Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022471.1 Corchorus olitorius cultivar O-4 contig22504, 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: 30305
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4448 original size:331 final size:328
Alignment explanation
Indices: 3680--6395 Score: 2513
Period size: 331 Copynumber: 8.3 Consensus size: 328
3670 TACATCTAAC
*** * *
3680 GCCCTTCAATCTTTTTTATGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTAAGGA
1 GCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * * * *
3745 AATATCTTTCGGG------TTTGCAAAAATTTAGCCGATATC--G---T---CA-C-GGTTTTTT
65 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTT
* * ** * * * * *
3794 GGCTGAAAACGTGTTCCG-GTGCCACGACTTTGTTTTGCATGATTTAAT-ACACAGGGGCTCCTT
130 GGCTAAAAACGCGTTCCGAG-GCC-CGACTCAGTTTTGCATGATTT-TTGGCTCA-AGACTCCTT
* * * * *
3857 GAAATATTTTTTTTCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGTGC
191 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* * * * *
3922 ATTTGAATCTTGTTTCGATTTAATCAGCAATTAATTTGGAAATAAAATAGGAAAAACGATATTAG
256 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAAA-AAAATATGAAAAACGATATTAG
3987 AAGCGTGAAAAA
318 AAGCGTG-AAAA
* * * *
3999 GCCCTTCAATCTTTTTGGCGTTGAGTCATATATTTTTACGAGTATTTTAGCAAAAAATTGAGGAA
1 GCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
* * * *
4064 ATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAATTTTTG
66 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTG
* * * * * * *
4129 GCTAAAAAAGCGATCCGAGGTCCTATCTCAGTTTAGCATGATTTTTGGCTCCAAGACTCCATGAG
131 GCTAAAAACGCGTTCCGAGGCCCGA-CTCAGTTTTGCATGATTTTTGGCT-CAAGACTCCTTGAA
* * * * * *
4194 ATATCCATATACTTCTAATCAAATCTCAGCCACACTGGATTTAAGCATTTGTTTTTACGAGCATC
194 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
*
4259 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGT
259 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAGAAGCGT
4324 GAAAA
324 GAAAA
* * * * * * * * *
4329 GTCCTCCAATATTTTTGACATTAAATTATATATATATTATGAATATTTTATCCAAAAATTGAGGA
1 GCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * * * * * *
4394 AACATTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCATGGTTTTT
65 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTT
* * * *
4459 GGCTAAAAACTCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGA
130 GGCTAAAAACGCGTTCCGAGG-CCCGACTCAGTTTTGCATGATTTTTGGC-TCAAGACTCCTTGA
** * * * **
4524 AATATCTATATTCATCTAATAAAATGTTAGCCACATTGCATTTAAGGATTTGTTTTTACGAAAAT
193 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * * *
4589 CTAAATTTTGTTTTGATTTAATTAGAAATT-ATATCAGAAAAATATGAAAAACGATATTAAAAGT
258 CTGAATCTTGTTTCGATTTAATTAGAAATTAAT-TCAAAAAAATATGAAAAACGATATTAGAAGC
4653 GTGAAAA
322 GTGAAAA
* * * * *
4660 GCCCTTCAATC-TTTTGGCGTTAAATTATATATTCTTTATGAGTATTGTGGCTAAAACTTGAGGA
1 GCCCTTCAATCTTTTTGGCGTTGAATTATATATT-TTTATGAGTATTTTAGCCAAAAATTGAGGA
* * * *
4724 AATATCTTTCGGGTCACATTTTTGCAAAATTTTAACCGAAATCGTGTACGTTAGTCGAAATCACG
65 AAAATCTTTCGGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA-AC--CATCACG
* * * *
4789 GTTTTTGGCTAAAAACGCG-T-CGTGGCCACGACTCTGTTTTGCATGATTTTTGGCGTCGA-ACT
124 ATTTTTGGCTAAAAACGCGTTCCGAGGCC-CGACTCAGTTTTGCATGATTTTTGGC-TCAAGACT
* * *
4851 CCATGAAATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTATTTAC
187 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
* * *
4916 GTGCATCTGAATCTTGTTTCGATTTAATTAGCAATTAATTTAGAAATAAA-ATAGAAAAAACGAT
252 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAA-AAATAT-G-AAAAACGAT
*
4980 ATTAGAAGCATGAAAAA
313 ATTAGAAGCGTG-AAAA
* * * *
4997 GGCTTTCAAT-TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTTA-CTAGAAATTGAGG
1 GCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTA-TTTTAGCCAAAAATTGAGG
* * * * * * *
5060 TAAAATCTTTCGGGGCAAATTTTGCCAAATTTTAGCCGAAATTGTGTACTGACCATCACG-GTTT
64 AAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
* * * * **
5124 TCGCTAAAAACGCGTTCCG-GGACCC-AGCTCAATTTTTCACGATTTTTGG-TGCCAATTCTCCT
129 TGGCTAAAAACGCGTTCCGAGG-CCCGA-CTCAGTTTTGCATGATTTTTGGCT--CAAGACTCCT
* *
5186 TGAAATATCTATA--CATCTAACCAAATCTCAGCCATATTGGATTTAAAGATTTGTTTTTACGAG
190 TGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* * *
5249 CATCTGAATCTTGTTTTGATTTAATTA-AAATTTAATTCAGATAAAAATAGGAAAAACAATATTA
255 CATCTGAATCTTGTTTCGATTTAATTAGAAA-TTAATTCA-A-AAAAATATGAAAAACGATATTA
*
5313 GAAGCGTTAAAA
317 GAAGCGTGAAAA
*** * * * *
5325 GCCCTTCAATCTTTTTTATGTCGAATTATATATTTTTTATGAGTGTTTTAGCCAAAAATTAAGTA
1 GCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * * *
5390 AATATACTTTC--G-C---GTTTGCAAAAATTTAGCCGAAATC---T--T---CAT-A-GTTTTT
65 AAAAT-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
* * * * * ** ** *** *
5439 TGGCTGAAGACGTGTTCCGGGGCAACGACTTTGTTTTGCATGATTTTTTACGTGGGGGCTCCTTG
129 TGGCTAAAAACGCGTTCCGAGGC-CCGACTCAGTTTTGCATGATTTTTGGC-TCAAGACTCCTTG
* * * *
5504 AAATATCTTTCTTCATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGTGCA
192 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* * * *
5569 TTTGAATCTTGTTTCGATTTAATCAGCAATTAATTTGCAAATAAAATAGGAAAAACGATATTAGA
257 TCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAAA-AAAATATGAAAAACGATATTAGA
5634 AGCGTGAAAAA
319 AGCGTG-AAAA
* * * * * ** * *
5645 GGCTTTCAATTTTTTTTGGCGTTGAATTATATATCTTTTATAAGTATTTTTGATAGAAATTAAGG
1 GCCCTTCAA-TCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGG
* * * * *
5710 AAAAATCTTTCGGGTCATTTTTTGTAAAATTTAATCCGAAATCGTGTACTAACCGTCACAGA-TT
64 AAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GATTT
* * * * * * *
5774 TCGGCTAAAAGCGCGTTCCGAGGCCCGGCTTAGTTTTGCATGATTTTTGGTGTCAAGACTCTTTT
128 TTGGCTAAAAACGCGTTCCGAGGCCCGACTCAGTTTTGCATGATTTTTGG-CTCAAGACTCCTTG
* *
5839 AAATATCTATATTCATCTAAGCAAATCTCAGCCACATTAGATTTAAGGA-TT-TTTTTACGAGCA
192 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* *
5902 TCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAAATAAAA-ATAGCAAAAACAATATTAGA
257 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAA-AAAATAT-G-AAAAACGATATTAGA
*
5966 AGCGTTAAAA
319 AGCGTGAAAA
* * *
5976 GCCCTTCAATATTTTTGATC-TCGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGAA
1 GCCCTTCAATCTTTTTG-GCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAG--
* * * * * * *
6040 AAAAATATCTTTAGGATCAATTTTTGCAAAATTTTGGCCGAGATCTTGTACTAACCCAATCATGA
63 GAAAA-ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CC-ATCACGA
* * * * * * * *
6105 TTTTTGGCTAATAACGCGTTTC-AGGGCCACGGCTCTGTTTTACGTGATTTTTGGCGCCAAGACA
125 TTTTTGGCTAAAAACGCGTTCCGA-GGCC-CGACTCAGTTTTGCATGATTTTTGGC-TCAAGACT
* * * *
6169 CCTTGAAATATCTTTATTCATTTAATCAAATCTGAGCCACATTGGATTTAAGGATTTGTTTTTAC
187 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
* * *
6234 GTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTA
252 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTA
* *
6299 AAAGCATG-AAA
317 GAAGCGTGAAAA
* * * * *
6310 GTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTTGTCAAAAATTGAGAA
1 GCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGA
6375 AAAATCTTTCGGGTC-ATTTTT
65 AAAATCTTTCGGGTCAATTTTT
6396 ACAATCATGG
Statistics
Matches: 1958, Mismatches: 335, Indels: 196
0.79 0.13 0.08
Matches are distributed among these distances:
314 1 0.00
315 20 0.01
316 37 0.02
317 1 0.00
318 118 0.06
319 60 0.03
320 19 0.01
321 47 0.02
322 1 0.00
323 1 0.00
324 40 0.02
326 20 0.01
327 1 0.00
328 18 0.01
329 89 0.05
330 214 0.11
331 377 0.19
332 99 0.05
333 153 0.08
334 226 0.12
335 198 0.10
336 96 0.05
337 117 0.06
338 5 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (328 bp):
GCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTG
GCTAAAAACGCGTTCCGAGGCCCGACTCAGTTTTGCATGATTTTTGGCTCAAGACTCCTTGAAAT
ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
AATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAGAAGCGTGA
AAA
Found at i:6670 original size:12 final size:12
Alignment explanation
Indices: 6653--6686 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
6643 AATCAACATT
6653 CACATTATATTG
1 CACATTATATTG
6665 CACATTATATTG
1 CACATTATATTG
*
6677 CACATGATAT
1 CACATTATAT
6687 GTAACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (12 bp):
CACATTATATTG
Found at i:9252 original size:2 final size:2
Alignment explanation
Indices: 9245--9282 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9235 AGAATTTAGC
9245 TA TA TA TA TA 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 TA TA TA TA TA
9283 AAGAAAAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18250 original size:10 final size:10
Alignment explanation
Indices: 18235--18259 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18225 AGAAGGTCGA
18235 GTGTGCTTGT
1 GTGTGCTTGT
18245 GTGTGCTTGT
1 GTGTGCTTGT
18255 GTGTG
1 GTGTG
18260 TGTGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.44, T:0.48
Consensus pattern (10 bp):
GTGTGCTTGT
Found at i:24332 original size:29 final size:29
Alignment explanation
Indices: 24263--24325 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
24253 ACTTGTAGCG
* * *
24263 TTTGGACGTTTTGTCCCTTGAACTTCAAT
1 TTTGGACATTTTGCCCCATGAACTTCAAT
24292 TTTGGACATTTTGCCCCATGAACTTCAAT
1 TTTGGACATTTTGCCCCATGAACTTCAAT
24321 TTTGG
1 TTTGG
24326 GACTTTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCATGAACTTCAAT
Found at i:24499 original size:29 final size:30
Alignment explanation
Indices: 24425--24502 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 30
24415 CATTAGCCTG
*
24425 AGGGGGCAAATCGTCTCAAAATTGAAATTCA
1 AGGGGACAAATCGTC-CAAAATTGAAATTCA
*
24456 GGGGGTA-AAAT-GTCCAAAATT-AAAGTT-A
1 AGGGG-ACAAATCGTCCAAAATTGAAA-TTCA
24484 AGGGGACAAATCGTCCAAA
1 AGGGGACAAATCGTCCAAA
24503 TGCTACAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
27 1 0.03
28 12 0.30
29 16 0.40
30 3 0.08
31 8 0.20
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (30 bp):
AGGGGACAAATCGTCCAAAATTGAAATTCA
Done.