Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 127 of 313
Found at i:41065830 original size:18 final size:19
Alignment explanation
Indices: 41065807--41065844 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
41065797 TTAAGAGTTT
*
41065807 AGTATTATTGTGAAA-AAA
1 AGTATTATTGAGAAATAAA
*
41065825 AGTATTTTTGAGAAATAAA
1 AGTATTATTGAGAAATAAA
41065844 A
1 A
41065845 TGTTCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (19 bp):
AGTATTATTGAGAAATAAA
Found at i:41065927 original size:5 final size:5
Alignment explanation
Indices: 41065917--41065943 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41065907 ATGATATTTC
41065917 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
41065944 AGTTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:41067513 original size:20 final size:21
Alignment explanation
Indices: 41067473--41067514 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
41067463 ACTGCTAACA
41067473 TAAATAATTATTAAATATTTT
1 TAAATAATTATTAAATATTTT
*
41067494 TAAA-AATTATT-AATAGTTT
1 TAAATAATTATTAAATATTTT
41067513 TA
1 TA
41067515 TTTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TAAATAATTATTAAATATTTT
Found at i:41067655 original size:21 final size:20
Alignment explanation
Indices: 41067630--41067668 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
41067620 AATTAAAAAT
41067630 TAAAAATAAAAAGAAATAAGA
1 TAAAAATAAAAA-AAATAAGA
41067651 TAAAAATAAAAAAAATAA
1 TAAAAATAAAAAAAATAA
41067669 ATATTATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (20 bp):
TAAAAATAAAAAAAATAAGA
Found at i:41067668 original size:15 final size:15
Alignment explanation
Indices: 41067631--41067669 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41067621 ATTAAAAATT
41067631 AAAAATAAAAAGAAA
1 AAAAATAAAAAGAAA
* * *
41067646 TAAGATAAAAATAAA
1 AAAAATAAAAAGAAA
41067661 AAAAATAAA
1 AAAAATAAA
41067670 TATTATCATT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAGAAA
Found at i:41068005 original size:29 final size:31
Alignment explanation
Indices: 41067968--41068033 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
41067958 TCTTTACAAA
* *
41067968 TTAAGAATTTAGTCTATATA-TTTTCAT-TT
1 TTAAAAATTTAATCTATATATTTTTCATATT
* *
41067997 TTAAAAATTTAATCTTTTTATTTTTCATATT
1 TTAAAAATTTAATCTATATATTTTTCATATT
41068028 TTAAAA
1 TTAAAA
41068034 TTTTGGTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.52
30 7 0.23
31 8 0.26
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (31 bp):
TTAAAAATTTAATCTATATATTTTTCATATT
Found at i:41073678 original size:19 final size:18
Alignment explanation
Indices: 41073654--41073708 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 18
41073644 AATGTTAAAT
41073654 AATATTTTTATAAATTTTA
1 AATATTTTT-TAAATTTTA
*
41073673 AATATTTTTTAGATTTT-
1 AATATTTTTTAAATTTTA
*
41073690 -ATATATTTTAAATTTTA
1 AATATTTTTTAAATTTTA
41073707 AA
1 AA
41073709 ATAATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 14 0.45
18 8 0.26
19 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATATTTTTTAAATTTTA
Found at i:41073688 original size:18 final size:19
Alignment explanation
Indices: 41073654--41073698 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
41073644 AATGTTAAAT
41073654 AATATTTTTATAAATTTTA
1 AATATTTTTATAAATTTTA
*
41073673 AATATTTTT-TAGATTTTA
1 AATATTTTTATAAATTTTA
*
41073691 TATATTTT
1 AATATTTT
41073699 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
AATATTTTTATAAATTTTA
Found at i:41073740 original size:19 final size:18
Alignment explanation
Indices: 41073718--41073761 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
41073708 AATAATAATG
**
41073718 TAAAAATTTAATATTTTAT
1 TAAAAATTTAA-AAATTAT
41073737 TAAAAAATTTAAAAATTAT
1 T-AAAAATTTAAAAATTAT
41073756 TAAAAA
1 TAAAAA
41073762 ATATGCCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 7 0.32
20 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAAATTTAAAAATTAT
Found at i:41073762 original size:19 final size:20
Alignment explanation
Indices: 41073719--41073763 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
41073709 ATAATAATGT
**
41073719 AAAAATTTAATATTTTATTA
1 AAAAATTTAATAAATTATTA
41073739 AAAAATTTAA-AAATTATTA
1 AAAAATTTAATAAATTATTA
41073758 AAAAAT
1 AAAAAT
41073764 ATGCCTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTTAATAAATTATTA
Found at i:41086413 original size:21 final size:19
Alignment explanation
Indices: 41086389--41086440 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
41086379 GATTAAAATG
41086389 ATTAAAGTTAGAATTTTATAT
1 ATTAAA-TTAGAATTTTAT-T
* *
41086410 ATTAAACAATAAAATTTTATT
1 ATT-AA-ATTAGAATTTTATT
41086431 ATTAAATTAG
1 ATTAAATTAG
41086441 TTGAGATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 7 0.28
22 12 0.48
23 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (19 bp):
ATTAAATTAGAATTTTATT
Found at i:41086694 original size:15 final size:16
Alignment explanation
Indices: 41086674--41086707 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41086664 GGCAAGAAGT
41086674 AAGAAA-TTAGAAGAA
1 AAGAAAGTTAGAAGAA
*
41086689 AAGAAAGTTGGAAGAA
1 AAGAAAGTTAGAAGAA
41086705 AAG
1 AAG
41086708 TGAAAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (16 bp):
AAGAAAGTTAGAAGAA
Found at i:41087305 original size:22 final size:21
Alignment explanation
Indices: 41087274--41087328 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
41087264 TTTCTGTAAT
*
41087274 TTTTTC-TCTTGCCAAACACCA
1 TTTTTCTTCTT-CAAAACACCA
41087295 TTTTTCTTCTTCAAAACACCA
1 TTTTTCTTCTTCAAAACACCA
*
41087316 ATTTTCTTCTTCA
1 TTTTTCTTCTTCA
41087329 TTACCTAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTTCTTCTTCAAAACACCA
Found at i:41092443 original size:26 final size:27
Alignment explanation
Indices: 41092390--41092443 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
41092380 ATTAAAATTT
* *
41092390 AAAAAGTAGAAGGACTAAATTCTTAAA
1 AAAAAGTAGAAGGAATAAATTCTCAAA
* *
41092417 AAAAAGTATAGGGAATAAATT-TCAAA
1 AAAAAGTAGAAGGAATAAATTCTCAAA
41092443 A
1 A
41092444 CTACAAAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAAAGTAGAAGGAATAAATTCTCAAA
Found at i:41099813 original size:30 final size:31
Alignment explanation
Indices: 41099774--41099833 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
41099764 GGAGATGGGA
*
41099774 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
41099805 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
41099834 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:41100005 original size:30 final size:30
Alignment explanation
Indices: 41099944--41100005 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
41099934 GGAGGGGAGG
* * **
41099944 GGAGTAAAAGTTTTGGGGGGAAAGTGGAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
41099974 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
41100004 GG
1 GG
41100006 TTTAGGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
Found at i:41100061 original size:9 final size:9
Alignment explanation
Indices: 41100047--41100083 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41100037 TATAGTTTGA
41100047 TATTCGAAT
1 TATTCGAAT
41100056 TATTCGAAT
1 TATTCGAAT
*
41100065 TATTCGAGT
1 TATTCGAAT
*
41100074 TCTTCGAAT
1 TATTCGAAT
41100083 T
1 T
41100084 TGAAAACTCA
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:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41105078 original size:3 final size:3
Alignment explanation
Indices: 41105070--41105103 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
41105060 CAACCGACCA
*
41105070 ATG ATG ATG ATG ATG ATG ATG CATG TTG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG -ATG ATG ATG ATG
41105104 GCAGTGCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:41107040 original size:6 final size:6
Alignment explanation
Indices: 41107031--41107068 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
41107021 TGCACCACCT
*
41107031 CCTCTG CCTCTC CCTCTC CCTCTC CCTCT- CCTCTC CCT
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCT
41107069 TCTCTCCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.00, C:0.63, G:0.03, T:0.34
Consensus pattern (6 bp):
CCTCTC
Found at i:41112662 original size:10 final size:11
Alignment explanation
Indices: 41112645--41112692 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
41112635 GGCCCATTTT
41112645 TATTTTAAAAA
1 TATTTTAAAAA
41112656 T-TTTT-AAAA
1 TATTTTAAAAA
*
41112665 -ATTTAAAAAA
1 TATTTTAAAAA
41112675 TTATTTTAAAAA
1 -TATTTTAAAAA
41112687 TATTTT
1 TATTTT
41112693 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 7 0.23
10 8 0.26
11 7 0.23
12 9 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:41112710 original size:33 final size:31
Alignment explanation
Indices: 41112644--41112705 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
41112634 CGGCCCATTT
*
41112644 TTATTTTAAAAATTTTTAAAAATTTAAAAAA
1 TTATTTTAAAAATTTTTAAAAATTAAAAAAA
*
41112675 TTATTTTAAAAATATTTT-TAAATTAAAAAAA
1 TTATTTTAAAAAT-TTTTAAAAATTAAAAAAA
41112706 AATTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TTATTTTAAAAATTTTTAAAAATTAAAAAAA
Found at i:41112719 original size:12 final size:11
Alignment explanation
Indices: 41112694--41112718 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41112684 AAATATTTTT
41112694 AAATTAAAAAA
1 AAATTAAAAAA
41112705 AAATTAAAAAA
1 AAATTAAAAAA
41112716 AAA
1 AAA
41112719 AAAGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTAAAAAA
Found at i:41112732 original size:12 final size:11
Alignment explanation
Indices: 41112717--41112784 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
41112707 ATTAAAAAAA
41112717 AAAAAGTATTTT
1 AAAAA-TATTTT
41112729 AAAAATATTTT
1 AAAAATATTTT
41112740 --AAA-A-TTT
1 AAAAATATTTT
* *
41112747 AAAAAAAATTT
1 AAAAATATTTT
* *
41112758 AAAAAGTATGTA
1 AAAAA-TATTTT
41112770 AAAAATATTTT
1 AAAAATATTTT
41112781 AAAA
1 AAAA
41112785 TTAAAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
7 3 0.07
8 1 0.02
9 6 0.13
10 1 0.02
11 22 0.49
12 12 0.27
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:41112735 original size:47 final size:47
Alignment explanation
Indices: 41112669--41112797 Score: 153
Period size: 47 Copynumber: 2.9 Consensus size: 47
41112659 TTAAAAATTT
* *
41112669 AAAAAATTATTTTAAAAATATTTTTAAATTAAAAAAAAATTAAAAAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAA
*
41112716 AAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAAATT------
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAA
* * *
41112757 TAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAATAAAT
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-AAAT
41112798 ATATTTATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
41 32 0.43
42 4 0.05
47 38 0.51
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (47 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAA
Found at i:41113140 original size:96 final size:96
Alignment explanation
Indices: 41112976--41113157 Score: 355
Period size: 96 Copynumber: 1.9 Consensus size: 96
41112966 GGACGGGCCG
*
41112976 CCCGGCCCATGAGCACCTCTAGTGTACGCGAATCCACTTTAAATATACACGTATTAATCTTAAAG
1 CCCGGCCCATGAGCACCTCTAGTGTACGCAAATCCACTTTAAATATACACGTATTAATCTTAAAG
41113041 TAGAGTACGTATCATCATGCATGAAAATCTA
66 TAGAGTACGTATCATCATGCATGAAAATCTA
41113072 CCCGGCCCATGAGCACCTCTAGTGTACGCAAATCCACTTTAAATATACACGTATTAATCTTAAAG
1 CCCGGCCCATGAGCACCTCTAGTGTACGCAAATCCACTTTAAATATACACGTATTAATCTTAAAG
41113137 TAGAGTACGTATCATCATGCA
66 TAGAGTACGTATCATCATGCA
41113158 GGCCCGGGCC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (96 bp):
CCCGGCCCATGAGCACCTCTAGTGTACGCAAATCCACTTTAAATATACACGTATTAATCTTAAAG
TAGAGTACGTATCATCATGCATGAAAATCTA
Found at i:41116084 original size:9 final size:9
Alignment explanation
Indices: 41116067--41116103 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41116057 TGAGTTTTCA
41116067 AATTCGAAT
1 AATTCGAAT
*
41116076 AACTCGAAT
1 AATTCGAAT
41116085 AATTCGAAT
1 AATTCGAAT
41116094 AATTCGAAT
1 AATTCGAAT
41116103 A
1 A
41116104 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41134751 original size:22 final size:22
Alignment explanation
Indices: 41134708--41134751 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41134698 CTAGTTTCAT
* *
41134708 TTAAAAGAAGGAAATGAGAAAA
1 TTAAAAGAAGGAAAGGAAAAAA
41134730 TTAAAAGAAGGAAAGGAAAAAA
1 TTAAAAGAAGGAAAGGAAAAAA
41134752 AAATAGGGGA
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:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (22 bp):
TTAAAAGAAGGAAAGGAAAAAA
Found at i:41142995 original size:18 final size:18
Alignment explanation
Indices: 41142972--41143006 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41142962 AATTCATGTC
41142972 AAATAAA-AAAATTAAAAT
1 AAATAAATAAAA-TAAAAT
41142990 AAATAAATAAAATAAAA
1 AAATAAATAAAATAAAA
41143007 CAATAAATCA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAAATAAAATAAAAT
Found at i:41143002 original size:13 final size:14
Alignment explanation
Indices: 41142972--41143006 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
41142962 AATTCATGTC
41142972 AAATAAAAAAATTA
1 AAATAAAAAAATTA
*
41142986 AAATAAATAAA-TA
1 AAATAAAAAAATTA
41142999 AAATAAAA
1 AAATAAAA
41143007 CAATAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAAAAATTA
Found at i:41143510 original size:59 final size:59
Alignment explanation
Indices: 41143437--41143556 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
41143427 AATTTGGAAT
* * *
41143437 AAAATAATAATAAAAGAATAAGGTCTGACAAGTATAATATTGGGCTCGTATATAATAAA
1 AAAATAATAATAAAAGAATAAGATCTGACAAATATAATATTGGGCTCATATATAATAAA
*
41143496 AAAATAATAATAAAATAATAAGATCTGACAAATATAATATTGGGCTCATATATAATAAA
1 AAAATAATAATAAAAGAATAAGATCTGACAAATATAATATTGGGCTCATATATAATAAA
41143555 AA
1 AA
41143557 TTAAGTCTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.28
Consensus pattern (59 bp):
AAAATAATAATAAAAGAATAAGATCTGACAAATATAATATTGGGCTCATATATAATAAA
Found at i:41146843 original size:36 final size:36
Alignment explanation
Indices: 41146796--41146867 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
41146786 ATTAAAGTAA
41146796 TAATTGTTAGTGTCACTTTTCAATGATAAAAATGGT
1 TAATTGTTAGTGTCACTTTTCAATGATAAAAATGGT
41146832 TAATTGTTAGTGTCACTTTTCAATGATAAAAATGGT
1 TAATTGTTAGTGTCACTTTTCAATGATAAAAATGGT
41146868 AGCTTTCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (36 bp):
TAATTGTTAGTGTCACTTTTCAATGATAAAAATGGT
Found at i:41154096 original size:20 final size:21
Alignment explanation
Indices: 41154062--41154101 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41154052 GATTTAATAT
*
41154062 AAATATATAGTATTATTATTTA
1 AAATATATAG-ATTAATATTTA
41154084 AAATATATA-ATTAATATT
1 AAATATATAGATTAATATT
41154102 ATATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATATATAGATTAATATTTA
Found at i:41155876 original size:19 final size:18
Alignment explanation
Indices: 41155835--41155887 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
41155825 TTACAAAAAT
41155835 ATTCAAAATAAATTT-TAAA
1 ATTCAAAAT--ATTTATAAA
41155854 ATTCAAAATATTTATAAA
1 ATTCAAAATATTTATAAA
*
41155872 CATTCTAAA-ATTTATA
1 -ATTCAAAATATTTATA
41155888 TATATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 11 0.35
19 16 0.52
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTCAAAATATTTATAAA
Found at i:41155884 original size:18 final size:17
Alignment explanation
Indices: 41155844--41155887 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
41155834 TATTCAAAAT
41155844 AAATTT-TAAAATTCAA
1 AAATTTATAAAATTCAA
*
41155860 AATATTTATAAACATTCTA
1 AA-ATTTATAAA-ATTCAA
41155879 AAATTTATA
1 AAATTTATA
41155888 TATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 4 0.17
18 11 0.46
19 7 0.29
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTATAAAATTCAA
Found at i:41155934 original size:20 final size:20
Alignment explanation
Indices: 41155891--41155951 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
41155881 ATTTATATAT
* *
41155891 ATTTTTTAAAAA-TATAAAT
1 ATTTTTAAAAAATTATAAAA
*
41155910 TTTTTTAAAAAATTATAAAA
1 ATTTTTAAAAAATTATAAAA
*
41155930 A-TTTTATAAAAATTTTAAAA
1 ATTTTTA-AAAAATTATAAAA
41155950 AT
1 AT
41155952 ATTCTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 15 0.44
20 19 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTTTAAAAAATTATAAAA
Found at i:41155959 original size:11 final size:11
Alignment explanation
Indices: 41155915--41155960 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
41155905 TAAATTTTTT
41155915 TAAAAA-ATTA
1 TAAAAATATTA
*
41155925 TAAAAATTTTA
1 TAAAAATATTA
41155936 TAAAAAT-TT-
1 TAAAAATATTA
*
41155945 TAAAAATATTC
1 TAAAAATATTA
41155956 TAAAA
1 TAAAA
41155961 TAATAAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
9 7 0.22
10 10 0.31
11 15 0.47
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAAAATATTA
Found at i:41155959 original size:20 final size:20
Alignment explanation
Indices: 41155917--41155960 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
41155907 AATTTTTTTA
*
41155917 AAAAATTATAAAAATTTTAT
1 AAAAATTATAAAAATATTAT
* *
41155937 AAAAATTTTAAAAATATTCT
1 AAAAATTATAAAAATATTAT
41155957 AAAA
1 AAAA
41155961 TAATAAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTATAAAAATATTAT
Found at i:41157153 original size:32 final size:33
Alignment explanation
Indices: 41157100--41157171 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
41157090 GAAGTCAAGT
*
41157100 AATTTTTTAGGGGGACCAAATAA-CATTTTATC
1 AATTTTTTAGGGGGACCAAATAATAATTTTATC
* *
41157132 AATATTTTT-GGGGGTCTAAATAATAATTTTATC
1 AAT-TTTTTAGGGGGACCAAATAATAATTTTATC
41157165 AATTTTT
1 AATTTTT
41157172 ATATGCAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 19 0.54
33 16 0.46
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (33 bp):
AATTTTTTAGGGGGACCAAATAATAATTTTATC
Found at i:41166765 original size:20 final size:20
Alignment explanation
Indices: 41166740--41166779 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41166730 ATAACCATGT
41166740 GTTGTACCTTCTGTTTGAAC
1 GTTGTACCTTCTGTTTGAAC
41166760 GTTGTACCTTCTGTTTGAAC
1 GTTGTACCTTCTGTTTGAAC
41166780 AATCATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (20 bp):
GTTGTACCTTCTGTTTGAAC
Found at i:41171438 original size:26 final size:26
Alignment explanation
Indices: 41171402--41171456 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
41171392 GAAGGGCATC
41171402 CAAACATTGAAGCTAAATTAGGAAAA
1 CAAACATTGAAGCTAAATTAGGAAAA
41171428 CAAACATTGAAGCTAAATTAGGAAAA
1 CAAACATTGAAGCTAAATTAGGAAAA
41171454 CAA
1 CAA
41171457 GGGAAGTGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.18
Consensus pattern (26 bp):
CAAACATTGAAGCTAAATTAGGAAAA
Found at i:41178535 original size:28 final size:28
Alignment explanation
Indices: 41178498--41178553 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
41178488 CACATAATCT
*
41178498 TCATTTTACTTCTTTTAACCCATCATCA
1 TCATTTTACTTCTCTTAACCCATCATCA
41178526 TCATTTTACTTCTCTTAACCCATCATCA
1 TCATTTTACTTCTCTTAACCCATCATCA
41178554 GAAACAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (28 bp):
TCATTTTACTTCTCTTAACCCATCATCA
Found at i:41180880 original size:7 final size:7
Alignment explanation
Indices: 41180868--41180892 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41180858 AGTCGTTTCA
41180868 TATTTAG
1 TATTTAG
41180875 TATTTAG
1 TATTTAG
41180882 TATTTAG
1 TATTTAG
41180889 TATT
1 TATT
41180893 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:41182792 original size:127 final size:127
Alignment explanation
Indices: 41182636--41182895 Score: 466
Period size: 127 Copynumber: 2.0 Consensus size: 127
41182626 ACTAATGTAG
* * * *
41182636 AAAAAGAGCGTCCACGTGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGCTTGTAGCG
1 AAAAATAGCGTCCACGTAGAAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGCTTGAAGCG
*
41182701 TTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAAA
66 TTTTTGACACTATTTGTTCAGAACAGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAAA
*
41182763 AAAAATAGCGTCCACGTAGAAGCTTTTTTCGTCAATTTTGCTGACAGTGCATCCTGCTTGAAGCG
1 AAAAATAGCGTCCACGTAGAAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGCTTGAAGCG
41182828 TTTTTGACACTATTTGTTCAGAACAGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAAA
66 TTTTTGACACTATTTGTTCAGAACAGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAAA
41182890 AAAAAT
1 AAAAAT
41182896 CCTTATTGTC
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (127 bp):
AAAAATAGCGTCCACGTAGAAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGCTTGAAGCG
TTTTTGACACTATTTGTTCAGAACAGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAAA
Found at i:41182995 original size:34 final size:33
Alignment explanation
Indices: 41182951--41183074 Score: 133
Period size: 34 Copynumber: 3.7 Consensus size: 33
41182941 AACTTATTTA
*
41182951 AAAAAATCTAAACCCTAATTTAATTAATTTTCTT
1 AAAAACTCTAAACCCTAATTTAATTAATTTT-TT
*
41182985 AAAAACTCTAAACCCTAAGTTAATTAATTTATTT
1 AAAAACTCTAAACCCTAATTTAATTAATTT-TTT
* * **
41183019 AAAACCCCTAAAATCTAATTTAATTATTATTTTTT
1 AAAAACTCTAAACCCTAATTTAATTA--ATTTTTT
* *
41183054 AAAAACAC-ATACCCTAATTTA
1 AAAAACTCTAAACCCTAATTTA
41183075 TTTTTTAAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
34 61 0.81
35 10 0.13
36 4 0.05
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.39
Consensus pattern (33 bp):
AAAAACTCTAAACCCTAATTTAATTAATTTTTT
Found at i:41183103 original size:28 final size:27
Alignment explanation
Indices: 41183044--41183106 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
41183034 TAATTTAATT
*
41183044 ATTATTTTTTAAAAACACATACCCTAA
1 ATTATTTTTTAAAAACACAAACCCTAA
* * * *
41183071 TTTATTTTTTAAAATCCCTAAACCTTAA
1 ATTATTTTTTAAAAACAC-AAACCCTAA
41183099 ATTATTTT
1 ATTATTTT
41183107 AACCCTAACC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTATTTTTTAAAAACACAAACCCTAA
Found at i:41197591 original size:46 final size:46
Alignment explanation
Indices: 41197524--41197708 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
41197514 ACATTGCTAT
* *
41197524 AACTCAGTATGGTTTTCTTCACGGAAATACCGTACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACGGAAACACCATACCTACTTTTCAC
41197570 AACTCAGTATGGTTTTCTTCACGGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACGGAAACACCATACCTACTTTTCAC
*
41197616 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACGGAAACACCATACCTACTTTTCAC
* * * *
41197662 AATTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACGGAAACACCATACCTACTTTTCAC
41197708 A
1 A
41197709 CTTTGCCATG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACGGAAACACCATACCTACTTTTCAC
Found at i:41198404 original size:252 final size:252
Alignment explanation
Indices: 41197959--41198470 Score: 1015
Period size: 252 Copynumber: 2.0 Consensus size: 252
41197949 GTTCAGAAAC
41197959 TAATTCAATACTTTTTCTTTTCCGCGTTTATCTTCGAATTCTCGATCTATAATATAAAATTTTCC
1 TAATTCAATACTTTTTCTTTTCCGCGTTTATCTTCGAATTCTCGATCTATAATATAAAATTTTCC
41198024 ATTTATTAGCATCTAATTCAATACTAATTTACTTCACAATTTATGCCTTTTAATTTTCGAAATTA
66 ATTTATTAGCATCTAATTCAATACTAATTTACTTCACAATTTATGCCTTTTAATTTTCGAAATTA
41198089 CACTTTTACCCCCAAAATTAACAATTTTTACAATTTGGTCCCTACTCAATTAACCCTTCAATTGA
131 CACTTTTACCCCCAAAATTAACAATTTTTACAATTTGGTCCCTACTCAATTAACCCTTCAATTGA
41198154 TCTAATTTTTCTCAATTAACACCTTATCCAACCATTTTAGACTACTAAAAAGCCTTT
196 TCTAATTTTTCTCAATTAACACCTTATCCAACCATTTTAGACTACTAAAAAGCCTTT
41198211 TAATTCAATACTTTTTCTTTTCCGCGTTTATCTTCGAATTCTCGATCTATAATATAAAATTTTCC
1 TAATTCAATACTTTTTCTTTTCCGCGTTTATCTTCGAATTCTCGATCTATAATATAAAATTTTCC
41198276 ATTTATTAGCATCTAATTCAATACTAATTTACTTCACAATTTATGCCTTTTAATTTTCGAAATTA
66 ATTTATTAGCATCTAATTCAATACTAATTTACTTCACAATTTATGCCTTTTAATTTTCGAAATTA
41198341 CACTTTTACCCCCAAAATTAACAATTTTTACAATTTGGTCCCTACTCAATTAACCCTTCAATTGA
131 CACTTTTACCCCCAAAATTAACAATTTTTACAATTTGGTCCCTACTCAATTAACCCTTCAATTGA
41198406 TCTAATTTTTCTCAATTAACACCTTATCCAACCATTTTAGACTACTAAAAAGCCTTT
196 TCTAATTTTTCTCAATTAACACCTTATCCAACCATTTTAGACTACTAAAAAGCCTTT
41198463 TATATTCA
1 TA-ATTCA
41198471 TAATTTCAGT
Statistics
Matches: 259, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
252 254 0.98
253 5 0.02
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (252 bp):
TAATTCAATACTTTTTCTTTTCCGCGTTTATCTTCGAATTCTCGATCTATAATATAAAATTTTCC
ATTTATTAGCATCTAATTCAATACTAATTTACTTCACAATTTATGCCTTTTAATTTTCGAAATTA
CACTTTTACCCCCAAAATTAACAATTTTTACAATTTGGTCCCTACTCAATTAACCCTTCAATTGA
TCTAATTTTTCTCAATTAACACCTTATCCAACCATTTTAGACTACTAAAAAGCCTTT
Found at i:41209873 original size:22 final size:21
Alignment explanation
Indices: 41209848--41209900 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
41209838 ATAATAAAAA
41209848 AATAAAAATTATTAAAAATTTT
1 AATAAAAATTATTAAAAA-TTT
*
41209870 AATAAAAA-TATTTAAAATTT
1 AATAAAAATTATTAAAAATTT
*
41209890 ACTAAAAATTA
1 AATAAAAATTA
41209901 GAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.36
21 10 0.36
22 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAAAAATTATTAAAAATTT
Found at i:41209909 original size:32 final size:32
Alignment explanation
Indices: 41209849--41209922 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
41209839 TAATAAAAAA
* ** *
41209849 ATAAAAATTATTAAAAATTTTAATAAAAATATT
1 ATAAAAATTACTAAAAATTAGAA-AAAAAAATT
*
41209882 -TAAAATTTACTAAAAATTAGAAAAAAAAATT
1 ATAAAAATTACTAAAAATTAGAAAAAAAAATT
41209913 ATAAAAATTA
1 ATAAAAATTA
41209923 GAAAAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (32 bp):
ATAAAAATTACTAAAAATTAGAAAAAAAAATT
Found at i:41209911 original size:13 final size:13
Alignment explanation
Indices: 41209893--41209941 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
41209883 AAAATTTACT
41209893 AAAAATTAGAAAA
1 AAAAATTAGAAAA
*
41209906 AAAAATT----AT
1 AAAAATTAGAAAA
41209915 AAAAATTAGAAAA
1 AAAAATTAGAAAA
*
41209928 AAAAATTATAAAA
1 AAAAATTAGAAAA
41209941 A
1 A
41209942 TCGTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
9 8 0.28
13 21 0.72
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAATTAGAAAA
Found at i:41209929 original size:19 final size:20
Alignment explanation
Indices: 41209892--41209969 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 20
41209882 TAAAATTTAC
41209892 TAAAAATTAGAAAAAAAAATTA
1 TAAAAATTAG--AAAAAAATTA
41209914 TAAAAATTAGAAAAAAAAATTA
1 TAAAAATTAG--AAAAAAATTA
* * *
41209936 TAAAAA-TCGTAAAAAAGTA
1 TAAAAATTAGAAAAAAATTA
41209955 TAAAATATATAGAAA
1 TAAAA-AT-TAGAAA
41209970 TATAGAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
19 13 0.27
20 1 0.02
21 2 0.04
22 32 0.67
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.23
Consensus pattern (20 bp):
TAAAAATTAGAAAAAAATTA
Found at i:41209940 original size:9 final size:9
Alignment explanation
Indices: 41209835--41210061 Score: 54
Period size: 10 Copynumber: 24.9 Consensus size: 9
41209825 ATGTGGTAAC
*
41209835 AAAATAATA
1 AAAATTATA
*
41209844 AAAA-AATA
1 AAAATTATA
41209852 AAAATTATTA
1 AAAATTA-TA
41209862 AAAATTTTAATA
1 AAAA--TT-ATA
*
41209874 AAAATATTTA
1 AAAAT-TATA
*
41209884 AAATTTACTA
1 AAAATTA-TA
41209894 AAAA-T-TA
1 AAAATTATA
*
41209901 GAAA--A-A
1 AAAATTATA
41209907 AAAATTATA
1 AAAATTATA
41209916 AAAA-T-TA
1 AAAATTATA
*
41209923 GAAA--A-A
1 AAAATTATA
41209929 AAAATTATA
1 AAAATTATA
41209938 AAAATCGTA-A
1 AAAAT--TATA
*
41209948 AAAAGTAT-
1 AAAATTATA
41209956 AAAATATATA
1 AAAAT-TATA
* *
41209966 GAAATATAGAA
1 AAAAT-TA-TA
41209977 AAAATTAT-
1 AAAATTATA
*
41209985 AAAATTTTA
1 AAAATTATA
*
41209994 TAAAGTCGTA-A
1 -AAAAT--TATA
41210005 GAAAATTATA
1 -AAAATTATA
41210015 AAAATATATA
1 AAAAT-TATA
41210025 AAAA-TATA
1 AAAATTATA
* *
41210033 AAATTTGTAAA
1 AAA-AT-TATA
41210044 AAGAATTATA
1 AA-AATTATA
41210054 AAAATTAT
1 AAAATTAT
41210062 CTTACCAAAG
Statistics
Matches: 163, Mismatches: 24, Indels: 62
0.65 0.10 0.25
Matches are distributed among these distances:
6 8 0.05
7 10 0.06
8 31 0.19
9 34 0.21
10 50 0.31
11 19 0.12
12 10 0.06
13 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:41209951 original size:22 final size:22
Alignment explanation
Indices: 41209883--41209942 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
41209873 AAAAATATTT
*
41209883 AAAATTTACTAAAAATTAGAAAA
1 AAAAATTA-TAAAAATTAGAAAA
41209906 AAAAATTATAAAAATTAGAAAA
1 AAAAATTATAAAAATTAGAAAA
41209928 AAAAATTATAAAAAT
1 AAAAATTATAAAAAT
41209943 CGTAAAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 29 0.81
23 7 0.19
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAAATTATAAAAATTAGAAAA
Found at i:41210018 original size:39 final size:38
Alignment explanation
Indices: 41209976--41210061 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
41209966 GAAATATAGA
* * *
41209976 AAAAATTATAAAATTTTATAAAGTCGTAAGAA-AATTAT
1 AAAAATTATAAAAATATA-AAAGTCGTAAAAAGAATTAT
* *
41210014 AAAAATATATAAAAATATAAAATTTGTAAAAAGAATTAT
1 AAAAAT-TATAAAAATATAAAAGTCGTAAAAAGAATTAT
41210053 AAAAATTAT
1 AAAAATTAT
41210062 CTTACCAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 19 0.46
39 22 0.54
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (38 bp):
AAAAATTATAAAAATATAAAAGTCGTAAAAAGAATTAT
Found at i:41210289 original size:20 final size:19
Alignment explanation
Indices: 41210238--41210279 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
41210228 TTAAATGTCC
*
41210238 TTTTTATGCATTTTAT-AT
1 TTTTTATGAATTTTATAAT
41210256 TTTTTATGAATTTTATAAT
1 TTTTTATGAATTTTATAAT
41210275 TTTTT
1 TTTTT
41210280 TTCTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTATGAATTTTATAAT
Found at i:41210343 original size:30 final size:29
Alignment explanation
Indices: 41210257--41210367 Score: 84
Period size: 31 Copynumber: 3.8 Consensus size: 29
41210247 ATTTTATATT
* * * *
41210257 TTTTATGAATTTTATAATTTTTTTTCTAAT
1 TTTTATAAATTTTATAATTTTTATT-AAAA
* *
41210287 TTTTAATAAATTTAAAATATTTTTTATTAAAA
1 TTTT-ATAAATTT--TATAATTTTTATTAAAA
41210319 TTTTATAAATTTTATAACTTTTTATT--AA
1 TTTTATAAATTTTATAA-TTTTTATTAAAA
**
41210347 TTTT-TATTTTTTATAATTTTT
1 TTTTATAAATTTTATAATTTTT
41210368 TTGCCACATG
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
26 5 0.07
27 10 0.15
28 6 0.09
29 3 0.04
30 12 0.18
31 15 0.22
32 6 0.09
33 10 0.15
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTATAAATTTTATAATTTTTATTAAAA
Found at i:41210351 original size:20 final size:20
Alignment explanation
Indices: 41210256--41210353 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 20
41210246 CATTTTATAT
* *
41210256 TTTTTATGAA-TTTTATAAT
1 TTTTTATTAATTTTTATAAA
*
41210275 TTTTTTTCTAATTTTTAATAAA
1 TTTTTAT-TAATTTTT-ATAAA
** * *
41210297 TTTAAAATATTTTTTATTAAA
1 TTTTTATTAATTTTTA-TAAA
* * *
41210318 ATTTTA-TAAATTTTATAAC
1 TTTTTATTAATTTTTATAAA
41210337 TTTTTATTAATTTTTAT
1 TTTTTATTAATTTTTAT
41210354 TTTTTATAAT
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
19 14 0.24
20 19 0.33
21 18 0.31
22 7 0.12
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTTATTAATTTTTATAAA
Found at i:41210366 original size:9 final size:9
Alignment explanation
Indices: 41210319--41210367 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
41210309 TTTATTAAAA
*
41210319 TTTTATAAA
1 TTTTATAAT
41210328 TTTTATAACT
1 TTTTATAA-T
41210338 TTTTATTAAT
1 TTTTA-TAAT
41210348 TTTTAT--T
1 TTTTATAAT
41210355 TTTTATAAT
1 TTTTATAAT
41210364 TTTT
1 TTTT
41210368 TTGCCACATG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 7 0.20
9 14 0.40
10 11 0.31
11 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTATAAT
Found at i:41213149 original size:40 final size:40
Alignment explanation
Indices: 41213079--41213204 Score: 139
Period size: 41 Copynumber: 3.0 Consensus size: 40
41213069 ACCAAAAATT
*
41213079 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTGAAA
1 TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTTAAAA
41213122 TATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTTTTAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTA--TTTTAAAA
* * *
41213163 -ATTTAAAAACTTTAAAAAATTTAAAAAAAAGTATTTTAAAA
1 TATTTTAAAA-TTAAAAAAAATT-AAAAAAAGTATTTTAAAA
41213204 T
1 T
41213205 TAAAAAAATA
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
39 9 0.12
40 15 0.21
41 28 0.38
42 6 0.08
43 15 0.21
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAA
Found at i:41213176 original size:9 final size:8
Alignment explanation
Indices: 41213156--41213189 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
41213146 AAAAGTATTT
41213156 TTTAAAAA
1 TTTAAAAA
41213164 TTTAAAAA
1 TTTAAAAA
41213172 CTTTAAAAAA
1 -TTT-AAAAA
41213182 TTTAAAAA
1 TTTAAAAA
41213190 AAAGTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 13 0.54
9 6 0.25
10 5 0.21
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (8 bp):
TTTAAAAA
Found at i:41213180 original size:41 final size:41
Alignment explanation
Indices: 41213082--41213219 Score: 142
Period size: 40 Copynumber: 3.4 Consensus size: 41
41213072 AAAAATTTAT
*
41213082 TTTAAAAATTAAAACAAAAATTAAAAAAAGTA-TTTTGAAATA
1 TTTAAAAATT-AAA-AAAAATTAAAAAAAGTATTTTTGAAAAA
* *
41213124 TTTTAAAATTAAAAAAAATT-AAAAAAGTATTTTTTAAAAA
1 TTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTTGAAAAA
* *
41213164 TTTAAAAACTTTAAAAAATTTAAAAAAAAGTA-TTTT--AAAA
1 TTTAAAAA-TTAAAAAAAATT-AAAAAAAGTATTTTTGAAAAA
* *
41213204 TTAAAAAAATAAAAAA
1 TTTAAAAATTAAAAAA
41213220 TAAAAATATT
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
39 15 0.18
40 33 0.40
41 13 0.16
42 13 0.16
43 9 0.11
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (41 bp):
TTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTTGAAAAA
Found at i:41213190 original size:9 final size:9
Alignment explanation
Indices: 41213159--41213190 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
41213149 AGTATTTTTT
41213159 AAAAATTTA
1 AAAAATTTA
*
41213168 AAAACTTTA
1 AAAAATTTA
41213177 AAAAATTTA
1 AAAAATTTA
41213186 AAAAA
1 AAAAA
41213191 AAGTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAATTTA
Found at i:41213303 original size:31 final size:32
Alignment explanation
Indices: 41213247--41213325 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 32
41213237 TTCGGGCTGA
41213247 GCCCG-GGCCGGGCCCGGGCCAAAAAAGTGGT
1 GCCCGAGGCCGGGCCCGGGCCAAAAAAGTGGT
*
41213278 GCCCGAGGCTGGGCCCGGGCCAAAAAAGTGGT
1 GCCCGAGGCCGGGCCCGGGCCAAAAAAGTGGT
41213310 GCCCGAGGCCGGGCCC
1 GCCCGAGGCCGGGCCC
41213326 TTTTTTAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 5 0.11
32 40 0.89
ACGTcount: A:0.18, C:0.34, G:0.42, T:0.06
Consensus pattern (32 bp):
GCCCGAGGCCGGGCCCGGGCCAAAAAAGTGGT
Found at i:41219790 original size:27 final size:28
Alignment explanation
Indices: 41219731--41219795 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
41219721 AATTTAAGAC
41219731 GAGATTTGGGGATTTTTTTTATTATTTA
1 GAGATTTGGGGATTTTTTTTATTATTTA
* *
41219759 AAGATTTGGGG-TTTTTTTTTTTAATTT-
1 GAGATTTGGGGATTTTTTTTATT-ATTTA
41219786 GAGATTTGGG
1 GAGATTTGGG
41219796 AATGTGAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.58
28 14 0.42
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (28 bp):
GAGATTTGGGGATTTTTTTTATTATTTA
Found at i:41224558 original size:30 final size:28
Alignment explanation
Indices: 41224523--41224601 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
41224513 TGATTCATCC
41224523 ATGGAAAATAAAATAAAAAAAATGATGAA
1 ATGGAAAATAAAATAAAAAAAATGAT-AA
* * *
41224552 ATTGGAAAGTGAAATAATAAAAGATGATAA
1 A-TGGAAAATAAAATAA-AAAAAATGATAA
41224582 AT-GATAAATAAAAATAAAAA
1 ATGGA-AAAT-AAAATAAAAA
41224602 TATCATCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.05
29 8 0.20
30 22 0.54
31 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (28 bp):
ATGGAAAATAAAATAAAAAAAATGATAA
Found at i:41225665 original size:25 final size:25
Alignment explanation
Indices: 41225631--41225688 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
41225621 GAGCGTCTTG
*
41225631 ATATGACTCGCTTGAACTTCCCAAT
1 ATATGGCTCGCTTGAACTTCCCAAT
*
41225656 ATATGGCTCGCTTGAACTTCCCGAT
1 ATATGGCTCGCTTGAACTTCCCAAT
41225681 ATATGGCT
1 ATATGGCT
41225689 ATCCGAAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (25 bp):
ATATGGCTCGCTTGAACTTCCCAAT
Found at i:41229759 original size:13 final size:13
Alignment explanation
Indices: 41229738--41229786 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
41229728 TTCTAGCACA
41229738 TGGGCGTGTGACC
1 TGGGCGTGTGACC
*
41229751 TGGGTGTGTGACC
1 TGGGCGTGTGACC
*
41229764 TGGGCGTATGACC
1 TGGGCGTGTGACC
41229777 TGGGCGTGTG
1 TGGGCGTGTG
41229787 TCCCCTGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.08, C:0.18, G:0.47, T:0.27
Consensus pattern (13 bp):
TGGGCGTGTGACC
Found at i:41230608 original size:24 final size:23
Alignment explanation
Indices: 41230555--41230666 Score: 106
Period size: 23 Copynumber: 4.9 Consensus size: 23
41230545 CTACTCTGTT
*
41230555 TTGGACAACATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
*
41230578 TTGGACAGCATTTATATACTCAAAA
1 TTGGACAGCATTTATACA-TC-AAA
41230603 TT-GACAGCA-TTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
* * *
41230624 TTGGACAACATCAATATGC-TCAAA
1 TTGGACAGCAT--TTATACATCAAA
*
41230648 ATGGACAGCA-TTATACATC
1 TTGGACAGCATTTATACATC
41230667 TAAAAACAAC
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
21 9 0.12
22 10 0.14
23 22 0.31
24 22 0.31
25 9 0.12
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (23 bp):
TTGGACAGCATTTATACATCAAA
Found at i:41230617 original size:46 final size:46
Alignment explanation
Indices: 41230556--41230666 Score: 159
Period size: 46 Copynumber: 2.4 Consensus size: 46
41230546 TACTCTGTTT
* * **
41230556 TGGACAACATTTATACATCAAATTGGACAGCATTTATATACTCAAAA
1 TGGACAGCA-TTATACATCAAATTGGACAACATCAATATACTCAAAA
* *
41230603 TTGACAGCATTATACATCAAATTGGACAACATCAATATGCTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAACATCAATATACTCAAAA
41230649 TGGACAGCATTATACATC
1 TGGACAGCATTATACATC
41230667 TAAAAACAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 50 0.88
47 7 0.12
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (46 bp):
TGGACAGCATTATACATCAAATTGGACAACATCAATATACTCAAAA
Found at i:41230672 original size:24 final size:23
Alignment explanation
Indices: 41230556--41230671 Score: 87
Period size: 24 Copynumber: 5.0 Consensus size: 23
41230546 TACTCTGTTT
* *
41230556 TGGACAACATTTATACATC-AAAT
1 TGGACAGCA-TTATACATCTAAAA
*
41230579 TGGACAGCATT-TATATACTCAAAA
1 TGGACAGCATTATACAT-CT-AAAA
* *
41230603 TTGACAGCATTATACATC-AAAT
1 TGGACAGCATTATACATCTAAAA
* * *
41230625 TGGACAACATCA-ATATGCTCAAAA
1 TGGACAGCATTATACAT-CT-AAAA
41230649 TGGACAGCATTATACATCTAAAA
1 TGGACAGCATTATACATCTAAAA
41230672 ACAACCACAT
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
21 7 0.10
22 16 0.23
23 12 0.17
24 29 0.41
25 7 0.10
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (23 bp):
TGGACAGCATTATACATCTAAAA
Found at i:41231357 original size:41 final size:38
Alignment explanation
Indices: 41231310--41231447 Score: 116
Period size: 41 Copynumber: 3.4 Consensus size: 38
41231300 TTGCCATCGT
41231310 ATAGCCGAAGCTATTATAATCCCGCACACTAAGTGCCTTA
1 ATAGCCGAAGCTATTA-AAT-CCGCACACTAAGTGCCTTA
* * *
41231350 CATAGCCGAAGCTATCTCAGTCACACACACTAAGTGCCATATA
1 -ATAGCCGAAGCTAT-TAAATC-CGCACACTAAGTGCC-T-TA
* * *
41231393 TATAACCGAAGCTATTCCAAAT-CGCACACTAAGTGTCATA
1 -ATAGCCGAAGCTATT--AAATCCGCACACTAAGTGCCTTA
41231433 ATTAGCCGAAGCTAT
1 A-TAGCCGAAGCTAT
41231448 CTCAAATTTC
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
39 1 0.01
40 15 0.19
41 30 0.38
42 16 0.20
43 15 0.19
44 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (38 bp):
ATAGCCGAAGCTATTAAATCCGCACACTAAGTGCCTTA
Found at i:41231624 original size:94 final size:94
Alignment explanation
Indices: 41231463--41231653 Score: 310
Period size: 94 Copynumber: 2.0 Consensus size: 94
41231453 ATTTCATACT
* ** * *
41231463 AAGTGCTAAACATAGCCGATTTATCGTTAAACATGATTGTATTCTCGTGTATACAATTTATGCAA
1 AAGTGCTAAACATAACCGATTTATCGTTAAACATGACCGTATTCTAGTGTATACAATTTATACAA
41231528 TAACAAAGCATTAAAAGCATAATTGTAAC
66 TAACAAAGCATTAAAAGCATAATTGTAAC
**
41231557 AAGTGCTAAACATAATTGATTTATCGTTAAACATGACCGTATTCTAGTGTATACAATTTATACAA
1 AAGTGCTAAACATAACCGATTTATCGTTAAACATGACCGTATTCTAGTGTATACAATTTATACAA
*
41231622 TAACAAAGCATTAAAATCATAATTGTAAC
66 TAACAAAGCATTAAAAGCATAATTGTAAC
41231651 AAG
1 AAG
41231654 GTTTATTGCG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 89 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (94 bp):
AAGTGCTAAACATAACCGATTTATCGTTAAACATGACCGTATTCTAGTGTATACAATTTATACAA
TAACAAAGCATTAAAAGCATAATTGTAAC
Found at i:41245482 original size:41 final size:41
Alignment explanation
Indices: 41245425--41245719 Score: 319
Period size: 41 Copynumber: 7.2 Consensus size: 41
41245415 TGAGCTTTCG
*
41245425 GGGCTTTAGCGGCGTTTTTGAGTAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCA
* *
41245466 GGGCTTTAGTGGCGTTTTTGGGGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCA
* * * *
41245507 GGGCTTTAGCGGCGTTTTTGGGGAAGCGCTGCTAATGTTTA
1 GGGCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCA
* *
41245548 GGGCTTTAGCAGCGTTTTT-AGGAAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAGG-AAGCGCCGCTAATGCTCA
*
41245589 GGGCTTTAGCGGCGTTTTTG-GGATAGCGCTGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGGA-AGCGCCGCTAATGCTCA
* * ** *
41245630 TGGCTTTTAGCGGTGTTTTTGATAAAGCGCCGCGAATGCTCTA
1 GGGC-TTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTC-A
** * * ** *
41245673 --TTTTTAGCGGTGTTTTTTAAAAAGCGCCGTTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCA
*
41245712 GGGATTTA
1 GGGCTTTA
41245720 AAATAATTTA
Statistics
Matches: 218, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.00
40 35 0.16
41 151 0.69
42 29 0.13
43 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCA
Found at i:41245689 original size:40 final size:40
Alignment explanation
Indices: 41245634--41245710 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
41245624 TGCTCATGGC
*
41245634 TTTTAGCGGTGTTTTTGATAAAGCGCCGCGAATGCTCTAT
1 TTTTAGCGGTGTTTTTGAAAAAGCGCCGCGAATGCTCTAT
* **
41245674 TTTTAGCGGTGTTTTTTAAAAAGCGCCGTTAATGCTC
1 TTTTAGCGGTGTTTTTGAAAAAGCGCCGCGAATGCTC
41245711 AGGGATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (40 bp):
TTTTAGCGGTGTTTTTGAAAAAGCGCCGCGAATGCTCTAT
Found at i:41245951 original size:7 final size:7
Alignment explanation
Indices: 41245912--41246049 Score: 68
Period size: 7 Copynumber: 19.6 Consensus size: 7
41245902 GGTGTTACCA
*
41245912 TTTAAGG
1 TTTATGG
*
41245919 TTTGTGG
1 TTTATGG
*
41245926 ATTATGGG
1 TTTAT-GG
41245934 TTTA-GG
1 TTTATGG
*
41245940 GTTATGG
1 TTTATGG
41245947 TTTATGG
1 TTTATGG
**
41245954 TTTACAG
1 TTTATGG
*
41245961 TTTACGG
1 TTTATGG
41245968 TTTATGG
1 TTTATGG
*
41245975 TTTAAAGG
1 TTT-ATGG
**
41245983 -TTGGGG
1 TTTATGG
*
41245989 TTTAAGG
1 TTTATGG
41245996 TTTA-GAG
1 TTTATG-G
*
41246003 GTTATGTG
1 TTTATG-G
*
41246011 TTAATGG
1 TTTATGG
41246018 TTTATGG
1 TTTATGG
*
41246025 TTTTAGGG
1 -TTTATGG
*
41246033 TTTA-AG
1 TTTATGG
41246039 TTTATGG
1 TTTATGG
41246046 TTTA
1 TTTA
41246050 AGATTTAGAT
Statistics
Matches: 99, Mismatches: 24, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
6 13 0.13
7 66 0.67
8 20 0.20
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (7 bp):
TTTATGG
Found at i:41245953 original size:21 final size:20
Alignment explanation
Indices: 41245912--41246026 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 20
41245902 GGTGTTACCA
* *
41245912 TTTAAGGTTTGTGGATTATGGG
1 TTTAAGG-TTATGGTTTAT-GG
*
41245934 TTTAGGGTTATGGTTTATGG
1 TTTAAGGTTATGGTTTATGG
* *
41245954 TTTACAGTTTACGGTTTATGG
1 TTTA-AGGTTATGGTTTATGG
** *
41245975 TTTAAAGGTTGGGGTTTAAGG
1 TTT-AAGGTTATGGTTTATGG
*
41245996 TTTAGAGGTTATGTGTTAATGG
1 TTTA-AGGTTATG-GTTTATGG
*
41246018 TTTATGGTT
1 TTTAAGGTT
41246027 TTAGGGTTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
20 7 0.09
21 50 0.68
22 17 0.23
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (20 bp):
TTTAAGGTTATGGTTTATGG
Found at i:41246357 original size:14 final size:14
Alignment explanation
Indices: 41246347--41246377 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41246337 GATTTAAGGT
41246347 TTAAGGGTTAAGAG
1 TTAAGGGTTAAGAG
*
41246361 TTATGGGTTAAGAG
1 TTAAGGGTTAAGAG
41246375 TTA
1 TTA
41246378 GTGATTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAAGAG
Found at i:41246371 original size:21 final size:21
Alignment explanation
Indices: 41246319--41246377 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
41246309 GATTTAGGAA
** *
41246319 TTATGGTTTAAGGGTTGGGAT
1 TTATGGTTTAAGGGTTAAGAG
*
41246340 TTAAGGTTTAAGGGTTAAGAG
1 TTATGGTTTAAGGGTTAAGAG
* *
41246361 TTATGGGTTAAGAGTTA
1 TTATGGTTTAAGGGTTA
41246378 GTGATTTAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (21 bp):
TTATGGTTTAAGGGTTAAGAG
Found at i:41248657 original size:14 final size:14
Alignment explanation
Indices: 41248638--41248666 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41248628 GATCGTACAG
41248638 CTTATTTGTAGTAA
1 CTTATTTGTAGTAA
41248652 CTTATTTGTAGTAA
1 CTTATTTGTAGTAA
41248666 C
1 C
41248667 GTGCTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (14 bp):
CTTATTTGTAGTAA
Found at i:41250318 original size:43 final size:43
Alignment explanation
Indices: 41250243--41250470 Score: 271
Period size: 43 Copynumber: 5.3 Consensus size: 43
41250233 AGATTATGTT
* ** * *
41250243 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
41250285 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCTTGGTC
*
41250329 TATAGCGGCGTTTGT-GGAAATAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAA-AGCGCCGCTAAAGGTCTTGGTC
* * * * *
41250372 TTTAGAGGCGTTTGTGGGAGAAGCGCCGCTAAAGATTTTTGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * *
41250415 TTTAGCGGCATTTGTGGGAGAAGCGCCGTTAAAAGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
41250458 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
41250471 AGCGGCGTAT
Statistics
Matches: 159, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
42 18 0.11
43 119 0.75
44 22 0.14
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:41258681 original size:43 final size:43
Alignment explanation
Indices: 41258632--41258714 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
41258622 CAAAAGAAAG
41258632 CAAAGAATTAATAGAGCATTAGATGAAGAATTCTAATGAAAAC
1 CAAAGAATTAATAGAGCATTAGATGAAGAATTCTAATGAAAAC
41258675 CAAAGAATTAATAGAGCATTAGATGAAGAATTCTAATGAA
1 CAAAGAATTAATAGAGCATTAGATGAAGAATTCTAATGAA
41258715 TTTTCATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (43 bp):
CAAAGAATTAATAGAGCATTAGATGAAGAATTCTAATGAAAAC
Found at i:41274748 original size:14 final size:14
Alignment explanation
Indices: 41274725--41274755 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41274715 TGTTGCATTC
*
41274725 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
41274739 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
41274753 TTA
1 TTA
41274756 AAACAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:41278530 original size:15 final size:16
Alignment explanation
Indices: 41278510--41278540 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
41278500 CCCATACCCA
41278510 CCCTTTCC-CCCTATT
1 CCCTTTCCTCCCTATT
41278525 CCCTTTCCTCCCTATT
1 CCCTTTCCTCCCTATT
41278541 TGAACCACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.06, C:0.52, G:0.00, T:0.42
Consensus pattern (16 bp):
CCCTTTCCTCCCTATT
Found at i:41279142 original size:6 final size:6
Alignment explanation
Indices: 41279131--41279202 Score: 65
Period size: 6 Copynumber: 11.7 Consensus size: 6
41279121 ATTCCATTTG
* ** *
41279131 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT GTTTAT GGTTATT TTCTTAG
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TT-TTAT
*
41279181 TCTTA- TTTTAT TTTTAT CTTTT
1 TTTTAT TTTTAT TTTTAT -TTTT
41279203 GAACTAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
5 4 0.07
6 42 0.76
7 6 0.11
8 3 0.05
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:41281887 original size:14 final size:14
Alignment explanation
Indices: 41281864--41281894 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41281854 TGTCTCGTTC
*
41281864 TTAGTCAATTTAGA
1 TTAGTAAATTTAGA
41281878 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
41281892 TTA
1 TTA
41281895 AAACAATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:41282651 original size:92 final size:92
Alignment explanation
Indices: 41282487--41282673 Score: 320
Period size: 92 Copynumber: 2.0 Consensus size: 92
41282477 CAATTTGTCA
** *
41282487 TTTTTAGGTGAAGGTGAAGTCTTTTTTGTTTGGGTTAATCATAGTATGGTTAATGATTACTTTGT
1 TTTTTAGGCAAAGGTGAAGTCTTTGTTGTTTGGGTTAATCATAGTATGGTTAATGATTACTTTGT
* *
41282552 GGTTATTTCAATGTACAAAATGACATC
66 AGCTATTTCAATGTACAAAATGACATC
*
41282579 TTTTTAGGCAAAGGTGAAGTCTTTGTTGTTTGGGTTAATCATTGTATGGTTAATGATTACTTTGT
1 TTTTTAGGCAAAGGTGAAGTCTTTGTTGTTTGGGTTAATCATAGTATGGTTAATGATTACTTTGT
41282644 AGCTATTTCAATGTACAAAATGACATC
66 AGCTATTTCAATGTACAAAATGACATC
41282671 TTT
1 TTT
41282674 AGTTAATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (92 bp):
TTTTTAGGCAAAGGTGAAGTCTTTGTTGTTTGGGTTAATCATAGTATGGTTAATGATTACTTTGT
AGCTATTTCAATGTACAAAATGACATC
Found at i:41289983 original size:42 final size:42
Alignment explanation
Indices: 41289866--41290198 Score: 227
Period size: 43 Copynumber: 7.8 Consensus size: 42
41289856 GTTTTTGTTC
*
41289866 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAA
1 AAAGCGCCGCTAAAGATCA-GGTCTTTAGCGGCGTTTGTGGAA
* *
41289909 AAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGT-GAG
1 AAAGCGCCGCTAAAGATCA-GGTCTTTAGCGGCGTTTGTGGAA
* * * *
41289951 ACAGCGCCGCTATAGATCAGAGTCTATT-GCGGCGTTTGAGGGGA
1 AAAGCGCCGCTAAAGATCAG-GTCT-TTAGCGGCGTTTG-TGGAA
* **
41289995 AAA-CGCCGCTAAAGAAT-AGGTCTTCTA-TGGCGTTTGTGGTC
1 AAAGCGCCGCTAAAG-ATCAGGTCTT-TAGCGGCGTTTGTGGAA
* *
41290036 AAAGCGCCGCTAAAGAAT-AGGTTCTTTAGTGGCGTTTGTGGTAT
1 AAAGCGCCGCTAAAG-ATCAGG-TCTTTAGCGGCGTTTGTGG-AA
* * *
41290080 AAA-TGCCGCTATAGATCAGGGTCTATT-GCGGCGTTT-TAGATA
1 AAAGCGCCGCTAAAGATCA-GGTCT-TTAGCGGCGTTTGTGGA-A
* * * * * * * **
41290122 AAAACGCCACTAAAGACCCTGATCTTTAGCGGCGCTTCTCCCAA
1 AAAGCGCCGCTAAAGA-TCAGGTCTTTAGCGGCGTTTGT-GGAA
*
41290166 AAATC-CCGCTAAAGATCAGGGTCTTTAGCGGCG
1 AAAGCGCCGCTAAAGATCA-GGTCTTTAGCGGCG
41290199 CTTCCACTAA
Statistics
Matches: 232, Mismatches: 37, Indels: 42
0.75 0.12 0.14
Matches are distributed among these distances:
41 8 0.03
42 74 0.32
43 130 0.56
44 19 0.08
45 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGATCAGGTCTTTAGCGGCGTTTGTGGAA
Found at i:41290088 original size:85 final size:83
Alignment explanation
Indices: 41289847--41290103 Score: 231
Period size: 85 Copynumber: 3.0 Consensus size: 83
41289837 TGTTGGCCTT
* *
41289847 TTTAGTGGCGTTTTTGTTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAA
1 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAA-GGTCTTTAGCGGCGTTTGTGG-AAAA
*
41289912 GCGCCACTAAAGATCATGGTC
64 -CGCCGCTAAAGATCATGGTC
* * * * *
41289933 TTTAGCGGCGTTTGTGAG--ACAGCGCCGCTATAGATCAGAGTCTATT-GCGGCGTTTGAGGGGA
1 TTTAGTGGCGTTTGTG-GTCAAAGCGCCGCTAAAGATAAG-GTCT-TTAGCGGCGTTT--GTGGA
41289995 AAACGCCGCTAAAGA--ATAGGTC
61 AAACGCCGCTAAAGATCAT-GGTC
*
41290017 TTCTA-TGGCGTTTGTGGTCAAAGCGCCGCTAAAGA-ATAGGTTCTTTAGTGGCGTTTGTGGTAT
1 TT-TAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATA-AGG-TCTTTAGCGGCGTTTGTGG-A-
* * *
41290080 AAATGCCGCTATAGATCAGGGTC
61 AAACGCCGCTAAAGATCATGGTC
41290103 T
1 T
41290104 ATTGCGGCGT
Statistics
Matches: 138, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
83 6 0.04
84 21 0.15
85 82 0.59
86 25 0.18
87 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (83 bp):
TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGTCTTTAGCGGCGTTTGTGGAAAACG
CCGCTAAAGATCATGGTC
Found at i:41290127 original size:128 final size:129
Alignment explanation
Indices: 41289870--41290137 Score: 316
Period size: 128 Copynumber: 2.1 Consensus size: 129
41289860 TTGTTCAAAG
41289870 CGCCGCTAAAG-ATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTCT
1 CGCCGCTAAAGAATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTCT
* * * *
41289934 TTAGCGGCGTTTGTGAGACAGCGCCGCTATAGATCAGAGTCTATTGCGGCGTTTGAGGGGAAAA
66 TTAGCGGCGTTTGTGAGAAAACGCCGCTATAGATCAGAGTCTATTGCGGCGTTTGAGAGAAAAA
* ** *
41289998 CGCCGCTAAAGAAT-A-GGTCTTCTA-TGGCGTTTGTGGTCAAAGCGCCGCTAAAGA--ATAGGT
1 CGCCGCTAAAGAATAAGGGTCTT-TAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAT-GG-
* * * * *
41290058 TCTTTAGTGGCGTTTGTG-GTATAAATGCCGCTATAGATCAGGGTCTATTGCGGCGTTTTAGATA
63 TCTTTAGCGGCGTTTGTGAG-A-AAACGCCGCTATAGATCAGAGTCTATTGCGGCGTTTGAGAGA
41290122 AAAA
126 AAAA
*
41290126 CGCCACTAAAGA
1 CGCCGCTAAAGA
41290138 CCCTGATCTT
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
125 2 0.02
126 3 0.03
127 50 0.42
128 63 0.52
129 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (129 bp):
CGCCGCTAAAGAATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTCT
TTAGCGGCGTTTGTGAGAAAACGCCGCTATAGATCAGAGTCTATTGCGGCGTTTGAGAGAAAAA
Found at i:41300069 original size:15 final size:15
Alignment explanation
Indices: 41300022--41300071 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
41300012 CAATTCAAAT
*
41300022 AATCAATATATATTC
1 AATCAATATAAATTC
41300037 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
41300054 AATCAATATAAATTC
1 AATCAATATAAATTC
41300069 AAT
1 AAT
41300072 AAATTTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:41302260 original size:4 final size:4
Alignment explanation
Indices: 41302237--41302304 Score: 52
Period size: 4 Copynumber: 16.8 Consensus size: 4
41302227 TTCTCCTTCA
*
41302237 TTTC TTTC CTT- TTTC TTTTC TTTC TTTC TTTC -TT- TTTC TTTCC GTTTC
1 TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC
* *
41302285 GTTTC TATC TTGC TTTC TTT
1 -TTTC TTTC TTTC TTTC TTT
41302305 TTATTTATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
3 6 0.12
4 32 0.62
5 11 0.21
6 3 0.06
ACGTcount: A:0.01, C:0.24, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:41302301 original size:33 final size:34
Alignment explanation
Indices: 41302237--41302306 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
41302227 TTCTCCTTCA
* * * *
41302237 TTTCTTTCCTTTTTCTTTTCTTTCTTTCTTTCTT
1 TTTCTTTCCTGTTTCGTTTCTATCTTGCTTTCTT
41302271 TTTCTTTCC-GTTTCGTTTCTATCTTGCTTTCTT
1 TTTCTTTCCTGTTTCGTTTCTATCTTGCTTTCTT
41302304 TTT
1 TTT
41302307 ATTTATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 23 0.72
34 9 0.28
ACGTcount: A:0.01, C:0.23, G:0.04, T:0.71
Consensus pattern (34 bp):
TTTCTTTCCTGTTTCGTTTCTATCTTGCTTTCTT
Found at i:41307896 original size:227 final size:227
Alignment explanation
Indices: 41307501--41307955 Score: 910
Period size: 227 Copynumber: 2.0 Consensus size: 227
41307491 CCTCATGAAC
41307501 CACTTTGGGGATTTTCAACAACCTTTGGCTAGATGGGTTTAGTGGCTCATGGTTGTGGTAGAAAA
1 CACTTTGGGGATTTTCAACAACCTTTGGCTAGATGGGTTTAGTGGCTCATGGTTGTGGTAGAAAA
41307566 GAAAATAAATAAAATAAAACTAGAGATTTTATTGAAAGGAAATATGAAAAGAACAAAAGCCTAAA
66 GAAAATAAATAAAATAAAACTAGAGATTTTATTGAAAGGAAATATGAAAAGAACAAAAGCCTAAA
41307631 CTTTTGGGGAGAGTGTGTTTACAGAAAAAGATAGATCCCCCCTTTTTGAGTCACTTCACCCCCTA
131 CTTTTGGGGAGAGTGTGTTTACAGAAAAAGATAGATCCCCCCTTTTTGAGTCACTTCACCCCCTA
41307696 TTTATAGTGCTAGGGGAGATAGTCTAATTCTA
196 TTTATAGTGCTAGGGGAGATAGTCTAATTCTA
41307728 CACTTTGGGGATTTTCAACAACCTTTGGCTAGATGGGTTTAGTGGCTCATGGTTGTGGTAGAAAA
1 CACTTTGGGGATTTTCAACAACCTTTGGCTAGATGGGTTTAGTGGCTCATGGTTGTGGTAGAAAA
41307793 GAAAATAAATAAAATAAAACTAGAGATTTTATTGAAAGGAAATATGAAAAGAACAAAAGCCTAAA
66 GAAAATAAATAAAATAAAACTAGAGATTTTATTGAAAGGAAATATGAAAAGAACAAAAGCCTAAA
41307858 CTTTTGGGGAGAGTGTGTTTACAGAAAAAGATAGATCCCCCCTTTTTGAGTCACTTCACCCCCTA
131 CTTTTGGGGAGAGTGTGTTTACAGAAAAAGATAGATCCCCCCTTTTTGAGTCACTTCACCCCCTA
41307923 TTTATAGTGCTAGGGGAGATAGTCTAATTCTA
196 TTTATAGTGCTAGGGGAGATAGTCTAATTCTA
41307955 C
1 C
41307956 TTAAATTCCT
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 228 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (227 bp):
CACTTTGGGGATTTTCAACAACCTTTGGCTAGATGGGTTTAGTGGCTCATGGTTGTGGTAGAAAA
GAAAATAAATAAAATAAAACTAGAGATTTTATTGAAAGGAAATATGAAAAGAACAAAAGCCTAAA
CTTTTGGGGAGAGTGTGTTTACAGAAAAAGATAGATCCCCCCTTTTTGAGTCACTTCACCCCCTA
TTTATAGTGCTAGGGGAGATAGTCTAATTCTA
Found at i:41315661 original size:5 final size:5
Alignment explanation
Indices: 41315645--41315674 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
41315635 TAACGAAAAT
41315645 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
41315675 GTGATGCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:41317314 original size:43 final size:43
Alignment explanation
Indices: 41317277--41317490 Score: 365
Period size: 43 Copynumber: 5.0 Consensus size: 43
41317267 GAAATCTTGT
* * *
41317277 ATCGATGCTAATAACCCAACTATGGTCTTACACGAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCAA
*
41317320 ATCGATGCCAATAGCCGAGCTATGGTCTTACACGAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCAA
* * *
41317363 ATTGATGCCAATAGCCCAACTATGGTCTTATACGAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCAA
41317406 ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCAA
1 ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCAA
41317449 ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCA
1 ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCA
41317491 CCTCGAAAGT
Statistics
Matches: 160, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 160 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (43 bp):
ATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCAA
Found at i:41317646 original size:31 final size:30
Alignment explanation
Indices: 41317605--41317687 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 30
41317595 ATCCAATGCT
* *
41317605 CAAATCAATTCGGCAATATATATCCATATA
1 CAAATCAATTCGGCAATGTATATCCACATA
* *
41317635 CGAATCAAATTCGGCAATGTATATCTACATA
1 CAAATC-AATTCGGCAATGTATATCCACATA
41317666 CAAATCAATTCGGCAATGTATA
1 CAAATCAATTCGGCAATGTATA
41317688 AAACATATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 21 0.45
31 26 0.55
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATATCCACATA
Found at i:41317698 original size:31 final size:30
Alignment explanation
Indices: 41317605--41317698 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 30
41317595 ATCCAATGCT
* **
41317605 CAAATCAATTCGGCAATATATATCCATATA
1 CAAATCAATTCGGCAATGTATAAACATATA
* * *
41317635 CGAATCAAATTCGGCAATGTAT-ATCTACATA
1 CAAATC-AATTCGGCAATGTATAAAC-ATATA
41317666 CAAATCAATTCGGCAATGTATAAAACATATA
1 CAAATCAATTCGGCAATGTAT-AAACATATA
41317697 CA
1 CA
41317699 TTTAAATTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 21 0.40
31 29 0.56
32 2 0.04
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.28
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATAAACATATA
Found at i:41321042 original size:25 final size:24
Alignment explanation
Indices: 41321006--41321059 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
41320996 TAAACTAATT
**
41321006 TAATTTTCTATTTTTTAAATTTTGTA
1 TAATTTTCTATTCATTAAA-TTTG-A
41321032 TAATTTT-TATTCATTAAATTTGA
1 TAATTTTCTATTCATTAAATTTGA
41321055 TAATT
1 TAATT
41321060 CGCCTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.23
24 4 0.15
25 9 0.35
26 7 0.27
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
TAATTTTCTATTCATTAAATTTGA
Found at i:41321247 original size:20 final size:20
Alignment explanation
Indices: 41321201--41321238 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41321191 ATGCTTTGGG
*
41321201 GTAATATTTTTTATTATTGA
1 GTAATATTTTTTATCATTGA
41321221 GTAATATTTTTTATCATT
1 GTAATATTTTTTATCATT
41321239 ATTATATATA
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:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (20 bp):
GTAATATTTTTTATCATTGA
Found at i:41334153 original size:11 final size:11
Alignment explanation
Indices: 41334137--41334164 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41334127 ATCGCCTCTT
41334137 CCTTCGTTCTA
1 CCTTCGTTCTA
41334148 CCTTCGTTCTA
1 CCTTCGTTCTA
41334159 CCTTCG
1 CCTTCG
41334165 CCTCCCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:41335976 original size:22 final size:22
Alignment explanation
Indices: 41335934--41336023 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 22
41335924 GAAGATGAAA
***
41335934 CTGGAAATTGTTGCAATTTGTT
1 CTGGAAATTGTTTTGATTTGTT
* *
41335956 -TTGATATTGTTATTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
41335978 CTGGAAATTGTTTTGA-TTGTCT
1 CTGGAAATTGTTTTGATTTGT-T
41336000 GCTGGAAATTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
41336024 AGTCAGTACA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
21 13 0.24
22 12 0.22
23 21 0.38
24 5 0.09
25 4 0.07
ACGTcount: A:0.19, C:0.07, G:0.22, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:41340632 original size:92 final size:91
Alignment explanation
Indices: 41340475--41340683 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
41340465 TTGATTTTAG
* * *
41340475 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
41340540 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
41340567 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
41340631 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
41340659 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
41340684 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:41340646 original size:24 final size:25
Alignment explanation
Indices: 41340611--41340658 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
41340601 TTATGAAATT
41340611 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
41340635 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
41340659 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:41340812 original size:66 final size:64
Alignment explanation
Indices: 41340737--41340945 Score: 190
Period size: 66 Copynumber: 3.3 Consensus size: 64
41340727 AAATATATTT
41340737 AATATTAATTATTTCAAATTTTAATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTTAATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
41340802 G
64 G
* * * * **
41340803 AATATTAATTATTAAGAATTTT-A-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTAATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
41340857 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TAATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
41340921 AG
63 AG
*
41340923 AATATTAATTATTAAGAATTTTA
1 AATATTAATTATTTA-AATTTTA
41340946 TTAAATTATA
Statistics
Matches: 110, Mismatches: 16, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
53 5 0.05
54 12 0.11
55 5 0.05
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 7 0.06
66 32 0.29
67 5 0.05
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (64 bp):
AATATTAATTATTTAAATTTTAATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:41340828 original size:120 final size:120
Alignment explanation
Indices: 41340699--41340991 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 120
41340689 AATTATTTTA
* * *
41340699 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATAAT
*
41340762 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
41340819 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAATTT
41340884 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41340939 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
41340992 TAAATATGAT
Statistics
Matches: 166, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
119 5 0.03
120 159 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAATTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:41340859 original size:15 final size:15
Alignment explanation
Indices: 41340824--41340875 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41340814 TTAAGAATTT
*
41340824 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41340838 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41340852 TATTTAATAATAAT-
1 TATTTAATTATAATA
41340866 TATGTTAATT
1 TAT-TTAATT
41340876 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41340974 original size:16 final size:16
Alignment explanation
Indices: 41340953--41340994 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41340943 TTATTAAATT
*
41340953 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41340969 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41340984 AT-TATGTTTAA
1 ATATAT-TTTAA
41340995 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41340979 original size:15 final size:15
Alignment explanation
Indices: 41340944--41340985 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41340934 TTAAGAATTT
*
41340944 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41340958 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41340972 TATTTAATAATAAT
1 TATTTAATTATAAT
41340986 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41341106 original size:157 final size:157
Alignment explanation
Indices: 41340928--41341244 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
41340918 ATAAGAATAT
*
41340928 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* * *
41340993 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAACATGATTAAATTATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
*
41341058 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
41341085 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
41341150 AAACATGATTAAATTATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
66 AAACATGATTAAATTATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
*
41341215 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
41341242 TAA
1 TAA
41341245 AGGTGTTCTA
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAACATGATTAAATTATTTATTATTGATAATAACAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:41341125 original size:18 final size:17
Alignment explanation
Indices: 41341097--41341131 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41341087 ATTATTAAGA
*
41341097 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41341114 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41341132 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41346315 original size:29 final size:29
Alignment explanation
Indices: 41346250--41346308 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
41346240 ACTAATAAAA
41346250 GCCG-TTTTTTTTAAATTTACCGAAATGG
1 GCCGATTTTTTTTAAATTTACCGAAATGG
* *
41346278 GCCGATTTTTTTTATTATTTACCGGAATGG
1 GCCGATTTTTTTTA-AATTTACCGAAATGG
41346308 G
1 G
41346309 TCATTTTCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 4 0.15
29 9 0.33
30 14 0.52
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.44
Consensus pattern (29 bp):
GCCGATTTTTTTTAAATTTACCGAAATGG
Found at i:41348001 original size:27 final size:27
Alignment explanation
Indices: 41347963--41348026 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
41347953 ATCATATTTA
41347963 ATTATCTATACTATATATTATGTCTAG
1 ATTATCTATACTATATATTATGTCTAG
41347990 ATTATCTATACTATATATTATGTCTAG
1 ATTATCTATACTATATATTATGTCTAG
*
41348017 AGTTACCTAT
1 A-TTATCTAT
41348027 GGACTTGGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 28 0.80
28 7 0.20
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (27 bp):
ATTATCTATACTATATATTATGTCTAG
Found at i:41351147 original size:26 final size:22
Alignment explanation
Indices: 41351100--41351143 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41351090 ATCACGAAAG
41351100 TTGCAAGAAAGAAGTTGTCTTT
1 TTGCAAGAAAGAAGTTGTCTTT
41351122 TTGCAAGAAAGAAGTTGTCTTT
1 TTGCAAGAAAGAAGTTGTCTTT
41351144 CTTTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (22 bp):
TTGCAAGAAAGAAGTTGTCTTT
Found at i:41359113 original size:29 final size:29
Alignment explanation
Indices: 41359080--41359139 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
41359070 TGAAGCCCAA
41359080 AGCGCTTTTGTACCAGGGCGTTTGATATC
1 AGCGCTTTTGTACCAGGGCGTTTGATATC
41359109 AGCGCTTTTGTACCAGGGCGTTTGATATC
1 AGCGCTTTTGTACCAGGGCGTTTGATATC
41359138 AG
1 AG
41359140 ACAATGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.33
Consensus pattern (29 bp):
AGCGCTTTTGTACCAGGGCGTTTGATATC
Found at i:41360632 original size:24 final size:24
Alignment explanation
Indices: 41360603--41360653 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
41360593 GTTGTTTTAT
* * *
41360603 TTTTATAATTTTAATTTTTTAATA
1 TTTTATAATTATAAATTTTGAATA
41360627 TTTTATAATTATAAATTTTGAATA
1 TTTTATAATTATAAATTTTGAATA
41360651 TTT
1 TTT
41360654 AAAATAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTATAATTATAAATTTTGAATA
Found at i:41360966 original size:21 final size:21
Alignment explanation
Indices: 41360941--41360996 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
41360931 AACAGCGGTG
* *
41360941 GCGGTGAGATTAGTTATTGTA
1 GCGGTGAGATTAGATACTGTA
*
41360962 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
41360983 GTGGTGAGATTAGA
1 GCGGTGAGATTAGA
41360997 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.38, T:0.32
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:41366774 original size:16 final size:16
Alignment explanation
Indices: 41366750--41366780 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41366740 TTAGGTATTT
*
41366750 GAACGGTTATGAAATA
1 GAACAGTTATGAAATA
41366766 GAACAGTTATGAAAT
1 GAACAGTTATGAAAT
41366781 GTAAGTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (16 bp):
GAACAGTTATGAAATA
Found at i:41366849 original size:28 final size:29
Alignment explanation
Indices: 41366818--41366880 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 29
41366808 AATTATATTG
*
41366818 AATTTTATTT-TTATT-TGATATATAATA
1 AATTTTATTTATTATTATGATATAAAATA
** *
41366845 TAATTAAATTTATTTTTATGATATAAAATA
1 -AATTTTATTTATTATTATGATATAAAATA
41366875 AATTTT
1 AATTTT
41366881 CATATTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
28 8 0.30
29 8 0.30
30 11 0.41
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
AATTTTATTTATTATTATGATATAAAATA
Found at i:41369741 original size:15 final size:16
Alignment explanation
Indices: 41369717--41369751 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41369707 CTTCTCGAAT
41369717 TATTACATAAATAT-A
1 TATTACATAAATATAA
*
41369732 TATTATATAAATATAA
1 TATTACATAAATATAA
41369748 TATT
1 TATT
41369752 TGTATATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTACATAAATATAA
Found at i:41369839 original size:25 final size:25
Alignment explanation
Indices: 41369805--41369854 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41369795 AGTTTAAAAT
41369805 GTATTGAATCACCACTGAATTGTAA
1 GTATTGAATCACCACTGAATTGTAA
* * * *
41369830 GTATTTAATCATCATTGAGTTGTAA
1 GTATTGAATCACCACTGAATTGTAA
41369855 AAAGCTCAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (25 bp):
GTATTGAATCACCACTGAATTGTAA
Done.