Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021875.1 Corchorus olitorius cultivar O-4 contig21908, 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: 37798
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35 TAATAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1414 original size:1 final size:1
Alignment explanation
Indices: 1403--1445 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
1393 GTGGGGTGGG
* * * *
1403 TTTTTTCTTTTTTCTTTTTTTTCTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1446 GATGATTATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (1 bp):
T
Found at i:1424 original size:16 final size:16
Alignment explanation
Indices: 1403--1445 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1393 GTGGGGTGGG
1403 TTTTTTCTTTTTTCTT
1 TTTTTTCTTTTTTCTT
*
1419 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTCTT
*
1435 TTTTTTGTTTT
1 TTTTTTCTTTT
1446 GATGATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (16 bp):
TTTTTTCTTTTTTCTT
Found at i:3153 original size:23 final size:24
Alignment explanation
Indices: 3109--3153 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
3099 TCATCATCAA
* *
3109 AAGGTAAGACTAGGCTTCTTTTAT
1 AAGGTAAGAATAGACTTCTTTTAT
*
3133 AAGG-AAGAATAGACTTTTTTT
1 AAGGTAAGAATAGACTTCTTTT
3154 TTATACCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (24 bp):
AAGGTAAGAATAGACTTCTTTTAT
Found at i:16271 original size:24 final size:26
Alignment explanation
Indices: 16244--16294 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
16234 TATTAAGCAG
16244 TAAACAACAA-A-TTTCCAGCCAACT
1 TAAACAACAATATTTTCCAGCCAACT
* * *
16268 TAAAGAGCAATATTTTCTAGCCAACT
1 TAAACAACAATATTTTCCAGCCAACT
16294 T
1 T
16295 GAAGAGCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 13 0.59
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (26 bp):
TAAACAACAATATTTTCCAGCCAACT
Found at i:16284 original size:26 final size:26
Alignment explanation
Indices: 16255--16307 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
16245 AAACAACAAA
16255 TTTCCAGCCAACTTAAAGAGCAATAT
1 TTTCCAGCCAACTTAAAGAGCAATAT
* *
16281 TTTCTAGCCAACTTGAAGAGCAATAT
1 TTTCCAGCCAACTTAAAGAGCAATAT
16307 T
1 T
16308 CGAGTGGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (26 bp):
TTTCCAGCCAACTTAAAGAGCAATAT
Found at i:17874 original size:65 final size:65
Alignment explanation
Indices: 17798--17920 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
17788 ATCCACATTT
*
17798 GAGATAACATGGCAAACCAAAATCTTTCCACGCAATAAGTGCTCTATTAATTTAGGTGCATATGA
1 GAGATAACATGGCAAACCAAAATCTTTCCACGAAATAAGTGCTCTATTAATTTAGGTGCATATGA
* * * *
17863 GAGATAACATGGCAAACCAACATCTTTCTAGGAAATAAGTGCTCTGTTAATTTAGGTG
1 GAGATAACATGGCAAACCAAAATCTTTCCACGAAATAAGTGCTCTATTAATTTAGGTG
17921 TATAACTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (65 bp):
GAGATAACATGGCAAACCAAAATCTTTCCACGAAATAAGTGCTCTATTAATTTAGGTGCATATGA
Found at i:18817 original size:43 final size:41
Alignment explanation
Indices: 18744--19273 Score: 458
Period size: 42 Copynumber: 12.8 Consensus size: 41
18734 AATCTTTAAC
*
18744 GGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAAAGACTAGAT
1 GGGATCTTT-CCCTAAATT-AAAACTTTGAAAAAAA-ACTGGAT
**
18787 GGGATCTTTCCCTAAATTAAAACTTCTG---AAAAACTATAT
1 GGGATCTTTCCCTAAATTAAAACTT-TGAAAAAAAACTGGAT
* * * *
18826 GAGATCTTTCCCTAAATTAAAGCTTCGAAAAAAAACTGAAT
1 GGGATCTTTCCCTAAATTAAAACTTTGAAAAAAAACTGGAT
* *
18867 GGGATCTTTCCCTAAATTAAAGCTTCTG---AAAAACTGAAT
1 GGGATCTTTCCCTAAATTAAAACTT-TGAAAAAAAACTGGAT
*
18906 AGGAT-TCTTCCCTAAATTAAAGACTTT-AAAAAGAAACTGGAT
1 GGGATCT-TTCCCTAAATTAAA-ACTTTGAAAAA-AAACTGGAT
*
18948 GAGATCTTTCCCTAAATTAAACACTTT-AAAAAGAAACTGGAT
1 GGGATCTTTCCCTAAATTAAA-ACTTTGAAAAA-AAACTGGAT
18990 GGGATCTTTCCCTAAATTAAAGACTTT-AAAAAGAAACTGGAT
1 GGGATCTTTCCCTAAATTAAA-ACTTTGAAAAA-AAACTGGAT
*
19032 GGGATCTTTCCCTAAACTAAAGACTTT-AAAAAGAAACTGGAT
1 GGGATCTTTCCCTAAATTAAA-ACTTTGAAAAA-AAACTGGAT
* *
19074 GGGATCTTTCCCT-AATTAGAAA-TCTTG----AAAGCTTGAT
1 GGGATCTTTCCCTAAATTA-AAACT-TTGAAAAAAAACTGGAT
* *
19111 GGGATCTTTCCCTAAACTAAAAACTTTG-AAAAATACTTTGG-T
1 GGGATCTTTCCCTAAA-TTAAAACTTTGAAAAAAAAC--TGGAT
*
19153 GGGATCTTTCCCTAAATTGAAAAACTTTG-AAAAATACTTTGG-T
1 GGGATCTTTCCCTAAATT--AAAACTTTGAAAAAAAAC--TGGAT
*
19196 GGGATCTTTCCCTAAATTGAAATCTTTGAAAAAAAATACTTTGG-T
1 GGGATCTTTCCCTAAATT-AAAACTTTG-AAAAAAA-AC--TGGAT
* *
19241 GGGATCTTTCCCTGAATTGAAATCTTTGAAAAA
1 GGGATCTTTCCCTAAATT-AAAACTTTGAAAAA
19274 TACTTTGGAA
Statistics
Matches: 429, Mismatches: 29, Indels: 57
0.83 0.06 0.11
Matches are distributed among these distances:
37 20 0.05
38 11 0.03
39 62 0.14
40 8 0.02
41 46 0.11
42 178 0.41
43 59 0.14
44 10 0.02
45 35 0.08
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (41 bp):
GGGATCTTTCCCTAAATTAAAACTTTGAAAAAAAACTGGAT
Found at i:19305 original size:88 final size:88
Alignment explanation
Indices: 18989--19281 Score: 237
Period size: 79 Copynumber: 3.5 Consensus size: 88
18979 AGAAACTGGA
* * * ** *
18989 TGGGATCTTTCCCTAAATT-AAAGACTTTAAAAAGAAAC--TGGATGGGATCTTTCCCTAAACT-
1 TGGGATCTTTCCCTAAATTGAAAAACTTTGAAAA-ATACTTTGG-TGGGATCTTTCAATAAATTG
*
19050 AAAGACTTT-AAAAAGAA-AC--TGG
64 AAA-ACTTTGAAAAAAAATACTTTGG
* * * ** * *
19072 ATGGGATCTTTCCCT-AATT-AGAAA-TCTTG--AAA-GC-TTGATGGGATCTTTCCCTAAACTA
1 -TGGGATCTTTCCCTAAATTGAAAAACT-TTGAAAAATACTTTGGTGGGATCTTTCAATAAATTG
19130 AAAACTTTG---AAAAATACTTTGG
64 AAAACTTTGAAAAAAAATACTTTGG
**
19152 TGGGATCTTTCCCTAAATTGAAAAACTTTGAAAAATACTTTGGTGGGATCTTTCCCTAAATTGAA
1 TGGGATCTTTCCCTAAATTGAAAAACTTTGAAAAATACTTTGGTGGGATCTTTCAATAAATTGAA
*
19217 ATCTTTGAAAAAAAATACTTTGG
66 AACTTTGAAAAAAAATACTTTGG
* *
19240 TGGGATCTTTCCCTGAATTG-AAATCTTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAAATTGAAAAACTTTGAAAAATACTTTGG
19282 AAACTTGATT
Statistics
Matches: 178, Mismatches: 14, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
77 4 0.02
78 2 0.01
79 39 0.22
80 13 0.07
81 9 0.05
82 2 0.01
83 12 0.07
84 15 0.08
85 29 0.16
87 21 0.12
88 32 0.18
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (88 bp):
TGGGATCTTTCCCTAAATTGAAAAACTTTGAAAAATACTTTGGTGGGATCTTTCAATAAATTGAA
AACTTTGAAAAAAAATACTTTGG
Found at i:21413 original size:19 final size:19
Alignment explanation
Indices: 21363--21415 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
21353 GAACATTCAT
*
21363 TAAACTGTGAAATGCTAAC
1 TAAAATGTGAAATGCTAAC
** **
21382 TAAAATGCCAAATGCTTGC
1 TAAAATGTGAAATGCTAAC
*
21401 TAACATGTGAAATGC
1 TAAAATGTGAAATGC
21416 AAACACAATG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (19 bp):
TAAAATGTGAAATGCTAAC
Found at i:22611 original size:35 final size:35
Alignment explanation
Indices: 22565--22634 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
22555 GCTAAGAGAG
22565 ACCTATCAATTGACCAAAATGATTCTAATGCAAAT
1 ACCTATCAATTGACCAAAATGATTCTAATGCAAAT
22600 ACCTATCAATTGACCAAAATGATTCTAATGCAAAT
1 ACCTATCAATTGACCAAAATGATTCTAATGCAAAT
22635 TAATAATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (35 bp):
ACCTATCAATTGACCAAAATGATTCTAATGCAAAT
Found at i:24313 original size:29 final size:29
Alignment explanation
Indices: 24271--24330 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
24261 TTACCGGTGC
*
24271 CGATCGCGGGAAGCGACGTTGGGCGGAAT
1 CGATCGCGGGAAGCGACGGTGGGCGGAAT
*
24300 CGATCGCGGGAAGCGACGGTGGTCGGAAT
1 CGATCGCGGGAAGCGACGGTGGGCGGAAT
24329 CG
1 CG
24331 CCGGGCCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.45, T:0.13
Consensus pattern (29 bp):
CGATCGCGGGAAGCGACGGTGGGCGGAAT
Found at i:26553 original size:46 final size:46
Alignment explanation
Indices: 26501--26595 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
26491 TGTGGAGATT
26501 TTAGAGTCTACCACCGCCTCAGATGATATGATAGTTTCTCCCGCCG
1 TTAGAGTCTACCACCGCCTCAGATGATATGATAGTTTCTCCCGCCG
*
26547 TTAGAGTCTACCACCGCCTCATATGATATGATAGTTTCTCCCGCCG
1 TTAGAGTCTACCACCGCCTCAGATGATATGATAGTTTCTCCCGCCG
26593 TTA
1 TTA
26596 TTTCTTCTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (46 bp):
TTAGAGTCTACCACCGCCTCAGATGATATGATAGTTTCTCCCGCCG
Found at i:32387 original size:24 final size:25
Alignment explanation
Indices: 32338--32388 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
32328 ATAATATGGC
* *
32338 TGCTTTGTAAAAGGGATATGAGCAT
1 TGCTGTGTAAAAGGGATATGAACAT
32363 TGCTGTGTAAAAGGG-TATGAACAT
1 TGCTGTGTAAAAGGGATATGAACAT
32387 TG
1 TG
32389 TAATGTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.31
Consensus pattern (25 bp):
TGCTGTGTAAAAGGGATATGAACAT
Found at i:32395 original size:24 final size:25
Alignment explanation
Indices: 32338--32396 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
32328 ATAATATGGC
* *
32338 TGCTTTGTAAAAGGGATATGAGCAT
1 TGCTATGTAAAAGGGATATGAACAT
*
32363 TGCTGTGTAAAAGGG-TATGAACAT
1 TGCTATGTAAAAGGGATATGAACAT
32387 TG-TAATGTAA
1 TGCT-ATGTAA
32397 GTGTGTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 15 0.50
25 14 0.47
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (25 bp):
TGCTATGTAAAAGGGATATGAACAT
Found at i:32732 original size:16 final size:16
Alignment explanation
Indices: 32713--32769 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
32703 ATTTGATGGA
32713 AAAAATATTGTTCAAT
1 AAAAATATTGTTCAAT
*
32729 AAAAATTATTATT-AACCT
1 AAAAA-TATTGTTCAA--T
*
32747 ATATAATATTGTTCAAT
1 A-AAAATATTGTTCAAT
32764 AAAAAT
1 AAAAAT
32770 TAAATAGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 11 0.34
17 8 0.25
18 8 0.25
19 5 0.16
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (16 bp):
AAAAATATTGTTCAAT
Found at i:33810 original size:175 final size:175
Alignment explanation
Indices: 33516--33854 Score: 536
Period size: 175 Copynumber: 1.9 Consensus size: 175
33506 GATACACCGG
* *
33516 CGGTGTAAATTTTGGACTTCATAAGCGGGTTGTGAAGTTGACACATGTCCATTTTCTGAATTAAT
1 CGGTGTAAATTTTGGACTCCATAAGCGGGTTGTGAAGTTGACACATATCCATTTTCTGAATTAAT
* *
33581 TAAATTCTAAATATTTCAATCTAGTCCATAGGGGACACATGTCACCTTTCAAGACCCGCGTGTGC
66 TAAATTCTAAATATTTCAATCTAGTCCATAGAGGACACATGTCACCTCTCAAGACCCGCGTGTGC
33646 AGCCTGCTAAACTCAACTGACGGTGTATTATATATAAACCCTTGC
131 AGCCTGCTAAACTCAACTGACGGTGTATTATATATAAACCCTTGC
* * *
33691 CGGTGTAAATTTTGGACTCCATAAGCGGGTTGTGGAGTTGATACATATCTATTTTCTGAATTAAT
1 CGGTGTAAATTTTGGACTCCATAAGCGGGTTGTGAAGTTGACACATATCCATTTTCTGAATTAAT
* * *
33756 TAAATTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCA-CTCCTCAAGACCCGCTTGTG
66 TAAATTCTAAATATTTCAATCTAGTCCATAGAGGACACATGTCACCT-CTCAAGACCCGCGTGTG
* * * *
33820 CAGTCTGCTAAATTCCACTGATGGTGTATTATATA
130 CAGCCTGCTAAACTCAACTGACGGTGTATTATATA
33855 ATTTTTTTTT
Statistics
Matches: 149, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
174 2 0.01
175 147 0.99
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (175 bp):
CGGTGTAAATTTTGGACTCCATAAGCGGGTTGTGAAGTTGACACATATCCATTTTCTGAATTAAT
TAAATTCTAAATATTTCAATCTAGTCCATAGAGGACACATGTCACCTCTCAAGACCCGCGTGTGC
AGCCTGCTAAACTCAACTGACGGTGTATTATATATAAACCCTTGC
Found at i:36437 original size:60 final size:59
Alignment explanation
Indices: 36340--36457 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 59
36330 ATTAATCAAA
* *
36340 TATCAAGTGATATGTTCTTTATTAGATGCATAAAAAAAAGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAAGACGTTTTAGGACCGAGACT
* * *
36399 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAAAGACGTTTTAGGACCGAGAC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAAGACGTTTTAGGACCGAGAC
36458 ATGATGCTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 12 0.23
60 41 0.77
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (59 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAAGACGTTTTAGGACCGAGACT
Found at i:37775 original size:36 final size:37
Alignment explanation
Indices: 37707--37777 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
37697 TTCAATAACC
* *
37707 TTACATTTTTTGTGATTTTGGTTATCATTATTTCTTA
1 TTACATTTTTTGTAATTTTGATTATCATTATTTCTTA
37744 TTACATTTTTTGTAATTTTGATTATCA-TATTTCT
1 TTACATTTTTTGTAATTTTGATTATCATTATTTCT
37778 CCAAAATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.62
Consensus pattern (37 bp):
TTACATTTTTTGTAATTTTGATTATCATTATTTCTTA
Done.