Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022532.1 Corchorus olitorius cultivar O-4 contig22565, 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: 56992
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4035 original size:442 final size:439
Alignment explanation
Indices: 3219--4365 Score: 1308
Period size: 442 Copynumber: 2.6 Consensus size: 439
3209 AAAACCACTT
* * * * **
3219 TTTTAGTTGTATTATTTATCAAATGACCCTCATACTTTTCTACTTTATATTATTTAGTCAGTTAC
1 TTTTATTTCTATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCTTTAC
* * * *
3284 AAATTCTATCTTAATCGATTTAACGCTTC-AGTTTTTTTTATTATTCTTTCTTTTATTTGTCCGA
66 AAATTCTATCTTAATCGATTTAACGCTTCAACTTTTTTTTTTTATTCTTTATTCTATTTGTCCGA
*
3348 TTAAGGTGATTTATGTGTCTATTAAAAGGTAATTTCATTATCTACAACTTTCATGAAGGACTCAA
131 TTAAGGTGATTTATGTGTCTATTAAAA-GTAATTTCATGATCTACAACTTTCATGAAGGACTCAA
* * * * *
3413 AAGTCAATTTTTATGTTTCAATTAAAAAAAAAAACTTTCGAAATTTGGTTGTTTCGATTGCCGGT
195 AAGCCAATTTTTATGTTTCAATTAAAAAAAAAAACTTCCCAAATTCGGTGGTTTCGATTGCCGGT
* ** * **
3478 CTATTTAAAATCATATAATTTTTTATCCACAAGTTCGATTAAAGTTATTCAAGTATCGTTTAAAA
260 CTATTTAAAACCATATAATTTTCGATCCACAAGTCCGATTAAAGTTATTCAAGTATCAATTAAAA
* * *
3543 GGTTATTGCATGATCTACGATTTTCAAAAAGGAACCGAAAGCTAAATTTGATCTATAAGTTTCAT
325 GGTTATTGCATGATCTAAGACTTTCAAAAAGGAACCGAAAGCTAAATTTGATCTACAAGTTTCAT
* * *
3608 TAAGGGTTCAAAAGGAAATTTTTATGTTTCAAAATCTCCATCAACAAACA
390 GAAGGGTTCAAAAGGAAACTTTTACGTTTCAAAATCTCCATCAACAAACA
* * * *
3658 TTTTATAATTCTATTATTTATAAAATGAACCTCCTA-TTTTCCTACTTTATACTACTTAATCCTT
1 TTTTAT--TTCTATTATTTATCAAATGACCCTCATACTTTT-CTACTTTATACTACTTAGTCCTT
* * *
3722 TACTAATTCTATCTTATTCGATTTAACGCTTCAACTTTTTTCTTTTTATTCTTTGTTCTATTTGT
63 TACAAATTCTATCTTAATCGATTTAACGCTTCAACTTTTTT-TTTTTATTCTTTATTCTATTTGT
* * *
3787 CCGATTAAGGTGATTCATATGTCTATTGAAAAGTAATTTCATGATTTACAACTTTCATGAAGGAC
127 CCGATTAAGGTGATTTATGTGTCTATT-AAAAGTAATTTCATGATCTACAACTTTCATGAAGGAC
* ***
3852 TCAAAAGCCAATTTGTATGTTTCAATT-AAAAAAAGTGCTTCCCAAATTCGGTGGTTTCGATTGC
191 TCAAAAGCCAATTTTTATGTTTCAATTAAAAAAAAAAACTTCCCAAATTCGGTGGTTTCGATTGC
* * * * * * *
3916 CGGTCTATTTGATACCATATAATTTTCGATCCATATGTCCGGTTAAAGTTATTCAAGTGTTAATT
256 CGGTCTATTTAAAACCATATAATTTTCGATCCACAAGTCCGATTAAAGTTATTCAAGTATCAATT
* ** *
3981 AAAAGGTTATTGTATGATCTAAGACTTTCATGAA-GAACCCGAAAGCTAAATTTGATCTACGAGT
321 AAAAGGTTATTGCATGATCTAAGACTTTCAAAAAGGAA-CCGAAAGCTAAATTTGATCTACAAGT
* * * * * *
4045 TTTATGAAGTGTTCAATAGGGAACTTTTACGTTTCAAGATCTCCATCAACAAATA
385 TTCATGAAGGGTTCAAAAGGAAACTTTTACGTTTCAAAATCTCCATCAACAAACA
* ** * * *
4100 TTTTCTTTGGATTAGTTATCAAATGACCCTCATACTTTTCTAATTTATATATGGTACTTAGTCCT
1 TTTTATTTCTATTATTTATCAAATGACCCTCATACTTTTCT-ACTT-TATA--CTACTTAGTCCT
* * *
4165 TTACAAATT-TAATTTTACTCGATTTAACGCTTCAAC----TTTTTTT-TTCTTTATTCTATTAG
62 TTACAAATTCT-ATCTTAATCGATTTAACGCTTCAACTTTTTTTTTTTATTCTTTATTCTATTTG
* * * * * * * *
4224 TCCAATTAAGCTAATTTAGGTGTCTATTAAACGGTAATTTTATGATCTACAACTTTCATAAAGGG
126 TCCGATTAAGGTGATTTATGTGTCTATTAAA-AGTAATTTCATGATCTACAACTTTCATGAAGGA
* * ** * * * ** *
4289 CTCAAAAGCGAATTTTTATGTTTTAATT-TTAGAAAAAACTTTCGAAATTTTGTGGTTTCGATTA
190 CTCAAAAGCCAATTTTTATGTTTCAATTAAAAAAAAAAACTTCCCAAATTCGGTGGTTTCGATTG
* *
4353 ACGATCTATTTAA
255 CCGGTCTATTTAA
4366 TATCATAGTA
Statistics
Matches: 593, Mismatches: 101, Indels: 29
0.82 0.14 0.04
Matches are distributed among these distances:
437 3 0.01
438 124 0.21
439 10 0.02
440 30 0.05
441 82 0.14
442 197 0.33
443 102 0.17
444 45 0.08
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (439 bp):
TTTTATTTCTATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCTTTAC
AAATTCTATCTTAATCGATTTAACGCTTCAACTTTTTTTTTTTATTCTTTATTCTATTTGTCCGA
TTAAGGTGATTTATGTGTCTATTAAAAGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAA
AGCCAATTTTTATGTTTCAATTAAAAAAAAAAACTTCCCAAATTCGGTGGTTTCGATTGCCGGTC
TATTTAAAACCATATAATTTTCGATCCACAAGTCCGATTAAAGTTATTCAAGTATCAATTAAAAG
GTTATTGCATGATCTAAGACTTTCAAAAAGGAACCGAAAGCTAAATTTGATCTACAAGTTTCATG
AAGGGTTCAAAAGGAAACTTTTACGTTTCAAAATCTCCATCAACAAACA
Found at i:6736 original size:117 final size:117
Alignment explanation
Indices: 6595--6807 Score: 336
Period size: 117 Copynumber: 1.8 Consensus size: 117
6585 CTTTTAAATG
* *
6595 ATTAAATTAGTAAAATGGTAAAAATAAAAAAGGTATAAGGATATTATATTTAATTAAATAAAAAT
1 ATTAAAATAGTAAAATGGTAAAAATAAAAAAGGTATAAGGATATTAGATTTAATTAAATAAAAAT
* * * *
6660 ATAGTTTTTAGTTGAGTAAAACTATAAAAGTATAATATATTTAAGTTTTTTA
66 AGAGTTCTTAGATGACTAAAACTATAAAAGTATAATATATTTAAGTTTTTTA
* * *
6712 ATTAAAATAGTAAAATGGTAAAAATAGAATAGTTATAAGGATATTAGATTTAATTAAATAAAAAT
1 ATTAAAATAGTAAAATGGTAAAAATAAAAAAGGTATAAGGATATTAGATTTAATTAAATAAAAAT
*
6777 AGAGTTCTTGGATGACTAAAACTATAAAAGT
66 AGAGTTCTTAGATGACTAAAACTATAAAAGT
6808 TTAAACAATG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 86 1.00
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (117 bp):
ATTAAAATAGTAAAATGGTAAAAATAAAAAAGGTATAAGGATATTAGATTTAATTAAATAAAAAT
AGAGTTCTTAGATGACTAAAACTATAAAAGTATAATATATTTAAGTTTTTTA
Found at i:24848 original size:30 final size:30
Alignment explanation
Indices: 24813--24873 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
24803 ATAAGAGACC
24813 CTTTCAATTTAACTAAAGAGACATCTCAGT
1 CTTTCAATTTAACTAAAGAGACATCTCAGT
24843 CTTTCAATTTAACTAAAGAGACATCTCAGT
1 CTTTCAATTTAACTAAAGAGACATCTCAGT
24873 C
1 C
24874 CATCGAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (30 bp):
CTTTCAATTTAACTAAAGAGACATCTCAGT
Found at i:24909 original size:14 final size:14
Alignment explanation
Indices: 24890--24923 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24880 GTTCGAATCT
*
24890 TGAAATGGATAAAA
1 TGAAATGAATAAAA
*
24904 TGAAATTAATAAAA
1 TGAAATGAATAAAA
24918 TGAAAT
1 TGAAAT
24924 TATTACAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (14 bp):
TGAAATGAATAAAA
Found at i:24924 original size:14 final size:14
Alignment explanation
Indices: 24898--24925 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24888 CTTGAAATGG
24898 ATAAAATGAAATTA
1 ATAAAATGAAATTA
24912 ATAAAATGAAATTA
1 ATAAAATGAAATTA
24926 TTACAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
ATAAAATGAAATTA
Found at i:49171 original size:3 final size:3
Alignment explanation
Indices: 49163--49195 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
49153 AAACAGATAT
49163 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
49196 ATTTTCTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:55334 original size:45 final size:45
Alignment explanation
Indices: 55283--55417 Score: 216
Period size: 45 Copynumber: 3.0 Consensus size: 45
55273 ATTTGTTTGA
*
55283 GAAAGCTCTCCCTTGACATCTTCCAACTGATCAGTTCCACAATGT
1 GAAAGCTCACCCTTGACATCTTCCAACTGATCAGTTCCACAATGT
* * *
55328 GCAAGCTCACCCTTGACATCCTCCAACTGACCAGTTCCACAATGT
1 GAAAGCTCACCCTTGACATCTTCCAACTGATCAGTTCCACAATGT
* *
55373 GAAAGCTCAGCCTTCACATCTTCCAACTGATCAGTTCCACAATGT
1 GAAAGCTCACCCTTGACATCTTCCAACTGATCAGTTCCACAATGT
55418 TTATTTCTCT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.26
Consensus pattern (45 bp):
GAAAGCTCACCCTTGACATCTTCCAACTGATCAGTTCCACAATGT
Done.