Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009933.1 Corchorus olitorius cultivar O-4 contig09965, 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: 3484
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:1485 original size:13 final size:13
Alignment explanation
Indices: 1467--1494 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1457 ACTTTTATAT
1467 ATAGTATAGATAG
1 ATAGTATAGATAG
1480 ATAGTATAGATAG
1 ATAGTATAGATAG
1493 AT
1 AT
1495 TTGGAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.32
Consensus pattern (13 bp):
ATAGTATAGATAG
Found at i:2142 original size:670 final size:670
Alignment explanation
Indices: 858--2148 Score: 2060
Period size: 670 Copynumber: 1.9 Consensus size: 670
848 TTCGGCCCAG
*
858 TAGGCCCATTAGGCCCGTTTGACTCCATGAAGCTCAAATTACCAAGCTAGATGTCTTGAAGTCTA
1 TAGGCCCATTAGGCCCGTTTGACTCCATGAAGCTCAAATTACCAAGCCAGATGTCTTGAAGTCTA
* *
923 AATATGATATTTTTAGACTCAATTCGTTAATATAGAAGCCCAAAGAAGGAGTTCAAGACTCCAAG
66 AATATGATATTCTTAGACCCAATTCGTTAATATAGAAGCCCAAAGAAGGAG-T--AGA-TCCAAG
* * * *
988 TCCAATCAGTAATTATGATGCAGTAATGATTTAGCCCTGATGCAGCATTGTTAAATCCTATTTAA
127 TCCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGACGCAACATTGTTAAATCATATTTAA
* * *
1053 AGGACTTAATAAGAGCAGTTTTGGAAGAAAATTCATAAGTTTTGATCCGGAGCTTAGAAAAATGC
192 AGGACTTAATAAGAGCAGTTTTGAAAGAAAATTCATAACTTTTGATCCAGAGCTTAGAAAAATGC
*
1118 AAATGAGGTGCCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTTACCTCGAGACCTAA
257 AAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTTACCTCGAGACCTAA
* * *
1183 TTCTGTCGTTCTGGTGGACGATTTTGCCCTTGAATTTTTGGACAGAATTGATCTTCTCTTAAACC
322 TTCTGTCGTTCTGGTGGACGATTTTACCCTTGAATTTCTGGACAGAATTGATCTTCTCCTAAACC
* * ***
1248 GACTTTGAGAATGTTTTGGACGAAAATTCAGATGCTAAAGATGATGTGGAGCATTTTTATTGGCC
387 GACTTGGAGAATGTTTTGGACGAAAATTCAGATGCTAAAGATGATGTAGAGCATCCCTATTGGCC
* *
1313 GCGTGGATCCTAATTAATGAGGATAATCTAAATTTTTATTATTTTAATAATGAAATAATTAAAAT
452 ACGTGGATCCTAATTAATGAGGATAATCTAAATTTTCATTATTTTAATAATGAAATAATTAAAAT
*
1378 ATTATTTAATAATGGCAATTTAGAAATATATTTGAAAAAAAAGGTACAATCGGAAAACATAAAGT
517 ATTATTTAATAATGGCAATTTAGAAATATATTTGAAAAAAAAGGTACAATCGAAAAACATAAAGT
1443 TTCCCCTTATTCGTACTTTTATATATAGTATAGATAGATAGTATAGATAGATTTGGAGAAACTAT
582 TTCCCCTTATTCGTACTTTTATATATAGTATAGATAGATAGTATAGATAGATTTGGAGAAACTAT
1508 TGATTTTGTCTCATTTAGGTCTAA
647 TGATTTTGTCTCATTTAGGTCTAA
* * * *
1532 TAGGCCCATTAGGCTCGTTTGAGTCCATTAAG-TCCAAATTGCCAAGCCAGATGTCTTGAAGTCT
1 TAGGCCCATTAGGCCCGTTTGACTCCATGAAGCT-CAAATTACCAAGCCAGATGTCTTGAAGTCT
* * *
1596 AAATCTGATATTCTTAGGCCCAATTCGTTAATATGGAAGCCCAAAGAA-G-G-AG-TCCAAGTCC
65 AAATATGATATTCTTAGACCCAATTCGTTAATATAGAAGCCCAAAGAAGGAGTAGATCCAAGTCC
* *
1657 AATCAGTAATTATGATGCAGTAATGATTCAGCCCTGACGTAATATTGTTAAATCATATTTAAAAG
130 AATCAGTAATTATGATGCAGTAATGATTCAGCCCTGACGCAACATTGTTAAATCATATTT--AA-
* *
1722 AGGACTTCATAAGAGTAGTTTTGAAAGAAAA-TCATAACTTTTGATCCAGAG-TTCAGAAAAATG
192 AGGACTTAATAAGAGCAGTTTTGAAAGAAAATTCATAACTTTTGATCCAGAGCTT-AGAAAAATG
* *
1785 CAAATGAGGTACCGTTGGAAAGAGGATTCCGAGATCTACAACTTTTATGTTTATCTCGAGACCTA
256 CAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTTACCTCGAGACCTA
1850 ATTCTGTCGTT-TCGGTGGACGATTTTACCCTTGAAATTTCTGGACAGAATTGATCTTCTCCTAA
321 ATTCTGTCGTTCT-GGTGGACGATTTTACCCTTG-AATTTCTGGACAGAATTGATCTTCTCCTAA
1914 ACCGACTTGGAGAATGTTTTGGACGAAAATTCAGATGCTAAAGATGATGTAGAGCATCCCTATTG
384 ACCGACTTGGAGAATGTTTTGGACGAAAATTCAGATGCTAAAGATGATGTAGAGCATCCCTATTG
* *
1979 GCCATGTTGGATCCTAATTAATGAGGATAATCTAAATTTTCATTATTTTAATAGT-AGAATAATT
449 GCCACG-TGGATCCTAATTAATGAGGATAATCTAAATTTTCATTATTTTAATAATGA-AATAATT
*
2043 AAAATATTATTTAATAATGGCAATTTAGAAATATATTTGAAAAAAAGGGTACAATCGAAAAACAT
512 AAAATATTATTTAATAATGGCAATTTAGAAATATATTTGAAAAAAAAGGTACAATCGAAAAACAT
2108 AAAGTTTCCCCTTATTCGTACTTTTATATATAGTATAGATA
577 AAAGTTTCCCCTTATTCGTACTTTTATATATAGTATAGATA
2149 AAAGTGTTAT
Statistics
Matches: 570, Mismatches: 38, Indels: 22
0.90 0.06 0.03
Matches are distributed among these distances:
666 63 0.11
667 3 0.01
668 123 0.22
669 121 0.21
670 157 0.28
672 1 0.00
673 2 0.00
674 100 0.18
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (670 bp):
TAGGCCCATTAGGCCCGTTTGACTCCATGAAGCTCAAATTACCAAGCCAGATGTCTTGAAGTCTA
AATATGATATTCTTAGACCCAATTCGTTAATATAGAAGCCCAAAGAAGGAGTAGATCCAAGTCCA
ATCAGTAATTATGATGCAGTAATGATTCAGCCCTGACGCAACATTGTTAAATCATATTTAAAGGA
CTTAATAAGAGCAGTTTTGAAAGAAAATTCATAACTTTTGATCCAGAGCTTAGAAAAATGCAAAT
GAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAACTTTTATGTTTACCTCGAGACCTAATTCT
GTCGTTCTGGTGGACGATTTTACCCTTGAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACT
TGGAGAATGTTTTGGACGAAAATTCAGATGCTAAAGATGATGTAGAGCATCCCTATTGGCCACGT
GGATCCTAATTAATGAGGATAATCTAAATTTTCATTATTTTAATAATGAAATAATTAAAATATTA
TTTAATAATGGCAATTTAGAAATATATTTGAAAAAAAAGGTACAATCGAAAAACATAAAGTTTCC
CCTTATTCGTACTTTTATATATAGTATAGATAGATAGTATAGATAGATTTGGAGAAACTATTGAT
TTTGTCTCATTTAGGTCTAA
Done.