Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011758.1 Corchorus olitorius cultivar O-4 contig11791, 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: 2767
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Found at i:471 original size:154 final size:154
Alignment explanation
Indices: 1--2767 Score: 4216
Period size: 154 Copynumber: 17.9 Consensus size: 154
* * *
1 TTAGGCCATAAACAATGGGAAGAAAAGCATTGAGGGTTGTCCGAAATCGAAGACGATTCAATAC-
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG-CC-AAATCGAAGACGATTCAAAACG
* *
65 GTACTAATGGG-CCCGACTAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
64 GAACTAATGGGCCCCGA-TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
129 GGCCTAATCTCACCAAAATGATTATAG
128 GGACTAATCTCACCAAAATGATTATAG
* *
156 TTAGGACCACTAAACAATGGAACGTAAAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAAC
1 TTAGG-CCA-TAAACAATGGAAAG-AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
** * * * *
221 GTCACAAATGGACCTCGATAGGACCCAAAATAACAAGGGGTTCCCAAAATGAGCTAAAAACTTCA
63 GGAACTAATGGGCCCCGATAGG-CCCAAAATAACAA-GTGTT-CC-AAATGAGCTAAAAACTTCA
286 CAGTGGACTAATCTCACCAAAATGATTATAG
124 CAGTGGACTAATCTCACCAAAATGATTATAG
*
317 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
*
382 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGC
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
447 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
*
471 TTAGGCCATAAACAATGGAAAGGAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* * *
536 ACTAATGGGCCTCGATAGGCCGAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
601 CTAATCTCACCGAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* *
625 TTAGGCCATAAACAATGGATAGAATAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* *
690 ACTAATGAGCCCCGTTAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
755 CTAATCTCACCGAAATGATTATTG
131 CTAATCTCACCAAAATGATTATAG
* * *
779 TTAGGCCATAAACAATGGATAGAATAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* * * *
844 ACTAATGAGCCCCGTTAGGCCCAAAATAACAAGTGTTCCGAATGAGCTAAAAACTTCACAGTGTA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
909 ATAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
933 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* * * *
998 ACTAATGGGCCCCGATAGGCCCAAAATAACACGTGTTCCAACTGACCTAAAAAGTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
1063 CTAAACTCACCAAACTGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * **
1087 TTAGGTCATAAAAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* *
1152 ACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
1217 CTAATCTCACCAAATTGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * * * *
1241 TTAGGCCATAAACAATTGAAAGAAAAGTATTGAGATTGGCCAAATC-ATAGACGATTCAATACGT
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA-AGACGATTCAAAACGG
* * * *
1305 CACTAATGGGCCCCGATAGGCCCAAAGTAACATGTGTTCCAAATGAGCTAAAAAGTTCACAGTGG
65 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
* *
1370 GCTAATCTCACCAAATTGATTATAG
130 ACTAATCTCACCAAAATGATTATAG
* * * **
1395 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGATGACGATTCAATACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* * ** *
1460 ACTAATGGGCCCCGATATGCCCAAAATAACAAGTATTTTAAATGAACTAAAAACTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
1525 CTAATATCACCAAAATGATTATAT
131 CTAATCTCACCAAAATGATTATAG
* * *
1549 TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTTCCAAAATCGAAGACGATTCAAAACGT
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC-AAATCGAAGACGATTCAAAACGG
* * *
1614 CACTAATGGGACCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAGCTTCACAGTG
65 AACTAATGGG-CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
1679 GACTAATCTCACCAAAATGATTATAG
129 GACTAATCTCACCAAAATGATTATAG
* * * * *
1705 TTAGGCCATAAATAATGAAAATAAAAGAATTGAGGTTTGCCAGATCGAAGACGATTCAAAA-GGT
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG-
* * * * * *
1769 CACTGATGGGCACCGATAGGCCCGAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGG
65 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG
*
1834 ACAAATCTCACCAAAATGATTATAG
130 ACTAATCTCACCAAAATGATTATAG
* * * * * * **
1859 TTAGGCCGTAAACAATGGAAAGAAAGGAATCGAAGTTTGCCAAATCGAAGACTATTCAAAACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* *
1924 ACTAATGGTCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1989 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * **
2013 GTAGGCCATAAACAATGGAAACAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTC
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
2078 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
2143 CTAATCTACGACC-AAATGAGTTATAG
131 CTAATCT-C-ACCAAAATGA-TTATAG
2169 TTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
*
2233 ACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
2298 CTAATCTCACCAAAATAATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * * * * **
2322 TTAGGCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTT
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
*
2387 ACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
2452 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
*
2476 TTAGGCCATAAACAATGGTAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
*
2541 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
2606 CTAATCTCACCGAAATGATTATAG
131 CTAATCTCACCAAAATGATTATAG
* * *
2630 CTAGGCCATAAACAATGGATAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGA
1 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* *
2695 ACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACAGTGTA
66 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
2759 ATAATCTCA
131 CTAATCTCA
Statistics
Matches: 2401, Mismatches: 191, Indels: 42
0.91 0.07 0.02
Matches are distributed among these distances:
153 54 0.02
154 1800 0.75
155 185 0.08
156 162 0.07
157 37 0.02
158 87 0.04
159 17 0.01
160 5 0.00
161 54 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAG
Done.