Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold937
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: 34325
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:129 original size:20 final size:20
Alignment explanation
Indices: 106--159 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
96 TAGTTTTCCC
*
106 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
126 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
146 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
160 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:140 original size:30 final size:30
Alignment explanation
Indices: 106--179 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
96 TAGTTTTCCC
106 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
136 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
166 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
180 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:169 original size:20 final size:20
Alignment explanation
Indices: 106--170 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
96 TAGTTTTCCC
* * * *
106 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
126 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
145 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
166 AGCTC
1 AGCTC
171 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:2847 original size:12 final size:12
Alignment explanation
Indices: 2835--2952 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
2825 GAAAGAGATT
*
2835 GAAAAAGAAATT
1 GAAAAAGAAATA
2847 G--AAAGAAA-A
1 GAAAAAGAAATA
*
2856 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
2867 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
2880 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
2892 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
2904 GAAAAAGTGAGA
1 GAAAAAGAAATA
2916 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
2927 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
2943 GAAAAAGAAA
1 GAAAAAGAAA
2953 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:2878 original size:18 final size:18
Alignment explanation
Indices: 2852--2955 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
2842 AAATTGAAAG
*
2852 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
2870 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
2888 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
2906 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
2924 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
2945 AAAAGAAAAAG
1 AAAAGAAAAAG
2956 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:2880 original size:6 final size:6
Alignment explanation
Indices: 2848--2955 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
2838 AAAGAAATTG
* * ** *
2848 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
2895 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
2946 AAAGAA AAAG
1 AAAGAA AAAG
2956 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:2937 original size:14 final size:13
Alignment explanation
Indices: 2916--2953 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2906 AAAAGTGAGA
2916 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
2928 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
2943 GAAAAAGAAAA
1 GAAAAAGAAAA
2954 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:2967 original size:21 final size:21
Alignment explanation
Indices: 2917--2967 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
2907 AAAGTGAGAG
*
2917 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
2938 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
2959 AAAAAGAAA
1 AAAAAGAAA
2968 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:3007 original size:33 final size:33
Alignment explanation
Indices: 2970--3032 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2960 AAAAGAAATT
2970 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
3003 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
3033 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:4827 original size:20 final size:20
Alignment explanation
Indices: 4804--4857 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
4794 AGTTTTTCCC
*
4804 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
4824 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
4844 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
4858 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:4839 original size:30 final size:30
Alignment explanation
Indices: 4804--4877 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
4794 AGTTTTTCCC
4804 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
4834 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
4864 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
4878 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:4867 original size:20 final size:20
Alignment explanation
Indices: 4804--4868 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
4794 AGTTTTTCCC
* * * *
4804 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
4824 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
4843 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
4864 AGCTC
1 AGCTC
4869 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:6514 original size:1 final size:1
Alignment explanation
Indices: 6451--6500 Score: 64
Period size: 1 Copynumber: 50.0 Consensus size: 1
6441 TATTGGATTT
*** *
6451 AAAAAAAAAAAAAAATTCAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6501 GGTGAGCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.92, C:0.02, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:7538 original size:12 final size:12
Alignment explanation
Indices: 7526--7643 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
7516 GAAAGAGATT
*
7526 GAAAAAGAAATT
1 GAAAAAGAAATA
7538 G--AAAGAAA-A
1 GAAAAAGAAATA
*
7547 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
7558 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
7571 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
7583 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
7595 GAAAAAGTGAGA
1 GAAAAAGAAATA
7607 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
7618 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
7634 GAAAAAGAAA
1 GAAAAAGAAA
7644 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:7569 original size:18 final size:18
Alignment explanation
Indices: 7543--7646 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
7533 AAATTGAAAG
*
7543 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
7561 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
7579 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
7597 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
7615 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
7636 AAAAGAAAAAG
1 AAAAGAAAAAG
7647 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:7571 original size:6 final size:6
Alignment explanation
Indices: 7539--7646 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
7529 AAAGAAATTG
* * ** *
7539 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
7586 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
7637 AAAGAA AAAG
1 AAAGAA AAAG
7647 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:7628 original size:14 final size:13
Alignment explanation
Indices: 7607--7644 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
7597 AAAAGTGAGA
7607 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
7619 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
7634 GAAAAAGAAAA
1 GAAAAAGAAAA
7645 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:7658 original size:21 final size:21
Alignment explanation
Indices: 7608--7658 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
7598 AAAGTGAGAG
*
7608 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
7629 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
7650 AAAAAGAAA
1 AAAAAGAAA
7659 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:7698 original size:33 final size:33
Alignment explanation
Indices: 7661--7723 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
7651 AAAAGAAATT
7661 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
7694 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
7724 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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:9523 original size:20 final size:20
Alignment explanation
Indices: 9500--9553 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
9490 AGTTTTTCCC
*
9500 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
9520 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
9540 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
9554 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:9535 original size:30 final size:30
Alignment explanation
Indices: 9500--9573 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
9490 AGTTTTTCCC
9500 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
9530 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
9560 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
9574 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:9563 original size:20 final size:20
Alignment explanation
Indices: 9500--9564 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
9490 AGTTTTTCCC
* * * *
9500 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
9520 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
9539 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
9560 AGCTC
1 AGCTC
9565 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:11175 original size:1 final size:1
Alignment explanation
Indices: 11171--11222 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
11161 AAAAAAATTC
** ** *
11171 AAAAAAAAATTAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11223 GTGAAAAGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.90, C:0.00, G:0.04, T:0.06
Consensus pattern (1 bp):
A
Found at i:11212 original size:21 final size:21
Alignment explanation
Indices: 11153--11229 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
11143 TATTGGATTT
**
11153 AAAAAAA-GAAAAAAATTCAAA
1 AAAAAAATGAAAAAAA-AAAAA
* *
11174 AAAAAATTAAAAAAAAAAAAAA
1 AAAAAAAT-GAAAAAAAAAAAA
*
11196 AAAAAAATGAAAAAAAAGAAA
1 AAAAAAATGAAAAAAAAAAAA
*
11217 AAAAAAGTGAAAA
1 AAAAAAATGAAAA
11230 GTCTTGCGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 29 0.63
22 10 0.22
23 7 0.15
ACGTcount: A:0.84, C:0.01, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAAAAATGAAAAAAAAAAAA
Found at i:11217 original size:23 final size:23
Alignment explanation
Indices: 11171--11222 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
11161 AAAAAAATTC
*
11171 AAAAAAAAATTAAAAAAAAAAAA
1 AAAAAAAAATGAAAAAAAAAAAA
*
11194 AAAAAAAAATGAAAAAAAAGAAA
1 AAAAAAAAATGAAAAAAAAAAAA
11217 AAAAAA
1 AAAAAA
11223 GTGAAAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.90, C:0.00, G:0.04, T:0.06
Consensus pattern (23 bp):
AAAAAAAAATGAAAAAAAAAAAA
Found at i:11223 original size:10 final size:10
Alignment explanation
Indices: 11153--11223 Score: 61
Period size: 10 Copynumber: 6.8 Consensus size: 10
11143 TATTGGATTT
11153 AAAAAAAGAA
1 AAAAAAAGAA
***
11163 AAAAATTCAA
1 AAAAAAAGAA
*
11173 AAAAAAATTAA
1 AAAAAAA-GAA
*
11184 AAAAAAAAAA
1 AAAAAAAGAA
*
11194 AAAAAAAAATGA
1 AAAAAAAGA--A
11206 AAAAAAAGAA
1 AAAAAAAGAA
11216 AAAAAAAG
1 AAAAAAAG
11224 TGAAAAGTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
10 32 0.64
11 9 0.18
12 9 0.18
ACGTcount: A:0.86, C:0.01, G:0.06, T:0.07
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:11228 original size:12 final size:11
Alignment explanation
Indices: 11153--11229 Score: 63
Period size: 11 Copynumber: 7.2 Consensus size: 11
11143 TATTGGATTT
11153 AAAAAAA-G-A
1 AAAAAAATGAA
* *
11162 AAAAAATTCAA
1 AAAAAAATGAA
*
11173 AAAAAAATTAAA
1 AAAAAAA-TGAA
**
11185 AAAAAAAAAAA
1 AAAAAAATGAA
11196 AAAAAAATG-A
1 AAAAAAATGAA
11206 AAAAAAA-GAA
1 AAAAAAATGAA
11216 AAAAAAAGTGAA
1 AAAAAAA-TGAA
11228 AA
1 AA
11230 GTCTTGCGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
9 7 0.13
10 16 0.29
11 17 0.31
12 15 0.27
ACGTcount: A:0.84, C:0.01, G:0.06, T:0.08
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:12236 original size:12 final size:12
Alignment explanation
Indices: 12224--12341 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
12214 GAAAGAGATT
*
12224 GAAAAAGAAATT
1 GAAAAAGAAATA
12236 G--AAAGAAA-A
1 GAAAAAGAAATA
*
12245 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
12256 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
12269 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
12281 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
12293 GAAAAAGTGAGA
1 GAAAAAGAAATA
12305 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
12316 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
12332 GAAAAAGAAA
1 GAAAAAGAAA
12342 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:12267 original size:18 final size:18
Alignment explanation
Indices: 12241--12344 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
12231 AAATTGAAAG
*
12241 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
12259 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
12277 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
12295 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
12313 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
12334 AAAAGAAAAAG
1 AAAAGAAAAAG
12345 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:12269 original size:6 final size:6
Alignment explanation
Indices: 12237--12344 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
12227 AAAGAAATTG
* * ** *
12237 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
12284 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
12335 AAAGAA AAAG
1 AAAGAA AAAG
12345 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:12326 original size:14 final size:13
Alignment explanation
Indices: 12305--12342 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
12295 AAAAGTGAGA
12305 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
12317 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
12332 GAAAAAGAAAA
1 GAAAAAGAAAA
12343 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:12356 original size:21 final size:21
Alignment explanation
Indices: 12306--12356 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
12296 AAAGTGAGAG
*
12306 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
12327 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
12348 AAAAAGAAA
1 AAAAAGAAA
12357 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:12396 original size:33 final size:33
Alignment explanation
Indices: 12359--12421 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
12349 AAAAGAAATT
12359 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
12392 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
12422 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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:14219 original size:20 final size:20
Alignment explanation
Indices: 14196--14249 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
14186 AGTTTTTCCC
*
14196 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14216 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14236 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14250 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:14231 original size:30 final size:30
Alignment explanation
Indices: 14196--14269 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
14186 AGTTTTTCCC
14196 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
14226 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
14256 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
14270 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:14259 original size:20 final size:20
Alignment explanation
Indices: 14196--14260 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
14186 AGTTTTTCCC
* * * *
14196 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
14216 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
14235 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
14256 AGCTC
1 AGCTC
14261 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:30693 original size:20 final size:20
Alignment explanation
Indices: 30670--30723 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
30660 AACTAAGAAG
30670 GAGCTGAATGAGCTAAGGA-T
1 GAGCTGAATGAGCT-AGGATT
* *
30690 GAGCTCAATGAGCTATGATT
1 GAGCTGAATGAGCTAGGATT
*
30710 GACCTGAATGAGCT
1 GAGCTGAATGAGCT
30724 TGAAGTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (20 bp):
GAGCTGAATGAGCTAGGATT
Done.