Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold858
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: 32457
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1406 original size:21 final size:21
Alignment explanation
Indices: 1382--1428 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1372 CGTATGTATA
* *
1382 TTTTT-TTTAATTTCGAATTT
1 TTTTTATTTTATTTCGAAATT
*
1402 TTTTTATTTTATTTTGAAATT
1 TTTTTATTTTATTTCGAAATT
1423 TTTTTA
1 TTTTTA
1429 CGTAGCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTTATTTTATTTCGAAATT
Found at i:3131 original size:20 final size:20
Alignment explanation
Indices: 3108--3153 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3098 CCAGCTCGAA
*
3108 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
3128 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
3148 TTAGCT
1 TTAGCT
3154 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:3135 original size:30 final size:30
Alignment explanation
Indices: 3100--3173 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
3090 AGTTTTTCCC
3100 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
3130 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
3160 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
3174 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:4671 original size:11 final size:10
Alignment explanation
Indices: 4655--4684 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
4645 TTCGTAATGT
4655 AAAAAAAAGTC
1 AAAAAAAA-TC
4666 AAAAAAAATC
1 AAAAAAAATC
4676 AAAAAAAAT
1 AAAAAAAAT
4685 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:5886 original size:6 final size:6
Alignment explanation
Indices: 5861--5958 Score: 61
Period size: 6 Copynumber: 15.8 Consensus size: 6
5851 GAAAGAAAAC
* * ** * **
5861 AAAAGA AAACGA AGAAGA AAAAGA AATTGC AAAAGA AAAAGA AATCGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * * *
5909 AAAAGT GAGAGA AAAAGA AAATGAA GAAAAGA AAATTGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAG-A -AAAAGA AAA-AGA AAAAGA AAAAG
5959 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 24, Indels: 6
0.68 0.25 0.06
Matches are distributed among these distances:
6 54 0.83
7 7 0.11
8 4 0.06
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.07
Consensus pattern (6 bp):
AAAAGA
Found at i:5912 original size:18 final size:18
Alignment explanation
Indices: 5839--5913 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
5829 GAAAGAGATT
*
5839 GAAAAAGAAATTGAAAGAA
1 GAAAAAGAAATCGAAA-AA
* * *
5858 AACAAAAGAAAACGAAGAA
1 GA-AAAAGAAATCGAAAAA
* *
5877 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAAAA
5895 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATCGAAAAA
5913 G
1 G
5914 TGAGAGAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
18 29 0.66
19 4 0.09
20 11 0.25
ACGTcount: A:0.69, C:0.05, G:0.19, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAATCGAAAAA
Found at i:5940 original size:14 final size:13
Alignment explanation
Indices: 5919--5956 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
5909 AAAAGTGAGA
5919 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
5931 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
5946 GAAAAAGAAAA
1 GAAAAAGAAAA
5957 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:5970 original size:21 final size:21
Alignment explanation
Indices: 5920--5970 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
5910 AAAGTGAGAG
*
5920 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
5941 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
5962 AAAAAGAAA
1 AAAAAGAAA
5971 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:6010 original size:33 final size:33
Alignment explanation
Indices: 5973--6035 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5963 AAAAGAAATT
5973 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
6006 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
6036 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:7836 original size:20 final size:20
Alignment explanation
Indices: 7813--7858 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
7803 CCAGCTCGAA
*
7813 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
7833 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
7853 TTAGCT
1 TTAGCT
7859 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:7840 original size:30 final size:30
Alignment explanation
Indices: 7805--7878 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
7795 AGTTTTTCCC
7805 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
7835 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
7865 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
7879 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:21524 original size:13 final size:13
Alignment explanation
Indices: 21500--21539 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
21490 GGATATCAAG
21500 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
21513 TTTGTGAAAAAAAA
1 -TTGTGAAAAAAAA
21527 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
21540 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:28069 original size:15 final size:14
Alignment explanation
Indices: 28033--28087 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
28023 TCTATTGATC
28033 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
28047 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
28061 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
28076 GAAAGAAAAGAA
1 GAGA-AAAAGAA
28088 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Done.