Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008870.1 Corchorus capsularis cultivar CVL-1 contig08891, 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: 25978
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:6965 original size:16 final size:16
Alignment explanation
Indices: 6929--7018 Score: 121
Period size: 16 Copynumber: 5.8 Consensus size: 16
6919 CGGGTTCGGG
* *
6929 TTCGAGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
6944 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
6960 TTCGGGTTCGGATATT
1 TTCGGGTTCGGGTATT
*
6976 TTCGGGTTTGGGTA-T
1 TTCGGGTTCGGGTATT
6991 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
7007 TTCAGGTTCGGG
1 TTCGGGTTCGGG
7019 CTCAGTTCGG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
15 27 0.41
16 39 0.59
ACGTcount: A:0.09, C:0.13, G:0.37, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:6969 original size:31 final size:31
Alignment explanation
Indices: 6929--7032 Score: 120
Period size: 31 Copynumber: 3.3 Consensus size: 31
6919 CGGGTTCGGG
* *
6929 TTCGAGTTCGGGTA-CTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATTTTCGGGTTCGGGTA-T
* *
6960 TTCGGGTTCGGATATTTTCGGGTTTGGGTAT
1 TTCGGGTTCGGGTATTTTCGGGTTCGGGTAT
* *
6991 TTCGGGTTCGGGTATTTTCAGGTTCGGGCTCAG
1 TTCGGGTTCGGGTATTTTCGGGTTCGGG-T-AT
7024 TTCGGGTTC
1 TTCGGGTTC
7033 TGGTTCGGGC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 38 0.61
32 14 0.23
33 10 0.16
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.40
Consensus pattern (31 bp):
TTCGGGTTCGGGTATTTTCGGGTTCGGGTAT
Found at i:7037 original size:6 final size:6
Alignment explanation
Indices: 7023--7067 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
7013 TTCGGGCTCA
* **
7023 GTTCGG GTTCTG GTTCGG GCCCGG G-TCGG GTTCGG GTTCGG GTTC
1 GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG GTTC
7068 ACTTTCGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.00, C:0.22, G:0.47, T:0.31
Consensus pattern (6 bp):
GTTCGG
Found at i:7039 original size:23 final size:23
Alignment explanation
Indices: 7011--7064 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
7001 GGTATTTTCA
* * *
7011 GGTTCGGGCTCAGTTCGGGTTCT
1 GGTTCGGGCCCAGGTCGGGTTCG
*
7034 GGTTCGGGCCCGGGTCGGGTTCG
1 GGTTCGGGCCCAGGTCGGGTTCG
7057 GGTTCGGG
1 GGTTCGGG
7065 TTCACTTTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.02, C:0.22, G:0.48, T:0.28
Consensus pattern (23 bp):
GGTTCGGGCCCAGGTCGGGTTCG
Found at i:7788 original size:20 final size:20
Alignment explanation
Indices: 7765--7806 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
7755 AAAAATTTTA
7765 TTTTATAA-ATAATTCTTGAT
1 TTTTATAATATAATT-TTGAT
* *
7785 TTTTTTAATATTATTTTGAT
1 TTTTATAATATAATTTTGAT
7805 TT
1 TT
7807 CGGGCTCGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTATAATATAATTTTGAT
Found at i:7833 original size:10 final size:11
Alignment explanation
Indices: 7806--7838 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
7796 TATTTTGATT
*
7806 TCGGGCTCGGG
1 TCGGGTTCGGG
7817 TCGGGTTCGGG
1 TCGGGTTCGGG
7828 -CGGGTTCGGG
1 TCGGGTTCGGG
7838 T
1 T
7839 TCCGGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.21, G:0.55, T:0.24
Consensus pattern (11 bp):
TCGGGTTCGGG
Found at i:7873 original size:16 final size:16
Alignment explanation
Indices: 7832--7876 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
7822 TTCGGGCGGG
* *
7832 TTCGGGTTCCGGTATT
1 TTCGGGTTCGGGTAAT
7848 TTCGGGTTCGGGTAAT
1 TTCGGGTTCGGGTAAT
7864 TTCGGGTTCGGGT
1 TTCGGGTTCGGGT
7877 TTGGGCGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.07, C:0.16, G:0.38, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTAAT
Found at i:8916 original size:44 final size:44
Alignment explanation
Indices: 8848--8936 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
8838 ATGTTATGGA
*
8848 TATGTCAAGAATAAGTGTGAGGGATTATCTATATAAAGGGTAAT
1 TATGTAAAGAATAAGTGTGAGGGATTATCTATATAAAGGGTAAT
*
8892 TATGTAAAGAATAAGTGTGGGGGATTATCTATATAAAGGGTAAT
1 TATGTAAAGAATAAGTGTGAGGGATTATCTATATAAAGGGTAAT
8936 T
1 T
8937 TAAAATTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (44 bp):
TATGTAAAGAATAAGTGTGAGGGATTATCTATATAAAGGGTAAT
Found at i:11619 original size:19 final size:18
Alignment explanation
Indices: 11595--11634 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11585 TTGAAGATTT
*
11595 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
11614 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
11632 ATT
1 ATT
11635 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:14419 original size:17 final size:17
Alignment explanation
Indices: 14397--14430 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
14387 GTTCATGTTA
14397 GCATTTAGTTTTAGTAG
1 GCATTTAGTTTTAGTAG
14414 GCATTTAGTTTTAGTAG
1 GCATTTAGTTTTAGTAG
14431 ATTACCTTCA
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:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (17 bp):
GCATTTAGTTTTAGTAG
Found at i:21177 original size:12 final size:12
Alignment explanation
Indices: 21141--21179 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
21131 ACGACCAAAG
*
21141 GAATAATAAAAA
1 GAATAATAATAA
* *
21153 TAATAATAGTAA
1 GAATAATAATAA
21165 GAATAATAATAA
1 GAATAATAATAA
21177 GAA
1 GAA
21180 GTGGAACGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (12 bp):
GAATAATAATAA
Found at i:21702 original size:28 final size:26
Alignment explanation
Indices: 21669--21726 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
21659 ACAAGAGGCA
21669 TTTTCCAAAATACGTTTTCAAGAGAAGG
1 TTTTCCAAAATACGTTTTCAA-A-AAGG
**
21697 TTTTCCAAAATGGGTTTTCAAAAAGG
1 TTTTCCAAAATACGTTTTCAAAAAGG
21723 TTTT
1 TTTT
21727 GAGTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.29
27 1 0.04
28 19 0.68
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (26 bp):
TTTTCCAAAATACGTTTTCAAAAAGG
Done.