Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010981.1 Corchorus olitorius cultivar O-4 contig11013, 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, 730
Length: 1218
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:922 original size:154 final size:153
Alignment explanation
Indices: 1--1218 Score: 1883
Period size: 153 Copynumber: 7.9 Consensus size: 153
* * * * *
1 GAAA-CATTTAGGGTTGCCAAATCGAAGACGATTCAAGATGGAACTAATGAGCCCCGGTAGGCAC
1 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCAC
* * *
65 AAAATAAAAAGTGTTCGAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAATAATTAT
66 AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
129 AGTTAGGCCATAAACAATGGAAA
131 AGTTAGGCCATAAACAATGGAAA
* * *
152 GAAAGCAATTAGAGGGTTGCCACATCGAAGACGATTCAAAACGGAACCAATGAGCCCCGATAGGC
1 GAAAGC-ATT-GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGC
*
217 AC-AAATAAAAAGTAGTTCCAAATTTAGCTAAAAACTTACACAGTGGACTAATCTCACCAAAATG
64 ACAAAATAAAAAGT-GTTCCAAA-TGAGCTAAAAACTT-CACAGTGGACTAATCTCACCAAAATG
281 ATTATAGTTAGGCCATAAACAATGGAAA
126 ATTATAGTTAGGCCATAAACAATGGAAA
* *
309 GAAAGCATTGAGGGTTGCCAAATCGAAGACGGTTCAAAACGGAACTAATGGGCCACGATA-G-AT
1 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCA-
* *
372 CGAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGCACTAATCTCACCAAAATGATT
65 C-AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
437 ATAGTTAGGCCATAAACAATGGAAA
129 ATAGTTAGGCCATAAACAATGGAAA
**
462 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTACCCGATAGGCAC
1 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCAC
*
527 AAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
66 AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
592 AGTTAGGCCATAAACAATGGAAA
131 AGTTAGGCCATAAACAATGGAAA
*
615 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGGCAC
1 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCAC
* *
680 -AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATAATTAT
66 AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
744 AGTTAGGCCATAAACAATGGAAA
131 AGTTAGGCCATAAACAATGGAAA
* * * ** ** *
767 GAAAACATTTAGAGTTGCCAAATCGAAGACGATTCAGGACGGAACTAATGATCCCCGGTAGGCAC
1 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCAC
* * *
832 AAAGTAAAAAGTGTTCGAAATTAGCTAAAAACTTACACAGTGGACTAATCTCACCAAAATGATTA
66 AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAATCTCACCAAAATGATTA
897 TAGTTAGGCCATAAACAATGGAAA
130 TAGTTAGGCCATAAACAATGGAAA
* *
921 GAAAGCATTGAGGGTTGCCAAATCGAAGACGGTTCAAAACGGAACTAATGGGCCCCGATAGATC-
1 GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG-GCA
985 CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
65 CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
1050 TAGTTAGGCCATAAACAATGGAAA
130 TAGTTAGGCCATAAACAATGGAAA
* * ** * *
1074 GAAAAGCATTGAGGGTTGCCAAATCCAAGATGATTCAAAACGTCACTAATGGGCCCCGATTGGCC
1 G-AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCA
* *
1139 CAAAATAAAAAGTGTTGCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTA
65 CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * *
1204 CACTTATGCCATAAA
130 TAGTTAGGCCATAAA
Statistics
Matches: 986, Mismatches: 64, Indels: 31
0.91 0.06 0.03
Matches are distributed among these distances:
151 4 0.00
152 143 0.15
153 358 0.36
154 339 0.34
155 70 0.07
156 34 0.03
157 38 0.04
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (153 bp):
GAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCAC
AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
AGTTAGGCCATAAACAATGGAAA
Done.