Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014773.1 Corchorus olitorius cultivar O-4 contig14806, 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: 20843
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:272 original size:60 final size:63
Alignment explanation
Indices: 153--276 Score: 191
Period size: 66 Copynumber: 2.0 Consensus size: 63
143 AGGTTAATTT
*
153 CTAGTCAGTTCTTGCCCTTGAACCCTTTTTTGTAATAAATCATATCGTCCTTGTCCTTAATTATT
1 CTAGCCAGTTCTTGCCCTTGAACCCTTTTTTGTAATAAATCATA-C-TCC-TGTCCTTAATTATT
218 C
63 C
219 CTAGCCAGTTCTTGCCCTTGAACCCTTTTTTGTAATAAATCATA-T-C-GTCCTTAATTAT
1 CTAGCCAGTTCTTGCCCTTGAACCCTTTTTTGTAATAAATCATACTCCTGTCCTTAATTAT
277 CTAGAATTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
60 12 0.21
62 1 0.02
63 1 0.02
66 43 0.75
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.43
Consensus pattern (63 bp):
CTAGCCAGTTCTTGCCCTTGAACCCTTTTTTGTAATAAATCATACTCCTGTCCTTAATTATTC
Found at i:5765 original size:25 final size:25
Alignment explanation
Indices: 5709--5759 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
5699 AATAATTGCC
5709 AAATGCCAACACAACATCCATAATA
1 AAATGCCAACACAACATCCATAATA
*
5734 AAGATGCCAACATAACAGCTCCATAA
1 AA-ATGCCAACACAACA--TCCATAA
5760 AAATGCTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 13 0.59
28 7 0.32
ACGTcount: A:0.49, C:0.27, G:0.08, T:0.16
Consensus pattern (25 bp):
AAATGCCAACACAACATCCATAATA
Found at i:10025 original size:17 final size:17
Alignment explanation
Indices: 10004--10045 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
9994 TTTGATTACC
**
10004 AGTGATCTTGCATCACT
1 AGTGATCTTAAATCACT
*
10021 GGTGATCTTAAATCACT
1 AGTGATCTTAAATCACT
10038 AGTGATCT
1 AGTGATCT
10046 AAGGGATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (17 bp):
AGTGATCTTAAATCACT
Found at i:13496 original size:21 final size:20
Alignment explanation
Indices: 13468--13506 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13458 GGGGCTTTTG
13468 AAATTATTTTGGCT-AAATTC
1 AAATTA-TTTGGCTCAAATTC
13488 AAATATATTTGGCTCAAAT
1 AAAT-TATTTGGCTCAAAT
13507 ATGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATTATTTGGCTCAAATTC
Found at i:19328 original size:3 final size:3
Alignment explanation
Indices: 19322--19470 Score: 77
Period size: 3 Copynumber: 49.7 Consensus size: 3
19312 AAGAAGGGAG
* ** * *
19322 TGA TGA TGA TGA GGA TGA TTC TGA TGA TGA TGT TGA -GA CTCA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA -TGA TGA
* * * * * *
19367 TGA TGA CGA -AA GTGA CGA CGA TGA TGA AGA TGA CGA TGA TGA TGA
1 TGA TGA TGA TGA -TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* * * * * * * * *
19412 CGA CGA AGA TGA TGA CGA AGG GGA TGA CGA TGA TGA TGA TGA TGA CGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
*
19460 GGA TGA TGA TG
1 TGA TGA TGA TG
19471 GGGATGGGGA
Statistics
Matches: 109, Mismatches: 33, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
2 3 0.03
3 104 0.95
4 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.35, T:0.23
Consensus pattern (3 bp):
TGA
Found at i:19393 original size:27 final size:27
Alignment explanation
Indices: 19363--19453 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
19353 GTTGAGACTC
*
19363 ATGATGATGACGAAAGTGACGACGATG
1 ATGATGATGACGAAAGTGATGACGATG
* * *
19390 ATGAAGATGACG-ATGATGATGACGACG
1 ATGATGATGACGAAAG-TGATGACGATG
* * *
19417 AAGATGATGACGAAGGGGATGACGATG
1 ATGATGATGACGAAAGTGATGACGATG
19444 ATGATGATGA
1 ATGATGATGA
19454 TGACGAGGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.04
27 48 0.92
28 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (27 bp):
ATGATGATGACGAAAGTGATGACGATG
Found at i:19469 original size:15 final size:15
Alignment explanation
Indices: 19379--19470 Score: 94
Period size: 15 Copynumber: 6.1 Consensus size: 15
19369 ATGACGAAAG
19379 TGACGACGATGATGA
1 TGACGACGATGATGA
* *
19394 AGATGACGATGATGA
1 TGACGACGATGATGA
*
19409 TGACGACGAAGATGA
1 TGACGACGATGATGA
* **
19424 TGACGAAGGGGATGA
1 TGACGACGATGATGA
* * *
19439 CGATGATGATGATGA
1 TGACGACGATGATGA
*
19454 TGACGAGGATGATGA
1 TGACGACGATGATGA
19469 TG
1 TG
19471 GGGATGGGGA
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.35, C:0.09, G:0.37, T:0.20
Consensus pattern (15 bp):
TGACGACGATGATGA
Done.