Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023299.1 Corchorus olitorius cultivar O-4 contig23332, 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: 37311
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37 AATTTGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1601 original size:2 final size:2
Alignment explanation
Indices: 1590--1630 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1580 TTTTCTTCCA
1590 AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1629 AT
1 AT
1631 GAATCTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1608 original size:11 final size:11
Alignment explanation
Indices: 1589--1629 Score: 54
Period size: 9 Copynumber: 4.1 Consensus size: 11
1579 ATTTTCTTCC
1589 AATAT-TATAT
1 AATATATATAT
1599 -ATATA-ATAT
1 AATATATATAT
1608 -ATATATATAT
1 AATATATATAT
1618 AATATATATAT
1 AATATATATAT
1629 A
1 A
1630 TGAATCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.46
10 4 0.14
11 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATATATATAT
Found at i:1614 original size:15 final size:15
Alignment explanation
Indices: 1589--1630 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1579 ATTTTCTTCC
1589 AATAT-TATATATAT
1 AATATATATATATAT
1603 AATATATATATATAT
1 AATATATATATATAT
1618 AATATATATATAT
1 AATATATATATAT
1631 GAATCTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:1641 original size:15 final size:14
Alignment explanation
Indices: 1589--1642 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
1579 ATTTTCTTCC
*
1589 AATATTATATATAT
1 AATATAATATATAT
1603 AATATATATATATAT
1 AATATA-ATATATAT
1618 AATAT-ATATATAT
1 AATATAATATATAT
*
1631 GAATCTAATATA
1 -AATATAATATA
1643 ATATTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 8 0.23
14 9 0.26
15 18 0.51
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
AATATAATATATAT
Found at i:1642 original size:13 final size:13
Alignment explanation
Indices: 1590--1630 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1580 TTTTCTTCCA
*
1590 ATATTATATATAT
1 ATATAATATATAT
1603 A-AT-ATATATAT
1 ATATAATATATAT
1614 ATATAATATATAT
1 ATATAATATATAT
1627 ATAT
1 ATAT
1631 GAATCTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.35
12 4 0.15
13 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:1642 original size:19 final size:17
Alignment explanation
Indices: 1590--1630 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1580 TTTTCTTCCA
1590 ATAT-TATATATAT-A-
1 ATATATATATATATAAT
1604 ATATATATATATATAAT
1 ATATATATATATATAAT
1621 ATATATATAT
1 ATATATATAT
1631 GAATCTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 1 0.04
17 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATATATATAAT
Found at i:1760 original size:44 final size:44
Alignment explanation
Indices: 1710--1793 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
1700 AGAAAATACT
**
1710 CCTACCACAAAATAATCCTAAAATGATCGAGTTGATTTCAATCC
1 CCTACCACAAAATAATCCTAAAATGATAAAGTTGATTTCAATCC
*
1754 CCTACCACAAAATAATCCTGAAATGATAAAGTTGATTTCA
1 CCTACCACAAAATAATCCTAAAATGATAAAGTTGATTTCA
1794 GTCTCCTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (44 bp):
CCTACCACAAAATAATCCTAAAATGATAAAGTTGATTTCAATCC
Found at i:2478 original size:69 final size:69
Alignment explanation
Indices: 2367--2504 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
2357 ATCCTATAGT
* * *
2367 AAATTTCAAATAAAATGTAAACAATATGCTGCAATAATGTAATAATAGGTAAGCACAATGCTTAG
1 AAATTTCAAATAAAATCTAAACAATATGCTGCAATAATGTAATAATAAGTAAGCACAATGCTCAG
2432 GACA
66 GACA
*
2436 AAATTTCAAATAAAATCTAATA-AATATGCTGCAATAATGTAATAGTAAGTAAGCACAATGCTCA
1 AAATTTCAAATAAAATCTAA-ACAATATGCTGCAATAATGTAATAATAAGTAAGCACAATGCTCA
2500 GGACA
65 GGACA
2505 GAAAACTTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 63 0.98
70 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (69 bp):
AAATTTCAAATAAAATCTAAACAATATGCTGCAATAATGTAATAATAAGTAAGCACAATGCTCAG
GACA
Found at i:4125 original size:15 final size:15
Alignment explanation
Indices: 4105--4145 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4095 CACCAAGTTC
4105 CTCTTCTTCAT-CGAT
1 CTCTTCTTCATAC-AT
4120 CTCTTCTTC-TACAT
1 CTCTTCTTCATACAT
4134 CGTCTTCTTCAT
1 C-TCTTCTTCAT
4146 TTTGGAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 18 0.78
16 1 0.04
ACGTcount: A:0.12, C:0.34, G:0.05, T:0.49
Consensus pattern (15 bp):
CTCTTCTTCATACAT
Found at i:9009 original size:21 final size:21
Alignment explanation
Indices: 8983--9026 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
8973 GTGGATCCCA
8983 TCATGATTCATGGCAGTTCCT
1 TCATGATTCATGGCAGTTCCT
9004 TCATGATTCATGGCAGTTCCT
1 TCATGATTCATGGCAGTTCCT
9025 TC
1 TC
9027 TTTTCTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (21 bp):
TCATGATTCATGGCAGTTCCT
Found at i:10263 original size:21 final size:21
Alignment explanation
Indices: 10239--10305 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
10229 AATTCTCTGT
10239 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
10260 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
10281 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
10302 AAAT
1 AAAT
10306 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:10285 original size:42 final size:42
Alignment explanation
Indices: 10226--10306 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
10216 GCTAAGTCTT
10226 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
10268 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
10307 CTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:10444 original size:56 final size:57
Alignment explanation
Indices: 10374--10485 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
10364 TATTTTGTAG
*
10374 AATAATTAAGTAGAGATA-GGGGGATAGGATTTATTATAACATTTATTGTGTGAAAA
1 AATAATTAAGTAGAGATAGGGGGGATAGGATTTATCATAACATTTATTGTGTGAAAA
*
10430 AATAATTAAGTAGAGATAGGGGGGATATGATTTATCATAACATTTATTGTGTGAAA
1 AATAATTAAGTAGAGATAGGGGGGATAGGATTTATCATAACATTTATTGTGTGAAA
10486 GGAAACAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 18 0.34
57 35 0.66
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (57 bp):
AATAATTAAGTAGAGATAGGGGGGATAGGATTTATCATAACATTTATTGTGTGAAAA
Found at i:17041 original size:18 final size:18
Alignment explanation
Indices: 17018--17053 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
17008 TAAATAAATC
17018 ATTTCTT-TGACTTATTAT
1 ATTTCTTGT-ACTTATTAT
17036 ATTTCTTGTACTTATTAT
1 ATTTCTTGTACTTATTAT
17054 GTTTTGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (18 bp):
ATTTCTTGTACTTATTAT
Found at i:19558 original size:18 final size:18
Alignment explanation
Indices: 19521--19565 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 18
19511 CACCTGCGGA
19521 AATAATAAATGAATACATT
1 AATAAT-AATGAATACATT
19540 AATAATAAT-AATAACATT
1 AATAATAATGAAT-ACATT
19558 AATAATAA
1 AATAATAA
19566 ATACTACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.12
18 16 0.64
19 6 0.24
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
AATAATAATGAATACATT
Found at i:21047 original size:29 final size:29
Alignment explanation
Indices: 21005--21075 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
20995 GTTATTCCAT
21005 GTTCTTGAAGATTTGAAATGTTCTTGAGC
1 GTTCTTGAAGATTTGAAATGTTCTTGAGC
21034 GTTCTTGAAGATTTGAAATGTTCTTGAGC
1 GTTCTTGAAGATTTGAAATGTTCTTGAGC
21063 GTTCTTGAAGATT
1 GTTCTTGAAGATT
21076 GCAGAGGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (29 bp):
GTTCTTGAAGATTTGAAATGTTCTTGAGC
Found at i:23663 original size:22 final size:22
Alignment explanation
Indices: 23622--23663 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
23612 GACAAATCTG
*
23622 TAACCTAAATGACCCGAGAAGT
1 TAACCTAAATGACCCAAGAAGT
* *
23644 TAACCTGAATGACTCAAGAA
1 TAACCTAAATGACCCAAGAA
23664 TATAATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
TAACCTAAATGACCCAAGAAGT
Found at i:25029 original size:129 final size:129
Alignment explanation
Indices: 24864--25125 Score: 377
Period size: 129 Copynumber: 2.0 Consensus size: 129
24854 GTCATTTAAG
* *
24864 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATA
1 AAATATATTTAAAAAATTCTAATATA-CTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATA
* * * * *
24929 AAATAGGTATAAAGATATTAGATTTTA-TACAATAGAAATAGAGTTTTTAGTTGAGTAAAATTAT
65 AAAAAGGTATAAAGATATTAGATTTAATTA-AATAAAAATAGAGTTTTTAGTTAAGTAAAACTAT
24993 GA
129 -A
24995 AAATATA-TTAAAAAATTCTAATATA-TAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATA
1 AAATATATTTAAAAAATTCTAATATACTAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAATA
* * *
25058 AAAAAGTTTTAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATA
65 AAAAAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATA
25123 AAA
1 AAA
25126 GTTTAAACAA
Statistics
Matches: 119, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
128 8 0.07
129 85 0.71
130 19 0.16
131 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (129 bp):
AAATATATTTAAAAAATTCTAATATACTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAA
AAAAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATA
Found at i:31372 original size:10 final size:10
Alignment explanation
Indices: 31359--31385 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31349 AAAAGGATTA
31359 AAAAAAATTC
1 AAAAAAATTC
31369 AAAAAAATTC
1 AAAAAAATTC
31379 AAAAAAA
1 AAAAAAA
31386 AATTTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Done.