Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015546.1 Corchorus olitorius cultivar O-4 contig15579, 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: 9662
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3840 original size:18 final size:18
Alignment explanation
Indices: 3817--3853 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3807 CTCAATAGTT
3817 GAATTTTAATTTTAAAGA
1 GAATTTTAATTTTAAAGA
3835 GAATTTTAATTTTAAAGA
1 GAATTTTAATTTTAAAGA
3853 G
1 G
3854 CTTATCTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (18 bp):
GAATTTTAATTTTAAAGA
Found at i:6309 original size:25 final size:25
Alignment explanation
Indices: 6279--6328 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6269 TTATAGATGC
6279 CTAAATGTAAATGTAAACTACTCTT
1 CTAAATGTAAATGTAAACTACTCTT
6304 CTAAATGTAAATGTAAACTACTCTT
1 CTAAATGTAAATGTAAACTACTCTT
6329 TAGTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (25 bp):
CTAAATGTAAATGTAAACTACTCTT
Found at i:8162 original size:22 final size:22
Alignment explanation
Indices: 8133--8213 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
8123 TGAATATTTT
8133 TATGAAATTTTGATAATTACCC
1 TATGAAATTTTGATAATTACCC
* *
8155 TATTAAATTTTGATAACTACCC
1 TATGAAATTTTGATAATTACCC
* *
8177 TATGAAATTTTGATAATCA-CG
1 TATGAAATTTTGATAATTACCC
*
8198 TATGAAATTGTGATAA
1 TATGAAATTTTGATAA
8214 ACTGCATATG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
21 16 0.31
22 36 0.69
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAATTACCC
Found at i:8224 original size:43 final size:44
Alignment explanation
Indices: 8133--8235 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 44
8123 TGAATATTTT
* * * *
8133 TATGAAATTTTGATAATTACCCTATTAAATTTTGATAACTACCC
1 TATGAAATTTTGATAATCACCCTATGAAATTGTGATAACTACCA
* *
8177 TATGAAATTTTGATAATCA-CGTATGAAATTGTGATAAACT-GCA
1 TATGAAATTTTGATAATCACCCTATGAAATTGTGAT-AACTACCA
*
8220 TATGAAACTTTGATAA
1 TATGAAATTTTGATAA
8236 CCTAACTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 29 0.57
44 22 0.43
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACCCTATGAAATTGTGATAACTACCA
Found at i:8289 original size:21 final size:22
Alignment explanation
Indices: 8133--8303 Score: 81
Period size: 22 Copynumber: 7.9 Consensus size: 22
8123 TGAATATTTT
*
8133 TATGAAATTTTGATAA--TTACCC
1 TATGAAATTTTGATAACCTT--TC
* **
8155 TATTAAATTTTGATAA-CTACCC
1 TATGAAATTTTGATAACCT-TTC
**
8177 TATGAAATTTTGATAA--TCAC
1 TATGAAATTTTGATAACCTTTC
* * *
8197 GTATGAAATTGTGATAAAC-TGC
1 -TATGAAATTTTGATAACCTTTC
* **
8219 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACCTTTC
* *
8242 TATAAAATTTTAATAAACC-TTC
1 TATGAAATTTTGAT-AACCTTTC
8264 TTATGAAATTTTG-TAACCTTTC
1 -TATGAAATTTTGATAACCTTTC
*
8286 TATG-ATTTTTGATAACCT
1 TATGAAATTTTGATAACCT
8304 CCCTGTGAGA
Statistics
Matches: 118, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.07
21 30 0.25
22 64 0.54
23 16 0.14
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTC
Done.