Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010281.1 Corchorus olitorius cultivar O-4 contig10313, 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: 14203
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1236 original size:41 final size:41
Alignment explanation
Indices: 1174--1612 Score: 433
Period size: 41 Copynumber: 10.8 Consensus size: 41
1164 TGACAAACTG
* * ***
1174 AACAACACCTTCAGACCGGGAAGGGCAAGCGGGGAAAAGTA
1 AACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
*
1215 AACAACACATTCCGACTGGGAAGGGCAAATTGGGAAAAG-A
1 AACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
* * * * * *
1255 AGACAACACCTCCCGACCGGGGAGGGCAAACTGGGAGACGTA
1 A-ACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
* *
1297 AACAAAACCTTTCGACTGGGAAGGGCAAATTGGGAAAAG-A
1 AACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
* * * * *
1337 AGACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTA
1 A-ACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
* * * * * *
1379 AAGAACACCTTTCGATTGGGAATGACAAATTGGGAAAAGAA
1 AACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
* *
1420 AACAACACC-TCTCGACCGGG-AGGGCAAATTGGGAAACGTA
1 AACAACACCTTC-CGACTGGGAAGGGCAAATTGGGAAAAGTA
*
1460 AACAACACTTTCCGACTGGGAAGGGCAAATTGGGAAAAG-A
1 AACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
* * * * *
1500 AGACAACACCTCCCGACCGGGGAGGGCAAAATGGGAAACG-A
1 A-ACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
* * * * *
1541 AGACAACACCTCCCGACTGGGGAGGGCAAACTGGGAGACGTA
1 A-ACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
*
1583 AACAACACCTTCCAACT-GGAAGGGCAAATT
1 AACAACACCTTCCGACTGGGAAGGGCAAATT
1613 TTTGGAATAT
Statistics
Matches: 326, Mismatches: 63, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
40 49 0.15
41 271 0.83
42 6 0.02
ACGTcount: A:0.38, C:0.22, G:0.29, T:0.11
Consensus pattern (41 bp):
AACAACACCTTCCGACTGGGAAGGGCAAATTGGGAAAAGTA
Found at i:1507 original size:163 final size:164
Alignment explanation
Indices: 1175--1592 Score: 563
Period size: 163 Copynumber: 2.6 Consensus size: 164
1165 GACAAACTGA
* * * * * * *
1175 ACAACACCTTCAGACCGGGAAGGGCAAGCGGGGAAAAGTAAACAACACATTCCGACTGGGAAGGG
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACATTCCGACTGGGAAGGA
* *
1240 CAAATTGGGAAAAGAAGACAACACCTCCCGACCGGGGAGGGCAAACTGGGAGACGTAAACAAAAC
66 CAAATTGGGAAAAGAAAACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAAAAC
1305 CTTTCGACTGGGAAGGGCAAATTGGGAAAAGAAG
131 CTTTCGACTGGGAAGGGCAAATTGGGAAAAGAAG
* * * * *
1339 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAAGAACACCTTTCGATTGGGAATGA
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACATTCCGACTGGGAAGGA
* * *
1404 CAAATTGGGAAAAGAAAACAACACCTCTCGACC-GGGAGGGCAAATTGGGAAACGTAAACAACA-
66 CAAATTGGGAAAAGAAAACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAAAAC
1467 CTTTCCGACTGGGAAGGGCAAATTGGGAAAAGAAG
131 CTTT-CGACTGGGAAGGGCAAATTGGGAAAAGAAG
* * * *
1502 ACAACACCTCCCGACCGGGGAGGGCAAAATGGGAAACG-AAGACAACACCTCCCGACTGGGGAGG
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAA-ACAACACATTCCGACTGGGAAGG
* * * * *
1566 GCAAACTGGGAGACGTAAACAACACCT
65 ACAAATTGGGAAAAGAAAACAACACCT
1593 TCCAACTGGA
Statistics
Matches: 223, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
162 6 0.03
163 133 0.60
164 84 0.38
ACGTcount: A:0.38, C:0.22, G:0.29, T:0.11
Consensus pattern (164 bp):
ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACATTCCGACTGGGAAGGA
CAAATTGGGAAAAGAAAACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAAAAC
CTTTCGACTGGGAAGGGCAAATTGGGAAAAGAAG
Found at i:1592 original size:82 final size:82
Alignment explanation
Indices: 1175--1576 Score: 574
Period size: 82 Copynumber: 4.9 Consensus size: 82
1165 GACAAACTGA
* * * * * * *
1175 ACAACACCTTCAGACCGGGAAGGGCAAGCGGGGAAAAGTAAACAACACATTCCGACTGGGAAGGG
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACCTTCCGACTGGGAAGGG
1240 CAAATTGGGAAAAGAAG
66 CAAATTGGGAAAAGAAG
* * *
1257 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAGACGTAAACAAAACCTTTCGACTGGGAAGGG
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACCTTCCGACTGGGAAGGG
1322 CAAATTGGGAAAAGAAG
66 CAAATTGGGAAAAGAAG
* * * * *
1339 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAAGAACACCTTTCGATTGGGAATGA
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACCTTCCGACTGGGAAGGG
*
1404 CAAATTGGGAAAAGAAA
66 CAAATTGGGAAAAGAAG
* * *
1421 ACAACACCTCTCGACC-GGGAGGGCAAATTGGGAAACGTAAACAACACTTTCCGACTGGGAAGGG
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACCTTCCGACTGGGAAGGG
1485 CAAATTGGGAAAAGAAG
66 CAAATTGGGAAAAGAAG
* * *
1502 ACAACACCTCCCGACCGGGGAGGGCAAAATGGGAAACG-AAGACAACACCTCCCGACTGGGGAGG
1 ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAA-ACAACACCTTCCGACTGGGAAGG
*
1566 GCAAACTGGGA
65 GCAAATTGGGA
1577 GACGTAAACA
Statistics
Matches: 286, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
81 74 0.26
82 212 0.74
ACGTcount: A:0.37, C:0.22, G:0.30, T:0.11
Consensus pattern (82 bp):
ACAACACCTCCCGACCGGGGAGGGCAAACTGGGAAACGTAAACAACACCTTCCGACTGGGAAGGG
CAAATTGGGAAAAGAAG
Found at i:1679 original size:48 final size:48
Alignment explanation
Indices: 1649--2075 Score: 507
Period size: 48 Copynumber: 8.7 Consensus size: 48
1639 CTCTCGACTA
* **
1649 GGAAGGGGCATTTTTGAATTTTGATGGAAAACAAGGACCTTCCGACCG
1 GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
** *
1697 GGAAGGTACATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGACCG
1 GGAAGGGGCATTTTT-GAATTTTGAAGGAAAACTGGGACCTTCCGACCG
*
1746 GGATGGGGCATTTTTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
1 GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
* * * *
1794 GGAAGGGGAATTTTTAAATTTTGTAGGAAAGCTGGGACCTTCCGACCG
1 GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
** * * * * **
1842 GGAAAGGGGCATTTTTGGAA-TAAGACGGTCTTAAAC-AGCACCTTCCGACAA
1 GG-AAGGGGCATTTTT-GAATTTTGAAGG---AAAACTGGGACCTTCCGACCG
* * *
1893 AGAAGGGCGGGCATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGTCCG
1 GGAA--G-GGGCATTTTT-GAATTTTGAAGGAAAACTGGGACCTTCCGACCG
1945 GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
1 GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
* * * *
1993 GGAAGGGACATTTTTGAAATATTGAAGGAAAACTAGGACCTTCCAACCG
1 GGAAGGGGCATTTTTG-AATTTTGAAGGAAAACTGGGACCTTCCGACCG
2042 GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTG
1 GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTG
2076 TTCTTTTGAA
Statistics
Matches: 319, Mismatches: 48, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
48 152 0.48
49 111 0.35
50 5 0.02
51 16 0.05
52 17 0.05
53 14 0.04
54 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (48 bp):
GGAAGGGGCATTTTTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
Found at i:1758 original size:97 final size:98
Alignment explanation
Indices: 1600--2074 Score: 552
Period size: 97 Copynumber: 4.8 Consensus size: 98
1590 CCTTCCAACT
* * * ** **
1600 GGAAGGGCAAATTTTTGGAATATTG-ACGAAAACTGAAACC-TCTCGACTAGGAAGGGGCATTTT
1 GGAAGGGGACATTTTTGGAATATTGAAGGAAAACTGGGACCTTC-CGACCGGGAAGGGGCATTTT
* *
1663 TGAATTTTGATGGAAAACAAGGACCTTCCGACCG
65 TGAATTTTGAAGGAAAACTAGGACCTTCCGACCG
* *
1697 GGAA-GGTACATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGACCGGGATGGGGCATTTTT
1 GGAAGGGGACATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT
*
1761 GAATTTTGAAGGAAAACTGGGACCTTCCGACCG
66 GAATTTTGAAGGAAAACTAGGACCTTCCGACCG
* * * *
1794 GGAAGGGGA-ATTTTT-AAATTTTGTAGGAAAGCTGGGACCTTCCGACCGGGAAAGGGGCATTTT
1 GGAAGGGGACATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGACCGGG-AAGGGGCATTTT
** * * * **
1857 TGGAA-TAAGACGGTCTTAAAC-AGCACCTTCCGACAA
65 T-GAATTTTGAAGG---AAAACTAGGACCTTCCGACCG
* * *
1893 AGAAGGGCGGGCATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGTCCGGGAAGGGGCATTT
1 GGAA-GG-GGACATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTT
*
1958 TTGAATTTTGAAGGAAAACTGGGACCTTCCGACCG
64 TTGAATTTTGAAGGAAAACTAGGACCTTCCGACCG
* * *
1993 GGAA-GGGACATTTTTGAAATATTGAAGGAAAACTAGGACCTTCCAACCGGGAAGGGGCATTTTT
1 GGAAGGGGACATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT
2057 GAATTTTGAAGGAAAACT
66 GAATTTTGAAGGAAAACT
2075 GTTCTTTTGA
Statistics
Matches: 318, Mismatches: 46, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
96 49 0.15
97 163 0.51
98 9 0.03
99 18 0.06
100 20 0.06
101 5 0.02
102 24 0.08
103 30 0.09
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (98 bp):
GGAAGGGGACATTTTTGGAATATTGAAGGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTT
GAATTTTGAAGGAAAACTAGGACCTTCCGACCG
Found at i:11767 original size:27 final size:28
Alignment explanation
Indices: 11729--11805 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
11719 GGTGTCCCTG
11729 AAATGACCAAAATGCCCCTAG-C-CTACA
1 AAATGACCAAAATGCCCCTAGTCAC-ACA
*
11756 AAATGACCAAAATGCCCCTGGTCACACA
1 AAATGACCAAAATGCCCCTAGTCACACA
*
11784 AAATGACCGAAAATTCCCCTAG
1 AAATGACC-AAAATGCCCCTAG
11806 ATGACCCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 20 0.45
28 12 0.27
29 12 0.27
ACGTcount: A:0.40, C:0.31, G:0.13, T:0.16
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGTCACACA
Found at i:11931 original size:20 final size:20
Alignment explanation
Indices: 11893--11931 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11883 TTGTAATCTT
*
11893 TGATTATTGATTAATAAAAG
1 TGATTATTGATTAAAAAAAG
11913 TGATTATTGGA-TAAAAAAA
1 TGATTATT-GATTAAAAAAA
11932 TTTATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (20 bp):
TGATTATTGATTAAAAAAAG
Found at i:13543 original size:19 final size:18
Alignment explanation
Indices: 13519--13554 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13509 TGAAGACTTA
*
13519 TTGAAGACTATTTGAAGAT
1 TTGAAGACCA-TTGAAGAT
13538 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
13555 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Done.