Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015198.1 Corchorus olitorius cultivar O-4 contig15231, 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: 2847
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:893 original size:325 final size:326
Alignment explanation
Indices: 283--2843 Score: 1507
Period size: 325 Copynumber: 7.9 Consensus size: 326
273 ATGGTAAAAA
* ** *
283 TGACTCGAAAAATTTTTCCTCAATTTTTGGAAAAAATACTCATAAAATATATAATTCAACGCC--
1 TGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCAAAAAATATATAATTCAACGCCAA
*
346 -----TTGGAGGACTTTTCACGCTTTTAATATCGATTTTCATATTTTTCCTAAATTAATTT-TAA
66 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTT-CT-AATTAATTTCTAA
* * *
405 TTAAATCGAAACAAGATTCAGATGCACATAAAAACAAATTCTTAAATCCAATGTGGTC-GAGATT
129 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACTGAGATT
* * * * *** *
469 TGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACAGAGTTGTG
194 TGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCACCAAAAATCATGCAAAACTGAACCGGG
* * * * * *
534 GCTCCAAAACGCGTTTTTAGCC-AAAAATCGTGATGATTAGTATATGATTTCAACTAAAATTTTG
259 GCCCCGAAACGCGTTTTTA-CCAAAAAACCGTGATGATTAGTAAACGATTTCAGCTAAAATTTTG
598 C-A-
323 CAAT
* *
600 TGACCCGAAAAATTTTACCGTCAATTTTTGGCTAAAATACTCAAAAAATATATAATTTAACGCCA
1 TGACCCGAAAAATTTTTCC-TCAATTTTTGGCTAAAATACTCAAAAAATATATAATTCAACGCCA
**
665 AAAAGATTGGAGGACTTTTCACGCTTTTTGTATCGTTTTTCATATTTTTCTAATTTAATTTCTAA
65 AAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAA-TTAATTTCTAA
* *
730 TTAAATCTG-AACAAGATTCAGATGCTCGTAAAAATAAATTCTTAAATCCAATGTAG-CT-ATGA
129 TTAAATC-GAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACTGA-GA
* * * * * *
792 TTTTATTAGATGAATATGGATATCTCAAAGAGTCTTGGCACAAAAAATCATGCAAAACTTAACCG
192 TTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCACCAAAAATCATGCAAAACTGAACCG
* * * * * *
857 GGGCCCCGTAACGCGTTTTTAGGC-AAAAACCGTGATGATTATTACACGATTTTCCGCTAGAATT
257 GGGCCCCGAAACGCGTTTTTA-CCAAAAAACCGTGATGATTAGTAAACGA-TTTCAGCTAAAATT
921 TTGCAAAAAT
320 TTGC---AAT
* * * ** * ** *
931 TGACTCG-AAAGTTATTTCCTCAAATTTAAGCCACGATACTCATAAAAATTATATGATTCAACGC
1 TGACCCGAAAAATT-TTTCCTCAATTTTTGGCTAAAATACTCA-AAAAA-TATATAATTCAACGC
* * * * * *
995 CAAAAAGATTGAAGGATTTTTCATGCTTATAATATCGTTTTTCGTATTATTTTCCGAATTAATTT
63 CAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTC--A-TATTTTTCTAATTAATTT
* *** * * *
1060 CTAATTAAATCGAAACATGATTCAGATGCT--TATTTTACAGATCCTTAAATTCAATGT-GACTG
125 CTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAAACAAATTCTTAAATCCAATGTGGACTG
* * * * * * *
1122 AGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTCGGCGCCGAAAATCATACAACACTGAA
189 AGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCACCAAAAATCATGCAAAACTGAA
* * * * * * *
1187 CAGGGTCCCCGGAACGCGTTTTTAGCGAAAAACCGTGATTTCGAATAACATAAACGATTTCAGCT
254 CCGGGGCCCCGAAACGCGTTTTTACCAAAAAACCGTGA--T-G-ATTA-GTAAACGATTTCAGCT
* *
1252 AATATTTTACAAAAAT
314 AAAATTTTGC---AAT
* * * **
1268 TGACCCGAAATA-TTTTCCTCAATTTTT-G-T----CA-T-AAAATATATATAATTCAATTCCAA
1 TGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCAAAAAATATATAATTCAACGCCAA
1324 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAAT
66 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-AATTAATTTCTAAT
* * ** * *
1389 TAAATTGAAAAAAGATTCAGATGCTCGTAAAAACAAATAGTTAAATACAATGTGG-TTGAGATTT
130 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACTGAGATTT
* * * * *
1453 GATTAGATGAATATAGATATTT-TAAGAAGTCTCGACGCC-AAAAT-ATGCAAAACTGAGCCTGG
195 GATTAGATGAATATAGATATTTCAAAG-AGTCTCGGCACCAAAAATCATGCAAAACTGAACCGGG
* *
1515 GCCCCGAAACGCATTTTTACCAAAAAACCGTGATGGTTAGTAAACGATTTCAGCTAAAATTTTGC
259 GCCCCGAAACGCGTTTTTACCAAAAAACCGTGATGATTAGTAAACGATTTCAGCTAAAATTTTGC
*
1580 AAAAAA
324 ---AAT
* * * *
1586 TGACCAGAGAAAA-TTTTCCTCAA---TT---T-AAA-GC-C---AAA-A-A-GATT----G--G
1 TGACCCGA-AAAATTTTTCCTCAATTTTTGGCTAAAATACTCAAAAAATATATAATTCAACGCCA
** ** ** * ** * * *
1629 AGGACTTTTCACG-CTTTTCATATCTTTTTTCATAT--TTTTCCGA-ATTAATTTCTAATTAA-A
65 AAAAGATTGGAGGACTTTTC--A-CGCTTTTAATATCGTTTTTC-ATATT--TTTCTAATTAATT
* ** * ** **** * **** * * *
1689 TCGAA--ACAA--GATTC-AGAATC--TCGCAAAAACAAATTCT----TAAATGCAATAT-AACT
124 TCTAATTA-AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACT
* * * * * **
1742 GAGTTTTGATCAGATGAATATGGATATTTCAAGGAATCTTAGCACCAAAAATCATGCAAAACTGA
188 GAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCACCAAAAATCATGCAAAACTGA
* ** * ** * * * *
1807 CCCGGGGCCTAGAACATGTTTTTTTGCC-AAAAACCGTGATGATTATTACACGATTTCGGCTAAA
253 ACCGGGGCCCCGAA-ACGCGTTTTTACCAAAAAACCGTGATGATTAGTAAACGATTTCAGCTAAA
1871 ATTTTGCAAAAAT
317 ATTTTGC---AAT
* * * * * *
1884 TGATCGGAAAGATATTACCTCAATTTTTGCCTAAAATACTCATAAAAAATATATAATTCAACGCC
1 TGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTC--AAAAAATATATAATTCAACGCC
* * * * * * *
1949 AAAAATATTGAAGG-TTTTTTACGCTTCTAATATTGTTTTTCCTACTTTTTCTGAATTAATTTCT
64 AAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCT-AATTAATTTCT
* * * *
2013 AATTAAATCGAAACAAAATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGG-CTGAGA
127 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACTGAGA
* * * * *
2077 TTTGATTCGATGAATATAGATATTTCAAAGAGTCTTGGCACAAAAAATCATGGACAACTG-ACCA
192 TTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCACCAAAAATCATGCAAAACTGAACC-
*** * ***** ** * *
2141 GGGGTTTC-ATAACGCGTTTTTAGCAAAAAAAAAAAAAAACCGTTATGTTACACGATTTCGGCTA
256 GGGGCCCCGA-AACGCGTTTTTACCAAAAAACCGTGATGA---TTA-G-TAAACGATTTCAGCTA
*
2205 ATATTTTGCAAAAAT
315 AAATTTTGC---AAT
* * * * * * *
2220 TGACCCGAAATATGTTTCCTCAATTTTTAGCCAAAATACTC--ATATTATATAATTCAATGCCAA
1 TGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCAAAAAATATATAATTCAACGCCAA
* * * * * * *
2283 AAAGATTGAAGGGCTTTTTACGCTTCTT-ATATCATTTTTCCTGTTTTTTCCGAATTAATTTCTA
66 AAAGATTGGAGGACTTTTCACGCTT-TTAATATCGTTTTTCAT-ATTTTT-CTAATTAATTTCTA
* *
2347 ATTAAAACGAAACAAGATTCAGATGCTTGT-------AA-----AAA--CAA--T-GACTGAGAT
128 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACTGAGAT
* * ** ** * *
2395 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGTCAAAAATCATTCAAAGCTGAACC-G
193 TTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCACCAAAAATCATGCAAAACTGAACCGG
* * * * * * * *
2459 GGCCCTGGAATGCGTTTTTAGCC-AAAAACTGTGATGATTATTACACGATTTCGGGTAAAATTTT
258 GGCCCCGAAACGCGTTTTTA-CCAAAAAACCGTGATGATTAGTAAACGATTTCAGCTAAAATTTT
*
2523 ACAAAAAT
322 GC---AAT
* * * * * * *
2531 TGACCC-AAAAGATATTTCCTCATTTTTTAGCCATAATACTCATAAAAATATATACTTCAACTCC
1 TGACCCGAAAA-ATTTTTCCTCAATTTTTGGCTAAAATACTCA-AAAAATATATAATTCAACGCC
* * * *
2595 AAAGAA-ATTGAAGGCCATTTCACGCTTTTAATATTGTTTCTTCATATTTTATTTCTGAATTAAT
64 AAA-AAGATTGGAGGACTTTTCACGCTTTTAATATCGTTT-TTCATA--TT-TTTCT-AATTAAT
* * * * *
2659 TTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAGCAAATCCTTAAATGCATTGT-GACT
123 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACT
* * * * * *
2723 AAGATTTTATTTGATAAATATAGATATTTC-AAGAAGTGTCGG-AGCCAAAAATCATGCAAAATT
188 GAGATTTGATTAGATGAATATAGATATTTCAAAG-AGTCTCGGCA-CCAAAAATCATGCAAAACT
* ** * *
2786 GAGCCGGGGCCCCG-AACGCGTTTTTAGCCGCAAAACCGTGATGGTTAGTACACGATTT
251 GAACCGGGGCCCCGAAACGCGTTTTTA-CCAAAAAACCGTGATGATTAGTAAACGATTT
2844 TGGC
Statistics
Matches: 1732, Mismatches: 364, Indels: 279
0.73 0.15 0.12
Matches are distributed among these distances:
296 44 0.03
297 10 0.01
298 80 0.05
299 9 0.01
300 6 0.00
301 2 0.00
302 5 0.00
303 2 0.00
304 2 0.00
305 11 0.01
306 19 0.01
307 9 0.01
308 14 0.01
310 3 0.00
311 61 0.04
312 6 0.00
313 7 0.00
314 45 0.03
315 12 0.01
316 27 0.02
317 116 0.07
318 86 0.05
319 24 0.01
320 13 0.01
321 20 0.01
322 2 0.00
323 51 0.03
324 60 0.03
325 248 0.14
326 72 0.04
327 10 0.01
328 1 0.00
329 4 0.00
330 35 0.02
331 95 0.05
332 87 0.05
333 237 0.14
334 72 0.04
335 11 0.01
336 76 0.04
337 30 0.02
338 8 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (326 bp):
TGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCAAAAAATATATAATTCAACGCCAA
AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAATTAATTTCTAATT
AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGACTGAGATTTG
ATTAGATGAATATAGATATTTCAAAGAGTCTCGGCACCAAAAATCATGCAAAACTGAACCGGGGC
CCCGAAACGCGTTTTTACCAAAAAACCGTGATGATTAGTAAACGATTTCAGCTAAAATTTTGCAA
T
Found at i:2381 original size:333 final size:328
Alignment explanation
Indices: 1615--2754 Score: 934
Period size: 331 Copynumber: 3.5 Consensus size: 328
1605 TCAATTTAAA
* * * * *
1615 GCCAAAAAGATTGGAGGACTTTTCACGCTT-TTCATATCTTTTTTCATATTTTTCCGAATTAATT
1 GCCAAAAAGATTGAAGGGCTTTTTACGCTTCTT-ATATCATTTTTCCTATTTTTCCGAATTAATT
* * *
1679 TCTAATTAAATCGAAACAAGATTCAGAAT-CTCGCAAAAACAAATTCTTAAATGCAATATAACTG
65 TCTAATTAAATCGAAACAAGATTCAG-ATGCTCGTAAAAACAAATCCTTAAATCCAATATAACTG
* * * *
1743 AGTTTTGATCAGATGAATATGGATATTTCAAGGAATCTTAGCACCAAAAATCATGCAAAACTGAC
129 AGATTTGATCAGATGAATATAGATATTTCAAAGAATCTTAGCACAAAAAATCATGCAAAACTGAC
* * * * ***** **
1808 CCGGGGCCTAGAACATGTTTTTTTGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAAT
194 CAGGGGCCTAGAACACGTTTTTTAGCAAAAAAAAAAAAAAATTATTACACGATTTCGGCTAAAAT
* *
1873 TTTGCAAAAATTGATCGGAAAGATATTACCTCAATTTTTGCCTAAAATACTCATAAAAAATATAT
259 TTTGCAAAAATTGACCCGAAAGATATTACCTCAATTTTTGCCTAAAATACTCAT---AAATATAT
1938 AATTCAAC
321 AATTCAAC
* * * ** *
1946 GCCAAAAATATTGAA-GGTTTTTTACGCTTCTAATATTGTTTTTCCTACTTTTTCTGAATTAATT
1 GCCAAAAAGATTGAAGGGCTTTTTACGCTTCTTATATCATTTTTCCTA-TTTTTCCGAATTAATT
* * * * **
2010 TCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
65 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATAACTGA
* * * *
2075 GATTTGATTC-GATGAATATAGATATTTCAAAGAGTCTTGGCACAAAAAATCATGGACAACTGAC
130 GATTTGA-TCAGATGAATATAGATATTTCAAAGAATCTTAGCACAAAAAATCATGCAAAACTGAC
** * *
2139 CAGGGGTTTCATAACGCG-TTTTTAGCAAAAAAAAAAAAAAACCGTTATGTTACACGATTTCGGC
194 CAGGGGCCT-AGAACACGTTTTTTAGCAAAAAAAAAAAAAAA---TTA--TTACACGATTTCGGC
* * * * *
2203 TAATATTTTGCAAAAATTGACCCGAAATATGTTTCCTCAATTTTTAGCC-AAAATACTCAT-ATT
253 TAAAATTTTGCAAAAATTGACCCGAAAGATATTACCTCAATTTTT-GCCTAAAATACTCATAAAT
*
2266 ATATAATTCAAT
317 ATATAATTCAAC
*
2278 GCCAAAAAGATTGAAGGGCTTTTTACGCTTCTTATATCATTTTTCCTGTTTTTTCCGAATTAATT
1 GCCAAAAAGATTGAAGGGCTTTTTACGCTTCTTATATCATTTTTCCT-ATTTTTCCGAATTAATT
* * *
2343 TCTAATTAAAACGAAACAAGATTCAGATGCTTGT-------AA-----AAA--C-A-ATGACTGA
65 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATAACTGA
* * * * * * * *
2392 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGTC-AAAAATCATTCAAAGCTGAA
130 GATTTGATCAGATGAATATAGATATTTCAAAGAATCTTAGC-ACAAAAAATCATGCAAAACTG-A
* * ** * ***** ** *
2456 CC-GGGCCCTGGAATGCG-TTTTTAGCCAAAAACTGTGATGATTATTACACGATTTCGGGTAAAA
193 CCAGGGGCCTAGAACACGTTTTTTAGCAAAAAAAAAAAAAAATTATTACACGATTTCGGCTAAAA
* * * * *
2519 TTTTACAAAAATTGACCCAAAAGATATTTCCTCATTTTTTAGCC-ATAATACTCATAAAAATATA
258 TTTTGCAAAAATTGACCCGAAAGATATTACCTCAATTTTT-GCCTAAAATACTCAT--AAATATA
*
2583 TACTTCAAC
320 TAATTCAAC
* * * * ** * *
2592 TCCAAAGAA-ATTGAAGGCCATTTCACGCTT-TTAATATTGTTTCTTCATATTTTATTTCTGAAT
1 GCCAAA-AAGATTGAAGGGCTTTTTACGCTTCTT-ATATCATTT-TTCCTA--TT-TTTCCGAAT
* * * * * *
2655 TAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAGCAAATCCTTAAATGCATTGTG
60 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATA
* * ** *
2720 ACTAAGATTTTATTTGATAAATATAGATATTTCAA
125 ACTGAGATTTGATCAGATGAATATAGATATTTCAA
2755 GAAGTGTCGG
Statistics
Matches: 651, Mismatches: 117, Indels: 80
0.77 0.14 0.09
Matches are distributed among these distances:
311 67 0.10
313 5 0.01
314 42 0.06
315 6 0.01
316 23 0.04
317 103 0.16
318 4 0.01
319 1 0.00
321 3 0.00
324 2 0.00
326 2 0.00
329 3 0.00
330 25 0.04
331 156 0.24
332 34 0.05
333 104 0.16
334 3 0.00
336 65 0.10
337 3 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (328 bp):
GCCAAAAAGATTGAAGGGCTTTTTACGCTTCTTATATCATTTTTCCTATTTTTCCGAATTAATTT
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATAACTGAG
ATTTGATCAGATGAATATAGATATTTCAAAGAATCTTAGCACAAAAAATCATGCAAAACTGACCA
GGGGCCTAGAACACGTTTTTTAGCAAAAAAAAAAAAAAATTATTACACGATTTCGGCTAAAATTT
TGCAAAAATTGACCCGAAAGATATTACCTCAATTTTTGCCTAAAATACTCATAAATATATAATTC
AAC
Done.