Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023165.1 Corchorus olitorius cultivar O-4 contig23198, 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: 4759
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:622 original size:5 final size:5
Alignment explanation
Indices: 612--640 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
602 AGTAATGAAT
612 TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
641 GAAATTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1645 original size:39 final size:39
Alignment explanation
Indices: 1578--1742 Score: 185
Period size: 39 Copynumber: 4.3 Consensus size: 39
1568 GATATCCTAA
* *
1578 AATAGGACTT-TGAAATTAACTGACAAAACAATGACCCTG
1 AATAGGA-TTCTGAAATTAACTGATAAAACAATGATCCTG
* *
1617 AACAGGATTCTGAAATTAACAGATAAAACAATGATCCT-
1 AATAGGATTCTGAAATTAACTGATAAAACAATGATCCTG
* * * * *
1655 AATTAGGCTTCTGAAATTGACGGTTATAACAATGATCCTG
1 AA-TAGGATTCTGAAATTAACTGATAAAACAATGATCCTG
*
1695 AATAGGATTCTGAAGTTAACTGATAAAGA-AATG-TCCTG
1 AATAGGATTCTGAAATTAACTGATAAA-ACAATGATCCTG
1733 AATAGGATTC
1 AATAGGATTC
1743 AAACATAAAT
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
38 19 0.18
39 84 0.79
40 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (39 bp):
AATAGGATTCTGAAATTAACTGATAAAACAATGATCCTG
Found at i:1782 original size:39 final size:39
Alignment explanation
Indices: 1685--1815 Score: 158
Period size: 39 Copynumber: 3.4 Consensus size: 39
1675 CGGTTATAAC
** * * * *
1685 AATGATCCTGAATAGGATTCTGA-AGTTAACTGATAAAGA
1 AATGATCCTGAATAGGATTCAAACAG-AAATTCATAAAGT
* **
1724 AATG-TCCTGAATAGGATTCAAACATAAATTCATTGAGT
1 AATGATCCTGAATAGGATTCAAACAGAAATTCATAAAGT
1762 AATGATCCTGAATAGGATTCAAACAGAAATTCATAAAGT
1 AATGATCCTGAATAGGATTCAAACAGAAATTCATAAAGT
1801 AATGATCCTGAATAG
1 AATGATCCTGAATAG
1816 CAATGATCCT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
38 27 0.35
39 51 0.65
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (39 bp):
AATGATCCTGAATAGGATTCAAACAGAAATTCATAAAGT
Found at i:1938 original size:20 final size:20
Alignment explanation
Indices: 1913--1953 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1903 AAAATATGGA
*
1913 ATGCCCAGAGGACTTGCCAG
1 ATGCCCAGAGGACTTGACAG
* *
1933 ATGCCCGGGGGACTTGACAG
1 ATGCCCAGAGGACTTGACAG
1953 A
1 A
1954 ATTAATACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.34, T:0.15
Consensus pattern (20 bp):
ATGCCCAGAGGACTTGACAG
Found at i:2345 original size:141 final size:140
Alignment explanation
Indices: 2077--2888 Score: 1183
Period size: 141 Copynumber: 5.7 Consensus size: 140
2067 AATGAGGTGG
* * *
2077 TACCCGGAGGTTTTTGAAATTATGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGTAAGGT
1 TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGG-
* * *
2142 TTTTTTGAAACTTAAACGCAACTTTGATTAACAACTTGATGAAATGAAGTGATACACAGAGGATT
65 TTTTTTGAAATTTAAACGCAACTTTGATTAACAACTTGATGAAATGAGGTGATACA-GGAGGATT
2207 TATCAGAATTAA
129 TATCAGAATTAA
** * * * * *
2219 TACCCGGAGGTGACTGAAATTGTGCCCGGAGGTCTTACAAACGCTAACTTGACCTTAAGCAGGGT
1 TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGT
* * *
2284 TTTTTGAAATTTAAACACAACTTTGATTAACGACTTGATGAAATGAGGTGATATCAGGAGGATTC
66 TTTTTGAAATTTAAACGCAACTTTGATTAACAACTTGATGAAATGAGGTGATA-CAGGAGGATTT
2349 ATCAGAATTAA
130 ATCAGAATTAA
* *
2360 TACCCGAAGGTTTCTAAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGT
1 TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGT
* *
2425 TTTTTGAAATTTAAACGCAACTTTGATTAACAACTTGATGAAATGAAGTGATACTTGGAGGATTT
66 TTTTTGAAATTTAAACGCAACTTTGATTAACAACTTGATGAAATGAGGTGATAC-AGGAGGATTT
2490 ATCAGAATTAA
130 ATCAGAATTAA
*
2501 TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCTAACTCGACCTTGAGCAAGGT
1 TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGT
** ** *
2566 TTTTTGAAATTTAAATACAACTTTGATTAACGGCTTGATGAAATGAGGTGATACCCGGAGGATTT
66 TTTTTGAAATTTAAACGCAACTTTGATTAACAACTTGATGAAATGAGGTGATA-CAGGAGGATTT
2631 ATCAGAATTAA
130 ATCAGAATTAA
* * * *
2642 TACCCTGAGGTTTCTGAAATTGTGCCCGGAGTTCTTACAAATGAAAACTCAACCTTGAGCAAGGT
1 TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGT
** *
2707 TTCTTTGAAATTTAAACGCAACTTTGATTAATGACTTGATGAAATGAGGTGATACCCGGAGGATT
66 TT-TTTGAAATTTAAACGCAACTTTGATTAACAACTTGATGAAATGAGGTGATA-CAGGAGGATT
2772 TATCAGAATTAA
129 TATCAGAATTAA
* * *
2784 TACACGGAGGTTTCTGAAATTGTGCCCGGAGGTTTTACAAATGCAAACTCGACCTTGGGCAAGGT
1 TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGG-
* *
2849 TTTTTTTTTGAAATTTAAACCCAGCTTTGATTAACAACTT
65 ---TTTTTTGAAATTTAAACGCAACTTTGATTAACAACTT
2889 ACCAAAATGA
Statistics
Matches: 603, Mismatches: 59, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
140 1 0.00
141 385 0.64
142 184 0.31
145 30 0.05
146 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (140 bp):
TACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCGACCTTGAGCAAGGT
TTTTTGAAATTTAAACGCAACTTTGATTAACAACTTGATGAAATGAGGTGATACAGGAGGATTTA
TCAGAATTAA
Found at i:4726 original size:40 final size:40
Alignment explanation
Indices: 4682--4759 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
4672 ATAGGAATAG
* *
4682 CACCTTCCGATGAGCAATGGCAAACTGGGAATATAAACAA
1 CACCTTCCGATGAGCAAGGGCAAACTAGGAATATAAACAA
* *
4722 CACCTTCCGATGAGGAAGGGCAAACTAGGAATTTAAAC
1 CACCTTCCGATGAGCAAGGGCAAACTAGGAATATAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (40 bp):
CACCTTCCGATGAGCAAGGGCAAACTAGGAATATAAACAA
Done.