Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 135 of 185
Found at i:41375862 original size:59 final size:59
Alignment explanation
Indices: 41375770--41375887 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
41375760 TCTAACCCTC
41375770 AGATATGGGCTTCGTACCACTCGAAGCTACTCCTTAAACGGAGGCTTGAGCGTTACTCT
1 AGATATGGGCTTCGTACCACTCGAAGCTACTCCTTAAACGGAGGCTTGAGCGTTACTCT
41375829 AGATATGGGCTTCGTACCACTCGAAGCTACTCCTTAAACGGAGGCTTGAGCGTTACTCT
1 AGATATGGGCTTCGTACCACTCGAAGCTACTCCTTAAACGGAGGCTTGAGCGTTACTCT
41375888 CTACTTTATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (59 bp):
AGATATGGGCTTCGTACCACTCGAAGCTACTCCTTAAACGGAGGCTTGAGCGTTACTCT
Found at i:41379740 original size:19 final size:19
Alignment explanation
Indices: 41379716--41379753 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41379706 TAATTAAATG
41379716 AATAAAATAATTTTATTTT
1 AATAAAATAATTTTATTTT
41379735 AATAAAATAATTTTATTTT
1 AATAAAATAATTTTATTTT
41379754 CATCATCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATAAAATAATTTTATTTT
Found at i:41380253 original size:21 final size:21
Alignment explanation
Indices: 41380228--41380269 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41380218 CTTTTGCCTA
*
41380228 AAATATGAATTGGATTGAATT
1 AAATATGAATTGGATTAAATT
*
41380249 AAATATGAATTGTATTAAATT
1 AAATATGAATTGGATTAAATT
41380270 GAGTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.40
Consensus pattern (21 bp):
AAATATGAATTGGATTAAATT
Found at i:41386015 original size:25 final size:25
Alignment explanation
Indices: 41385966--41386078 Score: 97
Period size: 25 Copynumber: 4.6 Consensus size: 25
41385956 TATCATATAT
41385966 GCTCATACGAGC--AATAAACGGGAA
1 GCTCATACGAGCTGAAT-AACGGGAA
* *
41385990 GCTCCTCCGAGCTGAATAACGGGAA
1 GCTCATACGAGCTGAATAACGGGAA
** *
41386015 GCTCATGTGAGCTAAATAACAGGG-A
1 GCTCATACGAGCTGAATAAC-GGGAA
* **
41386040 GCTCATACGAGCTGAGTATTGGGAA
1 GCTCATACGAGCTGAATAACGGGAA
* *
41386065 GTTCATAAGAGCTG
1 GCTCATACGAGCTG
41386079 TGGTGTGTCC
Statistics
Matches: 71, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
24 13 0.18
25 52 0.73
26 6 0.08
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGGAA
Found at i:41389044 original size:19 final size:22
Alignment explanation
Indices: 41389020--41389066 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
41389010 AAAAATATCT
41389020 TTATT-AAAT-TAAT-TAAAAA
1 TTATTAAAATATAATATAAAAA
41389039 TTATTAAAATATAATATAAAAA
1 TTATTAAAATATAATATAAAAA
41389061 TCTATT
1 T-TATT
41389067 TTCATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 4 0.17
22 7 0.29
23 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTAAAATATAATATAAAAA
Found at i:41396800 original size:34 final size:34
Alignment explanation
Indices: 41396752--41396826 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
41396742 GGGATGATAC
*
41396752 TCTATCGTGTAGTTATAATCTTTAAGCAGCTCAA
1 TCTATCGTGCAGTTATAATCTTTAAGCAGCTCAA
41396786 TCTATCGTGCAGTTATAATCTTTAAGCAGCTCAA
1 TCTATCGTGCAGTTATAATCTTTAAGCAGCTCAA
41396820 TCTATCG
1 TCTATCG
41396827 ACGCTGCCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (34 bp):
TCTATCGTGCAGTTATAATCTTTAAGCAGCTCAA
Found at i:41402625 original size:23 final size:23
Alignment explanation
Indices: 41402586--41402629 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
41402576 TGATTATGTC
41402586 AATGCAGTATTTTCAGAAAACAA
1 AATGCAGTATTTTCAGAAAACAA
41402609 AATGCAG-ATTTTGCAGAAAAC
1 AATGCAGTATTTT-CAGAAAAC
41402630 TTCCTACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (23 bp):
AATGCAGTATTTTCAGAAAACAA
Found at i:41411670 original size:21 final size:22
Alignment explanation
Indices: 41411622--41411671 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
41411612 ATTTCTAAAG
*
41411622 TTTTTAATATATATTTTTTATT
1 TTTTTAATATATATTTTTTATA
41411644 TATTTTAA-A-ATATTTTTTATGA
1 T-TTTTAATATATATTTTTTAT-A
41411666 TTTTTA
1 TTTTTA
41411672 TAAACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 16 0.64
22 3 0.12
23 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTAATATATATTTTTTATA
Found at i:41411820 original size:18 final size:18
Alignment explanation
Indices: 41411797--41411835 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
41411787 TAGAGTGAAC
41411797 TTTTTTT-CTATAGG-TTT
1 TTTTTTTCCTA-AGGATTT
41411814 TTTTTTTCCTAAGGATTT
1 TTTTTTTCCTAAGGATTT
41411832 TTTT
1 TTTT
41411836 ACCCTTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.13, C:0.08, G:0.10, T:0.69
Consensus pattern (18 bp):
TTTTTTTCCTAAGGATTT
Found at i:41415331 original size:17 final size:17
Alignment explanation
Indices: 41415311--41415345 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41415301 AAGTTTAGAG
41415311 AAAATAAACAA-AAATAA
1 AAAATAAA-AATAAATAA
41415328 AAAATAAAAATAAATAA
1 AAAATAAAAATAAATAA
41415345 A
1 A
41415346 GGGTAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAATAAAAATAAATAA
Found at i:41421693 original size:7 final size:6
Alignment explanation
Indices: 41421653--41421722 Score: 50
Period size: 6 Copynumber: 10.5 Consensus size: 6
41421643 TATTTTTCGA
*
41421653 AATTTT AATTTT AATTTT AATTTTT ATGAGTTT AATTTTT AAAATTTT
1 AATTTT AATTTT AATTTT AA-TTTT A--ATTTT AA-TTTT --AATTTT
* *
41421701 AAATTT AAATTT AATTATT AAT
1 AATTTT AATTTT AATT-TT AAT
41421723 GCTGTTAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
6 29 0.55
7 13 0.25
8 8 0.15
9 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (6 bp):
AATTTT
Found at i:41421701 original size:15 final size:15
Alignment explanation
Indices: 41421652--41421702 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
41421642 ATATTTTTCG
41421652 AAATTTTAA-TTTT-
1 AAATTTTAATTTTTA
41421665 -AATTTTAATTTTTA
1 AAATTTTAATTTTTA
** *
41421679 TGAGTTTAATTTTTA
1 AAATTTTAATTTTTA
41421694 AAATTTTAA
1 AAATTTTAA
41421703 ATTTAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.27
13 4 0.13
15 18 0.60
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
AAATTTTAATTTTTA
Found at i:41422861 original size:17 final size:17
Alignment explanation
Indices: 41422839--41422940 Score: 64
Period size: 17 Copynumber: 5.7 Consensus size: 17
41422829 TATTTTTCTC
* *
41422839 ATTAAAATTATAGAATT
1 ATTAAAAATATAAAATT
41422856 ATTAAAAATATAAAATT
1 ATTAAAAATATAAAATT
* **
41422873 AATATGAACTTATAAAAATT
1 -AT-TAAAAATAT-AAAATT
*
41422893 ATTAAAAAATTATAAAAAT
1 ATT-AAAAA-TATAAAATT
*
41422912 -TTAAAAAGATAATAAATT
1 ATTAAAAATAT-A-AAATT
41422930 A-TAAAAATATA
1 ATTAAAAATATA
41422941 TACATTTAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
16 2 0.03
17 22 0.34
18 17 0.26
19 15 0.23
20 9 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (17 bp):
ATTAAAAATATAAAATT
Found at i:41422892 original size:20 final size:20
Alignment explanation
Indices: 41422842--41422912 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 20
41422832 TTTTCTCATT
* *
41422842 AAAATTAT-AGAATT-ATTA
1 AAAATTATAAAAATTAATAA
*
41422860 AAAA-TAT-AAAATTAATAT
1 AAAATTATAAAAATTAATAA
* * *
41422878 GAACTTATAAAAATTATTAA
1 AAAATTATAAAAATTAATAA
41422898 AAAATTATAAAAATT
1 AAAATTATAAAAATT
41422913 TAAAAAGATA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
17 8 0.20
18 8 0.20
19 3 0.07
20 22 0.54
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAATTATAAAAATTAATAA
Found at i:41422909 original size:9 final size:9
Alignment explanation
Indices: 41422842--41423035 Score: 86
Period size: 9 Copynumber: 21.3 Consensus size: 9
41422832 TTTTCTCATT
41422842 AAAATTAT-
1 AAAATTATA
*
41422850 AGAATTATTA
1 AAAATTA-TA
41422860 AAAA-TAT-
1 AAAATTATA
41422867 AAAATTAATA
1 AAAATT-ATA
* *
41422877 TGAACTTATA
1 -AAAATTATA
41422887 AAAATTATTAA
1 AAAATTA-T-A
41422898 AAAATTATA
1 AAAATTATA
41422907 AAAATT-TA
1 AAAATTATA
*
41422915 AAAA-GATA
1 AAAATTATA
41422923 ATAAATTATA
1 A-AAATTATA
41422933 AAAA-TATA
1 AAAATTATA
* *
41422941 TACATTTAATA
1 -AAAATT-ATA
* *
41422952 AATATTTTTA
1 AA-AATTATA
41422962 AAATATT-TA
1 AAA-ATTATA
*
41422971 AAATTTTATA
1 AAA-ATTATA
*
41422981 AAAAATATA
1 AAAATTATA
41422990 AAAACTTATA
1 AAAA-TTATA
41423000 AATAA-TAT-
1 AA-AATTATA
41423008 -AAATT-TA
1 AAAATTATA
**
41423015 AAAAAAATA
1 AAAATTATA
41423024 AAAATTATA
1 AAAATTATA
41423033 AAA
1 AAA
41423036 GGAAAGTCAT
Statistics
Matches: 142, Mismatches: 21, Indels: 45
0.68 0.10 0.22
Matches are distributed among these distances:
6 3 0.02
7 6 0.04
8 24 0.17
9 57 0.40
10 31 0.22
11 21 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:41422950 original size:26 final size:26
Alignment explanation
Indices: 41422894--41422954 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
41422884 ATAAAAATTA
* *
41422894 TTAAAAAATTATAAAAATTTAAAAAG
1 TTAATAAATTATAAAAATATAAAAAG
* * * *
41422920 ATAATAAATTATAAAAATATATACAT
1 TTAATAAATTATAAAAATATAAAAAG
41422946 TTAATAAAT
1 TTAATAAAT
41422955 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TTAATAAATTATAAAAATATAAAAAG
Found at i:41422991 original size:19 final size:19
Alignment explanation
Indices: 41422949--41423029 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
41422939 TATACATTTA
*
41422949 ATAAATATTTT-TAAAATAT
1 ATAAA-ATTTTATAAAAAAT
*
41422968 TTAAAATTTTATAAAAAAT
1 ATAAAATTTTATAAAAAAT
** *
41422987 ATAAAAACTTATAAATAAT
1 ATAAAATTTTATAAAAAAT
*
41423006 AT-AAA-TTTAAAAAAAAT
1 ATAAAATTTTATAAAAAAT
41423023 A-AAAATT
1 ATAAAATT
41423030 ATAAAAGGAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
17 13 0.26
18 9 0.18
19 28 0.56
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAATTTTATAAAAAAT
Found at i:41423028 original size:17 final size:17
Alignment explanation
Indices: 41422969--41423035 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
41422959 TTAAAATATT
*
41422969 TAAAATTTTATAAAAAATA
1 TAAAAATTTA-AAAAAA-A
* * *
41422988 TAAAAACTTATAAATAA
1 TAAAAATTTAAAAAAAA
*
41423005 TATAAATTTAAAAAAAA
1 TAAAAATTTAAAAAAAA
41423022 TAAAAATTATAAAA
1 TAAAAATT-TAAAA
41423036 GGAAAGTCAT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 21 0.55
18 9 0.24
19 8 0.21
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATTTAAAAAAAA
Found at i:41423520 original size:58 final size:55
Alignment explanation
Indices: 41423422--41423556 Score: 135
Period size: 58 Copynumber: 2.4 Consensus size: 55
41423412 AGGAAGAAAC
* * * * ** **
41423422 AAATGAATTTTTATAATTTATTAACTGGTTTTGAATTTTTTATTAGTTTTATAATTAT
1 AAATAAATTTTTATAATTT-TTAAATAGTTTTGAAGTTTTTACCACATTTAT-ATT-T
* *
41423480 AGATAAATTTTTATAATTTTTAAATATTTTTAGAAGTTTTTACCACATTTATATTT
1 AAATAAATTTTTATAATTTTTAAATAGTTTT-GAAGTTTTTACCACATTTATATTT
41423536 AAATAAATTTTTTATAATTTT
1 AAATAAA-TTTTTATAATTTT
41423557 CATAAATTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
56 7 0.11
57 25 0.39
58 32 0.50
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (55 bp):
AAATAAATTTTTATAATTTTTAAATAGTTTTGAAGTTTTTACCACATTTATATTT
Found at i:41423549 original size:19 final size:20
Alignment explanation
Indices: 41423527--41423565 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41423517 TTTTACCACA
41423527 TTTAT-ATTTAAATAAATTT
1 TTTATAATTTAAATAAATTT
**
41423546 TTTATAATTTTCATAAATTT
1 TTTATAATTTAAATAAATTT
41423566 ATAGAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAATTTAAATAAATTT
Found at i:41428321 original size:21 final size:21
Alignment explanation
Indices: 41428297--41428511 Score: 177
Period size: 21 Copynumber: 10.3 Consensus size: 21
41428287 ATGCTTTACT
*
41428297 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
41428318 TTCTGTTTAACTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
41428339 TTCCGTTTAGCTCTT-TCGAGC
1 TTCTGTTCAGCTCTTAT-GAGC
* * * *
41428360 TTCTATTCAACTCATATGAGT
1 TTCTGTTCAGCTCTTATGAGC
*
41428381 TTCTATTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
41428402 TTCTGTTCA-ATCCTTATGGGT
1 TTCTGTTCAGCT-CTTATGAGC
* *
41428423 TTCTGTTTAGCTCTTATAAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * * *
41428444 TTTTGTTTAGTTCTCATAAGC
1 TTCTGTTCAGCTCTTATGAGC
*
41428465 TTCTGTTCAGCTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
*
41428486 TTCTGTTCAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTATGAGC
41428505 TTCTGTT
1 TTCTGTT
41428512 AATGATGTAC
Statistics
Matches: 154, Mismatches: 36, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
19 10 0.06
20 4 0.03
21 138 0.90
22 2 0.01
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:41428445 original size:84 final size:83
Alignment explanation
Indices: 41428296--41428494 Score: 224
Period size: 84 Copynumber: 2.4 Consensus size: 83
41428286 CATGCTTTAC
* * *
41428296 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACTCTTATGAGTTTCCGTTTAGCTCTTTCGAGCT
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAGTTTCCGTTTAGCTCTTTCAAGCT
41428361 TCTATTCA-ACTCATATGAG
66 TCTATTCAGACTCATA--AG
* * *
41428380 TTTCTATTCAGCTCTTATGAGCTTCTGTTCAA-TCCTTATGGGTTTCTGTTTAGCTCTTAT-AAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACT-CTTATGAGTTTCCGTTTAGCTCTT-TCAAG
* * * *
41428443 CTTTTGTTTAGTTCTCATAAG
64 CTTCTATTCAG-ACTCATAAG
* *
41428464 CTTCTGTTCAGCTCTTATGAGTTTCTGTTCA
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCA
41428495 GCTTTCGAGC
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
83 1 0.01
84 90 0.92
85 1 0.01
86 6 0.06
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.47
Consensus pattern (83 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAGTTTCCGTTTAGCTCTTTCAAGCT
TCTATTCAGACTCATAAG
Found at i:41429016 original size:25 final size:26
Alignment explanation
Indices: 41428963--41429022 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
41428953 TTATGTTTGC
*
41428963 ATGCAT-TAGCTTATGGCTATGGTGGT
1 ATGCATAT-GCTTATGACTATGGTGGT
*
41428989 ATG-ATATGCTTATGACT-TGTGTGTT
1 ATGCATATGCTTATGACTATG-GTGGT
41429014 ATGCATATG
1 ATGCATATG
41429023 GAATGACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 2 0.07
25 18 0.62
26 9 0.31
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.42
Consensus pattern (26 bp):
ATGCATATGCTTATGACTATGGTGGT
Found at i:41430910 original size:21 final size:21
Alignment explanation
Indices: 41430885--41430927 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41430875 CAAATTTGAC
* *
41430885 TCAATTTAATACAATTTATAT
1 TCAATTCAATACAATTCATAT
*
41430906 TCAATTCAATCCAATTCATAT
1 TCAATTCAATACAATTCATAT
41430927 T
1 T
41430928 TTAGGCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (21 bp):
TCAATTCAATACAATTCATAT
Found at i:41441399 original size:77 final size:77
Alignment explanation
Indices: 41441267--41441452 Score: 212
Period size: 77 Copynumber: 2.4 Consensus size: 77
41441257 ATTAGTTAAT
* * * * * *
41441267 ACATGAAAAGTTTTCTAAAAAATTAAATAATTCGTAAATCACAAAACAATTACTTAATACATGAA
1 ACATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCACAAAACAATCACTTAATACATGAA
41441332 ATGTTACATAAA
66 ATGTTACATAAA
* *** *
41441344 ATATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCATGGAAGAATCACTTAATACATGAA
1 ACATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCACAAAACAATCACTTAATACATGAA
* ** *
41441409 ATTTTATTTGAA
66 ATGTTACATAAA
*
41441421 ACATGACATGGTTT-TTAAGAAATTAAGTAATT
1 ACATGAAATGGTTTCTTAA-AAATTAAGTAATT
41441453 TTTTAATCAT
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
76 4 0.04
77 87 0.96
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (77 bp):
ACATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCACAAAACAATCACTTAATACATGAA
ATGTTACATAAA
Found at i:41441461 original size:77 final size:76
Alignment explanation
Indices: 41441267--41441476 Score: 206
Period size: 77 Copynumber: 2.7 Consensus size: 76
41441257 ATTAGTTAAT
* * * * * ** * *
41441267 ACATGAAAAGTTTTCTAAAAAATTAAATAATTCGTAAATCACAAAACAATTACTTAATACATGAA
1 ACATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCA-TGAAGAATCACTTAATACATGAA
41441332 ATGTTACATAAA
65 ATGTTACATAAA
*
41441344 ATATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCATGGAAGAATCACTTAATACATGAA
1 ACATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCAT-GAAGAATCACTTAATACATGAA
* ** *
41441409 ATTTTATTTGAA
65 ATGTTACATAAA
* ** * * *
41441421 ACATGACATGGTTT-TTAAGAAATTAAGTAATTTTTTAATCATGAATAATTACTTAA
1 ACATGAAATGGTTTCTTAA-AAATTAAGTAATTCATAAATCATGAAGAATCACTTAA
41441477 AAGCAGACTT
Statistics
Matches: 110, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
76 16 0.15
77 94 0.85
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (76 bp):
ACATGAAATGGTTTCTTAAAAATTAAGTAATTCATAAATCATGAAGAATCACTTAATACATGAAA
TGTTACATAAA
Found at i:41453865 original size:28 final size:28
Alignment explanation
Indices: 41453805--41453865 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
41453795 CTTTTAGTTG
* * **
41453805 TTATAATAGTAATTTTAGTCCTTTCTGT
1 TTATAACAATAATTTTAGTCCTTAATGT
* *
41453833 CTATAACAATAATTTTAGTCCTTAATTT
1 TTATAACAATAATTTTAGTCCTTAATGT
41453861 TTATA
1 TTATA
41453866 CTTTCTATCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (28 bp):
TTATAACAATAATTTTAGTCCTTAATGT
Found at i:41460009 original size:2 final size:2
Alignment explanation
Indices: 41460002--41460028 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41459992 CTTCTTCCTC
41460002 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
41460029 CATTCAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:41465192 original size:10 final size:10
Alignment explanation
Indices: 41465177--41465207 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
41465167 TTAAAACTTG
41465177 ACTATTTGAA
1 ACTATTTGAA
41465187 ACTATTTG-A
1 ACTATTTGAA
41465196 ACTATTTGAA
1 ACTATTTGAA
41465206 AC
1 AC
41465208 ACCCCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (10 bp):
ACTATTTGAA
Found at i:41472051 original size:24 final size:24
Alignment explanation
Indices: 41472024--41472075 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41472014 TTAGTAAGTC
*
41472024 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
41472048 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
41472072 AAAT
1 AAAT
41472076 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:41474021 original size:24 final size:24
Alignment explanation
Indices: 41473994--41474045 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41473984 TTAGTAAGTC
*
41473994 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
41474018 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
41474042 AAAT
1 AAAT
41474046 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:41477050 original size:21 final size:21
Alignment explanation
Indices: 41477026--41477066 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41477016 AAAAAAAACC
41477026 AACAACAAAACAGTAAAAAAT
1 AACAACAAAACAGTAAAAAAT
* *
41477047 AACAAGAAAATAGTAAAAAA
1 AACAACAAAACAGTAAAAAA
41477067 AAAAGGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (21 bp):
AACAACAAAACAGTAAAAAAT
Found at i:41478376 original size:21 final size:20
Alignment explanation
Indices: 41478352--41478405 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
41478342 AAAAATTACA
41478352 AAATAATTCAAAATAATTTTC
1 AAAT-ATTCAAAATAATTTTC
* *
41478373 AAATATTTAAAATAATTTTT
1 AAATATTCAAAATAATTTTC
*
41478393 AAA-ATTCTAAATA
1 AAATATTCAAAATA
41478406 TTTATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATATTCAAAATAATTTTC
Found at i:41478403 original size:20 final size:20
Alignment explanation
Indices: 41478356--41478422 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
41478346 ATTACAAAAT
41478356 AATTC-AAAATAATTTTCAAA
1 AATTCTAAAATAATTTT-AAA
* *
41478376 TATT-TAAAATAATTTTTAA
1 AATTCTAAAATAATTTTAAA
41478395 AATTCT-AAAT-ATTTATAAA
1 AATTCTAAAATAATTT-TAAA
41478414 AATTCTAAA
1 AATTCTAAA
41478423 TTTTACATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.10
19 18 0.46
20 17 0.44
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTCTAAAATAATTTTAAA
Found at i:41482246 original size:2 final size:2
Alignment explanation
Indices: 41482239--41482276 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
41482229 ATAACAACAG
41482239 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41482277 TTTCTTAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:41482848 original size:16 final size:16
Alignment explanation
Indices: 41482795--41482851 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
41482785 TGGGAGCAGA
* * *
41482795 GTGGCGAGCAAGCAGA
1 GTGGCGAGCTAGCGGG
* * *
41482811 GTGGCAAACTAGTGGG
1 GTGGCGAGCTAGCGGG
41482827 GTGGCGAGCTAGCGGG
1 GTGGCGAGCTAGCGGG
41482843 GTGGCGAGC
1 GTGGCGAGC
41482852 CGAATGACAT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.21, C:0.18, G:0.49, T:0.12
Consensus pattern (16 bp):
GTGGCGAGCTAGCGGG
Found at i:41499826 original size:18 final size:17
Alignment explanation
Indices: 41499800--41499838 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
41499790 ATTTTCCTTC
41499800 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
41499817 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
41499835 CACA
1 CACA
41499839 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:41504342 original size:15 final size:15
Alignment explanation
Indices: 41504317--41504351 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41504307 AACTCTATTT
*
41504317 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
41504331 TAATTAATATTAAGA
1 TAATTAATATTAAGA
41504346 TAATTA
1 TAATTA
41504352 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:41507259 original size:26 final size:25
Alignment explanation
Indices: 41507225--41507277 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
41507215 AATCAAAAGT
*
41507225 TCACAAAGAACTTTTAATCAGGAAGC
1 TCACAAAGAACCTTTAATCAGG-AGC
* *
41507251 TCACGAAGAGCCTTTAATCAGGAGC
1 TCACAAAGAACCTTTAATCAGGAGC
41507276 TC
1 TC
41507278 CGGATAGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (25 bp):
TCACAAAGAACCTTTAATCAGGAGC
Found at i:41509992 original size:22 final size:22
Alignment explanation
Indices: 41509951--41509992 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41509941 TTCATCTCAT
*
41509951 TAAGCTTTAGTGACACAACACC
1 TAAGCTTTAGTGACAAAACACC
* *
41509973 TAAGCTTTGGTGTCAAAACA
1 TAAGCTTTAGTGACAAAACA
41509993 TCCTCGGTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (22 bp):
TAAGCTTTAGTGACAAAACACC
Found at i:41514476 original size:18 final size:18
Alignment explanation
Indices: 41514445--41514482 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41514435 AAAAAATCAC
*
41514445 ATTTTTTATATTTAATAT
1 ATTTTTTATATTTAAAAT
41514463 ATTTTTTA-ATTTTAAAAT
1 ATTTTTTATA-TTTAAAAT
41514481 AT
1 AT
41514483 ATTGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTATATTTAAAAT
Found at i:41515854 original size:30 final size:31
Alignment explanation
Indices: 41515812--41515872 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
41515802 GGGTTGGGAG
* *
41515812 GGGAAGGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
41515843 GGGAA-GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
41515873 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:41515938 original size:9 final size:9
Alignment explanation
Indices: 41515921--41515957 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41515911 TATAGTTTGA
*
41515921 TATTTGAAT
1 TATTCGAAT
41515930 TATTCGAAT
1 TATTCGAAT
*
41515939 TATTCGAGT
1 TATTCGAAT
41515948 TATTCGAAT
1 TATTCGAAT
41515957 T
1 T
41515958 CGAAAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41521828 original size:41 final size:41
Alignment explanation
Indices: 41521771--41521853 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
41521761 TTCTATGCTC
41521771 ACATTTGGGATTTAGGTTTTATATTTTAATTTGATTTTCTG
1 ACATTTGGGATTTAGGTTTTATATTTTAATTTGATTTTCTG
41521812 ACATTTGGGATTTAGGTTTTATATTTTAATTTGATTTTCTG
1 ACATTTGGGATTTAGGTTTTATATTTTAATTTGATTTTCTG
41521853 A
1 A
41521854 TTTTATAACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.23, C:0.05, G:0.17, T:0.55
Consensus pattern (41 bp):
ACATTTGGGATTTAGGTTTTATATTTTAATTTGATTTTCTG
Found at i:41526010 original size:7 final size:7
Alignment explanation
Indices: 41525984--41526030 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
41525974 TTGCTATTAG
41525984 TATTTA-
1 TATTTAT
*
41525990 TATTCTAA
1 TATT-TAT
41525998 TATTTAT
1 TATTTAT
41526005 TATTTAT
1 TATTTAT
41526012 TATTTAT
1 TATTTAT
41526019 TATTTAT
1 TATTTAT
*
41526026 CATTT
1 TATTT
41526031 TAAATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 4 0.11
7 29 0.78
8 4 0.11
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (7 bp):
TATTTAT
Found at i:41530722 original size:21 final size:22
Alignment explanation
Indices: 41530696--41530742 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
41530686 CTCTGCTCAA
*
41530696 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
41530717 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
41530739 ACTC
1 ACTC
41530743 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:41537344 original size:18 final size:18
Alignment explanation
Indices: 41537321--41537358 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41537311 TTCAATTAAG
*
41537321 TCTTTCATT-AAGTGTTTT
1 TCTTTC-TTCAAGTATTTT
41537339 TCTTTCTTCAAGTATTTT
1 TCTTTCTTCAAGTATTTT
41537357 TC
1 TC
41537359 ATCTAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTTTCTTCAAGTATTTT
Found at i:41537406 original size:12 final size:12
Alignment explanation
Indices: 41537346--41537476 Score: 64
Period size: 12 Copynumber: 10.2 Consensus size: 12
41537336 TTTTCTTTCT
41537346 TCAAGTATTTTTCA
1 TCAAGT-TTTTT-A
*
41537360 TCTAGTTCTTTTA
1 TCAAGTT-TTTTA
41537373 TCAAGTTTTTAATTA
1 TCAAG-TTTT--TTA
*
41537388 CCAAGTTTTTTA
1 TCAAGTTTTTTA
**
41537400 TCAAGTTTTGCA
1 TCAAGTTTTTTA
* *
41537412 GCAAGTTCTTTTT
1 TCAAGTT-TTTTA
* *
41537425 TAAAGTTTTTCA
1 TCAAGTTTTTTA
*
41537437 TCAAGTCTTTTCA
1 TCAAGT-TTTTTA
* * **
41537450 TAAAATTTTCCA
1 TCAAGTTTTTTA
*
41537462 TCAAGTTTTTAA
1 TCAAGTTTTTTA
41537474 TCA
1 TCA
41537477 TTTCGTTTTT
Statistics
Matches: 89, Mismatches: 22, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
12 42 0.47
13 25 0.28
14 15 0.17
15 7 0.08
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
TCAAGTTTTTTA
Found at i:41537430 original size:25 final size:25
Alignment explanation
Indices: 41537389--41537468 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
41537379 TTTTAATTAC
*
41537389 CAAGTT-TTTTATCAAGTTTTGCAG
1 CAAGTTCTTTTATAAAGTTTTGCAG
* * *
41537413 CAAGTTCTTTTTTAAAGTTTTTCAT
1 CAAGTTCTTTTATAAAGTTTTGCAG
* * *
41537438 CAAG-TCTTTTCATAAAATTTTCCAT
1 CAAGTTCTTTT-ATAAAGTTTTGCAG
41537463 CAAGTT
1 CAAGTT
41537469 TTTAATCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 12 0.26
25 33 0.72
26 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (25 bp):
CAAGTTCTTTTATAAAGTTTTGCAG
Found at i:41539091 original size:9 final size:9
Alignment explanation
Indices: 41539037--41539095 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
41539027 TTTGGTTAAA
41539037 AATTACCCG
1 AATTACCCG
*
41539046 AATTAACCG
1 AATTACCCG
*
41539055 AATTAACCG
1 AATTACCCG
*
41539064 AATTA-TCG
1 AATTACCCG
*
41539072 AAAAATACCCG
1 --AATTACCCG
41539083 AATTACCCG
1 AATTACCCG
41539092 AATT
1 AATT
41539096 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 2 0.05
9 34 0.81
10 4 0.10
11 2 0.05
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:41539904 original size:246 final size:246
Alignment explanation
Indices: 41539470--41539917 Score: 869
Period size: 246 Copynumber: 1.8 Consensus size: 246
41539460 CACACCCCTA
*
41539470 GTTATAATGAACCGTTGAATGCAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAA
1 GTTATAATGAACCGTTGAATGCAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGATAAA
*
41539535 GTTGTCACGATTTTAACGAAATTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAA
66 GTCGTCACGATTTTAACGAAATTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAA
41539600 GTTTATTTTTGAGAAATAGAAAAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAA
131 GTTTATTTTTGAGAAATAGAAAAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAA
41539665 AAGTCTGTTTTTTGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTG
196 AAGTCTGTTTTTTGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTG
41539716 GTTATAATGAACCGTTGAATGCAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGATAAA
1 GTTATAATGAACCGTTGAATGCAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGATAAA
41539781 GTCGTCACGATTTTAACGAAATTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAA
66 GTCGTCACGATTTTAACGAAATTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAA
41539846 GTTTATTTTTGAGAAATAGAAAAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAA
131 GTTTATTTTTGAGAAATAGAAAAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAA
*
41539911 TAGTCTG
196 AAGTCTG
41539918 AGAAGTACTT
Statistics
Matches: 199, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
246 199 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (246 bp):
GTTATAATGAACCGTTGAATGCAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGATAAA
GTCGTCACGATTTTAACGAAATTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAA
GTTTATTTTTGAGAAATAGAAAAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAA
AAGTCTGTTTTTTGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTG
Found at i:41541862 original size:14 final size:14
Alignment explanation
Indices: 41541843--41541869 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41541833 AATCATAAAG
41541843 AAATGATGAATTGA
1 AAATGATGAATTGA
41541857 AAATGATGAATTG
1 AAATGATGAATTG
41541870 TAATTTGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (14 bp):
AAATGATGAATTGA
Found at i:41543858 original size:18 final size:18
Alignment explanation
Indices: 41543824--41543858 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41543814 ACATAACCGC
**
41543824 AAATTAGTATCGGTACTA
1 AAATTAGTATCAATACTA
41543842 AAATTAGTATCAATACT
1 AAATTAGTATCAATACT
41543859 TTATAGAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
AAATTAGTATCAATACTA
Found at i:41548707 original size:342 final size:343
Alignment explanation
Indices: 41548091--41548761 Score: 1182
Period size: 342 Copynumber: 2.0 Consensus size: 343
41548081 AGTTGGTACG
* *
41548091 AATATTTGAATAAGTAAATGGTAATGACTTGGTTGAGTTTCAGAGCATGGTTTGTAATGCGAATT
1 AATATTTAAATAAGTAAATGGTAATGACTTGGTTGAATTTCAGAGCATGGTTTGTAATGCGAATT
*
41548156 TGGTTTATGTAATTGAGTGAATTATGTCTACTTGGTTCATGAATGATTCATGATTTATTTAATGG
66 TGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTTCATGAATGATTCATGATTTATTTAATGG
41548221 GATATGTGATATATATATATGTAATGACTTGACATTTATGTATAATTAATGAGATGTTATTTGAG
131 GATATGTGA-ATATATATATGTAATGACTTGACATTTATGTATAATTAATGAGATGTTATTTGAG
*
41548286 CTTGAGAACTTTGATAAAGAAGTTGATAAAATTTTATACATGAATTGTAATAAGTGATTGTTCTG
195 CTTGAGAACTTTGATAAAGAAGTTGATAAAATTTTATACATGAATTGTAATAAGTGATTATTCTG
* * *
41548351 ATCTGTACTTATGTTCAGTAATGTCTCGTGACCCTAATCTGGCGACGGATACGGGTTTGGGGTAT
260 ATCTGTACTTATGTTCAGTAATGCCTCGTGACCCTAATCTGGCGACGGATACGAGTTTAGGGTAT
41548416 TACATTTGGTTGGTATCAC
325 TACATTTGGTTGGTATCAC
41548435 AATATTTAAATAAGTAAATGGTAATGACTTGGTTGAATTTCAGAGCATGGTTTGTAATGCGAATT
1 AATATTTAAATAAGTAAATGGTAATGACTTGGTTGAATTTCAGAGCATGGTTTGTAATGCGAATT
*
41548500 TGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTTCGTGAATGATTCATGATTTATTTAATGG
66 TGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTTCATGAATGATTCATGATTTATTTAATGG
* * * *
41548565 GATATGTG-ATATATATATGTAATTACTTGACATTTATGTATGATTAGTGATATGTTATTTGAGC
131 GATATGTGAATATATATATGTAATGACTTGACATTTATGTATAATTAATGAGATGTTATTTGAGC
41548629 TTGAGAACTTTGATAAAGAAGTTGATAAAATTTTATACATGAATTGTAATAAGTGATTATTCTGA
196 TTGAGAACTTTGATAAAGAAGTTGATAAAATTTTATACATGAATTGTAATAAGTGATTATTCTGA
* * * *
41548694 TTTGTACTTATGTTCAGTAATGCCTCGTGACCCTAATCTTGCTACGGATACGAGTTTAGGGTGTT
261 TCTGTACTTATGTTCAGTAATGCCTCGTGACCCTAATCTGGCGACGGATACGAGTTTAGGGTATT
41548759 ACA
326 ACA
41548762 ATAAATGTCG
Statistics
Matches: 311, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
342 177 0.57
344 134 0.43
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.40
Consensus pattern (343 bp):
AATATTTAAATAAGTAAATGGTAATGACTTGGTTGAATTTCAGAGCATGGTTTGTAATGCGAATT
TGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTTCATGAATGATTCATGATTTATTTAATGG
GATATGTGAATATATATATGTAATGACTTGACATTTATGTATAATTAATGAGATGTTATTTGAGC
TTGAGAACTTTGATAAAGAAGTTGATAAAATTTTATACATGAATTGTAATAAGTGATTATTCTGA
TCTGTACTTATGTTCAGTAATGCCTCGTGACCCTAATCTGGCGACGGATACGAGTTTAGGGTATT
ACATTTGGTTGGTATCAC
Found at i:41550548 original size:23 final size:23
Alignment explanation
Indices: 41550522--41550565 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
41550512 AGCAAATTGA
41550522 AAAT-ACATTAAGCAAAGTTACTT
1 AAATAACATTAA-CAAAGTTACTT
*
41550545 AAATAACATTAACATAGTTAC
1 AAATAACATTAACAAAGTTAC
41550566 AAATTAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.30
Consensus pattern (23 bp):
AAATAACATTAACAAAGTTACTT
Found at i:41550659 original size:49 final size:48
Alignment explanation
Indices: 41550546--41550665 Score: 111
Period size: 49 Copynumber: 2.5 Consensus size: 48
41550536 AAGTTACTTA
* * * * *
41550546 AATAACATTAACATAGTTACAAATTAGCAAGCAAATGCCTCTTAAAAT
1 AATAACAATAAAATAGTTACAAATTAGCAAGCAAATACATATTAAAAT
*
41550594 AGTATTAA-AAT-TAATAGTTACAAATTAGCAAGCAAATACAATATCT-AAAT
1 A--A-TAACAATAAAATAGTTACAAATTAGCAAGCAAATAC-ATAT-TAAAAT
*
41550644 AATAACAATAAAATAGTAACAA
1 AATAACAATAAAATAGTTACAA
41550666 TATAATAGCA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
47 3 0.05
48 5 0.09
49 35 0.61
50 10 0.18
51 4 0.07
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.27
Consensus pattern (48 bp):
AATAACAATAAAATAGTTACAAATTAGCAAGCAAATACATATTAAAAT
Found at i:41550663 original size:14 final size:14
Alignment explanation
Indices: 41550640--41550673 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41550630 TACAATATCT
*
41550640 AAATAATAACAATA
1 AAATAGTAACAATA
41550654 AAATAGTAACAATA
1 AAATAGTAACAATA
*
41550668 TAATAG
1 AAATAG
41550674 CAAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:41551674 original size:33 final size:33
Alignment explanation
Indices: 41551637--41551767 Score: 190
Period size: 33 Copynumber: 4.0 Consensus size: 33
41551627 TGGGACCCTG
* * *
41551637 ATTTCCAGGTATTCTAATTCTTGTTGGATCTCT
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
* * *
41551670 ATTTCCAGGGATTCTAATTCCTGTAGGAGCTCC
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
*
41551703 ATTTCCAGGCATTCCAATTCCTGTTGGATCTCC
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
*
41551736 ATTTCCAGGCATTCTAATTTCTGTTGGATCTC
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTC
41551768 TATGATCTCC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (33 bp):
ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
Found at i:41559067 original size:26 final size:26
Alignment explanation
Indices: 41559032--41559081 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
41559022 TATAAAGATA
41559032 CAAATAATAAAAA-AGTTTTAAAATT
1 CAAATAATAAAAATAGTTTTAAAATT
*
41559057 CAAATATATAAAAATATTTTTAAAA
1 CAAATA-ATAAAAATAGTTTTAAAA
41559082 ATAAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 9 0.41
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (26 bp):
CAAATAATAAAAATAGTTTTAAAATT
Found at i:41563454 original size:14 final size:14
Alignment explanation
Indices: 41563435--41563461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41563425 ATTATTTCAA
41563435 ATTTCTTTTCTCTC
1 ATTTCTTTTCTCTC
41563449 ATTTCTTTTCTCT
1 ATTTCTTTTCTCT
41563462 TTTCAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTCTTTTCTCTC
Found at i:41564862 original size:287 final size:287
Alignment explanation
Indices: 41564346--41564920 Score: 1150
Period size: 287 Copynumber: 2.0 Consensus size: 287
41564336 CTCCCATTTT
41564346 ATTTTCAAAGTCGATCCCCGTTTTTTCAAATAAAAAATGGTTTCAACAGCTTGGCGACTCCACTG
1 ATTTTCAAAGTCGATCCCCGTTTTTTCAAATAAAAAATGGTTTCAACAGCTTGGCGACTCCACTG
41564411 GGGACACCAAGAGAGTCAGGCCGTAAAATTGATTGTTTTTGTCTTGTTGTCGAAAATTAAAATTT
66 GGGACACCAAGAGAGTCAGGCCGTAAAATTGATTGTTTTTGTCTTGTTGTCGAAAATTAAAATTT
41564476 TGATTTGAAAAAACTACGATCTTCTCTTTGTATTTGTTTACATGATTATTGTAAATTGAATTTTA
131 TGATTTGAAAAAACTACGATCTTCTCTTTGTATTTGTTTACATGATTATTGTAAATTGAATTTTA
41564541 TATTTTGTCATCATATTGCATGAAGACTATTAGTCTTCCCCTTTTAAGTGGGAGTGAGAAGCTAC
196 TATTTTGTCATCATATTGCATGAAGACTATTAGTCTTCCCCTTTTAAGTGGGAGTGAGAAGCTAC
41564606 TCCTTCGTGAGGTTTTCACCTCCGTGC
261 TCCTTCGTGAGGTTTTCACCTCCGTGC
41564633 ATTTTCAAAGTCGATCCCCGTTTTTTCAAATAAAAAATGGTTTCAACAGCTTGGCGACTCCACTG
1 ATTTTCAAAGTCGATCCCCGTTTTTTCAAATAAAAAATGGTTTCAACAGCTTGGCGACTCCACTG
41564698 GGGACACCAAGAGAGTCAGGCCGTAAAATTGATTGTTTTTGTCTTGTTGTCGAAAATTAAAATTT
66 GGGACACCAAGAGAGTCAGGCCGTAAAATTGATTGTTTTTGTCTTGTTGTCGAAAATTAAAATTT
41564763 TGATTTGAAAAAACTACGATCTTCTCTTTGTATTTGTTTACATGATTATTGTAAATTGAATTTTA
131 TGATTTGAAAAAACTACGATCTTCTCTTTGTATTTGTTTACATGATTATTGTAAATTGAATTTTA
41564828 TATTTTGTCATCATATTGCATGAAGACTATTAGTCTTCCCCTTTTAAGTGGGAGTGAGAAGCTAC
196 TATTTTGTCATCATATTGCATGAAGACTATTAGTCTTCCCCTTTTAAGTGGGAGTGAGAAGCTAC
41564893 TCCTTCGTGAGGTTTTCACCTCCGTGC
261 TCCTTCGTGAGGTTTTCACCTCCGTGC
41564920 A
1 A
41564921 GTATAGTGGA
Statistics
Matches: 288, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 288 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (287 bp):
ATTTTCAAAGTCGATCCCCGTTTTTTCAAATAAAAAATGGTTTCAACAGCTTGGCGACTCCACTG
GGGACACCAAGAGAGTCAGGCCGTAAAATTGATTGTTTTTGTCTTGTTGTCGAAAATTAAAATTT
TGATTTGAAAAAACTACGATCTTCTCTTTGTATTTGTTTACATGATTATTGTAAATTGAATTTTA
TATTTTGTCATCATATTGCATGAAGACTATTAGTCTTCCCCTTTTAAGTGGGAGTGAGAAGCTAC
TCCTTCGTGAGGTTTTCACCTCCGTGC
Found at i:41574607 original size:13 final size:13
Alignment explanation
Indices: 41574589--41574614 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41574579 TTCTATTTCA
41574589 TTTTATTATACTT
1 TTTTATTATACTT
41574602 TTTTATTATACTT
1 TTTTATTATACTT
41574615 AATATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATTATACTT
Found at i:41574622 original size:16 final size:15
Alignment explanation
Indices: 41574590--41574643 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
41574580 TCTATTTCAT
41574590 TTTATTATACTT-T-
1 TTTATTATACTTATA
41574603 TTTATTATACTTAATA
1 TTTATTATACTT-ATA
*
41574619 TTTATT-TATCATATTA
1 TTTATTATA-CTTA-TA
41574635 TTTATTATA
1 TTTATTATA
41574644 ATACATATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 12 0.35
15 4 0.12
16 16 0.47
17 2 0.06
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTATACTTATA
Found at i:41576134 original size:41 final size:41
Alignment explanation
Indices: 41576089--41576291 Score: 268
Period size: 41 Copynumber: 5.0 Consensus size: 41
41576079 TTGTATAAAA
* * * * *
41576089 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTC
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATTT
*
41576130 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATTT
*
41576171 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATTT
41576212 CACCGGCACT-AAGCCTGCTAGACATAAAGTCTGAAGTA-A-TT
1 CACCGGCA-TAAAGCCTGCTAGACATAAAGTCTG-A-TACATTT
* * *
41576253 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACAT
41576292 CTTATTTTCA
Statistics
Matches: 147, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 139 0.95
42 2 0.01
43 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATTT
Found at i:41576962 original size:16 final size:17
Alignment explanation
Indices: 41576941--41576975 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41576931 ATCTAATAAT
41576941 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
41576957 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
41576974 TT
1 TT
41576976 CAACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:41597858 original size:25 final size:25
Alignment explanation
Indices: 41597817--41597873 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
41597807 ACAATCCATG
** * *
41597817 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
41597842 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
41597867 TATATCA
1 TAAATCA
41597874 ATTCTTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:41598200 original size:23 final size:23
Alignment explanation
Indices: 41598111--41598202 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 23
41598101 GAGCCATGAT
*
41598111 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCA-TACGAGCTG--AAA
*
41598137 CGGTAAGCTC-TATTGAGCTGAAA
1 CGGTAAGCTCATA-CGAGCTGAAA
*
41598160 CGGTAAGCTTCGTA-GAGCTGAAA
1 CGGTAAGC-TCATACGAGCTGAAA
41598183 CGGTAAGCTCATACGAGCTG
1 CGGTAAGCTCATACGAGCTG
41598203 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.07
23 34 0.58
24 3 0.05
25 8 0.14
26 10 0.17
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (23 bp):
CGGTAAGCTCATACGAGCTGAAA
Found at i:41606040 original size:54 final size:49
Alignment explanation
Indices: 41606017--41606135 Score: 114
Period size: 53 Copynumber: 2.3 Consensus size: 49
41606007 TATTTCATTA
* *
41606017 TTATTTACTTATTTATTTAATTTCAACTTTTCATTATTTTTTCCTTTTT
1 TTATTTACTTATTTATTTAATTTCAACTCTTCATTATTTTTTCATTTTT
* * * **
41606066 TTATTTACTTATTTATTATGGCAATTTCAGCCTTTTCATGATTTTTT-ATTTGC
1 TTATTTACTTATTTATT-T---AATTTCA-ACTCTTCATTATTTTTTCATTTTT
*
41606119 TTATTTATTTATTTATT
1 TTATTTACTTATTTATT
41606136 GTTGCCTTGC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
49 17 0.29
50 1 0.02
53 26 0.44
54 15 0.25
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (49 bp):
TTATTTACTTATTTATTTAATTTCAACTCTTCATTATTTTTTCATTTTT
Found at i:41606093 original size:53 final size:49
Alignment explanation
Indices: 41605966--41606135 Score: 132
Period size: 54 Copynumber: 3.3 Consensus size: 49
41605956 TTTCAATTTA
* *
41605966 ATTT-CTTATTTATTTAATTTCAG-CTCTTCATTAAATTTTTTTATTT-CATTATT
1 ATTTACTTATTTATTTAATTTCAGACTTTTCA-T-GA-TTTTTTATTTGC----TT
* * **
41606019 ATTTACTTATTTATTTAATTTCA-ACTTTTCATTATTTTTTCCTTTTTTT
1 ATTTACTTATTTATTTAATTTCAGACTTTTCATGATTTTTT-ATTTGCTT
*
41606068 ATTTACTTATTTATTATGGCAATTTCAGCCTTTTCATGATTTTTTATTTGCTT
1 ATTTACTTATTTATT-T---AATTTCAGACTTTTCATGATTTTTTATTTGCTT
*
41606121 ATTTATTTATTTATT
1 ATTTACTTATTTATT
41606136 GTTGCCTTGC
Statistics
Matches: 98, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
49 17 0.17
50 1 0.01
51 6 0.06
52 4 0.04
53 31 0.32
54 39 0.40
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (49 bp):
ATTTACTTATTTATTTAATTTCAGACTTTTCATGATTTTTTATTTGCTT
Found at i:41606537 original size:20 final size:20
Alignment explanation
Indices: 41606494--41606538 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41606484 TAGTACCATT
*
41606494 ATTATAAAATTGATATTATT
1 ATTATAAAATTGATATTATA
* *
41606514 ATTATAAAATTGGTATTCTA
1 ATTATAAAATTGATATTATA
41606534 ATTAT
1 ATTAT
41606539 TATTGTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTATAAAATTGATATTATA
Found at i:41606541 original size:23 final size:20
Alignment explanation
Indices: 41606491--41606530 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41606481 GATTAGTACC
41606491 ATTATTATAAAATTGATATT
1 ATTATTATAAAATTGATATT
*
41606511 ATTATTATAAAATTGGTATT
1 ATTATTATAAAATTGATATT
41606531 CTAATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTATTATAAAATTGATATT
Found at i:41607530 original size:10 final size:10
Alignment explanation
Indices: 41607517--41607557 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
41607507 CATATTTTTA
41607517 ATCTCAATTT
1 ATCTCAATTT
41607527 ATCTCATATTT
1 ATCTCA-ATTT
41607538 -TACT-AATTT
1 AT-CTCAATTT
41607547 ATCTCAATTT
1 ATCTCAATTT
41607557 A
1 A
41607558 ATTCTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.22
10 15 0.56
11 6 0.22
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (10 bp):
ATCTCAATTT
Found at i:41610277 original size:24 final size:24
Alignment explanation
Indices: 41610232--41610288 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
41610222 AATTAGTTCG
* *
41610232 TAATTTTATTGTGTTATAATAATT
1 TAATTTTATAGTGTTATAATAAAT
*
41610256 TAATTTTATAGT-TTGATTATAAAT
1 TAATTTTATAGTGTT-ATAATAAAT
*
41610280 TAATGTTAT
1 TAATTTTAT
41610289 TATGGTTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (24 bp):
TAATTTTATAGTGTTATAATAAAT
Found at i:41622863 original size:8 final size:8
Alignment explanation
Indices: 41622844--41622881 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
41622834 ATAGCATAGA
41622844 AATAATATG
1 AATAA-ATG
41622853 AATAAATG
1 AATAAATG
41622861 AATAAATG
1 AATAAATG
*
41622869 AATAAATA
1 AATAAATG
41622877 AATAA
1 AATAA
41622882 TTATGACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 23 0.82
9 5 0.18
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (8 bp):
AATAAATG
Found at i:41622871 original size:16 final size:17
Alignment explanation
Indices: 41622843--41622887 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
41622833 AATAGCATAG
41622843 AAATAATATGAATAAAT
1 AAATAATATGAATAAAT
*
41622860 GAATAA-ATGAATAAAT
1 AAATAATATGAATAAAT
41622876 AAATAATTATGA
1 AAATAA-TATGA
41622888 CATACAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 15 0.62
17 5 0.21
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
AAATAATATGAATAAAT
Found at i:41623752 original size:23 final size:22
Alignment explanation
Indices: 41623709--41623766 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
41623699 AAAGAGTATC
* *
41623709 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
41623730 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
41623753 TACATATCATATCT
1 TACAAATCATATCT
41623767 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:41623769 original size:19 final size:19
Alignment explanation
Indices: 41623722--41623819 Score: 115
Period size: 19 Copynumber: 4.8 Consensus size: 19
41623712 AAATTAAATC
*
41623722 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
41623742 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
41623764 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
41623785 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
41623804 TCTAAGATTACATATC
1 TCTAAGATTACATATC
41623820 CTCGAAGATT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
19 32 0.47
21 18 0.26
22 7 0.10
23 11 0.16
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:41623782 original size:21 final size:21
Alignment explanation
Indices: 41623756--41623818 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
41623746 CTAAGATTAC
41623756 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
41623777 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
*
41623796 ATATCATATCTAAGATTACAT
1 ATATCATATCTAAGATTGCAT
41623817 AT
1 AT
41623819 CCTCGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 18 0.46
21 21 0.54
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:41625423 original size:20 final size:19
Alignment explanation
Indices: 41625390--41625432 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
41625380 AGACTATGGC
41625390 ATTA-TTTTATGAATAAATAT
1 ATTATTTTTATGAAT--ATAT
41625410 ATTATTTTTA-GAATATAT
1 ATTATTTTTATGAATATAT
41625428 ATTAT
1 ATTAT
41625433 GACATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.41
20 8 0.36
21 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTATTTTTATGAATATAT
Found at i:41628095 original size:188 final size:189
Alignment explanation
Indices: 41627733--41628108 Score: 711
Period size: 189 Copynumber: 2.0 Consensus size: 189
41627723 TACTGCCTTA
41627733 TTTTTATTTTTTTTGTGGTAGCATTGGAGAAGTCGGAGACCAGTTGAGGAAACATGTAGAATCTA
1 TTTTTATTTTTTTTGTGGTAGCATTGGAGAAGTCGGAGACCAGTTGAGGAAACATGTAGAATCTA
*
41627798 AGGGTTTGTTGCAGTTTGTTTGAGTGCCTGTCAATGATTCTCAGTTTTGTTTAAGTGGGGCCGTG
66 AGGGTTTGTTGCAGTTTGTGTGAGTGCCTGTCAATGATTCTCAGTTTTGTTTAAGTGGGGCCGTG
41627863 GTTTGAATCCAGAAAAAGGGAAGGAAAGGACTTAAATAGTACTAGTCTAGTTTGTTTTG
131 GTTTGAATCCAGAAAAAGGGAAGGAAAGGACTTAAATAGTACTAGTCTAGTTTGTTTTG
41627922 TTTTT-TTTTTTTTGGTGGTAGCATTGGAGAAGTCGGAGACCAGTTGAGGAAACATGTAGAATCT
1 TTTTTATTTTTTTT-GTGGTAGCATTGGAGAAGTCGGAGACCAGTTGAGGAAACATGTAGAATCT
41627986 AAGGGTTTGTTGCAGTTTGTGTGAGTGCCTGTCAATGATTCTCAGTTTTGTTTAAGTGGGGCCGT
65 AAGGGTTTGTTGCAGTTTGTGTGAGTGCCTGTCAATGATTCTCAGTTTTGTTTAAGTGGGGCCGT
*
41628051 -GTTTGAATCCAGAAGAAGGGAAGGAAAGGACTTAAATAGTACTAGTCTAGTTTGTTTT
130 GGTTTGAATCCAGAAAAAGGGAAGGAAAGGACTTAAATAGTACTAGTCTAGTTTGTTTT
41628109 CTTTAGCTCT
Statistics
Matches: 184, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
188 65 0.35
189 119 0.65
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.36
Consensus pattern (189 bp):
TTTTTATTTTTTTTGTGGTAGCATTGGAGAAGTCGGAGACCAGTTGAGGAAACATGTAGAATCTA
AGGGTTTGTTGCAGTTTGTGTGAGTGCCTGTCAATGATTCTCAGTTTTGTTTAAGTGGGGCCGTG
GTTTGAATCCAGAAAAAGGGAAGGAAAGGACTTAAATAGTACTAGTCTAGTTTGTTTTG
Found at i:41629214 original size:14 final size:13
Alignment explanation
Indices: 41629195--41629224 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41629185 TGATTATCAT
*
41629195 AAAAAAACATTAA
1 AAAAAAACATGAA
41629208 AAAAAAACATGAA
1 AAAAAAACATGAA
41629221 AAAA
1 AAAA
41629225 GAAAATATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (13 bp):
AAAAAAACATGAA
Found at i:41640077 original size:126 final size:125
Alignment explanation
Indices: 41639887--41640128 Score: 421
Period size: 126 Copynumber: 1.9 Consensus size: 125
41639877 CCTCTAGCAG
* ** *
41639887 GATGCTATTTGAGAAGAAATTGTGAAATCGTGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCA
1 GATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
41639952 TGTAGGAAATAATTATTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAA
66 TGTAGGAAATAATTATTTTTTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAA
41640013 GATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
1 GATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
* *
41640078 TGTAGGAAATAATTATTTTTTGACGTTTCTGAGCAAATAGTGTCAAATCGC
66 TGTAGGAAATAATTATTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGC
41640129 GCTCTCGTGG
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 24 0.22
126 86 0.78
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (125 bp):
GATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
TGTAGGAAATAATTATTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAA
Found at i:41641525 original size:7 final size:7
Alignment explanation
Indices: 41641515--41641551 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
41641505 AATTAAAAAT
41641515 AATAATA
1 AATAATA
41641522 AATAATA
1 AATAATA
41641529 AATAATA
1 AATAATA
41641536 AAT--TA
1 AATAATA
41641541 AATATATA
1 AATA-ATA
41641549 AAT
1 AAT
41641552 TATTGGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.19
7 17 0.63
8 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATAATA
Found at i:41643781 original size:4 final size:4
Alignment explanation
Indices: 41643772--41643798 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41643762 ATAAAAAATA
41643772 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
41643799 ATAAGCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:41643785 original size:47 final size:46
Alignment explanation
Indices: 41643703--41643792 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 46
41643693 AAATGAGTAA
41643703 AATTATAAAAATAAAAAAGATATATATATATATGTACGTATGTTAG
1 AATTATAAAAATAAAAAAGATATATATATATATGTACGTATGTTAG
* * * *
41643749 AATTATAAAGTATATAAAAA-ATATATGTATGTATGTATGTATGT
1 AATTATAAA-AATA-AAAAAGATATATATATATATGTACGTATGT
41643793 ATGTATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 9 0.24
47 24 0.63
48 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (46 bp):
AATTATAAAAATAAAAAAGATATATATATATATGTACGTATGTTAG
Found at i:41643845 original size:8 final size:8
Alignment explanation
Indices: 41643824--41643894 Score: 58
Period size: 8 Copynumber: 9.1 Consensus size: 8
41643814 GTTTATAAAG
*
41643824 AGATATGT
1 AGATATAT
*
41643832 ATATATAT
1 AGATATAT
*
41643840 ACATATAT
1 AGATATAT
*
41643848 ATATA-AT
1 AGATATAT
41643855 AAGATATAT
1 -AGATATAT
41643864 AGATATAT
1 AGATATAT
*
41643872 ATA-ATA-
1 AGATATAT
*
41643878 AGATATAA
1 AGATATAT
41643886 AGATATAT
1 AGATATAT
41643894 A
1 A
41643895 AATAAATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 2 0.04
7 8 0.16
8 39 0.76
9 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (8 bp):
AGATATAT
Found at i:41643848 original size:12 final size:11
Alignment explanation
Indices: 41643831--41643907 Score: 63
Period size: 10 Copynumber: 7.2 Consensus size: 11
41643821 AAGAGATATG
41643831 TATATATATACA
1 TATATATATA-A
41643843 TATATATATAA
1 TATATATATAA
*
41643854 TA-AGATATATA
1 TATATATATA-A
*
41643865 GATATATATAA
1 TATATATATAA
*
41643876 TA-AGATATAA
1 TATATATATAA
*
41643886 -AGATATATAA
1 TATATATATAA
*
41643896 -ATAAATATAA
1 TATATATATAA
41643906 TA
1 TA
41643908 GTAATAACAA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 1 0.02
10 28 0.53
11 8 0.15
12 16 0.30
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (11 bp):
TATATATATAA
Found at i:41643861 original size:22 final size:22
Alignment explanation
Indices: 41643844--41643905 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
41643834 ATATATACAT
*
41643844 ATATATATAATAAGATATATAG
1 ATATATATAATAAGATATAAAG
41643866 ATATATATAATAAGATATAAAG
1 ATATATATAATAAGATATAAAG
41643888 ATATATA-AATAA-ATATAA
1 ATATATATAATAAGATATAA
41643906 TAGTAATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 6 0.15
21 5 0.13
22 28 0.72
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATATATAATAAGATATAAAG
Found at i:41643889 original size:30 final size:31
Alignment explanation
Indices: 41643817--41643907 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 31
41643807 AAAAAATGTT
* *
41643817 TATAAAGAGATAT-GTATATATATACATATATA
1 TATAAAGATATATAG-ATATATATA-ATATAGA
41643849 TATAATAAGATATATAGATATATATAATA-AGA
1 TAT-A-AAGATATATAGATATATATAATATAGA
* *
41643881 TATAAAGATATATAAATAAATATAATA
1 TATAAAGATATATAGATATATATAATA
41643908 GTAATAACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
30 21 0.40
31 1 0.02
32 8 0.15
33 4 0.08
34 17 0.33
35 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (31 bp):
TATAAAGATATATAGATATATATAATATAGA
Found at i:41645659 original size:46 final size:46
Alignment explanation
Indices: 41645592--41646166 Score: 757
Period size: 46 Copynumber: 12.5 Consensus size: 46
41645582 TACTGTATTG
* * ** * *
41645592 GGAAGACAAGAT-TCACCATCTTCGATCTCCTTTGCTGCTAGATACA
1 GGAAGACAAGATCT-GCTATCTTCGATCTCCTCCGCTGCCAAATACA
* * *
41645638 GGAAGAAAAGATCTTG-TATCTTTGATCTCTTCCGCTGCCAAATACA
1 GGAAGACAAGATC-TGCTATCTTCGATCTCCTCCGCTGCCAAATACA
* *
41645684 GGAAGACAAGATCTTG-TATCTTCGATCTCCTTCGTTGCCAAATACA
1 GGAAGACAAGATC-TGCTATCTTCGATCTCCTCCGCTGCCAAATACA
*
41645730 GGAAGACAAGATCTGCCATCTTCGATCTCCTCCGCTGCCAAATACA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
41645776 GGAAGACAAGATCTG-TCATCTTCGATCTCCTCCGCTGCCAAATACA
1 GGAAGACAAGATCTGCT-ATCTTCGATCTCCTCCGCTGCCAAATACA
* **
41645822 GGAAGACAAGATCTGTTATCTTCGATCTCC-CTCGCTG-CATTTACA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTC-CGCTGCCAAATACA
*
41645867 TGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
* * * * *
41645913 AGAAGACAAGATCTACTATCTTCGGTCTCCTCCGCTGCCAGATATA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
* ** * *
41645959 GGAAGACAAGATCTGCTATCTTCGATCTCCCCCATTGCTAAATATA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
** *
41646005 GGAAGACAAGATCTGCTATCTTCGATCTTTTCCACTGCCAAATACA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
* * * *
41646051 AGAAGACAAGATCTGCTATCTTCGATCTTCTTCACTGCCAAATACA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
*
41646097 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGTTGCCAAATACA
1 GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
41646143 GGAAGACAAGATCTGCTATCTTCG
1 GGAAGACAAGATCTGCTATCTTCG
41646167 TTGATCTGTT
Statistics
Matches: 470, Mismatches: 51, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
45 42 0.09
46 426 0.91
47 1 0.00
48 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (46 bp):
GGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACA
Found at i:41647316 original size:43 final size:44
Alignment explanation
Indices: 41647258--41647371 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 44
41647248 AGATCATCAT
* *
41647258 ATGCCCCGATCTGAT-CAAAATTTGAGCT-GCTCTGATCACCACC
1 ATGCCCCAATTTGATCCAAAATTTGAGCTCGCTCTGATCA-CACC
* **
41647301 ATGCCCCAATTTGATCCAAAATTTAAG-TCGCTCTGATCACTTC
1 ATGCCCCAATTTGATCCAAAATTTGAGCTCGCTCTGATCACACC
* * *
41647344 GTGCCCCATTTTGTTCCAAAATTTGAGC
1 ATGCCCCAATTTGATCCAAAATTTGAGC
41647372 CGCCCTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 39 0.66
44 20 0.34
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (44 bp):
ATGCCCCAATTTGATCCAAAATTTGAGCTCGCTCTGATCACACC
Found at i:41649306 original size:17 final size:18
Alignment explanation
Indices: 41649274--41649310 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
41649264 TCTGCACAGT
41649274 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
41649292 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
41649309 AT
1 AT
41649311 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:41653396 original size:4 final size:4
Alignment explanation
Indices: 41653387--41653417 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
41653377 ATAAAAAATA
*
41653387 TATG TATG TATG TATT TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
41653418 ATAAGCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (4 bp):
TATG
Found at i:41653408 original size:16 final size:16
Alignment explanation
Indices: 41653387--41653417 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41653377 ATAAAAAATA
41653387 TATGTATGTATGTATT
1 TATGTATGTATGTATT
41653403 TATGTATGTATGTAT
1 TATGTATGTATGTAT
41653418 ATAAGCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (16 bp):
TATGTATGTATGTATT
Found at i:41653478 original size:20 final size:20
Alignment explanation
Indices: 41653461--41653500 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
41653451 ATATATATAC
41653461 ATATATATAATAAGATATAAAG
1 ATATATA-AATAA-ATATAAAG
41653483 ATATATAAATAAATATAA
1 ATATATAAATAAATATAA
41653501 TAGTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATATATAAATAAATATAAAG
Found at i:41656662 original size:13 final size:11
Alignment explanation
Indices: 41656630--41656686 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 11
41656620 CCATTTTTTA
*
41656630 AATAAAATAAT
1 AATAAAATATT
41656641 AAT-AAATATCT
1 AATAAAATAT-T
41656652 AAGTAAAATATT
1 AA-TAAAATATT
41656664 AATAAAATAATATT
1 AAT--AA-AATATT
41656678 AATAAAATA
1 AATAAAATA
41656687 ATATTTAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
10 5 0.13
11 11 0.28
12 6 0.15
13 8 0.21
14 9 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAAAATATT
Found at i:41656677 original size:14 final size:14
Alignment explanation
Indices: 41656658--41656691 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
41656648 ATCTAAGTAA
41656658 AATATTAATAAAAT
1 AATATTAATAAAAT
41656672 AATATTAATAAAAT
1 AATATTAATAAAAT
41656686 AATATT
1 AATATT
41656692 TAACTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAATAAAAT
Found at i:41656890 original size:230 final size:230
Alignment explanation
Indices: 41656487--41656949 Score: 926
Period size: 230 Copynumber: 2.0 Consensus size: 230
41656477 AAATTTTCAA
41656487 AAACTTTGGGTAAAAATGTAAGTTTTCATGGCAAAGGACTAAATTGTAAAGAAAAGAAAACTTCC
1 AAACTTTGGGTAAAAATGTAAGTTTTCATGGCAAAGGACTAAATTGTAAAGAAAAGAAAACTTCC
41656552 TTTCTCACCCTTGCACTCACGTTGGAAGGATGATAAATTTCCTTCATCCTTCATTTCTTTTTATA
66 TTTCTCACCCTTGCACTCACGTTGGAAGGATGATAAATTTCCTTCATCCTTCATTTCTTTTTATA
41656617 CTACCATTTTTTAAATAAAATAATAATAAATATCTAAGTAAAATATTAATAAAATAATATTAATA
131 CTACCATTTTTTAAATAAAATAATAATAAATATCTAAGTAAAATATTAATAAAATAATATTAATA
41656682 AAATAATATTTAACTAATTAATTTAAAAAATTACC
196 AAATAATATTTAACTAATTAATTTAAAAAATTACC
41656717 AAACTTTGGGTAAAAATGTAAGTTTTCATGGCAAAGGACTAAATTGTAAAGAAAAGAAAACTTCC
1 AAACTTTGGGTAAAAATGTAAGTTTTCATGGCAAAGGACTAAATTGTAAAGAAAAGAAAACTTCC
41656782 TTTCTCACCCTTGCACTCACGTTGGAAGGATGATAAATTTCCTTCATCCTTCATTTCTTTTTATA
66 TTTCTCACCCTTGCACTCACGTTGGAAGGATGATAAATTTCCTTCATCCTTCATTTCTTTTTATA
41656847 CTACCATTTTTTAAATAAAATAATAATAAATATCTAAGTAAAATATTAATAAAATAATATTAATA
131 CTACCATTTTTTAAATAAAATAATAATAAATATCTAAGTAAAATATTAATAAAATAATATTAATA
41656912 AAATAATATTTAACTAATTAATTTAAAAAATTACC
196 AAATAATATTTAACTAATTAATTTAAAAAATTACC
41656947 AAA
1 AAA
41656950 ATATCATCAA
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
230 233 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (230 bp):
AAACTTTGGGTAAAAATGTAAGTTTTCATGGCAAAGGACTAAATTGTAAAGAAAAGAAAACTTCC
TTTCTCACCCTTGCACTCACGTTGGAAGGATGATAAATTTCCTTCATCCTTCATTTCTTTTTATA
CTACCATTTTTTAAATAAAATAATAATAAATATCTAAGTAAAATATTAATAAAATAATATTAATA
AAATAATATTTAACTAATTAATTTAAAAAATTACC
Found at i:41656892 original size:13 final size:11
Alignment explanation
Indices: 41656860--41656916 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 11
41656850 CCATTTTTTA
*
41656860 AATAAAATAAT
1 AATAAAATATT
41656871 AAT-AAATATCT
1 AATAAAATAT-T
41656882 AAGTAAAATATT
1 AA-TAAAATATT
41656894 AATAAAATAATATT
1 AAT--AA-AATATT
41656908 AATAAAATA
1 AATAAAATA
41656917 ATATTTAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
10 5 0.13
11 11 0.28
12 6 0.15
13 8 0.21
14 9 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAAAATATT
Found at i:41656907 original size:14 final size:14
Alignment explanation
Indices: 41656888--41656921 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
41656878 ATCTAAGTAA
41656888 AATATTAATAAAAT
1 AATATTAATAAAAT
41656902 AATATTAATAAAAT
1 AATATTAATAAAAT
41656916 AATATT
1 AATATT
41656922 TAACTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAATAAAAT
Found at i:41657826 original size:19 final size:20
Alignment explanation
Indices: 41657791--41657831 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41657781 AAAAGTATTT
*
41657791 AAAAATTATTAAGAATTATA
1 AAAAATTACTAAGAATTATA
*
41657811 AAAAATTACTAA-AATTTTA
1 AAAAATTACTAAGAATTATA
41657830 AA
1 AA
41657832 TTAATGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATTACTAAGAATTATA
Found at i:41658220 original size:31 final size:30
Alignment explanation
Indices: 41658142--41658221 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
41658132 TTTTTAATAA
41658142 ATTTTCAATAATTTTT-AATAATATCTTATC
1 ATTTT-AATAATTTTTAAATAATATCTTATC
* * *
41658172 ATTCTTATTAATTTTTAAATAACTTTTTTAT-
1 ATT-TTAATAATTTTTAAATAA-TATCTTATC
41658203 ATTTTAATAATTATTTAAA
1 ATTTTAATAATT-TTTAAA
41658222 AATTTATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
30 20 0.48
31 16 0.38
32 6 0.14
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTAATAATTTTTAAATAATATCTTATC
Found at i:41661446 original size:30 final size:29
Alignment explanation
Indices: 41661412--41661471 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
41661402 ACAATTTTCC
* *
41661412 CAAGTTGGTGCTGAAACTTTTTCTT-GGTTA
1 CAAG-TGGTACTGAAAC-TATTCTTCGGTTA
*
41661442 CAAGTGGTACTTAAACTATTCTTCGGTTA
1 CAAGTGGTACTGAAACTATTCTTCGGTTA
41661471 C
1 C
41661472 TCATTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (29 bp):
CAAGTGGTACTGAAACTATTCTTCGGTTA
Found at i:41662685 original size:29 final size:29
Alignment explanation
Indices: 41662653--41662708 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
41662643 AAAAAGCCCA
41662653 TTTTTTAAAAAATTACCGAAATGGGCCGG
1 TTTTTTAAAAAATTACCGAAATGGGCCGG
** * *
41662682 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAAAAAATTACCGAAATGGGCC
41662709 ATTTTCCGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (29 bp):
TTTTTTAAAAAATTACCGAAATGGGCCGG
Found at i:41662713 original size:28 final size:28
Alignment explanation
Indices: 41662650--41662713 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
41662640 CAAAAAAAGC
41662650 CCATTTTTTAAAAAATTACCGAAATGGG
1 CCATTTTTTAAAAAATTACCGAAATGGG
* ** * *
41662678 CCGGTTTTTTAATTATTTACCGGAATGGG
1 CC-ATTTTTTAAAAAATTACCGAAATGGG
41662707 CCATTTT
1 CCATTTT
41662714 CCGCGAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (28 bp):
CCATTTTTTAAAAAATTACCGAAATGGG
Found at i:41666326 original size:27 final size:27
Alignment explanation
Indices: 41666288--41666347 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
41666278 AGTTGAATGT
*
41666288 AATTATAGAAAAAATTACCTTTTATTC
1 AATTATAGAAAAAACTACCTTTTATTC
*
41666315 AATTATAGAAAAAGCTACCTTTTATTC
1 AATTATAGAAAAAACTACCTTTTATTC
41666342 AATTAT
1 AATTAT
41666348 TAATTGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (27 bp):
AATTATAGAAAAAACTACCTTTTATTC
Found at i:41666467 original size:29 final size:28
Alignment explanation
Indices: 41666406--41666916 Score: 561
Period size: 28 Copynumber: 18.5 Consensus size: 28
41666396 TTTCTTAAAT
**
41666406 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
41666434 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
*
41666462 GGGTTAGGGTTTTT-ATGTAAAATAGGTTA
1 -GGTTAGGGTTTTTAAT-TAAATTAGGTTA
*
41666491 GGGTTAGGGTTTTTAACTAAA-T--G--A
1 -GGTTAGGGTTTTTAATTAAATTAGGTTA
* *
41666515 TGTTAGGGTTTTTAACTAAATTA---T-
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
**
41666539 -GTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
41666566 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
**
41666594 GGGTTAGGGTTTTTAATTAAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTAGGTTA
* *
41666623 GGTTAGGGTTTTTAACTAAATTATGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
* **
41666651 GGTTAGGGTATTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
41666679 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
*
41666707 GGGTTAGGGTTTTTAATTAAATCAGGTTA
1 -GGTTAGGGTTTTTAATTAAATTAGGTTA
*
41666736 GGGTTAGGGTTTTTAACTAAATTA---T-
1 -GGTTAGGGTTTTTAATTAAATTAGGTTA
* * **
41666761 -GTTACGATTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
**
41666788 GGTTAGTCTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
* * *
41666816 TGGTTAGAG-TTTTCATGTAAAATAGGTTA
1 -GGTTAGGGTTTTTAAT-TAAATTAGGTTA
**
41666845 GGGTTAGGGTTTTTAATTAAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTAGGTTA
41666874 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTA
41666902 GGGTTAGGGTTTTTA
1 -GGTTAGGGTTTTTA
41666917 NNNNNNNNNN
Statistics
Matches: 418, Mismatches: 43, Indels: 43
0.83 0.09 0.09
Matches are distributed among these distances:
23 59 0.14
24 2 0.00
26 4 0.01
28 182 0.44
29 164 0.39
30 7 0.02
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (28 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:41667071 original size:28 final size:28
Alignment explanation
Indices: 41667031--41667997 Score: 863
Period size: 28 Copynumber: 35.1 Consensus size: 28
41667021 NNNNNNNNNN
*
41667031 AATTAGGTTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
* *
41667059 AATTAAATTAGGTTAGGGTTTTTAACTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
41667087 AATTATG-TTAGGTTAGGGTTTTTAATTA
1 AATTA-GATTAGGTTAGGGTTTTTAATTA
* * *
41667115 AATTAGGTTAATGTTAGGG-TTTTCATGTA
1 AATTAGATT-AGGTTAGGGTTTTTAAT-TA
* *
41667144 AAATAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
* * *
41667173 AATTAAATTATGTTAGGATTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
* *
41667201 AATTAGGTTAGGTTAGGGTTTTTAATCATTTTT
1 AATTAGATTAGGTTAGGGTTTTT-A--A--TTA
* * ** * *
41667234 AATTAAATTAGGTTATGG-TTAGAGTTTT
1 AATTAGATTAGGTTAGGGTTTTTA-ATTA
* * *
41667262 CATGTAAAATAGGTTAGGGTTAGGGTTTTTAATTA
1 AAT-TAGATTA------GGTTAGGGTTTTTAATTA
*
41667297 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667325 AATTAGGTTAGGGTTAGGGTTTTT-ATGTA
1 AATTAGATTA-GGTTAGGGTTTTTAAT-TA
* * *
41667354 AAATAGGTTAGGGTTAGGGTTTTTAACT-
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
41667382 -A--A-ATTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667406 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667434 AATTAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
* * *
41667463 AATCAGGTTAGGGTTAGGGTTTTTAACTA
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
* *
41667492 AATT--A-T--GTTACGATTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667515 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
* *
41667543 AATTAAATTAGGTTAGGATTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
* *
41667571 AATTAGGTTATGGTTAGAGTTTTTAATT-
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
41667599 -A--A-ATTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667623 AATTAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
* *
41667652 AATTAGGTTAGGGTTAGGGTTTTTAACTA
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
41667681 AATT--A-T--GTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667704 AATTAAATTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667732 AATTAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
*
41667761 AATTAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
* *
41667790 AATT--A-T--GTTAGGGTTATTAATTT
1 AATTAGATTAGGTTAGGGTTTTTAATTA
41667813 AATTA-AGTTAGGTTAGGGTTTTTAATT-
1 AATTAGA-TTAGGTTAGGGTTTTTAATTA
*
41667840 -A--AG-TTATGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
* **
41667864 AATTAGGTTAGGGTTTTGGTTTTTAATT-
1 AATTAGATTA-GGTTAGGGTTTTTAATTA
*
41667892 -A--A-ATTAGGTTAGGGTTTTGAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
*
41667916 AATTAGGTTAGGTTAGGGTTTTTAATT-
1 AATTAGATTAGGTTAGGGTTTTTAATTA
41667943 -A--A-ATTAGGTTAGGGTTTTTAATTA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
* *
41667967 AATTAGGTTAGGTTAGGGTTTTTAATCA
1 AATTAGATTAGGTTAGGGTTTTTAATTA
41667995 AAT
1 AAT
41667998 AATGTCAAAA
Statistics
Matches: 788, Mismatches: 83, Indels: 136
0.78 0.08 0.14
Matches are distributed among these distances:
23 142 0.18
24 12 0.02
25 10 0.01
26 8 0.01
27 10 0.01
28 300 0.38
29 258 0.33
30 7 0.01
31 2 0.00
32 2 0.00
33 17 0.02
34 6 0.01
35 11 0.01
36 3 0.00
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (28 bp):
AATTAGATTAGGTTAGGGTTTTTAATTA
Found at i:41667323 original size:23 final size:23
Alignment explanation
Indices: 41667297--41667978 Score: 428
Period size: 29 Copynumber: 25.7 Consensus size: 23
41667287 TTTTTAATTA
41667297 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
41667320 AATTAAATTAGGTTAGGGTTAGGGTTTT
1 AATTAAATTAGGTTAGGG-T----TTTT
*
41667348 TATGTAAAATAGGTTAGGGTTAGGGTTTTT
1 AAT-T-A-A-A--TTA-GGTTAGGGTTTTT
*
41667378 AACTAAATTAGGTTAGGGTTTTTAATT
1 AATTAAATTAGGTTAGGG--TTT--TT
41667405 AAATTAAATTAGGTTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTT
41667429 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTA-GGTTAGGGTTTTT
41667458 AATTAAATCAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTA-GGTTAGGGTTTTT
* * **
41667487 AACTAAATTATGTTACGATTTTTAATT
1 AATTAAATTAGGTTA-G-GGTTT--TT
41667514 AAATTAAATTAGGTTAGGGTTTTTAATT
1 -AATTAAATTAGGTTAGGG--TTT--TT
*
41667542 AAATTAAATTAGGTTAGGATTTTT
1 -AATTAAATTAGGTTAGGGTTTTT
41667566 AATTAAATTAGGTTATGGTTAGAGTTTTT
1 AATTAAATTAGGTTA--G---G-GTTTTT
41667595 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
41667618 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTA-GGTTAGGGTTTTT
41667647 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTA-GGTTAGGGTTTTT
* *
41667676 AACTAAATTATGTTAGGGTTTTTAATT
1 AATTAAATTAGGTTAGGG--TTT--TT
41667703 AAATTAAATTAGGTTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTT
41667727 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTA-GGTTAGGGTTTTT
41667756 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTA-GGTTAGGGTTTTT
*
41667785 AATTAAATTATGTTAGGGTTATTAATTT
1 AATTAAATTAGGTTAGGG---TT--TTT
*
41667813 AATTAAGTTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
* *
41667836 AATTAAGTTATGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
41667859 AATTAAATTAGGTTAGGGTTTTGGTTTTT
1 AATTAAATTAGGTTA--G----GGTTTTT
*
41667888 AATTAAATTAGGTTAGGGTTTTG
1 AATTAAATTAGGTTAGGGTTTTT
41667911 AATTAAATTAGGTTAGGTTAGGGTTTTT
1 AATT-AA--A--TTAGGTTAGGGTTTTT
41667939 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
41667962 AATTAAATTAGGTTAGG
1 AATTAAATTAGGTTAGG
41667979 TTAGGGTTTT
Statistics
Matches: 563, Mismatches: 27, Indels: 138
0.77 0.04 0.19
Matches are distributed among these distances:
23 158 0.28
24 29 0.05
25 14 0.02
26 19 0.03
27 12 0.02
28 132 0.23
29 179 0.32
30 6 0.01
31 1 0.00
32 1 0.00
34 4 0.01
35 8 0.01
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTTT
Found at i:41667417 original size:109 final size:109
Alignment explanation
Indices: 41667038--41667997 Score: 1088
Period size: 109 Copynumber: 8.7 Consensus size: 109
41667028 NNNAATTAGG
* *
41667038 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAACTAAATTATGTTA-GGTTA
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
** *
41667102 GGGTTTTTAATTAAATTAGGTTAATGTTAGGG-TTTTCATGTAAAATA
66 GGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAT-T--AA-A
* *
41667149 GGTTAGGGTTAGGGTTTTTAATTAAATTAAATTATGTTAGGATTTTTAATTAAATTAGGTTA-GG
1 --TTA-GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
* * *
41667213 TTAGGGTTTTTAATCATTTTTAATTAAATTAGGTTATGGTTAGAG-TTTTCATGTAAAATA
63 TTAGGG----------TTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAT-T--AA-A
41667273 GGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 --TTA-GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
41667338 TTAGGGTTTTT-ATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAA
63 TTAGGGTTTTTAAT-TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA
41667385 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
* *
41667450 GGGTTTTTAATTAAATCAGGTTAGGGTTAGGGTTTTTAACTAAA
66 GGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA
* * * **
41667494 TTATGTTACGATTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTA
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
* * *
41667558 GGATTTTTAATTAAATTAGGTTATGGTTAGAGTTTTTAATTAAA
66 GGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA
**
41667602 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
* *
41667667 AGGGTTTTTAACTAAATTATGTTAGGGTT----TTTAATTAAATTAAA
65 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT--TT-AATTAAA
**
41667711 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
* *
41667776 AGGGTTTTTAATTAAATTATGTTAGGGTTA---TTAATTTAATTAAG
65 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT--TTTAATTAAA
* *
41667820 TTAGGTTAGGGTTTTTAATTAAGTT--A-T--GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
* ** ** * **
41667880 TGGTTTTTAATTAAATTAGGTTAGGGTT-TTGAATTAAATTAGG
66 GGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA
41667923 TTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTA
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
*
41667982 GGGTTTTTAATCAAAT
66 GGGTTTTTAATTAAAT
41667998 AATGTCAAAA
Statistics
Matches: 764, Mismatches: 52, Indels: 73
0.86 0.06 0.08
Matches are distributed among these distances:
98 3 0.00
99 2 0.00
100 1 0.00
101 4 0.01
102 18 0.02
103 104 0.14
106 4 0.01
108 72 0.09
109 311 0.41
110 38 0.05
112 2 0.00
113 5 0.01
114 62 0.08
115 24 0.03
116 5 0.01
124 101 0.13
125 8 0.01
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (109 bp):
TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
GGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA
Found at i:41667972 original size:18 final size:21
Alignment explanation
Indices: 41667881--41667978 Score: 70
Period size: 23 Copynumber: 4.0 Consensus size: 21
41667871 TTAGGGTTTT
41667881 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAA-TA-GTTAG
*
41667904 GGTTTTGAATTAAATTAGGTTAGGTTAG
1 GGTTTTTAATT-AA--A---TA-GTTAG
41667932 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAA-TA-GTTAG
41667955 GGTTTTTAATTAAATTAGGTTAG
1 GGTTTTTAATTAAA-TA-GTTAG
41667978 G
1 G
41667979 TTAGGGTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
23 43 0.63
24 2 0.03
25 1 0.01
26 1 0.01
27 2 0.03
28 19 0.28
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (21 bp):
GGTTTTTAATTAAATAGTTAG
Found at i:41670159 original size:14 final size:15
Alignment explanation
Indices: 41670142--41670175 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41670132 AATAAATATC
41670142 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
41670156 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
41670171 TAAAA
1 TAAAA
41670176 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:41670403 original size:22 final size:22
Alignment explanation
Indices: 41670373--41670414 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41670363 ATTTGGAGAT
*
41670373 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
41670395 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
41670415 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:41670422 original size:30 final size:30
Alignment explanation
Indices: 41670386--41670444 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
41670376 TTGAAGGAAA
* *
41670386 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
41670416 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
41670445 AAATTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:41670435 original size:52 final size:51
Alignment explanation
Indices: 41670364--41670466 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
41670354 TTAATATGGA
* * *
41670364 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
41670415 TTTGAGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
41670467 AATTTTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:41670441 original size:22 final size:22
Alignment explanation
Indices: 41670416--41670506 Score: 123
Period size: 22 Copynumber: 4.1 Consensus size: 22
41670406 ATTTGAGAGT
41670416 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
41670438 TTGAGAGAAATTTT-GAAGGGAA
1 TTGAGAG-AATTTTGGAAGGAAA
*
41670460 TTGAGAGAATTTTTGAAAGG-AA
1 TTGAGAGAA-TTTTGGAAGGAAA
*
41670482 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
41670504 TTG
1 TTG
41670507 TTTGTGAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
21 10 0.16
22 41 0.67
23 10 0.16
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.31
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:41670465 original size:44 final size:44
Alignment explanation
Indices: 41670416--41670506 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
41670406 ATTTGAGAGT
* *
41670416 TTGAGAGAA-TTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAAGG-AATTGAGAGAAATTTTGAAGGAAA
*
41670460 TTGAGAGAATTTTTGAAAGGAATTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAAGGAATTGAGAGAAATTTTGAAGGAAA
41670504 TTG
1 TTG
41670507 TTTGTGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 34 0.79
45 9 0.21
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.31
Consensus pattern (44 bp):
TTGAGAGAATTTTTGAAAGGAATTGAGAGAAATTTTGAAGGAAA
Found at i:41680096 original size:37 final size:37
Alignment explanation
Indices: 41680039--41680190 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
41680029 TATGATCACT
*
41680039 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
41680074 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
41680111 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
41680156 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
41680191 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:41680174 original size:46 final size:46
Alignment explanation
Indices: 41680107--41680375 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
41680097 TAAGTGTAGC
* **
41680107 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
41680153 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
41680199 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
41680251 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
41680297 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
41680349 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
41680376 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:41680226 original size:52 final size:52
Alignment explanation
Indices: 41680150--41680369 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
41680140 TAGCTAAAGC
* *
41680150 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
41680203 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
41680255 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
41680301 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
41680353 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
41680370 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Done.