Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold672
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: 10870
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Found at i:4112 original size:18 final size:18
Alignment explanation
Indices: 4004--4184 Score: 146
Period size: 17 Copynumber: 10.3 Consensus size: 18
3994 CGGTCCCCCC
4004 CAAAAATTTTTCGTGTTTT
1 CAAAAA-TTTTCGTGTTTT
*
4023 CTAAAAA-CTTC-TGTGTTT
1 C-AAAAATTTTCGTGT-TTT
*
4041 CAAAAATTTTCGTATTTT
1 CAAAAATTTTCGTGTTTT
*
4059 -ATAAATTTTCGTG-TTT
1 CAAAAATTTTCGTGTTTT
* *
4075 CTAAAATTTTCGT-ATTT
1 CAAAAATTTTCGTGTTTT
*
4092 CAAAAATTTTCTTGTTTT
1 CAAAAATTTTCGTGTTTT
* *
4110 C-AAATTTTTCGT-ATTT
1 CAAAAATTTTCGTGTTTT
*
4126 CAAAAATCCTT-GTGTTTT
1 CAAAAAT-TTTCGTGTTTT
* *
4144 AAAAAATTTTGGTGTTTT
1 CAAAAATTTTCGTGTTTT
* *
4162 -GAAAATTTTCGTTTTTT
1 CAAAAATTTTCGTGTTTT
4179 CAAAAA
1 CAAAAA
4185 AAAAATCTCG
Statistics
Matches: 128, Mismatches: 22, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
16 7 0.05
17 74 0.58
18 39 0.30
19 3 0.02
20 5 0.04
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.50
Consensus pattern (18 bp):
CAAAAATTTTCGTGTTTT
Found at i:4119 original size:51 final size:51
Alignment explanation
Indices: 4007--4173 Score: 158
Period size: 52 Copynumber: 3.2 Consensus size: 51
3997 TCCCCCCCAA
* *
4007 AAATTTTTCGTGTTTTCTAAAAACTTCTGTGTTTCAAAAATTTTCGTATTTT
1 AAATTTTTCGTG-TTTCTAAAATCTTCTGTATTTCAAAAATTTTCGTATTTT
* * * *
4059 ATAAATTTTCGTGTTTCTAAAATTTTC-GTATTTCAAAAATTTTCTTGTTTT
1 A-AATTTTTCGTGTTTCTAAAATCTTCTGTATTTCAAAAATTTTCGTATTTT
* * * * * *
4110 CAAATTTTTCGTATTTCAAAAATCCTTGTGT-TTTAAAAAATTTTGGTGTTTT
1 -AAATTTTTCGTGTTTCTAAAAT-CTTCTGTATTTCAAAAATTTTCGTATTTT
*
4162 GAAAATTTTCGT
1 -AAATTTTTCGT
4174 TTTTTCAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
51 39 0.41
52 44 0.46
53 12 0.13
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (51 bp):
AAATTTTTCGTGTTTCTAAAATCTTCTGTATTTCAAAAATTTTCGTATTTT
Found at i:4256 original size:17 final size:17
Alignment explanation
Indices: 4005--4256 Score: 134
Period size: 17 Copynumber: 14.3 Consensus size: 17
3995 GGTCCCCCCC
4005 AAAAATTTTTCGTGTTTTCT
1 AAAAA-TTTTCGTG-TTT-T
* *
4025 AAAAA-CTTCTGTGTTTC
1 AAAAATTTTC-GTGTTTT
*
4042 AAAAATTTTCGTATTTT
1 AAAAATTTTCGTGTTTT
*
4059 ATAAATTTTCGTGTTTCT
1 AAAAATTTTCGTGTTT-T
* *
4077 -AAAATTTTCGTATTTC
1 AAAAATTTTCGTGTTTT
*
4093 AAAAATTTTCTTGTTTT
1 AAAAATTTTCGTGTTTT
* * * *
4110 CAAATTTTTCGTATTTC
1 AAAAATTTTCGTGTTTT
*
4127 AAAAATCCTT-GTGTTTT
1 AAAAAT-TTTCGTGTTTT
*
4144 AAAAAATTTTGGTGTTTT
1 -AAAAATTTTCGTGTTTT
* *
4162 GAAAATTTTCGTTTTTT
1 AAAAATTTTCGTGTTTT
* * *
4179 CAAAAAAAAAATCTCGTGTTTC
1 -----AAAAATTTTCGTGTTTT
* *
4201 ATAAATTTTCGTTTTTTT
1 AAAAATTTTCG-TGTTTT
** *
4219 TTAAATTTT-GTGTTTC
1 AAAAATTTTCGTGTTTT
* *
4235 CAAAATTCTCGTGTTTT
1 AAAAATTTTCGTGTTTT
4252 AAAAA
1 AAAAA
4257 AAAATTTCTC
Statistics
Matches: 173, Mismatches: 45, Indels: 31
0.69 0.18 0.12
Matches are distributed among these distances:
16 10 0.06
17 106 0.61
18 37 0.21
19 3 0.02
20 5 0.03
22 12 0.07
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTT
Found at i:8186 original size:20 final size:19
Alignment explanation
Indices: 8141--8189 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
8131 AAATTTTTAC
*
8141 TTTTTTAACTTTCTTTATA
1 TTTTTTAAATTTCTTTATA
8160 TATTTTTAGAATTTC-TTATAA
1 T-TTTTTA-AATTTCTTTAT-A
8181 TTTTTTAAA
1 TTTTTTAAA
8190 ATATATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 16 0.62
21 7 0.27
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTTAAATTTCTTTATA
Found at i:8230 original size:18 final size:18
Alignment explanation
Indices: 8175--8244 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
8165 TTAGAATTTC
*
8175 TTAT-AATTTTTTAAAAT
1 TTATAAATTTTTTGAAAT
* * *
8192 ATATAAA-TTTTGGAATTT
1 TTATAAATTTTTTGAA-AT
8210 TTATAAATTTTTTGAAAT
1 TTATAAATTTTTTGAAAT
*
8228 TTAAAAATTATTTTGAA
1 TTATAAATT-TTTTGAA
8245 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
17 9 0.22
18 18 0.44
19 14 0.34
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTATAAATTTTTTGAAAT
Found at i:8424 original size:14 final size:15
Alignment explanation
Indices: 8407--8445 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
8397 TGACTCTAAT
8407 AATTTGAATAACTC-
1 AATTTGAATAACTCA
*
8421 AATTTGATTAACTCGA
1 AATTTGAATAACTC-A
8437 AATTTGAAT
1 AATTTGAAT
8446 TTTTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
16 8 0.38
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (15 bp):
AATTTGAATAACTCA
Done.