Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3652
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: 27357
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:82 original size:12 final size:12
Alignment explanation
Indices: 65--90 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55 TTCAAAAAAA
65 TTTTTTGAATTT
1 TTTTTTGAATTT
77 TTTTTTGAATTT
1 TTTTTTGAATTT
89 TT
1 TT
91 CAAAATTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTTGAATTT
Found at i:869 original size:14 final size:14
Alignment explanation
Indices: 852--881 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
842 AAAACTAAGT
852 AAATAAATAAATAA
1 AAATAAATAAATAA
866 AAATAAATAAATAA
1 AAATAAATAAATAA
880 AA
1 AA
882 TCATTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:1864 original size:17 final size:18
Alignment explanation
Indices: 1832--1868 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1822 TGTTGAGCTG
1832 AACTTAATTAAATTAACT
1 AACTTAATTAAATTAACT
*
1850 AACTT-ATTTAATTAACT
1 AACTTAATTAAATTAACT
1867 AA
1 AA
1869 GTTTATTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AACTTAATTAAATTAACT
Found at i:6148 original size:14 final size:14
Alignment explanation
Indices: 6129--6178 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 14
6119 TAGCTTCTTC
6129 TTTTTTTCACGAAA
1 TTTTTTTCACGAAA
*
6143 TTTTTTTTTCACGAAT
1 --TTTTTTTCACGAAA
6159 TTTTTTTCACG-AA
1 TTTTTTTCACGAAA
6172 TTTTTTT
1 TTTTTTT
6179 TTCAACTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 8 0.25
14 11 0.34
16 13 0.41
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTTTTTCACGAAA
Found at i:6149 original size:15 final size:15
Alignment explanation
Indices: 6129--6182 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
6119 TAGCTTCTTC
6129 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAA-T
6145 TTTTTTTCACG-AAT
1 TTTTTTTCACGAAAT
*
6159 TTTTTTTCACGAATT
1 TTTTTTTCACGAAAT
6174 TTTTTTTCA
1 TTTTTTTCA
6183 ACTTGATATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
14 12 0.33
15 13 0.36
16 11 0.31
ACGTcount: A:0.20, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:6150 original size:16 final size:15
Alignment explanation
Indices: 6129--6182 Score: 92
Period size: 14 Copynumber: 3.6 Consensus size: 15
6119 TAGCTTCTTC
6129 TTTTTTTCACGAAATT
1 TTTTTTTCACG-AATT
6145 TTTTTTTCACGAA-T
1 TTTTTTTCACGAATT
6159 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
6174 TTTTTTTCA
1 TTTTTTTCA
6183 ACTTGATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
14 14 0.38
15 12 0.32
16 11 0.30
ACGTcount: A:0.20, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:6246 original size:21 final size:22
Alignment explanation
Indices: 6220--6261 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
6210 ATGGAAACCA
*
6220 AATTTTTTTT-CAATTTTTTTG
1 AATTTTTTTTGAAATTTTTTTG
6241 AATTTTTTTTGAAATTTTTTT
1 AATTTTTTTTGAAATTTTTTT
6262 TGAAGAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (22 bp):
AATTTTTTTTGAAATTTTTTTG
Found at i:6258 original size:10 final size:10
Alignment explanation
Indices: 6223--6261 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
6213 GAAACCAAAT
*
6223 TTTTTTTCAA
1 TTTTTTTGAA
6233 TTTTTTTGAA
1 TTTTTTTGAA
6243 TTTTTTTTGAAA
1 -TTTTTTTG-AA
6255 TTTTTTT
1 TTTTTTT
6262 TGAAGAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.35
11 15 0.58
12 2 0.08
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:6263 original size:12 final size:12
Alignment explanation
Indices: 6219--6265 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
6209 AATGGAAACC
6219 AAATTTTTTTT-
1 AAATTTTTTTTG
*
6230 CAA-TTTTTTTG
1 AAATTTTTTTTG
6241 -AATTTTTTTTG
1 AAATTTTTTTTG
6252 AAATTTTTTTTG
1 AAATTTTTTTTG
6264 AA
1 AA
6266 GAAACTACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 9 0.28
11 10 0.31
12 13 0.41
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (12 bp):
AAATTTTTTTTG
Found at i:7293 original size:21 final size:23
Alignment explanation
Indices: 7248--7294 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
7238 TCACCTACAA
* *
7248 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
7271 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
7292 TAA
1 TAA
7295 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:8539 original size:19 final size:19
Alignment explanation
Indices: 8515--8560 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
8505 GCTCTTTACA
8515 AGCTCAATGAGCTCGAACT
1 AGCTCAATGAGCTCGAACT
8534 AGCTCAATGAGCTCGAACT
1 AGCTCAATGAGCTCGAACT
8553 AGCTCAAT
1 AGCTCAAT
8561 AAACTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (19 bp):
AGCTCAATGAGCTCGAACT
Found at i:12082 original size:20 final size:21
Alignment explanation
Indices: 12049--12105 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
12039 GGTGGAATTG
* **
12049 AGCTC-AAGTGAGCTGATTGA
1 AGCTCGAATTGAGCTGAAGGA
12069 AG-TCGAATTGAGCT-AAGGA
1 AGCTCGAATTGAGCTGAAGGA
*
12088 AGCTGGAATTGAGCTGAA
1 AGCTCGAATTGAGCTGAA
12106 ATTAGCTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.23
20 21 0.70
21 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (21 bp):
AGCTCGAATTGAGCTGAAGGA
Found at i:14157 original size:17 final size:18
Alignment explanation
Indices: 14135--14168 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14125 TTTTTCTTTT
14135 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
14152 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
14169 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:14186 original size:27 final size:28
Alignment explanation
Indices: 14126--14192 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
14116 TTCAACATCT
14126 TTTTCTTTTTCAATTTTTTCTCAATCTCA
1 TTTTCTTTTTCAATTTTTTCTC-ATCTCA
* *
14155 ATTTCTTTTTCAATTTTCTTTTC-T-TCA
1 TTTTCTTTTTCAATTTT-TTCTCATCTCA
14182 TTTTCTTTTTC
1 TTTTCTTTTTC
14193 TCTCACTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 16 0.47
30 4 0.12
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTCTTTTTCAATTTTTTCTCATCTCA
Found at i:15061 original size:10 final size:10
Alignment explanation
Indices: 15041--15133 Score: 68
Period size: 10 Copynumber: 9.4 Consensus size: 10
15031 CTCGCAAGAC
15041 TTTTCAGTTTT
1 TTTTCA-TTTT
15052 TTTTCATTTT
1 TTTTCATTTT
15062 TTTTC--TTT
1 TTTTCATTTT
15070 TTTTC-TTTT
1 TTTTCATTTT
** *
15079 AACTTGATTTT
1 -TTTTCATTTT
*
15090 TTTGTCACTTT
1 TTT-TCATTTT
*
15101 TTTTCTTTTT
1 TTTTCATTTT
*
15111 TTTTGA-TTT
1 TTTTCATTTT
*
15120 TTTTAATTTT
1 TTTTCATTTT
15130 TTTT
1 TTTT
15134 TCGAATTTCT
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
8 8 0.12
9 11 0.17
10 28 0.43
11 18 0.28
ACGTcount: A:0.10, C:0.09, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:15584 original size:22 final size:21
Alignment explanation
Indices: 15548--15611 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
15538 TTGGTATTTG
15548 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
15569 GGAAGTTGGTATGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
15591 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
15612 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 4 0.11
22 32 0.86
23 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.34, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Done.