Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010940.1 Corchorus olitorius cultivar O-4 contig10972, 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: 3379
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Found at i:367 original size:154 final size:154
Alignment explanation
Indices: 1--2419 Score: 3684
Period size: 154 Copynumber: 15.7 Consensus size: 154
* * *
1 AAAAACATCACAGTGGACTAATCACACCAAAATGATTACAGTTAGTCCATAAACAATGG-AAG-A
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * ** *
64 AAGCATTGAGGTTTGCCAACTCGAAGACGAATCAAAACGTCACTAATGGGCCGCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
129 AAT---AAGTGTTCCAAATGAGTT
131 AATAACAAGTGTTCCAAATGAGCT
* *
150 AAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTAGTCCACAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
** *
215 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACGAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
280 AATAACAAGTGTTCCAAATCAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * * *
304 AAAAACTTTACAATGGACTAATCTCACCAAAATGATTATAGTTAGTCCATATATAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * *
369 AAGCATTAAGGTTTGCCAAATCGAAGACGATTCATAACGGAACTAATGGGCCCCGATAGGCCTAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
434 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * *
458 AAAAACATCACAGTGGACTAATCACACCAAAATGATTACAGTTAGTCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* *
523 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGCAACTAATGGGCCGCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
588 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
*
612 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGATAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * *
677 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTGGCCTCGATAGGCCCCA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
742 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * *
766 AAAAACTTCTCAGTGGACTAATTTCACGAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* ** * *
831 AGGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCGATAGACCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
896 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * *
920 AAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
*
985 AAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
1050 AATAACAAGTGTTCCAAATGAGTT
131 AATAACAAGTGTTCCAAATGAGCT
* * * *
1074 AAAAACTTCACAGTGGACTAATTTCACGAAAATGATTATAGTAAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* ** *
1139 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGACCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
1204 AATAACAAGTGTTCCAAATAAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * * * *
1228 AAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTAAGGCCATAAACAATGGAAAAAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * * *
1293 AAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGGAAATAATGGGCCACGAGAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
1358 AATAACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
1382 AAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTAGTCCACAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * *
1447 AAGCATTGAGGTTTGCCAAATCAAAGACGATTCAAAACGGAACTAATGGGGCTCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
1512 AATAATAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * *
1536 AAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
**
1601 AAGTC-TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCA
66 AAG-CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
* *
1665 GAATAACAAGTGATCCAAATGAGCT
130 AAATAACAAGTGTTCCAAATGAGCT
* * ** *
1690 AAAAACTTCACAGTGGACTAATCTCA-CAAATTGATTATAGTTAGGCCATAAACAATATAAGGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * * *
1754 AACCTTTGAGGTTTACCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCACGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
1819 AATAACAAGTGTTCCAAATGAAGCT
131 AATAACAAGTGTTCCAAATG-AGCT
* * * ***
1844 AAAAACTTCACAGTAGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACATAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * * ** * * *
1909 AA-CTTTAAGGTTTACCAAATCGAAGACGATTCGAAAAACGTCACTAATGGGCACCGATAGACCA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTC--AAAACGGAACTAATGGGCCCCGATAGGCCC
*
1973 AAAATAACAAGTGTTTCAAATGAGCT
129 AAAATAACAAGTGTTCCAAATGAGCT
* * *
1999 AAAAACTTCGCAGTGGACTAATCTCATCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* * *
2064 AAGCTTTGAGGTTTACCCAAACCGAAGACGATTACAAAACGGAACTAATGGGCCCCGATAGGACC
66 AAGCATTGAGGTTT-GCCAAATCGAAGACGATT-CAAAACGGAACTAATGGGCCCCGATAGG-CC
2129 CAAAATAACAAGTGTTACCAAATGAGCT
128 CAAAATAACAAGTGTT-CCAAATGAGCT
* * * *
2157 AAGAACTTTACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
* *
2222 AAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
2287 AATATCAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
2311 AAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGATAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
2376 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
2420 TGATACGAAT
Statistics
Matches: 2076, Mismatches: 178, Indels: 27
0.91 0.08 0.01
Matches are distributed among these distances:
149 54 0.03
150 3 0.00
151 65 0.03
152 1 0.00
153 110 0.05
154 1487 0.72
155 119 0.06
156 105 0.05
157 49 0.02
158 83 0.04
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
AATAACAAGTGTTCCAAATGAGCT
Done.