Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011915.1 Corchorus olitorius cultivar O-4 contig11948, 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: 4199
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:458 original size:154 final size:154
Alignment explanation
Indices: 27--4199 Score: 5796
Period size: 154 Copynumber: 27.2 Consensus size: 154
17 GTAGACTCCT
27 AAATAGAGCTAAATTAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAA
1 AAAT-GAGCTAAA--AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAA
** *
92 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACATCACTAATGGGCCT
63 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCC
* *
157 CGATAGGCCCCAAATAACAAGTGCTCC
128 CGATAGGCCCAAAATAACAAGTGTTCC
*
184 AAATGAGCTAAAATTCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACA
1 AAATGAGCTAAAA-ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACA
* * *
249 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATA-TGTCACTAATGGGCCCC
65 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCC
* *
313 GCTAGGCGCAAAATAACAAGTGTTCC
129 GATAGGCCCAAAATAACAAGTGTTCC
** * *
339 AAACAAGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCACAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* *
404 TGGAAAGAAAAGCATAGAGGTTTCCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
469 TAGGCCCAAAATAACAAGTGTTCC
131 TAGGCCCAAAATAACAAGTGTTCC
* * * *
493 AAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATAATTATAATTAGGCCATAAAC--
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * *
556 ----AA-ATAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATA-TGTCACTAATGGGCCCCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
*
615 ATAGGCCCAAAATAACAAGTCTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* * * * * *
640 AAATGAGCTAAAAACTTCAAAGTGAACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * * * * * *
705 TGGAAACAAACGCATTGAGGCTTGCCAATTCGAAGAAGATTCAATAC-GTCACCAATGGGCCCCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
769 ATAGGCCCAAAATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* * *
794 ACATGAGCTAAAAACTTCACAGTGGACTAATCCCACCAAAATGATTATAGTTAGGCCAT-AACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * *
858 TGGAAA-AAAAGCATTGAGGTTTGCCAAATCTAAGACTATTCAATAC-GTAACTAATGGGCTCCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
* *
921 ATAGGCCCAAAATAACAAGTATTCT
130 ATAGGCCCAAAATAACAAGTGTTCC
* * *
946 GAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAGCAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * *
1011 TGGAAAGAAAAGCATTGAGGTTTGCAAAACCGAAGACGATTCAAAACAAAACTAATGGGCGCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
*
1076 TAGCCCCAAAATAACAAGTGTTCC
131 TAGGCCCAAAATAACAAGTGTTCC
* * * * * * ** *
1100 AAATTAGCTAAGAACTTCATAGTAGACTAATCCCATCAAAATGATTATAACTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * *
1165 CT-TAACA-AAAA-CTTTGAGGTTT-CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
66 -TGGAA-AGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCC
* * *
1226 AGA-AGTCCTAAAGTAACAAGTGTTCC
129 -GATAGGCCCAAAATAACAAGTGTTCC
* * * *
1252 AAATTAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTTAGTCCCTAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * * * *
1317 TGGAAAGAAAAGCATTGAGGTTTGCCAAATTGAAGAGGATTCAATA-TGTCACTAATGGGCCCTG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
* *
1381 GTAGGCCCAAAATAAGAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
** * * *
1406 AAAAAAGTTAAAAACTTAACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCACAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * *
1471 TGGAAAGAAAAGCATAGAGGTTTGCCAAATCGAAGACGATTCAAAA-TGTCACTAATGGGCCTCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
* *
1535 ATATGCCCCAAATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* *** * *
1560 AAATTAGCTAAAAACTTCACAGTGGACTAATCTTTTCAAAATGATTATAGTTAGTCAATAAAAAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
** * *
1625 TGGAAAGAAAAGTTTTGAGGTTTGCCAAATTGAAGACGATTCAAAACAGAAATAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
* * *
1690 AAGACCTAAAATAACAAGTGTTCC
131 TAGGCCCAAAATAACAAGTGTTCC
* * * * *
1714 AAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTAAGTCCCTGAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* *
1779 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCTCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
* *
1843 ATAGGCCCCAAGTAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* * * * *
1868 AAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAGTAAGTCCCTAAACTA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* *
1933 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
* *
1998 AAGGCCTAAAATAACAAGTGTTCC
131 TAGGCCCAAAATAACAAGTGTTCC
*
2022 AAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * *
2087 TGGAAACAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
* * *
2152 AAGGCCTAAAATAACAAGTGTTTC
131 TAGGCCCAAAATAACAAGTGTTCC
**
2176 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTGTATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * *
2241 TGGAAAGAAAAGCATTGAGGTTTGTCAAATCGAAGAGGATTCAATA-TGTCAA-TAATGGGCCCC
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG--AACTAATGGGCCCC
*
2304 GATAGGCCCAAAATAACAAGTTTTCC
129 GATAGGCCCAAAATAACAAGTGTTCC
** *
2330 AAACAATCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* ** *
2395 TGGAAAGAAAAGCATTGAGGTTTTGCCAAATCGAAGAGGATTCAAAACATCACTAATGGGCCTCG
66 TGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCG
*
2460 ATAGGCCCCAAATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* * *
2485 AAATTAGCTAAAAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGTCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * *
2550 TGGAAAGAAAAGCATTAAGGTTTGCCAAATCGACGACGATTCAAAACGGAACTAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
*
2615 -ATGGCCTAAAATAACAAGTGTTCC
131 TA-GGCCCAAAATAACAAGTGTTCC
* * *
2639 AAATGAGCTAAAAACTTCACAATGGACTAATCTCAACAAAATGATTATAGTTAGTCCCTAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
*
2704 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
*
2769 TAGGCCCAAAATAAAAAGTGTTCC
131 TAGGCCCAAAATAACAAGTGTTCC
* * * * * * *
2793 AAATGAGCTAAAAATTTCACAATGAACTAATCTCATCAAAATGATTATAGTTAATCCCTAAATAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* *
2858 TGGAAAGAAAAGCACTGAGGTTTGCCAAATCGAAGACGATT-AGAAACGGAACTAATGGGCCCCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA-AAACAGAACTAATGGGCCCCG
2922 ATAGGCCC--AATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* * * * ** *
2945 AAATGAGCT-AAGACTTCATAGTAGACTAATCTCATCAAAATGATTATAACTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
** * * *
3009 CTTAAAAGAAAAACTTTGAGGTTT-CCAAATCG-TGACGATTCAAAAC-GTAACTAATGGGCCCC
66 -TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCC
*
3071 GATAGGCCTAAAATAACAAGTGTTCC
129 GATAGGCCCAAAATAACAAGTGTTCC
* * * *
3097 AAATGAGCTTAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTCAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* *
3162 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCTCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
*
3226 ATAGGCCCCAAATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* * *
3251 AAATTAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGTCCATAAAAAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
*
3316 TGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
3381 TAGGCCCAAAATAACAAGTGTTCC
131 TAGGCCCAAAATAACAAGTGTTCC
*
3405 AAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* *
3470 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTTACTAATGGGCCTCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
3534 ATAGGCCCAAAATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
*
3559 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
** *
3624 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACATCACTAATGGGCTCCGA
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
*
3689 TAGGCCCCAAATAACAAGTGTTCC
131 TAGGCCCAAAATAACAAGTGTTCC
*
3713 AAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGTTAGGT-CATAAACA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-GTCCATAAACA
*
3777 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCTCG
65 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCG
*
3842 ATAGGCACAAAATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
** * * * *
3867 AAAACAGCTAAAAACTTCAGAGTGGACTAATATCACCAAAATGATTATAGTTAGGCCATAAAGAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * * * * *
3932 TGGAAAGAAAAGAATTAAGGTTTGCCAAATCAAAGACGATTCAAAA-TGTCATTAATGGGCCCCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
*
3996 ATAGGCCCAAAATAACAACTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
* * * * *
4021 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGATTTTAGTTAGGCCGTACACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
* * *
4086 TGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGTCCCCG
66 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCG
4150 ATAGGCCCAAAATAACAAGTGTTCC
130 ATAGGCCCAAAATAACAAGTGTTCC
*
4175 ATATGAG---AAAACTTACACAGTGGAC
1 AAATGAGCTAAAAACTT-CACAGTGGAC
Statistics
Matches: 3607, Mismatches: 358, Indels: 107
0.89 0.09 0.03
Matches are distributed among these distances:
146 1 0.00
147 128 0.04
148 2 0.00
149 1 0.00
150 33 0.01
151 61 0.02
152 337 0.09
153 109 0.03
154 2633 0.73
155 290 0.08
156 8 0.00
157 4 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGA
TAGGCCCAAAATAACAAGTGTTCC
Done.