Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012541.1 Corchorus olitorius cultivar O-4 contig12574, 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: 28618
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Found at i:3624 original size:75 final size:75
Alignment explanation
Indices: 3493--3792 Score: 465
Period size: 75 Copynumber: 4.0 Consensus size: 75
3483 TTGAAGAAGC
*
3493 AAACGAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTCCC
1 AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTCCC
3558 CGTATAAAAT
66 CGTATAAAAT
* *
3568 AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCCACCTTAGTGTCCC
1 AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTCCC
*
3633 CGTATAATAT
66 CGTATAAAAT
*
3643 AAACAAAACGATCGTCTCCTGTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTCCC
1 AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTCCC
*
3708 CGTATAAAAAA
66 CGTAT-AAAAT
* * * * * **
3719 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACGAACGGTCGAACACCAGCCCAGGTGTCCC
1 AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTCCC
*
3784 CATATAAAA
66 CGTATAAAA
3793 ACAAAAGAAA
Statistics
Matches: 206, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
75 142 0.69
76 64 0.31
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (75 bp):
AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTCCC
CGTATAAAAT
Found at i:10572 original size:32 final size:32
Alignment explanation
Indices: 10508--10574 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
10498 ATAAAGATAG
* * *
10508 AAAAAAGTTTATGTGCTCTACCTAAAAGAAAA
1 AAAAAAGTTGATGTGCGCTACCTAAAACAAAA
*
10540 AAAAAAGTTGATGTGCGCTTCC-ACAAACAAAA
1 AAAAAAGTTGATGTGCGCTACCTA-AAACAAAA
10572 AAA
1 AAA
10575 GGTTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (32 bp):
AAAAAAGTTGATGTGCGCTACCTAAAACAAAA
Found at i:13518 original size:53 final size:53
Alignment explanation
Indices: 13438--13538 Score: 193
Period size: 53 Copynumber: 1.9 Consensus size: 53
13428 AAACAAATAA
13438 ATTACAAAGAAAACCCACATTCCGTGAGAGTAGAACCCAAGAACTCATGATCC
1 ATTACAAAGAAAACCCACATTCCGTGAGAGTAGAACCCAAGAACTCATGATCC
*
13491 ATTACAAAGAAAACCCACATTCCGTGAGAGTAGAACCCAATAACTCAT
1 ATTACAAAGAAAACCCACATTCCGTGAGAGTAGAACCCAAGAACTCAT
13539 AGTGCAGATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.18
Consensus pattern (53 bp):
ATTACAAAGAAAACCCACATTCCGTGAGAGTAGAACCCAAGAACTCATGATCC
Found at i:15038 original size:444 final size:431
Alignment explanation
Indices: 14013--15073 Score: 1157
Period size: 435 Copynumber: 2.4 Consensus size: 431
14003 ATTTTTTTCC
* *
14013 CTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTCA
1 CTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCA
* * * * *
14078 TG-AAGAACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAATATGCTTCCAAAATTTTGTGGTT
66 TGAAAG-ACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAATGCTT-CTAAATTTTGT-GTT
* * ** * *
14142 TTATTTGCCAGTCAATTTAATATCGTATAATTTTTTG-TCCACATGTCCGATTGAAATTATTAAA
128 TCAATTGATAGTCTATTTAATATCATATAA-TTTTTGATCCACATGTCCGATT-AAATTATTAAA
* * *
14206 GTGTCGGTTAAAAGATTATTGCATGATTTACGACTTTCATGAAGGACCCGAAAACTACATTTGAT
191 GTGTCGGTTAAAAGATTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAACTACATTTGAT
* * * * *
14271 CTACGAGTTTCACGAAGGGTTTAAAAGGGAGTTTTTATGTTAATATCTCCATCGACAAACATTTT
256 CTACGAGTTTCACGAAGGGTTTAAAAGGGAATTTTTATGTTAAGATATCAATCAACAAACATTTT
* ** * *
14336 CTTATTTGGATTATTTATCAAATGACCCTCATATTTTTCTATTTTATACTACTTAGTCCTTCATA
321 CTTATTTGAATTAGCTATCAAATGACCCTCATACTTTTCTATTTTATACTACTTAGTCCTTCACA
* *
14401 AATTATATTTTAATCTAACGTTTAAGACTTATTTTTTATTCTTTATT
386 AATTACATCTTAATCT-ACGTTTAAGACTTATTTTTTATTCTTTATT
* * * *
14448 CTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATAATCTACGACTTTCA
1 CTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCA
* ** *
14513 TGAACGACTCAAAAGCAAATTTTTATGTTTTAATTAAAAAAAATGCTTCCTAAATTTAGTCGTTT
66 TGAAAGACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAATGCTT-CTAAATTTTGT-GTTT
** * * *
14578 CAATTTTTGGTCTATTTAATACCATATAATTTTTGATCCACATGTCCGATTATAATTATTCAAGT
129 CAATTGATAGTCTATTTAATATCATATAATTTTTGATCCACATGTCCGATTA-AATTATTAAAGT
* * * * **
14643 GTTGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAAGAACTCGAAAGTTA-ATTTGATCT
193 GTCGGTTAAAAGATTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAACTACATTTGATCT
* * * * *
14707 ATGAGTTTCATGAAGGGTTTAAAAGGGAATTTTTATGTTTCAAGATATCAATTAAGAAATATTTT
258 ACGAGTTTCACGAAGGGTTTAAAAGGGAATTTTTATG-TT-AAGATATCAATCAACAAACATTTT
* *
14772 CTTATTTGAATTAGCTATCAGATGACTCTCATACTTTTCTATTTTATATTTTATGCTACTTAGTC
321 CTTATTTGAATTAGCTATCAAATGACCCTCATACTTTTCTA-TTT-TA---TA--CTACTTAGTC
* *
14837 CTTTACAAATTCCATCTT-A-CT-CGATTTAACG-CTTCATTTTTTTATTTTCTTTATT
379 CTTCACAAATTACATCTTAATCTACG-TTTAA-GACTT-A-TTTTTTA--TTCTTTATT
** * * * * *
14892 CTATTTGTCTAATTAAGATAATTCAGGTGTCTGTTAAAAAGTAATTTGATGATCTACAACTTTCA
1 CTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCA
* * * * *
14957 TGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATACTTTTGAAATTTTGTGATTT
66 TGAAAGACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAATGCTTCT-AAATTTTGTG-TTT
* * * * * * *
15022 CGATTGATAATCTATTTAATTTCATATTATTTTT-ATCTAGATGTTCGATTAA
129 CAATTGATAGTCTATTTAATATCATATAATTTTTGATCCACATGTCCGATTAA
15074 CAAAGATTCA
Statistics
Matches: 521, Mismatches: 85, Indels: 33
0.82 0.13 0.05
Matches are distributed among these distances:
434 50 0.10
435 206 0.40
436 54 0.10
437 3 0.01
438 2 0.00
439 2 0.00
440 8 0.02
441 6 0.01
442 9 0.02
443 39 0.07
444 142 0.27
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.43
Consensus pattern (431 bp):
CTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCA
TGAAAGACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAATGCTTCTAAATTTTGTGTTTCA
ATTGATAGTCTATTTAATATCATATAATTTTTGATCCACATGTCCGATTAAATTATTAAAGTGTC
GGTTAAAAGATTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAACTACATTTGATCTACG
AGTTTCACGAAGGGTTTAAAAGGGAATTTTTATGTTAAGATATCAATCAACAAACATTTTCTTAT
TTGAATTAGCTATCAAATGACCCTCATACTTTTCTATTTTATACTACTTAGTCCTTCACAAATTA
CATCTTAATCTACGTTTAAGACTTATTTTTTATTCTTTATT
Found at i:18483 original size:110 final size:109
Alignment explanation
Indices: 18291--18506 Score: 355
Period size: 110 Copynumber: 2.0 Consensus size: 109
18281 TCTAAACTTC
*
18291 AAAAATCTTGATCTGAAATATTTAAAATACCTTTTTTAATTTTAAAATTTTAGTATTCTTTTAAA
1 AAAAATCTTGATCTGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCTTTTAAA
18356 AGGTAAACATGTATTTTTA-TTTCATTTAGATTAATTAATTATTT
66 AGGTAAACATGTATTTTTAGTTT-ATTTAGATTAATTAATTATTT
* *
18400 AAAAATCTTGATCTGAATTATTTTAAAATACCCTTTTTAATTTTTAAATTTTAGTATT-TCTTTA
1 AAAAATCTTGATCTGAAATA-TTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCT-TTTA
*
18464 AAGGGTAAACATGTATTTTTAGTTTATTTAGATTAATTAATTA
64 AAAGGTAAACATGTATTTTTAGTTTATTTAGATTAATTAATTA
18507 ATTATGGAGT
Statistics
Matches: 100, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
109 20 0.20
110 77 0.77
111 3 0.03
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (109 bp):
AAAAATCTTGATCTGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCTTTTAAA
AGGTAAACATGTATTTTTAGTTTATTTAGATTAATTAATTATTT
Found at i:20215 original size:20 final size:20
Alignment explanation
Indices: 20190--20230 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
20180 AGTATCATAA
20190 TTGTTTTGA-TAACCTTTAAT
1 TTGTTTTGAGTAACC-TTAAT
*
20210 TTGTTTTTAGTAACCTTAAT
1 TTGTTTTGAGTAACCTTAAT
20230 T
1 T
20231 AGATAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
TTGTTTTGAGTAACCTTAAT
Done.