Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009790.1 Corchorus capsularis cultivar CVL-1 contig09811, 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: 29628
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1814 original size:18 final size:18
Alignment explanation
Indices: 1767--1816 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
1757 TGCTCCAACG
1767 GAAAGAAGAAAAAATGAAA
1 GAAA-AAGAAAAAATGAAA
* *
1786 GAAAAATAAAAAA-GGAA
1 GAAAAAGAAAAAATGAAA
1803 GAAAATAGAAAAAA
1 GAAAA-AGAAAAAA
1817 AAGGAGGTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.30
18 15 0.56
19 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (18 bp):
GAAAAAGAAAAAATGAAA
Found at i:3665 original size:10 final size:9
Alignment explanation
Indices: 3621--3667 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
3611 AATTTGAAGG
3621 AAAATGAAA
1 AAAATGAAA
* **
3630 AAAAAGAGG
1 AAAATGAAA
3639 AAAA-GAAA
1 AAAATGAAA
3647 AAAATGAAA
1 AAAATGAAA
3656 AAAATGGAAA
1 AAAAT-GAAA
3666 AA
1 AA
3668 CCAGAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
8 6 0.19
9 19 0.61
10 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (9 bp):
AAAATGAAA
Found at i:3675 original size:25 final size:26
Alignment explanation
Indices: 3620--3681 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
3610 CAATTTGAAG
* *
3620 GAAAATGAAAAAAAAGAGGAAAAGAA
1 GAAAATGAAAAAAAAGAGAAAAACAA
* * *
3646 AAAAATGAAAAAAATG-GAAAAACCA
1 GAAAATGAAAAAAAAGAGAAAAACAA
*
3671 GAAAATTAAAA
1 GAAAATGAAAA
3682 GATATAATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (26 bp):
GAAAATGAAAAAAAAGAGAAAAACAA
Found at i:11270 original size:23 final size:23
Alignment explanation
Indices: 11227--11270 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
11217 ATGCTTGCAA
*
11227 GGCACTCATAACTCTCCTGTGTG
1 GGCACTCATAACTCTCATGTGTG
*
11250 GGCACTCTCTAACTCT-ATGTG
1 GGCACTC-ATAACTCTCATGTG
11271 GTCCGTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.32
Consensus pattern (23 bp):
GGCACTCATAACTCTCATGTGTG
Found at i:14041 original size:17 final size:17
Alignment explanation
Indices: 14021--14060 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
14011 GATGCCATCC
14021 AGTACCTCATGCTACCT
1 AGTACCTCATGCTACCT
14038 AGTACCTCATGCTACCT
1 AGTACCTCATGCTACCT
*
14055 GGTACC
1 AGTACC
14061 ATGAGAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.28
Consensus pattern (17 bp):
AGTACCTCATGCTACCT
Found at i:17932 original size:19 final size:18
Alignment explanation
Indices: 17908--17943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17898 TTTAAAGGTG
17908 AAAAAAAAAGTAGTAAAAC
1 AAAAAAAAAGT-GTAAAAC
*
17927 AAAAAAAGAGTGTAAAA
1 AAAAAAAAAGTGTAAAA
17944 TCTTATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.03, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAGTGTAAAAC
Found at i:18957 original size:24 final size:23
Alignment explanation
Indices: 18913--18957 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
18903 CTTAGCTTTA
*
18913 TTTTTTTTTATCTCTCCTATCTC
1 TTTTTTTTTATCTCTCATATCTC
* *
18936 TTTTTCTTTTATTTCTTATATC
1 TTTTT-TTTTATCTCTCATATC
18958 ATGTTTATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTTTTTATCTCTCATATCTC
Found at i:28531 original size:30 final size:31
Alignment explanation
Indices: 28471--28531 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
28461 TTTATGTTTT
*
28471 CAATTGTACCCTTATTTTTAAAATATATTTC
1 CAATTGTACCCTTATTTTTAAAACATATTTC
28502 CAATTGTA-CCTT-TTTTTAAAAACATATTTC
1 CAATTGTACCCTTATTTTT-AAAACATATTTC
28532 TAAATTGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 5 0.18
30 15 0.54
31 8 0.29
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (31 bp):
CAATTGTACCCTTATTTTTAAAACATATTTC
Found at i:28538 original size:31 final size:31
Alignment explanation
Indices: 28468--28538 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
28458 AACTTTATGT
*
28468 TTTC-AATTGTACCCTTATTTTTAAAATATA
1 TTTCAAATTGTACCCTTATTTTTAAAACATA
*
28498 TTTCCAATTGTA-CCTT-TTTTTAAAAACATA
1 TTTCAAATTGTACCCTTATTTTT-AAAACATA
28528 TTTCTAAATTG
1 TTTC-AAATTG
28539 CCATTACTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 5 0.14
30 19 0.53
31 12 0.33
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.49
Consensus pattern (31 bp):
TTTCAAATTGTACCCTTATTTTTAAAACATA
Found at i:29165 original size:22 final size:22
Alignment explanation
Indices: 28965--29178 Score: 88
Period size: 22 Copynumber: 9.8 Consensus size: 22
28955 ACTTTGCAGA
* *
28965 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTATGG
* * * * *
28987 CTATCAAAATTTTATAATGTGA
1 TTATCAAAATTTCATAGTATGG
* * * *
29009 TTATCCAAATTTCAAAATGTGG
1 TTATCAAAATTTCATAGTATGG
* *
29031 TTA-CAAAAATTTCATTG-AAGG
1 TTATC-AAAATTTCATAGTATGG
*
29052 TAATCAAAA-TTCGAT-GT-TGTG
1 TTATCAAAATTTC-ATAGTATG-G
* *
29073 CTTATCAAAATTTAATAGTGA-GA
1 -TTATCAAAATTTCATAGT-ATGG
* * *
29096 TTAACAAAA-TTCTATAGGGA-AG
1 TTATCAAAATTTC-ATA-GTATGG
* *
29118 TTATCAACATTTC-TAGGGA-GG
1 TTATCAAAATTTCATA-GTATGG
29139 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGTATGG
*
29161 TTATCCAAATTTCATAGT
1 TTATCAAAATTTCATAGT
29179 GTACAAAATC
Statistics
Matches: 147, Mismatches: 30, Indels: 30
0.71 0.14 0.14
Matches are distributed among these distances:
20 5 0.03
21 35 0.24
22 98 0.67
23 8 0.05
24 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTATGG
Found at i:29297 original size:22 final size:22
Alignment explanation
Indices: 29272--29360 Score: 101
Period size: 22 Copynumber: 4.0 Consensus size: 22
29262 TCACTATTTT
29272 ATAGTGTGGTTATCAAAGTTTC
1 ATAGTGTGGTTATCAAAGTTTC
** * *
29294 ATAGTGTGGAAATCAAAATTTA
1 ATAGTGTGGTTATCAAAGTTTC
29316 ATAG-GATGGTTATCGAAA-TTTC
1 ATAGTG-TGGTTATC-AAAGTTTC
*
29338 ATAGTGTGGGTATCAAAGTTTC
1 ATAGTGTGGTTATCAAAGTTTC
29360 A
1 A
29361 CAGGGATTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.07
22 47 0.85
23 4 0.07
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (22 bp):
ATAGTGTGGTTATCAAAGTTTC
Done.