Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5929.1
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: 15887
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:75 original size:30 final size:30
Alignment explanation
Indices: 41--137 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31 TAAACTAAAA
*
41 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
71 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
101 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
130 ATGAGCTA
1 -TGAGCTA
138 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:1752 original size:24 final size:23
Alignment explanation
Indices: 1698--1753 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
1688 GGATAACTAA
* *
1698 GAAAGGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
1721 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
1745 GAAATGGTA
1 GAAATGGTA
1754 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:3972 original size:6 final size:6
Alignment explanation
Indices: 3956--4005 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
3946 TTTCTTTTTA
*
3956 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
4005 T
1 T
4006 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:3988 original size:37 final size:37
Alignment explanation
Indices: 3945--4015 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3935 CTTGCCTCTC
3945 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
3982 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
4016 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:4016 original size:16 final size:16
Alignment explanation
Indices: 3941--4001 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
3931 GCCTCTTGCC
*
3941 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
3957 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
3973 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
3989 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
4002 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:6695 original size:24 final size:23
Alignment explanation
Indices: 6641--6696 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
6631 GGATAACTAA
* *
6641 GAAAGGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
6664 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
6688 GAAATGGTA
1 GAAATGGTA
6697 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:8915 original size:6 final size:6
Alignment explanation
Indices: 8899--8948 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
8889 TTTCTTTTTA
*
8899 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
8948 T
1 T
8949 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:8931 original size:37 final size:37
Alignment explanation
Indices: 8888--8958 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
8878 CTTGCCTCTC
8888 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
8925 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
8959 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:8959 original size:16 final size:16
Alignment explanation
Indices: 8884--8944 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
8874 GCCTCTTGCC
*
8884 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
8900 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
8916 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
8932 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
8945 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:9892 original size:10 final size:10
Alignment explanation
Indices: 9879--9927 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
9869 TTTTCGATTT
9879 TTTTTTTAAA
1 TTTTTTTAAA
**
9889 TTTTTTTTCGA
1 -TTTTTTTAAA
9900 TTTTTTTAAA
1 TTTTTTTAAA
**
9910 TTTTTTTTCA
1 TTTTTTTAAA
9920 TTTTTTTA
1 TTTTTTTA
9928 CAATACCGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:9903 original size:21 final size:20
Alignment explanation
Indices: 9879--9927 Score: 89
Period size: 21 Copynumber: 2.4 Consensus size: 20
9869 TTTTCGATTT
9879 TTTTTTTAAATTTTTTTTCGA
1 TTTTTTTAAATTTTTTTTC-A
9900 TTTTTTTAAATTTTTTTTCA
1 TTTTTTTAAATTTTTTTTCA
9920 TTTTTTTA
1 TTTTTTTA
9928 CAATACCGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTTTAAATTTTTTTTCA
Found at i:14280 original size:12 final size:12
Alignment explanation
Indices: 14259--14338 Score: 81
Period size: 12 Copynumber: 6.6 Consensus size: 12
14249 TTTTTAATAC
*
14259 TTCAAATTTTTT
1 TTCAATTTTTTT
14271 TTCAATTTTTTT
1 TTCAATTTTTTT
*
14283 TTCGATTTTTTT
1 TTCAATTTTTTT
**
14295 TTCAAATTTCCTT
1 TTC-AATTTTTTT
*
14308 TTC-TTTTTTTT
1 TTCAATTTTTTT
*
14319 TTTAATTTTTTT
1 TTCAATTTTTTT
14331 GTTCAATT
1 -TTCAATT
14339 ACAATATGCT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
11 7 0.13
12 32 0.59
13 15 0.28
ACGTcount: A:0.16, C:0.10, G:0.03, T:0.71
Consensus pattern (12 bp):
TTCAATTTTTTT
Found at i:14301 original size:36 final size:37
Alignment explanation
Indices: 14259--14336 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 37
14249 TTTTTAATAC
* *
14259 TTCAAATTT-TTTTTCAATTTTTTTTTCGATTTTTTT-
1 TTCAAATTTCCTTTTC-ATTTTTTTTTCAATTTTTTTG
* *
14295 TTCAAATTTCCTTTTCTTTTTTTTTTTAATTTTTTTG
1 TTCAAATTTCCTTTTCATTTTTTTTTCAATTTTTTTG
14332 TTCAA
1 TTCAA
14337 TTACAATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.71
Consensus pattern (37 bp):
TTCAAATTTCCTTTTCATTTTTTTTTCAATTTTTTTG
Done.