Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019827.1 Corchorus olitorius cultivar O-4 contig19860, 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: 21333
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--25 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
26 CAACAAGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:467 original size:27 final size:27
Alignment explanation
Indices: 429--482 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
419 CAAAGAAACT
* *
429 GATAAATTAAACTCACATTCTGTGAGA
1 GATAAACTAAACTCACATTCCGTGAGA
*
456 GATAAACTAAACTCATATTCCGTGAGA
1 GATAAACTAAACTCACATTCCGTGAGA
483 CTTAGGACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (27 bp):
GATAAACTAAACTCACATTCCGTGAGA
Found at i:6707 original size:15 final size:16
Alignment explanation
Indices: 6676--6718 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
6666 ACAATAAGAA
*
6676 ATTTCATTGAGAAAAATT
1 ATTTCA-TGAG-AAATTT
*
6694 ATTTTATGAGAAATTT
1 ATTTCATGAGAAATTT
6710 ATTTCATGA
1 ATTTCATGA
6719 ATGAAATAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 4 0.18
18 5 0.23
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (16 bp):
ATTTCATGAGAAATTT
Found at i:7886 original size:437 final size:438
Alignment explanation
Indices: 6802--8008 Score: 1897
Period size: 438 Copynumber: 2.8 Consensus size: 438
6792 CAGAGCATGA
* * ** * * * *
6802 AATAA-CTTTTAACCGACACTTGAATAACTTCAATCAAACATGTGGATCAAAAATTATACGATAT
1 AATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACTATAT
* * *
6866 TAAATAAACCGTCAATCGAAACCACAAAATTTCGA-AAGCATTTTTTAGAATCAAAACATTAAAA
66 TAAATAGACCGACAATCGAGACCACAAAATTTC-ATAAGCATTTTTTAGAATCAAAACATTAAAA
* * *
6930 TTGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATGACATTTTAATAAACACTTGAATC
130 TTGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATC
* * * *
6995 ACCTTAATCGTACAAATAGAAAAAAAAATACAAAAATAAAAGGCGAAGCGTTAAATTGTCCAACC
195 ACCTTAATCGGACAAATAG-AACAAAAATACAAAAATAAAAGACGAAGCGTTAAATCGTCCAACC
7060 CATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCATTTGATAAATAATCCA
259 CATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCATTTGATAAATAATCCA
* *
7125 G-AAAAAAAATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTTGAACTCTCCACGAAACA
324 GCAAAAAAAATATTTATTTATGGAGACAAAACATAAAAATTCCCTCTTAAACTCTCCACGAAACA
7189 CATTAATCAAATTCAGCTTTCATGCCCTTGACAAAAGTCGTAATTCACAC
389 CATTAATCAAATTCAGCTTTCATGCCCTTGACAAAAGTCGTAATTCACAC
*
7239 AATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTGTACTATAT
1 AATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACTATAT
* *
7304 TAAATAGACCGACAATTGAGACAACAAAATTTCATAAGCATTTTTTAGAATCAAAACATTAAAAT
66 TAAATAGACCGACAATCGAGACCACAAAATTTCATAAGCATTTTTTAGAATCAAAACATTAAAAT
7369 TGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCA
131 TGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCA
*
7434 CCTTAATCGGACAAATAGAACAAAAA-AGAAAAA-AAAAGACGAAGCGTTAAATCGTCCAACCCA
196 CCTTAATCGGACAAATAGAACAAAAATACAAAAATAAAAGACGAAGCGTTAAATCGTCCAACCCA
* *
7497 TAATTGTAAAGGATTAAATATCATAAAGCATAAAAGTATGGGGATCATTTGATAAATAATCCAGC
261 TAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCATTTGATAAATAATCCAGC
* * *
7562 AAAAAAAATATTTATTTATGGAGACCAAACATAAAAATTCCCTCTTAAACTCTCTACGAAACTCA
326 AAAAAAAATATTTATTTATGGAGACAAAACATAAAAATTCCCTCTTAAACTCTCCACGAAACACA
**
7627 TTAATCAAATTCAGCTTTCA-GACCCTTGATGAAAGTCGTAGA-TCACAC
391 TTAATCAAATTCAGCTTTCATG-CCCTTGACAAAAGTCGTA-ATTCACAC
* *
7675 AATAACCTTTTAACTGACACTTGAACAACGTCAATCGGACAAGTGGACCGCAAAATTATACTATA
1 AATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCG-AAAATTATACTATA
*
7740 TTAGATAGACCGACAATCGAGACCACAAAATTTCATAAGCATTTTTTAGAATCAAAACATTAAAA
65 TTAAATAGACCGACAATCGAGACCACAAAATTTCATAAGCATTTTTTAGAATCAAAACATTAAAA
* *
7805 TTGGCTTCTGAGTACTTCATGAAAGTTGTAGATCATGAAATTACCTTTTGATAGACACTTGAATC
130 TTGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATC
* * * *
7870 AGCTTAATCGGACAAATAGAACAAAAAAATACAAAAATAAAAGCCGACGCGTTCAATCGTCCAAC
195 ACCTTAATCGGACAAATAGAAC--AAAAATACAAAAATAAAAGACGAAGCGTTAAATCGTCCAAC
* * * *
7935 CCAAAATTGTAAAGGATTAAATAGCAAAAAGCATAAAATTATGAGGATCATTTGATAAATAATAC
258 CCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCATTTGATAAATAATCC
*
8000 AACAAAAAA
323 AGCAAAAAA
8009 TTATTTGTTT
Statistics
Matches: 709, Mismatches: 51, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
435 91 0.13
436 156 0.22
437 173 0.24
438 187 0.26
439 5 0.01
440 6 0.01
441 91 0.13
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (438 bp):
AATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCGAAAATTATACTATAT
TAAATAGACCGACAATCGAGACCACAAAATTTCATAAGCATTTTTTAGAATCAAAACATTAAAAT
TGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCA
CCTTAATCGGACAAATAGAACAAAAATACAAAAATAAAAGACGAAGCGTTAAATCGTCCAACCCA
TAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCATTTGATAAATAATCCAGC
AAAAAAAATATTTATTTATGGAGACAAAACATAAAAATTCCCTCTTAAACTCTCCACGAAACACA
TTAATCAAATTCAGCTTTCATGCCCTTGACAAAAGTCGTAATTCACAC
Found at i:8228 original size:2 final size:2
Alignment explanation
Indices: 8216--8263 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
8206 TGTTATATGT
*
8216 TA TA T- TA TA TA TA TA TA TA T- TA TA AA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8255 TA TA TA TA T
1 TA TA TA TA T
8264 CACATGATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8236 original size:15 final size:15
Alignment explanation
Indices: 8216--8263 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
8206 TGTTATATGT
8216 TATATTATATATATA
1 TATATTATATATATA
*
8231 TATATTATAAATATA
1 TATATTATATATATA
8246 TATA-TATAT-TATA
1 TATATTATATATATA
8259 TATAT
1 TATAT
8264 CACATGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
15 18 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:8245 original size:21 final size:20
Alignment explanation
Indices: 8199--8263 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 20
8189 TTTTCAACTT
* *
8199 TAATATATGT-TATATGTTA
1 TAATATATATATATATATTA
*
8218 TATTATATATATATATATTA
1 TAATATATATATATATATTA
8238 TAA-ATATATATATATATTA
1 TAATATATATATATATATTA
8257 T-ATATAT
1 TAATATAT
8264 CACATGATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 29 0.73
20 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (20 bp):
TAATATATATATATATATTA
Found at i:11488 original size:2 final size:2
Alignment explanation
Indices: 11481--11511 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11471 CGCTTTAATC
*
11481 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11512 GCCAAATACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12517 original size:94 final size:94
Alignment explanation
Indices: 12402--12590 Score: 324
Period size: 94 Copynumber: 2.0 Consensus size: 94
12392 TAATTGGTTG
*
12402 TAAGTAAACTTAATTTAATTCTGATATAATCTAATTAAATTAATATTTTCACTCACCCAAAATAA
1 TAAGTAAACTTAATTTAATTCTAATATAATCTAATTAAATTAATATTTTCACTCACCCAAAATAA
* *
12467 TATATTGAGATAAAATTACAATTAATATA
66 TACATTAAGATAAAATTACAATTAATATA
* *
12496 TAAGTAAATTTAATTTTATTCTAATATAATCTAATTAAATTAATATTTTCACTCACCCAAAATAA
1 TAAGTAAACTTAATTTAATTCTAATATAATCTAATTAAATTAATATTTTCACTCACCCAAAATAA
*
12561 TACATTAAGATAATATTACAATTAATATA
66 TACATTAAGATAAAATTACAATTAATATA
12590 T
1 T
12591 TCACTTAGAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 89 1.00
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.40
Consensus pattern (94 bp):
TAAGTAAACTTAATTTAATTCTAATATAATCTAATTAAATTAATATTTTCACTCACCCAAAATAA
TACATTAAGATAAAATTACAATTAATATA
Found at i:19649 original size:18 final size:15
Alignment explanation
Indices: 19612--19650 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
19602 TTGCAGGTAA
19612 TTTTGTTTTACATTC
1 TTTTGTTTTACATTC
19627 TTTTGTTATTACCATTAC
1 TTTTGTT-TTA-CATT-C
19645 TTTTGT
1 TTTTGT
19651 GAGTACTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 3 0.14
17 4 0.19
18 7 0.33
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTTGTTTTACATTC
Done.