Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020572.1 Corchorus olitorius cultivar O-4 contig20605, 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: 13669
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1455 original size:74 final size:74
Alignment explanation
Indices: 1334--1485 Score: 295
Period size: 74 Copynumber: 2.1 Consensus size: 74
1324 TGGTTGGTAA
1334 TCTGTTTTTTCTTTTAATTGAATTAGGGTTTAGGGTTTGACTGTGGGCAAATTATTCTTATTTGA
1 TCTGTTTTTTCTTTTAATTGAATTAGGGTTTAGGGTTTGACTGTGGGCAAATTATTCTTATTTGA
1399 ATCTTTAAT
66 ATCTTTAAT
*
1408 TCTGTTTTTTCTTTTAATTGAATTAGGGTTTAGGGTTTGACTGTGGGCGAATTATTCTTATTTGA
1 TCTGTTTTTTCTTTTAATTGAATTAGGGTTTAGGGTTTGACTGTGGGCAAATTATTCTTATTTGA
1473 ATCTTTAAT
66 ATCTTTAAT
1482 TCTG
1 TCTG
1486 CAGATTCTGG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (74 bp):
TCTGTTTTTTCTTTTAATTGAATTAGGGTTTAGGGTTTGACTGTGGGCAAATTATTCTTATTTGA
ATCTTTAAT
Found at i:5348 original size:438 final size:439
Alignment explanation
Indices: 4549--5627 Score: 1100
Period size: 438 Copynumber: 2.5 Consensus size: 439
4539 TTTTAAATCT
* * * * *
4549 TTCATGAAAGTTGTAGATTATAAAATTA-CTTTTCAATAGACACCTGAATTATCTTAATTGGACA
1 TTCATGAAAGTTGTAGATCATAAAATTACCTTTT-AATAGACACATGAATCAACTTAATCGGACA
* * *
4613 AATAGAACAAAG-A-AAAAAAA-AATGAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAGGACT
65 AATAGAACAAAGAATAAAAAAATAAAGAAACGTTAAATCAAGTAAGATAGAATTTGTAAAGGACT
* ** * * * * *
4675 AAGTAGCATGAAATTGAAAGGTATGAGGGTGATTTGATAACTAATTCAAATAAGAAAATATTTGT
130 AAATAGCATGAAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGT
* *
4740 TAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTA
195 TAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTCACGAAACTCGTAGATCAAATTA
*** * * * * * *
4805 ACTTTCGGGTTTTTCATGAAAGTCGTAGATTATATAGTAACCTTTTAACCGACACTTGAATAACT
260 ACTTTCGGGCCCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAATAACT
* * ** * * * * * * *
4870 TTAATTGGACATATATATCGAACATTATATATGGTATTAAA-TAGACTAACAATCGAAACAACCA
325 TTAATCGGACATATAGATAAAAAAATATATACGATATTAAATTA-ACCAACAATCAAAACAACAA
* * **
4934 AATTTAGCAAGCATTTTTTTGAATTGAAACA-T-AA-TCACTTTTGAG-TC
389 AATTTAGCAAACATTTTTTAGAATCAAAACATTAAATTCACTTTTGAGTTC
* *
4981 ATTCATGAAGGTTGTA-ACTCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGAC
1 -TTCATGAAAGTTGTAGA-TCATAAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGAC
* * *
5045 AAATAGAACAAAGAATAAAAAAATAAAGCCCAAACGTTAAATTAATTAAGATAGAATTTGTAAAT
64 AAATAGAACAAAGAATAAAAAAATAAAG---AAACGTTAAATCAAGTAAGATAGAATTTGTAAAG
* *
5110 GACTAAATAGTAT-AAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGT
126 GACTAAATAGCATGAAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATAT
*
5174 TTGTTAATGGAGATCTTGAAACATAAAAATT-CTTTGTTGAACCATTCACGAAACTCGTAGATCA
191 TTGTTAATGGAGATCTTGAAACATAAAAATTCCCTT-TTGAACCATTCACGAAACTCGTAGATCA
* * * *
5238 AATTGAGCTTTGGGGCCCTTCATGAAAGTCATAAATCATGCAATAACCTTTTAACCGACCCTTCA
255 AATT-AACTTTCGGGCCCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCA
* * **
5303 ATAACTTTAATCGGACATGTGGATAAAAAAAT-TATACGATATTAAATTAACCGGCAATCAAAAC
319 ATAACTTTAATCGGACATATAGATAAAAAAATATATACGATATTAAATTAACCAACAATCAAAAC
* * * *
5367 CACAAAATTTCGGAAACATTTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTTC
384 AACAAAATTTAGCAAACATTTTTTAGAATCAAAACATT-AAATTCACTTTTGAGTTC
* * * * * * * *
5424 TTAATAAAAATTGCAGATCATCAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGAACAA
1 TTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAA
* * ** ** * *
5489 ATAGAA-AAAAAATACAAAAATAAAAGCCAGCGCGTTAAATC--GTCCAACCTATAA-TTGTGAA
66 ATAGAACAAAGAATAAAAAAAT-AAAG--A-AACGTTAAATCAAGT--AAGATAGAATTTGTAAA
* * * *
5550 GGACTAAATAGCAT-AAAGCATAAAAGTATAAGGATCATTTGATAAATAATCC-AAT-AGAAAAA
125 GGACTAAATAGCATGAAAG-AGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAG-AAAA
* *
5612 TATTAGTTTATGGAGA
188 TATTTGTTAATGGAGA
5628 ATGTGACCCA
Statistics
Matches: 533, Mismatches: 90, Indels: 38
0.81 0.14 0.06
Matches are distributed among these distances:
432 1 0.00
433 61 0.11
434 6 0.01
435 7 0.01
436 3 0.01
437 3 0.01
438 155 0.29
439 114 0.21
440 3 0.01
441 60 0.11
442 117 0.22
443 3 0.01
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (439 bp):
TTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAA
ATAGAACAAAGAATAAAAAAATAAAGAAACGTTAAATCAAGTAAGATAGAATTTGTAAAGGACTA
AATAGCATGAAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTT
AATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTCACGAAACTCGTAGATCAAATTAA
CTTTCGGGCCCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAATAACTT
TAATCGGACATATAGATAAAAAAATATATACGATATTAAATTAACCAACAATCAAAACAACAAAA
TTTAGCAAACATTTTTTAGAATCAAAACATTAAATTCACTTTTGAGTTC
Found at i:5884 original size:89 final size:89
Alignment explanation
Indices: 5733--5906 Score: 321
Period size: 89 Copynumber: 2.0 Consensus size: 89
5723 CAAAATACCC
* *
5733 CTCTCAATTTGTGAATGAATTCATAAAATCAATTCTTTACATTGGTTTTTTGGTAATTTCACTTT
1 CTCTCAATTTGTGAATGAATTCATAAAATCAATTCTTTACATTGGTTTTTTAGTAATTTCACTTC
5798 CTATTCTTATTGTTTCTTATTATA
66 CTATTCTTATTGTTTCTTATTATA
*
5822 CTCTCAATTTGTGAATGAATTCATAAAATCAATTTTTTACATTGGTTTTTTAGTAATTTCACTTC
1 CTCTCAATTTGTGAATGAATTCATAAAATCAATTCTTTACATTGGTTTTTTAGTAATTTCACTTC
5887 CTATTCTTATTGTTTCTTAT
66 CTATTCTTATTGTTTCTTAT
5907 AATTTCTTAT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 82 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.52
Consensus pattern (89 bp):
CTCTCAATTTGTGAATGAATTCATAAAATCAATTCTTTACATTGGTTTTTTAGTAATTTCACTTC
CTATTCTTATTGTTTCTTATTATA
Found at i:7323 original size:21 final size:21
Alignment explanation
Indices: 7294--7350 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
7284 GATTGCTAAA
7294 CACCGCCCCCCTTTTACTTAT
1 CACCGCCCCCCTTTTACTTAT
*
7315 CACCACCCCCCTTTTACTTAT
1 CACCGCCCCCCTTTTACTTAT
7336 CACCGCCCCCCTTTT
1 CACCGCCCCCCTTTT
7351 TACACTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.14, C:0.51, G:0.04, T:0.32
Consensus pattern (21 bp):
CACCGCCCCCCTTTTACTTAT
Found at i:8071 original size:27 final size:27
Alignment explanation
Indices: 8008--8075 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
7998 AAGGGATAAA
*
8008 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
*
8035 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
8062 GAGAG-GGAGGCTGC
1 GAG-GCGGAGGCTGC
8076 CGCTGGTGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (27 bp):
GAGGCGGAGGCTGCTCGGATGTATAGG
Found at i:8074 original size:33 final size:27
Alignment explanation
Indices: 8008--8064 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
7998 AAGGGATAAA
8008 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
8035 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
8062 GAG
1 GAG
8065 AGGGAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.14, G:0.46, T:0.21
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATGTATAGG
Found at i:8387 original size:20 final size:20
Alignment explanation
Indices: 8347--8388 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
8337 TATTATGTGA
**
8347 TATTATAAATTGAAATGAAT
1 TATTATAAATTGAAAAAAAT
8367 TATTATAAATTGAAAAAAAT
1 TATTATAAATTGAAAAAAAT
8387 TA
1 TA
8389 AATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
TATTATAAATTGAAAAAAAT
Found at i:10201 original size:20 final size:20
Alignment explanation
Indices: 10172--10210 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10162 TATTTTGGGA
10172 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
* *
10192 TTTTTTTGGATTTTTATGT
1 TTTTTATGGATGTTTATGT
10211 ATATTGGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.67
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Found at i:12418 original size:16 final size:13
Alignment explanation
Indices: 12395--12437 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 13
12385 CACCTGCGGC
12395 AATAATAAATGAAT
1 AATAATAAAT-AAT
12409 ACATTAATAAATAAT
1 A-A-TAATAAATAAT
12424 AATAATAAA-AAT
1 AATAATAAATAAT
12436 AA
1 AA
12438 CTAAACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.19
13 7 0.26
14 2 0.07
15 5 0.19
16 8 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (13 bp):
AATAATAAATAAT
Done.