Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002222.1 Corchorus olitorius cultivar O-4 contig02222, 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: 1957
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Found at i:1285 original size:2 final size:2
Alignment explanation
Indices: 1273--1333 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
1263 AGTTTAGACT
* * *
1273 TA TA TA GTA TA TA GA TA TA GA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1316 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1334 CTAGTATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1409 original size:22 final size:22
Alignment explanation
Indices: 1380--1430 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1370 ACGTGTTTAA
1380 ATGA-AATATTCATATGAAATT
1 ATGATAATATTCATATGAAATT
* *
1401 ATGATAATATTCTTATTAAATT
1 ATGATAATATTCATATGAAATT
1423 ATGATAAT
1 ATGATAAT
1431 TACACTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (22 bp):
ATGATAATATTCATATGAAATT
Found at i:1439 original size:22 final size:22
Alignment explanation
Indices: 1396--1439 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1386 TATTCATATG
* *
1396 AAATTATGATAATATTCTTATT
1 AAATTATGATAATATACCTATT
1418 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATATAC-CTATT
1440 TTTGATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATTATGATAATATACCTATT
Found at i:1546 original size:18 final size:18
Alignment explanation
Indices: 1519--1555 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1509 GAGAACCTTT
1519 TTATAAATTTT-TTAACC
1 TTATAAATTTTGTTAACC
1536 TTATGAAATTTTGTTAACC
1 TTAT-AAATTTTGTTAACC
1555 T
1 T
1556 CCGTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 7 0.39
19 7 0.39
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51
Consensus pattern (18 bp):
TTATAAATTTTGTTAACC
Found at i:1810 original size:46 final size:44
Alignment explanation
Indices: 1714--1817 Score: 138
Period size: 46 Copynumber: 2.3 Consensus size: 44
1704 AATCACACTC
* *
1714 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAAACACACTATAAAATTGTGATAACCTCGCTA
* *
1758 TGAAATTTTGATAAACATTC-CTATAAAATTTTGATAAACCTCGCTA
1 TAAAATTTTGATAAACA--CACTATAAAATTGTGAT-AACCTCGCTA
1804 TAAAATTTTGATAA
1 TAAAATTTTGATAA
1818 CCTCCTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 15 0.29
45 13 0.25
46 24 0.46
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (44 bp):
TAAAATTTTGATAAACACACTATAAAATTGTGATAACCTCGCTA
Found at i:1820 original size:68 final size:67
Alignment explanation
Indices: 1714--1839 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 67
1704 AATCACACTC
* * *
1714 TAAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGC-TATGAAATTTTGATAAACATTC
1 TAAAATTTTGATAACCACACTATAAAATTGTGATAACCTC-CTTATGAAATCTTGATAAACATTC
1778 CTA
65 CTA
* * *
1781 TAAAATTTTGATAAACCTCGCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAA
1 TAAAATTTTGAT-AACCACACTATAAAATTGTGATAACCTCCTTATGAAATCTTGATAA
1840 CTACAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
67 13 0.25
68 38 0.75
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (67 bp):
TAAAATTTTGATAACCACACTATAAAATTGTGATAACCTCCTTATGAAATCTTGATAAACATTCC
TA
Found at i:1831 original size:22 final size:21
Alignment explanation
Indices: 1439--1957 Score: 202
Period size: 22 Copynumber: 24.1 Consensus size: 21
1429 ATTACACTAT
* *
1439 TTTTGATGATCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* *
1461 TTTTGATAATCTTCTTATGAAA
1 TTTTGATAA-CCTCCTATGAAA
* * * *
1483 TTTTAATAACGATACTATAAAA
1 TTTTGATAAC-CTCCTATGAAA
* * **
1505 TTTCGAGAACCTTTTTAT-AAA
1 TTTTGATAACC-TCCTATGAAA
*
1526 TTTT-TTAACCT--TATGAAA
1 TTTTGATAACCTCCTATGAAA
* *
1544 TTTTGTTAACCTCCGTAAGAAA
1 TTTTGATAACCTCC-TATGAAA
1566 TTTTGA-AGACCTCACTATGAAA
1 TTTTGATA-ACCTC-CTATGAAA
* *
1588 TTTTGATAACTTCCCAATGAAA
1 TTTTGATAACCT-CCTATGAAA
* ** *
1610 TTTTGATAGCCAAC-ACTGAGA
1 TTTTGATAACCTCCTA-TGAAA
** * *
1631 CGTTGATAACTTCCATATGATA
1 TTTTGATAACCTCC-TATGAAA
* * *
1653 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* * * * *
1675 ATTTAAAAACATTCATATG-AA
1 TTTTGATAAC-CTCCTATGAAA
* * * *
1696 TTATT-AGTAATCACACTCTAAAA
1 TT-TTGA-TAACCTC-CTATGAAA
* *
1719 TTTTGATAATCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
*
1741 TTGTGATAACCTCGCTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
1763 TTTTGATAAACATTCCTATAAAA
1 TTTTGAT-AAC-CTCCTATGAAA
*
1786 TTTTGATAAACCTCGCTATAAAA
1 TTTTGAT-AACCTC-CTATGAAA
1809 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* *
1831 TCTTGATAA----CTA-CAAA
1 TTTTGATAACCTCCTATGAAA
**
1847 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCT-CCTATGAAA
* *
1869 TTTTGATAATCTCATTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
1891 TTTT-TTAATCTCCCTATGAAA
1 TTTTGATAACCT-CCTATGAAA
* * *
1912 TTTTGATCTACATACTATGAAA
1 TTTTGAT-AACCTCCTATGAAA
*
1934 TTTTGATAATCCTCTTATGAAA
1 TTTTGATAA-CCTCCTATGAAA
1956 TT
1 TT
Statistics
Matches: 372, Mismatches: 88, Indels: 74
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.03
17 5 0.01
18 8 0.02
19 8 0.02
20 5 0.01
21 49 0.13
22 234 0.63
23 50 0.13
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Done.