Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017172.1 Corchorus olitorius cultivar O-4 contig17205, 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: 4688
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:693 original size:327 final size:331
Alignment explanation
Indices: 28--722 Score: 856
Period size: 327 Copynumber: 2.1 Consensus size: 331
18 GCCTCGGCTT
* * **
28 AGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGATTATCTATATTCATCTAATCAAATCTCAGC
1 AGTTTTGCATGATTTTAGGCGCCGAGACTCCTTGAATATCTATATTCATCTAATCAAATCTCAAA
*
93 CACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
66 CACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTA
* * * *
158 ATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAAGGCTTTCAATTTTTTTGATATTGA
131 ATTCAGAAAAATATGAAAAACAATATTAAAAGCGTGAAAAAGCCCTTCAATTTTTTTGATATCGA
* * * ** * *
223 ATTATATGTTTTTTATGAGTATTTTTGTTAGAAATCGAGAAAAAATCTTTCAGATCAATTTTTGC
196 ATTATATATTTTTCATGAGTATTTTAGCCAAAAATCGAGAAAAAATCTTTCAGAGCAATTTTTGC
* * *
288 AAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTCTCGGCTAAAAACGCGTTCCGGGGCC
261 AAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTCTCGGCTAAAAACGCGTTCCAGGACC
**
353 CTGCTC
326 CAACTC
*
359 AGTTTTGCATGATTTTAGGTG-C-A-A-TCCTTGAAATATCTATATTCATCTAATCAAATCTCAA
1 AGTTTTGCATGATTTTAGGCGCCGAGACTCCTTG-AATATCTATATTCATCTAATCAAATCTCAA
420 ACACATT-AGATTTAAGGATT-TGTTTTT-CGAA-CATCTGAATCTTGTTTCGATTTAATTAAAA
65 ACACATTGA-ATTTAAGGATTGT-TTTTTAC-AAGCATCTGAATCTTGTTTCGATTTAATTAAAA
* * ** *
481 ATTAATTCGGAAAAA-ATTGGAAAAACAATATTAGAAGC-TTTAAAATCCCTTCAATCTTTTTT-
127 ATTAATTCAGAAAAATA-T-GAAAAACAATATTAAAAGCGTGAAAAAGCCCTTCAAT-TTTTTTG
* * * * * * *
543 ATCTCGAATTATGTATTTTTCATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGGCAA
189 ATATCGAATTATATATTTTTCATGAGTATTTTAGCCAAAAATCGAGAAAAAATCTTTCAGAGCAA
* * * * *
608 TTTTTGC-AAAGTTTTAGCCGAAATCGTGTACTAACCATCATGATTTTCGGCTAAAAACGTGTTT
254 TTTTTGCAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTCTCGGCTAAAAACGCGTTC
672 CAGGACCACAACTC
319 CAGGACC-CAACTC
* * *
686 TGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAT
1 AGTTTTGCATGATTTTAGGCGCCGAGACTCCTTGAAT
723 CGTGTACGTT
Statistics
Matches: 309, Mismatches: 43, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
326 57 0.18
327 143 0.46
328 77 0.25
329 2 0.01
330 5 0.02
331 25 0.08
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (331 bp):
AGTTTTGCATGATTTTAGGCGCCGAGACTCCTTGAATATCTATATTCATCTAATCAAATCTCAAA
CACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTA
ATTCAGAAAAATATGAAAAACAATATTAAAAGCGTGAAAAAGCCCTTCAATTTTTTTGATATCGA
ATTATATATTTTTCATGAGTATTTTAGCCAAAAATCGAGAAAAAATCTTTCAGAGCAATTTTTGC
AAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTCTCGGCTAAAAACGCGTTCCAGGACC
CAACTC
Found at i:2000 original size:22 final size:22
Alignment explanation
Indices: 1965--2006 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1955 TTCCCGCAAC
*
1965 AACTCCTGGACAGGACTTGTGT
1 AACTCCTGCACAGGACTTGTGT
* *
1987 AACTCCTGCCCAGGTCTTGT
1 AACTCCTGCACAGGACTTGT
2007 CCTGTATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (22 bp):
AACTCCTGCACAGGACTTGTGT
Found at i:3802 original size:328 final size:330
Alignment explanation
Indices: 3089--3849 Score: 811
Period size: 332 Copynumber: 2.3 Consensus size: 330
3079 TTTTTGGTGG
* * * *
3089 TGAATTATATATATTTTATGAGTATTTTAGCCAAATATTGACGG-AATAATTTTTCAGATCATTT
1 TGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGA-GGAAAT-ATCTTTCGGATCAATT
* * * *** *
3153 TTTGC-AAAATTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAAAGTGTTTCG
63 TTTGCAAAAAGTTTAGCCGAAATCGTGTACTAACCATCACGATTCTCAACTAAAAAAGCGTTTCG
* * *
3217 GGGCCCCGACTTAGTTTTGCATGATTTTTGTCGCCGAGACAACTTGATATATCTATATTCATCTA
128 GGGCCCCGACTCAGTTTTG-ATGATTTTTGTCGCCGAGACAACCTGAAATATCTATATTCATCTA
* *
3282 ATCAAATCTCAGCCACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGATT
192 ACCAAATCTCAGACACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGATT
* ** * *
3347 TAATCAGAAATTAATTCAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAAGGCTTTCAATCT
257 TAATCAAAAATTAATTCAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAAGCCCTTCAATCT
3412 TTTTGGCAT
322 TTTTGGCAT
* * ** * * * *
3421 TGAATTATATGTTTTTTATGAGTATTTTTGTTAGAAATCGAGAAAAAATCTTTCGGATCAATTTT
1 TGAATTATAT-ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTT
* *
3486 TGCAAAAAGTTTAGCCGAAATCGTGTACGTTA-CATCACGGTTCTCAACTAAAAACA-CGTTTCG
65 TGCAAAAAGTTTAGCCGAAATCGTGTAC-TAACCATCACGATTCTCAACTAAAAA-AGCGTTTCG
* *
3549 GGG-CCCGGCTCAGTTTTG-TGATTTTTGGT-G-C-A-AC-CCCTGAAATATCTATATTCATCTA
128 GGGCCCCGACTCAGTTTTGATGATTTTT-GTCGCCGAGACAACCTGAAATATCTATATTCATCTA
*
3607 ACCAAATCTCAGACACATT-AGATTTAAGGATTTGTTTTTTTCGAA-CATCTGAATCTTGTTTCG
192 ACCAAATCTCAGACACATTGA-ATTTAAGGA-TTGTTTTTTAC-AAGCATCTGAATCTTGTTTCG
* * * ** *
3670 ATTTAATTAAAAATTAATTCGAAAAAAATTTGGAAAAACAATATTAGAAGC-TTTAAAATCCCTT
254 ATTTAATCAAAAATTAATTC--AAAAAATAT-GAAAAACAATATTAAAAGCGTGAAAAAGCCCTT
3734 CAATCTTTTT-G-AT
316 CAATCTTTTTGGCAT
* * *
3747 CTCGAATTATGTATTTTTCATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCACTT
1 -T-GAATTATATATTTTT-ATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATT
*** *
3812 TTTGC--AAAGTTTTAGGAAAAATCGTGTAGTAACCATCA
63 TTTGCAAAAAG-TTTAGCCGAAATCGTGTACTAACCATCA
3850 TGGTTTTTTG
Statistics
Matches: 356, Mismatches: 56, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
324 1 0.00
325 47 0.13
326 56 0.16
327 30 0.08
328 77 0.22
329 25 0.07
330 2 0.01
331 32 0.09
332 82 0.23
333 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (330 bp):
TGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTTT
GCAAAAAGTTTAGCCGAAATCGTGTACTAACCATCACGATTCTCAACTAAAAAAGCGTTTCGGGG
CCCCGACTCAGTTTTGATGATTTTTGTCGCCGAGACAACCTGAAATATCTATATTCATCTAACCA
AATCTCAGACACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGATTTAAT
CAAAAATTAATTCAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAAGCCCTTCAATCTTTTT
GGCAT
Found at i:3867 original size:328 final size:328
Alignment explanation
Indices: 3089--3916 Score: 853
Period size: 328 Copynumber: 2.5 Consensus size: 328
3079 TTTTTGGTGG
* * * *
3089 TGAATTATATATATTTTATGAGTATTTTAGCCAAATATTGACGG-AATAATTTTTCAGATCATTT
1 TGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGA-GGAAAT-ATCTTTCGGATCAATT
* * * * *
3153 TTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAA-AGTGTTTCG
63 TTTGCAAAGTTTTAGCCGAAATCGTGTAGTAACCATCA-GGTTTTTGGCTAAAAACA-CGTTTCG
* * *
3217 GGGCCCCGACTTAGTTTTGCATGATTTTT-GTCGCCGAGACAACTTGATATATCTATATTCATCT
126 GGG-CCCGGCTTAGTTTTG-ATGATTTTTGGTCGCCGAGACAACCTGAAATATCTATATTCATCT
* *
3281 AATCAAATCTCAGCCACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGAT
189 AACCAAATCTCAGACACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGAT
* ** * *
3346 TTAATCAGAAATTAATTCAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAAGGCTTTCAATC
254 TTAATCAAAAATTAATTCAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAAGCCCTTCAATC
3411 TTTTTGGCAT
319 TTTTTGGCAT
* * ** * * * *
3421 TGAATTATATGTTTTTTATGAGTATTTTTGTTAGAAATCGAGAAAAAATCTTTCGGATCAATTTT
1 TGAATTATAT-ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTT
* * ***
3486 TGCAAAAAG-TTTAGCCGAAATCGTGTACGTTA-CATCACGGTTCTCAACTAAAAACACGTTTCG
65 TGC--AAAGTTTTAGCCGAAATCGTGTA-GTAACCATCA-GGTTTTTGGCTAAAAACACGTTTCG
* *
3549 GGGCCCGGCTCAGTTTTG-TGATTTTTGGT-G-C-A-AC-CCCTGAAATATCTATATTCATCTAA
126 GGGCCCGGCTTAGTTTTGATGATTTTTGGTCGCCGAGACAACCTGAAATATCTATATTCATCTAA
*
3608 CCAAATCTCAGACACATT-AGATTTAAGGATTTGTTTTTTTCGAA-CATCTGAATCTTGTTTCGA
191 CCAAATCTCAGACACATTGA-ATTTAAGGA-TTGTTTTTTAC-AAGCATCTGAATCTTGTTTCGA
* * * ** *
3671 TTTAATTAAAAATTAATTCGAAAAAAATTTGGAAAAACAATATTAGAAGC-TTTAAAATCCCTTC
253 TTTAATCAAAAATTAATTC--AAAAAATAT-GAAAAACAATATTAAAAGCGTGAAAAAGCCCTTC
3735 AATCTTTTT-G-AT
315 AATCTTTTTGGCAT
* * *
3747 CTCGAATTATGTATTTTTCATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCACTT
1 -T-GAATTATATATTTTT-ATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATT
*** * *
3812 TTTGCAAAGTTTTAGGAAAAATCGTGTAGTAACCATCATGGTTTTTTGGCTAAAAACGCGTTTCA
63 TTTGCAAAGTTTTAGCCGAAATCGTGTAGTAACCATCA-GG-TTTTTGGCTAAAAACACGTTTCG
* *
3877 GGACCACGGCTTAGTTTTGCATGATTTTTGG-CACCGAGAC
126 GGGCC-CGGCTTAGTTTTG-ATGATTTTTGGTCGCCGAGAC
3917 TCCTTGAATC
Statistics
Matches: 404, Mismatches: 66, Indels: 50
0.78 0.13 0.10
Matches are distributed among these distances:
324 1 0.00
325 47 0.12
326 57 0.14
327 32 0.08
328 98 0.24
329 37 0.09
330 2 0.00
331 42 0.10
332 78 0.19
333 8 0.02
334 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (328 bp):
TGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTTT
GCAAAGTTTTAGCCGAAATCGTGTAGTAACCATCAGGTTTTTGGCTAAAAACACGTTTCGGGGCC
CGGCTTAGTTTTGATGATTTTTGGTCGCCGAGACAACCTGAAATATCTATATTCATCTAACCAAA
TCTCAGACACATTGAATTTAAGGATTGTTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATCA
AAAATTAATTCAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAAGCCCTTCAATCTTTTTGG
CAT
Found at i:4588 original size:336 final size:331
Alignment explanation
Indices: 4029--4675 Score: 802
Period size: 336 Copynumber: 1.9 Consensus size: 331
4019 AAATATCTAC
*
4029 ATTCATCTAATCAAATTTCACCCAAATTGGATTTAAGGATTTATAAAACAAGCATTTGAATCTTG
1 ATTCATCTAATCAAATTTCACCCAAATTGGATTTAAGAATTTATAAAACAAGCATTTGAATCTTG
** *
4094 TTTCGATTTAATTAGAAATTAATTCTGAAAATAATATGAAAAACGATATTAAAAGCATGAAAACC
66 CATCGATTTAATTAGAAATTAATTCAGAAAATAATATGAAAAACGATATTAAAAGCATGAAAACC
* * * * *
4159 CCTTCAATCTTTTTGACGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTGAGGAAA
131 ACTCCAATCTTTTTGACATTGAATTATATAATTTTTATGAGTATTGTAGCCAAAAATTGAGGAAA
* *
4224 TAACTTTTCGAGTCAATTTTTACAAAATTCTAGCTGATCGAAATCGTGTAATAATCATCGCGGTT
196 TAACTTTTCGAGTCAATTTTTACAAAATTCTA---G-TCGAAATCGTGTAATAACCATCACGG-T
4289 TTTGGCTAAAAACTCATTCTA-GGGCCCCGACTAAGTTTTGCATGATTTTTGGCGCCAAAACTCT
256 TTTGGCTAAAAACT-ATT-TACGGGCCCCGACTAAGTTTTGCATGATTTTTGGCGCCAAAACTCT
4353 TTGAGATGTCCAT
319 TTGAGATGTCCAT
* * * * *** *
4366 ATTCATTTAATCAAATTTCAGCTAAATTGGATTTAAGAATTTGTTTTTACGAGCATTTGAATCTT
1 ATTCATCTAATCAAATTTCACCCAAATTGGATTTAAGAATTT-ATAAAACAAGCATTTGAATCTT
* * *
4431 GCATCGATTTAATTAGAAATTAATTCAGACAAAT-AT-TG-AATACGATATTAAAAGCGTGAAGA
65 GCATCGATTTAATTAGAAATTAATTCAGA-AAATAATATGAAAAACGATATTAAAAGCATGAAAA
** * * *
4493 GTACTCCAATTTTTTTGGCATTGAATTATAT-ATATTTTATGAGTATTTTAGCCAAAAATTGACG
129 CCACTCCAATCTTTTTGACATTGAATTATATAAT-TTTTATGAGTATTGTAGCCAAAAATTGA-G
* * * * * * *
4557 G-AATAATTTTTTGGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTATTAACCATCACGGTT
192 GAAATAACTTTTCGAGTCAATTTTTACAAAATTCTAGTCGAAATCGTGTAATAACCATCACGGTT
* * * *
4621 TTGGCTAAAAAGTGTTTACGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCC
257 TTGGCTAAAAACTATTTAC-GGGCCCCGACTAAGTTTTGCATGATTTTTGGCGCC
4676 GAGACTCCTT
Statistics
Matches: 266, Mismatches: 38, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
329 2 0.01
330 2 0.01
331 47 0.18
332 23 0.09
333 1 0.00
335 2 0.01
336 98 0.37
337 42 0.16
338 45 0.17
339 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (331 bp):
ATTCATCTAATCAAATTTCACCCAAATTGGATTTAAGAATTTATAAAACAAGCATTTGAATCTTG
CATCGATTTAATTAGAAATTAATTCAGAAAATAATATGAAAAACGATATTAAAAGCATGAAAACC
ACTCCAATCTTTTTGACATTGAATTATATAATTTTTATGAGTATTGTAGCCAAAAATTGAGGAAA
TAACTTTTCGAGTCAATTTTTACAAAATTCTAGTCGAAATCGTGTAATAACCATCACGGTTTTGG
CTAAAAACTATTTACGGGCCCCGACTAAGTTTTGCATGATTTTTGGCGCCAAAACTCTTTGAGAT
GTCCAT
Done.