Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022289.1 Corchorus olitorius cultivar O-4 contig22322, 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: 11930
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:7237 original size:438 final size:434
Alignment explanation
Indices: 6425--7458 Score: 1251
Period size: 438 Copynumber: 2.4 Consensus size: 434
6415 AATAGATTTT
* * * * * *
6425 CAATCGAAATCACAAAATTTCA-AAAACATTTTTTAGAATTGAAATATAAAAATTAGCTTTTGAG
1 CAATCAAAACCACAAAATTT-AGGAAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTTGAG
* * * * *
6489 TCTTTCATGAAAGTTGTAGAC-CATAAAATTACCTTTTAATAGACACTTGAATTAGCTTAATTGG
65 TCCTTCATGAAAGTTGTAG-CTCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATCGG
* * *
6553 ACAAATAGAACAAAGAAAATAAAAATAACTGAAGTGTTAAATCAAGTAAGATAGAATTTGGAAAT
129 ACAAATAGAACAAAG--AATAAAAAT-A-TAAAGTCTTAAATCAAGTAAGATAGAATTTGGAAAG
* * **
6618 GACTAAATAGCATAAAATAGAAAAGTATGAGGGTGATTTATAACTAATTGAAATAAGAAAATATT
190 GACTAAATAGCATAAAATAGAAAAGTATGAGGGTCATTTATAAATAATCCAAATAAGAAAATATT
*
6683 TGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTCATGAAACTCGTAGATCAAA
255 TGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTCACGAAACTCGTAGATCAAA
* * * * *
6748 TTAACTTTCGGGTTCTTCATGAAAGTCATAGATTATACAGTAACCTTTTAACCGACACTTGAATA
320 TTAACTTTCGGGTCCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAATA
* * * * *
6813 ACTTTAATTGGACATGTAGATC-GAAAATTATATGGTATTAAAT-AGACCAA
385 ACTTCAATCGGACATGTAGA-CAAAAAATTATACGATATTAAATCA-ACCAA
* * * *
6863 CAATCGAAACGAGC-AAATTTAGGAAGCATTTTTTTGAATTGAAACATAAAAATTTGGTTTTGAG
1 CAATCAAAACCA-CAAAATTTAGGAAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTTGAG
*
6927 TCCTTCATGAAAGTTGTAGCTCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGA
65 TCCTTCATGAAAGTTGTAGCTCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATCGGA
* *
6992 CAAATAGAACAAAGAATAAAAATATAAAG-CTTAAA-CGTTAGTTTAAGATAGAATTTGTAAAGG
130 CAAATAGAACAAAGAATAAAAATATAAAGTCTTAAATC--AAG--TAAGATAGAATTTGGAAAGG
* * * *
7055 ACTAAGTAGTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTT
191 ACTAAATAGCATAAAATAGAAAAGTATGAGGGTCATTT-ATAAATAATCCAAATAAGAAAATATT
* *
7120 TGTTAATGGAGATCTTGAAACATAGAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAA
255 TGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTCACGAAACTCGTAGATCAAA
* * ** * *
7185 TTTAGCTTTCGGGTCCTTCATTAAAGTTGTAAATCATGCAATAACGTTTTAACCGACACTTCAAT
320 -TTAACTTTCGGGTCCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAAT
* **
7250 AACTTCAATCGGACATGTGGACAAAAAATTATACGATATTAAATCAACCGG
384 AACTTCAATCGGACATGTAGACAAAAAATTATACGATATTAAATCAACCAA
* * ** *
7301 CAATCAAAACCACAAAATTTCGGAAGTATTTTTTAGAATCAAAACATTAAAA-TTGACTTTTGAG
1 CAATCAAAACCACAAAATTTAGGAAGCATTTTTTAGAATTGAAACATAAAAATTTG-CTTTTGAG
* * * * * *
7365 TTCTTAATGAGAA-TTTTAGATCATGAAATTACCTTTTAATAGACACTTCAATCACCTTAATCGG
65 TCCTTCATGA-AAGTTGTAGCTCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATCGG
* * *
7429 AAAAATAGAAAAAAAAATACAAAATA-AAAG
129 ACAAATAGAACAAAGAATA-AAAATATAAAG
7459 GCAACGCGTT
Statistics
Matches: 513, Mismatches: 68, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
432 1 0.00
433 5 0.01
434 6 0.01
435 1 0.00
436 61 0.12
437 91 0.18
438 338 0.66
439 10 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (434 bp):
CAATCAAAACCACAAAATTTAGGAAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTTGAGT
CCTTCATGAAAGTTGTAGCTCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATCGGAC
AAATAGAACAAAGAATAAAAATATAAAGTCTTAAATCAAGTAAGATAGAATTTGGAAAGGACTAA
ATAGCATAAAATAGAAAAGTATGAGGGTCATTTATAAATAATCCAAATAAGAAAATATTTGTTAA
TGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCATTCACGAAACTCGTAGATCAAATTAACT
TTCGGGTCCTTCATGAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCA
ATCGGACATGTAGACAAAAAATTATACGATATTAAATCAACCAA
Found at i:9991 original size:42 final size:43
Alignment explanation
Indices: 9940--10030 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 43
9930 AGTGCATTAC
*
9940 CTAA-ATTCTA-CTTCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTTCATCTCTAGATAATTCATCAAAATAAAA
*
9981 CTAATATTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTTCATCTCTAGATAATTCATCAAAATAAAA
10026 CTAAT
1 CTAAT
10031 CTTTTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTTCATCTCTAGATAATTCATCAAAATAAAA
Found at i:11437 original size:132 final size:131
Alignment explanation
Indices: 11224--11487 Score: 365
Period size: 132 Copynumber: 2.0 Consensus size: 131
11214 ATTTAAGAAA
** * *
11224 TATATTTTCAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATGATAAAAATAAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAATGATAAAAATAAAAA
* *
11289 AAGGTATAAGGATATTATG-TTTAATTAAATAAAAAATAGACTTTTTTAGTTGAGTAAAATTATA
66 AAGGTATAAGGATATTA-GATTTAATTAAAT-AAAAATAGA-GTTTTTAGTTGAGTAAAACTATA
11353 AAAG
128 AAAG
*
11357 TATATTTAAAAAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAATAT-AGTAAAAAT-TA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAA-ATGA-TAAAAATAAA
* * *
11419 AATAGTTATAAGGATATTAGATTTAATTAAATAAAAATGGAGTTTTTAGTTGAGTAAAACTATAA
64 AAAAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
11484 AAG
129 AAG
11487 T
1 T
11488 TCAAACAATG
Statistics
Matches: 118, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
130 26 0.22
131 9 0.08
132 48 0.41
133 35 0.30
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.39
Consensus pattern (131 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAATGATAAAAATAAAAA
AAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
G
Done.