Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1408
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: 67875
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2025 original size:20 final size:20
Alignment explanation
Indices: 2002--2055 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1992 TAGTTTTCCC
*
2002 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
2022 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
2042 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
2056 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:2036 original size:30 final size:30
Alignment explanation
Indices: 2002--2075 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
1992 TAGTTTTCCC
2002 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
2032 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
2062 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
2076 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:2065 original size:20 final size:20
Alignment explanation
Indices: 2002--2066 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1992 TAGTTTTCCC
* * * *
2002 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
2022 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
2041 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
2062 AGCTC
1 AGCTC
2067 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:3674 original size:12 final size:13
Alignment explanation
Indices: 3657--3745 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 13
3647 TTGGAGTAAC
3657 AAAAAAATC-AAA
1 AAAAAAATCGAAA
*
3669 AAAAAATTCGAAA
1 AAAAAAATCGAAA
*
3682 AAAAAAATTTGATTGAA
1 AAAAAAA-TCGA---AA
3699 AAAAAAAGT-G-AA
1 AAAAAAA-TCGAAA
3711 AAAAAAATCGAGCAA
1 AAAAAAATCGA--AA
*
3726 AAAAAAA-AGAAA
1 AAAAAAATCGAAA
3738 AGAAAAAA
1 A-AAAAAA
3746 AGGTGAGCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
11 1 0.02
12 21 0.34
13 15 0.24
14 5 0.08
15 9 0.15
16 1 0.02
17 10 0.16
ACGTcount: A:0.74, C:0.04, G:0.10, T:0.11
Consensus pattern (13 bp):
AAAAAAATCGAAA
Found at i:3683 original size:14 final size:13
Alignment explanation
Indices: 3666--3717 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 13
3656 CAAAAAAATC
3666 AAAAAAAAATTCGA
1 AAAAAAAAATT-GA
3680 AAAAAAAAATTTGA
1 AAAAAAAAA-TTGA
*
3694 TTGAAAAAAAAAGTGA
1 ---AAAAAAAAATTGA
3710 AAAAAAAA
1 AAAAAAAA
3718 TCGAGCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 8 0.24
14 11 0.33
15 2 0.06
16 3 0.09
17 9 0.27
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:3713 original size:13 final size:13
Alignment explanation
Indices: 3697--3783 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 13
3687 AATTTGATTG
3697 AAAAAAAAAGTGA
1 AAAAAAAAAGTGA
* *
3710 AAAAAAAATCGAGCA
1 AAAAAAAA-AGTG-A
*
3725 AAAAAAAAAG-AA
1 AAAAAAAAAGTGA
3737 AAGAAAAAAAGGTGA
1 AA-AAAAAAA-GTGA
* **
3752 GCAAAAAATCAAGTTT
1 --AAAAAA-AAAGTGA
3768 AAAAAAAAAGTGA
1 AAAAAAAAAGTGA
3781 AAA
1 AAA
3784 GTCTTGCGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
12 3 0.05
13 22 0.40
14 10 0.18
15 10 0.18
16 6 0.11
17 4 0.07
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAGTGA
Found at i:4807 original size:11 final size:12
Alignment explanation
Indices: 4791--4908 Score: 71
Period size: 12 Copynumber: 9.6 Consensus size: 12
4781 AAAGAAATTG
4791 AAAGAAAAC-AA
1 AAAGAAAACGAA
4802 AAAGAAAACGAA
1 AAAGAAAACGAA
*
4814 AAAGAAAAAGAA
1 AAAGAAAACGAA
** *
4826 ATTGCAAA-GAA
1 AAAGAAAACGAA
*
4837 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
4849 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
4861 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
**
4875 AAAGAAATTGAA
1 AAAGAAAACGAA
4887 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
4902 AAAGAAA
1 AAAGAAA
4909 TTGAAGAGAG
Statistics
Matches: 82, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
11 18 0.22
12 38 0.46
13 6 0.07
14 14 0.17
15 6 0.07
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:4823 original size:6 final size:6
Alignment explanation
Indices: 4791--4896 Score: 63
Period size: 6 Copynumber: 17.7 Consensus size: 6
4781 AAAGAAATTG
* * ** *
4791 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTG-C AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * **
4837 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA ATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AAAGAA
4887 AAAGAA AAAG
1 AAAGAA AAAG
4897 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 26, Indels: 7
0.68 0.25 0.07
Matches are distributed among these distances:
5 5 0.07
6 60 0.85
7 2 0.03
8 4 0.06
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:4879 original size:14 final size:12
Alignment explanation
Indices: 4777--4894 Score: 68
Period size: 12 Copynumber: 10.0 Consensus size: 12
4767 AGAAAGAGAT
*
4777 TGAAAAAGAAAT
1 TGAAAAAGAAAA
4789 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
4799 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
4810 CGAAAAAGAAAA
1 TGAAAAAGAAAA
* ** *
4822 AGAAATTGCAAA
1 TGAAAAAGAAAA
4834 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
4844 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
4858 -GAAAAAGAAAA
1 TGAAAAAGAAAA
*
4869 TGAAGAAAAGAAAT
1 TG-A-AAAAGAAAA
4883 TGAAAAAGAAAA
1 TGAAAAAGAAAA
4895 AGCGAAAAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
10 10 0.12
11 15 0.18
12 43 0.52
13 2 0.02
14 12 0.15
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:4893 original size:17 final size:17
Alignment explanation
Indices: 4769--4894 Score: 62
Period size: 17 Copynumber: 7.2 Consensus size: 17
4759 AGAAAAGGAG
*
4769 AAAGAGATTGAAAAAGA
1 AAAGAAATTGAAAAAGA
*
4786 AATTGAAA--GAAAACA-A
1 AA-AGAAATTGAAAA-AGA
**
4802 AAAGAAAACGAAAAAGAA
1 AAAGAAATTGAAAAAG-A
*
4820 AAAGAAATTG-CAAAGAA
1 AAAGAAATTGAAAAAG-A
* *
4837 AAAGAAATCGAAAAAGTG
1 AAAGAAATTGAAAAAG-A
* **
4855 AGAGAAAAAGAAAATGAAGA
1 AAAGAAATTG-AAA--AAGA
4875 AAAGAAATTGAAAAAGA
1 AAAGAAATTGAAAAAGA
4892 AAA
1 AAA
4895 AGCGAAAAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
15 4 0.05
16 9 0.11
17 30 0.37
18 23 0.28
19 6 0.07
20 7 0.09
21 3 0.04
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (17 bp):
AAAGAAATTGAAAAAGA
Found at i:4895 original size:27 final size:26
Alignment explanation
Indices: 4858--4913 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
4848 AAAAGTGAGA
*
4858 GAAAAAGAAAA-TGAAGAAAAGAAATT
1 GAAAAAGAAAAGCGAA-AAAAGAAATT
4884 GAAAAAGAAAAAGCGAAAAAAGAAATT
1 GAAAAAG-AAAAGCGAAAAAAGAAATT
4911 GAA
1 GAA
4914 GAGAGCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 17 0.63
28 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (26 bp):
GAAAAAGAAAAGCGAAAAAAGAAATT
Found at i:6770 original size:20 final size:20
Alignment explanation
Indices: 6747--6800 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
6737 AGTTTTTCCC
*
6747 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
6767 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
6787 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
6801 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:6782 original size:30 final size:30
Alignment explanation
Indices: 6747--6820 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
6737 AGTTTTTCCC
6747 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
6777 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
6807 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
6821 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:6810 original size:20 final size:20
Alignment explanation
Indices: 6747--6811 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
6737 AGTTTTTCCC
* * * *
6747 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
6767 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
6786 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
6807 AGCTC
1 AGCTC
6812 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:8419 original size:11 final size:11
Alignment explanation
Indices: 8403--8432 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
8393 TTGGAGTAAC
8403 AAAAAAATCAA
1 AAAAAAATCAA
*
8414 AAAAAATTCAA
1 AAAAAAATCAA
8425 AAAAAAAT
1 AAAAAAAT
8433 TTGATTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:13897 original size:6 final size:6
Alignment explanation
Indices: 13886--13919 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13876 AATTTTTTTC
* *
13886 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
13920 ATTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:13971 original size:21 final size:20
Alignment explanation
Indices: 13927--13971 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13917 CAAATTCTTT
*
13927 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
13947 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
13968 TTTC
1 TTTC
13972 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:14917 original size:32 final size:33
Alignment explanation
Indices: 14859--14939 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 33
14849 TTTCAATCAC
** *
14859 TCTTTTTTTTTTCAATTTTGATTTTTTTTTTCT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTTTTCT
14892 TCTTTTTTTTTT-AATTCCGAATTTTTTTTTCT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTTTTCT
14924 T-TTTTTTTTCTTCAAT
1 TCTTTTTTTT-TTCAAT
14940 ACTAAATACA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 8 0.19
32 20 0.47
33 15 0.35
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (33 bp):
TCTTTTTTTTTTCAATTCCGAATTTTTTTTTCT
Found at i:17158 original size:21 final size:21
Alignment explanation
Indices: 17113--17175 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
17103 TTTGAACCAT
* *
17113 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
17135 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
17156 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
17176 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:19309 original size:15 final size:15
Alignment explanation
Indices: 19289--19336 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19279 TCAAAGGTGG
19289 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
19304 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
19319 -TTTATGGATATAAA
1 GTTTATGGATATGAA
19333 GTTT
1 GTTT
19337 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:22233 original size:18 final size:19
Alignment explanation
Indices: 22210--22248 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
22200 TTTATCTTAA
*
22210 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
22228 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
22247 TT
1 TT
22249 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:22263 original size:18 final size:18
Alignment explanation
Indices: 22242--22303 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
22232 TTGTTCACAT
*
22242 TCTTTTTCTCTCTCAAAC
1 TCTTTTTCACTCTCAAAC
* ***
22260 TCTTTTTCAATCTCATTT
1 TCTTTTTCACTCTCAAAC
*
22278 TCTTTTTCACTCTCAACC
1 TCTTTTTCACTCTCAAAC
*
22296 TCCTTTTC
1 TCTTTTTC
22304 TTTTTCTTTC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTTTTCACTCTCAAAC
Found at i:22362 original size:42 final size:42
Alignment explanation
Indices: 22307--22403 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
22297 CCTTTTCTTT
* * *
22307 TTCTTTCA-TTTCTTTATTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTATTTCTTCTCTCGATTTCATTCAAAA
*
22348 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTATTTCTTCTCTCGATTTCATTCAAAA
*
22390 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
22404 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTATTTCTTCTCTCGATTTCATTCAAAA
Found at i:24619 original size:19 final size:19
Alignment explanation
Indices: 24574--24619 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
24564 ATTAACACAC
*
24574 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
24593 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
24611 AATTAATAA
1 AATTAATAA
24620 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:24867 original size:20 final size:20
Alignment explanation
Indices: 24833--24897 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
24823 AAGCTCGGTT
**
24833 GAGCTCAAACAAGCTGAAAC
1 GAGCTCAAATGAGCTGAAAC
*
24853 GAGCTCAAATGAGCTG-GAC
1 GAGCTCAAATGAGCTGAAAC
*
24872 GGAGCTC-AATGAGCTGGAAAT
1 -GAGCTCAAATGAGCT-GAAAC
24893 GAGCT
1 GAGCT
24898 AGGATCAGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 10 0.27
20 26 0.70
21 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.15
Consensus pattern (20 bp):
GAGCTCAAATGAGCTGAAAC
Found at i:25842 original size:24 final size:24
Alignment explanation
Indices: 25810--25864 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
25800 GTTAGGACAT
*
25810 ATTAAATTCGTCCACCAGCAACTC
1 ATTAAATTCGTCAACCAGCAACTC
*
25834 ATTAAATTCGTCAACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAACTC
25858 ATTAAAT
1 ATTAAAT
25865 CTGTCCAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAACTC
Found at i:31026 original size:9 final size:9
Alignment explanation
Indices: 31012--31037 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31002 TAATTATTAA
31012 AACTAATTT
1 AACTAATTT
31021 AACTAATTT
1 AACTAATTT
31030 AACTAATT
1 AACTAATT
31038 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (9 bp):
AACTAATTT
Found at i:34724 original size:19 final size:19
Alignment explanation
Indices: 34679--34724 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
34669 ATTAACACAC
*
34679 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
34698 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
34716 AATTAATAA
1 AATTAATAA
34725 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:34896 original size:11 final size:12
Alignment explanation
Indices: 34864--34896 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34854 GAGCTGTAGC
34864 AAACTTAATTAT
1 AAACTTAATTAT
*
34876 AAACTGAATTA-
1 AAACTTAATTAT
34887 AAACTTAATT
1 AAACTTAATT
34897 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:34964 original size:20 final size:21
Alignment explanation
Indices: 34917--34966 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
34907 AAAAGGAAAT
* *
34917 GAGCTGAATCAAGCTGAATTC
1 GAGCTCAAACAAGCTGAATTC
*
34938 TAGCTCAAACAAGCTGAA-TC
1 GAGCTCAAACAAGCTGAATTC
34958 GAGCTCAAA
1 GAGCTCAAA
34967 TGAACTGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
GAGCTCAAACAAGCTGAATTC
Found at i:35271 original size:19 final size:19
Alignment explanation
Indices: 35234--35292 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
35224 GAAAAAGTAT
**
35234 AAGAAAAAAAGATTG-AAA
1 AAGAAAAAAAGAAAGAAAA
35252 AAGAGAAAAAA-AAAGAAAA
1 AAGA-AAAAAAGAAAGAAAA
* *
35271 ATGAAAAAAAGAAAGGAAA
1 AAGAAAAAAAGAAAGAAAA
35290 AAG
1 AAG
35293 TGAGGGAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (19 bp):
AAGAAAAAAAGAAAGAAAA
Found at i:38566 original size:23 final size:22
Alignment explanation
Indices: 38514--38566 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
38504 TCCACGTCTT
*
38514 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
38536 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
38559 TTTCTTTT
1 TTTCTTTT
38567 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42227 original size:46 final size:45
Alignment explanation
Indices: 42153--42320 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 45
42143 GCCCATAAAC
* * * * *
42153 GAACTCGAACTCAACTCAATGAGCTCGGACGTTCAAATCCATGAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTT-ACATCCATAAGT
* *
42199 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTACATCCATAAGT
* * *
42246 GAACTCGGACTCAACTCAACGAGTTTGGACATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGAC-GTTACATCCATAAGT
42292 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
42321 TGCTCAACTA
Statistics
Matches: 102, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 54 0.53
47 28 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTACATCCATAAGT
Found at i:42310 original size:93 final size:93
Alignment explanation
Indices: 42151--42323 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
42141 CCGCCCATAA
* * *
42151 ACGAACTCGAACTCAACTCAATGAGCTCGGACGTTCAAATCCATGAGTGAACTCGGACTCAACTC
1 ACGAACTCGAACTCAACTCAACGAGCTCGGACATTCAAATCCATAAGTGAACTCGGACTCAACTC
42216 AACGAGTTCGGATGCCTAGTTACATCTC
66 AACGAGTTCGGATGCCTAGTTACATCTC
* * * ***
42244 ACGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCATCCATAAGTGAACTCGGACTCAACTC
1 ACGAACTCGAACTCAACTCAACGAGCTCGGACATTCAAATCCATAAGTGAACTCGGACTCAACTC
42309 AACGAGTTCGGATGC
66 AACGAGTTCGGATGC
42324 TCAACTATCC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
ACGAACTCGAACTCAACTCAACGAGCTCGGACATTCAAATCCATAAGTGAACTCGGACTCAACTC
AACGAGTTCGGATGCCTAGTTACATCTC
Found at i:43222 original size:21 final size:22
Alignment explanation
Indices: 43177--43216 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
43167 GCTTGGAAAC
43177 TTCAACGAAGCTTCCAAGGACG
1 TTCAACGAAGCTTCCAAGGACG
43199 TTCAA-GAAGCTT-CAAGGA
1 TTCAACGAAGCTTCCAAGGA
43217 AGGTTCCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTCAACGAAGCTTCCAAGGACG
Found at i:49217 original size:6 final size:6
Alignment explanation
Indices: 49206--49266 Score: 52
Period size: 6 Copynumber: 9.3 Consensus size: 6
49196 TTTTTCACAA
*
49206 TCTTTT TCTTTT TCTTCTT TCTCTTT TC-TTG TCTTTT TCTCATTT TCTTTT
1 TCTTTT TCTTTT TCTT-TT TCT-TTT TCTTTT TCTTTT TCT--TTT TCTTTT
49257 ATCATTTT TC
1 -TC-TTTT TC
49267 CTCTCTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
5 4 0.09
6 18 0.39
7 13 0.28
8 11 0.24
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (6 bp):
TCTTTT
Found at i:49232 original size:20 final size:19
Alignment explanation
Indices: 49209--49295 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 19
49199 TTCACAATCT
49209 TTTTCTTTTTCTTCTTTCTC
1 TTTTCTTTTTCTT-TTTCTC
*
49229 TTTTC-TTGTCTTTTTCTC
1 TTTTCTTTTTCTTTTTCTC
49247 ATTTTCTTTTATCATTTTTC-C
1 -TTTTCTTTT-TC-TTTTTCTC
*
49268 -TCTCTTTTTCTCATTTT-TC
1 TTTTCTTTTTCT--TTTTCTC
49287 TTTTCTTTT
1 TTTTCTTTT
49296 GTATTTTCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
17 1 0.02
18 8 0.15
19 23 0.42
20 14 0.25
21 3 0.05
22 6 0.11
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (19 bp):
TTTTCTTTTTCTTTTTCTC
Found at i:49266 original size:33 final size:32
Alignment explanation
Indices: 49206--49290 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 32
49196 TTTTTCACAA
* *
49206 TCTTTTTCT--TTTTCTTCTTTCTCTTTTCTTG
1 TCTTTTTCTCATTTTCTT-TTTCTCTTTTCCTC
49237 TCTTTTTCTCATTTTCTTTTATCAT-TTTTCCTC
1 TCTTTTTCTCATTTTCTTTT-TC-TCTTTTCCTC
49270 TCTTTTTCTCATTTTTCTTTT
1 TCTTTTTCTCA-TTTTCTTTT
49291 CTTTTGTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
31 9 0.19
32 2 0.04
33 26 0.55
34 10 0.21
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (32 bp):
TCTTTTTCTCATTTTCTTTTTCTCTTTTCCTC
Found at i:55020 original size:11 final size:10
Alignment explanation
Indices: 54995--55055 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
54985 ACCAATAAAA
54995 TAAA-TGAGC
1 TAAATTGAGC
*
55004 TGAATTGTAGC
1 TAAATTG-AGC
55015 TAAATTGAGC
1 TAAATTGAGC
**
55025 TCGATTGAGC
1 TAAATTGAGC
55035 TGAAA-TGAGC
1 T-AAATTGAGC
*
55045 TCAATTGAGC
1 TAAATTGAGC
55055 T
1 T
55056 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:55056 original size:20 final size:20
Alignment explanation
Indices: 54996--55056 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
54986 CCAATAAAAT
*
54996 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
55016 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
55037 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
55057 GTCGGAGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:56335 original size:29 final size:29
Alignment explanation
Indices: 56302--56361 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
56292 ATAACCAAAC
* *
56302 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
56331 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
56360 CT
1 CT
56362 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:56354 original size:15 final size:15
Alignment explanation
Indices: 56308--56355 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
56298 AAACCTACAA
*
56308 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
56323 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
56337 AAACTTCATATCCAT
1 AAACTTCATATCCAT
56352 AAAC
1 AAAC
56356 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:56593 original size:12 final size:13
Alignment explanation
Indices: 56576--56608 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
56566 AGTAAGTTTC
56576 AAAAAAAAAAT-A
1 AAAAAAAAAATCA
*
56588 AAAAAAAAATTCA
1 AAAAAAAAAATCA
56601 AAAAAAAA
1 AAAAAAAA
56609 CAAAATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATCA
Found at i:57533 original size:12 final size:12
Alignment explanation
Indices: 57518--57551 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57508 CTTGAAAGAT
*
57518 ATTGAGAAAGCC
1 ATTGAAAAAGCC
57530 ATTGAAAAAGCC
1 ATTGAAAAAGCC
*
57542 GTTGAAAAAG
1 ATTGAAAAAG
57552 AAAAAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (12 bp):
ATTGAAAAAGCC
Found at i:64015 original size:11 final size:10
Alignment explanation
Indices: 63990--64050 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
63980 ACCAATAAAA
63990 TAAA-TGAGC
1 TAAATTGAGC
*
63999 TGAATTGTAGC
1 TAAATTG-AGC
64010 TAAATTGAGC
1 TAAATTGAGC
**
64020 TCGATTGAGC
1 TAAATTGAGC
64030 TGAAA-TGAGC
1 T-AAATTGAGC
*
64040 TCAATTGAGC
1 TAAATTGAGC
64050 T
1 T
64051 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:64051 original size:20 final size:20
Alignment explanation
Indices: 63991--64051 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
63981 CCAATAAAAT
*
63991 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
64011 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
64032 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
64052 GTCGGAGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:65326 original size:29 final size:29
Alignment explanation
Indices: 65293--65352 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
65283 ATAACCAAAC
* *
65293 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
65322 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
65351 CT
1 CT
65353 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:65345 original size:15 final size:15
Alignment explanation
Indices: 65299--65346 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65289 AAACCTACAA
*
65299 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
65314 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
65328 AAACTTCATATCCAT
1 AAACTTCATATCCAT
65343 AAAC
1 AAAC
65347 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:65583 original size:12 final size:13
Alignment explanation
Indices: 65566--65598 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
65556 AGTAAGTTTC
65566 AAAAAAAAAAT-A
1 AAAAAAAAAATCA
*
65578 AAAAAAAAATTCA
1 AAAAAAAAAATCA
65591 AAAAAAAA
1 AAAAAAAA
65599 CAAAATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATCA
Found at i:66520 original size:12 final size:12
Alignment explanation
Indices: 66505--66538 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
66495 CTTGAAAGAT
*
66505 ATTGAGAAAGCC
1 ATTGAAAAAGCC
66517 ATTGAAAAAGCC
1 ATTGAAAAAGCC
*
66529 GTTGAAAAAG
1 ATTGAAAAAG
66539 AAAAAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (12 bp):
ATTGAAAAAGCC
Done.