Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6227.1
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: 13048
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5139 original size:56 final size:55
Alignment explanation
Indices: 5023--5140 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
5013 TCCATGCTTT
* * * *
5023 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
5077 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
5133 CATTAAAT
1 CATTAAAT
5141 TAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:5797 original size:20 final size:20
Alignment explanation
Indices: 5772--5818 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
5762 AATTAAGCTT
*
5772 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
5792 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
5812 GAATGAG
1 GAATGAG
5819 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:7142 original size:15 final size:16
Alignment explanation
Indices: 7103--7143 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
7093 AACAACACTC
7103 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
7119 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
7133 CTTTCTTTTTC
1 CTTTCTTTTTC
7144 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:7338 original size:17 final size:15
Alignment explanation
Indices: 7301--7339 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
7291 TATCTCCCAC
7301 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
7317 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
7334 TCATTT
1 TCATTT
7340 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:7369 original size:5 final size:6
Alignment explanation
Indices: 7352--7377 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7342 TCGCTCGCGC
7352 TCTTTT TCTTTT TCTTTT TCTTTT TC
1 TCTTTT TCTTTT TCTTTT TCTTTT TC
7378 ACATGCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:8253 original size:18 final size:17
Alignment explanation
Indices: 8231--8264 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8221 GACCTCTTCT
8231 TTTTTTTTAATTCTGAA
1 TTTTTTTTAATTCTGAA
*
8248 TTTTTTTTACTTCTGAA
1 TTTTTTTTAATTCTGAA
8265 ACTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTTTTAATTCTGAA
Found at i:10333 original size:30 final size:29
Alignment explanation
Indices: 10253--10334 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
10243 ATGACTCGTA
10253 TCACGAGCTAAACCTTAGCTCAACTTCAGC
1 TCACGAGCTAAA-CTTAGCTCAACTTCAGC
* * * * * *
10283 TTAGGAGTTTAATTTCAGCTCAACTTTAGC
1 TCACGAGCTAAACTT-AGCTCAACTTCAGC
10313 TCACGAGCTAAAGCTTAGCTCA
1 TCACGAGCTAAA-CTTAGCTCA
10335 TTTTAGTTTA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.90
31 2 0.05
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (29 bp):
TCACGAGCTAAACTTAGCTCAACTTCAGC
Found at i:11700 original size:11 final size:11
Alignment explanation
Indices: 11684--11734 Score: 95
Period size: 11 Copynumber: 4.7 Consensus size: 11
11674 ATACAAGTAT
11684 AAAAAAAATTC
1 AAAAAAAATTC
11695 -AAAAAAATTC
1 AAAAAAAATTC
11705 AAAAAAAATTC
1 AAAAAAAATTC
11716 AAAAAAAATTC
1 AAAAAAAATTC
11727 AAAAAAAA
1 AAAAAAAA
11735 ATGATTTGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.26
11 29 0.74
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:12670 original size:6 final size:5
Alignment explanation
Indices: 12635--12702 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
12625 ACATTCTTGT
* *
12635 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGTA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
12682 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
12703 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.56
6 18 0.35
7 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:12675 original size:15 final size:14
Alignment explanation
Indices: 12646--12702 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
12636 AAGAAAAAAC
12646 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
12662 AAAGTAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
12677 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
12693 AAAGAAAAGA
1 AAAGAAAAGA
12703 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:12775 original size:12 final size:13
Alignment explanation
Indices: 12750--12782 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
12740 TTAAGAGAAA
12750 TTGAAAAAAGCCT
1 TTGAAAAAAGCCT
12763 TTGAAAAAA-CCT
1 TTGAAAAAAGCCT
12775 TTGAAAAA
1 TTGAAAAA
12783 CAAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (13 bp):
TTGAAAAAAGCCT
Found at i:12799 original size:12 final size:12
Alignment explanation
Indices: 12776--12832 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
12766 AAAAAACCTT
*
12776 TGAAAAACAAAA
1 TGAAAAAGAAAA
* *
12788 AGAAAATGAAAA
1 TGAAAAAGAAAA
* * *
12800 TGAAAATGAGAT
1 TGAAAAAGAAAA
*
12812 TGAAAAAGAGAA
1 TGAAAAAGAAAA
12824 TGAAAAAGA
1 TGAAAAAGA
12833 GTTTGAGAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.12
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:12805 original size:18 final size:18
Alignment explanation
Indices: 12776--12829 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
12766 AAAAAACCTT
* *
12776 TGAAAAACAAAAAGAAAA
1 TGAAAAAGAAAATGAAAA
* * *
12794 TGAAAATGAAAATGAGAT
1 TGAAAAAGAAAATGAAAA
*
12812 TGAAAAAGAGAATGAAAA
1 TGAAAAAGAAAATGAAAA
12830 AGAGTTTGAG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TGAAAAAGAAAATGAAAA
Found at i:12816 original size:24 final size:24
Alignment explanation
Indices: 12789--12847 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
12779 AAAACAAAAA
* *
12789 GAAAATGAAAATGAAAATGAGATT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
12813 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
12837 GAGAGAGAAAA
1 GAAAAAGAAAA
12848 AGAATGTGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.15
Consensus pattern (24 bp):
GAAAAAGAAAATGAAAAAGAGATT
Found at i:12833 original size:12 final size:12
Alignment explanation
Indices: 12798--12833 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12788 AGAAAATGAA
*
12798 AATGAAAATGAG
1 AATGAAAAAGAG
*
12810 ATTGAAAAAGAG
1 AATGAAAAAGAG
12822 AATGAAAAAGAG
1 AATGAAAAAGAG
12834 TTTGAGAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (12 bp):
AATGAAAAAGAG
Done.