Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 101 of 253
Found at i:31495220 original size:17 final size:18
Alignment explanation
Indices: 31495181--31495222 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31495171 AAGAAGAAAA
31495181 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
31495198 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
31495215 TCAAAAGA
1 ACAAAAGA
31495223 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:31503069 original size:20 final size:20
Alignment explanation
Indices: 31503023--31503069 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31503013 AGCTCGTTTC
*
31503023 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31503043 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31503063 CAGCTCA
1 CAGCTCA
31503070 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31507425 original size:20 final size:20
Alignment explanation
Indices: 31507402--31507447 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31507392 CCAGCTCGAA
*
31507402 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
31507422 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
31507442 TTAGCT
1 TTAGCT
31507448 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:31507429 original size:30 final size:30
Alignment explanation
Indices: 31507394--31507467 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
31507384 AGTTTTTCCC
31507394 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
31507424 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
31507454 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
31507468 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:31510031 original size:30 final size:30
Alignment explanation
Indices: 31509997--31510093 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31509987 AGCTCACTCC
31509997 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31510027 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
31510057 CAGCTCAACTTTAGCTCACGGGCTAAACCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31510087 TAGCTCA
1 TAGCTCA
31510094 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31512555 original size:22 final size:22
Alignment explanation
Indices: 31512525--31512568 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31512515 TTTGGTATTT
31512525 GGGAATTGGTACAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
* *
31512547 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
31512569 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACAAAATGGTAA
Found at i:31518358 original size:20 final size:20
Alignment explanation
Indices: 31518314--31518351 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31518304 AGAAAGAAAG
*
31518314 AAGCTAAATCAAGCTCAAAC
1 AAGCTAAAACAAGCTCAAAC
31518334 AAGCTAAAACAAGCTCAA
1 AAGCTAAAACAAGCTCAA
31518352 GTGAGCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.11, T:0.13
Consensus pattern (20 bp):
AAGCTAAAACAAGCTCAAAC
Found at i:31522985 original size:22 final size:22
Alignment explanation
Indices: 31522955--31522998 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31522945 TTTGGTATTT
31522955 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31522977 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
31522999 TAGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:31525117 original size:20 final size:19
Alignment explanation
Indices: 31525094--31525158 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
31525084 AAGCTCAAAC
31525094 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
31525114 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
31525134 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
31525154 GAGCT
1 GAGCT
31525159 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:31525785 original size:18 final size:18
Alignment explanation
Indices: 31525759--31525862 Score: 66
Period size: 18 Copynumber: 5.6 Consensus size: 18
31525749 AAATTGAAAG
*
31525759 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
31525777 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
31525795 AAAAGAAAAAGAAATC-A
1 AAAAGAAAAAGAAAACGA
** * *
31525812 AAATAGTGAGAGAAAAAGA
1 AAA-AGAAAAAGAAAACGA
* *
31525831 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
31525852 AAAAGAAAAAG
1 AAAAGAAAAAG
31525863 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
17 3 0.05
18 38 0.59
19 9 0.14
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:31525787 original size:6 final size:6
Alignment explanation
Indices: 31525755--31525862 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
31525745 AAAGAAATTG
* * ** *
31525755 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * ** * * *
31525802 AAAGAA ATCA-AA ATAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
31525853 AAAGAA AAAG
1 AAAGAA AAAG
31525863 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:31525842 original size:14 final size:13
Alignment explanation
Indices: 31525823--31525860 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31525813 AATAGTGAGA
31525823 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31525835 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31525850 GAAAAAGAAAA
1 GAAAAAGAAAA
31525861 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:31525857 original size:13 final size:12
Alignment explanation
Indices: 31525741--31525860 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
31525731 AGAAAGAGAT
*
31525741 TGAAAAAGAAAT
1 TGAAAAAGAAAA
31525753 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
31525763 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
31525774 CGAAAAAGAAAA
1 TGAAAAAGAAAA
* **
31525786 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
31525799 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* * *
31525809 TCAAAATAGTGAGA
1 TGAAAA-AG-AAAA
31525823 -GAAAAAGAAAA
1 TGAAAAAGAAAA
31525834 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
31525848 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
31525861 AGCGAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 10 0.12
11 14 0.17
12 27 0.33
13 18 0.22
14 12 0.14
15 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:31525874 original size:21 final size:21
Alignment explanation
Indices: 31525824--31525874 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
31525814 ATAGTGAGAG
*
31525824 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
31525845 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
31525866 AAAAAGAAA
1 AAAAAGAAA
31525875 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:31525914 original size:33 final size:33
Alignment explanation
Indices: 31525877--31525939 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31525867 AAAAGAAATT
31525877 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
31525910 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
31525940 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:31528305 original size:30 final size:30
Alignment explanation
Indices: 31528271--31528367 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
31528261 TAAACTAAAA
31528271 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
31528301 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
31528331 TGAGCTGAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
31528360 ATGAGCTA
1 -TGAGCTA
31528368 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 44 0.90
31 3 0.06
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:31534203 original size:24 final size:25
Alignment explanation
Indices: 31534150--31534203 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
31534140 AACAAATTCT
* *
31534150 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
31534175 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
31534198 TTTTTT
1 TTTTTT
31534204 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:31538794 original size:17 final size:17
Alignment explanation
Indices: 31538774--31538811 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31538764 CAATTTTTTC
31538774 TCAATATCAATATCATA
1 TCAATATCAATATCATA
* *
31538791 TCAATATCAATCTCATC
1 TCAATATCAATATCATA
31538808 TCAA
1 TCAA
31538812 ATTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (17 bp):
TCAATATCAATATCATA
Found at i:31538832 original size:27 final size:27
Alignment explanation
Indices: 31538801--31538852 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
31538791 TCAATATCAA
31538801 TCTCA-TCTCAAATTATTTTTTTCTTTT
1 TCTCACTCTC-AATTATTTTTTTCTTTT
* *
31538828 TCTCACTCTCATTTCTTTTTTTCTT
1 TCTCACTCTCAATTATTTTTTTCTT
31538853 CTCTCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (27 bp):
TCTCACTCTCAATTATTTTTTTCTTTT
Found at i:31538844 original size:19 final size:20
Alignment explanation
Indices: 31538820--31538861 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
31538810 AAATTATTTT
31538820 TTTCTTTTTCTC-ACTCTCA
1 TTTCTTTTTCTCTACTCTCA
* *
31538839 TTTCTTTTTTTCTTCTCTCA
1 TTTCTTTTTCTCTACTCTCA
31538859 TTT
1 TTT
31538862 TCATCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTTTTTCTCTACTCTCA
Found at i:31539759 original size:31 final size:30
Alignment explanation
Indices: 31539722--31539791 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
31539712 TTCAATCACT
**
31539722 TTTTTTTTTTCAATTTTGATTTTTTTTCTTC
1 TTTTTTTTTTCAATTCCGA-TTTTTTTCTTC
*
31539753 TTTTTTTTTTTAATTCCGATTTTTTTCTTC
1 TTTTTTTTTTCAATTCCGATTTTTTTCTTC
31539783 TTTTTTTTT
1 TTTTTTTTT
31539792 CTTCAATACT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.09, C:0.10, G:0.03, T:0.79
Consensus pattern (30 bp):
TTTTTTTTTTCAATTCCGATTTTTTTCTTC
Found at i:31539851 original size:11 final size:11
Alignment explanation
Indices: 31539837--31539866 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31539827 ACAAATTTTT
*
31539837 TTTTTTTTGAA
1 TTTTTTTTCAA
31539848 TTTTTTTTCAA
1 TTTTTTTTCAA
31539859 TTTTTTTT
1 TTTTTTTT
31539867 TTTTTTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:31539868 original size:17 final size:17
Alignment explanation
Indices: 31539848--31539883 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31539838 TTTTTTTGAA
31539848 TTTTTTTTCAATTTTTT
1 TTTTTTTTCAATTTTTT
*
31539865 TTTTTTTTCGATTTTTT
1 TTTTTTTTCAATTTTTT
31539882 TT
1 TT
31539884 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.08, C:0.06, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCAATTTTTT
Found at i:31539872 original size:28 final size:28
Alignment explanation
Indices: 31539832--31539895 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
31539822 TGAATACAAA
31539832 TTTTTTTTTTTTT-GAATTTTTTTTCA-AT
1 TTTTTTTTTTTTTCG-ATTTTTTTT-ATAT
31539860 TTTTTTTTTTTTTCGATTTTTTTTATAT
1 TTTTTTTTTTTTTCGATTTTTTTTATAT
31539888 TTTTTTTT
1 TTTTTTTT
31539896 ACAATACCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 1 0.03
28 32 0.94
29 1 0.03
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (28 bp):
TTTTTTTTTTTTTCGATTTTTTTTATAT
Found at i:31567687 original size:13 final size:13
Alignment explanation
Indices: 31567669--31567695 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31567659 TTTATTTGTA
31567669 ATTATTTTTATTT
1 ATTATTTTTATTT
31567682 ATTATTTTTATTT
1 ATTATTTTTATTT
31567695 A
1 A
31567696 CTTAAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:31571228 original size:33 final size:34
Alignment explanation
Indices: 31571186--31571258 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
31571176 TTTCAATCAC
*
31571186 TTTTTTTTTTTCAATTTTG-A-TTTTTTTTCTTCT
1 TTTTTTTTTTTCAA-TTCGAATTTTTTTTTCTTCT
*
31571219 TTTTTTTTTTTTAATTCGAATTTTTTTTTCTTCT
1 TTTTTTTTTTTCAATTCGAATTTTTTTTTCTTCT
31571253 TTTTTT
1 TTTTTT
31571259 CTTCAATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 3 0.08
33 14 0.39
34 19 0.53
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (34 bp):
TTTTTTTTTTTCAATTCGAATTTTTTTTTCTTCT
Found at i:31571322 original size:13 final size:13
Alignment explanation
Indices: 31571304--31571365 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
31571294 AATACAAACT
31571304 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
**
31571317 TTTTTTTTTCAAA
1 TTTTTTTTTTGAA
31571330 TTTTTTTTTTTTCGAA
1 --TTTTTTTTTT-GAA
31571346 -TTTTTTTTT--A
1 TTTTTTTTTTGAA
31571356 TTTTTTTTTT
1 TTTTTTTTTT
31571366 ACAATACCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 1 0.02
11 9 0.22
13 20 0.49
15 9 0.22
16 2 0.05
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:31571324 original size:16 final size:16
Alignment explanation
Indices: 31571317--31571354 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
31571307 TTTTTTTGAA
*
31571317 TTTTTTTTTCAAATTT
1 TTTTTTTTTCGAATTT
31571333 TTTTTTTTTCGAATTT
1 TTTTTTTTTCGAATTT
31571349 TTTTTT
1 TTTTTT
31571355 ATTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTCGAATTT
Found at i:31571325 original size:17 final size:17
Alignment explanation
Indices: 31571317--31571359 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
31571307 TTTTTTTGAA
31571317 TTTTTTTTTCAAA-TTT
1 TTTTTTTTTCAAATTTT
*
31571333 TTTTTTTTTCGAATTTT
1 TTTTTTTTTCAAATTTT
31571350 TTTTTATTTT
1 TTTTT-TTTT
31571360 TTTTTTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 12 0.50
17 8 0.33
18 4 0.17
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTCAAATTTT
Found at i:31571338 original size:28 final size:29
Alignment explanation
Indices: 31571298--31571365 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
31571288 AAATTGAATA
*
31571298 CAAACTTTTTTTTTTT-GAATTTTTTTTT
1 CAAATTTTTTTTTTTTCGAATTTTTTTTT
31571326 CAAATTTTTTTTTTTTCGAATTTTTTTTT
1 CAAATTTTTTTTTTTTCGAATTTTTTTTT
31571355 ---ATTTTTTTTTT
1 CAAATTTTTTTTTT
31571366 ACAATACCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
26 11 0.29
28 15 0.39
29 12 0.32
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (29 bp):
CAAATTTTTTTTTTTTCGAATTTTTTTTT
Found at i:31575142 original size:27 final size:27
Alignment explanation
Indices: 31575108--31575257 Score: 167
Period size: 27 Copynumber: 5.6 Consensus size: 27
31575098 TAAATTGTAC
*
31575108 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
31575135 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
31575161 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
31575189 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * * *
31575216 AGCACTAAGTGTGTGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
31575243 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31575258 GACTTAATAT
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:31579727 original size:13 final size:12
Alignment explanation
Indices: 31579697--31579752 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
31579687 AATGTGAAAC
*
31579697 AAAAAGAAATTG
1 AAAAAGAAGTTG
31579709 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
31579721 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
31579733 AAAATG-AGTTAG
1 AAAAAGAAGTT-G
31579745 AAAAAGAA
1 AAAAAGAA
31579753 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.63
13 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:31581997 original size:27 final size:27
Alignment explanation
Indices: 31581958--31582309 Score: 318
Period size: 27 Copynumber: 13.1 Consensus size: 27
31581948 CCCTGTATCA
*
31581958 CCTT-GTTTGTAAAATTACTAAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
* *
31581984 CCTTGGTTTATAAAATCACCAAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
* *
31582011 CCCTGGTTTGTAAAATTACTAAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
* * * *
31582038 CCTTGATTTATAAAATCACAAAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
* *
31582065 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
* **
31582092 CCTTTGTTTACAAAATTACCAAAATA-
1 CCTTGGTTTGTAAAATTACCAAAATAC
* * *
31582118 CCTCTAGTTTGTAAAATTACTAGAATAC
1 CCT-TGGTTTGTAAAATTACCAAAATAC
*
31582146 CCTTGGTTTATAAAATTACCAAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
* *
31582173 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
* * * **
31582200 CCCTGATTTGTGAAATTACTGAAATAC
1 CCTTGGTTTGTAAAATTACCAAAATAC
** *
31582227 CCTT-GTAGGGTAGAATTACCAAAATAC
1 CCTTGGT-TTGTAAAATTACCAAAATAC
** *
31582254 CCTT-GTAGGGTAGAATTACCAAAATAC
1 CCTTGGT-TTGTAAAATTACCAAAATAC
* ** *
31582281 CCCT-GTAGGGTAAAATTATCAAAATAC
1 CCTTGGT-TTGTAAAATTACCAAAATAC
31582308 CC
1 CC
31582310 CTGTAGGGTA
Statistics
Matches: 272, Mismatches: 50, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
26 8 0.03
27 261 0.96
28 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
CCTTGGTTTGTAAAATTACCAAAATAC
Found at i:31582025 original size:54 final size:54
Alignment explanation
Indices: 31581962--31582201 Score: 381
Period size: 54 Copynumber: 4.4 Consensus size: 54
31581952 GTATCACCTT
*
31581962 GTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTG
1 GTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTA
* *
31582016 GTTTGTAAAATTACTAAAATACCCTTGATTTATAAAATCACAAAAATACCCCTA
1 GTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTA
* * * * *
31582070 GTTTGTAAAATTACCAAAATACCCTTTGTTTACAAAATTACCAAAATACCTCTA
1 GTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTA
* *
31582124 GTTTGTAAAATTACTAGAATACCCTTGGTTTATAAAATTACCAAAATACCCCTA
1 GTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTA
*
31582178 GTTTGTAAAATTACCAAAATACCC
1 GTTTGTAAAATTACTAAAATACCC
31582202 CTGATTTGTG
Statistics
Matches: 169, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 169 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (54 bp):
GTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTA
Found at i:31582216 original size:54 final size:53
Alignment explanation
Indices: 31581962--31582309 Score: 376
Period size: 54 Copynumber: 6.5 Consensus size: 53
31581952 GTATCACCTT
* * *
31581962 GTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTG
1 GTTTGTAAAATTACCAAAATACCCTT-GTTTATAAAATTACCAAAATACCCCTA
* * *
31582016 GTTTGTAAAATTACTAAAATACCCTTGATTTATAAAATCACAAAAATACCCCTA
1 GTTTGTAAAATTACCAAAATACCCTTG-TTTATAAAATTACCAAAATACCCCTA
* *
31582070 GTTTGTAAAATTACCAAAATACCCTTTGTTTACAAAATTACCAAAATACCTCTA
1 GTTTGTAAAATTACCAAAATACCC-TTGTTTATAAAATTACCAAAATACCCCTA
* *
31582124 GTTTGTAAAATTACTAGAATACCCTTGGTTTATAAAATTACCAAAATACCCCTA
1 GTTTGTAAAATTACCAAAATACCCTT-GTTTATAAAATTACCAAAATACCCCTA
* * * ** *
31582178 GTTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATA-CCCTT
1 GTTTGTAAAATTACCAAAATACCCTTG-TTTATAAAATTACCAAAATACCCCTA
** * *** *
31582231 GTAGGGTAGAATTACCAAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCT-
1 GT-TTGTAAAATTACCAAAATACCCTTGT-TTATAAAATTACCAAAATACCCCTA
** *
31582285 GTAGGGTAAAATTATCAAAATACCC
1 GT-TTGTAAAATTACCAAAATACCC
31582310 CTGTAGGGTA
Statistics
Matches: 256, Mismatches: 31, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
53 11 0.04
54 238 0.93
55 7 0.03
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (53 bp):
GTTTGTAAAATTACCAAAATACCCTTGTTTATAAAATTACCAAAATACCCCTA
Found at i:31582271 original size:81 final size:80
Alignment explanation
Indices: 31582105--31582366 Score: 262
Period size: 81 Copynumber: 3.2 Consensus size: 80
31582095 TTGTTTACAA
* *** *
31582105 AATTACCAAAATACCTCT-AGTTTGTAAAATTACTAGAATACCCTTGGT-TTATAAAATTACCAA
1 AATTACCAAAATACCCCTGA-TTTGTAAAATTACTA-AATACCCTT-GTAGGGTAGAATTACCAA
* ** *
31582168 AATACCCCTAGT-TTGTAA
63 AATA-CCCTTGTAGGGTAG
*
31582186 AATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATACCCTTGTAGGGTAGAATTACCAAAA
1 AATTACCAAAATACCCCTGATTTGTAAAATTACT-AAATACCCTTGTAGGGTAGAATTACCAAAA
31582251 TACCCTTGTAGGGTAG
65 TACCCTTGTAGGGTAG
** * * *
31582267 AATTACCAAAATACCCCTG-TAGGGTAAAATTATCAAAATACCCCTGTAGGGTAGAATTACCGAA
1 AATTACCAAAATACCCCTGAT-TTGTAAAATTA-CTAAATACCCTTGTAGGGTAGAATTACCAAA
*
31582331 ATACCCCTGTAGGGTAG
64 ATACCCTTGTAGGGTAG
***
31582348 AATTATTGAAATACCCCTG
1 AATTACCAAAATACCCCTG
31582367 TAGGGTAGAA
Statistics
Matches: 155, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
80 9 0.06
81 143 0.92
82 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (80 bp):
AATTACCAAAATACCCCTGATTTGTAAAATTACTAAATACCCTTGTAGGGTAGAATTACCAAAAT
ACCCTTGTAGGGTAG
Found at i:31582310 original size:27 final size:27
Alignment explanation
Indices: 31582156--31582404 Score: 268
Period size: 27 Copynumber: 9.2 Consensus size: 27
31582146 CCTTGGTTTA
**
31582156 TAAAATTACCAAAATACCCCTAGT-TTG
1 TAAAATTACCAAAATACCCCT-GTAGGG
**
31582183 TAAAATTACCAAAATACCCCTG-ATTTG
1 TAAAATTACCAAAATACCCCTGTA-GGG
* ** *
31582210 TGAAATTACTGAAATACCCTTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
* *
31582237 TAGAATTACCAAAATACCCTTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
*
31582264 TAGAATTACCAAAATACCCCTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
*
31582291 TAAAATTATCAAAATACCCCTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
* *
31582318 TAGAATTACCGAAATACCCCTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
* ***
31582345 TAGAATTATTGAAATACCCCTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
* * * *
31582372 TAGAATTACCAAGATACCCTTGTGGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
31582399 TAAAAT
1 TAAAAT
31582405 GGTAATTTTA
Statistics
Matches: 194, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 192 0.99
28 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCCTGTAGGG
Found at i:31582789 original size:22 final size:22
Alignment explanation
Indices: 31582756--31582814 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
31582746 CACGTTATCG
31582756 ATGGC-TCTGTGCCAACCTAAAT
1 ATGGCTTC-GTGCCAACCTAAAT
* * * *
31582778 ATGGCTTCGTGCCATCTTGACT
1 ATGGCTTCGTGCCAACCTAAAT
*
31582800 ATGGTTTCGTGCCAA
1 ATGGCTTCGTGCCAA
31582815 ACATATTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTCGTGCCAACCTAAAT
Found at i:31583217 original size:6 final size:6
Alignment explanation
Indices: 31583202--31583339 Score: 95
Period size: 6 Copynumber: 22.8 Consensus size: 6
31583192 ATTCTGTTAC
* * *
31583202 CTGATA CTGATT CTGATT TTGATT CT-ATT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * * * *
31583251 CTGATT TTAATT CTG-TCAC CTAATT CTGATT CTGATT CTGATT CTAATT
1 CTGATT CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGATT
* * * *
31583300 GTCA-C CTAATT CTGATT CTGATT CTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
31583340 AGTGTTTCTT
Statistics
Matches: 102, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
5 7 0.07
6 87 0.85
7 5 0.05
8 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:31583243 original size:37 final size:37
Alignment explanation
Indices: 31583202--31583328 Score: 159
Period size: 37 Copynumber: 3.5 Consensus size: 37
31583192 ATTCTGTTAC
* * * *
31583202 CTGATACTGATTCTGATTTTGATTCTATTACCTGATA
1 CTGATTCTGATTCTGATTTTAATTCTATCACCTAATA
* *
31583239 CTGATTCTGATTCTGATTTTAATTCTGTCACCTAATT
1 CTGATTCTGATTCTGATTTTAATTCTATCACCTAATA
* * *
31583276 CTGATTCTGATTCTGATTCTAA-T-TGTCACCTAATT
1 CTGATTCTGATTCTGATTTTAATTCTATCACCTAATA
31583311 CTGATTCTGATTCTGATT
1 CTGATTCTGATTCTGATT
31583329 CTAGTTCTGA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 30 0.36
36 1 0.01
37 52 0.63
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTTTAATTCTATCACCTAATA
Found at i:31583277 original size:31 final size:31
Alignment explanation
Indices: 31583179--31583330 Score: 124
Period size: 31 Copynumber: 4.5 Consensus size: 31
31583169 TTGCATTCAC
* * * *
31583179 ATTCTGATTTTTTATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTCACCTAATTCTG
* *
31583211 ATTCTGATTTTGATTCTATTACCTGATACTGATTCTG
1 ATTCTGATTTTGATTCTGTCACC---TA---ATTCTG
*
31583248 ATTCTGATTTTAATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTCACCTAATTCTG
*
31583279 ATTCTGATTCTGATTCTAATTGTCACCTAATTCTG
1 ATTCTGATTTTGATTC----TGTCACCTAATTCTG
*
31583314 ATTCTGATTCTGATTCT
1 ATTCTGATTTTGATTCT
31583331 AGTTCTGATA
Statistics
Matches: 101, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
31 35 0.35
32 7 0.07
34 3 0.03
35 31 0.31
37 25 0.25
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTCACCTAATTCTG
Found at i:31584373 original size:30 final size:30
Alignment explanation
Indices: 31584339--31584435 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31584329 AGCTCACTCC
31584339 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31584369 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
31584399 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31584429 TAGCTCA
1 TAGCTCA
31584436 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31588153 original size:19 final size:19
Alignment explanation
Indices: 31588131--31588172 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
31588121 TCACTTTCAA
31588131 CTCACGAGCTAAACCTTAG
1 CTCACGAGCTAAACCTTAG
*
31588150 CTCACGAGCTAAAGCTTAG
1 CTCACGAGCTAAACCTTAG
31588169 CTCA
1 CTCA
31588173 TTTTAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
CTCACGAGCTAAACCTTAG
Found at i:31589766 original size:30 final size:30
Alignment explanation
Indices: 31589732--31589808 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
31589722 TAAACTAAAA
* *
31589732 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCCTAAGCTAAAGT
* * *
31589762 TGAGCTGAAGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCCTAAGCTAAAGT
*
31589792 TGAGCTAAGGTTTAGCT
1 TGAGCTAAGCTTTAGCT
31589809 AAGGCAAGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 3 0.08
30 30 0.81
31 4 0.11
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCCTAAGCTAAAGT
Found at i:31592868 original size:15 final size:15
Alignment explanation
Indices: 31592822--31592869 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
31592812 AAACCTACAA
*
31592822 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
31592837 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
31592851 AAACTTCATATCCAT
1 AAACTTCATATCCAT
31592866 AAAC
1 AAAC
31592870 CCACCTTTGA
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:31594855 original size:9 final size:9
Alignment explanation
Indices: 31594841--31594866 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31594831 TTTCTTGTTT
31594841 TCAAGAAAA
1 TCAAGAAAA
31594850 TCAAGAAAA
1 TCAAGAAAA
31594859 TCAAGAAA
1 TCAAGAAA
31594867 TCGAATCTTG
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:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
TCAAGAAAA
Found at i:31597690 original size:14 final size:14
Alignment explanation
Indices: 31597671--31597715 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
31597661 AACTCATCTT
*
31597671 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
31597685 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
31597698 AATTTAATTTAATG
1 AGTTTAATTTAATG
31597712 AGTT
1 AGTT
31597716 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:31598608 original size:20 final size:20
Alignment explanation
Indices: 31598562--31598608 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31598552 AGCTCGTTTC
* *
31598562 CAGCTCGCTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31598582 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31598602 CAGCTCA
1 CAGCTCA
31598609 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31600550 original size:22 final size:22
Alignment explanation
Indices: 31600496--31600561 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
31600486 GGTATTTGGG
* *
31600496 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
31600517 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* * *
31600539 ATTTTGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
31600562 TCAAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 19 0.50
22 14 0.37
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:31602107 original size:17 final size:19
Alignment explanation
Indices: 31602075--31602109 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
31602065 AAAAAATTTC
31602075 AAACAAAAATTCTGAAAAA
1 AAACAAAAATTCTGAAAAA
31602094 AAAC-AAAA-TCTGAAAA
1 AAACAAAAATTCTGAAAA
31602110 TTTGAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (19 bp):
AAACAAAAATTCTGAAAAA
Found at i:31603174 original size:18 final size:19
Alignment explanation
Indices: 31603131--31603176 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
31603121 CGAGAGAAGC
*
31603131 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
31603149 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
31603167 GAAAAAGAAA
1 GAAAAAGAAA
31603177 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:31605616 original size:14 final size:14
Alignment explanation
Indices: 31605597--31605641 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
31605587 AACTCATCTT
*
31605597 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
31605611 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
31605624 AATTTAATTTAATG
1 AGTTTAATTTAATG
31605638 AGTT
1 AGTT
31605642 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:31606643 original size:29 final size:29
Alignment explanation
Indices: 31606610--31606669 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
31606600 ATAACCAAAC
*
31606610 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
31606639 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
31606668 CT
1 CT
31606670 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:31606662 original size:15 final size:15
Alignment explanation
Indices: 31606616--31606663 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
31606606 AAACCTACAA
*
31606616 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
31606631 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
31606645 AAACTTCATATCCAT
1 AAACTTCATATCCAT
31606660 AAAC
1 AAAC
31606664 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:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:31610049 original size:29 final size:29
Alignment explanation
Indices: 31610016--31610075 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
31610006 ATAACCAAAC
* *
31610016 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
31610045 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
31610074 CT
1 CT
31610076 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:31610068 original size:15 final size:15
Alignment explanation
Indices: 31610022--31610069 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
31610012 AAACCTACAA
*
31610022 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
31610037 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
31610051 AAACTTCATATCCAT
1 AAACTTCATATCCAT
31610066 AAAC
1 AAAC
31610070 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:31610308 original size:12 final size:12
Alignment explanation
Indices: 31610291--31610335 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
31610281 AGTAAGTTTC
31610291 AAAAAAAATCGA
1 AAAAAAAATCGA
* *
31610303 AAAAAAATTCCAA
1 AAAAAAAAT-CGA
*
31610316 AAAAAAAATTGA
1 AAAAAAAATCGA
31610328 AAAAAAAA
1 AAAAAAAA
31610336 CAAAATCTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:31610319 original size:14 final size:13
Alignment explanation
Indices: 31610302--31610335 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
31610292 AAAAAAATCG
31610302 AAAAAAAATTCCAA
1 AAAAAAAATT-CAA
*
31610316 AAAAAAAATTGAA
1 AAAAAAAATTCAA
31610329 AAAAAAA
1 AAAAAAA
31610336 CAAAATCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:31610334 original size:17 final size:18
Alignment explanation
Indices: 31610314--31610348 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31610304 AAAAAATTCC
31610314 AAAAAAAAAAT-TGAAAA
1 AAAAAAAAAATCTGAAAA
*
31610331 AAAAACAAAATCTGAAAA
1 AAAAAAAAAATCTGAAAA
31610349 TTTGAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAATCTGAAAA
Found at i:31610346 original size:18 final size:16
Alignment explanation
Indices: 31610314--31610348 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
31610304 AAAAAATTCC
31610314 AAAAAAAAAATTGAAA
1 AAAAAAAAAATTGAAA
31610330 AAAAAACAAAATCTGAAA
1 AAAAAA-AAAAT-TGAAA
31610348 A
1 A
31610349 TTTGAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAAAAAAAATTGAAA
Found at i:31611414 original size:30 final size:28
Alignment explanation
Indices: 31611378--31611433 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
31611368 AAGCGAAAAA
* *
31611378 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
31611408 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
31611434 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:31615691 original size:29 final size:29
Alignment explanation
Indices: 31615658--31615717 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
31615648 ATAACCAAAC
* *
31615658 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
31615687 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
31615716 CT
1 CT
31615718 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:31615710 original size:15 final size:15
Alignment explanation
Indices: 31615664--31615711 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
31615654 AAACCTACAA
*
31615664 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
31615679 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
31615693 AAACTTCATATCCAT
1 AAACTTCATATCCAT
31615708 AAAC
1 AAAC
31615712 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:31621789 original size:30 final size:30
Alignment explanation
Indices: 31621755--31621851 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
31621745 AGCTCACTCC
*
31621755 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
31621785 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
31621815 CAGCTCAACTTTAGCTCACGAGCTAAACCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31621845 TAGCTCA
1 TAGCTCA
31621852 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 48 0.91
31 5 0.09
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31623942 original size:30 final size:30
Alignment explanation
Indices: 31623857--31623953 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31623847 AAACTAAAAA
* *
31623857 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
31623887 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
31623917 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
31623946 ATGAGCTA
1 -TGAGCTA
31623954 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:31626905 original size:24 final size:23
Alignment explanation
Indices: 31626835--31626912 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 23
31626825 AAGATCAATT
31626835 AAAATTGACAGAAAAAGTAGAAGAAAA
1 AAAATTGA-A-AAAAAG-A-AAGAAAA
*
31626862 AAAGAGTGAAAAAGAA-AAAGACAAA
1 AAA-ATTGAAAAA-AAGAAAGA-AAA
*
31626887 AAAATTGAAAAAAAGAAAGGAAA
1 AAAATTGAAAAAAAGAAAGAAAA
31626910 AAA
1 AAA
31626913 TGAGAGAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 8 0.18
24 16 0.36
25 7 0.16
26 3 0.07
27 6 0.14
28 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (23 bp):
AAAATTGAAAAAAAGAAAGAAAA
Found at i:31629904 original size:19 final size:20
Alignment explanation
Indices: 31629867--31629905 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
31629857 AGAGCAGCAA
**
31629867 TAAAGGAGCTGCTGGTGCAT
1 TAAAGGAGCTGCTAATGCAT
31629887 TAAA-GAGCTGCTAATGCAT
1 TAAAGGAGCTGCTAATGCAT
31629906 AGAACAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (20 bp):
TAAAGGAGCTGCTAATGCAT
Found at i:31631986 original size:22 final size:22
Alignment explanation
Indices: 31631958--31632001 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31631948 TTTTGAACCA
31631958 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
31631980 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
31632002 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:31632317 original size:12 final size:12
Alignment explanation
Indices: 31632300--31632333 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
31632290 ATAGGTACGT
31632300 AAAAAAAATTTA
1 AAAAAAAATTTA
*
31632312 AAAAAAATTTTA
1 AAAAAAAATTTA
31632324 AAAAAAAATT
1 AAAAAAAATT
31632334 GCATACGGTT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAAAAATTTA
Found at i:31639751 original size:48 final size:48
Alignment explanation
Indices: 31639696--31639801 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
31639686 TTGTCTTTTC
*
31639696 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31639744 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
31639792 TTTCTTTTTC
1 TTTCTTTTTC
31639802 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:31642433 original size:20 final size:20
Alignment explanation
Indices: 31642410--31642456 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31642400 GGGTTAAGAT
*
31642410 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31642430 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31642450 TGAGCTG
1 TGAGCTG
31642457 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31643058 original size:18 final size:18
Alignment explanation
Indices: 31643020--31643061 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31643010 GCGAAAATAC
* *
31643020 AAAAGAAAAGAAAAATGA
1 AAAAAAAAAGAAAAATCA
*
31643038 AAAAAAAAAGAAAATTCA
1 AAAAAAAAAGAAAAATCA
31643056 AAAAAA
1 AAAAAA
31643062 GAGAATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAGAAAAATCA
Found at i:31645621 original size:20 final size:19
Alignment explanation
Indices: 31645577--31645628 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
31645567 CAAATGAGAG
31645577 AAAAAGAAAAGACGAAAATA
1 AAAAAGAAAAGAC-AAAATA
* *
31645597 CAAAAGAAAAGAAAAATGATAA
1 AAAAAGAAAAGACAAA--AT-A
31645619 AAAAAGAAAA
1 AAAAAGAAAA
31645629 TTCAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 11 0.42
21 2 0.08
22 10 0.38
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (19 bp):
AAAAAGAAAAGACAAAATA
Found at i:31645637 original size:17 final size:17
Alignment explanation
Indices: 31645590--31645643 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
31645580 AAGAAAAGAC
* *
31645590 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* * *
31645607 GAAAAATGATAAAAAAA
1 GAAAATTCAAAAAAAAA
*
31645624 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
31645641 GAA
1 GAA
31645644 TGAAAAGAGA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:31645679 original size:15 final size:15
Alignment explanation
Indices: 31645575--31645684 Score: 53
Period size: 17 Copynumber: 6.9 Consensus size: 15
31645565 ATCAAATGAG
31645575 AGAAAAAG-AAAAGA
1 AGAAAAAGAAAAAGA
* * *
31645589 CGAAAATACAAAAGAAA
1 AGAAAA-AGAAAA-AGA
*
31645606 AGAAAAATGATAAAAAA
1 AGAAAAA-GA-AAAAGA
**
31645623 AGAAAATTCAAAAA-A
1 AGAAAA-AGAAAAAGA
* *
31645638 AGAGAATGAAAAGAGA
1 AGAAAAAGAAAA-AGA
*
31645654 GCGATAAAAGAAAAAGA
1 -AGA-AAAAGAAAAAGA
31645671 AGAAAAAGAAAAAG
1 AGAAAAAGAAAAAG
31645685 TGAGTGAAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
14 10 0.14
15 19 0.26
16 11 0.15
17 23 0.32
18 10 0.14
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (15 bp):
AGAAAAAGAAAAAGA
Found at i:31649932 original size:21 final size:21
Alignment explanation
Indices: 31649883--31649949 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
31649873 CCTCTTTGAA
* * *
31649883 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
31649906 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
31649927 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
31649948 CC
1 CC
31649950 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:31654012 original size:22 final size:22
Alignment explanation
Indices: 31653984--31654027 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31653974 TTTTGAACCA
31653984 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
31654006 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
31654028 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:31658662 original size:14 final size:14
Alignment explanation
Indices: 31658643--31658687 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
31658633 AACTCATCTT
*
31658643 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
31658657 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
31658670 AATTTAATTTAATG
1 AGTTTAATTTAATG
31658684 AGTT
1 AGTT
31658688 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:31663567 original size:13 final size:14
Alignment explanation
Indices: 31663546--31663595 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
31663536 TTGATCGAGA
31663546 AAAAGAAAAAGA-G
1 AAAAGAAAAAGAGG
*
31663559 AAAACAAAAAGAGTG
1 AAAAGAAAAAGAG-G
*
31663574 AAAAGAAAAAGAAAG
1 AAAAGAAAAAG-AGG
31663589 AAAAGAA
1 AAAAGAA
31663596 TGAGGAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 11 0.35
15 19 0.61
16 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAGAGG
Found at i:31669984 original size:18 final size:18
Alignment explanation
Indices: 31669961--31669996 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31669951 GTGAACATCA
31669961 AGCTTGAAAGGTCTCTTG
1 AGCTTGAAAGGTCTCTTG
31669979 AGCTTGAAAGGTCTCTTG
1 AGCTTGAAAGGTCTCTTG
31669997 GATGTGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (18 bp):
AGCTTGAAAGGTCTCTTG
Found at i:31672022 original size:28 final size:27
Alignment explanation
Indices: 31671991--31672074 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
31671981 AACTTCGATC
31671991 ACGTGTGTAGTACTAAGTACAGGCTACT
1 ACGTGTGTAGTACTAAGT-CAGGCTACT
* * *
31672019 ACGTGTATCAG-A-T-GGTTAGG-T-C-
1 ACGTGTGT-AGTACTAAGTCAGGCTACT
31672041 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGT-CAGGCTACT
31672069 ACGTGT
1 ACGTGT
31672075 ACCAGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (27 bp):
ACGTGTGTAGTACTAAGTCAGGCTACT
Found at i:31672064 original size:50 final size:49
Alignment explanation
Indices: 31671888--31672118 Score: 313
Period size: 50 Copynumber: 4.7 Consensus size: 49
31671878 TCTATTGTGA
* *
31671888 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGT-TATCGGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
*
31671936 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTA-CTAGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATAA-TT
* * * **
31671986 CGATCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
* *
31672036 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
*
31672086 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
31672119 TGCGTACCAG
Statistics
Matches: 161, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
48 36 0.22
49 37 0.23
50 48 0.30
51 39 0.24
52 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT
Found at i:31672102 original size:99 final size:99
Alignment explanation
Indices: 31671888--31672118 Score: 340
Period size: 99 Copynumber: 2.3 Consensus size: 99
31671878 TCTATTGTGA
* *
31671888 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTTATCGGATTATTGGTCACATGTGTAGTAC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTTATCAGATGATTGGTCACATGTGTAGTAC
* *
31671953 TAAGTGCAGGCTACTATGTGTACTAGATAACTTC
66 TAAGTGCAGGCTACTACGTGTACCAGATAACTTC
* * * * *
31671987 GATCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGT-TATCAGATGATT-GGTCACATGTGTAGT
31672052 ACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-
64 ACTAAGTGCAGGCTACTACGTGTACCAGATAACTTC
*
31672086 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
31672119 TGCGTACCAG
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
99 62 0.53
100 11 0.09
101 44 0.38
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (99 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTTATCAGATGATTGGTCACATGTGTAGTAC
TAAGTGCAGGCTACTACGTGTACCAGATAACTTC
Found at i:31673389 original size:14 final size:13
Alignment explanation
Indices: 31673365--31673403 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31673355 TTTTGATCTC
31673365 CTTTTTGCTTTTCAT
1 CTTTTT-CTTTTC-T
31673380 CTTTTTCTTTTCT
1 CTTTTTCTTTTCT
*
31673393 CATTTTCTTTT
1 CTTTTTCTTTT
31673404 TACAAGAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 6 0.26
15 6 0.26
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (13 bp):
CTTTTTCTTTTCT
Found at i:31675037 original size:20 final size:20
Alignment explanation
Indices: 31675014--31675060 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31675004 GGGTTAAGAT
*
31675014 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31675034 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31675054 TGAGCTG
1 TGAGCTG
31675061 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31676784 original size:48 final size:48
Alignment explanation
Indices: 31676729--31676834 Score: 139
Period size: 48 Copynumber: 2.2 Consensus size: 48
31676719 TTGTCTTTTC
*
31676729 TTTCTTTTTC-A-TT-TTTCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCGATTTCTTTCTC-TTTT--TCACATCCTTT-TTCAATCTCAA
31676777 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
31676825 TTTCTTTTTC
1 TTTCTTTTTC
31676835 CATGACACTC
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
48 36 0.68
49 5 0.09
50 6 0.11
51 6 0.11
ACGTcount: A:0.13, C:0.25, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:31676831 original size:18 final size:17
Alignment explanation
Indices: 31676810--31676894 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
31676800 TTTTCACATC
31676810 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTC-ATTT
*
31676828 CTTTTTCCATGACACTCATTT
1 CTTTTT-CA--A-TCTCATTT
* * *
31676849 CTTTTACACTCTCGTTT
1 CTTTTTCAATCTCATTT
*
31676866 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCA-TTT
31676885 CTTTTTCAAT
1 CTTTTTCAAT
31676895 TTCTTGTTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
17 10 0.19
18 19 0.37
19 8 0.15
20 2 0.04
21 10 0.19
22 3 0.06
ACGTcount: A:0.18, C:0.28, G:0.02, T:0.52
Consensus pattern (17 bp):
CTTTTTCAATCTCATTT
Found at i:31677877 original size:11 final size:10
Alignment explanation
Indices: 31677860--31677897 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
31677850 AGACTTTTCA
31677860 CTTTTTTTTT
1 CTTTTTTTTT
*
31677870 CTTCTTTTTTA
1 CTT-TTTTTTT
31677881 CTTTTTTTTT
1 CTTTTTTTTT
31677891 CTTTTTT
1 CTTTTTT
31677898 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:31677883 original size:21 final size:20
Alignment explanation
Indices: 31677854--31677914 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
31677844 CTCGCAAGAC
31677854 TTTTCACTTTTTTTTTCTTCT
1 TTTTCACTTTTTTTTTCTT-T
*
31677875 TTTTTACTTTTTTTTTCTTT
1 TTTTCACTTTTTTTTTCTTT
31677895 TTTGCTCACTTCTTTTTTTC
1 TTT--TCACTT-TTTTTTTC
31677915 GAATGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 18 0.51
22 5 0.14
23 8 0.23
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTCACTTTTTTTTTCTTT
Found at i:31681425 original size:14 final size:14
Alignment explanation
Indices: 31681406--31681450 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
31681396 AACTCATCTT
*
31681406 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
31681420 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
31681433 AATTTAATTTAATG
1 AGTTTAATTTAATG
31681447 AGTT
1 AGTT
31681451 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:31685110 original size:18 final size:18
Alignment explanation
Indices: 31685087--31685136 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
31685077 GAAAGACAGA
*
31685087 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
31685105 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
31685123 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
31685137 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:31689569 original size:93 final size:93
Alignment explanation
Indices: 31689463--31689635 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
31689453 CGCCCATAAG
* * * * * *
31689463 CGAACTCGAACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGAGTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCA
31689528 ACGAGCTCGGATGCCTAGTTACACCTCT
66 ACGAGCTCGGATGCCTAGTTACACCTCT
* *
31689556 CGAACTCGAACTCAACTCAACGAGTTCAGACATTTGCATCCATAAATGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCA
*
31689621 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
31689636 CAAATATCCT
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:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACACCTCT
Found at i:31693866 original size:38 final size:38
Alignment explanation
Indices: 31693815--31693891 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
31693805 CCGATCACAC
31693815 TATCGAAGAAATCACATTGGTATAGTTAGACGTTTCGT
1 TATCGAAGAAATCACATTGGTATAGTTAGACGTTTCGT
31693853 TATCGAAGAAATCACATTGGTATAGTTAGACGTTTCGT
1 TATCGAAGAAATCACATTGGTATAGTTAGACGTTTCGT
31693891 T
1 T
31693892 TTGTGTACGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (38 bp):
TATCGAAGAAATCACATTGGTATAGTTAGACGTTTCGT
Found at i:31694171 original size:20 final size:20
Alignment explanation
Indices: 31694125--31694171 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31694115 AGCTCGTTTC
*
31694125 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31694145 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31694165 CAGCTCA
1 CAGCTCA
31694172 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31696681 original size:20 final size:21
Alignment explanation
Indices: 31696634--31696681 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
31696624 ATTTTGTCCA
*
31696634 AATTA-GTTAAGTTGTTATTT
1 AATTATGTTAAGTTGCTATTT
*
31696654 AAGT-TGTT-AGTTGCTATTT
1 AATTATGTTAAGTTGCTATTT
31696673 AATTATGTT
1 AATTATGTT
31696682 TAAATGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (21 bp):
AATTATGTTAAGTTGCTATTT
Found at i:31714207 original size:68 final size:67
Alignment explanation
Indices: 31714135--31714284 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
31714125 CATCATGTGT
* * * *
31714135 ACAAGAGAGCTACAAGACATCATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACAT-AT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
31714197 ATGTAG
62 ATGTAG
** * *
31714203 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
31714268 AG
66 AG
31714270 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
31714285 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 6 0.09
66 5 0.07
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:31714240 original size:64 final size:64
Alignment explanation
Indices: 31714159--31714342 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
31714149 AGACATCATG
* *
31714159 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
31714223 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
31714288 AA
63 AA
* * * *
31714290 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
31714343 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:31717455 original size:20 final size:19
Alignment explanation
Indices: 31717423--31717467 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
31717413 AAATTCTATC
31717423 AAGCTTGAATGAGCTAAATT
1 AAGC-TGAATGAGCTAAATT
* *
31717443 AAGCTGAAGTGAGCTGATTT
1 AAGCTGAA-TGAGCTAAATT
31717463 AAGCT
1 AAGCT
31717468 TCGACGGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (19 bp):
AAGCTGAATGAGCTAAATT
Found at i:31718974 original size:14 final size:14
Alignment explanation
Indices: 31718957--31718996 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31718947 CGAATGGAAT
*
31718957 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
31718971 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
31718985 GATATGAACAAA
1 GGTAGGAACAAA
31718997 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:31720660 original size:22 final size:22
Alignment explanation
Indices: 31720630--31720673 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31720620 TTTGGTATTT
31720630 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31720652 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
31720674 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:31728096 original size:6 final size:6
Alignment explanation
Indices: 31728087--31728206 Score: 71
Period size: 6 Copynumber: 19.2 Consensus size: 6
31728077 GAAAGAGATT
** * * **
31728087 GAAAAA GAAATT GAAAGAA AAAAAAA GAAAAC GAAAAA GAAAAA GAAATT
1 GAAAAA GAAAAA GAAA-AA GAA-AAA GAAAAA GAAAAA GAAAAA GAAAAA
* * ** *
31728137 GCAAAA GAAAAA GAAATCA -AAAAA GTGAAA GAAAAA GAAAAT GAAGAAAA
1 GAAAAA GAAAAA GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA
*
31728187 GAAAATT GAAAAA GAAAAA G
1 GAAAA-A GAAAAA GAAAAA G
31728207 CGAAAAAAGA
Statistics
Matches: 83, Mismatches: 24, Indels: 14
0.69 0.20 0.12
Matches are distributed among these distances:
5 1 0.01
6 63 0.76
7 14 0.17
8 5 0.06
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:31728124 original size:7 final size:6
Alignment explanation
Indices: 31728100--31728206 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
31728090 AAAGAAATTG
* ** *
31728100 AAAG-A AAA-AA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * *
31728146 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
31728197 AAAGAA AAAG
1 AAAGAA AAAG
31728207 CGAAAAAAGA
Statistics
Matches: 77, Mismatches: 18, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
5 8 0.10
6 57 0.74
7 8 0.10
8 4 0.05
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:31728186 original size:14 final size:13
Alignment explanation
Indices: 31728167--31728204 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31728157 AAAAGTGAAA
31728167 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31728179 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31728194 GAAAAAGAAAA
1 GAAAAAGAAAA
31728205 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:31728241 original size:12 final size:12
Alignment explanation
Indices: 31728210--31728241 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31728200 GAAAAAGCGA
*
31728210 AAAAAGAATTTG
1 AAAAAGAGTTTG
31728222 AAAAAGAGTTTG
1 AAAAAGAGTTTG
31728234 AAAAAGAG
1 AAAAAGAG
31728242 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:31732935 original size:23 final size:22
Alignment explanation
Indices: 31732883--31732935 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31732873 TCCACGTCTT
*
31732883 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
31732905 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
31732928 TTTCTTTT
1 TTTCTTTT
31732936 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:31735289 original size:4 final size:4
Alignment explanation
Indices: 31735280--31735310 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
31735270 TTAAACTAAG
31735280 TAAA TAAA TAAA TAAA TAAA TAAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
31735311 AATAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:31742146 original size:18 final size:18
Alignment explanation
Indices: 31742125--31742159 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31742115 TTTTTCTTTT
31742125 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
31742143 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
31742160 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:31743646 original size:20 final size:20
Alignment explanation
Indices: 31743623--31743669 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
31743613 GGGTTAAGAT
31743623 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
* *
31743643 TGAGTTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
31743663 TGAGCTG
1 TGAGCTG
31743670 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTTGAG
Found at i:31745390 original size:48 final size:48
Alignment explanation
Indices: 31745335--31745440 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
31745325 TTGTCTTTTC
*
31745335 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31745383 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
31745431 TTTCTTTTTC
1 TTTCTTTTTC
31745441 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:31746609 original size:31 final size:31
Alignment explanation
Indices: 31746550--31746609 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
31746540 TTAAACTTGA
* *
31746550 TTTTTTTTGCTCACCTTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCACATTTTTTTTACTTTTCT
31746581 TTTTTTTTGCTCA-ATTTTTTTTCACTTTT
1 TTTTTTTTGCTCACATTTTTTTT-ACTTTT
31746610 TTTGAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (31 bp):
TTTTTTTTGCTCACATTTTTTTTACTTTTCT
Found at i:31746617 original size:21 final size:22
Alignment explanation
Indices: 31746593--31746635 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31746583 TTTTTTGCTC
31746593 AATTT-TTTTTCACTTTTTTTG
1 AATTTATTTTTCACTTTTTTTG
* *
31746614 AATTTATTTTTGATTTTTTTTG
1 AATTTATTTTTCACTTTTTTTG
31746636 TTACTCCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (22 bp):
AATTTATTTTTCACTTTTTTTG
Found at i:31747488 original size:18 final size:18
Alignment explanation
Indices: 31747424--31747477 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
31747414 CTTCATTTTC
31747424 TCTCA-TTTCTTTTTCAA
1 TCTCATTTTCTTTTTCAA
*
31747441 -CATCTTTTTCTTTTTCAA
1 TC-TCATTTTCTTTTTCAA
*
31747459 TCTCAATTTCTTTTTCAA
1 TCTCATTTTCTTTTTCAA
31747477 T
1 T
31747478 TTTCTTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 2 0.06
18 27 0.87
19 1 0.03
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (18 bp):
TCTCATTTTCTTTTTCAA
Found at i:31748937 original size:20 final size:20
Alignment explanation
Indices: 31748914--31748955 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31748904 GGGTTAAGAT
*
31748914 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31748934 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31748954 TG
1 TG
31748956 CACTGGAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.36, T:0.31
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31752906 original size:14 final size:14
Alignment explanation
Indices: 31752889--31752928 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31752879 CGAATGGAAT
*
31752889 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
31752903 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
31752917 GATATGAACAAA
1 GGTAGGAACAAA
31752929 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:31760460 original size:30 final size:30
Alignment explanation
Indices: 31760375--31760471 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31760365 TAAACTAAAA
* *
31760375 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
31760405 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
31760435 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
31760464 ATGAGCTA
1 -TGAGCTA
31760472 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:31762754 original size:30 final size:30
Alignment explanation
Indices: 31762684--31762765 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
31762674 TTTTGTTTCA
* *
31762684 ATTTCTTTTTCATCTTCTTTTTCACTCTCAG
1 ATTTCTTTTTCTTC-TCTTTTTCAATCTCAG
31762715 ATTTC-TTTTCGTTCTCTTTTTCAATCTCA-
1 ATTTCTTTTTC-TTCTCTTTTTCAATCTCAG
* *
31762744 TTTTCTTTTTCTTTTTCTTTTT
1 ATTTCTTTTTC-TTCTCTTTTT
31762766 GATTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 33 0.75
31 7 0.16
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.66
Consensus pattern (30 bp):
ATTTCTTTTTCTTCTCTTTTTCAATCTCAG
Found at i:31762783 original size:12 final size:12
Alignment explanation
Indices: 31762768--31762798 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31762758 TTCTTTTTGA
31762768 TTTTCAAAGGAT
1 TTTTCAAAGGAT
*
31762780 TTTTCAAAGGCT
1 TTTTCAAAGGAT
31762792 TTTTCAA
1 TTTTCAA
31762799 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGAT
Found at i:31762856 original size:5 final size:5
Alignment explanation
Indices: 31762846--31762907 Score: 65
Period size: 5 Copynumber: 12.0 Consensus size: 5
31762836 CTCTTGCCTC
*
31762846 TCTTT TCTTT T-TATT TCTTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
31762893 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
31762908 GTTTTCTCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 34 0.69
6 6 0.12
7 5 0.10
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:31762866 original size:15 final size:14
Alignment explanation
Indices: 31762846--31762914 Score: 66
Period size: 16 Copynumber: 4.6 Consensus size: 14
31762836 CTCTTGCCTC
31762846 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
31762861 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
31762876 TCTTTTGCTTTTTCTTT
1 TCTTTT-C-TTTT-TTT
*
31762893 TCTTTTCTTTTCTT
1 TCTTTTCTTTTTTT
*
31762907 TGTTTTCT
1 TCTTTTCT
31762915 CTTTCCAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
14 13 0.28
15 10 0.22
16 15 0.33
17 8 0.17
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.78
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:31762919 original size:15 final size:14
Alignment explanation
Indices: 31762848--31762919 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 14
31762838 CTTGCCTCTC
*
31762848 TTTTCTTTTTATTTCT
1 TTTTCTTTTT-CTT-T
31762864 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTT-T
*
31762879 TTTGCTTTTTCTTT
1 TTTTCTTTTTCTTT
31762893 TCTTT-TCTTTTCTTT
1 T-TTTCT-TTTTCTTT
*
31762908 GTTTTCTCTTTC
1 -TTTTCTTTTTC
31762920 CAAGAATGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
14 3 0.06
15 33 0.69
16 12 0.25
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Done.