Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019833.1 Corchorus olitorius cultivar O-4 contig19866, 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: 29973
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:10762 original size:20 final size:20
Alignment explanation
Indices: 10737--10774 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10727 CAAACTAAAC
10737 CCATTTACTCATTAAAAAAA
1 CCATTTACTCATTAAAAAAA
10757 CCATTTACTCATTAAAAA
1 CCATTTACTCATTAAAAA
10775 TATACTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (20 bp):
CCATTTACTCATTAAAAAAA
Found at i:12498 original size:123 final size:123
Alignment explanation
Indices: 12095--12472 Score: 639
Period size: 123 Copynumber: 3.0 Consensus size: 123
12085 ATTTAATTAA
12095 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT----
*
12160 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTATTTGAGTAAAACTGTAAAA
62 TA--TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
12225 G
123 G
*
12226 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATAAAAATAGTAAAATGGTAAAAATTATA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
*
12291 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTGTAAAAG
66 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
*
12349 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATTATA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
*
12414 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
12472 T
1 T
12473 TTAAACAATA
Statistics
Matches: 240, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
123 174 0.73
124 2 0.01
125 2 0.01
127 2 0.01
131 60 0.25
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (123 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATA
AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
Found at i:13919 original size:131 final size:132
Alignment explanation
Indices: 13766--14029 Score: 410
Period size: 131 Copynumber: 2.0 Consensus size: 132
13756 GTCATTTAAT
* *
13766 AAATATATTTTAAAAATTCTAATATATCTAAG-TTTTTT-AATTAAATTAGTAAAATGGTAAAAA
1 AAATATATTTAAAAAATTCTAATATA--TAAGTTTTTTTAAATTAAAATAGTAAAATGGTAAAAA
* * *
13829 TAAAATAGGTATAAAGATATTAGATTTTA-TACAATAGAAATAGAGTTTTTAGTTGAGTAAAATT
64 TAAAATAGGTATAAAGATATTAGATTTAATTA-AATAAAAATAGAGTTTTTAGTTGAGTAAAACT
13893 ATAAA
128 ATAAA
13898 AAATATA-TTAAAAAATTCTAATATATAAGTTTTTTTAAATTAAAATAGTAAAATGGTAAAAATA
1 AAATATATTTAAAAAATTCTAATATATAAGTTTTTTTAAATTAAAATAGTAAAATGGTAAAAATA
* *
13962 AAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
66 AAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
14027 AA
131 AA
14029 A
1 A
14030 GTTTAACTAA
Statistics
Matches: 122, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
129 4 0.03
130 6 0.05
131 103 0.84
132 9 0.07
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (132 bp):
AAATATATTTAAAAAATTCTAATATATAAGTTTTTTTAAATTAAAATAGTAAAATGGTAAAAATA
AAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
AA
Found at i:14133 original size:11 final size:11
Alignment explanation
Indices: 14117--14144 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
14107 GTACTTTTTA
14117 ATATAGTATAG
1 ATATAGTATAG
14128 ATATAGTATAG
1 ATATAGTATAG
14139 ATATAG
1 ATATAG
14145 ATGAATAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (11 bp):
ATATAGTATAG
Found at i:14459 original size:2 final size:2
Alignment explanation
Indices: 14454--14480 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14444 CCAAGTGTGT
14454 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
14481 GAGTGTAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15331 original size:30 final size:30
Alignment explanation
Indices: 15255--15331 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
15245 ATATCGTACA
* *
15255 GGTCCCTCTATTTACAAAAATGAATCAATTC
1 GGTCCCTCTACTTATAAAAATG-ATCAATTC
* * *
15286 GGTCCCCCTAC-TATAAAAACTG-TGAATTT
1 GGTCCCTCTACTTATAAAAA-TGATCAATTC
15315 GGTCCCTCTACTTATAA
1 GGTCCCTCTACTTATAA
15332 TTTGTTGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 15 0.39
30 12 0.32
31 11 0.29
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (30 bp):
GGTCCCTCTACTTATAAAAATGATCAATTC
Found at i:15697 original size:30 final size:30
Alignment explanation
Indices: 15623--15698 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 30
15613 TGACACCAAA
* **
15623 TTGTAAGTAGAGAGACCAAATTGATAGTTT
1 TTGTAAGTAGAGGGACCAAATTGATACCTT
* *
15653 TTGT-AGTAGGGGGACCAAATTGATCCCTT
1 TTGTAAGTAGAGGGACCAAATTGATACCTT
15682 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
15699 TGTACGGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (30 bp):
TTGTAAGTAGAGGGACCAAATTGATACCTT
Found at i:19720 original size:57 final size:57
Alignment explanation
Indices: 19629--19744 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
19619 TATCCGTTTC
* *
19629 CTTTCACACAATAAATGTTATAATAAATCTTATCCCCCCTATTTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
19686 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
19743 CT
1 CT
19745 ACAAAATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.41
Consensus pattern (57 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
Found at i:19869 original size:42 final size:42
Alignment explanation
Indices: 19810--19890 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
19800 TAAGGATCAG
*
19810 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
19852 GATTTGAATTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTC
19891 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (42 bp):
GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.