Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013175.1 Corchorus capsularis cultivar CVL-1 contig13196, 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: 40070
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:14105 original size:3 final size:3
Alignment explanation
Indices: 14090--14120 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
14080 AGCTAAGATT
*
14090 CTG CTG GTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
14121 GCACTTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:14733 original size:2 final size:2
Alignment explanation
Indices: 14726--14751 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14716 ATTTCATGTT
14726 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
14752 AAGTTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15529 original size:3 final size:3
Alignment explanation
Indices: 15521--15573 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
15511 GTACTAAAAG
15521 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
15569 GAA GA
1 GAA GA
15574 GACAAAGCCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19747 original size:22 final size:22
Alignment explanation
Indices: 19719--19857 Score: 133
Period size: 22 Copynumber: 6.3 Consensus size: 22
19709 TTTTTTTATA
*
19719 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTACCCTATG
*
19741 AAATTTTGATAA-TCACGCTATG
1 AAATTTTGATAACT-ACCCTATG
*
19763 AAATTTTGATAATTA-CCTATG
1 AAATTTTGATAACTACCCTATG
* *
19784 AAATTATGATAAACT-CCATATG
1 AAATTTTGAT-AACTACCCTATG
*
19806 AAATTTTGATAACCTA-ACTATG
1 AAATTTTGATAA-CTACCCTATG
* * *
19828 AAATTTTAATAAACAATCCTATG
1 AAATTTTGAT-AACTACCCTATG
19851 AAATTTT
1 AAATTTT
19858 TTAACCTTCC
Statistics
Matches: 97, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
21 17 0.18
22 65 0.67
23 15 0.15
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATG
Found at i:19794 original size:43 final size:43
Alignment explanation
Indices: 19719--19857 Score: 147
Period size: 43 Copynumber: 3.2 Consensus size: 43
19709 TTTTTTTATA
* * *
19719 AAATTTTGATAACTACCCTATTAAATTTTGATAATCACGC-TATG
1 AAATTTTGATAACTA-CCTATGAAATTATGATAAACAC-CATATG
* *
19763 AAATTTTGATAATTACCTATGAAATTATGATAAACTCCATATG
1 AAATTTTGATAACTACCTATGAAATTATGATAAACACCATATG
* * *
19806 AAATTTTGATAACCTAACTATGAAATTTTAATAAACAATCC-TATG
1 AAATTTTGATAA-CTACCTATGAAATTATGATAAAC-A-CCATATG
19851 AAATTTT
1 AAATTTT
19858 TTAACCTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.01
43 34 0.42
44 33 0.41
45 11 0.14
46 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (43 bp):
AAATTTTGATAACTACCTATGAAATTATGATAAACACCATATG
Found at i:19841 original size:44 final size:42
Alignment explanation
Indices: 19719--19888 Score: 162
Period size: 44 Copynumber: 3.9 Consensus size: 42
19709 TTTTTTTATA
* * *
19719 AAATTTTGATAACTACCCTATTAAATTTTGATAATCACGCTATG
1 AAATTTTGATAACTA-CCTATGAAATTTTGATAAACTC-CTATG
* *
19763 AAATTTTGATAATTACCTATGAAATTATGATAAACTCCATATG
1 AAATTTTGATAACTACCTATGAAATTTTGATAAACTCC-TATG
* *
19806 AAATTTTGATAACCTAACTATGAAATTTTAATAAACAATCCTATG
1 AAATTTTGATAA-CTACCTATGAAATTTTGATAAAC--TCCTATG
* * * * *
19851 AAATTTT-TTAACCTTCCTATGAGATTTTGTTAATCTCC
1 AAATTTTGATAA-CTACCTATGAAATTTTGATAAACTCC
19889 CTATAATTTT
Statistics
Matches: 106, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 4 0.04
43 34 0.32
44 54 0.51
45 11 0.10
46 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (42 bp):
AAATTTTGATAACTACCTATGAAATTTTGATAAACTCCTATG
Found at i:19870 original size:21 final size:22
Alignment explanation
Indices: 19802--19892 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
19792 ATAAACTCCA
**
19802 TATGAAATTTTGA-TAACCTAAC
1 TATGAAATTTT-ATTAACCTTCC
* **
19824 TATGAAATTTTAATAAACAATCC
1 TATGAAATTTT-ATTAACCTTCC
19847 TATGAAATTTT-TTAACCTTCC
1 TATGAAATTTTATTAACCTTCC
* * * *
19868 TATGAGATTTTGTTAATCTCCC
1 TATGAAATTTTATTAACCTTCC
19890 TAT
1 TAT
19893 AATTTTTTGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 17 0.31
22 23 0.42
23 15 0.27
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTATTAACCTTCC
Found at i:19891 original size:22 final size:21
Alignment explanation
Indices: 19778--19900 Score: 63
Period size: 22 Copynumber: 5.7 Consensus size: 21
19768 TTGATAATTA
** *
19778 CCTATGAAATTATGATAAACTC
1 CCTATGAAATT-TTTTAACCTC
* * *
19800 CATATGAAATTTTGATAACCTA
1 CCTATGAAATTTT-TTAACCTC
* * *
19822 ACTATGAAATTTTAATAAACAAT-
1 CCTATGAAATTTT--TTAAC-CTC
*
19845 CCTATGAAATTTTTTAACCTT
1 CCTATGAAATTTTTTAACCTC
* *
19866 CCTATGAGATTTTGTTAATCTC
1 CCTATGAAATTTT-TTAACCTC
19888 CCTAT--AATTTTTT
1 CCTATGAAATTTTTT
19901 GATATTATAG
Statistics
Matches: 79, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.03
20 6 0.08
21 17 0.22
22 38 0.48
23 15 0.19
24 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.41
Consensus pattern (21 bp):
CCTATGAAATTTTTTAACCTC
Found at i:23554 original size:55 final size:55
Alignment explanation
Indices: 23490--23652 Score: 247
Period size: 55 Copynumber: 3.0 Consensus size: 55
23480 CAGGACTTTC
* ** *
23490 TTCAAGGAACACTGGGAGATCAC-GAAGATTTCGGGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCACAG-AGATCTCAAGCGAGCGTCAGCATTGAAGCT
23545 TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGCGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGCGTCAGCATTGAAGCT
* * *
23600 TTCAAGGAAAACTGGAAAATCACAGAGATCTCAAGCGAGCGTCAGCATTGAAG
1 TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGCGTCAGCATTGAAG
23653 ATTGATAGGA
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 99 0.99
56 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.19
Consensus pattern (55 bp):
TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGCGTCAGCATTGAAGCT
Found at i:36974 original size:55 final size:55
Alignment explanation
Indices: 36881--37043 Score: 247
Period size: 55 Copynumber: 3.0 Consensus size: 55
36871 CAGGACTTTC
* **
36881 TTCAAGGAACACTGGGAGATCAC-GAAGATTTCGGGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCACAG-AGATCTCAAGCGAGTGTCAGCATTGAAGCT
36936 TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
* * * *
36991 TTCAAGGAATACTAGGAAATCACAGAGATCTCAAGCGAGCGTCAGCATTGAAG
1 TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGTGTCAGCATTGAAG
37044 ATTGATAGGA
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 99 0.99
56 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (55 bp):
TTCAAGGAACACTGGGAGATCACAGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
Found at i:37443 original size:17 final size:17
Alignment explanation
Indices: 37416--37465 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
37406 CCCTCCTCAT
37416 GGTACCTAGGTAACATGA
1 GGTA-CTAGGTAACATGA
*
37434 GGTACTAGGTAGCATGA
1 GGTACTAGGTAACATGA
* *
37451 GGTGCTAGATAACAT
1 GGTACTAGGTAACAT
37466 CTGCTGTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (17 bp):
GGTACTAGGTAACATGA
Found at i:38112 original size:156 final size:155
Alignment explanation
Indices: 37812--38104 Score: 353
Period size: 156 Copynumber: 1.9 Consensus size: 155
37802 TCACCCCAAA
* *
37812 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGATGAAATTTTTCC
1 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGATG-AATTTTTCC
* * * * *
37877 AAGGGACTTATATTATCCACATAAGACTATGGAAAAAATTCTAAGTAAAATCGAGCTCCCCTTGA
65 AAGAGACTTAGATTATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTAGA
* *
37942 TGGTGAACTAGGTTTCTCTCCCTGAG
130 TAGAGAACTAGGTTTCTCTCCCTGAG
* *
37968 TTGTCCTTAGATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAGGCTG-A-TTTTCC
1 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGA-GATGAATTTTTCC
* * * *
38030 ACCAGTAGACTTAGATTATCCCCATGAAG-CTGTGGGAAAAATTCTAAGTAAAACCGAACT-CTC
65 A--AG-AGACTTAGATTATCCACAT-AAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCC
38093 TAGCATAGAGAA
126 TAG-ATAGAGAA
38105 GTTGGTTTGA
Statistics
Matches: 116, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
153 7 0.06
154 1 0.01
155 10 0.09
156 95 0.82
157 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (155 bp):
TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGATGAATTTTTCCA
AGAGACTTAGATTATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTAGAT
AGAGAACTAGGTTTCTCTCCCTGAG
Done.