Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023687.1 Corchorus olitorius cultivar O-4 contig23720, 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: 17363
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:6064 original size:19 final size:18
Alignment explanation
Indices: 6031--6066 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6021 TTGAGATAAT
6031 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
6049 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
6067 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:6074 original size:11 final size:10
Alignment explanation
Indices: 6026--6077 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
6016 TTCTCTTGAG
6026 ATAATTCTTCA
1 ATAA-TCTTCA
6037 ATAATCTTC-
1 ATAATCTTCA
6046 A-AATCTTCAA
1 ATAATCTTC-A
*
6056 ATTATCTTCA
1 ATAATCTTCA
6066 ATAAGTCTTCA
1 ATAA-TCTTCA
6077 A
1 A
6078 ACACGAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 10 0.29
11 17 0.49
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (10 bp):
ATAATCTTCA
Found at i:7696 original size:15 final size:15
Alignment explanation
Indices: 7676--7707 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7666 AAGCGCCTTT
7676 CTTTAAGGTCTTTGG
1 CTTTAAGGTCTTTGG
7691 CTTTAAGGTCTTTGG
1 CTTTAAGGTCTTTGG
7706 CT
1 CT
7708 AGACTGCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (15 bp):
CTTTAAGGTCTTTGG
Found at i:7899 original size:21 final size:21
Alignment explanation
Indices: 7870--7923 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
7860 AGCTTGGAAT
* **
7870 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATAACC
* * *
7891 GGTGGTGGCTCGGGCTTAATC
1 GGTGGTGGCACGGGCATAACC
7912 GGTGGTGGCACG
1 GGTGGTGGCACG
7924 ATGCTTGGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.11, C:0.20, G:0.48, T:0.20
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:11005 original size:9 final size:9
Alignment explanation
Indices: 10991--11020 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
10981 AACTTCCTAG
10991 AAAAACTCA
1 AAAAACTCA
11000 AAAAACTCA
1 AAAAACTCA
11009 AAAAACTCA
1 AAAAACTCA
11018 AAA
1 AAA
11021 GAAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAACTCA
Found at i:11163 original size:30 final size:26
Alignment explanation
Indices: 11116--11179 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
11106 GCAGAAACAA
11116 TTTTTTTTTTTAGAAAA-CGTAAAATCT
1 TTTTTTTTTTTAGAAAACCG-AAAA-CT
*
11143 CTTTTTTTTTTATCGCAAAACCGAAAACT
1 -TTTTTTTTTT-TAG-AAAACCGAAAACT
11172 TTTTTTTT
1 TTTTTTTT
11180 CTTTTTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 18 0.56
29 4 0.12
30 8 0.25
31 2 0.06
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.53
Consensus pattern (26 bp):
TTTTTTTTTTTAGAAAACCGAAAACT
Found at i:14631 original size:32 final size:32
Alignment explanation
Indices: 14595--14785 Score: 189
Period size: 32 Copynumber: 6.0 Consensus size: 32
14585 TTTTTTTCTG
*
14595 AAGACGCCGCTAAATAAGGGCGTTTTGGTTTT
1 AAGACGCCGCTAAATAAGGGCGTTTTCGTTTT
* *
14627 AAGACGCCGCTAAATAATGGCG-TTTCGTTCTG
1 AAGACGCCGCTAAATAAGGGCGTTTTCGTT-TT
*
14659 GAGACGCCGCTAAATAAGGGCG-TTTCGTTTTT
1 AAGACGCCGCTAAATAAGGGCGTTTTCG-TTTT
* *
14691 AAAACGCCGCTAAAT-AGTGGCG-TTTCATTCTGT
1 AAGACGCCGCTAAATAAG-GGCGTTTTCGTT-T-T
* *
14724 -AGACGCCGCCAAATAAGGGCGTTTT-GTTCT
1 AAGACGCCGCTAAATAAGGGCGTTTTCGTTTT
* *
14754 ATAGACGCCGCTAAATAAGTGCATTTTC-TTTT
1 A-AGACGCCGCTAAATAAGGGCGTTTTCGTTTT
14786 CACATGCTCC
Statistics
Matches: 132, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.01
31 10 0.08
32 113 0.86
33 8 0.06
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (32 bp):
AAGACGCCGCTAAATAAGGGCGTTTTCGTTTT
Found at i:14682 original size:64 final size:64
Alignment explanation
Indices: 14581--14771 Score: 267
Period size: 64 Copynumber: 3.0 Consensus size: 64
14571 TAAATATAGC
**
14581 GGCGTTTTTTTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAAATAAT
1 GGCGTTTCATTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAAATAAT
* * * * * *
14645 GGCGTTTCGTTCTGGAGACGCCGCTAAATAAGGGCGTTTCGTTTTTAAAACGCCGCTAAATAGT
1 GGCGTTTCATTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAAATAAT
* * *
14709 GGCGTTTCATTCTGTAGACGCCGCCAAATAAGGGCGTTTT-GTTCTATAGACGCCGCTAAATAA
1 GGCGTTTCATTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTA-AGACGCCGCTAAATAA
14772 GTGCATTTTC
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
63 4 0.04
64 107 0.96
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (64 bp):
GGCGTTTCATTCTGAAGACGCCGCTAAATAAGGGCGTTTTGGTTTTAAGACGCCGCTAAATAAT
Found at i:17198 original size:27 final size:27
Alignment explanation
Indices: 17168--17286 Score: 184
Period size: 27 Copynumber: 4.4 Consensus size: 27
17158 CGAAATAACT
* *
17168 GGATCCACTGCTAGGGTCGAAGTGTGA
1 GGATCCACTGCTGGGGTCGAAGTGGGA
17195 GGATCCACTGCTGGGGTCGAAGTGGGA
1 GGATCCACTGCTGGGGTCGAAGTGGGA
17222 GGATCCACTGCTGGGGTCGAAGTGGGA
1 GGATCCACTGCTGGGGTCGAAGTGGGA
* ** *
17249 GGATCCACTACTGGGGTCGAAGCAGAA
1 GGATCCACTGCTGGGGTCGAAGTGGGA
17276 GGATCCACTGC
1 GGATCCACTGC
17287 GGTAACAGTC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.22, C:0.21, G:0.39, T:0.18
Consensus pattern (27 bp):
GGATCCACTGCTGGGGTCGAAGTGGGA
Done.