Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2804
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: 34793
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4896 original size:22 final size:22
Alignment explanation
Indices: 4871--4915 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4861 AAACTTAAGC
4871 AGTTGTTGTGGGTCGGCTTACA
1 AGTTGTTGTGGGTCGGCTTACA
4893 AGTTGTTGTGGGTCGGCTTACA
1 AGTTGTTGTGGGTCGGCTTACA
4915 A
1 A
4916 ACTTGATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.36, T:0.36
Consensus pattern (22 bp):
AGTTGTTGTGGGTCGGCTTACA
Found at i:5087 original size:14 final size:13
Alignment explanation
Indices: 5068--5115 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
5058 ACTAGCTCTC
5068 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
5081 TTTTTTTTTCACAA
1 TTTTTTTTTCA-AA
*
5095 TTTTTTTTCCAAA
1 TTTTTTTTTCAAA
5108 TTTTTTTT
1 TTTTTTTT
5116 CACAACTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:5111 original size:26 final size:27
Alignment explanation
Indices: 5068--5120 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
5058 ACTAGCTCTC
*
5068 TTTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTCCAAATTTTTTTTTCACAA
5095 TTTTTTTTCCAAA-TTTTTTTTCACAA
1 TTTTTTTTCCAAATTTTTTTTTCACAA
5121 CTTGATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTTTTCCAAATTTTTTTTTCACAA
Found at i:5131 original size:26 final size:27
Alignment explanation
Indices: 5077--5132 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
5067 CTTTTTTTTT
* ** *
5077 CAAATTTTTTTTTCACAATTTTTTTTC
1 CAAATTTTTTTTTCACAACTTGATATC
5104 CAAA-TTTTTTTTCACAACTTGATATC
1 CAAATTTTTTTTTCACAACTTGATATC
5130 CAA
1 CAA
5133 TCTTTTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.52
Consensus pattern (27 bp):
CAAATTTTTTTTTCACAACTTGATATC
Found at i:7494 original size:23 final size:22
Alignment explanation
Indices: 7443--7494 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
7433 CTCGTCTTTT
*
7443 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
7465 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
7488 TTCTTTT
1 TTCTTTT
7495 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:11663 original size:24 final size:25
Alignment explanation
Indices: 11635--11682 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
11625 TGACTCGTAT
11635 CAAGAATTT-TCT-TTGAGTTTTCTC
1 CAAG-ATTTCTCTCTTGAGTTTTCTC
11659 CAAGATTTCTCTCTTGAGTTTTCT
1 CAAGATTTCTCTCTTGAGTTTTCT
11683 TTAGAAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 7 0.32
25 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (25 bp):
CAAGATTTCTCTCTTGAGTTTTCTC
Found at i:16795 original size:22 final size:21
Alignment explanation
Indices: 16763--16826 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
16753 TTGGTATTTA
16763 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
16784 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
16806 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
16827 ATGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:19128 original size:11 final size:12
Alignment explanation
Indices: 19107--19155 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
19097 ATAGTAGTTT
19107 CTCGAAAAAAAA
1 CTCGAAAAAAAA
19119 CTCGAAAAAAAA
1 CTCGAAAAAAAA
*
19131 TTC-AAAAAAAA
1 CTCGAAAAAAAA
*
19142 TTCGAAAAAAAA
1 CTCGAAAAAAAA
19154 CT
1 CT
19156 AGTTTCCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 11 0.32
12 23 0.68
ACGTcount: A:0.65, C:0.14, G:0.06, T:0.14
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:19216 original size:13 final size:13
Alignment explanation
Indices: 19198--19244 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
19188 AAGTTGTGAA
*
19198 AAAAAAAATTTTG
1 AAAAAAAATTGTG
19211 AAAAAAAATTGTG
1 AAAAAAAATTGTG
19224 AAAAAAAAATTGTG
1 -AAAAAAAATTGTG
19238 AAAAAAA
1 AAAAAAA
19245 GAGCTAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 19 0.59
14 13 0.41
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTGTG
Found at i:19216 original size:14 final size:14
Alignment explanation
Indices: 19191--19244 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
19181 GGATATCAAG
19191 TTGTGAAAAAAAAAA
1 TTGTG-AAAAAAAAA
*
19206 TTTTG-AAAAAAAA
1 TTGTGAAAAAAAAA
19219 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
19233 TTGTGAAAAAAA
1 TTGTGAAAAAAA
19245 GAGCTAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 12 0.33
14 20 0.56
15 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:23044 original size:11 final size:11
Alignment explanation
Indices: 23028--23072 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
23018 TAGTAGTTTC
23028 TTCAAAAAAAA
1 TTCAAAAAAAA
23039 TTCAAAAAAAAA
1 TTC-AAAAAAAA
23051 TTCAAAAAAAA
1 TTCAAAAAAAA
23062 TTCAAAAAAAA
1 TTCAAAAAAAA
23073 ATTTGGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:23048 original size:12 final size:12
Alignment explanation
Indices: 23031--23075 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
23021 TAGTTTCTTC
23031 AAAAAAAATTCA
1 AAAAAAAATTCA
23043 AAAAAAAATTC-
1 AAAAAAAATTCA
23054 AAAAAAAATTCA
1 AAAAAAAATTCA
23066 AAAAAAAATT
1 AAAAAAAATT
23076 TGGTTTCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.34
12 21 0.66
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:23058 original size:23 final size:23
Alignment explanation
Indices: 23028--23075 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
23018 TAGTAGTTTC
23028 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
23051 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
23074 TT
1 TT
23076 TGGTTTCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (23 bp):
TTCAAAAAAAATTCAAAAAAAAA
Found at i:23133 original size:15 final size:16
Alignment explanation
Indices: 23113--23154 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
23103 GATATCAAGT
23113 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
23128 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
23144 TGAAAAAAAAA
1 TGAAAAAAAAA
23155 AGAAGCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:31355 original size:20 final size:20
Alignment explanation
Indices: 31332--31385 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
31322 AGTTTTTCCC
*
31332 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
31352 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
31372 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
31386 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:31367 original size:30 final size:30
Alignment explanation
Indices: 31332--31405 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
31322 AGTTTTTCCC
31332 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
31362 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
31392 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
31406 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:31395 original size:20 final size:20
Alignment explanation
Indices: 31332--31396 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31322 AGTTTTTCCC
* * * *
31332 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
31352 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
31371 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
31392 AGCTC
1 AGCTC
31397 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:32992 original size:12 final size:12
Alignment explanation
Indices: 32975--33004 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
32965 TTGGAGTAAC
32975 AAAAAAAATCAA
1 AAAAAAAATCAA
32987 AAAAAAAATCAA
1 AAAAAAAATCAA
32999 AAAAAA
1 AAAAAA
33005 TTTGATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:33028 original size:12 final size:12
Alignment explanation
Indices: 32975--33043 Score: 59
Period size: 12 Copynumber: 5.5 Consensus size: 12
32965 TTGGAGTAAC
32975 AAAAAAAA-TCA
1 AAAAAAAATTCA
*
32986 AAAAAAAAATCA
1 AAAAAAAATTCA
*
32998 AAAAAAATTTGATTGA
1 AAAAAAA----ATTCA
33014 AAAAAAAATTCA
1 AAAAAAAATTCA
* *
33026 AAAAAAAAGTGA
1 AAAAAAAATTCA
33038 AAAAAA
1 AAAAAA
33044 TCGAGCAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.17
12 30 0.62
16 10 0.21
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:34120 original size:5 final size:5
Alignment explanation
Indices: 34103--34158 Score: 58
Period size: 5 Copynumber: 10.4 Consensus size: 5
34093 AAAGAAATTG
* *
34103 AAAGA AAACA AAAGA AAACGA AAAGAA AAAGA AAAGA AATTGCA AAAGA
1 AAAGA AAAGA AAAGA AAA-GA AAAG-A AAAGA AAAGA AA-AG-A AAAGA
34152 AAAGA AA
1 AAAGA AA
34159 TCGAAAAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 28 0.65
6 12 0.28
7 3 0.07
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:34128 original size:11 final size:11
Alignment explanation
Indices: 34103--34141 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
34093 AAAGAAATTG
34103 AAAGAAAAC-A
1 AAAGAAAACGA
34113 AAAGAAAACGA
1 AAAGAAAACGA
*
34124 AAAGAAAAAGA
1 AAAGAAAACGA
34135 AAAGAAA
1 AAAGAAA
34142 TTGCAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAACGA
Found at i:34132 original size:6 final size:6
Alignment explanation
Indices: 34112--34211 Score: 55
Period size: 6 Copynumber: 16.8 Consensus size: 6
34102 GAAAGAAAAC
* ** *
34112 AAAAGA AAACG- AAAAGA AAAAG- AAAAGA AATTGC AAAAG- AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
** * * * *
34157 AATCGA AAAAGT GAGAGA AAAAGA AAATA-A GAAAAGA AAATTGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA -AAAAGA AAA-AGA AAAAGA
34207 AAAAG
1 AAAAG
34212 CGAAAAAAGA
Statistics
Matches: 68, Mismatches: 19, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
5 14 0.21
6 44 0.65
7 10 0.15
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAAGA
Found at i:34137 original size:22 final size:22
Alignment explanation
Indices: 34103--34158 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
34093 AAAGAAATTG
*
34103 AAAGAAAACAAAAGAAAACG-A
1 AAAGAAAAGAAAAGAAAACGCA
**
34124 AAAGAAAAAGAAAAGAAATTGCA
1 AAAG-AAAAGAAAAGAAAACGCA
34147 AAAGAAAAGAAA
1 AAAGAAAAGAAA
34159 TCGAAAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.13
22 21 0.70
23 5 0.17
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAGAAAAGAAAAGAAAACGCA
Found at i:34149 original size:12 final size:11
Alignment explanation
Indices: 34081--34153 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
34071 AGAAAAGGAG
*
34081 AAAGAGATTGAA
1 AAAGAAATTG-A
34093 AAAGAAATTG-
1 AAAGAAATTGA
**
34103 AAAGAAA-ACA
1 AAAGAAATTGA
**
34113 AAAGAAAACGA
1 AAAGAAATTGA
**
34124 AAAGAAAAAGA
1 AAAGAAATTGA
34135 AAAGAAATTGCA
1 AAAGAAATTG-A
34147 AAAGAAA
1 AAAGAAA
34154 AGAAATCGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
10 14 0.28
11 19 0.38
12 17 0.34
ACGTcount: A:0.70, C:0.04, G:0.18, T:0.08
Consensus pattern (11 bp):
AAAGAAATTGA
Found at i:34149 original size:17 final size:17
Alignment explanation
Indices: 34103--34159 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
34093 AAAGAAATTG
34103 AAAGAAA-A-CAAAAGA
1 AAAGAAATAGCAAAAGA
*
34118 AAACGAAA-AGAAAAAGA
1 AAA-GAAATAGCAAAAGA
*
34135 AAAGAAATTGCAAAAGA
1 AAAGAAATAGCAAAAGA
34152 AAAGAAAT
1 AAAGAAAT
34160 CGAAAAAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 3 0.08
16 9 0.25
17 24 0.67
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAGAAATAGCAAAAGA
Found at i:34166 original size:17 final size:17
Alignment explanation
Indices: 34112--34209 Score: 81
Period size: 17 Copynumber: 5.5 Consensus size: 17
34102 GAAAGAAAAC
34112 AAAAGAAAACGAAA-AGA
1 AAAAGAAAA-GAAATAGA
* *
34129 AAAAGAAAAGAAATTGC
1 AAAAGAAAAGAAATAGA
*
34146 AAAAGAAAAGAAATCGA
1 AAAAGAAAAGAAATAGA
* * *
34163 AAAAGTGAGAGAAAAAGAA
1 AAAAG-AAAAGAAATAG-A
*
34182 AATAAGAAAAGAAAATTGA
1 AA-AAGAAAAG-AAATAGA
34201 AAAAGAAAA
1 AAAAGAAAA
34210 AGCGAAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
16 4 0.06
17 30 0.47
18 14 0.22
19 9 0.14
20 7 0.11
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAGAAATAGA
Found at i:34204 original size:13 final size:12
Alignment explanation
Indices: 34089--34209 Score: 56
Period size: 12 Copynumber: 10.0 Consensus size: 12
34079 AGAAAGAGAT
*
34089 TGAAAAAGAAAT
1 TGAAAAAGAAAA
*
34101 TGAAAGAAAACAAA
1 TGAAA-AAGA-AAA
* *
34115 AGAAAACGAAAA
1 TGAAAAAGAAAA
34127 -GAAAAAGAAAA
1 TGAAAAAGAAAA
**
34138 -GAAATTGCAAAA
1 TGAAAAAG-AAAA
34150 -G-AAAAG-AAA
1 TGAAAAAGAAAA
* *
34159 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
34173 -GAAAAAGAAAA
1 TGAAAAAGAAAA
*
34184 TAAGAAAAGAAAA
1 TGA-AAAAGAAAA
34197 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
34210 AGCGAAAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 21
0.70 0.13 0.18
Matches are distributed among these distances:
9 3 0.04
11 21 0.25
12 26 0.31
13 23 0.28
14 10 0.12
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:34216 original size:26 final size:27
Alignment explanation
Indices: 34173--34229 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
34163 AAAAGTGAGA
*
34173 GAAAAAGAAAATAAGAAAAGA-AAATT
1 GAAAAAGAAAATAAGAAAAAAGAAATT
*
34199 GAAAAAGAAAA-AGCGAAAAAAGAAATT
1 GAAAAAGAAAATA-AGAAAAAAGAAATT
34226 GAAA
1 GAAA
34230 GAGAGCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 17 0.63
27 9 0.33
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAATAAGAAAAAAGAAATT
Found at i:34263 original size:33 final size:33
Alignment explanation
Indices: 34226--34288 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
34216 AAAAGAAATT
34226 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
34259 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
34289 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
Done.