Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008587.1 Corchorus capsularis cultivar CVL-1 contig08608, 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: 29467
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1842 original size:30 final size:30
Alignment explanation
Indices: 1767--1842 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
1757 TGTCAACAAA
* **
1767 ATTTTGAAAGTTTAGGGGTAAAATATCAAG
1 ATTTTAAAAGTTTAGGGACAAAATATCAAG
*
1797 ATTTTAAAA-TTTAGGGACAAAATTTCAAG
1 ATTTTAAAAGTTTAGGGACAAAATATCAAG
1826 ATTTTAAAAGTTTAGGG
1 ATTTTAAAAGTTTAGGG
1843 GGCAAAATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 26 0.63
30 15 0.37
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.36
Consensus pattern (30 bp):
ATTTTAAAAGTTTAGGGACAAAATATCAAG
Found at i:2504 original size:11 final size:10
Alignment explanation
Indices: 2476--2526 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
2466 GGTTCAAATG
2476 GGGGAGGGGT
1 GGGGAGGGGT
2486 GGGGAGGGGT
1 GGGGAGGGGT
*
2496 GGGTTAGGGAG-
1 GGG-GAGGG-GT
*
2507 GGGGAGGAGT
1 GGGGAGGGGT
*
2517 TGGGAGGGGT
1 GGGGAGGGGT
2527 TTTAGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 1 0.03
10 24 0.73
11 7 0.21
12 1 0.03
ACGTcount: A:0.14, C:0.00, G:0.73, T:0.14
Consensus pattern (10 bp):
GGGGAGGGGT
Found at i:2510 original size:16 final size:16
Alignment explanation
Indices: 2475--2525 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2465 TGGTTCAAAT
* *
2475 GGGGGAGGGGTGGGGA
1 GGGGGAGGAGTTGGGA
*
2491 -GGGGTGG-GTTAGGGA
1 GGGGGAGGAGTT-GGGA
2506 GGGGGAGGAGTTGGGA
1 GGGGGAGGAGTTGGGA
2522 GGGG
1 GGGG
2526 TTTTAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 14 0.48
17 3 0.10
ACGTcount: A:0.14, C:0.00, G:0.75, T:0.12
Consensus pattern (16 bp):
GGGGGAGGAGTTGGGA
Found at i:3837 original size:28 final size:28
Alignment explanation
Indices: 3786--3839 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3776 TTAGAAATTC
* ** *
3786 AGTAAACCTCATAATTTTTTTTGAAGAA
1 AGTAAACCACATAATTAATATTGAAGAA
3814 AGTAAACCACATAATTAATATTGAAG
1 AGTAAACCACATAATTAATATTGAAG
3840 GAAAATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (28 bp):
AGTAAACCACATAATTAATATTGAAGAA
Found at i:4517 original size:11 final size:11
Alignment explanation
Indices: 4497--4527 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4487 TCTAAAGTTA
*
4497 TATATAATTAT
1 TATATTATTAT
4508 TATATTATTAT
1 TATATTATTAT
4519 TATATTATT
1 TATATTATT
4528 TGTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTATTAT
Found at i:7246 original size:2 final size:2
Alignment explanation
Indices: 7235--7306 Score: 60
Period size: 2 Copynumber: 36.5 Consensus size: 2
7225 ATATGTAGTG
* * * *
7235 TA TA TA -A TA TA TA TA TA TA TA TA TA TA AA CTA AA TC T- TCA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T-A TA
*
7277 TA TA T- TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7307 TCAATTAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
1 3 0.05
2 51 0.91
3 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7910 original size:45 final size:45
Alignment explanation
Indices: 7859--7948 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
7849 AATTACTTCT
7859 CCAGCTCATCATTAATCCGGGGTAGAGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGAGATCTTTTAGTAATTCCAC
* *
7904 CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGAGATCTTTTAGTAATTCCAC
7949 TACTCTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGAGATCTTTTAGTAATTCCAC
Found at i:10597 original size:30 final size:30
Alignment explanation
Indices: 10563--10624 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
10553 TTCCAAAGAA
**
10563 AAAGATTTTCACAAGCAGTTTAGATTTCAT
1 AAAGATTTTCACAAGCAGTCCAGATTTCAT
*
10593 AAAGATTTTCACAAGTAGTCCAGATTTCAT
1 AAAGATTTTCACAAGCAGTCCAGATTTCAT
10623 AA
1 AA
10625 GTCATCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (30 bp):
AAAGATTTTCACAAGCAGTCCAGATTTCAT
Found at i:11121 original size:2 final size:2
Alignment explanation
Indices: 11114--11141 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11104 CTTGCACCTT
11114 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
11142 AAAAGTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16466 original size:76 final size:76
Alignment explanation
Indices: 16324--16466 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
16314 CTCGACTCCT
* * *
16324 CCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAAGACCCAGTTGGGTAGTG
1 CCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAAGACCCAGTAGGCTAGTG
16389 TCCCAACTCTA
66 TCCCAACTCTA
* * * * **
16400 CCTGGGTGCCCACATGGTTTGTC-TGAGGACCCATGTGATTTGCTTGATTACCCAGGTAGGCT-G
1 CCTGGGCGCCCACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAAGACCCA-GTAGGCTAG
16463 TGTC
64 TGTC
16467 ATGACTCGGC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
76 47 0.84
77 9 0.16
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (76 bp):
CCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAAGACCCAGTAGGCTAGTG
TCCCAACTCTA
Found at i:16964 original size:35 final size:35
Alignment explanation
Indices: 16856--16966 Score: 114
Period size: 35 Copynumber: 3.1 Consensus size: 35
16846 TTTTGGTAGG
*
16856 AATTGTGGTTTTGCTTGCTGTTAGTACATAGGTTTT
1 AATTGTGGTTTTGCTTGCTGCTAGTACATAGG-TTT
* *** *
16892 AATATGTATGTTTAATTTGCTGCTCGTACATAGGTTT
1 AAT-TGT-GGTTTTGCTTGCTGCTAGTACATAGGTTT
* * *
16929 AATTGTGGTTTTGCTTGCTGCTAGAAAATATGTTT
1 AATTGTGGTTTTGCTTGCTGCTAGTACATAGGTTT
16964 AAT
1 AAT
16967 ATTTTGGTAG
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
35 24 0.41
36 6 0.10
37 9 0.15
38 20 0.34
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.47
Consensus pattern (35 bp):
AATTGTGGTTTTGCTTGCTGCTAGTACATAGGTTT
Found at i:17050 original size:23 final size:23
Alignment explanation
Indices: 17019--17062 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17009 GTGGCAATTC
*
17019 ATGTATGAGTTTTGCGTGCTAGT
1 ATGTATGAGTTTTGCCTGCTAGT
*
17042 ATGTTTGAGTTTTGCCTGCTA
1 ATGTATGAGTTTTGCCTGCTA
17063 CTTGATCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.45
Consensus pattern (23 bp):
ATGTATGAGTTTTGCCTGCTAGT
Found at i:22015 original size:18 final size:19
Alignment explanation
Indices: 21992--22029 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
21982 TTTTACTAAG
21992 AAAATAATTATTATT-TTC
1 AAAATAATTATTATTATTC
*
22010 AAAATAATTTTTATTATTC
1 AAAATAATTATTATTATTC
22029 A
1 A
22030 TATATGCCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATAATTATTATTATTC
Found at i:25011 original size:15 final size:16
Alignment explanation
Indices: 24991--25024 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
24981 GATTGTTTTC
*
24991 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
25006 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
25022 TTA
1 TTA
25025 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:28283 original size:6 final size:6
Alignment explanation
Indices: 28274--28312 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
28264 AAAGCAAAGC
28274 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
28313 GCAGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:28324 original size:12 final size:13
Alignment explanation
Indices: 28309--28353 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
28299 AATCTAAATC
28309 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
28321 TAAAGCAAATTAA
1 TAAAGCAGATTAA
28334 TAAAGCAGATTAA
1 TAAAGCAGATTAA
28347 TAAAGCA
1 TAAAGCA
28354 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:28360 original size:25 final size:25
Alignment explanation
Indices: 28309--28361 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
28299 AATCTAAATC
*
28309 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
28334 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
28359 TAA
1 TAA
28362 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.