Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022029.1 Corchorus olitorius cultivar O-4 contig22062, 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: 41749
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:46 original size:27 final size:26
Alignment explanation
Indices: 15--103 Score: 84
Period size: 27 Copynumber: 3.6 Consensus size: 26
5 TTATTTGTTA
15 TTTATCTTTTTATTTATTAATTTAAT
1 TTTATCTTTTTATTTATTAATTTAAT
* *
41 TATTATC----TATTTATTTA-CT-A-
1 T-TTATCTTTTTATTTATTAATTTAAT
61 TTTATCTTTTTATTTATTAATTTAAT
1 TTTATCTTTTTATTTATTAATTTAAT
*
87 TGTTATCTATTTATTTA
1 T-TTATCTTTTTATTTA
104 CTATTTATCT
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
19 5 0.10
20 1 0.02
21 1 0.02
22 1 0.02
23 18 0.37
24 1 0.02
25 1 0.02
26 2 0.04
27 19 0.39
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTATCTTTTTATTTATTAATTTAAT
Found at i:54 original size:8 final size:8
Alignment explanation
Indices: 52--214 Score: 57
Period size: 8 Copynumber: 21.9 Consensus size: 8
42 ATTATCTATT
52 TATTTA-C
1 TATTTATC
59 TATTTATC
1 TATTTATC
* *
67 TTTTTATT
1 TATTTATC
* *
75 TATTAATT
1 TATTTATC
* *
83 TAATTGT-
1 TATTTATC
* *
90 TATCTATT
1 TATTTATC
98 TATTTA-C
1 TATTTATC
105 TATTTATC
1 TATTTATC
113 T-TTT-TC
1 TATTTATC
119 --TTTAT-
1 TATTTATC
*
124 TAATTTAGC
1 T-ATTTATC
133 TA-TTATC
1 TATTTATC
*
140 TATTTATT
1 TATTTATC
148 TA-TTAT-
1 TATTTATC
154 TA-TTATC
1 TATTTATC
* *
161 T-TTTCTT
1 TATTTATC
** *
168 TAGCTACC
1 TATTTATC
176 TATTTATC
1 TATTTATC
184 TA-TTATTC
1 TATTTA-TC
* *
192 TCTGTATC
1 TATTTATC
200 TATTTATC
1 TATTTATC
208 TATTTAT
1 TATTTAT
215 TTCTATACCT
Statistics
Matches: 113, Mismatches: 29, Indels: 27
0.67 0.17 0.16
Matches are distributed among these distances:
5 3 0.03
6 9 0.08
7 37 0.33
8 61 0.54
9 3 0.03
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (8 bp):
TATTTATC
Found at i:65 original size:19 final size:18
Alignment explanation
Indices: 12--76 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
2 TATTTATTTG
*
12 TTATTTATCTTTTTATTTAT
1 TTATTTA-C-TTTTATCTAT
* *
32 TAATTTAATTATTATCTAT
1 TTATTTACTT-TTATCTAT
*
51 TTATTTACTATTTATCTTT
1 TTATTTACT-TTTATCTAT
70 TTATTTA
1 TTATTTA
77 TTAATTTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
18 2 0.05
19 28 0.76
20 7 0.19
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTACTTTTATCTAT
Found at i:68 original size:46 final size:46
Alignment explanation
Indices: 1--164 Score: 247
Period size: 46 Copynumber: 3.5 Consensus size: 46
**
1 CTATTTATTTGTTATTTATCTTTTTATTTATTAATTTAATTATTAT
1 CTATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTATTAT
*
47 CTATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTGTTAT
1 CTATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTATTAT
* **
93 CTATTTATTTACTATTTATCTTTTTCTTTATTAATTTAGCTATTAT
1 CTATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTATTAT
*
139 CTATTTATTTATTATTATTATCTTTT
1 CTATTTATTTACTA-T-TTATCTTTT
165 CTTTAGCTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
46 98 0.91
47 1 0.01
48 9 0.08
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (46 bp):
CTATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTATTAT
Found at i:124 original size:27 final size:27
Alignment explanation
Indices: 89--152 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
79 AATTTAATTG
* * *
89 TTATCTATTTATTTA-CTATTTATCTTT
1 TTATTTATTAATTTAGCTA-TTATCTAT
*
116 TTCTTTATTAATTTAGCTATTATCTAT
1 TTATTTATTAATTTAGCTATTATCTAT
143 TTATTTATTA
1 TTATTTATTA
153 TTATTATCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATTTATTAATTTAGCTATTATCTAT
Found at i:216 original size:36 final size:32
Alignment explanation
Indices: 135--216 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 32
125 AATTTAGCTA
*
135 TTATCTATTTATTTATTATTATTATCTTTTCT
1 TTATCTATTTATTTATTATTATTATCTTTTAT
* ** *
167 TTAGCTACCTATTTATCTATTATTCTCTGTATCTAT
1 TTATCTATTTATTTAT-TATTATTATCT-T-T-TAT
203 TTATCTATTTATTT
1 TTATCTATTTATTT
217 CTATACCTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
32 13 0.34
33 10 0.26
34 1 0.03
35 1 0.03
36 13 0.34
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.62
Consensus pattern (32 bp):
TTATCTATTTATTTATTATTATTATCTTTTAT
Found at i:4215 original size:16 final size:16
Alignment explanation
Indices: 4194--4237 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
4184 AATACCCGAG
4194 TATTAT-TATGTATATA
1 TATTATATAT-TATATA
4210 TATTATATATTATATA
1 TATTATATATTATATA
*
4226 TCTATATATATT
1 TAT-TATATATT
4238 GGTGAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
TATTATATATTATATA
Found at i:4218 original size:7 final size:7
Alignment explanation
Indices: 4197--4234 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
4187 ACCCGAGTAT
*
4197 TATTATG
1 TATTATA
4204 TA-TATA
1 TATTATA
4210 TATTATA
1 TATTATA
4217 TATTATA
1 TATTATA
4224 TATCTATA
1 TAT-TATA
4232 TAT
1 TAT
4235 ATTGGTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (7 bp):
TATTATA
Found at i:20674 original size:5 final size:5
Alignment explanation
Indices: 20664--20710 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
20654 ATACACTTTG
20664 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
20711 GTAGATCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:30263 original size:6 final size:6
Alignment explanation
Indices: 30252--30278 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30242 AAATTGTGAG
30252 GGAACC GGAACC GGAACC GGAACC GGA
1 GGAACC GGAACC GGAACC GGAACC GGA
30279 TGGATTGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.37, T:0.00
Consensus pattern (6 bp):
GGAACC
Found at i:37828 original size:2 final size:2
Alignment explanation
Indices: 37823--37859 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
37813 CCCAAATATT
*
37823 TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
37860 TATAAGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:41533 original size:27 final size:27
Alignment explanation
Indices: 41495--41551 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
41485 ACGGGATAAA
* *
41495 GAGGTTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATCTATAGG
*
41522 GAGGCTGAGGCTGCTCGGATCTATATG
1 GAGGCTGAGGCTGCTCGGATCTATAGG
41549 GAG
1 GAG
41552 AGGGAGCCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.14, G:0.42, T:0.25
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATCTATAGG
Done.