Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014362.1 Corchorus olitorius cultivar O-4 contig14395, 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: 30368
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:1412 original size:22 final size:23
Alignment explanation
Indices: 1382--1951 Score: 193
Period size: 22 Copynumber: 25.6 Consensus size: 23
1372 CATAGGAAGT
1382 TTATCAAAATTTCATAATGTA-G
1 TTATCAAAATTTCATAATGTAGG
*
1404 TTA-CAAAAATTTCAT-ATGGAGG
1 TTATC-AAAATTTCATAATGTAGG
* *
1426 TTATCAAAACTTCA-AA-GTATAG
1 TTATCAAAATTTCATAATGTA-GG
1448 TTATCAAAATTTCATACA-G-AGG
1 TTATCAAAATTTCATA-ATGTAGG
* **
1470 TTACCAAAATTTCATAA-AAAGG
1 TTATCAAAATTTCATAATGTAGG
* * *
1492 TTATCAAAATTTC-TTAGGGAGG
1 TTATCAAAATTTCATAATGTAGG
* * *
1514 TTAACAAAATTTCAT-ACGAAGG
1 TTATCAAAATTTCATAATGTAGG
* *
1536 TTATCGAAAGTTT-ATAGTGT-GG
1 TTATC-AAAATTTCATAATGTAGG
**
1558 TTATCAAAATTTCATAA-AAAGG
1 TTATCAAAATTTCATAATGTAGG
* * * * *
1580 TTAACAAAATATCATAGGGAGGGAGA
1 TTATCAAAATTTCATA---ATGTAGG
*
1606 TTATCAAAATTTCCT-A-G-AGG
1 TTATCAAAATTTCATAATGTAGG
* * *
1626 TTAACAAAATTTCAT-AGGGAGG
1 TTATCAAAATTTCATAATGTAGG
* * *
1648 TTATGAAAATTTTATGGA-G-AGG
1 TTATCAAAATTTCAT-AATGTAGG
1670 TTATCAAAA-TT-ATATATAG-AGG
1 TTATCAAAATTTCATA-AT-GTAGG
* * * *
1692 ATATCATAATTTCATTCTCATAGGGAGG
1 TTATCAAAATTTCA---T-A-ATGTAGG
* * *
1720 TTATCGAAATTTCACAGTGT-GG
1 TTATCAAAATTTCATAATGTAGG
* *
1742 TTATCAAAATTTTCATAGTG-CGG
1 TTATCAAAA-TTTCATAATGTAGG
* *
1765 TTA-C-CAATTAT-ATAGTGT-GG
1 TTATCAAAATT-TCATAATGTAGG
* * *
1785 TTATCAAAATTTCAT-AGGGAGA
1 TTATCAAAATTTCATAATGTAGG
* * * *
1807 TTATTAAAATTTTACACTG-AGG
1 TTATCAAAATTTCATAATGTAGG
* *
1829 TTATCAAAATTTTATAGTGT-GG
1 TTATCAAAATTTCATAATGTAGG
* *
1851 TTATCAAAATTTCACAGTGT-GG
1 TTATCAAAATTTCATAATGTAGG
* * *
1873 TTATCAAACTTTCAT-AGGAAGG
1 TTATCAAAATTTCATAATGTAGG
* * * *
1895 TAATCGAAGTTTCATAATG-AAG
1 TTATCAAAATTTCATAATGTAGG
* * *
1917 TTATCAAATTTTCATAGTGT-TG
1 TTATCAAAATTTCATAATGTAGG
*
1939 TTATCAATATTTC
1 TTATCAAAATTTC
1952 TACGTTTGAG
Statistics
Matches: 417, Mismatches: 86, Indels: 90
0.70 0.15 0.15
Matches are distributed among these distances:
20 32 0.08
21 27 0.06
22 287 0.69
23 32 0.08
24 5 0.01
25 1 0.00
26 14 0.03
27 2 0.00
28 17 0.04
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (23 bp):
TTATCAAAATTTCATAATGTAGG
Found at i:1635 original size:46 final size:47
Alignment explanation
Indices: 1558--1647 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
1548 TATAGTGTGG
1558 TTATCAAAATTTCATAAAAAGGTTAACAAAATATCATAGGGAGGGAGA
1 TTATCAAAATTTCAT-AAAAGGTTAACAAAATATCATAGGGAGGGAGA
* * *
1606 TTATCAAAATTTCCT-AGAGGTTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAAAAGGTTAACAAAATATCATAGGGAGG
1648 TTATGAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 25 0.64
48 14 0.36
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (47 bp):
TTATCAAAATTTCATAAAAGGTTAACAAAATATCATAGGGAGGGAGA
Found at i:14296 original size:34 final size:34
Alignment explanation
Indices: 14253--14317 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
14243 CCTTTAGATA
*
14253 AGTGCTTACATGGCATTTTTTAGTTGACGTGGAT
1 AGTGCTTACATGGCATTTTTTAGCTGACGTGGAT
14287 AGTGCTTACATGGCATTTTTTAGCTGACGTG
1 AGTGCTTACATGGCATTTTTTAGCTGACGTG
14318 CCACGTCAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (34 bp):
AGTGCTTACATGGCATTTTTTAGCTGACGTGGAT
Found at i:18843 original size:25 final size:25
Alignment explanation
Indices: 18815--18862 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18805 ATAAATTTAG
18815 AACATGATCAACTAAAACAAAATCA
1 AACATGATCAACTAAAACAAAATCA
* * *
18840 AACATGATTAATTGAAACAAAAT
1 AACATGATCAACTAAAACAAAAT
18863 TGCACAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (25 bp):
AACATGATCAACTAAAACAAAATCA
Found at i:19009 original size:16 final size:18
Alignment explanation
Indices: 18977--19009 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
18967 CTTCGGGTTA
18977 TATTGTTGGGCTATTTGC
1 TATTGTTGGGCTATTTGC
18995 TATT-TTGGG-TATTTG
1 TATTGTTGGGCTATTTG
19010 GTCAGCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.12, C:0.06, G:0.27, T:0.55
Consensus pattern (18 bp):
TATTGTTGGGCTATTTGC
Found at i:28619 original size:13 final size:13
Alignment explanation
Indices: 28588--28630 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
28578 GTCTGACTGT
*
28588 TTTGGTTAATTA-
1 TTTGGTTTATTAC
28600 TTCTGGTTTATTAC
1 TT-TGGTTTATTAC
*
28614 TTTGGTTTATAAC
1 TTTGGTTTATTAC
28627 TTTG
1 TTTG
28631 ATTATGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 2 0.07
13 23 0.85
14 2 0.07
ACGTcount: A:0.19, C:0.07, G:0.16, T:0.58
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:30276 original size:2 final size:2
Alignment explanation
Indices: 30269--30354 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
30259 AAATGCACTG
30269 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
30311 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
30353 GA
1 GA
30355 CGACGACGAC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.