Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011894.1 Corchorus olitorius cultivar O-4 contig11927, 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: 2112
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Found at i:599 original size:154 final size:154
Alignment explanation
Indices: 191--2112 Score: 2744
Period size: 154 Copynumber: 12.7 Consensus size: 154
181 CGAAGTCGAT
* *
191 TCTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* ** * * * *
256 -AATATCTCTTCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGTTTTGC
66 CTA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
*
320 CAAATCGAAGTCTATTCAAAACGGA
130 CAAATCGAAGTCGATTCAAAACGGA
* * *
345 ACTAATGCGCCCCGAAAGG-CC-------CAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
402 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
66 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
467 AAATCGAAGTCGATTCAAAACGGA
131 AAATCGAAGTCGATTCAAAACGGA
* * * *
491 TCTAATGGGCCCCGAAAGACCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACTGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
556 CTAATCTCACCAAAATGATTATAGTTAGTTCATAAACAGTGGAAAGAAAAGCTTTGAGGTTTGCC
66 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
621 AAATCGAAGTCGA-T---------
131 AAATCGAAGTCGATTCAAAACGGA
* * *
635 TCTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAATTTCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
** * * * *
700 C-ATATCTCTTCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGTTTTGC
66 CTA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
764 CAAATCGAAGTCGA-T---------
130 CAAATCGAAGTCGATTCAAAACGGA
* *
779 TCTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
** * *
844 C-ATATCTCTTCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTTTTGAGGTTTGC
66 CTA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
908 CAAATCGAAGTCGATTCAAAACGGA
130 CAAATCGAAGTCGATTCAAAACGGA
* * *
933 TCTAATGGGCCCCCGAAAGACCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGG
1 TCTAATGGG-CCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
*
998 ACTAATCTCACCAAAATGACTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
65 ACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
*
1063 CAAATCGATGTCGATTCAAAACGGA
130 CAAATCGAAGTCGATTCAAAACGGA
* * *
1088 TCTAATGGACCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAATTTCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
1153 C-ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCTTTGAGGTTTGC
66 CTA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
*
1217 CGAATCGAAGTCGATTCAAAACGGA
130 CAAATCGAAGTCGATTCAAAACGGA
* * ** *
1242 ACTAATGGGCCCCGAATGGCCCAAAATAGTAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* ** * * * *
1307 -AATATCTCTTCAAAATGATTATAGTTAGGCCATAAATAATGGAAAG-AAAGACTTTTAGTTTTG
66 CTA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAG-CTTTGAGGTTTG
*
1370 CCAAATCGAAGTCTATTCAAAACGGA
129 CCAAATCGAAGTCGATTCAAAACGGA
* * * * *
1396 ACTAATGGGCCCCGAAAGGCCCAAAATTACAAGTGTTTCAAATGAGCTAAAAACTACGCAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
1461 CTAATCTCACCAAAATGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
66 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
*
1526 AAATCGATGTCGATTCAAAACGGA
131 AAATCGAAGTCGATTCAAAACGGA
* * *
1550 TCTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTCGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * * *
1615 C-ATATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAACTTTTAGTTTTGC
66 CTA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
*
1679 CAAATCGAAGTCTATTCAAAACGGA
130 CAAATCGAAGTCGATTCAAAACGGA
* * * *
1704 ACTAATGCGCCCCGAAAGGCCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1769 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
66 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
1834 AAATCGAAGTCGATTCAAAACGGA
131 AAATCGAAGTCGATTCAAAACGGA
* * *
1858 TCTAATGGTCCCCGAAAGACCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * *
1923 CTAATCTCACCAAAATGATTAGAGTTAGTCCATAAAAAATAGAAAGAAAAGCTTTGAGGTTTGCC
66 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
1988 AAATCGAAGTCGATTCAAAACGGA
131 AAATCGAAGTCGATTCAAAACGGA
* * *
2012 TCTAATGGGCCCCGAAAGACCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1 TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
2077 CTAATCTCACCAAAATGATTATAGTTAGTTCATAAA
66 CTAATCTCACCAAAATGATTATAGTTAGTCCATAAA
Statistics
Matches: 1601, Mismatches: 138, Indels: 58
0.89 0.08 0.03
Matches are distributed among these distances:
143 1 0.00
144 265 0.17
145 1 0.00
146 129 0.08
147 3 0.00
153 9 0.01
154 1045 0.65
155 147 0.09
156 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (154 bp):
TCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
AAATCGAAGTCGATTCAAAACGGA
Found at i:1565 original size:462 final size:461
Alignment explanation
Indices: 1--2104 Score: 3169
Period size: 462 Copynumber: 4.6 Consensus size: 461
** * *
1 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGTTCTGAAAGG
1 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGA
* * *
66 CCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAACTGA
66 CCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGA
*
130 TTATAGTTAGTTCATAAACAGTGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGA-T---
130 TTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAA
*
191 ------TCTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCAC
195 AACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCAC
* **
250 AGTGGAAATATCTCTTCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGT
260 AGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGT
*
315 TTTGCCAAATCGAAGTCTATTCAAAACGGAACTAATGCGCCCCGAAAGG-CC------CAAGTGT
325 TTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGCGCCCCGAAAGGCCCAAAATACAAGTGT
* *
373 TCCAAATGAGCTAAAAACTCCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAA
390 TCCAAATGAGCTAAAAACTCCACAGTGGAATAATCTCACCAAAATGATTATAGTTAGGCCATAAA
438 CAATGGA
455 CAATGGA
445 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGA
1 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGA
* *
510 CCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACTGTGGACTAATCTCACCAAAATGAT
66 CCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
*
575 TATAGTTAGTTCATAAACAGTGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGA-T----
131 TATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAA
* *
635 -----TCTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAATTTCACA
196 ACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACA
**
695 GTGGACATATCTCTTCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGTT
261 GTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGTT
760 TTGCCAAATCGAAGTCGATT----------CTAATG-GTCCCCGAAAGGCCCAAAATAACAAGTG
326 TTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGCG-CCCCGAAAGGCCCAAAAT-ACAAGTG
* * **
814 TTCCAAATGAGCTAAAAATTTCACAGTGGACAT-ATCTCTTCAAAATGATTATAGTTAGGCCATA
389 TTCCAAATGAGCTAAAAACTCCACAGTGGA-ATAATCTCACCAAAATGATTATAGTTAGGCCATA
878 AACAATGGA
453 AACAATGGA
*
887 AAGAAAAGTTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCCGAAAG
1 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGG-CCCCGAAAG
*
952 ACCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
65 ACCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * *
1017 CTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAA
130 TTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAA
* *
1082 AACGGATCTAATGGACCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAATTTCAC
195 AACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCAC
* * * *
1147 AGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCTTTGAGG
260 AGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGT
* * * *
1212 TTTGCCGAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAATGGCCCAAAATAGTAAGTG
325 TTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGCGCCCCGAAAGGCCCAAAATA-CAAGTG
* * **
1277 TTCCAAATGAGCTAAAAATTTCACAGTGGAA-ATATCTCTTCAAAATGATTATAGTTAGGCCATA
389 TTCCAAATGAGCTAAAAACTCCACAGTGGAATA-ATCTCACCAAAATGATTATAGTTAGGCCATA
*
1341 AATAATGGA
453 AACAATGGA
* * * *
1350 AAG-AAAGACTTTTAGTTTTGCCAAATCGAAGTCTATTCAAAACGGAACTAATGGGCCCCGAAAG
1 AAGAAAAG-CTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAG
* * * *
1414 GCCCAAAATTACAAGTGTTTCAAATGAGCTAAAAACTACGCAGTGGACTAATCTCACCAAAATGA
65 ACCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
1479 TTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGATGTCGATTCAA
130 TTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAA
*
1544 AACGGATCTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCAC
195 AACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCAC
* *
1609 AGTCGACATATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAACTTTTAGT
260 AGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGT
*
1674 TTTGCCAAATCGAAGTCTATTCAAAACGGAACTAATGCGCCCCGAAAGGCCCAAAATTACAAGTG
325 TTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGCGCCCCGAAAGGCCCAAAA-TACAAGTG
* *
1739 TTCCAAATGAGCTAAAAACTCCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAA
389 TTCCAAATGAGCTAAAAACTCCACAGTGGAATAATCTCACCAAAATGATTATAGTTAGGCCATAA
1804 ACAATGGA
454 ACAATGGA
*
1812 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGTCCCCGAAAGA
1 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGA
* *
1877 CCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
66 CCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * * *
1942 TAGAGTTAGTCCATAAAAAATAGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAA
131 TATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAA
* * * *
2007 ACGGATCTAATGGGCCCCGAAAGACCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACA
196 ACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACA
2072 GTGGAC-TAATCTCACCAAAATGATTATAGTTAG
261 GTGGACAT-ATCTCACCAAAATGATTATAGTTAG
2105 TTCATAAA
Statistics
Matches: 1527, Mismatches: 92, Indels: 64
0.91 0.05 0.04
Matches are distributed among these distances:
433 1 0.00
434 16 0.01
435 2 0.00
442 125 0.08
443 130 0.09
444 322 0.21
445 1 0.00
453 135 0.09
461 1 0.00
462 644 0.42
463 149 0.10
464 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (461 bp):
AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGA
CCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
TATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAA
ACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACA
GTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACTTTTAGTT
TTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGCGCCCCGAAAGGCCCAAAATACAAGTGTT
CCAAATGAGCTAAAAACTCCACAGTGGAATAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
AATGGA
Done.