Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014822.1 Corchorus olitorius cultivar O-4 contig14855, 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: 25733
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:144 original size:25 final size:27
Alignment explanation
Indices: 97--146 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
87 AATTTAAATA
97 TATTAGATAATAGAATATTATTATTTT
1 TATTAGATAATAGAATATTATTATTTT
*
124 TATTA-ATAATA-TATATTATTATT
1 TATTAGATAATAGAATATTATTATT
147 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 6 0.27
27 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TATTAGATAATAGAATATTATTATTTT
Found at i:242 original size:35 final size:35
Alignment explanation
Indices: 196--270 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
186 TTATATAAAC
*
196 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
231 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
266 GAACA
1 GAACA
271 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:3264 original size:15 final size:14
Alignment explanation
Indices: 3232--3290 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
3222 CCTTATTTCC
3232 TTCTTCTTCTTT-TT
1 TTCTTCTT-TTTCTT
3246 TTCTTCCTTTTTCTT
1 TTCTT-CTTTTTCTT
*
3261 TTCTT-TCTTTTCCT
1 TTCTTCT-TTTTCTT
*
3275 TTC-TATTTTTCTT
1 TTCTTCTTTTTCTT
3288 TTC
1 TTC
3291 CCTTTTTGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 11 0.28
14 18 0.46
15 10 0.26
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (14 bp):
TTCTTCTTTTTCTT
Found at i:3273 original size:21 final size:20
Alignment explanation
Indices: 3227--3297 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
3217 AATTTCCTTA
*
3227 TTTCCTTCTTCTTCTTTTT-T
1 TTTCCTTTTTCTT-TTTTTCT
3247 TCTTCCTTTTTCTTTTCTTTCT
1 T-TTCCTTTTTCTTTT-TTTCT
*
3269 TTTCC--TTTCTATTTTTCT
1 TTTCCTTTTTCTTTTTTTCT
3287 TTTCCCTTTTT
1 TTT-CCTTTTT
3298 GGGCCAAGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
18 8 0.19
19 9 0.21
20 3 0.07
21 21 0.49
22 2 0.05
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTCCTTTTTCTTTTTTTCT
Found at i:5875 original size:16 final size:16
Alignment explanation
Indices: 5849--5884 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
5839 TTACATAAAT
5849 AAATCATATAATATATC
1 AAATCATATAATA-ATC
5866 AAAT-ATATAATAATC
1 AAATCATATAATAATC
5881 AAAT
1 AAAT
5885 TTTTTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 8 0.42
17 4 0.21
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATCATATAATAATC
Found at i:6163 original size:15 final size:15
Alignment explanation
Indices: 6143--6173 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6133 TAGGGTGGGT
6143 GTTAAAAATTTTAAA
1 GTTAAAAATTTTAAA
6158 GTTAAAAATTTTAAA
1 GTTAAAAATTTTAAA
6173 G
1 G
6174 AGTAAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (15 bp):
GTTAAAAATTTTAAA
Found at i:6180 original size:15 final size:15
Alignment explanation
Indices: 6145--6181 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
6135 GGGTGGGTGT
*
6145 TAAAAATTTTAAAGT
1 TAAAAATTTTAAAGG
6160 TAAAAATTTTAAAGAG
1 TAAAAATTTTAAAG-G
6176 TAAAAA
1 TAAAAA
6182 GGGAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (15 bp):
TAAAAATTTTAAAGG
Found at i:6392 original size:2 final size:2
Alignment explanation
Indices: 6378--6414 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
6368 CGTATATTGG
*
6378 AT AT AT GT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6415 TTTGAGTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7002 original size:42 final size:42
Alignment explanation
Indices: 6923--7002 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
6913 TATTGGCTCA
* **
6923 CCCAAATTGGCTTTAGCCCAAATATTGGCTCCAAAATTTTCG
1 CCCAAATTGGCTTTAGCCCAAATATAGGAGCCAAAATTTTCG
* *
6965 CCCAAATTGGAC-TTGGCCCAAATATAGGAGCCCAAATT
1 CCCAAATTGG-CTTTAGCCCAAATATAGGAGCCAAAATT
7003 AATAAGTCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.97
43 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
CCCAAATTGGCTTTAGCCCAAATATAGGAGCCAAAATTTTCG
Found at i:7516 original size:13 final size:12
Alignment explanation
Indices: 7472--7520 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
7462 CGAGCTTTCT
*
7472 TCCTCTTTCC-C
1 TCCTCCTTCCTC
7483 TCCTCCTTCCTC
1 TCCTCCTTCCTC
7495 -CCT-CTTCCTC
1 TCCTCCTTCCTC
7505 TCCATCCTTCCTC
1 TCC-TCCTTCCTC
7518 TCC
1 TCC
7521 CCGATTCCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 7 0.21
11 14 0.42
12 2 0.06
13 10 0.30
ACGTcount: A:0.02, C:0.57, G:0.00, T:0.41
Consensus pattern (12 bp):
TCCTCCTTCCTC
Found at i:12971 original size:78 final size:78
Alignment explanation
Indices: 12868--13024 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 78
12858 TTTAGGCTGG
* *
12868 AAGAGTCATAGATAAAATTTTAGAAAGATTCCATGTGGGCTTCATACAGCAATTCAATACATAAA
1 AAGAGTCATAGATAAAATTTTAGAAAGATTCCATGCGGGCTTCATACAGCAATTCAATAAATAAA
12933 CTCAGAGTAGAAC
66 CTCAGAGTAGAAC
12946 AAGAGTCATAGAT-AAATTTTGAGAAAGATTCCATGCGGGCTTCATACAGCAATTCAATAAATAA
1 AAGAGTCATAGATAAAATTTT-AGAAAGATTCCATGCGGGCTTCATACAGCAATTCAATAAATAA
13010 ACTCAGAGTAGAAC
65 ACTCAGAGTAGAAC
13024 A
1 A
13025 TGTAATCTCA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 7 0.09
78 69 0.91
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (78 bp):
AAGAGTCATAGATAAAATTTTAGAAAGATTCCATGCGGGCTTCATACAGCAATTCAATAAATAAA
CTCAGAGTAGAAC
Found at i:25229 original size:32 final size:32
Alignment explanation
Indices: 25182--25242 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
25172 TGTAAAACTT
25182 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACTATTATACCCTTATTTTTCTAA
*
25214 TTGAATCGA-TCATTATATCCTTATTTTTC
1 TTGAATCGACT-ATTATACCCTTATTTTTC
25243 AAACATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (32 bp):
TTGAATCGACTATTATACCCTTATTTTTCTAA
Done.