Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold853
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: 5218
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Found at i:3761 original size:341 final size:341
Alignment explanation
Indices: 3146--4061 Score: 1679
Period size: 341 Copynumber: 2.7 Consensus size: 341
3136 GATTGTCATG
* *
3146 ATTCGTGTATGCATATATATTTTCTTTTTCATACTGCTGGGTGGTTGCATTCATCAGTAAGGATT
1 ATTCGTGTATGCATATATGTTTTCTTTTTCATACTGCTAGGTGGTTGCATTCATCAGTAAGGATT
* *
3211 GGGTATATTTTCTTTAAAATA-----G-TT-CT-GTGTTCTGTTGGGTATGATTTGCAAATGGAT
66 GGGTATATTTTCTTTAAAATAGTTGGGATTGTTCGTGTTCTGTTGGGTAAGATTTGCAAATGGAT
* *
3268 TTTGATTGGAAGTTTTAGGTAGACCCATGGTATCTCTGTATATCAACTGAATGGGAAGTTTTGTG
131 CTTGATTGGAAGCTTTAGGTAGACCCATGGTATCTCTGTATATCAACTGAATGGGAAGTTTTGTG
3333 TGATTATTGATATATCCATGTGGTGAAAATACTCTGATTTTGGTTAAAGATAGAATTATATTCAT
196 TGATTATTGATATATCCATGTGGTGAAAATACTCTGATTTTGGTTAAAGATAGAATTATATTCAT
3398 CTGTGTTACCTAGCCTTACATGAAGGGAAAATTGAGTTGTAATCTTTTAAGTAAATAGGTTCTAT
261 CTGTGTTACCTAGCCTTACATGAAGGGAAAATTGAGTTGTAATCTTTTAAGTAAATAGGTTCTAT
3463 GAGATTGATTAACATA
326 GAGATTGATTAACATA
3479 ATTCGTGTATGCATATATGTTTTCTTTTTCATACTGCTAGGTGGTTGCATTCATCAGTAAGGATT
1 ATTCGTGTATGCATATATGTTTTCTTTTTCATACTGCTAGGTGGTTGCATTCATCAGTAAGGATT
3544 GGGTATATTTTCTTTAAAATAGTTGGGATTGTTCGTGTTCTGTTGGGTAAGATTTGCAAATGGAT
66 GGGTATATTTTCTTTAAAATAGTTGGGATTGTTCGTGTTCTGTTGGGTAAGATTTGCAAATGGAT
3609 CTTGATTGGAAGCTTTAGGTAGACCCATGGTATCTCTGTATATCAACTGAATGGGAAGTTTTGTG
131 CTTGATTGGAAGCTTTAGGTAGACCCATGGTATCTCTGTATATCAACTGAATGGGAAGTTTTGTG
3674 TGATTATTGATATATCCATGTGGTGAAAATACTCTGATTTTGGTTAAAGATAGAATTATATTCAT
196 TGATTATTGATATATCCATGTGGTGAAAATACTCTGATTTTGGTTAAAGATAGAATTATATTCAT
3739 CTGTGTTACCTAGCCTTACATGAAGGGAAAATTGAGTTGTAATCTTTTAAGTAAATAGGTTCTAT
261 CTGTGTTACCTAGCCTTACATGAAGGGAAAATTGAGTTGTAATCTTTTAAGTAAATAGGTTCTAT
3804 GAGATTGATTAACATA
326 GAGATTGATTAACATA
3820 ATTCGTGTATGCATATATGTTTTCTTTTTCATACTGCTAGGTGGTTGCATTCATCAGTAAGGATT
1 ATTCGTGTATGCATATATGTTTTCTTTTTCATACTGCTAGGTGGTTGCATTCATCAGTAAGGATT
3885 GGGTATATTTTCTTTAAAATAGTTGGGATTGTTCGTGTTCTGTTGGGTAAGATTTGCAAATGGAT
66 GGGTATATTTTCTTTAAAATAGTTGGGATTGTTCGTGTTCTGTTGGGTAAGATTTGCAAATGGAT
*
3950 CTTGATTGGAAGCTTTAGGTAGACCCATGGTATCTCTGTATATCAGCTGAATGGGAAAGTTTTGT
131 CTTGATTGGAAGCTTTAGGTAGACCCATGGTATCTCTGTATATCAACTGAATGGG-AAGTTTTGT
* *
4015 GTGATTATTGATGTATCCATGTGGTG-AAATACTCAGATTTTGGTTAA
195 GTGATTATTGATATATCCATGTGGTGAAAATACTCTGATTTTGGTTAA
4062 CAATGGAAGT
Statistics
Matches: 565, Mismatches: 9, Indels: 10
0.97 0.02 0.02
Matches are distributed among these distances:
333 84 0.15
338 1 0.00
339 2 0.00
340 1 0.00
341 443 0.78
342 34 0.06
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (341 bp):
ATTCGTGTATGCATATATGTTTTCTTTTTCATACTGCTAGGTGGTTGCATTCATCAGTAAGGATT
GGGTATATTTTCTTTAAAATAGTTGGGATTGTTCGTGTTCTGTTGGGTAAGATTTGCAAATGGAT
CTTGATTGGAAGCTTTAGGTAGACCCATGGTATCTCTGTATATCAACTGAATGGGAAGTTTTGTG
TGATTATTGATATATCCATGTGGTGAAAATACTCTGATTTTGGTTAAAGATAGAATTATATTCAT
CTGTGTTACCTAGCCTTACATGAAGGGAAAATTGAGTTGTAATCTTTTAAGTAAATAGGTTCTAT
GAGATTGATTAACATA
Found at i:4881 original size:20 final size:21
Alignment explanation
Indices: 4856--4905 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
4846 ATATCCTATC
* * *
4856 CCGGTTCAGTATCTTT-GTGT
1 CCGGTTCAGCAGCTTTGGTGG
4876 CCGGTTCAGCAGCTTTGGTGG
1 CCGGTTCAGCAGCTTTGGTGG
4897 CCGGTTCAG
1 CCGGTTCAG
4906 ATTTTTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.10, C:0.24, G:0.32, T:0.34
Consensus pattern (21 bp):
CCGGTTCAGCAGCTTTGGTGG
Found at i:5012 original size:31 final size:31
Alignment explanation
Indices: 4953--5017 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
4943 ATTCCAGATA
* * *
4953 GGGATATCCCATCCCAGGGATATACCGGCTT
1 GGGATATCCCATCCAAGAGATACACCGGCTT
* *
4984 GGGATATCCCATTCAAGAGATACCCCGGCTT
1 GGGATATCCCATCCAAGAGATACACCGGCTT
5015 GGG
1 GGG
5018 GTCTAGGGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.22
Consensus pattern (31 bp):
GGGATATCCCATCCAAGAGATACACCGGCTT
Done.