Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024635.1 Corchorus olitorius cultivar O-4 contig24668, 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: 13624
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:414 original size:26 final size:26
Alignment explanation
Indices: 385--437 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
375 TTTCTTAAAC
*
385 TATTTTCTTAATCTCTAGTTTAATTT
1 TATTTTATTAATCTCTAGTTTAATTT
** *
411 TATTTTATTGTTTTCTAGTTTAATTT
1 TATTTTATTAATCTCTAGTTTAATTT
437 T
1 T
438 CTATTTCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.06, T:0.66
Consensus pattern (26 bp):
TATTTTATTAATCTCTAGTTTAATTT
Found at i:615 original size:26 final size:26
Alignment explanation
Indices: 586--638 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
576 TTTCTTAAAC
*
586 TATTTTCTTAATCTCTAGTTTAATTT
1 TATTTTATTAATCTCTAGTTTAATTT
** *
612 TATTTTATTGTTTTCTAGTTTAATTT
1 TATTTTATTAATCTCTAGTTTAATTT
638 T
1 T
639 CTATTTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.06, T:0.66
Consensus pattern (26 bp):
TATTTTATTAATCTCTAGTTTAATTT
Found at i:635 original size:201 final size:200
Alignment explanation
Indices: 290--693 Score: 774
Period size: 201 Copynumber: 2.0 Consensus size: 200
280 TTTAAGTCAA
290 ATTCATGTCTTGTGTCCATGATCCATGATTTATTAGATCAAAATAATTACCTAAAGGAGAAGAAG
1 ATTCATGTCTTGTGTCCATGATCCATGATTTATTAGATCAAAATAATTACCTAAAGGAGAAGAAG
355 TATGTTTTTAATCCATTGTTTTTCTTAAACTATTTTCTTAATCTCTAGTTTAATTTTATTTTATT
66 TATGTTTTTAATCCATTGTTTTTCTTAAACTATTTTCTTAATCTCTAGTTTAATTTTATTTTATT
420 GTTTTCTAGTTTAATTTTCTATTTCGAAAAAAACCCAT-AAAATCCCCTTTGGTAAGACTTTCTT
131 GTTTTCTAGTTTAATTTTCTATTTC--AAAAAACCCATAAAAATCCCCTTTGGTAAGACTTTCTT
484 TAGTGTG
194 TAGTGTG
491 ATTCATGTCTTGTGTCCATGATCCATGATTTATTAGATCAAAATAATTACCTAAAGGAGAAGAAG
1 ATTCATGTCTTGTGTCCATGATCCATGATTTATTAGATCAAAATAATTACCTAAAGGAGAAGAAG
556 TATGTTTTTAATCCATTGTTTTTCTTAAACTATTTTCTTAATCTCTAGTTTAATTTTATTTTATT
66 TATGTTTTTAATCCATTGTTTTTCTTAAACTATTTTCTTAATCTCTAGTTTAATTTTATTTTATT
*
621 GTTTTCTAGTTTAATTTTCTATTTCTAAAAACCCATAAAAATCCCCTTTGGTAAGACTTTCTTTA
131 GTTTTCTAGTTTAATTTTCTATTTCAAAAAACCCATAAAAATCCCCTTTGGTAAGACTTTCTTTA
686 GTGTG
196 GTGTG
691 ATT
1 ATT
694 TGGATTTAAT
Statistics
Matches: 201, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
199 10 0.05
200 36 0.18
201 155 0.77
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (200 bp):
ATTCATGTCTTGTGTCCATGATCCATGATTTATTAGATCAAAATAATTACCTAAAGGAGAAGAAG
TATGTTTTTAATCCATTGTTTTTCTTAAACTATTTTCTTAATCTCTAGTTTAATTTTATTTTATT
GTTTTCTAGTTTAATTTTCTATTTCAAAAAACCCATAAAAATCCCCTTTGGTAAGACTTTCTTTA
GTGTG
Found at i:4128 original size:314 final size:314
Alignment explanation
Indices: 3097--4722 Score: 1355
Period size: 314 Copynumber: 5.1 Consensus size: 314
3087 AATGATTCCA
* * * * * **
3097 TTTTGTTGCCGTTGAATTATATATTGTTTATG-AGTATTGTGGCAAAAAATTGAGAAAAAAAAAA
1 TTTT-TTGGCGTTGAATTATATATTTTTTCTGAAGTATTATCGCAAAAAATTGAG--AAAAAACT
* * *
3161 TTTCGGGTCAGTTTTTAGCCGAAATCGGGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTT
63 TTTCAGGTCA-ATTTTAGCCGAAATC--GTGCT-----TCACGGTTTTTGGCTAAAAACGCGTTT
** * * * * *
3226 CAGGG-CCTCGACTCAGCCTTCCATGGTTTTT-GCAATAAAGACTCCATAAAATATCTATATTCA
120 C-GGGACC-CGACTCAGTTTTGCATGATTTTTGGC-AGAAAGACTCCTTGAAATATCTATATTCA
* * * * * * *
3289 TCTAACCAAATCACAACTACATTGGATTTAAGGATTTGGTTTTACAAGCATTTGAATCTTGTTTC
182 TCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
* * * *
3354 AATTTAATTAGAAATAAATTTGGGGAAAAAAAAGGAAAAACGATATTAGAAGCATGAAAAACCCT
247 GATTTAATTAGAAATAAA-TT-CGG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCT
3419 TCAAT-
309 TCAATC
* * * * *
3424 TTCTTTGGTGTTAAATTATATA-TTTTTCT-AAGTATTCTGGCAAAAAATTGAGAAAAAACTTTG
1 TTTTTTGGCGTTGAATTATATATTTTTTCTGAAGTATTATCGCAAAAAATTGAGAAAAAACTTT-
* * *
3487 CGGGTCAGTTTTTGCGAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTCTTGGCTAAAAA
65 ----TCAG---GT-C--AATTTTAGCCGAAATCGTG--CT-----TCACGGTTTTTGGCTAAAAA
* * * * * * * * * * *
3552 TGCGTTCCGAAGTCCGGGCTCAATTTGGCATGATTTTTGG-TGCAAAGATTCCTTGAAATACCTA
113 CGCGTTTCG-GGACCCGACTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTA
* * * * * * *
3616 TATTCATCGAAGCAAATCTCAGGCACATTGGATATAACGATTTG-TTTTACGAACATCTGAATCT
176 TATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* * ** * *
3680 TGATTCGATTTAATAAGAAATTGATTCAGAAAAAAAAATGGAAAAACGATATTAGAAACGTGAAA
241 TGTTTCGATTTAATTAGAAATAAATTC-G--GAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
*
3745 AACCCATCAATC
303 AACCCTTCAATC
* *
3757 -TTTTTGGCATTGAATTATATATTTTTTCTGAA-TAATT-T-GCAAAGAATTGAG-AAAAACTTT
1 TTTTTTGGCGTTGAATTATATATTTTTTCTGAAGT-ATTATCGCAAAAAATTGAGAAAAAACTTT
** * *
3817 TCATTTCAGTTTTAGCTGAAATCGTGTACTTCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCC
65 TCAGGTCAATTTTAGCCGAAATCGTG--CTTCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCC
*
3882 GACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAC
128 GACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
*
3947 CTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAG
193 CTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * ** *
4012 AAATTAATTCGGAAAAAATGGAAAAGCGATATTAGAAGCTTGAAAAGTCCGTCAATC
258 AAATAAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATC
*
4069 TTTTTTGGCGTTTAATTATATATTTTTTCTGAA-TAGTT-T-GC-AAAAATTGAGAAAAAAACTT
1 TTTTTTGGCGTTGAATTATATATTTTTTCTGAAGTA-TTATCGCAAAAAATTGAG-AAAAAACTT
* * * ** * * **
4130 TTCGGGTCAGTTTTTAGCCGAAATCGTGCATCATTGTTTTCGGCTAAAAACGCATTTCAGGGTTC
64 TTCAGGTCA-ATTTTAGCCGAAATCGTGCTTCACGGTTTTTGGCTAAAAACGCGTTTC-GGGACC
* * ** * **
4195 TGTCTCAGTTTTAAATGATTTTTGGCAGAAAGACTCCTTGAAATATTTATAAACATCTAACCAAA
127 CGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
* *
4260 TCTCAGCCACAATGCATTTGAA-TATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
192 TCTCAGCCACAATGGATTT-AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * * * *
4324 AGAAATAAATTCAGGGAAAAAAAAAAGAAAAAACGAAATTAAAAGCGTG-AAAATCCTTCATTC
256 AGAAATAAATTC--GG---AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATC
* * * *
4387 -TTTTTGGCGTTGAATTATATTTTTTTTTTACAAGTATTATCGCAAAAAATTGAGAAAAAAATTT
1 TTTTTTGGCGTTGAATTATATATTTTTTCT-GAAGTATTATCGCAAAAAATTGAGAAAAAACTTT
* * *
4451 TC-GGTCAATTTT--TC---A--G-G--T--CGGTTTTTGGCTAAAAACGCGTTTCGCGGACTCA
65 TCAGGTCAATTTTAGCCGAAATCGTGCTTCACGGTTTTTGGCTAAAAACGCGTTTCG-GGACCCG
* * * * *
4503 ACTCAATTTTGCATTG-TTTTTGGCATAAAAACTCCCTGAAATACCTATATTCATCTAACCAAAT
129 ACTCAGTTTTGCA-TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * * *
4567 CTCAGCCA-AATTGGATTTTAGGATTTGTTTATACGAGCATATCTAAATCTTGTTTCGAATTAAT
193 CTCAGCCACAA-TGGATTTAAGGATTTGTTTTTACGAGC--ATCTGAATCTTGTTTCGATTTAAT
* * *
4631 TAGAAATAAAATTTGGAAAAAATTGGAAAAACGATATAAGAAGCGTGAAAAACCCTTTAA--
255 TAGAAAT-AAATTCGGAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATC
**
4691 TTTTTTAACGTTGAATTATATATTTTTTCTGA
1 TTTTTTGGCGTTGAATTATATATTTTTTCTGA
4723 GTTTTGTGGC
Statistics
Matches: 1068, Mismatches: 177, Indels: 131
0.78 0.13 0.10
Matches are distributed among these distances:
304 7 0.01
305 48 0.04
306 111 0.10
307 4 0.00
308 30 0.03
309 5 0.00
310 1 0.00
311 1 0.00
312 49 0.05
313 62 0.06
314 225 0.21
315 86 0.08
316 3 0.00
317 26 0.02
318 19 0.02
319 32 0.03
320 34 0.03
321 10 0.01
322 1 0.00
323 10 0.01
325 26 0.02
326 18 0.02
327 3 0.00
328 3 0.00
331 15 0.01
332 107 0.10
333 123 0.12
334 9 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (314 bp):
TTTTTTGGCGTTGAATTATATATTTTTTCTGAAGTATTATCGCAAAAAATTGAGAAAAAACTTTT
CAGGTCAATTTTAGCCGAAATCGTGCTTCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCGAC
TCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC
AGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
TAAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATC
Found at i:8030 original size:2 final size:2
Alignment explanation
Indices: 8023--8056 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8013 AGGGACAATC
8023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8057 AGAGAATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10664 original size:19 final size:18
Alignment explanation
Indices: 10640--10675 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10630 TGAAGACTTA
10640 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
10659 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
10676 ATTATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.