Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2214
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: 22551
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Found at i:3539 original size:33 final size:34
Alignment explanation
Indices: 3481--3547 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 34
3471 AATTAAAAGT
*
3481 TATCATCAATTTGCATAAGCATTTTATAATCTGATG
1 TATCATCAATTTG-A-AAGCATTTTAGAATCTGATG
3517 TATCATCAATTTG-AAGCATTTTAGAATCTGA
1 TATCATCAATTTGAAAGCATTTTAGAATCTGA
3548 GTTAATTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 17 0.57
36 13 0.43
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (34 bp):
TATCATCAATTTGAAAGCATTTTAGAATCTGATG
Found at i:4676 original size:20 final size:20
Alignment explanation
Indices: 4651--4690 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4641 TGATACAAAC
4651 AGTGAATGTATCGATACATG
1 AGTGAATGTATCGATACATG
4671 AGTGAATGTATCGATACATG
1 AGTGAATGTATCGATACATG
4691 TCTAAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
AGTGAATGTATCGATACATG
Found at i:4701 original size:21 final size:20
Alignment explanation
Indices: 4655--4707 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4645 ACAAACAGTG
* *
4655 AATGTATCGATACATGAGTG
1 AATGTATCGATACATGACTA
*
4675 AATGTATCGATACATGTCTAA
1 AATGTATCGATACATGACT-A
4696 AATGTATCGATA
1 AATGTATCGATA
4708 TAGGATCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATGACTA
Found at i:7171 original size:41 final size:41
Alignment explanation
Indices: 7113--7209 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
7103 TTTATAAAAT
7113 AATTTCT-CCCCTTTGTCAAATGCCAAATTTATTTTCATAA
1 AATTTCTCCCCCTTTGTCAAATGCCAAATTTATTTTCATAA
7153 AATTTCTCCCCCTTTGTCAAATGCCAAATTTATTTTCATAA
1 AATTTCTCCCCCTTTGTCAAATGCCAAATTTATTTTCATAA
7194 AATTTTCTCCCCCTTT
1 AA-TTTCTCCCCCTTT
7210 TTGTTATAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 7 0.13
41 35 0.64
42 13 0.24
ACGTcount: A:0.27, C:0.26, G:0.04, T:0.43
Consensus pattern (41 bp):
AATTTCTCCCCCTTTGTCAAATGCCAAATTTATTTTCATAA
Found at i:9091 original size:33 final size:33
Alignment explanation
Indices: 9040--9120 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
9030 AAATAGTAAC
* *
9040 CCTTATATCGATACAGTGTATTGATGCAAAGAT
1 CCTTGTATCGATACAGTGTATTGATACAAAGAT
*
9073 CCTTGTATTGATACAGTGTATTGATACAAAGAT
1 CCTTGTATCGATACAGTGTATTGATACAAAGAT
9106 CCTTGTATCGATACA
1 CCTTGTATCGATACA
9121 TCTAGGTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (33 bp):
CCTTGTATCGATACAGTGTATTGATACAAAGAT
Found at i:9094 original size:13 final size:13
Alignment explanation
Indices: 9076--9100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9066 CAAAGATCCT
9076 TGTATTGATACAG
1 TGTATTGATACAG
9089 TGTATTGATACA
1 TGTATTGATACA
9101 AAGATCCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TGTATTGATACAG
Found at i:9539 original size:13 final size:13
Alignment explanation
Indices: 9521--9546 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9511 TACACAAAGT
9521 ATGTATCGATACA
1 ATGTATCGATACA
9534 ATGTATCGATACA
1 ATGTATCGATACA
9547 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9544 original size:32 final size:33
Alignment explanation
Indices: 9503--9566 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
9493 TAGCCAAACT
*
9503 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAT-TGTATCGATACAA
9535 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
9567 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:9631 original size:20 final size:22
Alignment explanation
Indices: 9600--9643 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
9590 GCTATATTTT
9600 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
9621 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
9642 CA
1 CA
9644 CGGAAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:11803 original size:22 final size:21
Alignment explanation
Indices: 11776--11826 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
11766 TTGCAAGTTG
11776 AAATAAAAAATTTAGCTAATG-A
1 AAATAAAAAA-TTAGCTAA-GAA
**
11798 AAATAATGAATTAGCTAAGAA
1 AAATAAAAAATTAGCTAAGAA
11819 AAATAAAA
1 AAATAAAA
11827 CTTGCATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.62
22 8 0.33
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.24
Consensus pattern (21 bp):
AAATAAAAAATTAGCTAAGAA
Found at i:15750 original size:13 final size:13
Alignment explanation
Indices: 15732--15770 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
15722 ACATTTTCCT
15732 TTGTATCGATACA
1 TTGTATCGATACA
15745 TTGTATCGATACA
1 TTGTATCGATACA
* *
15758 CTGTATTGATACA
1 TTGTATCGATACA
15771 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:18362 original size:13 final size:13
Alignment explanation
Indices: 18344--18369 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18334 TACACAAAGT
18344 ATGTATCGATACA
1 ATGTATCGATACA
18357 ATGTATCGATACA
1 ATGTATCGATACA
18370 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:18367 original size:32 final size:33
Alignment explanation
Indices: 18326--18389 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
18316 TAGCCAAACT
*
18326 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAT-TGTATCGATACAA
18358 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
18390 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:18454 original size:20 final size:22
Alignment explanation
Indices: 18423--18466 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
18413 GCTATATTTT
18423 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
18444 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
18465 CA
1 CA
18467 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:19780 original size:3 final size:3
Alignment explanation
Indices: 19774--19816 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
19764 TGTGGCAAGC
19774 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19817 ACATTTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:19827 original size:14 final size:14
Alignment explanation
Indices: 19774--19816 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
19764 TGTGGCAAGC
19774 TAATAATATAATAA
1 TAATAATATAATAA
19788 TAAT-A-ATAATAA
1 TAATAATATAATAA
19800 TAATAATATAATAA
1 TAATAATATAATAA
19814 TAA
1 TAA
19817 ACATTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 11 0.41
13 2 0.07
14 14 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:21296 original size:21 final size:22
Alignment explanation
Indices: 21268--21309 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
21258 AAACGGAGGG
21268 GGAAGGCGA-A-GGAGGAGAGA
1 GGAAGGCGAGATGGAGGAGAGA
21288 GGAACGGCGAGATGGAGGAGAG
1 GGAA-GGCGAGATGGAGGAGAG
21310 GAGGTGAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 1 0.05
23 9 0.47
ACGTcount: A:0.36, C:0.07, G:0.55, T:0.02
Consensus pattern (22 bp):
GGAAGGCGAGATGGAGGAGAGA
Done.