bp):
TTTGAA
Found at i:4224 original size:23 final size:24
Alignment explanation
Indices: 4181--4229 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
4171 TTTAATTCAC
4181 TTTTGATTTGAACTTTGATTTGAA
1 TTTTGATTTGAACTTTGATTTGAA
4205 TTTTGATTTGAA-TTTGATTTGAA
1 TTTTGATTTGAACTTTGATTTGAA
4228 TT
1 TT
4230 ACTTAACGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.57
Consensus pattern (24 bp):
TTTTGATTTGAACTTTGATTTGAA
Found at i:4551 original size:13 final size:14
Alignment explanation
Indices: 4512--4560 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
4502 CTTAAAAGGC
4512 TCAAAACC--TTTT
1 TCAAAACCTATTTT
*
4524 TGAAAACCTATTTT
1 TCAAAACCTATTTT
*
4538 TCAAAAACTATTTT
1 TCAAAACCTATTTT
4552 TCAAAACCT
1 TCAAAACCT
4561 TTTCTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 7 0.23
14 24 0.77
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (14 bp):
TCAAAACCTATTTT
Found at i:4571 original size:14 final size:13
Alignment explanation
Indices: 4514--4587 Score: 60
Period size: 14 Copynumber: 5.4 Consensus size: 13
4504 TAAAAGGCTC
4514 AAAACC-TTTTTG
1 AAAACCTTTTTTG
*
4526 AAAACCTATTTTTC
1 AAAACCT-TTTTTG
* *
4540 AAAAACTATTTTTC
1 AAAACCT-TTTTTG
4554 AAAACCTTTTCTTG
1 AAAACCTTTT-TTG
*
4568 AAAACAATTTTCTTG
1 AAAAC-CTTTT-TTG
4583 AAAAC
1 AAAAC
4588 ATGTCTTGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
12 6 0.11
13 3 0.06
14 31 0.58
15 13 0.25
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:4580 original size:15 final size:15
Alignment explanation
Indices: 4560--4588 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4550 TTTCAAAACC
4560 TTTTCTTGAAAACAA
1 TTTTCTTGAAAACAA
4575 TTTTCTTGAAAACA
1 TTTTCTTGAAAACA
4589 TGTCTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTTCTTGAAAACAA
Found at i:7640 original size:23 final size:22
Alignment explanation
Indices: 7595--7637 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7585 TATTATTGCA
*
7595 TCTTTTTGTTTTCTGATTTTTC
1 TCTTTTTGATTTCTGATTTTTC
7617 TCTTTTTGATTT-TGATCTTTT
1 TCTTTTTGATTTCTGAT-TTTT
7638 TCTATCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.07, C:0.12, G:0.09, T:0.72
Consensus pattern (22 bp):
TCTTTTTGATTTCTGATTTTTC
Done.