Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016989.1 Corchorus olitorius cultivar O-4 contig17022, 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: 13605
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Found at i:702 original size:169 final size:168
Alignment explanation
Indices: 421--740 Score: 561
Period size: 169 Copynumber: 1.9 Consensus size: 168
411 AAAGAATACC
* *
421 TCAAGTCTAAGGCATTCAGATCCGTCGACGGTGGGCGAACGGAGGGGCGACCATCGTGGATTTGG
1 TCAAGTCTAAGGCATTCAGATCCGTCGACGGTGGGCGAACGGACGGGCGACCATCG-GGATTTGA
* *
486 AAATGAAGGAGGCGGAGGGAGAGAGTGAAAGAGAGTTGAGAGAGCTCGCGCAAAAGAGGGAATTA
65 AAATGAAGGAGGCGGAAGGAGAGAGTGAAAGAGAGTTGAGAGAGCTCGAGCAAAAGA-GGAATTA
551 GGGATTAGGTTTATGAAAATTTAAGAAAGGAGAAGAATGGG
129 GGGATTAGGTTTA-GAAAATTTAAGAAAGGAGAAGAATGGG
*
592 TCAAGTCTCAGGCATTCAGATCCGTCGACGGTGGGCGAACGGACGGGCGACCATC-GGATTTGAA
1 TCAAGTCTAAGGCATTCAGATCCGTCGACGGTGGGCGAACGGACGGGCGACCATCGGGATTTGAA
656 AATGAAGGAGGCGGAAGGAGAGAGTGAAAGAGAGTTGAGAGAGCTCGAGCAAAAGAGGAATTAGG
66 AATGAAGGAGGCGGAAGGAGAGAGTGAAAGAGAGTTGAGAGAGCTCGAGCAAAAGAGGAATTAGG
721 GATTAGGTTTAGAAAATTTA
131 GATTAGGTTTAGAAAATTTA
741 TATATATATA
Statistics
Matches: 144, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
167 9 0.06
168 20 0.14
169 62 0.43
171 53 0.37
ACGTcount: A:0.33, C:0.12, G:0.37, T:0.18
Consensus pattern (168 bp):
TCAAGTCTAAGGCATTCAGATCCGTCGACGGTGGGCGAACGGACGGGCGACCATCGGGATTTGAA
AATGAAGGAGGCGGAAGGAGAGAGTGAAAGAGAGTTGAGAGAGCTCGAGCAAAAGAGGAATTAGG
GATTAGGTTTAGAAAATTTAAGAAAGGAGAAGAATGGG
Found at i:8834 original size:36 final size:36
Alignment explanation
Indices: 8713--8852 Score: 210
Period size: 37 Copynumber: 3.9 Consensus size: 36
8703 GAACGCTTTG
** *
8713 AAAAC-TGATGGGAACTTTCCCAATTTGACAATTTTG
1 AAAACTTGATGGGAACTTTCCCAATTTGA-AAACTTA
*
8749 AAAACTGGATGGGAACTTTCCCAATTTGAAAACTATA
1 AAAACTTGATGGGAACTTTCCCAATTTGAAAACT-TA
*
8786 GAAACTTGATGGGAACTTTCCCAATTTGAAAACTTA
1 AAAACTTGATGGGAACTTTCCCAATTTGAAAACTTA
8822 AAAACTTGATGGGAACTTTCCCAATTTGAAA
1 AAAACTTGATGGGAACTTTCCCAATTTGAAA
8853 GAGCTAAATT
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
36 40 0.42
37 55 0.58
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (36 bp):
AAAACTTGATGGGAACTTTCCCAATTTGAAAACTTA
Found at i:8835 original size:73 final size:73
Alignment explanation
Indices: 8714--8852 Score: 226
Period size: 73 Copynumber: 1.9 Consensus size: 73
8704 AACGCTTTGA
** *
8714 AAACTGATGGGAACTTTCCCAATTTGACAATTTTGAAAACTGGATGGGAACTTTCCCAATTTGAA
1 AAACTGATGGGAACTTTCCCAATTTGACAAACTTAAAAACTGGATGGGAACTTTCCCAATTTGAA
8779 AACTATAG
66 AACTATAG
*
8787 AAACTTGATGGGAACTTTCCCAATTTGA-AAACTTAAAAACTTGATGGGAACTTTCCCAATTTGA
1 AAAC-TGATGGGAACTTTCCCAATTTGACAAACTTAAAAACTGGATGGGAACTTTCCCAATTTGA
8851 AA
65 AA
8853 GAGCTAAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 38 0.62
74 23 0.38
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (73 bp):
AAACTGATGGGAACTTTCCCAATTTGACAAACTTAAAAACTGGATGGGAACTTTCCCAATTTGAA
AACTATAG
Found at i:8877 original size:51 final size:52
Alignment explanation
Indices: 8822--8957 Score: 204
Period size: 52 Copynumber: 2.6 Consensus size: 52
8812 TGAAAACTTA
8822 AAAACTTGATGGGAACTTTCCCAATTTG-AAAGAGC-TAAATTGAATACTTTG
1 AAAACTTGATGGGAACTTTCCCAATTTGAAAAGA-CTTAAATTGAATACTTTG
** *
8873 AAAACTTGATGGGAACTTTCCCGCTTTGAAAAGACTTAAATTGAATGCTTTG
1 AAAACTTGATGGGAACTTTCCCAATTTGAAAAGACTTAAATTGAATACTTTG
*
8925 AAAACTTGATGGGAACTTTCCCTAAATTGAAAA
1 AAAACTTGATGGGAACTTTCCC-AATTTGAAAA
8958 CCTTTGAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
51 27 0.36
52 42 0.55
53 7 0.09
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (52 bp):
AAAACTTGATGGGAACTTTCCCAATTTGAAAAGACTTAAATTGAATACTTTG
Found at i:8991 original size:65 final size:65
Alignment explanation
Indices: 8901--9061 Score: 268
Period size: 65 Copynumber: 2.5 Consensus size: 65
8891 TCCCGCTTTG
* * * * *
8901 AAAAGACTTAAATTGAATGCTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAAAACCTTTGAA
1 AAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGAACTCTCCCTAAATTGAAAACCCTTGAA
*
8966 AAAAAACTTGAATTGAATATTTTGAAAACTTGATGGGAACTCTCCCTAAATTGAAAACCCTTGAA
1 AAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGAACTCTCCCTAAATTGAAAACCCTTGAA
9031 AAAAAACTTGAATTGAATACTTTGAAAACTT
1 AAAAAACTTGAATTGAATACTTTGAAAACTT
9062 TGAATGACAT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 89 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (65 bp):
AAAAAACTTGAATTGAATACTTTGAAAACTTGATGGGAACTCTCCCTAAATTGAAAACCCTTGAA
Found at i:9105 original size:19 final size:20
Alignment explanation
Indices: 9077--9115 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
9067 GACATTCTTT
9077 TTTTTATTTTTGAATTTTTG
1 TTTTTATTTTTGAATTTTTG
*
9097 TTTTT-TTTTTGGATTTTTG
1 TTTTTATTTTTGAATTTTTG
9116 AAAACCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTTGAATTTTTG
Found at i:12252 original size:19 final size:19
Alignment explanation
Indices: 12209--12259 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
12199 AGGGTTCCCC
*
12209 AATTTTCTCTTTTCTGTTG
1 AATTTTCTCTTTTATGTTG
*
12228 AA-TTTCTCCTTTTAT-TTT
1 AATTTTCT-CTTTTATGTTG
12246 AATTTTCCTCTTTT
1 AATTTT-CTCTTTT
12260 GTCTGTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 9 0.33
19 16 0.59
20 2 0.07
ACGTcount: A:0.14, C:0.18, G:0.04, T:0.65
Consensus pattern (19 bp):
AATTTTCTCTTTTATGTTG
Done.