Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015286.1 Corchorus olitorius cultivar O-4 contig15319, 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: 19382
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Found at i:9939 original size:27 final size:27
Alignment explanation
Indices: 9873--9973 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
9863 TGTGAACTTA
* * *
9873 AAATGACCACAATGCCCCTTGAGTATGC
1 AAATGACCAAAATGCCCCTGGA-TATAC
* *
9901 AAATGACCAAAATGCCCCTGGACATTC
1 AAATGACCAAAATGCCCCTGGATATAC
* * * *
9928 AAATGACTAAAATACCCCTGAATATAA
1 AAATGACCAAAATGCCCCTGGATATAC
9955 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
9974 AGATGACCCT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
27 41 0.67
28 20 0.33
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATATAC
Found at i:10506 original size:50 final size:50
Alignment explanation
Indices: 10431--10696 Score: 469
Period size: 50 Copynumber: 5.3 Consensus size: 50
10421 CTCATTAAAC
*
10431 TTGGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
*
10481 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAAT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
10531 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
*
10581 TTGACTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
* *
10631 TTGGCCTGTGGAAAAGCCTATGTAGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
* *
10681 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
10697 TCAAAGCATT
Statistics
Matches: 206, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 206 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (50 bp):
TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
Found at i:10887 original size:92 final size:92
Alignment explanation
Indices: 10783--10957 Score: 289
Period size: 92 Copynumber: 1.9 Consensus size: 92
10773 ATACCTTTGG
*
10783 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAAGGACCAAT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATG-AAAAAGGACCAAT
10848 GTGCGGTCAACTTGAAAAACAA-CTTGA
65 GTGCGGTCAACTTGAAAAACAATCTTGA
* * *
10875 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAACAGGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
*
10940 TGCAGTCAACTTGAAAAA
66 TGCGGTCAACTTGAAAAA
10958 TAACTCTGAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 29 0.37
92 49 0.63
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (92 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
TGCGGTCAACTTGAAAAACAATCTTGA
Found at i:10998 original size:79 final size:79
Alignment explanation
Indices: 10867--11037 Score: 290
Period size: 79 Copynumber: 2.2 Consensus size: 79
10857 ACTTGAAAAA
**
10867 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTCTTGATTGATGATGAAACA-
1 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAA-AG
10931 GGACCAATTTGCAGT
65 GGACCAATTTGCAGT
10946 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAAGG
1 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAA-G
*
11011 GGACCAATTTGCGGT
65 GGACCAATTTGCAGT
11026 CAACTTGAAAAA
1 CAACTTGAAAAA
11038 CAATTTTGAA
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
78 1 0.01
79 60 0.69
80 26 0.30
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.29
Consensus pattern (79 bp):
CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAAGG
GACCAATTTGCAGT
Found at i:11068 original size:171 final size:170
Alignment explanation
Indices: 10783--11108 Score: 521
Period size: 171 Copynumber: 1.9 Consensus size: 170
10773 ATACCTTTGG
*
10783 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAAGGACCAAT
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAAAAGGACCAAT
10848 GTGCGGTCAACTTGAAAAACAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAATTTC
66 GTGCGGTCAACTTGAAAAACAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTG-AAATTTC
*
10913 TTGATTGA-TGATGAAACAGGACCAATTTGCAGTCAACTTGA
130 TTGATT-ACTGATGAAAAAGGACCAATTTGCAGTCAACTTGA
* **
10954 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAAGGGGACCAAT
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAAAAGGACCAAT
* * * * *
11019 TTGCGGTCAACTTGAAAAACAATTTTGAAAAATAACTCTG-GTCTGATGTTGTGATTGAAATTTT
66 GTGCGGTCAACTTGAAAAACAA-CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAATTTC
11083 TTGATTACTGATGAAAAAGGACCAAT
130 TTGATTACTGATGAAAAAGGACCAAT
11109 GCATAGTCAA
Statistics
Matches: 143, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
169 1 0.01
170 29 0.20
171 97 0.68
172 16 0.11
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (170 bp):
AAAATAACTCTGAATCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAAAAGGACCAAT
GTGCGGTCAACTTGAAAAACAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAATTTCT
TGATTACTGATGAAAAAGGACCAATTTGCAGTCAACTTGA
Found at i:11129 original size:90 final size:90
Alignment explanation
Indices: 10949--11176 Score: 300
Period size: 90 Copynumber: 2.5 Consensus size: 90
10939 TTGCAGTCAA
* * * * *
10949 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACGTCTTGATTGATGATGAAAAGGGGA
1 CTTGAAAAATAACTCTG-GTCTGATGTTGTGATTG-AAACTTTTTGATTGATGATGAAAAGAGGA
* *
11014 CCAATTTGCGGTCAACTTGAAAAACAAT
64 CCAA-TTGCAGTCAAATTGAAAAACAAT
* *
11042 TTTGAAAAATAACTCTGGTCTGATGTTGTGATTGAAATTTTTTGATT-ACTGATGAAAA-AGGAC
1 CTTGAAAAATAACTCTGGTCTGATGTTGTGATTGAAACTTTTTGATTGA-TGATGAAAAGAGGAC
11105 CAA-TGCATAGTCAAATTGAAAAACAAT
65 CAATTGC--AGTCAAATTGAAAAACAAT
11132 CTTGAAAAATAACTCTGGTCTGATGTTGTGATTGAAACTTTTTGA
1 CTTGAAAAATAACTCTGGTCTGATGTTGTGATTGAAACTTTTTGA
11177 CTGTTCCTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
88 3 0.02
90 68 0.56
91 19 0.16
92 15 0.12
93 16 0.13
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (90 bp):
CTTGAAAAATAACTCTGGTCTGATGTTGTGATTGAAACTTTTTGATTGATGATGAAAAGAGGACC
AATTGCAGTCAAATTGAAAAACAAT
Found at i:11630 original size:50 final size:50
Alignment explanation
Indices: 11576--11820 Score: 386
Period size: 50 Copynumber: 4.9 Consensus size: 50
11566 CCTAAATGCC
* **
11576 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
*
11626 CTTTGAAAAGCGAATTTTGATCTT-GACTTACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
11675 CTTTGAAAAGCGAATTTTGATCTT-GACTTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGAC-TCACAAATGGAAAGCAATTTTA
* *
11725 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAGAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
* * *
11775 CTTTGAAAAGCGAATTTTCATCTTGAACTCACAAATGGAATGCAAT
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAAT
11821 CTTATTATAA
Statistics
Matches: 183, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
49 48 0.26
50 133 0.73
51 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
Found at i:11747 original size:99 final size:99
Alignment explanation
Indices: 11576--11821 Score: 404
Period size: 99 Copynumber: 2.5 Consensus size: 99
11566 CCTAAATGCC
11576 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTACTTTGAAAAGCGAAT
1 CTTTGAAAAGCGAATTTTGATCTT-GACTCACAAATGGAATGCAATCCTACTTTGAAAAGCGAAT
*
11641 TTTGATCTTG-ACTTACAAATGGAAAGCAATTTTA
65 TTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* **
11675 CTTTGAAAAGCGAATTTTGATCTTGACTTCACAAATGGAAAGCAATTTTACTTTGAAAAGCGAAT
1 CTTTGAAAAGCGAATTTTGATCTTGAC-TCACAAATGGAATGCAATCCTACTTTGAAAAGCGAAT
*
11740 TTTGATCTTGAACTCACAAATGGAGAGCAATTTTA
65 TTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
*
11775 CTTTGAAAAGCGAATTTTCATCTTGAACTCACAAATGGAATGCAATC
1 CTTTGAAAAGCGAATTTTGATCTTG-ACTCACAAATGGAATGCAATC
11822 TTATTATAAA
Statistics
Matches: 136, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
98 3 0.02
99 68 0.50
100 63 0.46
101 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (99 bp):
CTTTGAAAAGCGAATTTTGATCTTGACTCACAAATGGAATGCAATCCTACTTTGAAAAGCGAATT
TTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:12210 original size:20 final size:21
Alignment explanation
Indices: 12187--12229 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12177 TAATCGTGTC
12187 AAGACACGACTAACACG-TTT
1 AAGACACGACTAACACGCTTT
* *
12207 AAGACACGAGTGACACGCTTT
1 AAGACACGACTAACACGCTTT
12228 AA
1 AA
12230 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (21 bp):
AAGACACGACTAACACGCTTT
Found at i:13142 original size:15 final size:16
Alignment explanation
Indices: 13116--13149 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
13106 TTTGAATTGA
13116 TTTGATTTTTGATTTT
1 TTTGATTTTTGATTTT
13132 TTTGA-TTTTGATTTT
1 TTTGATTTTTGATTTT
13147 TTT
1 TTT
13150 TTGAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (16 bp):
TTTGATTTTTGATTTT
Found at i:13150 original size:26 final size:27
Alignment explanation
Indices: 13112--13163 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
13102 TTTGTTTGAA
* *
13112 TTGATTTGATTTTTGATTTTTTTGATT
1 TTGATTTGATTTTTGAATTTCTTGATT
*
13139 TTGATTT-TTTTTTGAATTTCTTGAT
1 TTGATTTGATTTTTGAATTTCTTGAT
13164 GGAGTGGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.69
Consensus pattern (27 bp):
TTGATTTGATTTTTGAATTTCTTGATT
Found at i:18583 original size:16 final size:17
Alignment explanation
Indices: 18562--18599 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
18552 TTTTATTACT
18562 TTTTTTAATTTTCT-GA
1 TTTTTTAATTTTCTGGA
* *
18578 TTTTTTCATTTTTTGGA
1 TTTTTTAATTTTCTGGA
18595 TTTTT
1 TTTTT
18600 CCTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTTTAATTTTCTGGA
Done.