Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007158.1 Corchorus capsularis cultivar CVL-1 contig07179, 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: 18647
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1586 original size:41 final size:41
Alignment explanation
Indices: 1454--1596 Score: 139
Period size: 41 Copynumber: 3.4 Consensus size: 41
1444 CTTGTGTTAC
* * *
1454 ATGTATTTAGGGACTTTGATATAGATGCCTTTGTGTTATGA
1 ATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATGA
* * *
1495 ATGTGCTTGAGGGA-TTTGAAAAAGAATTGACC-CTGTGTTAT-A
1 ATGTGTTTG-GGGACTTTGATATAG-A-TG-CCTCTGTGTTATGA
*
1537 ATTTTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATGA
1 A-TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATGA
* *
1579 ACGTGTTTGAGGACTTTG
1 ATGTGTTTGGGGACTTTG
1597 GTCATTGGGT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
40 2 0.02
41 39 0.48
42 14 0.17
43 24 0.30
44 2 0.02
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.41
Consensus pattern (41 bp):
ATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATGA
Found at i:14634 original size:47 final size:47
Alignment explanation
Indices: 14575--14683 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
14565 TTTTATCCGT
*
14575 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAATTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAAATTG
* *
14622 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGTTTTCTGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAAATTG
14669 TGCCCGGAGGACTTA
1 TGCCCGGAGGACTTA
14684 CCAATACAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (47 bp):
TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAAATTG
Found at i:14653 original size:25 final size:25
Alignment explanation
Indices: 14577--14655 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
14567 TTATCCGTTG
14577 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGGACTTATCAGAATTAATA
* * *
14602 CCCGGAGG--TT-TCTGAAATT-GTG
1 CCCGGAGGACTTATCAG-AATTAATA
*
14624 CCCGGAGGACTTATCAGAATTAACA
1 CCCGGAGGACTTATCAGAATTAATA
14649 CCCGGAG
1 CCCGGAG
14656 TTTTCTGAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
22 12 0.29
23 6 0.14
24 6 0.14
25 18 0.43
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (25 bp):
CCCGGAGGACTTATCAGAATTAATA
Found at i:14810 original size:25 final size:25
Alignment explanation
Indices: 14780--14859 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
14770 TTACCAATTG
14780 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGGACTTATCAGAATTAATA
* * ** *
14805 CTCGGAGG--TT-TCTGAATTTGTG
1 CCCGGAGGACTTATCAGAATTAATA
*
14827 CCCGGAGGACTTATCAGAATTAACA
1 CCCGGAGGACTTATCAGAATTAATA
14852 CCCGGAGG
1 CCCGGAGG
14860 TTTCTGAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 15 0.37
23 2 0.05
24 2 0.05
25 22 0.54
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (25 bp):
CCCGGAGGACTTATCAGAATTAATA
Found at i:14821 original size:22 final size:22
Alignment explanation
Indices: 14796--14869 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
14786 GGACTTATCA
*
14796 GAATTAATACTCGGAGGTTTCT
1 GAATTAATACCCGGAGGTTTCT
** * *
14818 GAATTTGTGCCCGGAGGACTTATCA
1 GAATTAATACCCGGAGG--TT-TCT
*
14843 GAATTAACACCCGGAGGTTTCT
1 GAATTAATACCCGGAGGTTTCT
14865 GAATT
1 GAATT
14870 TGTGCTCGGA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (22 bp):
GAATTAATACCCGGAGGTTTCT
Found at i:14833 original size:47 final size:47
Alignment explanation
Indices: 14778--14886 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
14768 TTTTACCAAT
* *
14778 TGCCCGGAGGACTTATCAGAATTAATACTCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTG
14825 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTG
*
14872 TGCTCGGAGGACTTA
1 TGCCCGGAGGACTTA
14887 CCAATGCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (47 bp):
TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTG
Found at i:14879 original size:22 final size:22
Alignment explanation
Indices: 14807--14881 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
14797 AATTAATACT
14807 CGGAGGTTTCTGAATTTGTGCC
1 CGGAGGTTTCTGAATTTGTGCC
* ****
14829 CGGAGGACTTATCAGAATTAACACC
1 CGGAGG--TT-TCTGAATTTGTGCC
*
14854 CGGAGGTTTCTGAATTTGTGCT
1 CGGAGGTTTCTGAATTTGTGCC
14876 CGGAGG
1 CGGAGG
14882 ACTTACCAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (22 bp):
CGGAGGTTTCTGAATTTGTGCC
Found at i:14882 original size:203 final size:203
Alignment explanation
Indices: 14527--15150 Score: 1115
Period size: 203 Copynumber: 3.1 Consensus size: 203
14517 CATGAATCTT
* *
14527 TGATGAAAAACTTGACGAAATGAAATGGTACCCGGAGGTTTTATCC-GTTGCCCGGAGGACTTAT
1 TGAT-AAAAACTTGATGGAATGAAATGGTACCCGGAGGTTTTA-CCAGTTGCCCGGAGGACTTAT
*
14591 CAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGACTTATCAGAATTAACACCCGGAG
64 CAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTATCAGAATTAACACCCGGAG
* * *
14656 TTTTCTGAATTTGTGCCCGGAGGACTTACCAATACAAACTCTGAATTGACACCTTCGATCAAGGA
129 GTTTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAACTCTGAATTGACACCTTCGATCAAGGA
14721 TTTTAAAATA
194 TTTTAAAATA
*
14731 TGATAAAAACTTGATGGAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCA
1 TGATAAAAACTTGATGGAATGAAATGGTACCCGGAGGTTTTACCAGTTGCCCGGAGGACTTATCA
*
14796 GAATTAATACTCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTATCAGAATTAACACCCGGAGGT
66 GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTATCAGAATTAACACCCGGAGGT
*
14861 TTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAACTCTGAATTGACACATTCGATCAAGGATT
131 TTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAACTCTGAATTGACACCTTCGATCAAGGATT
14926 TTAAAATA
196 TTAAAATA
14934 TGATAAAAACTTGATGGAATGAAATGGTACCCGGAGGTTTTACCAGTTGCCCGGAGGACTTATCA
1 TGATAAAAACTTGATGGAATGAAATGGTACCCGGAGGTTTTACCAGTTGCCCGGAGGACTTATCA
14999 GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTATCAGAATTAACACCCGGAGGT
66 GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTATCAGAATTAACACCCGGAGGT
* *
15064 TTCAGAATTTGTGCTCGGAGGACTTACCAATGCAAACTTTGAATTGACACCTTCGATCAAGGATT
131 TTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAACTCTGAATTGACACCTTCGATCAAGGATT
15129 TTAAAATA
196 TTAAAATA
*
15137 TAATAAAAACTTGA
1 TGATAAAAACTTGA
15151 ACTAATTCGT
Statistics
Matches: 404, Mismatches: 15, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
202 2 0.00
203 398 0.99
204 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (203 bp):
TGATAAAAACTTGATGGAATGAAATGGTACCCGGAGGTTTTACCAGTTGCCCGGAGGACTTATCA
GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTATCAGAATTAACACCCGGAGGT
TTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAACTCTGAATTGACACCTTCGATCAAGGATT
TTAAAATA
Found at i:15033 original size:22 final size:22
Alignment explanation
Indices: 14981--15084 Score: 73
Period size: 22 Copynumber: 4.5 Consensus size: 22
14971 TTTTACCAGT
**
14981 TGCCCGGAGGACTTATCAGAATTAA
1 TGCCCGGAGG--TT-TCAGAATTTG
* *
15006 TACCCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGTTTCAGAATTTG
**
15028 TGCCCGGAGGACTTATCAGAATTAA
1 TGCCCGGAGG--TT-TCAGAATTTG
**
15053 CACCCGGAGGTTTCAGAATTTG
1 TGCCCGGAGGTTTCAGAATTTG
*
15075 TGCTCGGAGG
1 TGCCCGGAGG
15085 ACTTACCAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 9
0.72 0.18 0.11
Matches are distributed among these distances:
22 31 0.51
23 4 0.07
24 2 0.03
25 24 0.39
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (22 bp):
TGCCCGGAGGTTTCAGAATTTG
Found at i:15040 original size:47 final size:47
Alignment explanation
Indices: 14981--15089 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
14971 TTTTACCAGT
* *
14981 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCAGAATTTG
15028 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCAGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCAGAATTTG
*
15075 TGCTCGGAGGACTTA
1 TGCCCGGAGGACTTA
15090 CCAATGCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (47 bp):
TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCAGAATTTG
Found at i:15058 original size:25 final size:25
Alignment explanation
Indices: 14983--15062 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
14973 TTACCAGTTG
14983 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGGACTTATCAGAATTAATA
* ** *
15008 CCCGGAGG--TT-TCTGAATTTGTG
1 CCCGGAGGACTTATCAGAATTAATA
*
15030 CCCGGAGGACTTATCAGAATTAACA
1 CCCGGAGGACTTATCAGAATTAATA
15055 CCCGGAGG
1 CCCGGAGG
15063 TTTCAGAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 16 0.37
23 2 0.05
24 2 0.05
25 23 0.53
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (25 bp):
CCCGGAGGACTTATCAGAATTAATA
Found at i:16438 original size:12 final size:13
Alignment explanation
Indices: 16410--16438 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16400 AGTTAACCCG
16410 AAAACTCTTTTCA
1 AAAACTCTTTTCA
16423 AAAACTCTTTTCA
1 AAAACTCTTTTCA
16436 AAA
1 AAA
16439 GTTTTGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAACTCTTTTCA
Found at i:16733 original size:19 final size:20
Alignment explanation
Indices: 16709--16782 Score: 82
Period size: 19 Copynumber: 3.7 Consensus size: 20
16699 TTCAGTTTAC
16709 TTTTTTTGA-TGATTTGA-T
1 TTTTTTTGATTGATTTGATT
*
16727 TTTTTTTGATTGATTTTATT
1 TTTTTTTGATTGATTTGATT
*
16747 ATTATTATTTGATTTATTTGA-T
1 -TT-TT-TTTGATTGATTTGATT
16769 TTTTTTTGATTGAT
1 TTTTTTTGATTGAT
16783 GCCTTCTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.19
19 16 0.34
20 3 0.06
21 4 0.09
22 3 0.06
23 12 0.26
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (20 bp):
TTTTTTTGATTGATTTGATT
Found at i:16739 original size:14 final size:13
Alignment explanation
Indices: 16722--16782 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
16712 TTTTGATGAT
16722 TTGATTTTTTTTGA
1 TTGATTTTTTTT-A
16736 TTGATTTTATTATTA
1 TTGATTTT-TT-TTA
**
16751 TT-ATTTGATTTA
1 TTGATTTTTTTTA
16763 TTTGATTTTTTTTGA
1 -TTGATTTTTTTT-A
16778 TTGAT
1 TTGAT
16783 GCCTTCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 24 0.63
15 6 0.16
16 2 0.05
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (13 bp):
TTGATTTTTTTTA
Found at i:17092 original size:15 final size:14
Alignment explanation
Indices: 17072--17132 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 14
17062 AACGAGTTTC
17072 AAAAACCGTTTTTTG
1 AAAAACC-TTTTTTG
* *
17087 AAAAA-CATTTTAG
1 AAAAACCTTTTTTG
*
17100 AAAAACATTTTTTTG
1 AAAAAC-CTTTTTTG
* *
17115 AAAATCATTTTTTG
1 AAAAACCTTTTTTG
17129 AAAA
1 AAAA
17133 CCATGACTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
13 10 0.27
14 12 0.32
15 15 0.41
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (14 bp):
AAAAACCTTTTTTG
Found at i:17103 original size:28 final size:28
Alignment explanation
Indices: 17072--17125 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
17062 AACGAGTTTC
*
17072 AAAAACCGTTTTTTGAAAAACATTTTAG
1 AAAAACAGTTTTTTGAAAAACATTTTAG
* *
17100 AAAAACATTTTTTTGAAAATCATTTT
1 AAAAACAGTTTTTTGAAAAACATTTT
17126 TTGAAAACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (28 bp):
AAAAACAGTTTTTTGAAAAACATTTTAG
Found at i:17125 original size:13 final size:14
Alignment explanation
Indices: 17080--17132 Score: 72
Period size: 13 Copynumber: 3.8 Consensus size: 14
17070 TCAAAAACCG
17080 TTTTTTGAAAAACA
1 TTTTTTGAAAAACA
*
17094 -TTTTAGAAAAACA
1 TTTTTTGAAAAACA
*
17107 TTTTTTTGAAAATCA
1 -TTTTTTGAAAAACA
17122 TTTTTTGAAAA
1 TTTTTTGAAAA
17133 CCATGACTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.35
14 11 0.32
15 11 0.32
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (14 bp):
TTTTTTGAAAAACA
Found at i:17201 original size:7 final size:7
Alignment explanation
Indices: 17189--17236 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
17179 CAAGTGCTTT
17189 TTTTTTC
1 TTTTTTC
17196 TTTTTTC
1 TTTTTTC
17203 -TTTTTC
1 TTTTTTC
17209 TTTTTTC
1 TTTTTTC
*
17216 ATTTTTC
1 TTTTTTC
*
17223 ATCCTTTTC
1 -T-TTTTTC
17232 TTTTT
1 TTTTT
17237 CAAAATTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 6 0.18
7 22 0.65
8 1 0.03
9 5 0.15
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:17260 original size:7 final size:7
Alignment explanation
Indices: 17190--17260 Score: 51
Period size: 7 Copynumber: 10.1 Consensus size: 7
17180 AAGTGCTTTT
*
17190 TTTTTCT
1 TTTTTCA
17197 TTTTTC-
1 TTTTTCA
*
17203 TTTTTCT
1 TTTTTCA
17210 TTTTTCA
1 TTTTTCA
17217 TTTTTCA
1 TTTTTCA
17224 TCCTTTTC-
1 T--TTTTCA
17232 TTTTTCAAA
1 TTTTTC--A
*
17241 ATTTTCA
1 TTTTTCA
17248 --TTTCA
1 TTTTTCA
17253 TTTTTCA
1 TTTTTCA
17260 T
1 T
17261 CATTTTTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
5 5 0.09
6 11 0.20
7 27 0.50
8 1 0.02
9 10 0.19
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Done.