Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014338.1 Corchorus capsularis cultivar CVL-1 contig14359, 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: 46395
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Found at i:2371 original size:23 final size:22
Alignment explanation
Indices: 2328--2407 Score: 60
Period size: 23 Copynumber: 3.6 Consensus size: 22
2318 TTTCAAATAA
2328 AATTATTTTTTTTTATTTTTAAT
1 AATTATTTTTTTTTA-TTTTAAT
2351 AATTATTATTTTATTTA-TTT-AT
1 AATTATT-TTTT-TTTATTTTAAT
* *
2373 --TTATTTTGTTTTTATTAATAAA
1 AATTATTTT-TTTTTATT-TTAAT
*
2395 AATAATTTTTTTT
1 AATTATTTTTTTT
2408 CACATGCGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
19 6 0.13
20 8 0.17
21 1 0.02
22 3 0.07
23 14 0.30
24 10 0.22
25 4 0.09
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (22 bp):
AATTATTTTTTTTTATTTTAAT
Found at i:4190 original size:21 final size:21
Alignment explanation
Indices: 4166--4213 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
4156 GGTCATGGTC
4166 CCATGCGATGGCGCGGCTACT
1 CCATGCGATGGCGCGGCTACT
** *
4187 CCATGCTTTGGCGCGGCTTCT
1 CCATGCGATGGCGCGGCTACT
4208 CCATGC
1 CCATGC
4214 TTTGGCCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.35, G:0.29, T:0.25
Consensus pattern (21 bp):
CCATGCGATGGCGCGGCTACT
Found at i:4214 original size:21 final size:21
Alignment explanation
Indices: 4174--4219 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
4164 TCCCATGCGA
4174 TGGCGCGGCTACTCCATGCTT
1 TGGCGCGGCTACTCCATGCTT
*
4195 TGGCGCGGCTTCTCCATGCTT
1 TGGCGCGGCTACTCCATGCTT
4216 TGGC
1 TGGC
4220 CGGTCATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.07, C:0.33, G:0.30, T:0.30
Consensus pattern (21 bp):
TGGCGCGGCTACTCCATGCTT
Found at i:9661 original size:8 final size:8
Alignment explanation
Indices: 9648--9678 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
9638 GGTCGAAAGT
9648 TTTTTTTA
1 TTTTTTTA
9656 TTTTTTTA
1 TTTTTTTA
9664 TTTTTTTA
1 TTTTTTTA
*
9672 TATTTTT
1 TTTTTTT
9679 CAATATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:10733 original size:10 final size:12
Alignment explanation
Indices: 10706--10739 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
10696 TCCCATGTGA
10706 TGGCCGGTCATG
1 TGGCCGGTCATG
10718 TGGCCGGTC-T-
1 TGGCCGGTCATG
10728 TGGCCGGTCATG
1 TGGCCGGTCATG
10740 GTCCCATGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.06, C:0.26, G:0.41, T:0.26
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:10769 original size:21 final size:21
Alignment explanation
Indices: 10743--10790 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10733 GGTCATGGTC
10743 CCATGCGATAGCGCGGCTACT
1 CCATGCGATAGCGCGGCTACT
** * *
10764 CCATGCTTTGGCGCGGCTTCT
1 CCATGCGATAGCGCGGCTACT
10785 CCATGC
1 CCATGC
10791 TTTTGGCCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.12, C:0.35, G:0.27, T:0.25
Consensus pattern (21 bp):
CCATGCGATAGCGCGGCTACT
Found at i:10791 original size:21 final size:21
Alignment explanation
Indices: 10753--10793 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10743 CCATGCGATA
10753 GCGCGGCTACTCCATGCTTTG
1 GCGCGGCTACTCCATGCTTTG
*
10774 GCGCGGCTTCTCCATGCTTT
1 GCGCGGCTACTCCATGCTTT
10794 TGGCCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.34, G:0.27, T:0.32
Consensus pattern (21 bp):
GCGCGGCTACTCCATGCTTTG
Found at i:15035 original size:21 final size:20
Alignment explanation
Indices: 15005--15054 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 20
14995 CATTTTTAGA
15005 TTTAATTTTCTTGTTTGCATG
1 TTTAA-TTTCTTGTTTGCATG
15026 TTTAGATTTCTTGTTTGCATG
1 TTTA-ATTTCTTGTTTGCATG
15047 TTTAATTT
1 TTTAATTT
15055 TGTTTTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.14
21 23 0.82
22 1 0.04
ACGTcount: A:0.16, C:0.08, G:0.14, T:0.62
Consensus pattern (20 bp):
TTTAATTTCTTGTTTGCATG
Found at i:25668 original size:19 final size:18
Alignment explanation
Indices: 25644--25680 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
25634 TTGAAGATTT
25644 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
25663 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
25681 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:31711 original size:89 final size:88
Alignment explanation
Indices: 31598--31777 Score: 315
Period size: 89 Copynumber: 2.0 Consensus size: 88
31588 CGGATACCTC
** *
31598 TAGTTTGCTAGTCTGTCATGCACTAATCCAACCAAAACCTTCAACACCTAAGACTTAAAACCAAC
1 TAGTTTGCTAGTCAATCATACACTAATCCAACCAAAACCTTCAACACCTAAGACTTAAAACCAAC
*
31663 ATATCAAATCCGAATCAAACCAAG
66 ATATC-AATCCCAATCAAACCAAG
31687 TAGTTTGCTAGTCAATCATACACTAATCCAACCAAAACCTTCAACACCTAAGACTTAAAACCAAC
1 TAGTTTGCTAGTCAATCATACACTAATCCAACCAAAACCTTCAACACCTAAGACTTAAAACCAAC
31752 ATATCAATCCCAATCAAACCAAG
66 ATATCAATCCCAATCAAACCAAG
31775 TAG
1 TAG
31778 CACGAACATA
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 20 0.23
89 67 0.77
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (88 bp):
TAGTTTGCTAGTCAATCATACACTAATCCAACCAAAACCTTCAACACCTAAGACTTAAAACCAAC
ATATCAATCCCAATCAAACCAAG
Found at i:40522 original size:21 final size:21
Alignment explanation
Indices: 40486--40541 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
40476 GTGCTTAGGC
40486 ATGGCCGGGTCATGCGATGGTG
1 ATGGCCGGG-CATGCGATGGTG
*
40508 ATGGTCGGGCATGCGATGGTG
1 ATGGCCGGGCATGCGATGGTG
40529 ATGGCCGGGCATG
1 ATGGCCGGGCATG
40542 TGGCCTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.14, C:0.18, G:0.46, T:0.21
Consensus pattern (21 bp):
ATGGCCGGGCATGCGATGGTG
Found at i:45977 original size:10 final size:10
Alignment explanation
Indices: 45962--45987 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
45952 TCTGGTTGAA
45962 ATTTTTTTAT
1 ATTTTTTTAT
45972 ATTTTTTTAT
1 ATTTTTTTAT
45982 ATTTTT
1 ATTTTT
45988 GGATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTTAT
Done.