Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011692.1 Corchorus olitorius cultivar O-4 contig11725, 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: 1912
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Found at i:353 original size:154 final size:154
Alignment explanation
Indices: 1--1912 Score: 2936
Period size: 154 Copynumber: 12.4 Consensus size: 154
**
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* * *
66 GGTTTGCCAAATCGATGTCGATTCAAAACGGTTCTAATGGGGCCCCTAGAAAGGCCCAAAATAAA
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAAT-GGGCCCC--GAAAGGCCCAAAATAAC
* *
131 AAGTGTTCCAAATGAGCTATAAACTCC
128 AAGTGTTCCAAATGAGCTAAAAACTTC
* * *
158 ACAGTGGA-GTAATCTCACCAAAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCTTTG
1 ACAGTGGACAT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTG
* * *
222 AGGTTTGCTAAATCGAAGTCGATTCAAAACGTATCTAATGGGCCCCAAAAGGCCCAAAATAACAA
65 AGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAA
287 GTGTTCCAAATGAGCTAAAAACTTC
130 GTGTTCCAAATGAGCTAAAAACTTC
* * * *
312 AGAGTGGAGAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCTTTGA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
377 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAG
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAG
442 TGTTCCAAATGAGCTAAAAACTTC
131 TGTTCCAAATGAGCTAAAAACTTC
* * * * *
466 ATACTGGAAATATCTCTCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTTA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* *
531 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCTGACAGGCCCAAAATAACAAG
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAG
596 TGTTCCAAATGAGCTAAAAACTTC
131 TGTTCCAAATGAGCTAAAAACTTC
* * *
620 ACATTGGACATATCTCACCAAAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCTTTGA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* *
685 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGACCTAAAATAACAAG
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAG
* * * *
750 GGTTCCAATTGACCTAAAAATTTC
131 TGTTCCAAATGAGCTAAAAACTTC
* * *
774 ACAGTGGACATATCTCTCCAAAATGATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTTA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* * *
839 GGTTT-CCCAATCGAAGTCTATTCAAAACGGAAT-TAATGCGCCCCGAAAGGCCCAAAATAACAA
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGG-ATCTAATGGGCCCCGAAAGGCCCAAAATAACAA
*
902 GTGTTGCAAATGAGCTAAAAACTTC
130 GTGTTCCAAATGAGCTAAAAACTTC
* **
927 ACAGTGGAAATATCTCACCAAAATGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* * *
992 GGTATGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATTACAAT
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAG
*
1057 TCTTCCAAATGAGCTAAAAACTTC
131 TGTTCCAAATGAGCTAAAAACTTC
* * *
1081 ACAGTGGACATATCTCTCCAAAATGATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTTA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* * *
1146 GGTTT-CCCAATCGAAGTCTATTCAAAACGGAAT-TAATGCGCCCCGAAAGGCCCAAAATAACAA
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGG-ATCTAATGGGCCCCGAAAGGCCCAAAATAACAA
*
1209 GTGTTGCAAATGAGCTAAAAACTTC
130 GTGTTCCAAATGAGCTAAAAACTTC
* **
1234 ACAGTGGAAATATCTCACCAAAATGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* *
1299 GGTATGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGGCCCCCGAAAAGGCCCAAAAATTA
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAAT-GGG-CCCCG-AAAGGCCC-AAAATAA
* * *
1364 CAATTCTTCCAAAATGAGCTAAAAATTTC
127 CAAGTGTTCC-AAATGAGCTAAAAACTTC
* *
1393 ACAGTGGACATATCTCTCCAAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAAGCTTTG
1 ACAGTGGACATATCTCACC-AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTG
* * **
1458 AGGTTTGCCAAACCGAAGTCGATTCAAAACGGAACTAATGGTTCCCGAAAGGCCCAAAATAACAA
65 AGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAA
1523 GTGTTCCAAATGAGCTAAAAACTTC
130 GTGTTCCAAATGAGCTAAAAACTTC
** * *
1548 ACAGTGGACATATCTCACCAAAATGATTATAGTTAATCCATAAAAAATGGATAGAAAAGCTTTGA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
*
1613 GGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAG
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAG
1678 TGTTCCAAATGAGCTAAAAACTTC
131 TGTTCCAAATGAGCTAAAAACTTC
* *
1702 ACAGTGGACATATCTCACCAAAATGATTATGGTTAGGCCATAAACAATGGATAGAAAAGCTTTGA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
* *
1767 GGTTTGCCAAATCGAAGTCGATTCAAAACGGTAT-TAATGAGCCCCGAAAGGCCCAAGATAACAA
66 GGTTTGCCAAATCGAAGTCGATTCAAAACGG-ATCTAATGGGCCCCGAAAGGCCCAAAATAACAA
* *
1831 GTGTTCCCAAATCAGCTAAAAATTTC
130 GTGTT-CCAAATGAGCTAAAAACTTC
*
1857 ACAGTGGACATATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
Statistics
Matches: 1602, Mismatches: 137, Indels: 34
0.90 0.08 0.02
Matches are distributed among these distances:
153 273 0.17
154 952 0.59
155 109 0.07
156 27 0.02
157 110 0.07
158 17 0.01
159 36 0.02
160 78 0.05
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (154 bp):
ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGA
GGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAG
TGTTCCAAATGAGCTAAAAACTTC
Done.