Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014249.1 Corchorus capsularis cultivar CVL-1 contig14270, 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: 28550
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1538 original size:18 final size:20
Alignment explanation
Indices: 1515--1553 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1505 TTCCTTGTGG
1515 ACGTGGCAT-T-AAAATTCC
1 ACGTGGCATCTGAAAATTCC
*
1533 ACGTGGCCTCTGAAAATTCC
1 ACGTGGCATCTGAAAATTCC
1553 A
1 A
1554 TGTGTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
ACGTGGCATCTGAAAATTCC
Found at i:2047 original size:14 final size:14
Alignment explanation
Indices: 2024--2063 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2014 AATAATGTAC
*
2024 TAATATAAAAATGA
1 TAATACAAAAATGA
2038 TAATACAAAAATGA
1 TAATACAAAAATGA
2052 TAATACGAAAAA
1 TAATAC-AAAAA
2064 AAAATGAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (14 bp):
TAATACAAAAATGA
Found at i:2482 original size:17 final size:17
Alignment explanation
Indices: 2428--2475 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2418 ATCACCCCTT
* **
2428 AGATCACTAGTGATTTA
1 AGATCACCAGTGATGCA
2445 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
*
2462 AGATCACCGGTGAT
1 AGATCACCAGTGAT
2476 CAAAGATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:6525 original size:1 final size:1
Alignment explanation
Indices: 6519--6544 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
6509 CAATGGTAAA
6519 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
6545 GTAAAAGGCA
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12723 original size:77 final size:77
Alignment explanation
Indices: 12629--12778 Score: 273
Period size: 77 Copynumber: 1.9 Consensus size: 77
12619 GATGTATCAT
*
12629 ATAATTACCTTTATTATAAAATTGAAAACAATTTTATTTAACAAACTTTAGTCCCAAAACTCATA
1 ATAATTACCCTTATTATAAAATTGAAAACAATTTTATTTAACAAACTTTAGTCCCAAAACTCATA
12694 ATGTGTAAAAAG
66 ATGTGTAAAAAG
* *
12706 ATAATTACCCTTGTTATAAAATTGAAAACAATTTTATTTAATAAACTTTAGTCCCAAAACTCATA
1 ATAATTACCCTTATTATAAAATTGAAAACAATTTTATTTAACAAACTTTAGTCCCAAAACTCATA
12771 ATGTGTAA
66 ATGTGTAA
12779 GACTCGTAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (77 bp):
ATAATTACCCTTATTATAAAATTGAAAACAATTTTATTTAACAAACTTTAGTCCCAAAACTCATA
ATGTGTAAAAAG
Found at i:13837 original size:16 final size:16
Alignment explanation
Indices: 13818--13860 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
13808 CTCGAACCCG
13818 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
13834 CCCGAACCCGAAATTA
1 CCCGAACCCGAAAATA
13850 CCCGAACCCGA
1 CCCGAACCCGA
13861 GACAACCCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.37, C:0.42, G:0.14, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:13868 original size:16 final size:16
Alignment explanation
Indices: 13818--13876 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
13808 CTCGAACCCG
13818 CCCGAACCCGA-AAATA
1 CCCGAACCCGAGAAA-A
*
13834 CCCGAACCCGA-AATTA
1 CCCGAACCCGAGAA-AA
*
13850 CCCGAACCCGAGACAA
1 CCCGAACCCGAGAAAA
13866 CCCG-ACCCGAG
1 CCCGAACCCGAG
13877 CCCGAGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 7 0.18
16 30 0.79
17 1 0.03
ACGTcount: A:0.36, C:0.42, G:0.17, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGAGAAAA
Found at i:14665 original size:16 final size:16
Alignment explanation
Indices: 14642--14702 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
14632 CCGACCCGGG
14642 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
* *
14658 CACGAACCAGAAAATA
1 CCCGAACCCGAAAATA
*
14674 CCCGAATCCGAAAATA
1 CCCGAACCCGAAAATA
14690 CCCGAACCCGAAA
1 CCCGAACCCGAAA
14703 GGCAGTACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.46, C:0.34, G:0.13, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:23129 original size:3 final size:3
Alignment explanation
Indices: 23117--23168 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
23107 CCCTTTTCCC
* * * *
23117 TCT T-T TCT TCT TCT TCC TCT TCG TCT TCT TCT TCT GCT TCT TCT TTT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
23164 TCT TC
1 TCT TC
23169 AACCCGTGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.00, C:0.33, G:0.04, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:24554 original size:18 final size:18
Alignment explanation
Indices: 24511--24561 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
24501 TAACTCACAA
*
24511 ATTTATTTAAAAGATAATT
1 ATTTATTT-AAATATAATT
*
24530 ATTTATTTAAATATATTT
1 ATTTATTTAAATATAATT
*
24548 GTTTATTTAAATAT
1 ATTTATTTAAATAT
24562 TCGTTAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
ATTTATTTAAATATAATT
Found at i:25324 original size:31 final size:31
Alignment explanation
Indices: 25289--25354 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
25279 TTAGTCAAGC
* *
25289 TCAATTTGATTAGTTTTGATGTCAAAATGGT
1 TCAATTTGATTAGTGTTAATGTCAAAATGGT
25320 TCAATTTGATTAGTGTTAATGTCAAAATGGT
1 TCAATTTGATTAGTGTTAATGTCAAAATGGT
25351 TCAA
1 TCAA
25355 CTTGTTGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (31 bp):
TCAATTTGATTAGTGTTAATGTCAAAATGGT
Done.