Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024272.1 Corchorus olitorius cultivar O-4 contig24305, 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: 17221
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:589 original size:31 final size:31
Alignment explanation
Indices: 551--610 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
541 CATTTTTTAC
*
551 AGGTTTGGATCAATTTAGTCCCTCTACTTAT
1 AGGTTTGGACCAATTTAGTCCCTCTACTTAT
*
582 AGGTTTGGGCCAATTTAGTCCCTCTACTT
1 AGGTTTGGACCAATTTAGTCCCTCTACTT
611 GCGAAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (31 bp):
AGGTTTGGACCAATTTAGTCCCTCTACTTAT
Found at i:728 original size:31 final size:31
Alignment explanation
Indices: 685--751 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
675 TGATCATTTT
*
685 TTGACCCAATTTCACATA-TAGAGGGACTAAA
1 TTGATCCAATTTCACA-AGTAGAGGGACTAAA
*
716 TTGATCCAATTTCACAAGTAGAGGGATTAAA
1 TTGATCCAATTTCACAAGTAGAGGGACTAAA
747 TTGAT
1 TTGAT
752 GGTGTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (31 bp):
TTGATCCAATTTCACAAGTAGAGGGACTAAA
Found at i:4051 original size:60 final size:60
Alignment explanation
Indices: 3979--4105 Score: 227
Period size: 60 Copynumber: 2.1 Consensus size: 60
3969 TCCTCACCGA
* *
3979 ATTCATCATCTTGGTCAGTCTCACTCCCCATATGCGTCTGTAAAGAATGGTTCTCCCCAT
1 ATTCTTCATCTTGGTCAGTCTCACTCCCCATATGCATCTGTAAAGAATGGTTCTCCCCAT
*
4039 ATTCTTCATCTTGGTCATTCTCACTCCCCATATGCATCTGTAAAGAATGGTTCTCCCCAT
1 ATTCTTCATCTTGGTCAGTCTCACTCCCCATATGCATCTGTAAAGAATGGTTCTCCCCAT
4099 ATTCTTC
1 ATTCTTC
4106 CTCCTCTTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (60 bp):
ATTCTTCATCTTGGTCAGTCTCACTCCCCATATGCATCTGTAAAGAATGGTTCTCCCCAT
Found at i:5739 original size:168 final size:168
Alignment explanation
Indices: 5395--6238 Score: 1139
Period size: 168 Copynumber: 5.0 Consensus size: 168
5385 ACATTCGGAA
* * * *
5395 TTTTGAGAACTTGCAAT-GTAATCATTTCCTGAAAGAAA-CTTTTGTTGA--A-GAGAAGCAGGA
1 TTTTGAGAACTTGCAGTAG-AATCATCTCCTGAAAGAAATC-TTTGTGGAGGAGGAGAAGCAGAA
* * ** * *
5455 GGATTTGTAACTGTAGATGGCTGTTGGTTGGAGTATGGTA-TCTGATCACCATGTTGAGAGTGAT
64 GG---TGTAACTGGAGATGGCTGTTGGTTGGGGTA-GAAACTCTGATTA-C-TG-T--G-TTGAT
* * *
5519 TGTTTTTTGGAGGGGCCGAAACTGGAGATGTCTTACTTTTGGAAGCGTAG
119 TGTTTTTTGGAGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
* *
5569 TTTTGAGAACTTGCAGTAGAATCATCTCCTGAAAGAAATGTTTCTGGAGGAGGAGAAGCAGAAGG
1 TTTTGAGAACTTGCAGTAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGAAGG
*
5634 TGTAACTGGAGATTGCTGTTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGTTTTTTGGAG
66 TGTAACTGGAGATGGCTGTTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGTTTTTTGGAG
5699 AGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
131 AGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
* * * * *
5737 TTTTGAGAACTTGAATTAGAATCATCTCCTGAAAGATATCTTTGTGGGGGAGGAGTAGCAGGAGG
1 TTTTGAGAACTTGCAGTAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCA-GA--
* **
5802 AGGTGTAACTGGAGACGGCTGTTGGTTGGGGTAGAAACTCTGATTACCATGTTGATTGTTTTTTG
63 AGGTGTAACTGGAGATGGCTGTTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGTTTTTTG
5867 GAGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
128 GAGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
* * * *
5908 TTTTGAGAACTTG-ATGTAGAATCATCTCCTGAAAGATATCTTTGTGGGGGAGGAGTAGCAGGAG
1 TTTTGAGAACTTGCA-GTAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGAAG
*
5972 GTGTAACTGGAGATGGTTGTTGGTTGGGGTAGAAACTCTGATTACCT-TGTTGATTGTTTTTTGG
65 GTGTAACTGGAGATGGCTGTTGGTTGGGGTAGAAACTCTGATTA-CTGTGTTGATTGTTTTTTGG
6036 AGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
129 AGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
* * * *
6076 TTTTGAGAACTTGCAATAGAATCATTTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGGACG
1 TTTTGAGAACTTGCAGTAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGAAGG
* *
6141 TGTAACTGGAGATTGCTGTTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGATTTTTGGAG
66 TGTAACTGGAGATGGCTGTTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGTTTTTTGGAG
*
6206 AGGCTGAAGCTGGAGATGT-TTGACTTTTGGAAG
131 AGGCTGAAACTGGAGATGTCTT-ACTTTTGGAAG
6239 GCTTGGAACT
Statistics
Matches: 614, Mismatches: 42, Indels: 34
0.89 0.06 0.05
Matches are distributed among these distances:
167 4 0.01
168 350 0.57
169 5 0.01
170 2 0.00
171 160 0.26
172 2 0.00
173 3 0.00
174 74 0.12
175 1 0.00
176 1 0.00
177 12 0.02
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.33
Consensus pattern (168 bp):
TTTTGAGAACTTGCAGTAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGAAGG
TGTAACTGGAGATGGCTGTTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGTTTTTTGGAG
AGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAG
Found at i:6074 original size:339 final size:336
Alignment explanation
Indices: 5395--6238 Score: 1171
Period size: 339 Copynumber: 2.5 Consensus size: 336
5385 ACATTCGGAA
* * * * * *
5395 TTTTGAGAACTTGCAAT-GTAATCATTTCCTGAAAGAAA-CTTTTGTTGAAGAGAAGCAGGAGGA
1 TTTTGAGAACTTGCAATAG-AATCATCTCCTGAAAGAAATC-TTTGTGGAGGAGGAGAAGCAGGA
** * * * ** *
5458 TTTGTAACTGTAGATGGCTGTTGGTTGGAGTATGGTA-TCTGATCACCATGTTGAGAGTGATTGT
64 CGTGTAACTGGAGACGGCTGTTGGTTGGGGTA-GAAACTCTGATTACCATG-T-----TGATTGT
* * *
5522 TTTTTGGAGGGGCCGAAACTGGAGATGTCTTACTTTTGGAAGCGTAGTTTTGAGAACTTGCAGTA
122 TTTTTGGAGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAGTTTTGAGAACTTGCAGTA
* *
5587 GAATCATCTCCTGAAAGAAATGTTTCTGGAGGAGGAGAAGCAGAAGGTGTAACTGGAGATTGCTG
187 GAATCATCTCCTGAAAGAAATCTTTCTGGAGGAGGAGAAGCAGAAGGTGTAACTGGAGATGGCTG
5652 TTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGTTTTTTGGAGAGGCTGAAACTGGAGATG
252 TTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGTTTTTTGGAGAGGCTGAAACTGGAGATG
5717 TCTTACTTTTGGAAGAGTAG
317 TCTTACTTTTGGAAGAGTAG
* * *
5737 TTTTGAGAACTTG-AATTAGAATCATCTCCTGAAAGATATCTTTGTGGGGGAGGAGTAGCAGGAG
1 TTTTGAGAACTTGCAA-TAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAG-A--AGCAG
*
5801 GAGGTGTAACTGGAGACGGCTGTTGGTTGGGGTAGAAACTCTGATTACCATGTTGATTGTTTTTT
62 GACGTGTAACTGGAGACGGCTGTTGGTTGGGGTAGAAACTCTGATTACCATGTTGATTGTTTTTT
5866 GGAGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAGTTTTGAGAACTTG-ATGTAGAAT
127 GGAGAGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAGTTTTGAGAACTTGCA-GTAGAAT
* * * * * *
5930 CATCTCCTGAAAGATATCTTTGTGGGGGAGGAGTAGCAGGAGGTGTAACTGGAGATGGTTGTTGG
191 CATCTCCTGAAAGAAATCTTTCTGGAGGAGGAGAAGCAGAAGGTGTAACTGGAGATGGCTGTTGG
5995 TTGGGGTAGAAACTCTGATTACCT-TGTTGATTGTTTTTTGGAGAGGCTGAAACTGGAGATGTCT
256 TTGGGGTAGAAACTCTGATTA-CTGTGTTGATTGTTTTTTGGAGAGGCTGAAACTGGAGATGTCT
6059 TACTTTTGGAAGAGTAG
320 TACTTTTGGAAGAGTAG
*
6076 TTTTGAGAACTTGCAATAGAATCATTTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGGACG
1 TTTTGAGAACTTGCAATAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGGACG
** ** *
6141 TGTAACTGGAGATTGCTGTTGGTTGGGGTAGAAACTCTGATTACTGTGTTGATTGATTTTTGGAG
66 TGTAACTGGAGACGGCTGTTGGTTGGGGTAGAAACTCTGATTACCATGTTGATTGTTTTTTGGAG
*
6206 AGGCTGAAGCTGGAGATGT-TTGACTTTTGGAAG
131 AGGCTGAAACTGGAGATGTCTT-ACTTTTGGAAG
6239 GCTTGGAACT
Statistics
Matches: 454, Mismatches: 37, Indels: 28
0.87 0.07 0.05
Matches are distributed among these distances:
335 2 0.00
336 96 0.21
338 2 0.00
339 255 0.56
340 4 0.01
341 2 0.00
342 42 0.09
343 2 0.00
344 3 0.01
345 46 0.10
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.33
Consensus pattern (336 bp):
TTTTGAGAACTTGCAATAGAATCATCTCCTGAAAGAAATCTTTGTGGAGGAGGAGAAGCAGGACG
TGTAACTGGAGACGGCTGTTGGTTGGGGTAGAAACTCTGATTACCATGTTGATTGTTTTTTGGAG
AGGCTGAAACTGGAGATGTCTTACTTTTGGAAGAGTAGTTTTGAGAACTTGCAGTAGAATCATCT
CCTGAAAGAAATCTTTCTGGAGGAGGAGAAGCAGAAGGTGTAACTGGAGATGGCTGTTGGTTGGG
GTAGAAACTCTGATTACTGTGTTGATTGTTTTTTGGAGAGGCTGAAACTGGAGATGTCTTACTTT
TGGAAGAGTAG
Found at i:10641 original size:9 final size:9
Alignment explanation
Indices: 10629--10653 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10619 TACAACTAGA
10629 ACAACAATC
1 ACAACAATC
10638 ACAACAATC
1 ACAACAATC
10647 ACAACAA
1 ACAACAA
10654 CATTTAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (9 bp):
ACAACAATC
Found at i:13559 original size:5 final size:5
Alignment explanation
Indices: 13549--13588 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
13539 TACCAGAATG
*
13549 CTTTT CTTTT CTTTT CTTCT CTTTT CGTTTT CCTTTT CTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT C-TTTT -CTTTT CTT
13589 CTTAAAGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 22 0.71
6 8 0.26
7 1 0.03
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (5 bp):
CTTTT
Found at i:13586 original size:22 final size:20
Alignment explanation
Indices: 13549--13590 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
13539 TACCAGAATG
13549 CTTTTCTTTTCTTTTCTTCT
1 CTTTTCTTTTCTTTTCTTCT
13569 CTTTTCGTTTTCCTTTTCTTCT
1 CTTTTC-TTTT-CTTTTCTTCT
13591 TAAAGCAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 4 0.20
22 10 0.50
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.71
Consensus pattern (20 bp):
CTTTTCTTTTCTTTTCTTCT
Found at i:14910 original size:30 final size:29
Alignment explanation
Indices: 14838--14910 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
14828 CTTGTAGCGT
*
14838 TTGGACGTTTTGTCCCCTGAACTTCAATA
1 TTGGACGTTTTGCCCCCTGAACTTCAATA
* *
14867 TTGGACATTTTGCCCCCTGAACTTCAATT
1 TTGGACGTTTTGCCCCCTGAACTTCAATA
14896 TTGGGACGTTTTGCC
1 TT-GGACGTTTTGCC
14911 ACCATTAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (29 bp):
TTGGACGTTTTGCCCCCTGAACTTCAATA
Found at i:16685 original size:22 final size:22
Alignment explanation
Indices: 16657--16700 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
16647 GAAATCACAT
16657 ACACCATTGGCGTCAAGGCGGA
1 ACACCATTGGCGTCAAGGCGGA
16679 ACACCATTGGCGTCAAGGCGGA
1 ACACCATTGGCGTCAAGGCGGA
16701 TAGACGTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (22 bp):
ACACCATTGGCGTCAAGGCGGA
Done.