Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002647.1 Corchorus capsularis cultivar CVL-1 contig02655, 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: 1984
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34
Found at i:170 original size:24 final size:22
Alignment explanation
Indices: 91--268 Score: 94
Period size: 22 Copynumber: 7.8 Consensus size: 22
81 GATAATCTTT
91 CTATGAAATTGTGATAATTAACC-AC
1 CTATGAAATT-T--TAA-TAACCAAC
*
116 CTTATGAAATTTCAATAACCAAC
1 C-TATGAAATTTTAATAACCAAC
* *
139 CTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTTAATAACC--AAC
**
163 CTATGAAATTTTGGTAACC-AC
1 CTATGAAATTTTAATAACCAAC
**
184 TCTATGAAATTTTGGTAACC-AC
1 -CTATGAAATTTTAATAACCAAC
* * **
206 ACTATGGAATTTTGATAACC-TT
1 -CTATGAAATTTTAATAACCAAC
* * *
228 CTCATGGAATTATAATAACCATC
1 CT-ATGAAATTTTAATAACCAAC
* *
251 TTATGAAATTTTGATAAC
1 CTATGAAATTTTAATAAC
269 GACATAGAGA
Statistics
Matches: 126, Mismatches: 20, Indels: 17
0.77 0.12 0.10
Matches are distributed among these distances:
21 3 0.02
22 87 0.69
23 7 0.06
24 18 0.14
25 2 0.02
26 9 0.07
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCAAC
Found at i:191 original size:22 final size:22
Alignment explanation
Indices: 109--268 Score: 114
Period size: 22 Copynumber: 7.2 Consensus size: 22
99 TTGTGATAAT
**
109 TAACCAC-CTTATGAAATTTCAA
1 TAACCACTC-TATGAAATTTTGA
* *
131 TAACCAAC-CTAAGAAATTTTAA
1 TAACC-ACTCTATGAAATTTTGA
*
153 TAACCTGA-TCCTATGAAATTTTGG
1 TAACC--ACT-CTATGAAATTTTGA
*
177 TAACCACTCTATGAAATTTTGG
1 TAACCACTCTATGAAATTTTGA
* *
199 TAACCACACTATGGAATTTTGA
1 TAACCACTCTATGAAATTTTGA
* * * *
221 TAACC-TTCTCATGGAATTATAA
1 TAACCACTCT-ATGAAATTTTGA
243 TAACCA-TCTTATGAAATTTTGA
1 TAACCACTC-TATGAAATTTTGA
265 TAAC
1 TAAC
269 GACATAGAGA
Statistics
Matches: 114, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.02
22 90 0.79
23 6 0.05
24 16 0.14
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCACTCTATGAAATTTTGA
Found at i:582 original size:31 final size:31
Alignment explanation
Indices: 547--617 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
537 TGGCAATTTA
* *
547 GAAATATGTTTTAAAAA-AAGGGGTATAATTG
1 GAAATATGTTTTAAAAATAA-GGGCACAATTG
578 GAAATATGTTTTAAAAATAAGGGCACAATTG
1 GAAATATGTTTTAAAAATAAGGGCACAATTG
609 GAAATATGT
1 GAAATATGT
618 AATAAGGGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGCACAATTG
Found at i:1835 original size:332 final size:324
Alignment explanation
Indices: 688--1884 Score: 1031
Period size: 333 Copynumber: 3.6 Consensus size: 324
678 ATATATATAT
* * * * * * * *
688 ATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTATTATCGTTTTTC-ATATC
1 ATATATAATTCAACGTCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTCCTATTTT
* * *
752 TTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCAT-ATAAAAAGAAATCCTTAA
66 TTTC-AAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGC-TCGTAAAAACAAATCCTTAA
* * * * *
816 ATCCAATGTGGCTGAGATTTGATTAGATAAATAAAGATATTTCAAGGAGACTCGGCGCAAAAAAA
129 ATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGC-C--AAAAA
* * * * *** * * *
881 TCATGCAAAACAAAGCCGTGGCCCTGAAAAGCGTTTTTAGTCAAAAACCGTGATTGTTAGTAAAC
191 TCATGCAAAACTAAGCCG-GGTCCTGAACA-CGTTTTTAG-CAAAAAACACCA-TGATGGTACAC
* * * ** * *
946 GATTTCGGCTAAAATTTTGTAAATATTGAAT-TGAAAGATATTTCCTTGATTTTTGGCTAAAATA
252 GATTTCGGCTAAAATTTTGCAAAAATTG-ATCTGAAAGAT-TTTTCTCAATTTTTAGCCAAAATA
1010 TCCATAAAAA
315 TCCATAAAAA
* ** * * * * * * *
1020 TTTATATAATTTGACATCAAAAAGATGGAAGGGCTTTTAACGTTTATAATATTGTTTTTCCTA-T
1 -ATATATAATTCAACGTCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCG-TTTTCCTATT
* * * * * * * * *
1084 TTTCTCGAATTGATTTTTGATTAAATCAAAACAAGATTCAGATTCTCGTAAAAACAAATCTTTAA
64 TTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAA
** * * *
1149 ATTTAATATGGCTAATATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAAT
129 ATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGG--CCAAAAAT
* * * ** **
1214 CATGCAAAACTGAGCCGGATCCCGGAACACGTTTTTAGC-TGAAA-ACTGTGATGGTTAGCACAC
192 CATGCAAAACTAAGCCGGGT-CCTGAACACGTTTTTAGCAAAAAACACCATGATGG-T---ACAC
* * * ** *
1277 GATTTTGGCTAAAATTTTGCAAAAATTGATCTGAAAGATTTTTCCTCTAGTTTTAGAGAAAATAA
252 GATTTCGGCTAAAATTTTGCAAAAATTGATCTGAAAGATTTTT-CTCAATTTTTAGCCAAAATAT
*
1342 CCATAAACA
316 CCATAAAAA
* * ** * * * *
1351 ATATATAATTCAATGTCAAAAATATTGAAGGGTTTTTCACGATTCAAATATCATTTTTTTCTATT
1 ATATATAATTCAACGTCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATC--GTTTTCCTATT
* * * * *
1416 TTACTTTTACATTAATTTCTGATTAAATCGAAACAAGATTTAGAA-ACTCGTAAAAACAAATCCT
64 TT--TTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCA-AATGCTCGTAAAAACAAATCCT
** * * * * *
1480 TAAATAAAATGTGTCTAAGATTTGGTTAGATAAATATAGATGTATTTTTAAGGTTTGTTTTAGCC
126 TAAATCCAATGTGGCTAAGATTTGGTTAGATAAATATAGA--TA-TTTCAAGG--AGTCTTGGCC
* * *
1545 AAAAATTATTCAAAACTAACCCAGGGTCCTAGAACACGTTTTTAGCCAAAAAACACCATGATGGT
186 AAAAATCATGCAAAACTAAGCC-GGGTCCT-GAACACGTTTTTAG-CAAAAAACACCATGATGGT
* ** *
1610 ACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAATTATTTTTCTCAATTTTTAGCCACAA
248 ACACGATTTCGGCTAAAATTTTGCAAAAATTGATCTGAAAGATTTTTCTCAATTTTTAGCCAAAA
*
1675 TATTCATAAAAA
313 TATCCATAAAAA
* * *
1687 ATACATTATTCAACGTCAAAAAGATTGAAGGACTTCTCACGCTTCTAATATCGTTTTCCTATTTT
1 ATATATAATTCAACGTCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTCCTATTTT
*
1752 TTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAAT
66 TTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT
* * * * * * *
1817 CCAATGTGGATAAGATTTGGTCAGATGAATTTAGATATTTTAAGGAGTTTTGCCACAAAAAATCA
131 CCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGC-C-AAAAATCA
1882 TGC
194 TGC
1885 TGACCTGGTC
Statistics
Matches: 681, Mismatches: 152, Indels: 66
0.76 0.17 0.07
Matches are distributed among these distances:
327 10 0.01
328 2 0.00
329 19 0.03
330 47 0.07
331 77 0.11
332 115 0.17
333 132 0.19
334 102 0.15
335 3 0.00
336 67 0.10
337 72 0.11
338 17 0.02
339 6 0.01
340 4 0.01
341 8 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (324 bp):
ATATATAATTCAACGTCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTCCTATTTT
TTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT
CCAATGTGGCTAAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGCCAAAAATCATG
CAAAACTAAGCCGGGTCCTGAACACGTTTTTAGCAAAAAACACCATGATGGTACACGATTTCGGC
TAAAATTTTGCAAAAATTGATCTGAAAGATTTTTCTCAATTTTTAGCCAAAATATCCATAAAAA
Done.