Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018688.1 Corchorus olitorius cultivar O-4 contig18721, 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: 15026
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Found at i:1969 original size:15 final size:14
Alignment explanation
Indices: 1947--1981 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
1937 ATAACAAACA
1947 TAATTGTTTTGCTT
1 TAATTGTTTTGCTT
1961 TATATTGTTTTGCTT
1 TA-ATTGTTTTGCTT
1976 TAATTG
1 TAATTG
1982 ATGATTCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.63
Consensus pattern (14 bp):
TAATTGTTTTGCTT
Found at i:2859 original size:66 final size:66
Alignment explanation
Indices: 2785--2915 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
2775 GATTTCTAAG
*
2785 CCGATTATTATGTAGGCTATTTTGTAGTAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
1 CCGATTATTATGTAGGCTATTTTGTAGCAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
2850 A
66 A
* *
2851 CCGATTATTATGTAGGCTATTTTGTAGCATATTTATTTCTTTCTTCTTTTCCTTTTAATTTACTT
1 CCGATTATTATGTAGGCTATTTTGTAGCAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
2916 TAAGAATTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (66 bp):
CCGATTATTATGTAGGCTATTTTGTAGCAAATTTATTTCTTCCTTCTTTTCCTTTTAATTTACTT
A
Found at i:2996 original size:99 final size:99
Alignment explanation
Indices: 2887--3084 Score: 369
Period size: 99 Copynumber: 2.0 Consensus size: 99
2877 GCATATTTAT
*
2887 TTCTTTCTTCTTTTCCTTTTAATTTACTTTAAGAATTTATTTTAGAATTAATTAAATTAAGTATG
1 TTCTTTCTTCTTTTCCTTTTAATTTACTTTAAGAATTTATTTTAGAATTAATTAAATTAAGTAGG
2952 AATGTAAGACTTTTTCTAATAATTTGTTTACGCA
66 AATGTAAGACTTTTTCTAATAATTTGTTTACGCA
**
2986 TTCTTTCTTCTTTTCCTTTTAATTTACTTTAAGGGTTTATTTTAGAATTAATTAAATTAAGTAGG
1 TTCTTTCTTCTTTTCCTTTTAATTTACTTTAAGAATTTATTTTAGAATTAATTAAATTAAGTAGG
3051 AATGTAAGACTTTTTCTAATAATTTGTTTACGCA
66 AATGTAAGACTTTTTCTAATAATTTGTTTACGCA
3085 GGTTGGTAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (99 bp):
TTCTTTCTTCTTTTCCTTTTAATTTACTTTAAGAATTTATTTTAGAATTAATTAAATTAAGTAGG
AATGTAAGACTTTTTCTAATAATTTGTTTACGCA
Found at i:4244 original size:178 final size:176
Alignment explanation
Indices: 4042--4370 Score: 622
Period size: 176 Copynumber: 1.9 Consensus size: 176
4032 AAGTTTGTTA
*
4042 TAACTCGCAATAATTAGATTATTAGAACCTTGAATGTATCATGGGTGATTTCTTTTGTAGTTTTA
1 TAACTCGCAATAATTAGATTATTAGAACCTTGAATGTATCATGGATGATTT-TTTTGTAGTTTTA
4107 GTACTCATTTATAGTTTTAATTGTCTATAATTTTTATTTTTCAATTAAAGCGAAGTTGGCATTTT
65 GTACTCATTTATAGTTTTAATTGTCTATAATTTTTA-TTTTCAATTAAAGCGAAGTTGGCATTTT
4172 CAATAATATAACACGTTAACATACTTAGAAGATTTGTTAATAAAGTTG
129 CAATAATATAACACGTTAACATACTTAGAAGATTTGTTAATAAAGTTG
4220 TAACTCGCAATAATTAGATTATTAGAACCTTGAATGTATCATGGATGATTTTTTTGTAGTTTTAG
1 TAACTCGCAATAATTAGATTATTAGAACCTTGAATGTATCATGGATGATTTTTTTGTAGTTTTAG
*
4285 TACTCATTTATAGTTTTAATTGTCTATAATTTTTATTTTCAATTAAAGCGAAGTTGGTATTTTCA
66 TACTCATTTATAGTTTTAATTGTCTATAATTTTTATTTTCAATTAAAGCGAAGTTGGCATTTTCA
4350 ATAATATAACACGTTAACATA
131 ATAATATAACACGTTAACATA
4371 GATGGAGATT
Statistics
Matches: 149, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
176 50 0.34
177 49 0.33
178 50 0.34
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (176 bp):
TAACTCGCAATAATTAGATTATTAGAACCTTGAATGTATCATGGATGATTTTTTTGTAGTTTTAG
TACTCATTTATAGTTTTAATTGTCTATAATTTTTATTTTCAATTAAAGCGAAGTTGGCATTTTCA
ATAATATAACACGTTAACATACTTAGAAGATTTGTTAATAAAGTTG
Found at i:5373 original size:22 final size:22
Alignment explanation
Indices: 5348--5394 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5338 CCTATTTTTA
5348 GTAACCTTGAATAAAAAGAATG
1 GTAACCTTGAATAAAAAGAATG
* *
5370 GTAACCTTGAATAAGAAGATTG
1 GTAACCTTGAATAAAAAGAATG
5392 GTA
1 GTA
5395 TAACCTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.26
Consensus pattern (22 bp):
GTAACCTTGAATAAAAAGAATG
Found at i:6681 original size:18 final size:17
Alignment explanation
Indices: 6654--6690 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
6644 GAGCATGGTT
*
6654 AAAAATTTACGAATACA
1 AAAAATTTACAAATACA
6671 AAAACATTTACAAATACA
1 AAAA-ATTTACAAATACA
6689 AA
1 AA
6691 TATAACACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.14, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAAATTTACAAATACA
Found at i:7935 original size:36 final size:36
Alignment explanation
Indices: 7873--8020 Score: 161
Period size: 36 Copynumber: 4.1 Consensus size: 36
7863 GAATCTGAGC
* *
7873 CACCAGCTGTAACAGAGAAAATAAAGGAAGAAGAGG
1 CACCAGCTGCAACAGAGAAAACAAAGGAAGAAGAGG
* * *
7909 CACCGGCTGCAGCAGAGAACACAAAGGAAGAAGAGG
1 CACCAGCTGCAACAGAGAAAACAAAGGAAGAAGAGG
* * * * *
7945 CACCAGCTGCAACAGAGAAAGCAGAGGAAAAAGTGA
1 CACCAGCTGCAACAGAGAAAACAAAGGAAGAAGAGG
* * * * *
7981 TACCATCTGTAACAGAGAAAACGAAGGAAGAAGTGG
1 CACCAGCTGCAACAGAGAAAACAAAGGAAGAAGAGG
8017 CACC
1 CACC
8021 GGAAGCAACT
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 90 1.00
ACGTcount: A:0.45, C:0.19, G:0.28, T:0.07
Consensus pattern (36 bp):
CACCAGCTGCAACAGAGAAAACAAAGGAAGAAGAGG
Found at i:11411 original size:18 final size:18
Alignment explanation
Indices: 11388--11424 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11378 AATATGAAAC
11388 ATGCTTAAGAACTCAACA
1 ATGCTTAAGAACTCAACA
11406 ATGCTTAAGAACTCAACA
1 ATGCTTAAGAACTCAACA
11424 A
1 A
11425 ATTGTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ATGCTTAAGAACTCAACA
Done.