Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012330.1 Corchorus capsularis cultivar CVL-1 contig12351, 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: 15976
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:250 original size:18 final size:19
Alignment explanation
Indices: 224--261 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
214 ATAATTATTC
224 ATTAAAAAGAATTA-TAAT
1 ATTAAAAAGAATTAGTAAT
* *
242 ATTATAAAGATTTAGTAAT
1 ATTAAAAAGAATTAGTAAT
261 A
1 A
262 ATTTTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
ATTAAAAAGAATTAGTAAT
Found at i:1543 original size:21 final size:22
Alignment explanation
Indices: 1499--1546 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1489 TTAGAACCGA
*
1499 CGGGTCGGTTCCGTCGGGTTCT
1 CGGGTCGGTTCCGTCGGATTCT
1521 CGGGTCGGTTCCGT-GGATTCT
1 CGGGTCGGTTCCGTCGGATTCT
1542 CGGGT
1 CGGGT
1547 TGAGTCGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.02, C:0.25, G:0.42, T:0.31
Consensus pattern (22 bp):
CGGGTCGGTTCCGTCGGATTCT
Found at i:1652 original size:15 final size:15
Alignment explanation
Indices: 1566--1717 Score: 76
Period size: 15 Copynumber: 9.5 Consensus size: 15
1556 TTATTTATTT
*
1566 ATATATATAAAATAA
1 ATATATATAAATTAA
*
1581 AGT-TATA-AAAGTAA
1 A-TATATATAAATTAA
**
1595 ATATATATTTATTATA
1 ATATATATAAATTA-A
* *
1611 ATATATACAATTATAA
1 ATATATATAAAT-TAA
1627 TTATAATATATAAATTAA
1 --AT-ATATATAAATTAA
*
1645 ATATATATAAAGTAA
1 ATATATATAAATTAA
* *
1660 ATATATAATTACTTTATATAT
1 ATATAT-A-TA---AAT-TAA
*
1681 ATATATATAAAGTAA
1 ATATATATAAATTAA
1696 ATATATAT-AATTATA
1 ATATATATAAATTA-A
1711 ATATATA
1 ATATATA
1718 ATTTATATTT
Statistics
Matches: 104, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
13 1 0.01
14 15 0.14
15 44 0.42
16 15 0.14
17 4 0.04
18 5 0.05
19 10 0.10
20 2 0.02
21 8 0.08
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (15 bp):
ATATATATAAATTAA
Found at i:1719 original size:13 final size:13
Alignment explanation
Indices: 1622--1720 Score: 64
Period size: 13 Copynumber: 7.5 Consensus size: 13
1612 TATATACAAT
1622 TATAATTATAATA
1 TATAATTATAATA
*
1635 TATAAATTAAATATA
1 TAT-AATTATA-ATA
*
1650 TATAAAGTA-AATA
1 TAT-AATTATAATA
*
1663 TATAATTACT-TTA
1 TATAATTA-TAATA
1676 TAT-A-TAT-ATA
1 TATAATTATAATA
* *
1686 TATAAAGTAAATATA
1 TAT-AATTATA-ATA
1701 TATAATTATAATA
1 TATAATTATAATA
1714 TATAATT
1 TATAATT
1721 TATATTTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
10 6 0.09
11 2 0.03
12 6 0.09
13 26 0.38
14 12 0.17
15 17 0.25
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (13 bp):
TATAATTATAATA
Found at i:1719 original size:51 final size:47
Alignment explanation
Indices: 1584--1729 Score: 152
Period size: 51 Copynumber: 3.0 Consensus size: 47
1574 AAAATAAAGT
*
1584 TATA-AAAGTAAATATATATTTATTATAATATATACAATTATAATTATAA
1 TATATAAAGTAAATATATA-TAATTATAATATAT--AATTATAATTATAA
* * *
1633 TATATAAATTAAATATATATAAAGTA-AATATATAATTACTTTATATATATA
1 TATATAAAGTAAATATATAT-AATTATAATATATAATTA--TAAT-TATA-A
*
1684 TATATAAAGTAAATATATATAATTATAATATATAATTTATATTTAT
1 TATATAAAGTAAATATATATAATTATAATATATAA-TTATAATTAT
1730 TATTTTTTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
47 5 0.06
49 18 0.22
50 26 0.32
51 29 0.36
52 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (47 bp):
TATATAAAGTAAATATATATAATTATAATATATAATTATAATTATAA
Found at i:9458 original size:15 final size:15
Alignment explanation
Indices: 9440--9472 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9430 GGAGTTACTT
*
9440 TCCCTAGAATCACTC
1 TCCCAAGAATCACTC
9455 TCCCAAGAATCACTC
1 TCCCAAGAATCACTC
9470 TCC
1 TCC
9473 TATGGAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.42, G:0.06, T:0.24
Consensus pattern (15 bp):
TCCCAAGAATCACTC
Found at i:10010 original size:100 final size:100
Alignment explanation
Indices: 9837--10038 Score: 316
Period size: 100 Copynumber: 2.0 Consensus size: 100
9827 TAATTAAATC
* *
9837 ATGGATAATTATTTGATACACTGACAGTATAAATTTTGGACTCCACAAGTGGGATGGAGAGTTCA
1 ATGGATAATTATTTGATACACTGACAGTATAAATTTTGGACTACACAAGCGGGATGGAGAGTTCA
9902 CACATACCCATTTTCTGAATAAATTTCTTTTTAAA
66 CACATACCCATTTTCTGAATAAATTTCTTTTTAAA
* * * *
9937 ATGGATAATTATTTGATACACTGACAGTGTAAATTTTGGACTACATAAGCGGGCTGG-GAAGTTG
1 ATGGATAATTATTTGATACACTGACAGTATAAATTTTGGACTACACAAGCGGGATGGAG-AGTTC
* *
10001 ACACATACCCATTTTCTGAATTAATTTGTTTTTAAA
65 ACACATACCCATTTTCTGAATAAATTTCTTTTTAAA
10037 AT
1 AT
10039 TCAAAACTAT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.01
100 92 0.99
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (100 bp):
ATGGATAATTATTTGATACACTGACAGTATAAATTTTGGACTACACAAGCGGGATGGAGAGTTCA
CACATACCCATTTTCTGAATAAATTTCTTTTTAAA
Found at i:10228 original size:101 final size:101
Alignment explanation
Indices: 10030--10228 Score: 274
Period size: 101 Copynumber: 2.0 Consensus size: 101
10020 ATTAATTTGT
* * *
10030 TTTTAAAATTCAAAACTATTCGCTAAAGGGCACATATCAACCCTTAGACCCCGCATGCGTAGTCT
1 TTTTAAAATTCAAAACTATTCCCTAAAGGACACATATCAACCCTTAGAACCCGCATGCGTAGTCT
** * * * *
10095 GTTAAACTCCATTGACAGTGTATTGTATATTTTTTC
66 ACTAAACTCCACTAACAGAGTATGGTATATTTTTTC
* *
10131 TTTTAAAATTCAAAACTATTCCCTAAAGGACACATGTCAACCCTTA-AACCCGCATGTGTAGTCT
1 TTTTAAAATTCAAAACTATTCCCTAAAGGACACATATCAACCCTTAGAACCCGCATGCGTAGTCT
* *
10195 ACTAAACTCCACTAAGAGAGTATGGTATAATTTT
66 ACTAAACTCCACTAACAGAGTATGGTATATTTTT
10229 CATTAAATCA
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 42 0.49
101 43 0.51
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (101 bp):
TTTTAAAATTCAAAACTATTCCCTAAAGGACACATATCAACCCTTAGAACCCGCATGCGTAGTCT
ACTAAACTCCACTAACAGAGTATGGTATATTTTTTC
Found at i:15315 original size:24 final size:24
Alignment explanation
Indices: 15288--15348 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
15278 AAAATGGGGA
*
15288 AAACTTGGCTGATCCTCCTGTTGT
1 AAACTTGGGTGATCCTCCTGTTGT
15312 AAACTTGGGTGATCCTCCTGTTGT
1 AAACTTGGGTGATCCTCCTGTTGT
*
15336 CAACTTGGGTGAT
1 AAACTTGGGTGAT
15349 TCTGTTGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (24 bp):
AAACTTGGGTGATCCTCCTGTTGT
Found at i:15355 original size:21 final size:23
Alignment explanation
Indices: 15288--15355 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 23
15278 AAAATGGGGA
*
15288 AAACTTGGCTGATCCTCCTGTTGT
1 AAACTTGGGTGAT-CTCCTGTTGT
15312 AAACTTGGGTGATCCTCCTGTTGT
1 AAACTTGGGTGAT-CTCCTGTTGT
*
15336 CAACTTGGGTGAT-T-CTGTTG
1 AAACTTGGGTGATCTCCTGTTG
15356 AGAATGTTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
21 6 0.14
22 1 0.02
24 35 0.83
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (23 bp):
AAACTTGGGTGATCTCCTGTTGT
Done.