Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010900.1 Corchorus olitorius cultivar O-4 contig10932, 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: 2034
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Found at i:615 original size:154 final size:154
Alignment explanation
Indices: 331--2033 Score: 2636
Period size: 154 Copynumber: 11.1 Consensus size: 154
321 TCCTTGGCGC
**
331 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* * * *
396 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCATAGTAGACTAATCTCATCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
** *
461 ATGATTATAACTAGGCCATAAACA
131 ATGATTATAGTTAGTCCATAAACA
* * * ** *
485 ACT-TAAAGAAAAACTTTGAGGTTTATCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCC
1 A-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
*
549 GATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
614 AATGATTATAGTTAGTCCATAAACA
130 AATGATTATAGTTAGTCCATAAACA
*
639 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
704 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
769 ATGATTATAGTTAGTCCATAAACA
131 ATGATTATAGTTAGTCCATAAACA
*
793 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATTCGAAGACGATTCAAAATGTCACTAATGGGCCCC
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAA-TCGAAGACGATTCAAAACGTCACTAATGGGCCCC
*
858 GATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
923 AATGATTATAGTTAGTCCATAAACA
130 AATGATTATAGTTAGTCCATAAACA
*
948 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* *
1013 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTTACCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* * *
1078 TTGATTATAGTTAGGCCATATACA
131 ATGATTATAGTTAGTCCATAAACA
** * * * *
1102 ATATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAATGGGCACCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
*
1167 ATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1232 ATGATTATAGTTAGTCCATAAACA
131 ATGATTATAGTTAGTCCATAAACA
* * *
1256 ATAGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* ** *
1321 ATAGGCGCAAAATAACAAGTGTTCCAAACAAGCTAAAAATTTCACAGTGGACTAATCTCACCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1386 ATGATTATAGTTAGTCCATAAACA
131 ATGATTATAGTTAGTCCATAAACA
* * *
1410 ATGGAAAGAAAAGCATAGAGG-TT------T-GAAGACGATTCAAAACAG-AACAAATGGGCCCC
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCC
* * * * **
1466 GATAGGCCCCAAATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTAGATTAATCTTTCCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
1531 AATGATTATAGTTAGTCCATAAACA
130 AATGATTATAGTTAGTCCATAAACA
* * * *
1556 ATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* * * *
1621 GTAGGCGCAAAATAACAAGTGTTCCAAA-CAGGCTAAAAATTTCACAGTGGACTAATCTCACCAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGA-GCTAAAAACTTCACAGTGGACTAATCTCACCAA
1685 AATGATTATAGTTAGTCCATAAACA
130 AATGATTATAGTTAGTCCATAAACA
* * *
1710 ATAGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* * ** *
1775 ATAGGACCAAAATAACAAGTTTTCCAAACAATCTAAAAACTTCACAGTGGACTAATCTCACCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1840 ATGATTATAGTTAGTCCATAAACA
131 ATGATTATAGTTAGTCCATAAACA
* * * * *
1864 ATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCTG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* **
1929 GTAGGCCCAAAATAACAAGTGTTCCAAACAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1994 ATGATTATAGTTAGTCCATAAACA
131 ATGATTATAGTTAGTCCATAAACA
*
2018 ATGGAAAGAGAAGCAT
1 ATGGAAAGAAAAGCAT
2034 A
Statistics
Matches: 1423, Mismatches: 111, Indels: 30
0.91 0.07 0.02
Matches are distributed among these distances:
146 125 0.09
147 4 0.00
153 6 0.00
154 1135 0.80
155 153 0.11
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
ATGATTATAGTTAGTCCATAAACA
Found at i:1779 original size:608 final size:610
Alignment explanation
Indices: 331--2034 Score: 2754
Period size: 608 Copynumber: 2.8 Consensus size: 610
321 TCCTTGGCGC
**
331 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* * *
396 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCATAGTAGACTAATCTCATCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAA
** *
461 ATGATTATAACTAGGCCATAAACAACT-TAAAGAAAAACTTTGAGGTTTATCAAATCGAAGACGA
131 ATGATTATAGTTAGGCCATAAACAA-TATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGA
*
525 TTCAAAACGTAACTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
195 TTCAAAACGTCACTAATGGGCCCCGATAGGCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAAC
590 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCAT
259 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCAT
*
655 TGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
324 TGAGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
**
720 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTC
389 AAGTGTTCCAAACAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTC
* * * *
785 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATTCGAAGACGATTCAAAATGTCACTAA
454 CATAAACAATGGAAAGAAAAGCATAGAGG-TT-----ATTCGAAGACGATTCAAAAAGTAACAAA
*
850 TGGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
513 TGGGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTAGACTAAT
915 CTCACCAAAATGATTATAGTTAGTCCATAAACA
578 CTCACCAAAATGATTATAGTTAGTCCATAAACA
*
948 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
*
1013 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTTACCAAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAA
* *
1078 TTGATTATAGTTAGGCCATATACAATATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGAT
131 ATGATTATAGTTAGGCCATAAACAATATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGAT
*
1143 TCAAAACGTCACTAATGGGCACCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
196 TCAAAACGTCACTAATGGGCCCCGATAGGCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACT
*
1208 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATAGAAAGAAAAGCATT
260 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATT
*
1273 GAGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCGCAAAATAACA
325 GAGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAAATAACA
*
1338 AGTGTTCCAAACAAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCC
390 AGTGTTCCAAACAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCC
1403 ATAAACAATGGAAAGAAAAGCATAGAGG-T-TT-GAAGACGATTCAAAACAG-AACAAATGGGCC
455 ATAAACAATGGAAAGAAAAGCATAGAGGTTATTCGAAGACGATTCAAAA-AGTAACAAATGGGCC
* * * * **
1464 CCGATAGGCCCCAAATAACAAGTGTTGCAAATGAGCTAAAAACTTCACAGTAGATTAATCTTTCC
519 CCGATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACC
1529 AAAATGATTATAGTTAGTCCATAAACA
584 AAAATGATTATAGTTAGTCCATAAACA
* * * *
1556 ATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCCG
1 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
* * * * *
1621 GTAGGCGCAAAATAACAAGTGTTCCAAA-CAGGCTAAAAATTTCACAGTGGACTAATCTCACCAA
66 ATAGGCCCAAAATAACAAGTGTTCCAAATGA-GCTAAGAACTTCACAGTGGACTAATCTCACCAA
* * * * *
1685 AATGATTATAGTTAGTCCATAAACAATAGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
130 AATGATTATAGTTAGGCCATAAACAATATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGA
* * * ** *
1750 TTCAATATGTCACTAATGGGCCCCGATAGGACCAAAATAACAAGTTTTCCAAACAATCTAAAAAC
195 TTCAAAACGTCACTAATGGGCCCCGATAGG-CCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
*
1815 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCCT
259 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCAT
* * *
1880 TGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCTGGTAGGCCCAAAATAAC
324 TGAGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
1945 AAGTGTTCCAAACAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTC
389 AAGTGTTCCAAACAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTC
*
2010 CATAAACAATGGAAAGAGAAGCATA
454 CATAAACAATGGAAAGAAAAGCATA
Statistics
Matches: 1018, Mismatches: 65, Indels: 17
0.93 0.06 0.02
Matches are distributed among these distances:
607 1 0.00
608 551 0.54
609 5 0.00
615 1 0.00
616 1 0.00
617 459 0.45
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (610 bp):
ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCG
ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAA
ATGATTATAGTTAGGCCATAAACAATATAAAGAAAAACTTTGAGGTTTACCAAATCGAAGACGAT
TCAAAACGTCACTAATGGGCCCCGATAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTG
AGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA
GTGTTCCAAACAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
TAAACAATGGAAAGAAAAGCATAGAGGTTATTCGAAGACGATTCAAAAAGTAACAAATGGGCCCC
GATAGGCCCAAAATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAA
AATGATTATAGTTAGTCCATAAACA
Done.