Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008974.1 Corchorus olitorius cultivar O-4 contig09001, 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, 649
Length: 1083
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Found at i:573 original size:154 final size:154
Alignment explanation
Indices: 264--1082 Score: 1222
Period size: 154 Copynumber: 5.3 Consensus size: 154
254 CAGATTCTCC
* *
264 TTCCAAATGAGCTAAAAACTCCACAGTGGACTAATCTCACCAAAATGATTATAGTTTGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
* * *
329 ACAATGGAAAG-AAAGCTTTGAGGTTTGCCAAATCGAAGCCGATTCAAAACGGATCTAATGGGCC
66 ACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
393 CCGAAAGGCCCAAAATAACAAGTG
131 CCGAAAGGCCCAAAATAACAAGTG
417 TTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATGATTATAGTTAGAT-CAT
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAG-TCCAT
*
480 AAACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGG
64 AAACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
*
545 CCCCGAAAGGCCTAAAATAACAAGTG
129 CCCCGAAAGGCCCAAAATAACAAGTG
* * ** *
571 TTCCAAATGAGCTAAAAATTTCACAGTGGAC-ATGTCTCTAAAAAAATGATTATAGTTTGTCCAT
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTC-ACCAAAATGATTATAGTTAGTCCAT
* * * *
635 AAACAATGAAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAATCGGAACTAATGGG
64 AAACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
*
700 CCCCGAAAGGCCTAAAATAACAAGTG
129 CCCCGAAAGGCCCAAAATAACAAGTG
* * *
726 TTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTTAGTCCCTAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
* *
791 CCAATGGAAAGAAAAGCA-TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGC
66 ACAATGGAAAGAAAAG-ATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
*
855 CCCGATAGGCCCAAAATAACAAGTG
130 CCCGAAAGGCCCAAAATAACAAGTG
*
880 TTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
**
945 ACAATGGAAAGAAAAGCA-TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGC
66 ACAATGGAAAGAAAAG-ATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
** * *
1009 CTGGATAGGCCC-CAAT-ACAAGTG
130 CCCGAAAGGCCCAAAATAACAAGTG
* * *
1032 TTCCAAATTAGCTAAAAACTTCACAGTGAACTAATCTTACCGAAAATGATT
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAATGATT
1083 C
Statistics
Matches: 616, Mismatches: 42, Indels: 16
0.91 0.06 0.02
Matches are distributed among these distances:
152 45 0.07
153 82 0.13
154 347 0.56
155 141 0.23
156 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (154 bp):
TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
ACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
CCGAAAGGCCCAAAATAACAAGTG
Found at i:873 original size:309 final size:307
Alignment explanation
Indices: 264--1082 Score: 1245
Period size: 309 Copynumber: 2.7 Consensus size: 307
254 CAGATTCTCC
*
264 TTCCAAATGAGCTAAAAACTCCACAGTGGACTAATCTCACCAAAATGATTATAGTTTGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTTGTCCATAA
* *
329 ACAATGGAAAG-AAAGCTTTGAGGTTTGCCAAATCGAAGCCGATTCAAAACGGATCTAATGGGCC
66 ACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
393 CCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCAC
131 CCGAAAGG-CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCAC
*
457 CAAAATGATTATAGTTAGATCATAAACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGT
194 CAAAATGATTATAGTTAGATCATAAACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGA
*
522 CGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTG
259 CGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
* * **
571 TTCCAAATGAGCTAAAAATTTCACAGTGGAC-ATGTCTCTAAAAAAATGATTATAGTTTGTCCAT
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTC-ACCAAAATGATTATAGTTTGTCCAT
* * *
635 AAACAATGAAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAATCGGAACTAATGGG
64 AAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
*
700 CCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCA
129 CCCCGAAAGGCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
* * *
765 TCAAAATGATTATAGTTAG-TCCCTAACCAATGGAAAGAAAAGCA-TTGAGGTTTGCCAAATCGA
193 CCAAAATGATTATAGTTAGAT-CATAAACAATGGAAAGAAAAG-ATTTGAGGTTTGCCAAATCGA
* *
828 AGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
256 AGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
* *
880 TTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
1 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTTGTCCATAA
* **
945 ACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
66 ACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
** * ** * * *
1010 TGGATAGGCCCCAAT-ACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGAACTAATCTTACCG
131 CCGAAAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-
1074 AAAATGATT
195 AAAATGATT
1083 C
Statistics
Matches: 464, Mismatches: 39, Indels: 18
0.89 0.07 0.03
Matches are distributed among these distances:
306 44 0.09
307 45 0.10
308 128 0.28
309 244 0.53
310 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (307 bp):
TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTTGTCCATAA
ACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
CCGAAAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
AAATGATTATAGTTAGATCATAAACAATGGAAAGAAAAGATTTGAGGTTTGCCAAATCGAAGACG
ATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
Done.