Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012596.1 Corchorus olitorius cultivar O-4 contig12629, 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: 2940
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Found at i:420 original size:154 final size:154
Alignment explanation
Indices: 135--2688 Score: 3943
Period size: 154 Copynumber: 16.7 Consensus size: 154
125 GACGTCGACT
* *
135 CTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* * *
200 ATATCTCTCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTTAGGTTTTCCA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
*
265 AATCGAAATCGATTCAAAACGGAA
131 AATCGAAGTCGATTCAAAACGGAA
289 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
354 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
419 AATCGAAGTCGATTCAAAACGGAA
131 AATCGAAGTCGATTCAAAACGGAA
*
443 CTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
508 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
573 AATCGAAGTCGATTCAAAACGGAA
131 AATCGAAGTCGATTCAAAACGGAA
*
597 C-AATTGGGCCCCGAAAGGCCCAAAATAACAACTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1 CTAA-TGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * * * *
661 CATATCTCACCAAAATGATTATAGTTATGTCATAATCAACT-TATAGAAAAGCTTTGAGGTTTGC
65 CATATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTGC
725 CAAATCGAAGTCGATTCAAAACGGAA
129 CAAATCGAAGTCGATTCAAAACGGAA
* * *
751 CTAATGGGCCCCGAAAGTCCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTCCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* * *
816 -TAATCTCACCAAAATGATTATAGTTAGTCCATAAACAACGGAAAGAAGAGCTTTGAGGTTTGCC
66 AT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
*
880 AAATCGAAGTCGATTCAAAACGGTA
130 AAATCGAAGTCGATTCAAAACGGAA
* *
905 CTAATGGGCCCCGAAAGGCCGAAAATAACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
970 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCTTTGAGGTTTGCCA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
*
1035 AATCGAAGTCGATTCAAAACGGAT
131 AATCGAAGTCGATTCAAAACGGAA
* * *
1059 CTAATGCGCCCCGAATGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
1124 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCTTTGAGGTTTGCC-
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
1188 AATCGAAGTCGATT----------
131 AATCGAAGTCGATTCAAAACGGAA
* * *
1202 CTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGTC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
** * *
1267 ATATCTCTTCAAAATGATTATAGTTAGGCCATAAACAACGGATAGAAAAGCTTTGAGGTTTGCCA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
1332 AATCGAAGTCGATTCCAAAACGGAA
131 AATCGAAGTCGATT-CAAAACGGAA
* * *
1357 CTAATGGGCCCCGAAAGGCCCAACATAACAAGTCTTCCAAATGAGCTAAAAACTCCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* * * ** *
1422 -TAATCTCGCCAAATTGATTATACTCTAGTTCATAAACAATGGAAAGAAAAACTTTGAGGTTTGC
66 AT-ATCTCACCAAAATGATTATAGT-TAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGC
*
1486 CAAATCGAAGTCGATTCAAAACAGAA
129 CAAATCGAAGTCGATTCAAAACGGAA
*
1512 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* *
1577 -TAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAATGCTTTGAGGTTTGCC
66 AT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
* * *
1641 AAATCGATGTCAATTCAAAACGGAT
130 AAATCGAAGTCGATTCAAAACGGAA
*
1666 CTAATGGGCCCCGAAAGGCCCAAAATAATAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
** * *
1731 ATATCTCACCAAAATGATTATAGTTAGTTCATAAACATTGGAAAGAAAAGCTTTGAGAGGTTTAC
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTT--GAGGTTTGC
*
1796 CAAATCGATGTCGATTCAAAACGGAA
129 CAAATCGAAGTCGATTCAAAACGGAA
* * * * *
1822 CTAATAGGCCCCGAAAGTCCCAAAATAATAAGTGTTCCAAATGAGCTAAAAACTCCACAGTTGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*** **
1887 -TAATCTCGTTAAAATGATTATAGTTAGTTCATAAAC-----AAAGAAAAGCTTTGAGGTTTGCC
66 AT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
*
1946 AAATCGAAGTCGATTCAAAACAGAA
130 AAATCGAAGTCGATTCAAAACGGAA
1971 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
2036 -TAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
66 AT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCC
* *
2100 AAATCGATGTCGATTCAAAACGGAT
130 AAATCGAAGTCGATTCAAAACGGAA
* *
2125 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAGCTTCACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* *
2190 ATATCTCACCAAAATGATTATTGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCC
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCTTTGAGGTTTGCC
* *
2254 AAATCGAAGACGATTCAAAGCGGAA
130 AAATCGAAGTCGATTCAAAACGGAA
* * * *
2279 CTAATGGTCCCCGAAAGGCCCAAAATAAAAAGTGTTCCGAATGAGCTAAAAACTTGACAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* * ** * *
2344 ATATCTCACAAAAATTATTATAGTTAGTTCATAAAC-ATAGAAAGATAAGCTTTGAGGTTTGCCA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
*
2408 AATCGAAGTCGATTCAAAACGGAT
131 AATCGAAGTCGATTCAAAACGGAA
* * * * * *
2432 CTAATGGGTCCCGAAAGGCCCAAAATTACAATTGTTCCAAAAGAGTTAAAAACTTCTCAGTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
2497 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
2562 AATCGAAGTCGATTCAAAACGGAA
131 AATCGAAGTCGATTCAAAACGGAA
* * *
2586 CTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACATTGGAC
1 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
2651 ATATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
66 ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
2689 GTAGCACATG
Statistics
Matches: 2204, Mismatches: 163, Indels: 66
0.91 0.07 0.03
Matches are distributed among these distances:
143 120 0.05
144 14 0.01
149 124 0.06
151 13 0.01
152 1 0.00
153 149 0.07
154 1433 0.65
155 176 0.08
156 174 0.08
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (154 bp):
CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCA
AATCGAAGTCGATTCAAAACGGAA
Done.