Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020857.1 Corchorus olitorius cultivar O-4 contig20890, 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: 5116
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1646 original size:333 final size:333
Alignment explanation
Indices: 33--3184 Score: 3078
Period size: 332 Copynumber: 9.6 Consensus size: 333
23 TTTTAGCATA
*
33 GTTAGTATACGATTTCGGCTAAAATTTAGCAAAAACTG-TCCCGAAAAATTTTTCCTCAATTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGAT-CCGAAAAATTTTTCCTCAATTTTT
**
97 TTTCACAATATTCATAAAAGAATATATAATTCAATCTCCAAAGATTGGAGGGCTTTTCACGCTTC
65 TGCCACAATATTCATAAAA-AATATATAATTCAATCTCCAAAGATTGGAGGGCTTTTCACGCTTC
* **
162 TAATATCGCTTTCCCTAA-TTTTTCTAAATTAATTTCTAATTAAATTTAAACCGGTTTCAGATGC
129 TAATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATGC
* * * *
226 TCATAAAA-CATAATTCTTAAATCCAATGTGGTTAAGATTTAATTAGATGAATATAGATATTAAA
194 TCATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTAA
* ** *
290 AGGAGTTTCTGCGCCAAAAATCATGCAAAAATGAGACGGGATCCCGGAACGCGTTTTTAGCTAAA
259 AGGAGTTTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAA
* *
355 AAACGTGATATT
324 AACCGTG--ATG
* * *
367 TTTAGTATACGATTTCGGCTAAAATTTAGCAAAAA-TTATCCAGAAAAATTTTTCCTCAATTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGATCC-GAAAAATTTTTCCTCAATTTTT
* * *
431 TGCCACAATATTCAGAAAAAAATATATAACTCAATCTCCAAAGATCGGAGGGCTTTTCACGCTTC
65 TGCCACAATATTCA-TAAAAAATATATAATTCAATCTCCAAAGATTGGAGGGCTTTTCACGCTTC
* * * *
496 TAATATC-TCTTTCCCTAATTTTTTCTAAAGTAATTTCTAATTAAATCAAAACTGGTTTCAAACG
129 TAATATCGT-TTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATG
* * *
560 CTCGTAAACT-AT-A-T-TTAAATCCAATGTGTTTGAGATTTGATTAGATGAATATAGATATTTA
193 CTCATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTA
* * * * * * *
621 AAGGAGTTTCTGCGCCAAAAACCATGCAAAAATAAGACAGGGTCCCGGAACGCGTTTTTAACTAA
258 AAGGAGTTTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAA
*
686 AAAAC--G-T-
323 AAACCGTGATG
* * * **
693 G-TAGT-----ATTTCTGCTAAAATTTAGCAAAAATTGTTCCGAAAAAGATTTCCTCAATTTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGATCCGAAAAATTTTTCCTCAATTTTTT
*** * *
752 GCCACAATATTCATAAAAAATATATAATTCAAGGGCTAGAAGATTGGAGGG--TTTCAAGCTTCT
66 GCCACAATATTCATAAAAAATATATAATTCAATCTCCA-AAGATTGGAGGGCTTTTCACGCTTCT
* * *
815 AATATCGTTTTTCCTAATTTTTTCTAAATTAATTTCTAATTAAATCTAAACCGATTTCAGATGCT
130 AATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATGCT
* * *
880 CATAAAAACATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATGGATACTTAAA
195 CATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTAAA
* * * *
945 GGAGTTTCTGCGCCAAAAATCATACAAAAATGAGACGGGGTCCCGGAACGCGTTTTTAGCTAAAA
260 GGAGTTTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAA
*
1010 A-CGTGATA
325 ACCGTGATG
* * * *
1018 TTTAGTATACGATTTCGGCTAAAATTTAGCAAAAA-TTATCCAGAAAAATTTTTCCTCAAGTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGATCC-GAAAAATTTTTCCTCAATTTTT
*
1082 TGCCACAATATTCATAAAAAAATATATAATTCAATCTCCAAAGATCGGAGGGCTTTTCACGCTTC
65 TGCCACAATATTCAT-AAAAAATATATAATTCAATCTCCAAAGATTGGAGGGCTTTTCACGCTTC
* *
1147 TAATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACTGGTTTTCAGACG
129 TAATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGG-TTTCAGATG
* * * * * * *
1212 CTCGTAAACT-AT-ATTTTTAAATCCAATGTGGCTGAGATTTGATTACATGAATTTAGATATTTA
193 CTCATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTA
* * * *
1275 AAGGAGTCTCTGCGGCAAAAATCATGCAAAACTGAGACGGGGCCCCGAAACGTGTTTTTAGCCAA
258 AAGGAGTTTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAA
1340 AAACCGTGATG
323 AAACCGTGATG
* * * * *
1351 GTTAGTACACGATTTCGGTTAAAATTTTGTCAAAAGCTGAGCCGAAAAAATTTT-CTCAATTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAG-CAAAAACTGATCCGAAAAATTTTTCCTCAATTTTT
* * *** * *
1415 GGACACAATGA-TCATAAAAAATATATAATTCAAGGGCTAGAAGATTGGA-GGATTTTCACGCTT
65 TGCCACAAT-ATTCATAAAAAATATATAATTCAATCTCCA-AAGATTGGAGGGCTTTTCACGCTT
* * * *
1478 CTAATATTGTTTTTCCTAATTTTTTCTAAATTAATTTCTAATTAAATCTAAACCGGTTTCAAATG
128 CTAATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATG
1543 CTCATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTA
193 CTCATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTA
* * * * *
1608 AAGGAGTTTCTGCGTCAAAAATCATTCAATAA-TGAGACGGGGTCCCGGAACGCCTTTTTAGCTA
258 AAGGAGTTTCTGCGCCAAAAATCATGCAA-AACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCA
* *
1672 AAAAACGTGATA
322 AAAACCGTGATG
* * *
1684 GTTAGTATACGATTTCGTCTAAAATTTAGCAAAAGCTG-TCCCGAAAAATTTTTCCTC-ATTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGAT-CCGAAAAATTTTTCCTCAATTTTT
* *
1747 TGCCACAATATTCATAAAAAATATATATTTCAATCTCCAAAGATCGGAGGGCTTTTCACGCTTCT
65 TGCCACAATATTCATAAAAAATATATAATTCAATCTCCAAAGATTGGAGGGCTTTTCACGCTTCT
* * *
1812 AATATCGTTTTCCCTAATTTTTTTCTAATTTAATTTCTAATTAAATCAAAACTGGTTTCAGACGC
130 AATATCGTTTTCCCTAA-TTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATGC
* * * * * * * *
1877 TCGTAAACT-AT-ATTTTTAAATCCAATATGGCTGAAATTTGATTAGATGAATTTAGATATTTAA
194 TCATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTAA
* * * * *
1940 AGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGAC-GGCCCCCGAAACGTGTTTTTAGCCAAA
259 AGGAGTTTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAA
2004 AACCGTGAT-
324 AACCGTGATG
** * * * *
2013 GTTA-T--ACGATTTCGGCTAAAATTTTTCAAAAACTGACCCTAAAAGTTTTACCTCAATTTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGATCCGAAAAATTTTTCCTCAATTTTTT
* *
2075 GCCACAATATTCATAAGAAATATATAATTCAATCTCCAAAAGATTGGAGGGTTTTTCACGCTTCT
66 GCCACAATATTCATAAAAAATATATAATTCAATCTCC-AAAGATTGGAGGGCTTTTCACGCTTCT
* * ** *
2140 AATATCGTTTT-CATTATTTTAAACTAAATTAATTTCTAATTAAATCAAAATCGGTTTCAGATGC
130 AATATCGTTTTCCCTAATTTT-TTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATGC
** * * * * * * * *
2204 TTGTAAAAACATATC-CTTAAATCCAATGTGGCTGATATTTGATTATATGAATAAAGATGTTTCA
194 TCATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTAA
* * *** * *
2268 AGGAGTCTT-GGTGCCAAAAATCATGCAAAACTGACTTGGGGCCCCAGAACGCGTTTTTAGCAAA
259 AGGAGT-TTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAA
2332 AAACCGCT-ATG
323 AAACCG-TGATG
** * * * * *
2343 GTTAGTACACGATTTCGGCTAAAATTTTTCAAAAACTTGATCTGAAATATTTCTCATCAATTTTC
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAAC-TGATCCGAAAAATTTTTCCTCAATTTTT
* * * * *
2408 GGCTAAAATACTCATAAAAAATATATAATTCAA-CGCCAAAAAGATTGGATGGGC----CACGCT
65 TGCCACAATATTCATAAAAAATATATAATTCAATCTCC--AAAGATTGGA-GGGCTTTTCACGCT
*
2468 TCTAATATCGTTTTCCC---------C-----T--TTT-T-ATT--AT-----CCGGTTTCTGAT
127 TCTAATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGAT
* * ** * * * *
2508 GCTCGTAAAAACA-AATCT-TTAAATCCAATGTGACTGAAATTTGGTTAAATGAATATAGTTATT
192 GCTCATAAAATCATAA-CTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATT
* ** * * * * * ***
2571 TCACTGAGTCTTGC-GCGCAAAAAATCATGCAAAAGTGAGCCGAGGCCCCGGGATATGTTTTTAG
256 TAAAGGAGT-TT-CTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAG
* * *
2635 CCTAAAATCGCGATG
319 CCAAAAACCGTGATG
* * * * * * * ** *
2650 GTTGGTATACACAATTTC-GCTAAATTTTTGCAAGAATTGACACCTGAAAGTTTTTTTTCTCAAT
1 GTTAG--TACACGATTTCGGCTAAAATTTAGCAAAAACTGA-TCC-GAAA-AATTTTTCCTCAAT
* * * * * * *
2714 TTTTAGCCACAATAATCATAGAAAATATATAATTCAA-CGTCAAAAAGATTGAATGACTTTTCAC
61 TTTTTGCCACAATATTCATAAAAAATATATAATTCAATC-TC-CAAAGATTGGAGGGCTTTTCAC
* * * * * * * *
2778 GCTTCTTATATTGTTTTTTCCTATTTTTTTCCAAATTAGTTTCTAATTAAATCGAAACCGATTTC
124 GCTTCTAATATCG-TTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTC
* * *
2843 AAATGCTCA-AAAA--A-AA-TCTTTATATCCAATGTGGTTGAG-TTCTG-TTAGATGAATATAT
188 AGATGCTCATAAAATCATAACTC-TTAAATCCAATGTGGTTGAGATT-TGATTAGATGAATATAG
* * * * * * ** * *
2901 ATATTTCAATGAGTCTTC-GCGCGAAAATTTATGCAAAACTGAGTCGGGGCCCCATAAGGCATTT
251 ATATTTAAAGGAGT-TTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTT
*
2965 TTAGCCTAAAACCGTGATG
315 TTAGCCAAAAACCGTGATG
* * * * * *
2984 GTTAGTACACAATTTCGGCTAAATTTTTGCAAAAGCTGA-CCCAAAATATTTATCCTCAATTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGATCCGAAAA-ATTTTTCCTCAATTTTT
* ** * * *** * * * * *
3048 TGTCCAAAATACCCACAAGAAATATATAATTCAAGAACAAAAAAATTGAAAGGCTTTTCTCGCTT
65 TG-CCACAATATTCATAAAAAATATATAATTCAATCTC-CAAAGATTGGAGGGCTTTTCACGCTT
* * * * *
3113 CTAAAATCGTTTTCCCT-A-TTTTTCTGAATTAATTTATAATTAAATCGAAACCAGTTTCAGATG
128 CTAATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATG
3176 CTCATAAAA
193 CTCATAAAA
3185 ACAGATCTTT
Statistics
Matches: 2358, Mismatches: 351, Indels: 223
0.80 0.12 0.08
Matches are distributed among these distances:
305 1 0.00
306 71 0.03
307 55 0.02
308 16 0.01
309 16 0.01
310 51 0.02
311 3 0.00
313 17 0.01
314 7 0.00
315 3 0.00
317 1 0.00
318 72 0.03
319 22 0.01
320 69 0.03
321 6 0.00
322 108 0.05
323 2 0.00
324 1 0.00
325 4 0.00
326 48 0.02
327 89 0.04
328 153 0.06
329 38 0.02
330 69 0.03
331 247 0.10
332 423 0.18
333 362 0.15
334 278 0.12
335 88 0.04
336 21 0.01
338 4 0.00
339 13 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (333 bp):
GTTAGTACACGATTTCGGCTAAAATTTAGCAAAAACTGATCCGAAAAATTTTTCCTCAATTTTTT
GCCACAATATTCATAAAAAATATATAATTCAATCTCCAAAGATTGGAGGGCTTTTCACGCTTCTA
ATATCGTTTTCCCTAATTTTTTCTAAATTAATTTCTAATTAAATCAAAACCGGTTTCAGATGCTC
ATAAAATCATAACTCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTAAAG
GAGTTTCTGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAA
CCGTGATG
Found at i:3270 original size:328 final size:329
Alignment explanation
Indices: 2514--3234 Score: 693
Period size: 331 Copynumber: 2.2 Consensus size: 329
2504 TGATGCTCGT
* * * ** *
2514 AAAAACAAATCTTTAAATCCAATGTGACTGAAATT-TGGTTAAATGAATATAGTTATTTCACTGA
1 AAAAA-AAATCTTTATATCC-ATGTG-CTG-AGTTCT-GTTAGATGAATATAAATATTTCAATGA
* * * * * *
2578 GTCTTGCGCGCAAAAAATCATGCAAAAGTGAGCCGAGGCCCCGGGAT-ATG--TTTTTAGCCTAA
61 GTCTT-CGCGCGAAAATTCATGCAAAACTGAGTCGGGGCCCC---ATAAGGCATTTTTAGCCTAA
* * * * *
2640 AATCGCGATGGTTGGTATACACAATTTCGCTAAATTTTTGCAAGAATTGACACCTGAAAGTTTTT
122 AACCGCGATGGTTAG-ATACACAATTTCGCTAAATTTTTGCAAGAACTGACACC-GAAAATATTT
* * * * * * * *
2705 TTTCTCAATTTTTAGCCACAATAATCATAGAAAATATATAATTCAACGTCAAAAAGATTGAATGA
185 ATCCTCAATTTTTAGCCAAAATAACCAAAGAAAATATATAATTCAACGACAAAAAAATTGAAAGA
* * * * * *
2770 CTTTTCACGCTTCTTATATTGTTTTTTCCTATTTTTTTCCAAATTAGTTTCTAATTAAATCGAAA
250 CTTTTCACGCTTCTAAAATCGTTTTTCCCTA-TTTTTTCCAAATTAATTTATAATTAAATCGAAA
2835 CCGATTTCAAATGCTC
314 CCGATTTCAAATGCTC
* *
2851 AAAAAAAATCTTTATATCCAATGTGGTTGAGTTCTGTTAGATGAATATATATATTTCAATGAGTC
1 AAAAAAAATCTTTATATCC-ATGT-GCTGAGTTCTGTTAGATGAATATAAATATTTCAATGAGTC
* *
2916 TTCGCGCGAAAATTTATGCAAAACTGAGTCGGGGCCCCATAAGGCATTTTTAGCCTAAAACCGTG
64 TTCGCGCGAAAATTCATGCAAAACTGAGTCGGGGCCCCATAAGGCATTTTTAGCCTAAAACCGCG
2981 ATGGTTAG-TACACAATTTCGGCTAAATTTTTGCAA-AAGCTGAC-CC-AAAATATTTATCCTCA
129 ATGGTTAGATACACAATTTC-GCTAAATTTTTGCAAGAA-CTGACACCGAAAATATTTATCCTCA
* * *
3042 ATTTTTTGTCCAAAATACCCACAAG-AAATATATAATTCAA-GAACAAAAAAATTGAAAGGCTTT
192 ATTTTTAG-CCAAAATAACCA-AAGAAAATATATAATTCAACG-ACAAAAAAATTGAAAGACTTT
* **
3105 TCTCGCTTCTAAAATCG-TTTTCCCTA-TTTTTCTGAATTAATTTATAATTAAATCGAAACC-AG
254 TCACGCTTCTAAAATCGTTTTTCCCTATTTTTTCCAAATTAATTTATAATTAAATCGAAACCGA-
*
3167 TTTCAGATGCTC
318 TTTCAAATGCTC
* *
3179 ATAAAAACAGATCTTTGA-ATTC-TGT-CTGAGATT-TGATTTGATGAATATAAATATTT
1 A-AAAAA-A-ATCTTT-ATATCCATGTGCTGAG-TTCTG-TTAGATGAATATAAATATTT
3235 TGAAGAAGTC
Statistics
Matches: 322, Mismatches: 45, Indels: 43
0.79 0.11 0.10
Matches are distributed among these distances:
327 7 0.02
328 62 0.19
329 8 0.02
330 29 0.09
331 65 0.20
332 20 0.06
333 19 0.06
334 54 0.17
335 31 0.10
336 21 0.07
337 6 0.02
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (329 bp):
AAAAAAAATCTTTATATCCATGTGCTGAGTTCTGTTAGATGAATATAAATATTTCAATGAGTCTT
CGCGCGAAAATTCATGCAAAACTGAGTCGGGGCCCCATAAGGCATTTTTAGCCTAAAACCGCGAT
GGTTAGATACACAATTTCGCTAAATTTTTGCAAGAACTGACACCGAAAATATTTATCCTCAATTT
TTAGCCAAAATAACCAAAGAAAATATATAATTCAACGACAAAAAAATTGAAAGACTTTTCACGCT
TCTAAAATCGTTTTTCCCTATTTTTTCCAAATTAATTTATAATTAAATCGAAACCGATTTCAAAT
GCTC
Found at i:4427 original size:31 final size:31
Alignment explanation
Indices: 4392--4464 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
4382 GCATGTCACA
**
4392 TGTACCAAAAAGCGACATGTGA-CACGCCATG
1 TGTACCAAAAAGCGACACAT-ATCACGCCATG
*
4423 TGTACCAAAAAGTGACACATATCACGCCATG
1 TGTACCAAAAAGCGACACATATCACGCCATG
4454 TGTACCAAAAA
1 TGTACCAAAAA
4465 AGTGACCATG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.18
Consensus pattern (31 bp):
TGTACCAAAAAGCGACACATATCACGCCATG
Found at i:4475 original size:21 final size:20
Alignment explanation
Indices: 4449--4490 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4439 ACATATCACG
4449 CCATGTGTACCAAAAAAGTGA
1 CCATGTGTACC-AAAAAGTGA
**
4470 CCATGTGTTTCAAAAAGTGA
1 CCATGTGTACCAAAAAGTGA
4490 C
1 C
4491 ACGTGGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
CCATGTGTACCAAAAAGTGA
Done.