Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012341.1 Corchorus olitorius cultivar O-4 contig12374, 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: 14023
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Found at i:8784 original size:57 final size:57
Alignment explanation
Indices: 8696--8809 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
8686 GTTGTTGTCA
8696 TTCCATAATAGCCATGAGCCTCCACAAAATCATGCTGCATCGAGACTCTTGAGTGAT
1 TTCCATAATAGCCATGAGCCTCCACAAAATCATGCTGCATCGAGACTCTTGAGTGAT
8753 TTCCATAATAGCCATGAGCCTCCACAAAATCATGCTGCATCGAGACTCTTGAGTGAT
1 TTCCATAATAGCCATGAGCCTCCACAAAATCATGCTGCATCGAGACTCTTGAGTGAT
8810 CACCTTCTCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (57 bp):
TTCCATAATAGCCATGAGCCTCCACAAAATCATGCTGCATCGAGACTCTTGAGTGAT
Found at i:10913 original size:863 final size:863
Alignment explanation
Indices: 9227--10952 Score: 2337
Period size: 863 Copynumber: 2.0 Consensus size: 863
9217 AAATTATACA
** * **
9227 ATATTAAATAGATTGGCAATCAAAACTACAAAATTTCAGAAGCATTTTTTAGGGTCAAAAAATTA
1 ATATTAAATAGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAAAATTA
* *
9292 AAATTGGCTTCCGAGTTCTTCATGAAAGTTGTAGATCATGAAATCACATTTTAATGGACACATGA
66 AAAATGGCTTCCGAGTTCTTCATGAAAGTTGTAGATCATGAAATCACATTTTAATAGACACATGA
** *
9357 ATCACCTTAATCGGACAAATAGAGCAAAAAATACAAAAATAAAAGTCGAATCGTTAAATCGTCCA
131 ATCACCTTAATCGGACAAATAGAAAAAAAAATACAAAAATAAAAGTCGAATCGTTAAATCATCCA
** *
9422 ACCCATAATTGTAAAAGATTAAATAGCATAAATTATAAAAGTATGGGGGGATCATTTGATAAATA
196 ACCCATAATTGTAAAAGATTAAATAGCATAAAGCATAAAAGTAT-GGAGGATCATTTGATAAATA
* * *
9487 ATCCAGCAAAAAAAATATTTGTTTATAGAGACCAAACATAAAAATTCCCTCTTGAACCCTCCACG
260 ATCCAACAAAAAAAATATTTGTTTATAGAGACCAAACATAAAAATTCCATCTTGAACCCTCCACA
* * **
9552 AAACTCGTTAATCAAATTCAGGTTCAGGCCCTTGACGAAAGTTTTAGATCACACAATAACCTTTT
325 AAACTCATTAATCAAATTCAGGTTCAGGCCCTCGACGAAAGTCGTAGATCACACAATAACCTTTT
* * * ** *
9617 AACCGACACTTGAATAACTTCAATCGGACATATGGACAAAAAATTATACGATATTAGATAGACCG
390 AACCGACACTTGAACAACCTCAATCAGACATATAAACAAAAAATTATACAATATTAGATAGACCG
* * *
9682 ACAATCGAGACCACAAAATTTCTGAAGCATTTTTTAGAATAAAAACATCAAAATTGGCTTTCGAG
455 ACAATCAAGACCACAAAATTTCTGAAGCATTTTTTAAAATAAAAACATCAAAATAGGCTTTCGAG
* * * *
9747 TTCTTCATGAAAGTTGTAGATCATTAAATTACCATTCAATAGACACCTGAATCACCTTGATCCGA
520 TTCTTCATGAAAGTTGTAGATCATGAAATTACCATTCAATAGAAACCTGAATCAACTTAATCCGA
* * *
9812 CAAATAGAACGAAAACTACAAAAATAAAAGCCGACGCATTAAATCGTCCAACCCATAATTTGTGA
585 CAAATAGAACAAAAAATACAAAAATAAAAGCCGACGCATTAAATCGTCCAACCCATAATTTGTAA
* * **
9877 GGGATTAAATAGCATAAAACATAAAAGTATAGGGATCATTTGATAAATAATCCAAAAAAAATGAT
650 AGGAATAAATAGCATAAAACATAAAAGTATAGGGATCATTCAATAAATAATCCAAAAAAAATGAT
* * * * * * **
9942 TTGTTTATTGAGAGTGGGACCCACCAATAGTAACTTTTAACCAAAGTTCCGAAAACGCCCTTGGT
715 TTCTTTATGGAGAATGGGACCCACCAAGAGTAACTTTTAACCAAACTTCCCAAAACGCCCTCAGT
* * * *
10007 CATCAATTCAAATAATGAAAAAATATGAGCACGAAAGTACCGAAATACCCCCGACAATTTGTTCT
780 CATCAATCCAAATAACGAAAAAATACGAGCACGAAAATACCGAAATA-CCCCGACAATTTGTTCT
*
10072 TTGGTGAATGTAGTGCATCG
844 TGGGTGAATGTAGTGCATCG
* * * *
10092 ATATTAAATAGACCGTCAATCAAAACCACAAAATTTCGGAAGTATTTTTTAGAATCAAAATATTA
1 ATATTAAATAGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAAAATTA
* * *
10157 AAAATGGCTTCTGAGTTCTTCATGAAAGTTGTAGATCGTGAAATCACATTTTAATAGACACTTGA
66 AAAATGGCTTCCGAGTTCTTCATGAAAGTTGTAGATCATGAAATCACATTTTAATAGACACATGA
* *
10222 ATCATCTTAATCGGATAAATAGAAAAAAAAATACAAAAATAAAAGTCGAAGT-GTTAAATCATCC
131 ATCACCTTAATCGGACAAATAGAAAAAAAAATACAAAAATAAAAGTCGAA-TCGTTAAATCATCC
* * *
10286 AACCCATAATTGTAAAGGATTAGATAGCATAAAGCATAAAAGTAT-GAGGTTCATTTGATAAATA
195 AACCCATAATTGTAAAAGATTAAATAGCATAAAGCATAAAAGTATGGAGGATCATTTGATAAATA
* *
10350 ATCCAAC-AAAAAAATATTT-TCTTATGGAGACCAAACAT-AAAATGTCCATCTTGAACTCTCCA
260 ATCCAACAAAAAAAATATTTGT-TTATAGAGACCAAACATAAAAAT-TCCATCTTGAACCCTCCA
* *
10412 CAAAACTCATTAATCAAATTCTGCTTTCAGGCCCTCGACGAAAGTCGTAGATCACACAATAACCT
323 CAAAACTCATTAATCAAATTCAG-GTTCAGGCCCTCGACGAAAGTCGTAGATCACACAATAACCT
* ***
10477 TTTAAGCGACACTTGAACAACCTCAATCAGACA-AGTAAACCGGAAATTATACAATATTAGATAG
387 TTTAACCGACACTTGAACAACCTCAATCAGACATA-TAAACAAAAAATTATACAATATTAGATAG
* * * *
10541 ACCGGCAATTAAGACCACAAAATTTCAT-AAGCATTTTTTAAAATCAAAACATTAAAATAGGC-T
451 ACCGACAATCAAGACCACAAAATTTC-TGAAGCATTTTTTAAAATAAAAACATCAAAATAGGCTT
* * * *
10604 TCTGAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTATTAGAAACTTGAATCAACTTA
515 TC-GAGTTCTTCATGAAAGTTGTAGATCATGAAATTACCATTCAATAGAAACCTGAATCAACTTA
* * *
10669 ATCGGACAAATAGAACAAAAAATACAAAAATAAAAGCCGACGCGTTAAATTGTCCAACCCATAA-
579 ATCCGACAAATAGAACAAAAAATACAAAAATAAAAGCCGACGCATTAAATCGTCCAACCCATAAT
* *
10733 TTGTAAAGGAATAAATAGCATAAAGCATAAAAGTAT-GAGTATCATTCAATAAATAATCCAACAA
644 TTGTAAAGGAATAAATAGCATAAAACATAAAAGTATAG-GGATCATTCAATAAATAAT-C--CAA
* * ***
10797 AAAAAAT-ATTTCTTTATGGAGAATGGGCCCCA-CAGAGGGTAACTTTTTTGCAAACTTCCCAAA
705 AAAAAATGATTTCTTTATGGAGAATGGGACCCACCA-AGAGTAACTTTTAACCAAACTTCCCAAA
* * * * *
10860 ACGCCCTCAGTCGTCAA-CCAAAATAACGAAAAAA-CCGAGTATGAAAATACCGAAATACCCTGA
769 ACGCCCTCAGTCATCAATCC-AAATAACGAAAAAATACGAGCACGAAAATACCGAAATACCCCGA
* *
10923 GAATTTGTTCTTGGGTGAATGTGGTGCATC
833 CAATTTGTTCTTGGGTGAATGTAGTGCATC
10953 TTATAGCTGG
Statistics
Matches: 750, Mismatches: 98, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
861 7 0.01
862 148 0.20
863 300 0.40
864 70 0.09
865 224 0.30
866 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (863 bp):
ATATTAAATAGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAAAATTA
AAAATGGCTTCCGAGTTCTTCATGAAAGTTGTAGATCATGAAATCACATTTTAATAGACACATGA
ATCACCTTAATCGGACAAATAGAAAAAAAAATACAAAAATAAAAGTCGAATCGTTAAATCATCCA
ACCCATAATTGTAAAAGATTAAATAGCATAAAGCATAAAAGTATGGAGGATCATTTGATAAATAA
TCCAACAAAAAAAATATTTGTTTATAGAGACCAAACATAAAAATTCCATCTTGAACCCTCCACAA
AACTCATTAATCAAATTCAGGTTCAGGCCCTCGACGAAAGTCGTAGATCACACAATAACCTTTTA
ACCGACACTTGAACAACCTCAATCAGACATATAAACAAAAAATTATACAATATTAGATAGACCGA
CAATCAAGACCACAAAATTTCTGAAGCATTTTTTAAAATAAAAACATCAAAATAGGCTTTCGAGT
TCTTCATGAAAGTTGTAGATCATGAAATTACCATTCAATAGAAACCTGAATCAACTTAATCCGAC
AAATAGAACAAAAAATACAAAAATAAAAGCCGACGCATTAAATCGTCCAACCCATAATTTGTAAA
GGAATAAATAGCATAAAACATAAAAGTATAGGGATCATTCAATAAATAATCCAAAAAAAATGATT
TCTTTATGGAGAATGGGACCCACCAAGAGTAACTTTTAACCAAACTTCCCAAAACGCCCTCAGTC
ATCAATCCAAATAACGAAAAAATACGAGCACGAAAATACCGAAATACCCCGACAATTTGTTCTTG
GGTGAATGTAGTGCATCG
Found at i:13949 original size:25 final size:24
Alignment explanation
Indices: 13913--13959 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
13903 AATACTTACA
13913 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
13937 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
13960 GTGCAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Done.