Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024475.1 Corchorus olitorius cultivar O-4 contig24508, 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: 13853
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:677 original size:18 final size:18
Alignment explanation
Indices: 654--691 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
644 CCCATTCAAG
654 TGCTGATGTGGCTATTTT
1 TGCTGATGTGGCTATTTT
672 TGCTGATGTGGCTATTTT
1 TGCTGATGTGGCTATTTT
690 TG
1 TG
692 TCAACTCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.29, T:0.50
Consensus pattern (18 bp):
TGCTGATGTGGCTATTTT
Found at i:2617 original size:2 final size:2
Alignment explanation
Indices: 2610--2641 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2600 TATCTATGCA
2610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2642 GAATTCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7846 original size:27 final size:27
Alignment explanation
Indices: 7792--7874 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
7782 GTACAGCCAC
*
7792 CGGTAAGTTCA-TCTCAAG-TTTTCCTG
1 CGGTAA-TTCATTCTCCAGATTTTCCTG
7818 CGGTGAATTCATT-TCCA-ATGTTTCCTG
1 CGGT-AATTCATTCTCCAGAT-TTTCCTG
* *
7845 CGGTAATTGATTCTCCAGATCTTCCTG
1 CGGTAATTCATTCTCCAGATTTTCCTG
7872 CGG
1 CGG
7875 CATCCACTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 19 0.40
27 27 0.56
28 2 0.04
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.37
Consensus pattern (27 bp):
CGGTAATTCATTCTCCAGATTTTCCTG
Found at i:10521 original size:23 final size:21
Alignment explanation
Indices: 10478--10521 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
10468 TTAAAATTTT
*
10478 TTTAAAATAAATTTTGGAAAA
1 TTTAAAATAAATTTTGCAAAA
*
10499 TTTAAAACTTAAATTTTTCAAAA
1 TTTAAAA--TAAATTTTGCAAAA
10522 CATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
TTTAAAATAAATTTTGCAAAA
Found at i:10929 original size:5 final size:5
Alignment explanation
Indices: 10919--10943 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10909 TGGTGTGTAA
10919 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
10944 AATAGCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:11705 original size:14 final size:14
Alignment explanation
Indices: 11686--11713 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11676 AAAGCCTGTT
11686 GAATCTAAATTAAA
1 GAATCTAAATTAAA
11700 GAATCTAAATTAAA
1 GAATCTAAATTAAA
11714 ATTATGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
GAATCTAAATTAAA
Found at i:12427 original size:304 final size:303
Alignment explanation
Indices: 11974--13097 Score: 859
Period size: 304 Copynumber: 3.6 Consensus size: 303
11964 TATTTTTTTG
*
11974 AATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAA-
* * * * * * * **
12039 A-TGCCTGAGATTTGATTAAAT-AATATAGATATTTCAACAAGTCTCGGCGCCAAAAATCATATA
65 AGTGGCTGAGATTTGATTAGATGAATATAGAAATTTCAAGAAGTCTTGGCACAAAAAATCATGCA
** * * *
12102 AAACTGAGCCGGGATCCCGGAATGTGTTTTTATAGCC-AAAAAC-CATGATGGT-AAAAATGACC
130 AAACTGAGCTAGGACCCCGGAATGCG-TTTT-TAGCCAAAAAACGCAAGATGGTAAAAAATGACC
* * *
12164 CGAAAGATTTTTACTCAATTTTTGGCTAAAATACTCATAAAAATATATAGTTCGACATCAAAAAG
193 CGAAAGATTTTT-CTCAATTTTTAGCCAAAATACTCATAAAAATATATA-TTCAACATCAAAAA-
* * *
12229 ATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTTCTATTTTTCTCCG
255 ATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTCTCCA
*
12278 AATTAATTTCTAATTAAATCGAAATAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAAA
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAAA
* *
12343 GTGGCTGAGATTTGGTTAGATGAATATAGAAATTTCAAGGAGTCTTGGCACAAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGAAATTTCAAGAAGTCTTGGCACAAAAAATCATGCAA
** *** * * * **
12408 AACTGAGCTAGG-CCCCGGAACACGTTTTTAGCCGACACGATTTCGGCTAAAAGTTTGCAAAAGT
131 AACTGAGCTAGGACCCCGGAATGCGTTTTTAGCC-A-A--AAAAC-GC---AAGATGGTAAAAAA
* * * *
12472 TGACCCGAAAGATTTTTCTTCAATTTTTAACGAAAATACTCATAAAAAATATTTAATTCAAAAAC
188 TGACCCGAAAGATTTTTC-TCAATTTTTAGCCAAAATACTCAT-AAAAATATAT-ATTC-AACA-
* * * * *
12537 TAAAAAAATTGAAAGCCTTTTTTCACGCTTCAAATATTGTTTTTCCTATTTTATTTCCA
248 TCAAAAAATTGAAGGGC--TTTTCACGCTTCTAATATTGTTTTTCCTATTTT-TCTCCA
* * * * * * * * * * * * *
12596 AATTAATTGCTGATTAAATCGAGACAATATTTAGATACTCTTGAAAATAAATCCTTAAATACGAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAAA
* * * * ** * *
12661 GTGGTTGAGATTCGATTAGATGAATAAAGATATATTTTAAGGCGTCTTGACACCAAAAATCATGC
66 GTGGCTGAGATTTGATTAGATGAATATAGA-A-ATTTCAAGAAGTCTTGGCACAAAAAATCATGC
* *
12726 AAAATTGA-C-ACGGGGCCCCGGAATGCGTTTTTAGCCAAAAAAAAAAAACCGTGCTGCTACACG
129 AAAACTGAGCTA--GGACCCCGGAATGCGTTTTTAGCC------AAAAAA-----C-GC-A-A-G
* * *
12789 ATTTCGGCTAAAATTTTACAAAAATTGACCTGAAATA-TTTTCTCAATTTTTAGCCACAATACTA
177 A--T-GG-T--AA-------AAAA-TGACCCGAAAGATTTTTCTCAATTTTTAGCCAAAATACT-
* * * **
12853 AATAAAAATATA-ATTCAACATCAAATAATTGAAGGGCTTCTCACGCTTCTAATATCATTTTTCC
227 CATAAAAATATATATTCAACATCAAAAAATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCC
12917 T-TTTTTCT-CA
292 TATTTTTCTCCA
* * * *
12927 AATCAATTTCTAATTAAATCGAAATATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAAA
* * * ** *
12992 GTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGAAGTTTTACCACAAAATATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGAAATTTCAAGAAGTCTTGGCACAAAAAATCATGCAA
* ** * *
13057 AACTGACCTAGGACCCCATAATGCGTTTTTAGTCTAAAAAC
131 AACTGAGCTAGGACCCCGGAATGCGTTTTTAGCCAAAAAAC
13098 CGTGATGGTA
Statistics
Matches: 636, Mismatches: 129, Indels: 96
0.74 0.15 0.11
Matches are distributed among these distances:
302 5 0.01
303 5 0.01
304 87 0.14
305 46 0.07
307 2 0.00
309 1 0.00
312 5 0.01
313 41 0.06
314 12 0.02
315 11 0.02
316 6 0.01
317 30 0.05
318 83 0.13
319 2 0.00
320 37 0.06
321 19 0.03
323 6 0.01
325 1 0.00
326 2 0.00
327 1 0.00
328 4 0.01
329 51 0.08
330 2 0.00
331 80 0.13
332 2 0.00
333 4 0.01
334 26 0.04
336 13 0.02
337 3 0.00
338 4 0.01
340 26 0.04
341 9 0.01
342 10 0.02
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (303 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAAA
GTGGCTGAGATTTGATTAGATGAATATAGAAATTTCAAGAAGTCTTGGCACAAAAAATCATGCAA
AACTGAGCTAGGACCCCGGAATGCGTTTTTAGCCAAAAAACGCAAGATGGTAAAAAATGACCCGA
AAGATTTTTCTCAATTTTTAGCCAAAATACTCATAAAAATATATATTCAACATCAAAAAATTGAA
GGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTCTCCA
Found at i:13832 original size:2 final size:2
Alignment explanation
Indices: 13825--13852 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13815 AAATACTCAT
13825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13853 C
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.