Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020601.1 Corchorus olitorius cultivar O-4 contig20634, 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: 36972
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1633 original size:16 final size:16
Alignment explanation
Indices: 1614--1647 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1604 ATTATTATAT
1614 ATATT-ATTAATTATTA
1 ATATTAATTAA-TATTA
1630 ATATTAATTAATATTA
1 ATATTAATTAATATTA
1646 AT
1 AT
1648 TGAGGGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAATTAATATTA
Found at i:4433 original size:85 final size:82
Alignment explanation
Indices: 4325--4502 Score: 225
Period size: 85 Copynumber: 2.1 Consensus size: 82
4315 TCTATTCTTA
* * * *
4325 TTTAAGTAAATCTAATTTCTTTATAACTATTTTATTTTTACTA-TTTTACTATTTTAATTAAAAA
1 TTTAAATAAATCTAATTTCTTTATAACTATTTTA-CTTTACCATTTTTAATATTTTAATT--AAA
*
4389 AAACTTAGATATATTATAATT
63 AAACTTAGATATATTAGAA-T
* * *
4410 TTTAATTAAATCTAATCTT-TTTATAATTATTTTACTTTACCATTTTTAATATTTTAATTACAAA
1 TTTAAATAAATCTAAT-TTCTTTATAACTATTTTACTTTACCATTTTTAATATTTTAATTAAAAA
4474 ACTTAGATATATTAGAAT
65 ACTTAGATATATTAGAAT
4492 TTTAAATAAAT
1 TTTAAATAAAT
4503 TTCTTAAATG
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
82 11 0.13
83 20 0.24
84 6 0.07
85 44 0.53
86 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (82 bp):
TTTAAATAAATCTAATTTCTTTATAACTATTTTACTTTACCATTTTTAATATTTTAATTAAAAAA
CTTAGATATATTAGAAT
Found at i:4723 original size:65 final size:62
Alignment explanation
Indices: 4646--4771 Score: 191
Period size: 65 Copynumber: 2.0 Consensus size: 62
4636 TCTCTTTATA
*
4646 ATTATTTTATTTTTACCATTTTACTATTTTTAATTAAAAAAGACTTAGATATATTTA-AATTTTT
1 ATTAATTTATTTTTACCATTTTACT-TTTTTAATTAAAAAA-A-TTAGATATA-TTAGAATTTTT
4710 G
62 G
*
4711 ATTAATTTATTTTTACCATTTTACTTTTTTAATTGAAAAAATTAGATATATTAGAATTTTT
1 ATTAATTTATTTTTACCATTTTACTTTTTTAATTAAAAAAATTAGATATATTAGAATTTTT
4772 AAATATATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 3 0.05
62 16 0.28
63 1 0.02
64 14 0.24
65 24 0.41
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.54
Consensus pattern (62 bp):
ATTAATTTATTTTTACCATTTTACTTTTTTAATTAAAAAAATTAGATATATTAGAATTTTTG
Found at i:12193 original size:19 final size:19
Alignment explanation
Indices: 12171--12221 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
12161 GGGCTGAAAT
12171 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
12190 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
12209 TAATT-ATTATTAA
1 TAATTAATTATTAA
12222 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:13685 original size:51 final size:50
Alignment explanation
Indices: 13584--13685 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
13574 GTTCTTCATA
* **
13584 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
*
13634 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAA-AAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACA-AACAAACACTCGTACA-GTGT
13685 T
1 T
13686 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 7 0.16
51 34 0.77
52 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:18402 original size:2 final size:2
Alignment explanation
Indices: 18397--18425 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18387 TGTGTGTGTC
18397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18426 TATTTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27737 original size:1 final size:1
Alignment explanation
Indices: 27731--27775 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
27721 TGATAGTGAG
* * * *
27731 TTTTTTTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27776 AGTTTTAGGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:27746 original size:11 final size:11
Alignment explanation
Indices: 27730--27781 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
27720 GTGATAGTGA
27730 GTTTTTTTTTT
1 GTTTTTTTTTT
27741 GTTTTTTTTTT
1 GTTTTTTTTTT
27752 GTTTTTTTGTTT
1 GTTTTTTT-TTT
*
27764 TTTTGTTTTTTT
1 GTTT-TTTTTTT
27776 AGTTTT
1 -GTTTT
27782 AGGAGCAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
11 19 0.53
12 10 0.28
13 7 0.19
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.87
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:27747 original size:8 final size:8
Alignment explanation
Indices: 27730--27781 Score: 72
Period size: 8 Copynumber: 6.6 Consensus size: 8
27720 GTGATAGTGA
27730 GTTTTTTT
1 GTTTTTTT
*
27738 -TTTGTTT
1 GTTTTTTT
27745 -TTTTTTT
1 GTTTTTTT
27752 GTTTTTTT
1 GTTTTTTT
27760 GTTTTTTT
1 GTTTTTTT
27768 GTTTTTTT
1 GTTTTTTT
27776 AGTTTT
1 -GTTTT
27782 AGGAGCAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
7 12 0.30
8 23 0.57
9 5 0.12
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.87
Consensus pattern (8 bp):
GTTTTTTT
Found at i:27747 original size:9 final size:9
Alignment explanation
Indices: 27733--27781 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
27723 ATAGTGAGTT
27733 TTTTTTTTG
1 TTTTTTTTG
*
27742 TTTTTTTTT
1 TTTTTTTTG
27751 TGTTTTTTTG
1 T-TTTTTTTG
27761 -TTTTTTTG
1 TTTTTTTTG
*
27769 TTTTTTTAG
1 TTTTTTTTG
27778 TTTT
1 TTTT
27782 AGGAGCAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.23
9 20 0.57
10 7 0.20
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:28314 original size:2 final size:2
Alignment explanation
Indices: 28307--28352 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
28297 TGTGCTTTCG
*
28307 AT AT AT AT AT AT A- AT AT AT AT A- AT AC AT AT A- 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
28346 A- AT AT AT
1 AT AT AT AT
28353 TATTTTTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:28325 original size:9 final size:9
Alignment explanation
Indices: 28307--28352 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
28297 TGTGCTTTCG
28307 ATAT-ATAT
1 ATATAATAT
28315 ATATAATAT
1 ATATAATAT
*
28324 ATATAATAC
1 ATATAATAT
28333 ATATAATAT
1 ATATAATAT
28342 ATATAATAT
1 ATATAATAT
28351 AT
1 AT
28353 TATTTTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 4 0.11
9 31 0.89
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATAATAT
Found at i:28556 original size:22 final size:23
Alignment explanation
Indices: 28517--28642 Score: 107
Period size: 23 Copynumber: 5.2 Consensus size: 23
28507 AATTTACTAT
28517 TTTTATATTTATGATTAAGTGTG
1 TTTTATATTTATGATTAAGTGTG
28540 TTTTA-ATTATAT-ATTAATTGTGTG
1 TTTTATATT-TATGATTAA--GTGTG
28564 ATTTTTATATTTATGATTAAGTGTG
1 --TTTTATATTTATGATTAAGTGTG
*
28589 TTTTA-ATTACAT-ATTAATTGTGTG
1 TTTTATATT-TATGATTAA--GTGTG
* *
28613 ATTTTTATATTTATGATTAATTATG
1 --TTTTATATTTATGATTAAGTGTG
28638 TTTTA
1 TTTTA
28643 ATTACACATT
Statistics
Matches: 85, Mismatches: 4, Indels: 28
0.73 0.03 0.24
Matches are distributed among these distances:
22 16 0.19
23 20 0.24
24 10 0.12
25 8 0.09
26 15 0.18
27 16 0.19
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.58
Consensus pattern (23 bp):
TTTTATATTTATGATTAAGTGTG
Found at i:28577 original size:49 final size:49
Alignment explanation
Indices: 28515--28660 Score: 256
Period size: 49 Copynumber: 3.0 Consensus size: 49
28505 GTAATTTACT
*
28515 ATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTAATTGTGTG
1 ATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTG
28564 ATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTG
1 ATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTG
* * *
28613 ATTTTTATATTTATGATTAATTATGTTTTAATTACACATTAATTGTGT
1 ATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGT
28661 ATGGATATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 93 1.00
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (49 bp):
ATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTG
Found at i:29770 original size:29 final size:28
Alignment explanation
Indices: 29708--29773 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
29698 AACTTGTACG
* *
29708 ATTTTGACGTTTTGCCTCCTAAACTTTA
1 ATTTGGACGTTTTGCCTCCTAAACTTCA
*
29736 ATTTTGGACGTTTTGCC-CCATACACTTGCA
1 A-TTTGGACGTTTTGCCTCC-TAAACTT-CA
29766 ATTTGGAC
1 ATTTGGAC
29774 TTGGAGACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.09
29 27 0.84
30 2 0.06
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (28 bp):
ATTTGGACGTTTTGCCTCCTAAACTTCA
Found at i:29900 original size:33 final size:31
Alignment explanation
Indices: 29831--29914 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 31
29821 CACGTTGATG
29831 ACGTGGCATTTTGGTCTGACGTGGCATTGCC
1 ACGTGGCATTTTGGTCTGACGTGGCATTGCC
* * *
29862 TCGTGGCATTTTGGT-TGACGACGTGGCTTTGTC
1 ACGTGGCATTTTGGTCT---GACGTGGCATTGCC
29895 ACGTGGCATTTTTGGTCTGA
1 ACGTGGCA-TTTTGGTCTGA
29915 TATGGCAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
30 1 0.02
31 14 0.32
32 2 0.05
33 19 0.43
34 7 0.16
35 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.32, T:0.37
Consensus pattern (31 bp):
ACGTGGCATTTTGGTCTGACGTGGCATTGCC
Done.