Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011679.1 Corchorus olitorius cultivar O-4 contig11712, 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: 1999
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Found at i:286 original size:154 final size:153
Alignment explanation
Indices: 5--1999 Score: 2847
Period size: 154 Copynumber: 13.1 Consensus size: 153
1 AACT
*
5 TTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGG-AAG-AAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * * **
68 CGAGGTTTGCCAAATCGAAGACGATTCAAAATTGAACTAATGGGCCCCGAAAGGGACAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGATAGGCCCAAAATAAC
133 AAGTGTTCCAAATGAGCTAAAAAC
130 AAGTGTTCCAAATGAGCTAAAAAC
* * *
157 TTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACGATGGAAAGAAACGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
*
222 TGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCTCGATAGGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAAC
*
287 AAGTATTCCAAATGAGCTAAAAAC
130 AAGTGTTCCAAATGAGCTAAAAAC
311 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* *
376 TAAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAGGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGATAGGCCCAAAATAAC
* * * *
441 ACGTGTTCCAACTGACCTAAAAAG
130 AAGTGTTCCAAATGAGCTAAAAAC
* * * *
465 TTCACAGTGGACTAAACTCACCAAACTGATTATAGTTTGGTCATAAACAATGGAAAGAAAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
*
530 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAAC
595 AAGTGTTCCAAATGAGCTAAAAAC
130 AAGTGTTCCAAATGAGCTAAAAAC
* * * * * * *
619 ATAAAAGTGGACTAATCTAAACAAAATGATTATGGGTAGGCCATAAACAATGGAAAGAAAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * * * * * * *
684 TGAGGCTTACCAATTCGAAGAAGATTCAATACGTCACTAATGAGCCCCGATAGGCCCAAAATAAG
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAAC
749 AAGTGTTCCAAATGAGCTAAAAAC
130 AAGTGTTCCAAATGAGCTAAAAAC
773 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
*
838 TGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAGGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGATAGGCCCAAAATAAC
903 AAGTGTTCCAAATGAGCTAAAAAC
130 AAGTGTTCCAAATGAGCTAAAAAC
* * * *
927 TTCATAGTGGACTAATCTAAACAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * * *
992 TGAAGTTTGCCAAATCGTAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAAC
* *
1057 AAGTGTTCCAAATGATCTAAAAAG
130 AAGTGTTCCAAATGAGCTAAAAAC
1081 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
*
1146 TGAGGTTTCCCAAATCGAAGACGATTCAAAACAGAACTAAT-------G---GGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAAC
1201 AAGTGTTCCAAATGAGCTAAAAAC
130 AAGTGTTCCAAATGAGCTAAAAAC
* * * *
1225 TTCATAGTGGACTAATCTAAACAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * * *
1290 TGAAGTTTGCCAAATCGTAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAAC
* *
1355 AAGTGTTCCAAATGATCTAAAAAG
130 AAGTGTTCCAAATGAGCTAAAAAC
1379 TTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCCATAAAC-ATAGGAAAGAAAAGC
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG-CCATAAACAAT-GGAAAGAAAAGC
* *
1442 ATTGAAGGTTTCCCAAATCGAAGACGATTCAAAACAGAACTAA--------G-TGGGCCC-AAAT
64 ATTG-AGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAAT
1497 -ACAAGTGTTCCAAATGAGCTAAAAAC
127 AACAAGTGTTCCAAATGAGCTAAAAAC
* * * *
1523 TTCATAGTGGACTAATCTAAACAAAATGATTATAGTTAGGCCATAAACAATTGAAAG-AAAGCAT
1 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * * *
1587 TGAAGTTTGCCAAATCGTAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
66 TGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAAC
*
1652 AAGTGTTACCAAATGAGCTAAAAAG
130 AAGTGTT-CCAAATGAGCTAAAAAC
*
1677 TTCACAGTGGACTAATCTCACCAAAAATGATTATAGTTAGGCCATAAACGATGGAAAGAAAAGCA
1 TTCACAGTGGACTAATCTCACC-AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * *
1742 TTGAGGTTTGCCAAACCGAAGACGATTCAAAATAGACCTAATGGGCCCCGATAGGCCCAAAATAA
65 TTGAGGTTTGCCAAATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGATAGGCCCAAAATAA
** * *
1807 CACTTGTTCCAAATGAGCTAAATAG
129 CAAGTGTTCCAAATGAGCTAAAAAC
*
1832 TTCACTA-TGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCA
1 TTCAC-AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * * * * *
1896 TTGAGGTTTGCCAAATCGAAGACGATGCAATACGTCACTAATGGGTCCTGATAGGCCCAAAATAT
65 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAA
*
1961 CAAGTATTCCAAATGAGCTAAAAAAC
129 CAAGTGTTCCAAATGAGCT-AAAAAC
1987 TTCACAGTGGACT
1 TTCACAGTGGACT
Statistics
Matches: 1641, Mismatches: 156, Indels: 89
0.87 0.08 0.05
Matches are distributed among these distances:
141 1 0.00
142 31 0.02
143 10 0.01
144 186 0.11
145 23 0.01
146 6 0.00
147 2 0.00
150 1 0.00
151 7 0.00
152 54 0.03
153 34 0.02
154 1098 0.67
155 117 0.07
156 70 0.04
157 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (153 bp):
TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
TGAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGATAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAAC
Done.