Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5309.1
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: 26824
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.31
Warning! 778 characters in sequence are not A, C, G, or T
Found at i:227 original size:123 final size:123
Alignment explanation
Indices: 5--249 Score: 463
Period size: 123 Copynumber: 2.0 Consensus size: 123
1 TCTT
5 TCAGTTCGTAGAATATCCAAAACGGTTCGAACATGGAAAACATGATCATCTAATGACTTTGAGTA
1 TCAGTTCGTAGAATATCCAAAACGGTTCGAACATGGAAAACATGATCATCTAATGACTTTGAGTA
*
70 AATTAAAATATCATCAAAGTAAACTACTATAAATTTAACCAAATGTAGCCTCAAAACG
66 AATTAAAATATCATCAAAGTAAACTACTACAAATTTAACCAAATGTAGCCTCAAAACG
128 TCAGTTCGTAGAATATCCAAAACGGTTCGAACATGGAAAACATGATCATCTAATGACTTTGAGTA
1 TCAGTTCGTAGAATATCCAAAACGGTTCGAACATGGAAAACATGATCATCTAATGACTTTGAGTA
* *
193 AATTAAAATATCATCAAAGTAAACTACTACAAATTTACCCACATGTAGCCTCAAAAC
66 AATTAAAATATCATCAAAGTAAACTACTACAAATTTAACCAAATGTAGCCTCAAAAC
250 ATGATTCATT
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (123 bp):
TCAGTTCGTAGAATATCCAAAACGGTTCGAACATGGAAAACATGATCATCTAATGACTTTGAGTA
AATTAAAATATCATCAAAGTAAACTACTACAAATTTAACCAAATGTAGCCTCAAAACG
Found at i:2776 original size:20 final size:19
Alignment explanation
Indices: 2722--2779 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
2712 ATTGGATTTA
* *
2722 AAAAAAAAGAGAAGAAATTC
1 AAAAAAAAG-GAAAAAAATC
**
2742 AAAAAAAATTCAAAAAAATC
1 AAAAAAAA-GGAAAAAAATC
2762 GAAAAAAAAGGAAAAAAA
1 -AAAAAAAAGGAAAAAAA
2780 GAAGTGACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.09
Consensus pattern (19 bp):
AAAAAAAAGGAAAAAAATC
Found at i:3071 original size:29 final size:29
Alignment explanation
Indices: 3038--3094 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3028 TTTGTGAGAT
3038 GAGGTCGAGTGGTAAAAGGCAAGAGAGCA
1 GAGGTCGAGTGGTAAAAGGCAAGAGAGCA
*
3067 GAGGTCGAGTGGTAAAAGGTAAGAGAGC
1 GAGGTCGAGTGGTAAAAGGCAAGAGAGC
3095 GTGAGTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.09, G:0.42, T:0.12
Consensus pattern (29 bp):
GAGGTCGAGTGGTAAAAGGCAAGAGAGCA
Found at i:3896 original size:18 final size:18
Alignment explanation
Indices: 3870--3955 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
3860 AAATTGAAAG
*
3870 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
* *
3888 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAAACGA
** * *
3906 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
3924 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
3945 AAAAGAAAAAG
1 AAAAGAAAAAG
3956 CGAAAAAAGA
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
18 31 0.62
19 5 0.10
20 8 0.16
21 6 0.12
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:3898 original size:6 final size:6
Alignment explanation
Indices: 3866--3955 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
3856 AAAGAAATTG
* * * **
3866 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATCA-AA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
* * *
3913 AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
3956 CGAAAAAAGA
Statistics
Matches: 63, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
5 4 0.06
6 47 0.75
7 8 0.13
8 4 0.06
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:3935 original size:14 final size:13
Alignment explanation
Indices: 3916--3953 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
3906 AAAAGTGAGA
3916 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
3928 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
3943 GAAAAAGAAAA
1 GAAAAAGAAAA
3954 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:3950 original size:13 final size:12
Alignment explanation
Indices: 3852--3953 Score: 50
Period size: 12 Copynumber: 8.0 Consensus size: 12
3842 AGAAAGAGAT
*
3852 TGAAAAAGAAAT
1 TGAAAAAGAAAA
3864 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
3874 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
3885 CGAAAAAGAAAA
1 TGAAAAAGAAAA
*
3897 AGAAATCAA-AAAA
1 TGAAA--AAGAAAA
3910 GTGAGAGAAAAAGAAAA
1 -T----GAAAAAGAAAA
3927 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
3941 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
3954 AGCGAAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.10
11 8 0.11
12 17 0.24
13 14 0.20
14 12 0.17
15 2 0.03
16 3 0.04
17 4 0.06
18 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:3990 original size:12 final size:12
Alignment explanation
Indices: 3959--3990 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3949 GAAAAAGCGA
*
3959 AAAAAGAATTTG
1 AAAAAGAGTTTG
3971 AAAAAGAGTTTG
1 AAAAAGAGTTTG
3983 AAAAAGAG
1 AAAAAGAG
3991 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:7181 original size:15 final size:15
Alignment explanation
Indices: 7161--7214 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
7151 TAGCTTCTTC
7161 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAA--T
*
7178 TTTTTTTCACGAATT
1 TTTTTTTCACGAAAT
7193 TTTTTTTCACGAAAT
1 TTTTTTTCACGAAAT
7208 TTTTTTT
1 TTTTTTT
7215 GAATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 22 0.63
17 13 0.37
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:7183 original size:17 final size:17
Alignment explanation
Indices: 7161--7214 Score: 94
Period size: 17 Copynumber: 3.3 Consensus size: 17
7151 TAGCTTCTTC
7161 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAATTT
7178 TTTTTTTCACG-AA-TT
1 TTTTTTTCACGAAATTT
7193 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAATTT
7210 TTTTT
1 TTTTT
7215 GAATTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.37
16 4 0.11
17 18 0.51
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (17 bp):
TTTTTTTCACGAAATTT
Found at i:7219 original size:11 final size:11
Alignment explanation
Indices: 7205--7245 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
7195 TTTTTCACGA
7205 AATTTTTTTTG
1 AATTTTTTTTG
7216 AA-TTTTTTTG
1 AATTTTTTTTG
7226 AATTTTTTTTG
1 AATTTTTTTTG
7237 AATTTTTTT
1 AATTTTTTT
7246 GAAGAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:7223 original size:10 final size:10
Alignment explanation
Indices: 7208--7248 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
7198 TTCACGAAAT
7208 TTTTTTTGAA
1 TTTTTTTGAA
7218 TTTTTTTGAA
1 TTTTTTTGAA
7228 TTTTTTTTGAA
1 -TTTTTTTGAA
7239 TTTTTTTGAA
1 TTTTTTTGAA
7249 GAAACTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.71
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:7231 original size:21 final size:21
Alignment explanation
Indices: 7205--7248 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
7195 TTTTTCACGA
7205 AATTTTTTTTGAATTTTTTTG
1 AATTTTTTTTGAATTTTTTTG
7226 AATTTTTTTTGAATTTTTTTG
1 AATTTTTTTTGAATTTTTTTG
7247 AA
1 AA
7249 GAAACTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (21 bp):
AATTTTTTTTGAATTTTTTTG
Found at i:19672 original size:16 final size:16
Alignment explanation
Indices: 19643--19678 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19633 CCGTATACAA
19643 TTTT-TTTTCAATTTT
1 TTTTCTTTTCAATTTT
*
19658 TTTTCTTTTCGATTTT
1 TTTTCTTTTCAATTTT
19674 TTTTC
1 TTTTC
19679 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTCAATTTT
Done.