Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013455.1 Corchorus olitorius cultivar O-4 contig13488, 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: 56035
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:274 original size:12 final size:12
Alignment explanation
Indices: 257--283 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
247 TTCCTTTTTT
257 TTTCTGAATTTA
1 TTTCTGAATTTA
269 TTTCTGAATTTA
1 TTTCTGAATTTA
281 TTT
1 TTT
284 TTAATAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTCTGAATTTA
Found at i:777 original size:333 final size:328
Alignment explanation
Indices: 8--2513 Score: 3064
Period size: 333 Copynumber: 7.7 Consensus size: 328
1 GTGGACT
* *
8 GAGATTTGGTTAGATGAATATAGATATTTCGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGA
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGA
* * * *
73 GCCATAGG-CCCGAAACGCGTTTTTAGCCAAAAA-TCAT-GTACACGATTTCGGCTAAAATTTTT
66 GCCA-GGGCCCCGAAACGCATTTTTAGCCAAAAAGTGATGGTACACGATTTCGGCTAAAATTTTG
* ** * * * *
135 CAAAAAACTGACCTGATGTGTTTTTCCCCAATTTTTTTCCACAGTACTCGGAAAAATTATATAAT
130 CAAAAAACTGACCCGA-AAGTTTTTCCCCAA-TTTTTGCCACAATACTCAGAAAAATCATATAAT
* * *
200 TCAACGCCAAAATTATTTTAGGTTTTTTTCATGCTTCTAATATCG-TTTTCCTTTTTTTTTCTGA
193 TCAACGCCAAAATTATTTTAGG-GTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCTGA
* * *** * * * * * * *
264 ATTTATTTCTGAATTTATTTTTAATAAGATTCAGATGCTCGTAAAAACAAATCCATAAATCCAAT
257 ATTTATTTCT-AATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAAATGCATT
329 GTTGGCTGA
321 G-TGGCTGA
* *
338 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTACCAAAAATCATGCAAAACTTA
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGA
** * *
403 GTGAGGGCCCCGAAACGCGTTTTTAGCCGAAAACCGTGATGGTACACGATTTTC-GCTAAAATTT
66 GCCAGGGCCCCGAAACGCATTTTTAGCC-AAAA-AGTGATGGTACACGA-TTTCGGCTAAAATTT
467 TGCAAAAAACTGACCCGACAAGTTTTTCCCCAATTTTTGGCCACAATACTCAGAAAAATCATATA
128 TGCAAAAAACTGACCCGA-AAGTTTTTCCCCAATTTTT-GCCACAATACTCAGAAAAATCATATA
532 ATTCAACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTGTCT
191 ATTCAACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTT-TCT
* * * *
597 GAATTTATTTCTAATTATATCGGAACAAGATTCGGAAACTTGTAAAAATAAATCCGTAAATGCAT
255 GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAAATGCAT
662 TGTGGCTGA
320 TGTGGCTGA
* * * *
671 GAGATTTGATTAGATGACTATAGATAATTCGATAAGTCATTT-TGCCAAAAATTATGCAAAACTG
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTC-TTTCTGCCAAAAATCATGCAAAACTG
* *
735 AGCCAGGGCCCCGAAACGCATTTTTAGCCAAAAACAGTGATGGTACATGATTTTGGCTAAAATTT
65 AGCCAGGGCCCCGAAACGCATTTTTAGCC-AAAA-AGTGATGGTACACGATTTCGGCTAAAATTT
* *
800 TGTAAAAAACTGACCCGAAAGGTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATG
128 TGCAAAAAACTGACCCGAAA-GTTTTTCCCCAA-TTTTTGCCACAATACTCAGAAAAATCATATA
* * *
865 ATTCAACGCCAAAATTATTTTAGGGGTTATCACGCTTCTAGTATCGTTTTTCCA-TTTTTTTCTG
191 ATTCAACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCTG
* * * * **
929 AACTTATTTCTGATTAAATCGAAATAAGATTCAGATACGTGTAAAAATAAATCCGTAAATGTGTT
256 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAAATGCATT
* *
994 GTAGTTGA
321 GTGGCTGA
* *
1002 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTATT-TGCCAAAACTTATGCAAAACTG
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCT-TTCTGCCAAAAATCATGCAAAACTG
* * ** *
1066 AGTCAGGG--CC-AAA---AATCGT-G-----ATG-GA--GTACACGATTTTC-GCTAAAATTTT
65 AGCCAGGGCCCCGAAACGCATTTTTAGCCAAAAAGTGATGGTACACGA-TTTCGGCTAAAATTTT
* * *
1115 GCAAAAAACTGACCCGAAA----------AGTTTTTGCCCCAATACTCA-AACAAATCATATGAT
129 GCAAAAAACTGACCCGAAAGTTTTTCCCCAATTTTTGCCACAATACTCAGAA-AAATCATATAAT
* * * * *
1169 TCAACGGCAAAAATATTTTTGGATTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTATTTCTG
193 TCAACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTT-TTTCTG
*
1234 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCATAAATGCATT
256 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAAATGCATT
1299 GTGGCTGA
321 GTGGCTGA
*
1307 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCATTCTGCCAAAAATCATGCAAAACTGA
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGA
** *
1372 GCCAGGGCCTAGAAACGCATTTTTAGCCAAAAACCGTGATGGCTAGTACACGATTTCGTCTAAAA
66 GCCAGGGCCCCGAAACGCATTTTTAGCCAAAAA--GTGAT-G---GTACACGATTTCGGCTAAAA
*
1437 TTATGCAAAAAACTGACCCGAAAAGTGTTTGT-CCCAATTTTTTAG-CACAATACTCAGAAAAAT
125 TTTTGCAAAAAACTGACCCG-AAAGT-TTT-TCCCCAA-TTTTT-GCCACAATACTCAGAAAAAT
* *
1500 CATATAATTCAACGCCAAAATTATTTTAGGGGTTTTCACGCTTTTAATATCGTTTTTCCATCTTT
185 CATATAATTCAACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT-TTT
* * * *
1565 TTTTCTGAATTTATTTCTAATTAAATCGTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAA
249 TTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAA
* * *
1630 ATCCAATGTGACT--
314 ATGCATTGTGGCTGA
* * * *
1643 GAGATTTGTTTAGATGAATATAGATATTTCGAGGAGTCTTTCTGGCAAAAATCATGTAAAACTGA
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGA
** * *
1708 GCCATAGCCCCGAAACGCGTTTTTAGCCAAAAA-TCAT-GTACACGATTTCGGCTAAAATTTTGC
66 GCCAGGGCCCCGAAACGCATTTTTAGCCAAAAAGTGATGGTACACGATTTCGGCTAAAATTTTGC
*
1771 AAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTTTTCCACAATACTCAGAAAAATCATATAATT
131 AAAAAACTGACCCG-AAAGTTTTTCCCCAA-TTTTTGCCACAATACTCAGAAAAATCATATAATT
*
1836 CAACGCCAAAACTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTT-TGAAT
194 CAACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCTGAAT
*** * * * * * *
1899 TTATTTCTAATTAAATTTTAATAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCAATGTG
259 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAAATGCATTGTG
1964 GCTGA
324 GCTGA
* *
1969 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGCCTTTCTACCAAAAATCATGCAAAACTGA
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGA
** *
2034 GTGAGGGCCCCGAAACGCATTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
66 GCCAGGGCCCCGAAACGCATTTTTAGCC-AAAA-AGTGAT-G---GTACACGATTTCGGCTAAAA
* *
2099 TTTTGC-AAAAACTTACCCGTAAAGTTTTTCCTCAATTTCTTGCCACAATACTCAGAAAAATCAT
125 TTTTGCAAAAAACTGACCCG-AAAGTTTTTCCCCAATTT-TTGCCACAATACTCAGAAAAATCAT
* * *
2163 ATAATTTAACGCCAAAACTATTTTAGGGTTTTTCACGCTTTTAATATCGTTTTTCCA--TTTTTT
188 ATAATTCAACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTT
* * * *
2226 CTGAATTTCTTTCTAAATAAATCGAAACAAGATTCAAATACTTCTAAAAATAAATCCGTAAATGC
253 CTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAAATGC
2291 ATTGTGGCTGA
318 ATTGTGGCTGA
* *
2302 GAGATTTGATTAAATGAATATAGATATTTCGAGAAGTCATTCTGCCAAAAATCATGCAAAACTGA
1 GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGA
** * *
2367 GCCAGGGCCTAGAAACGCATTTTTAGCC-AAAA---ATCG--CACGATTTCGGCTAAAATTTTGG
66 GCCAGGGCCCCGAAACGCATTTTTAGCCAAAAAGTGATGGTACACGATTTCGGCTAAAATTTTGC
* **
2426 AAAAAATTGACCCGAAAAGCGTTTCCCCAACTTTTTGCCACAATACTCAGAAAAATCATATAATT
131 AAAAAACTGACCCG-AAAGTTTTTCCCCAA-TTTTTGCCACAATACTCAGAAAAATCATATAATT
*
2491 CAACGCCAAAACTATTTTAGGGT
194 CAACGCCAAAATTATTTTAGGGT
2514 AAACAAGAAG
Statistics
Matches: 1904, Mismatches: 198, Indels: 156
0.84 0.09 0.07
Matches are distributed among these distances:
301 2 0.00
302 73 0.04
303 1 0.00
304 6 0.00
305 135 0.07
308 3 0.00
311 3 0.00
312 1 0.00
314 36 0.02
315 3 0.00
316 2 0.00
317 2 0.00
318 1 0.00
319 1 0.00
320 2 0.00
321 22 0.01
322 76 0.04
323 4 0.00
324 70 0.04
325 14 0.01
326 116 0.06
327 98 0.05
328 47 0.02
329 7 0.00
330 84 0.04
331 137 0.07
332 20 0.01
333 503 0.26
334 179 0.09
335 19 0.01
336 88 0.05
338 71 0.04
339 75 0.04
340 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (328 bp):
GAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGA
GCCAGGGCCCCGAAACGCATTTTTAGCCAAAAAGTGATGGTACACGATTTCGGCTAAAATTTTGC
AAAAAACTGACCCGAAAGTTTTTCCCCAATTTTTGCCACAATACTCAGAAAAATCATATAATTCA
ACGCCAAAATTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCTGAATTT
ATTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAATAAATCCGTAAATGCATTGTGGC
TGA
Found at i:14040 original size:5 final size:5
Alignment explanation
Indices: 14029--14069 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
14019 TCTCAAATTG
* *
14029 GAAAA AAAAA AAAAA GAAAA GAAAA GAAAA GAAAA GGAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA -GAAAA
14070 CAAACAGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:30415 original size:27 final size:26
Alignment explanation
Indices: 30372--30422 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
30362 TCTTACTCTC
* *
30372 TTTTTTTTTCTTTTTTGCCATAAATT
1 TTTTTTTTTATTATTTGCCATAAATT
30398 TTTTTTTTTATATATTTGCCATAAA
1 TTTTTTTTTAT-TATTTGCCATAAA
30423 AAAAGTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.22, C:0.10, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTTTTTTATTATTTGCCATAAATT
Found at i:33616 original size:2 final size:2
Alignment explanation
Indices: 33609--33633 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33599 TGTTAACTTC
33609 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
33634 GCCATTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39861 original size:26 final size:26
Alignment explanation
Indices: 39823--39874 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
39813 CCTTTCTAAT
*
39823 TATTTTATTTTCATATATATACTCAC
1 TATTTTATCTTCATATATATACTCAC
*
39849 TATTTTATCTTCATGTATATACTCAC
1 TATTTTATCTTCATATATATACTCAC
39875 GTAGTTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (26 bp):
TATTTTATCTTCATATATATACTCAC
Found at i:44172 original size:7 final size:7
Alignment explanation
Indices: 44160--44192 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
44150 CTTTGTGAGG
44160 TGGAGCC
1 TGGAGCC
44167 TGGAGCC
1 TGGAGCC
44174 TGGAGCC
1 TGGAGCC
44181 TGGAGCC
1 TGGAGCC
44188 TGGAG
1 TGGAG
44193 GGTCATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.24, G:0.45, T:0.15
Consensus pattern (7 bp):
TGGAGCC
Found at i:49322 original size:6 final size:6
Alignment explanation
Indices: 49311--49358 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
49301 GGTTTGGTGG
* *
49311 TCTATA TCTATA TCTATA TATATA TCTATA TCTATA TCTATA TATATA
1 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA
49359 CACACAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTATA
Found at i:49343 original size:24 final size:24
Alignment explanation
Indices: 49311--49358 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
49301 GGTTTGGTGG
49311 TCTATATCTATATCTATATATATA
1 TCTATATCTATATCTATATATATA
49335 TCTATATCTATATCTATATATATA
1 TCTATATCTATATCTATATATATA
49359 CACACAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (24 bp):
TCTATATCTATATCTATATATATA
Found at i:52535 original size:21 final size:21
Alignment explanation
Indices: 52511--52550 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52501 GCCCTCAACA
* *
52511 GCCTCATGCATGCGTTCCACC
1 GCCTCATCCATGCGGTCCACC
*
52532 GCCTCCTCCATGCGGTCCA
1 GCCTCATCCATGCGGTCCA
52551 TGCGCTCTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.45, G:0.20, T:0.23
Consensus pattern (21 bp):
GCCTCATCCATGCGGTCCACC
Found at i:53277 original size:10 final size:10
Alignment explanation
Indices: 53262--53302 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
53252 ACGGGCCACG
53262 CGCGGGCCAT
1 CGCGGGCCAT
*
53272 CGCGGGCCAC
1 CGCGGGCCAT
**
53282 CGCGGGCTGT
1 CGCGGGCCAT
53292 CGCGGGCCAT
1 CGCGGGCCAT
53302 C
1 C
53303 TCGGCCCAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.07, C:0.41, G:0.41, T:0.10
Consensus pattern (10 bp):
CGCGGGCCAT
Found at i:53287 original size:20 final size:21
Alignment explanation
Indices: 53253--53300 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
53243 GGGTCACGCA
53253 CGGGCCACGCGCGGGCCATCG
1 CGGGCCACGCGCGGGCCATCG
**
53274 CGGGCCAC-CGCGGGCTGTCG
1 CGGGCCACGCGCGGGCCATCG
53294 CGGGCCA
1 CGGGCCA
53301 TCTCGGCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.08, C:0.42, G:0.44, T:0.06
Consensus pattern (21 bp):
CGGGCCACGCGCGGGCCATCG
Found at i:54459 original size:73 final size:73
Alignment explanation
Indices: 54376--54522 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
54366 CCGTCCTGTT
54376 TTGCAGATTATTATATATGTAATGTTAAATAAGGCAGGATTAGCCTGAGAAGAAATTATAACCAC
1 TTGCAGATTATTATATATGTAATGTTAAATAAGGCAGGATTAGCCTGAGAAGAAATTATAACCAC
54441 GCAAAAGA
66 GCAAAAGA
54449 TTGCAGATTATTATATATGTAATGTTAAATAAGGCAGGATTAGCCTGAGAAGAAATTATAACCAC
1 TTGCAGATTATTATATATGTAATGTTAAATAAGGCAGGATTAGCCTGAGAAGAAATTATAACCAC
54514 GCAAAAGA
66 GCAAAAGA
54522 T
1 T
54523 AGTTAGCAGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (73 bp):
TTGCAGATTATTATATATGTAATGTTAAATAAGGCAGGATTAGCCTGAGAAGAAATTATAACCAC
GCAAAAGA
Done.