Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010786.1 Corchorus capsularis cultivar CVL-1 contig10807, 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: 68908
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:4678 original size:205 final size:202
Alignment explanation
Indices: 4308--4690 Score: 473
Period size: 205 Copynumber: 1.9 Consensus size: 202
4298 GTCGCTCTTG
* * *
4308 TTTATATTTTTGCGACGTTTCAGAGACGTTTTCTCAAATGTCATTCAATTATGCAACATTTTTCA
1 TTTATATTTTTACGACGTTTCAGAGACGTTTTCTCAAATCTCATTCAATCATGCAACATTTTTCA
* * * * * * * *
4373 ACAAATGTCGTTTTAAGATCGACTTTTTCGACATTTATAACAACGTTTTTCTGAAACTTCATTTT
66 ACAAACGTCGCTTAAAGATCGACTTCTCCGACATTTATAACAACGTTTTACGGAAACGTCATTTT
* * * *
4438 AATATATGAAATTTTAATAAATGTCACATTACCTTGTGAGTCTTTTTTTAAATTGAGTGAACGTT
131 AAAATATGAAATTTTAATAAATGTCACAATACCTTGCGACTCTTTTTTTAAATTGAGTGAACGTT
4503 ACTCTAC
196 ACTCTAC
* * ** *
4510 TTTATATTTTTACGACGTTTGTAGAGACATTTTTCTCAAATCTCATTCAATCATGTGACTTTTTT
1 TTTATATTTTTACGACGTTT-CAGAGAC-GTTTTCTCAAATCTCATTCAATCATGCAAC--ATTT
** *
4575 TTTTACAAACGTCGCTTAAAGA-CAGACTTCTCCGACATTTATAACAACG-TTTAGGGAAACGTC
62 TTCAACAAACGTCGCTTAAAGATC-GACTTCTCCGACATTTATAACAACGTTTTACGGAAACGTC
* * *
4638 GTTTTAAAATATGACATTTTAATAAATGTCGCAATACCTTGCGACTCTTTTTT
126 ATTTTAAAATATGAAATTTTAATAAATGTCACAATACCTTGCGACTCTTTTTT
4691 AATTTAAGTG
Statistics
Matches: 150, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
202 19 0.13
203 6 0.04
204 25 0.17
205 57 0.38
206 43 0.29
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (202 bp):
TTTATATTTTTACGACGTTTCAGAGACGTTTTCTCAAATCTCATTCAATCATGCAACATTTTTCA
ACAAACGTCGCTTAAAGATCGACTTCTCCGACATTTATAACAACGTTTTACGGAAACGTCATTTT
AAAATATGAAATTTTAATAAATGTCACAATACCTTGCGACTCTTTTTTTAAATTGAGTGAACGTT
ACTCTAC
Found at i:14405 original size:2 final size:2
Alignment explanation
Indices: 14398--14432 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
14388 CATGATCGTA
* *
14398 AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14433 CTTAATTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:15668 original size:11 final size:11
Alignment explanation
Indices: 15652--15680 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
15642 TCTAATTCTC
15652 TTTGAAAAATG
1 TTTGAAAAATG
15663 TTTGAAAAATG
1 TTTGAAAAATG
15674 TTTGAAA
1 TTTGAAA
15681 CATTCCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (11 bp):
TTTGAAAAATG
Found at i:30151 original size:15 final size:15
Alignment explanation
Indices: 30131--30161 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30121 GTTACTAGCC
30131 TTAGAGGTGATTGAA
1 TTAGAGGTGATTGAA
30146 TTAGAGGTGATTGAA
1 TTAGAGGTGATTGAA
30161 T
1 T
30162 CGAACCGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (15 bp):
TTAGAGGTGATTGAA
Found at i:44478 original size:18 final size:17
Alignment explanation
Indices: 44436--44478 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
44426 TCAAGCATAC
*
44436 ATAAACTATGACAAGAA
1 ATAAACTAAGACAAGAA
44453 ATAGAACTAAGACAAGGAA
1 ATA-AACTAAGACAA-GAA
*
44472 CTAAACT
1 ATAAACT
44479 TGATTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 14 0.64
19 5 0.23
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (17 bp):
ATAAACTAAGACAAGAA
Found at i:50438 original size:12 final size:12
Alignment explanation
Indices: 50421--50445 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50411 AGTAGTGCCT
50421 ATTTCCAGAAAC
1 ATTTCCAGAAAC
50433 ATTTCCAGAAAC
1 ATTTCCAGAAAC
50445 A
1 A
50446 GAGCATGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
ATTTCCAGAAAC
Found at i:50964 original size:28 final size:28
Alignment explanation
Indices: 50924--50979 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
50914 TAACTCAGCT
*
50924 CTACGCCCATACCTTACAGATCTTGATG
1 CTACGCCCATACCTTAAAGATCTTGATG
50952 CTACGCCCATACCTTAAAGATCTTGATG
1 CTACGCCCATACCTTAAAGATCTTGATG
50980 AAGATTGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (28 bp):
CTACGCCCATACCTTAAAGATCTTGATG
Found at i:51107 original size:18 final size:18
Alignment explanation
Indices: 51073--51107 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51063 ATAATGAGAA
*
51073 GAGAAGAAGAACGACAAG
1 GAGAAGAAGAACAACAAG
*
51091 GAGAAGAAGAATAACAA
1 GAGAAGAAGAACAACAA
51108 AAAAAAAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.09, G:0.29, T:0.03
Consensus pattern (18 bp):
GAGAAGAAGAACAACAAG
Found at i:54243 original size:173 final size:174
Alignment explanation
Indices: 53925--54270 Score: 676
Period size: 173 Copynumber: 2.0 Consensus size: 174
53915 ATACCTTGAT
53925 GTATAATAGGAATGCTACTGTTGTGCCTCCCAAAGTATCTTATTTGAACTCATATCATAGGAAAA
1 GTATAATAGGAATGCTACTGTTGTGCCTCCCAAAGTATCTTATTTGAACTCATATCATAGGAAAA
53990 ATACTAAAAACGAAACCAAGGGAAGACATAGCTGCTATTTTATGGGTGTCCAGTGAATATTAGAC
66 ATACTAAAAACGAAACCAAGGGAAGACATAGCTGCTATTTTATGGGTGTCCAGTGAATATTAGAC
54055 AGCTACAAAATGACTCTAAATATAAACTTCAATTGTAAATGGCA
131 AGCTACAAAATGACTCTAAATATAAACTTCAATTGTAAATGGCA
54099 GTATAATAGGAATGCTACTGTTGTGCCTCCCAAAGTATCTTATTTGAACTCATATCATAGGAAAA
1 GTATAATAGGAATGCTACTGTTGTGCCTCCCAAAGTATCTTATTTGAACTCATATCATAGGAAAA
*
54164 ATACT-AAAACGAAACCAAGGGAAGGCATAGCTGCTATTTTATGGGTGTCCAGTGAATATTAGAC
66 ATACTAAAAACGAAACCAAGGGAAGACATAGCTGCTATTTTATGGGTGTCCAGTGAATATTAGAC
54228 AGCTACAAAATGACTCTAAATATAAACTTCAATTGTAAATGGC
131 AGCTACAAAATGACTCTAAATATAAACTTCAATTGTAAATGGC
54271 GGTACACAGA
Statistics
Matches: 171, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
173 101 0.59
174 70 0.41
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (174 bp):
GTATAATAGGAATGCTACTGTTGTGCCTCCCAAAGTATCTTATTTGAACTCATATCATAGGAAAA
ATACTAAAAACGAAACCAAGGGAAGACATAGCTGCTATTTTATGGGTGTCCAGTGAATATTAGAC
AGCTACAAAATGACTCTAAATATAAACTTCAATTGTAAATGGCA
Found at i:55059 original size:164 final size:164
Alignment explanation
Indices: 54788--55117 Score: 644
Period size: 164 Copynumber: 2.0 Consensus size: 164
54778 TATATATTAT
54788 ACGAGCTGGCACCACTAAACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCTTACCA
1 ACGAGCTGGCACCACTAAACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCTTACCA
54853 ACCTTTATTCGATGCACCATTATACATAGATGTATAATAGGAATGTCATCCCTTTTACTGCAAAA
66 ACCTTTATTCGATGCACCATTATACATAGATGTATAATAGGAATGTCATCCCTTTTACTGCAAAA
54918 TAGAAATTCCCATAGCCAACTTTTACTCAGATGC
131 TAGAAATTCCCATAGCCAACTTTTACTCAGATGC
54952 ACGAGCTGGCACCACTAAACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCTTACCA
1 ACGAGCTGGCACCACTAAACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCTTACCA
55017 ACCTTTATT-GAATGCACCATTATACATAGATGTATAATAGGAATGTCATCCCTTTTACTGCAAA
66 ACCTTTATTCG-ATGCACCATTATACATAGATGTATAATAGGAATGTCATCCCTTTTACTGCAAA
55081 ATAGAAATTCCCATAGCCAACTTTTACTCAGATGC
130 ATAGAAATTCCCATAGCCAACTTTTACTCAGATGC
55116 AC
1 AC
55118 CATCATAACC
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
163 1 0.01
164 164 0.99
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (164 bp):
ACGAGCTGGCACCACTAAACCTTTATGTATAGTAGGAATGCCACCACCACAAAGAATTCTTACCA
ACCTTTATTCGATGCACCATTATACATAGATGTATAATAGGAATGTCATCCCTTTTACTGCAAAA
TAGAAATTCCCATAGCCAACTTTTACTCAGATGC
Found at i:57596 original size:17 final size:17
Alignment explanation
Indices: 57574--57607 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
57564 TTGCCCTCTC
57574 TTTCTTTTCTTGGAATT
1 TTTCTTTTCTTGGAATT
57591 TTTCTTTTCTTGGAATT
1 TTTCTTTTCTTGGAATT
57608 GGAACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTCTTTTCTTGGAATT
Found at i:59656 original size:14 final size:14
Alignment explanation
Indices: 59637--59664 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59627 GCAGCTAAAA
59637 GCAAGTCATATTGT
1 GCAAGTCATATTGT
59651 GCAAGTCATATTGT
1 GCAAGTCATATTGT
59665 TAGTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
GCAAGTCATATTGT
Done.