Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010868.1 Corchorus olitorius cultivar O-4 contig10900, 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: 4437
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Found at i:939 original size:154 final size:154
Alignment explanation
Indices: 659--4437 Score: 5662
Period size: 154 Copynumber: 24.6 Consensus size: 154
649 GATTCGTATC
659 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * * * *
724 CATTAAGGTTTGCCCAATAGAAGACGATTTAAAATGTCACTAATGGGCCCCGATAGGCCCAACAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
789 AACAAGTGTTCCAAATGAGCTAAG
131 AACAAGTGTTCCAAATGAGCTAAA
* *
813 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAGG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** * *
878 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAATAGGCCCAAAAG
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
943 AAAAAGTGTTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
** *
967 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGATCATAAACAGTGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
1032 CATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGTAAATAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* *
1097 AACAAG-GATTCTAAATGAGCAAAA
131 AACAAGTG-TTCCAAATGAGCTAAA
* *
1121 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
1186 CATTGAGGGTTGTCAAATTGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCTAAAAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
1251 AACAAGTGTTCCAAACGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * *
1275 AACTTCACAGTGGACTAATGTCACCAATATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * *
1340 CATTGAGGTTTGTCAAATTGAAGACGATTCAAAACGTCTCTAATGGGCCCCGATAGGCCCAACAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
1405 AACAAGTGTTCCAAATGAGCTAAG
131 AACAAGTGTTCCAAATGAGCTAAA
* *
1429 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
1494 CAATGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG-CCC---A-----AACAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* *
1550 AACAAGTGTTCCAAATGAGCCAAG
131 AACAAGTGTTCCAAATGAGCTAAA
*
1574 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
1639 CAATGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAACAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
1704 AACAAGTGTTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * *
1728 AACTTCACAGTGGACTAATGTCACCAAAATTATTATAGTTAGGCCATAACCAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * * *
1793 CATTGAGGTTTGCCCAATCTAAGACGATTCAAAACGTCACTAAAGGGCCCCGATAGGCTCAAATT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
1858 AACAAGTGTTCCAAATGCGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
*
1882 AACATT-ACAGTGGACTAATCTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
1 AAC-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* * *
1946 GCATTGAGGGTTGCCAAATCGAAGACAATTCAAAACGTCACTAAAGGGCCCTGATAGGCCCAAAA
65 GCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAA
2011 TAACAAGTGTTCCAAATGAGC-AAA
130 TAACAAGTGTTCCAAATGAGCTAAA
*
2035 AACCTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTTGGCCATAAACAATGGAAAGAAAA
1 AA-CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* ** * * * *
2100 GCTTTGAGATTTGTCAAATTGAAGACGATTCAAAACGTCTCTAATGGGCGCCGATAGGCCCAAAA
65 GCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAA
2165 TAACAAGTGTTCCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
* *
2190 AACTTCACAATGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * * *
2255 CATTCAGGTTTGCCTAATCGAAGACCATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAACAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
2320 AACAAGTGTTCCAAATGAGCTAAG
131 AACAAGTGTTCCAAATGAGCTAAA
* *
2344 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** * * *
2409 CATTGAGATTTGTCAAATTGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAAAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
2474 AACAAGTGTTCTAAATGAAGCTAAA
131 AACAAGTGTTCCAAATG-AGCTAAA
* * * *
2499 AACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGACAATAAACAATGAAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
2564 CAATGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAACAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
2629 AACAAGTGTTCCAAATGAGCTAAG
131 AACAAGTGTTCCAAATGAGCTAAA
* * * * *
2653 AACTTCTCAGTGGACTAATCTCACCCAAAATAATTATAGATAGGCCATAAACAATGGAACGTAAA
1 AACTTCACAGTGGACTAATCTCA-CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* * *
2718 GCATTGAGGGTTAGTCAAATTGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAA
65 GCATTGAGGGTT-GCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAA
*
2783 ATAACAAGTGTTCTAAATGAGCTAAA
129 ATAACAAGTGTTCCAAATGAGCTAAA
* * * * *
2809 AACTTCATAGTGGACTAATCTCACTAAAATGATTATAGTTAGACAATAAACAATGAAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
*
2874 CAATGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
2939 AACAAGTGTTCCAAATGAGCAAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * *
2963 AACTTCACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCAAAAACAATGGAACGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
3028 CATTGAGGGTTGTCAAATTGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
3093 AACAAGTGTTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * *
3117 AACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
3182 CAATGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAACAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* *
3247 AACAAGTGTTCCAAAGGAGCTAAG
131 AACAAGTGTTCCAAATGAGCTAAA
* **
3271 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGTGAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
3336 CATTGTGGGTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCAATAGGCCCAAAA
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGATAGGCCCAAAA
* * *
3400 GAAAAAGTGTTCCAAATGCGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
* *
3425 AACATT-ACAGTGGACTAATCTGACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAA
1 AAC-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* *
3489 GCATTGAGGGTTGCCAAATCGAAGACAATTCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAA
65 GCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAA
3554 TAACAAGTGTTCCAAATGAGC-AAA
130 TAACAAGTGTTCCAAATGAGCTAAA
* * * *
3578 AACCTTCACAGTGGACTAATCTCACCAAAATGATAATTGTTTGGCCATAAACAATGGAAAAAAAA
1 AA-CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
** * * *
3643 GCATTGAGATTTGTCAAATTGAAGACGATTCAAAACGTCTCTAATGGGCCCCGATAGGCCCAAAA
65 GCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAA
*
3708 TAACAAGTGTTCCAAACGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
* * *
3733 AACTTCACAGTGGACTAATGTCACCAAAATTATTATAGTTAGGCCATAACCAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * * *
3798 CATTGAGGTTTGCCCAATCTAAGACGATTCAAAACGTCACTAAAGGGCCCCGATAGGCTCAAATT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
*
3863 AACAAGTGTTCCAAATGCGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
*
3887 AACATT-ACAGTGGACTAATCTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
1 AAC-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* * ** * * *
3951 GCATTGAGGGTTGCCAAATCGAAGACAATTCAAAAAGGAACTAA-AGGACCCTATAGGCCCAAAA
65 GCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAA
4015 TAACAAGTGTTCCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
*
4040 AACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT----AA---AAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * ** * *
4098 CATTGAGGGTTGCCAAATCGAAGATGATTCAATACGGAACTAATGGGTCCTGATAGGCCCAAAAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* *
4163 AACAAGTGTTCCAAATGTGTTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* *
4187 AACTTCACAGTGGACTAACCTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** * **
4252 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAATTAATGGGCCCATATAGGCCCAAAAT
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
* *
4317 AAAAAGTGTTCCAAATGAGCTAAC
131 AACAAGTGTTCCAAATGAGCTAAA
* *
4341 AACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
4406 CATTGAGGGTTGCCAAATCGAAGACGATTCAA
66 CATTGAGGGTTGCCAAATCGAAGACGATTCAA
Statistics
Matches: 3281, Mismatches: 310, Indels: 68
0.90 0.08 0.02
Matches are distributed among these distances:
145 137 0.04
146 51 0.02
147 83 0.03
149 3 0.00
150 1 0.00
151 2 0.00
152 2 0.00
153 100 0.03
154 2563 0.78
155 246 0.07
156 93 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
AACAAGTGTTCCAAATGAGCTAAA
Done.