Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010046.1 Corchorus capsularis cultivar CVL-1 contig10067, 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: 77863
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4054 original size:20 final size:22
Alignment explanation
Indices: 4017--4068 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
4007 TATAAGTATA
4017 AATATTTTTAATGATAATAA-T
1 AATATTTTTAATGATAATAATT
* *
4038 AATATTTTT-TTGTTAATAATT
1 AATATTTTTAATGATAATAATT
*
4059 TATATTTTTA
1 AATATTTTTA
4069 TTGCTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
AATATTTTTAATGATAATAATT
Found at i:4881 original size:17 final size:17
Alignment explanation
Indices: 4861--4894 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4851 CATTGTTTTT
*
4861 AAAAAAGGAAAAAGAAA
1 AAAAAAAGAAAAAGAAA
*
4878 AAAAAAAGAAAAGGAAA
1 AAAAAAAGAAAAAGAAA
4895 TGTTGAGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAA
Found at i:5593 original size:55 final size:55
Alignment explanation
Indices: 5509--5620 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
5499 AACAAGAACG
5509 TTCTAGTTGGAATTTATCAAGATAACGTTTTGAATTCGAAACCTTATTAATTTTT
1 TTCTAGTTGGAATTTATCAAGATAACGTTTTGAATTCGAAACCTTATTAATTTTT
5564 TTCTAGTTGGAATTTATCAAGATAACGTTTTGAATTCGAAACCTTATTAATTTTT
1 TTCTAGTTGGAATTTATCAAGATAACGTTTTGAATTCGAAACCTTATTAATTTTT
5619 TT
1 TT
5621 GTGAAAAACC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.46
Consensus pattern (55 bp):
TTCTAGTTGGAATTTATCAAGATAACGTTTTGAATTCGAAACCTTATTAATTTTT
Found at i:15787 original size:45 final size:45
Alignment explanation
Indices: 15719--15853 Score: 243
Period size: 45 Copynumber: 3.0 Consensus size: 45
15709 GGGAAACCAC
15719 CTTTGCCTCCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
1 CTTTGCCTCCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
* *
15764 CTTTGCCTGCCCCTTCACCTAGGCCACAGATTAATTCACCCTCCT
1 CTTTGCCTCCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
*
15809 CTTTGCCTTCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
1 CTTTGCCTCCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
15854 TGCAGCAAAG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.18, C:0.41, G:0.10, T:0.31
Consensus pattern (45 bp):
CTTTGCCTCCCCCTTCACTTAGGCCACAGATTAATTCACCCTCCT
Found at i:15968 original size:30 final size:30
Alignment explanation
Indices: 15934--16202 Score: 351
Period size: 30 Copynumber: 9.0 Consensus size: 30
15924 GCAACAACAG
*
15934 CATGTATCATCTCAACAGGTGCCACAACCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
*
15964 CATGTATCATCTCCTCAGGTGCCACAACCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* **
15994 CATGTGTCATCTCCACAGGTGCCACAGTCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
**
16024 CATGTATCATCTCCACAGGTGCCACAGTCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
*
16054 CATGTATCATCTCCACAGGTGACACAACCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* *
16084 CATGTATCGTCTGCAC-GTGTGCCACAACCT
1 CATGTATCATCTCCACAG-GTGCCACAACCT
* * *
16114 CGTGCATCATCTCCACATGTGCCACAACCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* * *
16144 CATGTATCATCTACACATGTGCCACAATCT
1 CATGTATCATCTCCACAGGTGCCACAACCT
* * *
16174 CATGTATCATCTTCACATGTGTCACAACC
1 CATGTATCATCTCCACAGGTGCCACAACC
16203 ATCTCCTCAT
Statistics
Matches: 212, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
29 1 0.00
30 211 1.00
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.26
Consensus pattern (30 bp):
CATGTATCATCTCCACAGGTGCCACAACCT
Found at i:26373 original size:25 final size:25
Alignment explanation
Indices: 26337--26384 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
26327 AGGGTTTTAA
26337 GTGAAATACTAACATTTGGGTAGTG
1 GTGAAATACTAACATTTGGGTAGTG
* *
26362 GTGAAATGCTAACGTTTGGGTAG
1 GTGAAATACTAACATTTGGGTAG
26385 CGGGGTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.31
Consensus pattern (25 bp):
GTGAAATACTAACATTTGGGTAGTG
Found at i:26921 original size:67 final size:67
Alignment explanation
Indices: 26808--26942 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
26798 ATCCGGCAGT
* *
26808 AATTAGGATACCCATGGTGCAGCAAGTTGCCGTATCCGCAGGTAATTAGGCACATGTGGAATCCG
1 AATTAAGATACCCATGGTGCAGCAAGTTGCCGTATCCGCAGATAATTAGGCACATGTGGAATCCG
26873 TG
66 TG
26875 AATTAAGATACCCATGGTGCAGCAAGTTGCCGTATCCGCAGATAATTAGGCACATGTGGAATCCG
1 AATTAAGATACCCATGGTGCAGCAAGTTGCCGTATCCGCAGATAATTAGGCACATGTGGAATCCG
26940 TG
66 TG
26942 A
1 A
26943 TTCCACAATC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (67 bp):
AATTAAGATACCCATGGTGCAGCAAGTTGCCGTATCCGCAGATAATTAGGCACATGTGGAATCCG
TG
Found at i:40150 original size:27 final size:28
Alignment explanation
Indices: 40120--40188 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
40110 GTTTCTGGTT
*
40120 GAGAAGAGCTTTC-TGCTGGTTCTGGAA
1 GAGAAGAGCTTTCAAGCTGGTTCTGGAA
*
40147 GAGAAGAGAAGC-TTCAAGTTGGTTCTGGAA
1 GAG-A-AG-AGCTTTCAAGCTGGTTCTGGAA
40177 GAGAAGAGCTTT
1 GAGAAGAGCTTT
40189 AAGAGCATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 6 0.17
28 5 0.14
29 6 0.17
30 18 0.51
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (28 bp):
GAGAAGAGCTTTCAAGCTGGTTCTGGAA
Found at i:40328 original size:46 final size:45
Alignment explanation
Indices: 40259--40345 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
40249 ATTATGCATA
40259 TCGGAAAAAAGGACCGCCAGAAAAGCTAGTGAAGGTAGAACTAGG
1 TCGGAAAAAAGGACCGCCAGAAAAGCTAGTGAAGGTAGAACTAGG
** * *
40304 TCGGAAAAAAAGGACCGCTGGAAAAGCTGGTGAAGGTGGAAC
1 TCGG-AAAAAAGGACCGCCAGAAAAGCTAGTGAAGGTAGAAC
40346 CAGGAAAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.11
46 33 0.89
ACGTcount: A:0.40, C:0.15, G:0.33, T:0.11
Consensus pattern (45 bp):
TCGGAAAAAAGGACCGCCAGAAAAGCTAGTGAAGGTAGAACTAGG
Found at i:42067 original size:31 final size:31
Alignment explanation
Indices: 42025--42089 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
42015 AACTAAACTA
* *
42025 ACTCAAACATCCAAGATTTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAAATCTGGAG
*
42056 ACTCAAGCATCCAAGATCTAAAAATCTGGAG
1 ACTCAAACATCCAAGATCTAAAAATCTGGAG
42087 ACT
1 ACT
42090 GATAACCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAAATCTGGAG
Found at i:47580 original size:25 final size:25
Alignment explanation
Indices: 47533--47590 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
47523 CATATTTATT
47533 TTTTAAAATAAAATAATAATTAAAG
1 TTTTAAAATAAAATAATAATTAAAG
47558 TTTTAATAA-AAAATAA-AATTTAAA-
1 TTTTAA-AATAAAATAATAA-TTAAAG
*
47582 TATTAAAAT
1 TTTTAAAAT
47591 TTATATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 7 0.24
25 18 0.62
26 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TTTTAAAATAAAATAATAATTAAAG
Found at i:47732 original size:29 final size:30
Alignment explanation
Indices: 47674--47734 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
47664 GTTCTAATTA
* *
47674 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
47704 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
47733 AT
1 AT
47735 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:48919 original size:13 final size:13
Alignment explanation
Indices: 48901--48928 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48891 ATTAGTTTAA
48901 AATTTATTAATGT
1 AATTTATTAATGT
48914 AATTTATTAATGT
1 AATTTATTAATGT
48927 AA
1 AA
48929 CTATTGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
AATTTATTAATGT
Found at i:51705 original size:29 final size:29
Alignment explanation
Indices: 51661--51735 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
51651 GGACGCTGAG
* * *
51661 AGTTTAGGGGGTAAAATGTTTAAAATTAA
1 AGTTTAGGGGGCAAAACGTTCAAAATTAA
51690 AGTTTAGGGGGCAAAACGTTCAAAATTAA
1 AGTTTAGGGGGCAAAACGTTCAAAATTAA
* *
51719 AATTTAGGGGACAAAAC
1 AGTTTAGGGGGCAAAAC
51736 ATCTAAACTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.27
Consensus pattern (29 bp):
AGTTTAGGGGGCAAAACGTTCAAAATTAA
Found at i:70053 original size:30 final size:30
Alignment explanation
Indices: 70017--70073 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
70007 AGATTTCAAT
70017 TGTAATTGTCGGGGAAAAGGTTCGTTGAGA
1 TGTAATTGTCGGGGAAAAGGTTCGTTGAGA
* * *
70047 TGTAATTGTTGGGGAAAGGGTTTGTTG
1 TGTAATTGTCGGGGAAAAGGTTCGTTG
70074 GCTCATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.23, C:0.04, G:0.39, T:0.35
Consensus pattern (30 bp):
TGTAATTGTCGGGGAAAAGGTTCGTTGAGA
Found at i:71403 original size:18 final size:17
Alignment explanation
Indices: 71375--71415 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
71365 CTAATTAATA
71375 ATTTAATATTAAATTTT
1 ATTTAATATTAAATTTT
*
71392 ATTTATATATTATATTTT
1 ATTTA-ATATTAAATTTT
*
71410 ACTTAA
1 ATTTAA
71416 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAATATTAAATTTT
Done.