Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021278.1 Corchorus olitorius cultivar O-4 contig21311, 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: 19577
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:5993 original size:1 final size:1
Alignment explanation
Indices: 5987--6012 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5977 GATTTATGAT
5987 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
6013 CTCAAATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10518 original size:110 final size:109
Alignment explanation
Indices: 10326--10524 Score: 262
Period size: 110 Copynumber: 1.8 Consensus size: 109
10316 TGATAATAAT
10326 TAAGGTTTAGTCCAACTATAAATTTGTTTTATATTTTTAAAGGGTAAATTTCAAATTTTAGGACT
1 TAAGGTTTAGTCCAACTATAAATTTGTTTTATATTTTTAAAGGGTAAATTTCAAATTTTAGGACT
* *
10391 CATTCTCTTAGGATTTTAGAAAAATAAGTTTAAACACTTATCAA
66 CATTATCATAGGATTTTAGAAAAATAAGTTTAAACACTTATCAA
* *
10435 TAAGGTTTAG-CACAATTATTAAA-TTGTTTTATTTTTTTAAAAGGGTAAATCTT-AAATTTT-G
1 TAAGGTTTAGTC-CAACTA-TAAATTTGTTTTATATTTTT-AAAGGGTAAAT-TTCAAATTTTAG
* * *
10496 ATACTCTTTATCATAGGGTTTTAGAAAAA
62 -GACTCATTATCATAGGATTTTAGAAAAA
10525 AAAAATTATA
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
108 1 0.01
109 30 0.38
110 45 0.58
111 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (109 bp):
TAAGGTTTAGTCCAACTATAAATTTGTTTTATATTTTTAAAGGGTAAATTTCAAATTTTAGGACT
CATTATCATAGGATTTTAGAAAAATAAGTTTAAACACTTATCAA
Found at i:10829 original size:21 final size:19
Alignment explanation
Indices: 10787--10841 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
10777 TTTAGCAACA
10787 GTACAGATGAGATTACACT
1 GTACAGATGAGATTACACT
* *
10806 GTACAGATTAGATTAGGTACT
1 GTACAGATGAGATTA--CACT
10827 GTACAGATGAGATTA
1 GTACAGATGAGATTA
10842 TTAGAGCAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
21 17 0.55
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (19 bp):
GTACAGATGAGATTACACT
Found at i:12114 original size:69 final size:70
Alignment explanation
Indices: 12018--12178 Score: 243
Period size: 69 Copynumber: 2.3 Consensus size: 70
12008 ATTTCCCGCA
* * *
12018 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTA-ATTTGCGCTCCTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA
12082 ACAGC
66 ACAGC
* * * *
12087 ACAAGTCCGGGACAGGAATTGGGTAACTCCCGCCCAGGTCTTGTCCTGTATTTTTGCATTCCTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA
12152 ACAGC
66 ACAGC
*
12157 CCAAGTCCTGGACAGGACTTGG
1 ACAAGTCCTGGACAGGACTTGG
12179 CCAAGATCTG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 46 0.57
70 35 0.43
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (70 bp):
ACAAGTCCTGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA
ACAGC
Found at i:17926 original size:22 final size:22
Alignment explanation
Indices: 17900--18474 Score: 130
Period size: 22 Copynumber: 26.4 Consensus size: 22
17890 ATTACACTAT
*
17900 TTTTGATGATCTCCTTATGAAA
1 TTTTGATAATCTCCTTATGAAA
*
17922 TTTTGATAATCTTCTTATGAAA
1 TTTTGATAATCTCCTTATGAAA
* * *
17944 TTTTAATAA-CGATAC-TATAAAA
1 TTTTGATAATC--TCCTTATGAAA
* * * ** *
17966 TTTCGAGAACCTTTTTATAAAA
1 TTTTGATAATCTCCTTATGAAA
* *
17988 TTTT-ATAACCTTCTTATGAAA
1 TTTTGATAATCTCCTTATGAAA
* * * *
18009 TTTTGTTAACCTCCGTAAGAAA
1 TTTTGATAATCTCCTTATGAAA
*
18031 TTTTGA-AGACCTCAC-TATGAAA
1 TTTTGATA-ATCTC-CTTATGAAA
**
18053 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAATC-TCCTTATGAAA
*** *
18075 TTTTGATAA-C-CAACACTGAGA
1 TTTTGATAATCTCCTTA-TGAAA
** * *
18096 CGTTGATAA-CTTCCATATGATA
1 TTTTGATAATC-TCCTTATGAAA
* * * *
18118 TATTGATAACCACGTTATGAAA
1 TTTTGATAATCTCCTTATGAAA
* * * * *
18140 ATTT-AAAAGCATTCATATG-AA
1 TTTTGATAATC-TCCTTATGAAA
*
18161 TTATT-AGTAATCACACTCTA--AAA
1 TT-TTGA-TAATCTC-CT-TATGAAA
*
18184 TTTTGATAATCACAC-TATGAAA
1 TTTTGATAATCTC-CTTATGAAA
* * *
18206 TTGTGATAACCTCGC-TATGGAA
1 TTTTGATAATCTC-CTTATGAAA
* *
18228 TTTTGATAAACATTCC-TATAAAA
1 TTTTGATAATC--TCCTTATGAAA
* *
18251 TTTTGATAAACCTCGC-TATAAAA
1 TTTTGAT-AATCTC-CTTATGAAA
*
18274 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAATCTCCTTATGAAA
* *
18296 TCTTGATAA----C-TA-CAAA
1 TTTTGATAATCTCCTTATGAAA
* * **
18312 TTTTGATAACCTCCCTATGATT
1 TTTTGATAATCTCCTTATGAAA
* *
18334 TTTTGATAACCTCATTATGAAA
1 TTTTGATAATCTCCTTATGAAA
* *
18356 TTATT-TTAATCTCCCTATTGAAA
1 TT-TTGATAATCTCCTTA-TGAAA
* *
18379 TTTTGAT-CTACATAC-TATGAAA
1 TTTTGATAAT-C-TCCTTATGAAA
18401 TTTTGATAATC-CTCTTATGAAA
1 TTTTGATAATCTC-CTTATGAAA
* * *
18423 TTTTGA-AAACTAAAC-TATAAAA
1 TTTTGATAATCT--CCTTATGAAA
* * *
18445 TTTTGATAACCTTCATATGAAA
1 TTTTGATAATCTCCTTATGAAA
18467 TTTTGATA
1 TTTTGATA
18475 TCATGCCTAA
Statistics
Matches: 420, Mismatches: 86, Indels: 94
0.70 0.14 0.16
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
20 5 0.01
21 50 0.12
22 277 0.66
23 65 0.15
24 9 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAATCTCCTTATGAAA
Found at i:18269 original size:46 final size:44
Alignment explanation
Indices: 18179--18282 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 44
18169 AATCACACTC
* *
18179 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAAACACACTATAAAATTGTGATAACCTCGCTA
** *
18223 TGGAATTTTGATAAACATTC-CTATAAAATTTTGATAAACCTCGCTA
1 TAAAATTTTGATAAACA--CACTATAAAATTGTGAT-AACCTCGCTA
18269 TAAAATTTTGATAA
1 TAAAATTTTGATAA
18283 CCTCCTTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 14 0.28
45 13 0.26
46 23 0.46
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (44 bp):
TAAAATTTTGATAAACACACTATAAAATTGTGATAACCTCGCTA
Found at i:18302 original size:68 final size:67
Alignment explanation
Indices: 18179--18304 Score: 164
Period size: 68 Copynumber: 1.9 Consensus size: 67
18169 AATCACACTC
* * * *
18179 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATGGAATTTTGATAAACATTCC
1 TAAAATTTTGATAACCACACTATAAAATTGTGATAACCTCGCTATGAAATCTTGATAAACATTCC
18244 TA
66 TA
* * *
18246 TAAAATTTTGATAAACCTCGCTATAAAATTTTGATAACCTC-CTTATGAAATCTTGATAA
1 TAAAATTTTGAT-AACCACACTATAAAATTGTGATAACCTCGC-TATGAAATCTTGATAA
18305 CTACAAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 13 0.26
68 37 0.74
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (67 bp):
TAAAATTTTGATAACCACACTATAAAATTGTGATAACCTCGCTATGAAATCTTGATAAACATTCC
TA
Found at i:18624 original size:44 final size:44
Alignment explanation
Indices: 18574--18769 Score: 159
Period size: 44 Copynumber: 4.4 Consensus size: 44
18564 AGAAATACCA
* *
18574 TTATGAAATTTTGGTAATCACATTTTGAAAA-TTTGATAACCTCT
1 TTATGAAATTTTGATAATCACATTAT-AAAATTTTGATAACCTCT
* * * * * *
18618 TTATGAAAATTTTTGGTAACCTC-TCTATAAAATTTTGTTGACCCCT
1 TTATG-AAA-TTTTGATAATCACAT-TATAAAATTTTGATAACCTCT
* * ** *
18664 CTATAAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGC
1 TTATGAAATTTTGATAATCACATTATAAAATTTTGATAACCTC-T
* * *
18709 TT-TGAAATTTTGATAATAACACTATAAAATTTTGATAATCT-T
1 TTATGAAATTTTGATAATCACATTATAAAATTTTGATAACCTCT
18751 CTTAT-AAATTTTGATAATC
1 -TTATGAAATTTTGATAATC
18770 TGATCTCTAT
Statistics
Matches: 118, Mismatches: 26, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
43 15 0.13
44 64 0.54
45 13 0.11
46 26 0.22
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (44 bp):
TTATGAAATTTTGATAATCACATTATAAAATTTTGATAACCTCT
Found at i:18802 original size:22 final size:22
Alignment explanation
Indices: 18575--18815 Score: 132
Period size: 22 Copynumber: 10.8 Consensus size: 22
18565 GAAATACCAT
* *
18575 TATGAAATTTTGGTAATCACAT-
1 TATGAAATTTTGATAACCAC-TC
* * * *
18597 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACTC
* *
18619 TATGAAAATTTTTGGTAACCTCTC
1 TATG-AAA-TTTTGATAACCACTC
* * * *
18643 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCACTC
* *
18665 TATAAAATTTTGATAATCACAT-
1 TATGAAATTTTGATAACCAC-TC
* * *
18687 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCACTC
* ** *
18709 TTTGAAATTTTGATAATAACAC
1 TATGAAATTTTGATAACCACTC
* * *
18731 TATAAAATTTTGATAATC-TTC
1 TATGAAATTTTGATAACCACTC
*
18752 TTAT-AAATTTTGATAATCTGATCTC
1 -TATGAAATTTTGATAA-C-CA-CTC
*
18777 TATGAAATTTCGATAACCACTC
1 TATGAAATTTTGATAACCACTC
*
18799 TATGAGA-TTTGATAACC
1 TATGAAATTTTGATAACC
18816 TTCTCAAATC
Statistics
Matches: 168, Mismatches: 40, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
21 23 0.14
22 105 0.62
23 8 0.05
24 19 0.11
25 13 0.08
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACTC
Done.