Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011567.1 Corchorus olitorius cultivar O-4 contig11600, 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: 1833
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Found at i:485 original size:154 final size:154
Alignment explanation
Indices: 1--1833 Score: 2781
Period size: 154 Copynumber: 11.9 Consensus size: 154
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
*
66 AAACTTCACACGTGGACTAATCCCACTAAAATGATTATAGTTTAGGCCATAAACAATAGGAAAGA
66 AAACTTCACA-GTGGACTAATCTCACTAAAATGATTATAG-TTAGGCCATAAACAAT-GGAAAGA
* *
131 AAACCATCGAGGTTTAGCCAAATCGAAG
128 AAAGCATTGAGGTTT-GCCAAATCGAAG
** ** *
159 ACGATTCAATTAA-GGAACCTAATGGGACCC-GA-A-GTACAAAATAACAAGTGTTCCAAATGGG
1 ACGATTCAA--AACGTCA-CTAATGGG-CCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
*
220 CTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTA-AATTAGGCCATAAACAATGGAAAG
62 CTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
284 AAAAGCATTGAGGTTTGCCAAATCGAAG
127 AAAAGCATTGAGGTTTGCCAAATCGAAG
312 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
*
377 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAG
66 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
442 GCATTGAGGTTTGCCAAATCGAAG
131 GCATTGAGGTTTGCCAAATCGAAG
** * ** *
466 ACGATTCAAAACGGAACTAATGGGCCCCGATAGATCCAAAATAAAAAGTGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* * *
531 AAACTTTAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
66 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
596 GCATTGAGGTTTGCCAAATCGAAG
131 GCATTGAGGTTTGCCAAATCGAAG
* * * *
620 ACGATTCAAAACATCACTAATTGGCCCTGATAGGCCCAAAATAACAGGGGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* * * * *
685 AAACTCCACAGTGGACTGATCTCACTAAAATGATTAAACTTAGGCCATAAACAATGGAAAGAAAC
66 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
750 GCATTGAGGTTTGCCAAATCGAAG
131 GCATTGAGGTTTGCCAAATCGAAG
*
774 ACGATTCAAAACGTCAGTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* * * *
839 AAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACGATGGAAAGAAAC
66 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
904 GCATTGAGGTTTGCCAAATCGAAG
131 GCATTGAGGTTTGCCAAATCGAAG
*
928 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
993 AAACTTCACAGTGGACTGATGTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
66 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* *
1058 GCATCGAGGGTTGCCAAATCGAAG
131 GCATTGAGGTTTGCCAAATCGAAG
* * * * *
1082 ACGATTCAAAACAG-AACTAATGGAACCC-GAAAGGCACAAAATAACAAGTGTTCCAAATTAGCT
1 ACGATTCAAAAC-GTCACTAATGG-GCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*
1145 AAAAACCTTCACAGTGGACTAATCTCACTAAAAATGATTGTAGTTAGGCCATAAACAATGGAAAG
64 AAAAA-CTTCACAGTGGACTAATCTCACT-AAAATGATTATAGTTAGGCCATAAACAATGGAAAG
*
1210 AATAGCATTGAGGTTTGCCAAATCGAAG
127 AAAAGCATTGAGGTTTGCCAAATCGAAG
* *
1238 ACGATTCAAAACGTCACTAATGGGCCCTGATAAGCCCAGAATAACAAGTGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
1303 AAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA-AAAA
66 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* *
1367 GCATCGAGGTTTGCCAAATCGAGG
131 GCATTGAGGTTTGCCAAATCGAAG
* ** * * * *
1391 ACGATTCAAAATGGAACTAATGGGCCCCGAAAGGCACAAAATATA-AAGTGTTCCAAATGAGCTT
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATA-ACAAGTGTTCCAAATGAGCTA
1455 AAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
65 AAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* *
1520 ACCATTAAGGTTTGCCAAATCGAAG
130 AGCATTGAGGTTTGCCAAATCGAAG
*
1545 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAA
1 ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
1610 AAACTTCACAGTGGACTGATGTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
66 AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
*
1675 GACATCGAGCG-TTGCCAAATCGAAG
131 G-CATTGAG-GTTTGCCAAATCGAAG
* * * * *
1700 ACGATTCAAAACAG-AACTAATGGAACCC-GAAAGGCACAAAATAACAAGTGTTCCAAATTAGCT
1 ACGATTCAAAAC-GTCACTAATGG-GCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* * *
1763 AAAACCTTCACAGTGGACTTATCTCACTAAAATGATTATACTTAGGCCATAAACAATGGAAAGAA
64 AAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1828 AAGCAT
129 AAGCAT
Statistics
Matches: 1524, Mismatches: 129, Indels: 48
0.90 0.08 0.03
Matches are distributed among these distances:
150 3 0.00
151 12 0.01
152 3 0.00
153 224 0.15
154 871 0.57
155 200 0.13
156 120 0.08
157 25 0.02
158 48 0.03
159 3 0.00
160 12 0.01
161 3 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
ACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
AAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
GCATTGAGGTTTGCCAAATCGAAG
Done.