Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 29 of 135
Found at i:11458366 original size:5 final size:5
Alignment explanation
Indices: 11458356--11458380 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11458346 AAGAGTGAGT
11458356 ATGGG ATGGG ATGGG ATGGG ATGGG
1 ATGGG ATGGG ATGGG ATGGG ATGGG
11458381 CTTATGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (5 bp):
ATGGG
Found at i:11461552 original size:2 final size:2
Alignment explanation
Indices: 11461545--11461569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11461535 TGCTCACTCA
11461545 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 C
11461570 AATCACGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:11466650 original size:4 final size:4
Alignment explanation
Indices: 11466643--11466680 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
11466633 TCTCTATCTT
11466643 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TC
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TC
11466681 TATCTAGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.50, G:0.00, T:0.26
Consensus pattern (4 bp):
TCCA
Found at i:11480058 original size:11 final size:12
Alignment explanation
Indices: 11480035--11480066 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
11480025 AATACTTATT
11480035 AAACAATAAAAA
1 AAACAATAAAAA
11480047 AAACAA-AAAAA
1 AAACAATAAAAA
11480058 AAAC-ATAAA
1 AAACAATAAA
11480067 GACAACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 12 0.63
12 6 0.32
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.06
Consensus pattern (12 bp):
AAACAATAAAAA
Found at i:11482573 original size:21 final size:21
Alignment explanation
Indices: 11482548--11482603 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
11482538 TAATATATAT
*
11482548 ATTTTTTATATTTTTAAAATG
1 ATTTTTTATATTTTTAAAATA
11482569 ATTTTATTA-ATTTTTAAAATA
1 ATTTT-TTATATTTTTAAAATA
11482590 ATTTTTT-TATTTTT
1 ATTTTTTATATTTTT
11482604 TTTGAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.25
21 21 0.66
22 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTTTTTATATTTTTAAAATA
Found at i:11482775 original size:2 final size:2
Alignment explanation
Indices: 11482768--11482797 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11482758 AACATAATTT
11482768 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11482798 ATGTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11483077 original size:4 final size:4
Alignment explanation
Indices: 11483068--11483101 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
11483058 ATTCTCCATG
11483068 GGAT GGAT GGAT GGAT GGAT GGAT GGAT GGAT GG
1 GGAT GGAT GGAT GGAT GGAT GGAT GGAT GGAT GG
11483102 GGCCATCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.53, T:0.24
Consensus pattern (4 bp):
GGAT
Found at i:11489081 original size:17 final size:17
Alignment explanation
Indices: 11489059--11489092 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11489049 ATATATATAA
*
11489059 AAAAATATTTTTATTTT
1 AAAAATATTTCTATTTT
11489076 AAAAATATTTCTATTTT
1 AAAAATATTTCTATTTT
11489093 TAGTAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
AAAAATATTTCTATTTT
Found at i:11495481 original size:5 final size:5
Alignment explanation
Indices: 11495471--11495496 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11495461 ACAAATACTA
11495471 ACAAT ACAAT ACAAT ACAAT ACAAT A
1 ACAAT ACAAT ACAAT ACAAT ACAAT A
11495497 GCGTATCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
ACAAT
Found at i:11499345 original size:18 final size:18
Alignment explanation
Indices: 11499309--11499346 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11499299 TGAGTTTTCG
*
11499309 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCAAAT
11499327 AATTCGAATAAACT-AAAT
1 AATTCGAAT-AACTCAAAT
11499345 AA
1 AA
11499347 CAAACTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:11500782 original size:24 final size:24
Alignment explanation
Indices: 11500731--11500782 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
11500721 TTCGTAGGTC
* *
11500731 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
11500755 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
11500779 AAAT
1 AAAT
11500783 CTTATAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:11502632 original size:19 final size:19
Alignment explanation
Indices: 11502608--11502646 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11502598 TAATAAGCGT
11502608 GTTTTCTAAGGTTGTAAAA
1 GTTTTCTAAGGTTGTAAAA
11502627 GTTTTCTAAGGTTGTAAAA
1 GTTTTCTAAGGTTGTAAAA
11502646 G
1 G
11502647 AGTTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (19 bp):
GTTTTCTAAGGTTGTAAAA
Found at i:11502726 original size:24 final size:24
Alignment explanation
Indices: 11502675--11502726 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11502665 TTCGTAGGCC
*
11502675 AAATAAATTATACTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
11502699 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
11502723 AAAT
1 AAAT
11502727 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:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:11506753 original size:87 final size:89
Alignment explanation
Indices: 11506654--11506846 Score: 232
Period size: 87 Copynumber: 2.2 Consensus size: 89
11506644 GTCATAATTT
* * * * *
11506654 TTTTTTAAAAAAATAATTAAGTCCCTGCTTTTATTTTGTATTCACTT-AGATACTTAAACTTTTA
1 TTTTTTAAAAAAAAAATTAAGTCCCTGCTTTTATTTTGCACTCAATTGAG-TACTTAAACTTTCA
*
11506718 AAATACATTAA-AAGACT-CTCAAAC
65 AAATACATCAAGAAGA-TACTCAAAC
** *
11506742 TTTTTT-AAAAAAAAATTAAGTCTTTGCTTTTATTTTGCACTCAATTGAGTACTTGAACTTTCAA
1 TTTTTTAAAAAAAAAATTAAGTCCCTGCTTTTATTTTGCACTCAATTGAGTACTTAAACTTTCAA
*
11506806 AATATATCAAGAAGATACTCAAAC
66 AATACATCAAGAAGATACTCAAAC
*
11506830 TTTTTTTTAAAAAAAAA
1 -TTTTTTAAAAAAAAAA
11506847 CAATTAAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
87 56 0.62
88 19 0.21
89 6 0.07
90 9 0.10
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (89 bp):
TTTTTTAAAAAAAAAATTAAGTCCCTGCTTTTATTTTGCACTCAATTGAGTACTTAAACTTTCAA
AATACATCAAGAAGATACTCAAAC
Found at i:11506987 original size:10 final size:10
Alignment explanation
Indices: 11506974--11507136 Score: 75
Period size: 10 Copynumber: 17.3 Consensus size: 10
11506964 AAAAAACAAT
11506974 AAAAATTATA
1 AAAAATTATA
11506984 AAAAA-TAT-
1 AAAAATTATA
* *
11506992 AGAAATTATT
1 AAAAATTATA
* *
11507002 TAAAATTAGA
1 AAAAATTATA
11507012 AAAAA--ATA
1 AAAAATTATA
11507020 AAAAATTAT-
1 AAAAATTATA
*
11507029 AAAAATCAT-
1 AAAAATTATA
*
11507038 AAAAA-TGTA
1 AAAAATTATA
* *
11507047 ATAAGTTAT-
1 AAAAATTATA
11507056 -AAAA-TATA
1 AAAAATTATA
*
11507064 AAAAAATATA
1 AAAAATTATA
11507074 GAAAAATTAT-
1 -AAAAATTATA
*
11507084 -AAAATTTTA
1 AAAAATTATA
* * *
11507093 TACAGTTATA
1 AAAAATTATA
11507103 AGAAAATTATA
1 A-AAAATTATA
11507114 AATAAA-TATA
1 AA-AAATTATA
11507124 AATAAA-TATA
1 AA-AAATTATA
11507134 AAA
1 AAA
11507137 TTCTTAAAGA
Statistics
Matches: 116, Mismatches: 23, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
7 3 0.03
8 21 0.18
9 27 0.23
10 46 0.40
11 19 0.16
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:11507068 original size:27 final size:29
Alignment explanation
Indices: 11506983--11507088 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 29
11506973 TAAAAATTAT
*
11506983 AAAAAATATAGAAATTATT-TAAAAT-T-A
1 AAAAAATATAGAAA-AATTATAAAATATCA
11507010 GAAAAAA-ATA-AAAAATTATAAAA-ATCA
1 -AAAAAATATAGAAAAATTATAAAATATCA
* * * *
11507037 TAAAAATGTA-ATAAGTTATAAAATAT-A
1 AAAAAATATAGAAAAATTATAAAATATCA
11507064 AAAAAATATAGAAAAATTATAAAAT
1 AAAAAATATAGAAAAATTATAAAAT
11507089 TTTATACAGT
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
25 3 0.05
26 14 0.22
27 26 0.41
28 20 0.32
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (29 bp):
AAAAAATATAGAAAAATTATAAAATATCA
Found at i:11507087 original size:9 final size:9
Alignment explanation
Indices: 11506949--11507158 Score: 83
Period size: 9 Copynumber: 22.7 Consensus size: 9
11506939 CATGTGGCAA
*
11506949 AAAAATGAT
1 AAAAATTAT
11506958 AAAAA-TA-
1 AAAAATTAT
**
11506965 AAAAACAAT
1 AAAAATTAT
11506974 AAAAATTAT
1 AAAAATTAT
*
11506983 AAAAAATAT
1 AAAAATTAT
*
11506992 AGAAATTATT
1 AAAAATTA-T
* *
11507002 TAAAATTAG
1 AAAAATTAT
*
11507011 AAAAA-AAT
1 AAAAATTAT
11507019 AAAAAATTAT
1 -AAAAATTAT
*
11507029 AAAAATCAT
1 AAAAATTAT
11507038 AAAAATGTA-
1 AAAAAT-TAT
* *
11507047 ATAAGTTAT
1 AAAAATTAT
*
11507056 -AAAATATAA
1 AAAAAT-TAT
*
11507065 AAAAATATAG
1 AAAAAT-TAT
11507075 AAAAATTAT
1 AAAAATTAT
*
11507084 -AAAATTTT
1 AAAAATTAT
* *
11507092 ATACAGTTAT
1 A-AAAATTAT
11507102 AAGAAAATTAT
1 -A-AAAATTAT
*
11507113 AAATAAATAT
1 AAA-AATTAT
*
11507123 AAATAAATAT
1 AAA-AATTAT
*
11507133 -AAAATTCTT
1 AAAAATT-AT
11507142 AAAGATATTAT
1 AAA-A-ATTAT
11507153 AAAAAT
1 AAAAAT
11507159 CATGTACTAA
Statistics
Matches: 150, Mismatches: 34, Indels: 34
0.69 0.16 0.16
Matches are distributed among these distances:
7 5 0.03
8 18 0.12
9 64 0.43
10 48 0.32
11 12 0.08
12 3 0.02
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:11507100 original size:46 final size:46
Alignment explanation
Indices: 11506974--11507138 Score: 119
Period size: 46 Copynumber: 3.5 Consensus size: 46
11506964 AAAAAACAAT
* * * *
11506974 AAAAATTATAAAAAATATAGAAATTATTTAA-AA-TTAGAAAAA-AATA
1 AAAAAATATAAAAAAT-TATAAA--ATTTAATAAGTTATAAAAATTATA
* * *
11507020 AAAAATTAT-AAAAATCATAAAAATGTAATAAGTTAT-AAAA-TATA
1 AAAAAATATAAAAAATTAT-AAAATTTAATAAGTTATAAAAATTATA
*
11507064 AAAAAATATAGAAAAATTATAAAATTTTATACAGTTATAAGAAAATTATA
1 AAAAAATATA-AAAAATTATAAAATTTAATA-AGTTAT-A-AAAATTATA
*
11507114 AATAAATATAAATAAA-TATAAAATT
1 AAAAAATATAAA-AAATTATAAAATT
11507139 CTTAAAGATA
Statistics
Matches: 98, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
43 5 0.05
44 18 0.18
45 21 0.21
46 23 0.23
49 15 0.15
50 16 0.16
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (46 bp):
AAAAAATATAAAAAATTATAAAATTTAATAAGTTATAAAAATTATA
Found at i:11507679 original size:92 final size:90
Alignment explanation
Indices: 11507502--11507732 Score: 233
Period size: 92 Copynumber: 2.6 Consensus size: 90
11507492 TTGACCGTTT
* * * * * *
11507502 AAGTATCCAATTAAGTGTAAAA-AAAATCGAGAGCTTAATTAC--TTTTTTTTTTTAAGTTTGAG
1 AAGTATTCAATTGAGTGCAAAATAAAAAC-AGAGCTTAATTGCTTTTTTTTTTTTTAAGATTGAG
* *
11507564 GCTTTTTTGATGTATTTTAAAAGTTCA
65 GCTCTTTTGATGCATTTTAAAAGTT-A
11507591 AA-TATTCAATTGAGTGCAAAATAAAAACAAGAGCTTAATTGCTTTTTTTTTTTTTAAAAGATTG
1 AAGTATTCAATTGAGTGCAAAATAAAAAC-AGAGCTTAATTGCTTTTTTTTTTTTT--AAGATTG
*
11507655 AGAGC-CTTTT-ATGCATTTTGAAAGTTA
63 AG-GCTCTTTTGATGCATTTTAAAAGTTA
* * * *
11507682 AAGTATTCAAGTGAATGCAAAATAAAAGCAGTAACTTAATTG-TTTTTTTTT
1 AAGTATTCAATTGAGTGCAAAATAAAAACAG-AGCTTAATTGCTTTTTTTTT
11507733 AAAGTTTGAT
Statistics
Matches: 120, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
88 16 0.13
89 19 0.16
91 25 0.21
92 46 0.38
93 12 0.10
94 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (90 bp):
AAGTATTCAATTGAGTGCAAAATAAAAACAGAGCTTAATTGCTTTTTTTTTTTTTAAGATTGAGG
CTCTTTTGATGCATTTTAAAAGTTA
Found at i:11519118 original size:3 final size:3
Alignment explanation
Indices: 11519112--11519142 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11519102 ATAATAATAA
11519112 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11519143 TAAATTGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11523758 original size:3 final size:3
Alignment explanation
Indices: 11523750--11523775 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11523740 TCTTGTTATA
11523750 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
11523776 ATACAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:11543123 original size:16 final size:16
Alignment explanation
Indices: 11543099--11543148 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
11543089 TAACTAATTT
11543099 TTATACATTATTTTTA
1 TTATACATTATTTTTA
*
11543115 TTCTACATTTATTTTTA
1 TTATACA-TTATTTTTA
* *
11543132 GTATAGATTATTTTTA
1 TTATACATTATTTTTA
11543148 T
1 T
11543149 ACATAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (16 bp):
TTATACATTATTTTTA
Found at i:11543161 original size:16 final size:16
Alignment explanation
Indices: 11543095--11543171 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 16
11543085 TAATTAACTA
*
11543095 ATTTTTATACATTATT
1 ATTTTTATACATAATT
*
11543111 -TTTATTCTACAT--TT
1 ATTT-TTATACATAATT
11543125 ATTTTTAGT--ATAGATT
1 ATTTTTA-TACATA-ATT
11543141 ATTTTTATACATAATT
1 ATTTTTATACATAATT
* *
11543157 TTTTTTATAAATAAT
1 ATTTTTATACATAAT
11543172 GTCATGAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
13 2 0.04
14 4 0.08
15 8 0.16
16 32 0.65
17 3 0.06
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (16 bp):
ATTTTTATACATAATT
Found at i:11546073 original size:12 final size:12
Alignment explanation
Indices: 11546056--11546080 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11546046 CGTATAACTT
11546056 AAAATTTCTGTC
1 AAAATTTCTGTC
11546068 AAAATTTCTGTC
1 AAAATTTCTGTC
11546080 A
1 A
11546081 TTTTGTTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAATTTCTGTC
Found at i:11548026 original size:23 final size:23
Alignment explanation
Indices: 11547988--11548031 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11547978 TGTGACACGT
* *
11547988 TTTTCTTCTGCCTTGTGGCACAC
1 TTTTCTTCTACATTGTGGCACAC
11548011 TTTTCTTCTACATTGTGGCAC
1 TTTTCTTCTACATTGTGGCAC
11548032 GCTTCTGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.27, G:0.16, T:0.45
Consensus pattern (23 bp):
TTTTCTTCTACATTGTGGCACAC
Found at i:11553962 original size:24 final size:24
Alignment explanation
Indices: 11553915--11553959 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
11553905 TGGATTTGTT
*
11553915 ATTTAAGAATAAAATACTATTTAA
1 ATTTAAGAATAAAATAATATTTAA
11553939 ATTTAAGAATAAAATAA-ATTT
1 ATTTAAGAATAAAATAATATTT
11553960 TAATACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTTAAGAATAAAATAATATTTAA
Found at i:11555518 original size:18 final size:18
Alignment explanation
Indices: 11555495--11555537 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
11555485 GAATAGATTT
11555495 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
11555513 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
11555531 TTAATTA
1 TTAATTA
11555538 CATTTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:11559816 original size:59 final size:58
Alignment explanation
Indices: 11559725--11559839 Score: 194
Period size: 59 Copynumber: 2.0 Consensus size: 58
11559715 TCCAACTGAG
* *
11559725 TATGTTCCGTAACTATTATGTAACCGCTGTAACGCTAATTAAGTTGCGTGCACATAGT
1 TATGTTCCGTAACTATTACGTAACCGCTGTAACGCTAATGAAGTTGCGTGCACATAGT
*
11559783 TATGTTCCGTTAACTATTACGTAACCGCTGTAACGCTAATGAAGTTGTGTGCACATA
1 TATGTTCCG-TAACTATTACGTAACCGCTGTAACGCTAATGAAGTTGCGTGCACATA
11559840 CACAGTTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 9 0.17
59 44 0.83
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (58 bp):
TATGTTCCGTAACTATTACGTAACCGCTGTAACGCTAATGAAGTTGCGTGCACATAGT
Found at i:11562024 original size:20 final size:20
Alignment explanation
Indices: 11561999--11562044 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
11561989 TAAAAAATTA
11561999 ATAATTATTAAAAAGTTTT-T
1 ATAATTATTAAAAA-TTTTAT
* *
11562019 ATAATTCTTAATAATTTTAT
1 ATAATTATTAAAAATTTTAT
11562039 ATAATT
1 ATAATT
11562045 TTTTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAATTATTAAAAATTTTAT
Found at i:11562165 original size:21 final size:21
Alignment explanation
Indices: 11562139--11562183 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
11562129 TTCGACATGA
* *
11562139 TTTTTAATCATTT-TTATACT
1 TTTTTTATCATTTCTTATAAT
*
11562159 TTTTTTATGATTTCTTATAAT
1 TTTTTTATCATTTCTTATAAT
11562180 TTTT
1 TTTT
11562184 AAATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTATCATTTCTTATAAT
Found at i:11562198 original size:21 final size:23
Alignment explanation
Indices: 11562169--11562210 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
11562159 TTTTTTATGA
11562169 TTTCTTATAA-TTTTTAAATATT
1 TTTCTTATAACTTTTTAAATATT
11562191 TTTC-TATAACTTTTTAAATA
1 TTTCTTATAACTTTTTAAATA
11562211 ATTATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTCTTATAACTTTTTAAATATT
Found at i:11565453 original size:28 final size:32
Alignment explanation
Indices: 11565412--11565485 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 32
11565402 CATTAAAAGT
* * *
11565412 TTAAGATAACTATATAAAT-TTTTTA-ATAAAA
1 TTAAAATAA-TATATAAATCTGTTAATATAAAA
11565443 -TAAAA-AATATATAAATCTGTTAATATAAAA
1 TTAAAATAATATATAAATCTGTTAATATAAAA
11565473 TTAAAATAATATA
1 TTAAAATAATATA
11565486 AATATGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 9 0.25
29 6 0.17
30 10 0.28
31 5 0.14
32 6 0.17
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (32 bp):
TTAAAATAATATATAAATCTGTTAATATAAAA
Found at i:11565473 original size:30 final size:30
Alignment explanation
Indices: 11565437--11565493 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
11565427 AAATTTTTTA
*
11565437 ATAAAATAAAAA-ATATATAAATCTGTTAAT
1 ATAAAATAAAAATA-ATATAAATATGTTAAT
*
11565467 ATAAAATTAAAATAATATAAATATGTT
1 ATAAAATAAAAATAATATAAATATGTT
11565494 TTCTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (30 bp):
ATAAAATAAAAATAATATAAATATGTTAAT
Found at i:11565500 original size:29 final size:30
Alignment explanation
Indices: 11565422--11565508 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 30
11565412 TTAAGATAAC
* *
11565422 TATATAAATTTTTTAATA-AAATAA--AAAA
1 TATATAAATATGTTAATATAAA-AATTAAAA
*
11565450 TATATAAATCTGTTAATAT-AAAATTAAAA
1 TATATAAATATGTTAATATAAAAATTAAAA
* *
11565479 TAATATAAATATGTT-TTCTAAAAATTAAAA
1 T-ATATAAATATGTTAATATAAAAATTAAAA
11565509 AGAAATAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.04
28 18 0.37
29 7 0.14
30 22 0.45
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
TATATAAATATGTTAATATAAAAATTAAAA
Found at i:11566665 original size:19 final size:19
Alignment explanation
Indices: 11566622--11566682 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
11566612 AGAATTATAG
* *
11566622 AAAATTATTAAAAATTATG
1 AAAATTATTAAAAATCATT
11566641 ATAAATTA-TAAATAATCATT
1 A-AAATTATTAAA-AATCATT
*
11566661 AAAATTATTAAAAATTATT
1 AAAATTATTAAAAATCATT
11566680 AAA
1 AAA
11566683 TATATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATTATTAAAAATCATT
Found at i:11566679 original size:10 final size:10
Alignment explanation
Indices: 11566598--11566682 Score: 79
Period size: 10 Copynumber: 8.5 Consensus size: 10
11566588 AAGTGATTTC
11566598 TTAAATAATTA
1 TTAAA-AATTA
11566609 -TAAAGAATTA
1 TTAAA-AATTA
11566619 -TAGAAAATTA
1 TTA-AAAATTA
11566629 TTAAAAATTA
1 TTAAAAATTA
* *
11566639 TGATAAATTA
1 TTAAAAATTA
*
11566649 -TAAATAATCA
1 TTAAA-AATTA
11566659 TT-AAAATTA
1 TTAAAAATTA
11566668 TTAAAAATTA
1 TTAAAAATTA
11566678 TTAAA
1 TTAAA
11566683 TATATATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.13
10 49 0.79
11 5 0.08
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.38
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:11566986 original size:21 final size:21
Alignment explanation
Indices: 11566962--11567012 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
11566952 ACATTGTAAT
* *
11566962 ATTTTTTTATAA-TTTATTATA
1 ATTTTTTAATAACTTT-CTATA
*
11566983 ATTTTTAAATAACTTTCTATA
1 ATTTTTTAATAACTTTCTATA
11567004 ATTTTTTAA
1 ATTTTTTAA
11567013 ATAATTATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTTAATAACTTTCTATA
Found at i:11590707 original size:51 final size:51
Alignment explanation
Indices: 11590626--11590729 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
11590616 TGATATGAGG
* ** *
11590626 TTGGAGCAGGCTGTTGAATCAAGAAAAGAAGTTGGAATATCAGGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCAGGGAGAAGT
* * *
11590677 TTGGAACAGGCTGCCGAATCTAGAAGAGAAGTTGGAATAGCTGGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCAGGGAGAAGT
11590728 TT
1 TT
11590730 CGAGCCAAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.34, T:0.22
Consensus pattern (51 bp):
TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCAGGGAGAAGT
Found at i:11595329 original size:24 final size:24
Alignment explanation
Indices: 11595272--11595331 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
11595262 ATAATATCCA
*
11595272 AACAACAAAAATAACAATCAAAAC
1 AACAACAAAAATAACAAGCAAAAC
* **
11595296 AGCAGTAAAAATAAC-AGCAAAAC
1 AACAACAAAAATAACAAGCAAAAC
11595319 AACAACAAAAATA
1 AACAACAAAAATA
11595332 GTAAAAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.08
Consensus pattern (24 bp):
AACAACAAAAATAACAAGCAAAAC
Found at i:11595342 original size:36 final size:35
Alignment explanation
Indices: 11595302--11595408 Score: 112
Period size: 36 Copynumber: 3.1 Consensus size: 35
11595292 AAACAGCAGT
*
11595302 AAAAATAACAGCAAAACAACAACAAAAATAGTAAAA
1 AAAAATAACAACAAAACAACAAC-AAAATAGTAAAA
* * *
11595338 AAAAATAACAACAAAAACAATACCAAAACAGT---A
1 AAAAATAACAAC-AAAACAACAACAAAATAGTAAAA
* *
11595371 AAAAATAACATCAAAACAACAATCAAAATAATAAAA
1 AAAAATAACAACAAAACAACAA-CAAAATAGTAAAA
11595407 AA
1 AA
11595409 GCATCAAAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
32 8 0.14
33 19 0.33
36 21 0.37
37 9 0.16
ACGTcount: A:0.72, C:0.15, G:0.03, T:0.10
Consensus pattern (35 bp):
AAAAATAACAACAAAACAACAACAAAATAGTAAAA
Found at i:11595353 original size:12 final size:12
Alignment explanation
Indices: 11595272--11595354 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 12
11595262 ATAATATCCA
11595272 AACAACAAAAAT
1 AACAACAAAAAT
*
11595284 AACAATC-AAAAC
1 AACAA-CAAAAAT
* **
11595296 AGCAGTAAAAAT
1 AACAACAAAAAT
* *
11595308 AACAGC-AAAAC
1 AACAACAAAAAT
11595319 AACAACAAAAAT
1 AACAACAAAAAT
*
11595331 AGTA-AAAAAAAAT
1 A--ACAACAAAAAT
11595344 AACAACAAAAA
1 AACAACAAAAA
11595355 CAATACCAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
11 10 0.19
12 32 0.60
13 10 0.19
14 1 0.02
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:11595358 original size:69 final size:69
Alignment explanation
Indices: 11595275--11595408 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 69
11595265 ATATCCAAAC
*
11595275 AACAAAAATAACAAT-CAAAACAGCAGT-AAAAATAACAGCAAAACAACAA-CAAAAATAGTAAA
1 AACAAAAATAACAATACAAAA-A-CAGTAAAAAATAACAGCAAAACAACAATC-AAAATAATAAA
11595337 AAAAAAT
63 AAAAAAT
* *
11595344 AACAACAAA-AACAATACCAAAACAGTAAAAAATAACATCAAAACAACAATCAAAATAATAAAAA
1 AACAA-AAATAACAATACAAAAACAGTAAAAAATAACAGCAAAACAACAATCAAAATAATAAAAA
11595408 A
65 A
11595409 GCATCAAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
68 4 0.07
69 46 0.79
70 8 0.14
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.10
Consensus pattern (69 bp):
AACAAAAATAACAATACAAAAACAGTAAAAAATAACAGCAAAACAACAATCAAAATAATAAAAAA
AAAT
Found at i:11606189 original size:22 final size:21
Alignment explanation
Indices: 11606159--11606204 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
11606149 AAAATTGTAT
* *
11606159 AAAATTATTAAATATTAAAATA
1 AAAAATATT-AATATTAAAACA
11606181 AAAAATATTAATATTAAAACA
1 AAAAATATTAATATTAAAACA
11606202 AAA
1 AAA
11606205 TGAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATATTAATATTAAAACA
Found at i:11607308 original size:15 final size:15
Alignment explanation
Indices: 11607290--11607341 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
11607280 TAGTCCCTAT
11607290 ATTTTAATTTGATCA
1 ATTTTAATTTGATCA
* **
11607305 ATTTTAATTTTCATTT
1 ATTTTAA-TTTGATCA
*
11607321 TTTTTAATTTGATCA
1 ATTTTAATTTGATCA
11607336 ATTTTA
1 ATTTTA
11607342 GTTTCTATAC
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (15 bp):
ATTTTAATTTGATCA
Found at i:11607340 original size:16 final size:16
Alignment explanation
Indices: 11607291--11607340 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
11607281 AGTCCCTATA
11607291 TTTTAATTTGATCAA-
1 TTTTAATTTGATCAAT
*
11607306 TTTTAATTT--TCATTTT
1 TTTTAATTTGATCA--AT
11607322 TTTTAATTTGATCAAT
1 TTTTAATTTGATCAAT
11607338 TTT
1 TTT
11607341 AGTTTCTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.11
15 9 0.32
16 13 0.46
18 3 0.11
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (16 bp):
TTTTAATTTGATCAAT
Found at i:11608844 original size:28 final size:28
Alignment explanation
Indices: 11608797--11608850 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
11608787 TTTAATACCA
*
11608797 TTAAAAATAATTACGAGTATGGGTCATT
1 TTAAAAATAATTACGAGTATGAGTCATT
11608825 TTAAAAATAATTACCG-GTATGAGTCA
1 TTAAAAATAATTA-CGAGTATGAGTCA
11608851 AAAACATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (28 bp):
TTAAAAATAATTACGAGTATGAGTCATT
Found at i:11610176 original size:14 final size:14
Alignment explanation
Indices: 11610159--11610211 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
11610149 TTATTTAAGT
11610159 TATTAATTTTTTTG
1 TATTAATTTTTTTG
**
11610173 TATTATATTTTGGTG
1 TATTA-ATTTTTTTG
11610188 TA-TAATTTTTTTTG
1 TATTAA-TTTTTTTG
*
11610202 TATTAGTTTT
1 TATTAATTTT
11610212 GTAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 1 0.03
14 19 0.61
15 11 0.35
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (14 bp):
TATTAATTTTTTTG
Found at i:11610269 original size:27 final size:27
Alignment explanation
Indices: 11610239--11610294 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
11610229 TGGTGCTACT
* *
11610239 TGACAGAAAGGCACCATTGGTGCCGCC
1 TGACAGAAAGGCACCACTAGTGCCGCC
**
11610266 TGACAGGTAGGCACCACTAGTGCCGCC
1 TGACAGAAAGGCACCACTAGTGCCGCC
11610293 TG
1 TG
11610295 TCAAGTAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (27 bp):
TGACAGAAAGGCACCACTAGTGCCGCC
Found at i:11610302 original size:27 final size:27
Alignment explanation
Indices: 11610247--11610309 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
11610237 CTTGACAGAA
* * *
11610247 AGGCACCATTGGTGCCGCCTGACAGGT
1 AGGCACCACTAGTGCCGCCTGACAAGT
*
11610274 AGGCACCACTAGTGCCGCCTGTCAAGT
1 AGGCACCACTAGTGCCGCCTGACAAGT
11610301 AGGCACCAC
1 AGGCACCAC
11610310 CCACTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (27 bp):
AGGCACCACTAGTGCCGCCTGACAAGT
Found at i:11610485 original size:15 final size:15
Alignment explanation
Indices: 11610465--11610506 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
11610455 AATGGGGAGA
11610465 ATATATTATTTTGGT
1 ATATATTATTTTGGT
**
11610480 ATATATTATTTTTTT
1 ATATATTATTTTGGT
*
11610495 TTATATTATTTT
1 ATATATTATTTT
11610507 AGTAAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (15 bp):
ATATATTATTTTGGT
Found at i:11611940 original size:22 final size:22
Alignment explanation
Indices: 11611914--11611957 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11611904 GAATTCCAAT
11611914 TAATAAGCACAATAATAAAAAA
1 TAATAAGCACAATAATAAAAAA
*
11611936 TAATAAGGACAATAATAAAAAA
1 TAATAAGCACAATAATAAAAAA
11611958 ATATCACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
TAATAAGCACAATAATAAAAAA
Found at i:11620894 original size:45 final size:45
Alignment explanation
Indices: 11620830--11620918 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
11620820 TTTGATTTGC
*
11620830 TTTCATAATTTGGAAAGCTTGATTTGTGATTAAACTCAAACTATT
1 TTTCACAATTTGGAAAGCTTGATTTGTGATTAAACTCAAACTATT
11620875 TTTCACAATTTGGAAAGCTTGATTTGTGATTAAACTCAAACTAT
1 TTTCACAATTTGGAAAGCTTGATTTGTGATTAAACTCAAACTAT
11620919 CTATAGTGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (45 bp):
TTTCACAATTTGGAAAGCTTGATTTGTGATTAAACTCAAACTATT
Found at i:11621762 original size:16 final size:17
Alignment explanation
Indices: 11621727--11621764 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11621717 AAACTACACG
*
11621727 AAATAAAATGATTAAGC
1 AAATAAAACGATTAAGC
*
11621744 AAATAAAACGA-TGAGC
1 AAATAAAACGATTAAGC
11621760 AAATA
1 AAATA
11621765 CGAAACGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (17 bp):
AAATAAAACGATTAAGC
Found at i:11621891 original size:29 final size:29
Alignment explanation
Indices: 11621859--11622000 Score: 103
Period size: 29 Copynumber: 4.9 Consensus size: 29
11621849 TTGGATACCC
*
11621859 GGGGGTAAAATGGTAATTTTGATGAA-ATT
1 GGGGGTAAAATGGTAATTTTG-GGAAGATT
* *
11621888 GGGGTTGAAAATGG-AATTTTGGGAAGTTT
1 GGGGGT-AAAATGGTAATTTTGGGAAGATT
* *
11621917 GGGGGTAAAATGGTAATTTTTGGTAA-AAT
1 GGGGGTAAAATGGTAA-TTTTGGGAAGATT
* * * * *
11621946 CGAGGTCAAAAAT-GAAATTTTGGAAAGTTT
1 GGGGGT--AAAATGGTAATTTTGGGAAGATT
* *
11621976 TGGGGTAAAATGGTAATTTTTGGAA
1 GGGGGTAAAATGGTAATTTTGGGAA
11622001 AAGTTTAGGG
Statistics
Matches: 87, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
28 15 0.17
29 44 0.51
30 23 0.26
31 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.31, T:0.34
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTGGGAAGATT
Found at i:11622043 original size:29 final size:29
Alignment explanation
Indices: 11621859--11622188 Score: 278
Period size: 30 Copynumber: 11.1 Consensus size: 29
11621849 TTGGATACCC
*
11621859 GGGGGTAAAATGGTAATTTTGATGAAA--TT-
1 GGGGTTAAAAT-GTAATTTTG--GAAAGTTTA
* *
11621888 GGGGTTGAAAATGGAATTTTGGGAAGTTT-
1 GGGGTT-AAAATGTAATTTTGGAAAGTTTA
* * *
11621917 GGGGGTAAAATGGTAATTTTTGGTAAA--ATC
1 GGGGTTAAAAT-GTAA-TTTTGG-AAAGTTTA
* * * *
11621947 GAGGTCAAAAATGAAATTTTGGAAAGTTTT
1 GGGGT-TAAAATGTAATTTTGGAAAGTTTA
11621977 GGGG-TAAAATGGTAATTTTTGGAAAAGTTTA
1 GGGGTTAAAAT-GTAA-TTTTGG-AAAGTTTA
* *
11622008 GGGGTTAGAATGTAATTTTGGAAATTTTA
1 GGGGTTAAAATGTAATTTTGGAAAGTTTA
* * * *
11622037 AGGGTTAAAATGTAATTTTAGAAAATCTA
1 GGGGTTAAAATGTAATTTTGGAAAGTTTA
11622066 GGGGTTAAAATGTAATTTTGGGAAAGTTTA
1 GGGGTTAAAATGTAATTTT-GGAAAGTTTA
* *
11622096 GGGGTTAAAATATAATTTTGAAAAAGTTTA
1 GGGGTTAAAATGTAATTTTG-GAAAGTTTA
* *
11622126 GGGGTCAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTA
**
11622156 GGGGTTAAAAAATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTA
11622186 GGG
1 GGG
11622189 TTTTAGGGTA
Statistics
Matches: 250, Mismatches: 34, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.01
28 13 0.05
29 83 0.33
30 124 0.50
31 22 0.09
32 5 0.02
ACGTcount: A:0.37, C:0.01, G:0.27, T:0.35
Consensus pattern (29 bp):
GGGGTTAAAATGTAATTTTGGAAAGTTTA
Found at i:11622101 original size:59 final size:60
Alignment explanation
Indices: 11621859--11622180 Score: 292
Period size: 59 Copynumber: 5.4 Consensus size: 60
11621849 TTGGATACCC
* *
11621859 GGGGGTAAAATGGTAATTTT-GATGAAAT-T-GGGGTTGAAAATGGAATTTTGGG-AAGTTT-
1 GGGGTTAAAATGGTAATTTTGGA--AAATCTAGGGGTT-AAAATGTAATTTTGGGAAAGTTTA
* * * * *
11621917 GGGGGTAAAATGGTAATTTTTGGTAAAATC--GAGGTCAAAAATGAAATTTT-GGAAAGTTTT
1 GGGGTTAAAATGGTAA-TTTTGG-AAAATCTAGGGGT-TAAAATGTAATTTTGGGAAAGTTTA
* * *
11621977 GGGG-TAAAATGGTAATTTTTGGAAAAGTTTAGGGGTTAGAATGTAATTTT-GGAAATTTTA
1 GGGGTTAAAATGGTAA-TTTTGGAAAA-TCTAGGGGTTAAAATGTAATTTTGGGAAAGTTTA
* *
11622037 AGGGTTAAAAT-GTAATTTTAGAAAATCTAGGGGTTAAAATGTAATTTTGGGAAAGTTTA
1 GGGGTTAAAATGGTAATTTTGGAAAATCTAGGGGTTAAAATGTAATTTTGGGAAAGTTTA
* * * * * *
11622096 GGGGTTAAAAT-ATAATTTTGAAAAAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATGGTAATTTTGGAAAA-TCTAGGGGTTAAAATGTAATTTTGGGAAAGTTTA
**
11622156 GGGGTTAAAA-AATAATTTTGGAAAA
1 GGGGTTAAAATGGTAATTTTGGAAAA
11622181 GTTTAGGGTT
Statistics
Matches: 226, Mismatches: 24, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
58 43 0.19
59 88 0.39
60 84 0.37
61 11 0.05
ACGTcount: A:0.37, C:0.01, G:0.27, T:0.35
Consensus pattern (60 bp):
GGGGTTAAAATGGTAATTTTGGAAAATCTAGGGGTTAAAATGTAATTTTGGGAAAGTTTA
Found at i:11622171 original size:30 final size:30
Alignment explanation
Indices: 11621954--11622188 Score: 298
Period size: 30 Copynumber: 7.9 Consensus size: 30
11621944 ATCGAGGTCA
* *
11621954 AAAATGAAATTTTGG-AAAGTTTTGGGG-T
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
11621982 AAAATGGTAATTTTTGGAAAAGTTTAGGGGTT
1 AAAAT-GTAA-TTTTGGAAAAGTTTAGGGGTT
* * *
11622014 AGAATGTAATTTTGG-AAATTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
11622043 AAAATGTAATTTTAGAAAA-TCTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
*
11622072 AAAATGTAATTTTGGGAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * *
11622102 AAAATATAATTTTGAAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
*
11622132 AAAATATAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
**
11622162 AAAAAATAATTTTGGAAAAGTTTAGGG
1 AAAATGTAATTTTGGAAAAGTTTAGGG
11622189 TTTTAGGGTA
Statistics
Matches: 182, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.03
29 53 0.29
30 104 0.57
31 15 0.08
32 5 0.03
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGGTT
Found at i:11623286 original size:25 final size:22
Alignment explanation
Indices: 11623249--11623300 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
11623239 ATCTTCCTTT
11623249 TTTATT-TTAAT-AT-TAATAAA
1 TTTATTATTAATAATATAA-AAA
11623269 TATTATTATTAATAATATAAAAA
1 T-TTATTATTAATAATATAAAAA
11623292 TTTATTATT
1 TTTATTATT
11623301 TATTGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.04
21 5 0.18
22 13 0.46
23 6 0.21
24 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATTATTAATAATATAAAAA
Found at i:11624029 original size:18 final size:19
Alignment explanation
Indices: 11624003--11624049 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
11623993 GCTTGTACCT
*
11624003 TTTTGAATTTATA-ATAAG
1 TTTTAAATTTATATATAAG
*
11624021 TTTTAAATTCATATATAAG
1 TTTTAAATTTATATATAAG
*
11624040 -TCTAAATTTA
1 TTTTAAATTTA
11624050 AATTAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (19 bp):
TTTTAAATTTATATATAAG
Found at i:11624058 original size:11 final size:11
Alignment explanation
Indices: 11624042--11624100 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
11624032 TATATAAGTC
11624042 TAAATTTAAAT
1 TAAATTTAAAT
11624053 TAAATTTAAATTT
1 TAAATTTAAA--T
***
11624066 TAAAACAAAATT
1 TAAATTTAAA-T
*
11624078 TAAATTTAAAA
1 TAAATTTAAAT
11624089 TAAATTTAAAT
1 TAAATTTAAAT
11624100 T
1 T
11624101 CAAAAATCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 21 0.55
12 9 0.24
13 8 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:11624069 original size:7 final size:6
Alignment explanation
Indices: 11624042--11624100 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
11624032 TATATAAGTC
** * *
11624042 TAAATT TAAA-T TAAATT TAAATTT TAAAAC AAAATT TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT TAAATT
11624089 TAAATT TAAATT
1 TAAATT TAAATT
11624101 CAAAAATCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
5 9 0.21
6 27 0.64
7 6 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:11624082 original size:36 final size:35
Alignment explanation
Indices: 11624008--11624134 Score: 121
Period size: 36 Copynumber: 3.5 Consensus size: 35
11623998 TACCTTTTTG
* * * * * *
11624008 AATTTATAATAAGTTTTAAATTCATATATAAGTCTA
1 AATTTAAAATAA-ATTTAAATTCAAAAATAAATTTA
* *
11624044 AATTTAAATTAAATTTAAATTTTAAAACA-AAATTTA
1 AATTTAAAATAAATTTAAA-TTCAAAA-ATAAATTTA
*
11624080 AATTTAAAATAAATTTAAATTCAAAAATCAATTTA
1 AATTTAAAATAAATTTAAATTCAAAAATAAATTTA
*
11624115 AACTTAAAATAAATCTTAAA
1 AATTTAAAATAAAT-TTAAA
11624135 ATGGGTTTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
34 1 0.01
35 31 0.41
36 42 0.56
37 1 0.01
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (35 bp):
AATTTAAAATAAATTTAAATTCAAAAATAAATTTA
Found at i:11624106 original size:18 final size:17
Alignment explanation
Indices: 11624042--11624134 Score: 82
Period size: 17 Copynumber: 5.2 Consensus size: 17
11624032 TATATAAGTC
* *
11624042 TAAATTTAAATTAAATT
1 TAAATTAAAAATAAATT
11624059 TAAATTTTAAAACA-AAATT
1 TAAA--TTAAAA-ATAAATT
*
11624078 TAAATTTAAAATAAATT
1 TAAATTAAAAATAAATT
*
11624095 TAAATTCAAAAATCAATT
1 TAAATT-AAAAATAAATT
11624113 TAAACTT-AAAATAAATCT
1 TAAA-TTAAAAATAAAT-T
11624131 TAAA
1 TAAA
11624135 ATGGGTTTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
16 1 0.02
17 28 0.44
18 18 0.29
19 16 0.25
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAAAAATAAATT
Found at i:11625511 original size:26 final size:26
Alignment explanation
Indices: 11625457--11625511 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
11625447 CCTACTCTAC
*
11625457 ATATAATATAAATATTTTATCTAATA
1 ATATAATATAAATATTTTATCTAAAA
* *
11625483 ATATAATATAAATATTTTTTTTAAAA
1 ATATAATATAAATATTTTATCTAAAA
11625509 ATA
1 ATA
11625512 ATATGTGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATAATATAAATATTTTATCTAAAA
Found at i:11626138 original size:19 final size:20
Alignment explanation
Indices: 11626114--11626156 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
11626104 TCAATTCAAA
* *
11626114 TTAAATAATAA-AAAAGTAT
1 TTAAATAAAAATAAAAATAT
11626133 TTAAATAAAAATAAAAATAT
1 TTAAATAAAAATAAAAATAT
11626153 TTAA
1 TTAA
11626157 TATTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAATAAAAATAAAAATAT
Found at i:11628644 original size:12 final size:11
Alignment explanation
Indices: 11628609--11628657 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 11
11628599 TATGCCCTTG
11628609 ATAATTTTTAAA
1 ATAATTTTT-AA
11628621 ATTAATTATTTAA
1 A-TAATT-TTTAA
*
11628634 ATAATCTTTTAT
1 ATAAT-TTTTAA
11628646 ATAATTTTTAA
1 ATAATTTTTAA
11628657 A
1 A
11628658 ATTAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 6 0.19
12 14 0.44
13 9 0.28
14 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
ATAATTTTTAA
Found at i:11650975 original size:31 final size:29
Alignment explanation
Indices: 11650939--11651007 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
11650929 TTACAAAAGC
* *
11650939 AGTCACTTTTGTTTGCATCATATTACATTTT
1 AGTCACTTATGTTTG-A-AATATTACATTTT
* *
11650970 AGTCACTTATGTTTGAAATGTTACGTTTT
1 AGTCACTTATGTTTGAAATATTACATTTT
11650999 AGTCACTTA
1 AGTCACTTA
11651008 CGTTATCGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
30 1 0.03
31 14 0.41
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (29 bp):
AGTCACTTATGTTTGAAATATTACATTTT
Found at i:11651162 original size:17 final size:17
Alignment explanation
Indices: 11651142--11651174 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11651132 TTTCAATTGT
*
11651142 AATTAATTTAAAATTTC
1 AATTAATTAAAAATTTC
11651159 AATTAATTAAAAATTT
1 AATTAATTAAAAATTT
11651175 ATTCTCATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAATTAAAAATTTC
Found at i:11652150 original size:26 final size:24
Alignment explanation
Indices: 11652109--11652182 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
11652099 TTCATGTATT
*
11652109 TATTTTTTGAATTTTTATGAATTATATA
1 TATTTTTT-AA-TTTTA--AATTATAGA
* *
11652137 TATTTTTTAATTTTAATTTTTAGA
1 TATTTTTTAATTTTAAATTATAGA
11652161 TATTTTTATAATTTTAAATTAT
1 TATTTTT-TAATTTTAAATTAT
11652183 TTGTTGACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 13 0.32
25 12 0.30
26 5 0.12
27 2 0.05
28 8 0.20
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
TATTTTTTAATTTTAAATTATAGA
Found at i:11654832 original size:28 final size:28
Alignment explanation
Indices: 11654771--11654860 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
11654761 AACATTAAAA
* *
11654771 AAATGATAAGATAACTATATTAAAATTTT
1 AAATAATAAAATAA-TATATTAAAATTTT
*
11654800 CAATAAATAAAA-AATATA-TAAAATTATT
1 AAAT-AATAAAATAATATATTAAAATT-TT
* *
11654828 AAATATTAAAATAATATAATATAAATATTT
1 AAATAATAAAATAATATATTA-AAAT-TTT
11654858 AAA
1 AAA
11654861 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
27 13 0.26
28 15 0.30
29 7 0.14
30 14 0.28
31 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATAATAAAATAATATATTAAAATTTT
Found at i:11657514 original size:24 final size:22
Alignment explanation
Indices: 11657485--11657548 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 22
11657475 TTTAAAATTA
*
11657485 AAAATTAAAAATAATATATTTTTT
1 AAAATTAAAAATAATA-A-TCTTT
11657509 AAAATTAGGAAAAGTAA-AATCTTT
1 AAAATTA--AAAA-TAATAATCTTT
11657533 AAAATTAAAAA-AATAA
1 AAAATTAAAAATAATAA
11657549 ATTCATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 4 0.11
24 18 0.51
25 1 0.03
26 5 0.14
27 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAATTAAAAATAATAATCTTT
Found at i:11658953 original size:39 final size:38
Alignment explanation
Indices: 11658910--11658994 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 38
11658900 TTTTTTAAAA
*
11658910 TTTTAAAATTCAAAA-ATTCAAAAATACAAAAAAAAATAT
1 TTTTAAAATT-AAAATATT-AAAAAAACAAAAAAAAATAT
* *
11658949 TTTTAAAAATTAAAATTATTAAAAAAATATAAAAAAATAT
1 TTTT-AAAATTAAAA-TATTAAAAAAACAAAAAAAAATAT
11658989 TTTTAA
1 TTTTAA
11658995 TTTTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 10 0.25
40 27 0.68
41 3 0.08
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (38 bp):
TTTTAAAATTAAAATATTAAAAAAACAAAAAAAAATAT
Found at i:11680529 original size:23 final size:23
Alignment explanation
Indices: 11680488--11680539 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
11680478 AAGGTTGCGG
* * *
11680488 GATGTTCCGCCTCATGAGGAGTT
1 GATGTTCCACCTCACGAGGAGCT
* *
11680511 GATGTTCCACCTCGCGAGGTGCT
1 GATGTTCCACCTCACGAGGAGCT
11680534 GATGTT
1 GATGTT
11680540 TGCGAGGCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (23 bp):
GATGTTCCACCTCACGAGGAGCT
Found at i:11684875 original size:4 final size:4
Alignment explanation
Indices: 11684866--11684928 Score: 65
Period size: 4 Copynumber: 15.2 Consensus size: 4
11684856 AGGTTTGAAG
* * *
11684866 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA G-AA GGAA GAAT GAGAA GAAT
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
11684915 GAGAA GAAA GAAA G
1 GA-AA GAAA GAAA G
11684929 GAGAAGGAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
3 3 0.06
4 37 0.74
5 10 0.20
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:11684885 original size:9 final size:9
Alignment explanation
Indices: 11684866--11684927 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
11684856 AGGTTTGAAG
11684866 GAAAG-AAA
1 GAAAGAAAA
11684874 GAAAGAAAA
1 GAAAGAAAA
11684883 GAAAG-AAA
1 GAAAGAAAA
11684891 GAAAGAAGGAA
1 GAAAGAA--AA
* *
11684902 GAATGAGAA
1 GAAAGAAAA
* *
11684911 GAATGAGAA
1 GAAAGAAAA
11684920 GAAAGAAA
1 GAAAGAAA
11684928 GGAGAAGGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
8 13 0.28
9 26 0.57
11 7 0.15
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:11684885 original size:13 final size:12
Alignment explanation
Indices: 11684866--11684928 Score: 65
Period size: 13 Copynumber: 5.1 Consensus size: 12
11684856 AGGTTTGAAG
11684866 GAAAGAAAGAAA
1 GAAAGAAAGAAA
11684878 GAAAAGAAAGAAA
1 G-AAAGAAAGAAA
*
11684891 GAAAG-AAGGAA
1 GAAAGAAAGAAA
* *
11684902 GAATGAGAAGAAT
1 GAAAGA-AAGAAA
11684915 GAGAAGAAAGAAA
1 GA-AAGAAAGAAA
11684928 G
1 G
11684929 GAGAAGGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 9 0.22
12 5 0.12
13 24 0.59
14 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (12 bp):
GAAAGAAAGAAA
Found at i:11684913 original size:33 final size:33
Alignment explanation
Indices: 11684862--11684928 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
11684852 CAACAGGTTT
11684862 GAAGGAAAGAAAGAAAGAAA-AGAAAGAAAGAAA
1 GAAGGAAAGAAAGAAAGAAAGAG-AAGAAAGAAA
* *
11684895 GAAGG-AAGAATGAGAAGAATGAGAAGAAAGAAA
1 GAAGGAAAGAAAGA-AAGAAAGAGAAGAAAGAAA
11684928 G
1 G
11684929 GAGAAGGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.23
33 21 0.70
34 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (33 bp):
GAAGGAAAGAAAGAAAGAAAGAGAAGAAAGAAA
Found at i:11684952 original size:33 final size:33
Alignment explanation
Indices: 11684885--11684953 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
11684875 AAAGAAAAGA
11684885 AAGAAAGAAAGAAGGAAGAATGAGAAGAATGAG
1 AAGAAAGAAAGAAGGAAGAATGAGAAGAATGAG
* * *
11684918 AAGAAAGAAAGGA-GAAGGA-GAGGAGAATGAG
1 AAGAAAGAAAGAAGGAAGAATGAGAAGAATGAG
11684949 -AGAAA
1 AAGAAA
11684954 AGTAATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 5 0.15
31 11 0.33
32 5 0.15
33 12 0.36
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.04
Consensus pattern (33 bp):
AAGAAAGAAAGAAGGAAGAATGAGAAGAATGAG
Found at i:11686979 original size:18 final size:18
Alignment explanation
Indices: 11686952--11687003 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
11686942 CTTCTGCCTT
* *
11686952 AGAGTCAGAGCCAGAGCA
1 AGAGTAAGAGCAAGAGCA
11686970 AGAGTAAGAGCAAGAGCA
1 AGAGTAAGAGCAAGAGCA
* *
11686988 AGAGCAAGAGGAAGAG
1 AGAGTAAGAGCAAGAG
11687004 GCATTGGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.13, G:0.37, T:0.04
Consensus pattern (18 bp):
AGAGTAAGAGCAAGAGCA
Found at i:11687004 original size:6 final size:6
Alignment explanation
Indices: 11686958--11687003 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
11686948 CCTTAGAGTC
* * *
11686958 AGAGCC AGAGCA AGAGTA AGAGCA AGAGCA AGAGCA AGAGGA AGAG
1 AGAGCA AGAGCA AGAGCA AGAGCA AGAGCA AGAGCA AGAGCA AGAG
11687004 GCATTGGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.48, C:0.13, G:0.37, T:0.02
Consensus pattern (6 bp):
AGAGCA
Found at i:11692221 original size:24 final size:24
Alignment explanation
Indices: 11692189--11692259 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
11692179 CACCATACAC
* *
11692189 GGAGTTGGATTTTCATTTTCTGCT
1 GGAGTTGGATCTTCATTTTCTACT
* *
11692213 GGAGTTGGATCTTCATTTTTTATT
1 GGAGTTGGATCTTCATTTTCTACT
*
11692237 GGATTTGGATCTTCATTTTCTAC
1 GGAGTTGGATCTTCATTTTCTAC
11692260 AAGTTCCACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (24 bp):
GGAGTTGGATCTTCATTTTCTACT
Found at i:11692654 original size:15 final size:15
Alignment explanation
Indices: 11692621--11692654 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11692611 AATCTGTTAA
**
11692621 AAATAAATAAAATTT
1 AAATAAATAAAATAC
11692636 AAATAAATAAAATAC
1 AAATAAATAAAATAC
11692651 AAAT
1 AAAT
11692655 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAATAAAATAC
Found at i:11692671 original size:21 final size:21
Alignment explanation
Indices: 11692621--11692659 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11692611 AATCTGTTAA
11692621 AAAT-AAATA-AAATTTAAAT
1 AAATAAAATACAAATTTAAAT
11692640 AAATAAAATACAAATTTAAA
1 AAATAAAATACAAATTTAAA
11692660 AATATATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAAATACAAATTTAAAT
Found at i:11702890 original size:8 final size:9
Alignment explanation
Indices: 11702810--11702892 Score: 64
Period size: 9 Copynumber: 8.9 Consensus size: 9
11702800 AATTAAGATT
11702810 ATTTTTAAA
1 ATTTTTAAA
**
11702819 ATTTTTGTA
1 ATTTTTAAA
*
11702828 TTTTTTAAATA
1 ATTTTT-AA-A
11702839 ATTTTT--A
1 ATTTTTAAA
11702846 ATTTTATAAAATA
1 ATTTT-T--AA-A
11702859 ATTTTTAAA
1 ATTTTTAAA
11702868 ATTTTTAAA
1 ATTTTTAAA
11702877 ATTTTT-AA
1 ATTTTTAAA
11702885 ATTTTTAA
1 ATTTTTAA
11702893 TTAATTATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
7 6 0.10
8 9 0.15
9 29 0.49
10 2 0.03
11 6 0.10
12 1 0.02
13 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:11705320 original size:22 final size:23
Alignment explanation
Indices: 11705287--11705330 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
11705277 TTAATAAAAA
*
11705287 TTTATAATTTTTTATTAATTTTG
1 TTTATAATTTTTTATGAATTTTG
11705310 TTTATAA-TTTTTATGAATTTT
1 TTTATAATTTTTTATGAATTTT
11705331 TAAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTATAATTTTTTATGAATTTTG
Found at i:11705331 original size:23 final size:23
Alignment explanation
Indices: 11705286--11705355 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
11705276 TTTAATAAAA
*
11705286 ATTTATAATTTTTTATTAA-TTTT
1 ATTTATAA-TTTTTATGAATTTTT
*
11705309 GTTTATAATTTTTATGAATTTTT
1 ATTTATAATTTTTATGAATTTTT
*** *
11705332 AAAAATAATTTGTATGAATTTTT
1 ATTTATAATTTTTATGAATTTTT
11705355 A
1 A
11705356 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.23
23 30 0.77
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (23 bp):
ATTTATAATTTTTATGAATTTTT
Found at i:11705356 original size:23 final size:23
Alignment explanation
Indices: 11705313--11705357 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
11705303 AATTTTGTTT
*
11705313 ATAATTTTTATGAATTTTTAAAA
1 ATAATTTGTATGAATTTTTAAAA
11705336 ATAATTTGTATGAATTTTTAAA
1 ATAATTTGTATGAATTTTTAAA
11705358 TTTTAAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
ATAATTTGTATGAATTTTTAAAA
Found at i:11709759 original size:8 final size:8
Alignment explanation
Indices: 11709746--11709770 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11709736 CAAGGTTCAG
11709746 ATCATCAC
1 ATCATCAC
11709754 ATCATCAC
1 ATCATCAC
11709762 ATCATCAC
1 ATCATCAC
11709770 A
1 A
11709771 GTCTAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (8 bp):
ATCATCAC
Found at i:11718827 original size:14 final size:14
Alignment explanation
Indices: 11718791--11718829 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11718781 TGTTATCATT
* * *
11718791 TTATTATTATATTT
1 TTATTATTTTGTTG
11718805 TTATTATTTTGTTG
1 TTATTATTTTGTTG
11718819 TTATTATTTTG
1 TTATTATTTTG
11718830 ATATGGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (14 bp):
TTATTATTTTGTTG
Found at i:11720622 original size:5 final size:5
Alignment explanation
Indices: 11720612--11720636 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11720602 CACCCTCAAA
11720612 ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT
11720637 TTACTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:11721404 original size:23 final size:23
Alignment explanation
Indices: 11721378--11721423 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11721368 TTATTATTTA
11721378 ATAAATAACATA-TTAATATGATT
1 ATAAA-AACATATTTAATATGATT
* *
11721401 ATAAAAATATATTTAATTTGATT
1 ATAAAAACATATTTAATATGATT
11721424 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
ATAAAAACATATTTAATATGATT
Found at i:11722434 original size:28 final size:27
Alignment explanation
Indices: 11722343--11722437 Score: 76
Period size: 28 Copynumber: 3.6 Consensus size: 27
11722333 CAGGTTATTT
11722343 ATATTATT-ATT-TT-AAAAA-TAAAA
1 ATATTATTAATTATTAAAAAATTAAAA
* *
11722366 ATATATATATAATTTTTTAAAATAATT-ACA
1 ATAT-TAT-TAA-TTATTAAAA-AATTAAAA
*
11722396 ATA-TATAAATTATTAAAAAATTTAAAA
1 ATATTATTAATTATTAAAAAA-TTAAAA
11722423 ATATTATTAATTATT
1 ATATTATTAATTATT
11722438 TTATATATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
23 4 0.07
24 3 0.05
25 3 0.05
26 11 0.20
27 9 0.16
28 15 0.27
29 3 0.05
30 7 0.12
31 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATTATTAATTATTAAAAAATTAAAA
Found at i:11722459 original size:18 final size:18
Alignment explanation
Indices: 11722436--11722477 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
11722426 TTATTAATTA
* *
11722436 TTTTATATATTTATATAT
1 TTTTATAAATTTATAAAT
11722454 TTTTATAAATTTATAAAT
1 TTTTATAAATTTATAAAT
11722472 TTTTAT
1 TTTTAT
11722478 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATAAATTTATAAAT
Found at i:11729835 original size:11 final size:11
Alignment explanation
Indices: 11729819--11729851 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11729809 TGATATTACT
11729819 TAAAATAAAAA
1 TAAAATAAAAA
*
11729830 TAAAATATAAA
1 TAAAATAAAAA
11729841 T-AAATAAAAA
1 TAAAATAAAAA
11729851 T
1 T
11729852 TCTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:11731190 original size:23 final size:23
Alignment explanation
Indices: 11731147--11731190 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
11731137 ATTTTAAACT
* *
11731147 CTTTAATTTATTTATTTATTATA
1 CTTTAATTAATTTATTAATTATA
11731170 CTTT-ATTAATTTAATTAATTA
1 CTTTAATTAATTT-ATTAATTA
11731191 GATACTGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (23 bp):
CTTTAATTAATTTATTAATTATA
Found at i:11740525 original size:21 final size:19
Alignment explanation
Indices: 11740494--11740537 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
11740484 AAATATATTT
11740494 ATAATAAAATTAAATTAAA
1 ATAATAAAATTAAATTAAA
* *
11740513 ATAATACACAATTATATTGAA
1 ATAATA-A-AATTAAATTAAA
11740534 ATAA
1 ATAA
11740538 AATCTATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATAAAATTAAATTAAA
Found at i:11740979 original size:17 final size:17
Alignment explanation
Indices: 11740957--11740998 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
11740947 CTTAGTAAAA
11740957 TAATAATTTTATCAT-TT
1 TAATAATTTTAT-ATATT
11740974 TAATAA-TTTATATATT
1 TAATAATTTTATATATT
11740990 T-ATAATTTT
1 TAATAATTTT
11740999 TAAAAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATAATTTTATATATT
Found at i:11741060 original size:23 final size:24
Alignment explanation
Indices: 11741034--11741083 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
11741024 ATTTTGAGAG
*
11741034 TTAAAAGTATAA-TTTTATTATTA
1 TTAAAAGTAAAACTTTTATTATTA
**
11741057 TT-AATTTAAAACTTTTATTATTA
1 TTAAAAGTAAAACTTTTATTATTA
11741080 TTAA
1 TTAA
11741084 CTTATAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 6 0.27
23 15 0.68
24 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTAAAAGTAAAACTTTTATTATTA
Found at i:11746077 original size:95 final size:95
Alignment explanation
Indices: 11745954--11746142 Score: 360
Period size: 95 Copynumber: 2.0 Consensus size: 95
11745944 ACAACCAAAA
*
11745954 AGAAAGAATGCTAAGTGTCTATAAACATTCCAAGCACCAAATAAAAGGAAAAACCTTTGTTGAAG
1 AGAAAGAATGCTAAGTGTCCATAAACATTCCAAGCACCAAATAAAAGGAAAAACCTTTGTTGAAG
11746019 GAAAAATACAAAAGAAAGATGGGTAGATAC
66 GAAAAATACAAAAGAAAGATGGGTAGATAC
*
11746049 AGAAAGAATGCTAAGTTTCCATAAACATTCCAAGCACCAAATAAAAGGAAAAACCTTTGTTGAAG
1 AGAAAGAATGCTAAGTGTCCATAAACATTCCAAGCACCAAATAAAAGGAAAAACCTTTGTTGAAG
11746114 GAAAAATACAAAAGAAAGATGGGTAGATA
66 GAAAAATACAAAAGAAAGATGGGTAGATA
11746143 TAGACATGAA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.50, C:0.13, G:0.19, T:0.19
Consensus pattern (95 bp):
AGAAAGAATGCTAAGTGTCCATAAACATTCCAAGCACCAAATAAAAGGAAAAACCTTTGTTGAAG
GAAAAATACAAAAGAAAGATGGGTAGATAC
Found at i:11752261 original size:10 final size:10
Alignment explanation
Indices: 11752236--11752283 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
11752226 GAAACTTATT
11752236 TAAAAA-TTA
1 TAAAAATTTA
*
11752245 TAGAAATTTA
1 TAAAAATTTA
*
11752255 TAAAAATTCA
1 TAAAAATTTA
* *
11752265 AAAAAAATTA
1 TAAAAATTTA
11752275 TAAAAATTT
1 TAAAAATTT
11752284 TGAATAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:11752279 original size:9 final size:9
Alignment explanation
Indices: 11752236--11752512 Score: 56
Period size: 9 Copynumber: 30.0 Consensus size: 9
11752226 GAAACTTATT
11752236 TAAAAATTA
1 TAAAAATTA
*
11752245 TAGAAATTTA
1 TA-AAAATTA
11752255 TAAAAATTCAA
1 TAAAAATT--A
*
11752266 AAAAAATTA
1 TAAAAATTA
*
11752275 TAAAAATTT
1 TAAAAATTA
11752284 TGAATAAATTA
1 T-AA-AAATTA
** *
11752295 TTAAAGCTAA
1 -TAAAAATTA
*
11752305 TAGAAATT-
1 TAAAAATTA
11752313 TGAAAAATT-
1 T-AAAAATTA
*
11752322 TAAAAA-GA
1 TAAAAATTA
*
11752330 GTAAAATTTA
1 -TAAAAATTA
* *
11752340 AAAAAATAA
1 TAAAAATTA
*
11752349 TAATAATT-
1 TAAAAATTA
* *
11752357 TATTAAACTA
1 TA-AAAATTA
11752367 TAAAAA-T-
1 TAAAAATTA
*
11752374 GAAAAATTA
1 TAAAAATTA
*
11752383 TTAAAAATCA
1 -TAAAAATTA
*
11752393 T-AACATTA
1 TAAAAATTA
*
11752401 TAAAAA-AA
1 TAAAAATTA
*
11752409 CTGCAAAAAAATA
1 -T---AAAAATTA
*
11752422 TTAAACATTA
1 -TAAAAATTA
* *
11752432 T-GAAATTT
1 TAAAAATTA
11752440 TGAAAAATTA
1 T-AAAAATTA
*
11752450 TCAAAAATTT
1 T-AAAAATTA
11752460 TAAAAATTA
1 TAAAAATTA
11752469 GTAAAAATT-
1 -TAAAAATTA
**
11752478 TTGAAA--A
1 TAAAAATTA
11752485 TAAAAATATA
1 TAAAAAT-TA
*
11752495 TTAAAATTA
1 TAAAAATTA
*
11752504 CAAAAATTA
1 TAAAAATTA
11752513 AATTAAACAT
Statistics
Matches: 187, Mismatches: 53, Indels: 56
0.63 0.18 0.19
Matches are distributed among these distances:
7 9 0.05
8 26 0.14
9 71 0.38
10 58 0.31
11 15 0.08
12 6 0.03
13 2 0.01
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:11752466 original size:19 final size:19
Alignment explanation
Indices: 11752434--11752485 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
11752424 AAACATTATG
11752434 AAATTTTGAAAAATTA-TCAA
1 AAATTTT-AAAAATTAGT-AA
11752454 AAATTTTAAAAATTAGTAA
1 AAATTTTAAAAATTAGTAA
*
11752473 AAATTTTGAAAAT
1 AAATTTTAAAAAT
11752486 AAAAATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (19 bp):
AAATTTTAAAAATTAGTAA
Found at i:11753334 original size:22 final size:20
Alignment explanation
Indices: 11753308--11753348 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
11753298 GAAATGCCAA
11753308 CAAAACAGTGGCAAAACAACAC
1 CAAAACAGT-G-AAAACAACAC
*
11753330 CAAAATAGTGAAAACAACA
1 CAAAACAGTGAAAACAACA
11753349 GTAGCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.07
Consensus pattern (20 bp):
CAAAACAGTGAAAACAACAC
Found at i:11753677 original size:219 final size:221
Alignment explanation
Indices: 11753297--11753725 Score: 648
Period size: 220 Copynumber: 2.0 Consensus size: 221
11753287 AATATCATAA
* *
11753297 CGAAATGCCAACAAAACAGTGGCAAAACAACACCAAAATAGTGAAAACAACAGTAGCTTTTTTTG
1 CGAAATGCCAACAAAACAGTGGCAAAACAACACCAAAACAATGAAAACAACAGTAGCTTTTTTTG
** * * * * * *
11753362 GTAAATTCAAGACAGGCAAGGCCAAGAAAAACTGCTAAAAAAAATTACTCGATGCTCGGCCCGTT
66 ACAAATTCAAGACAGGCAAGGCCAAAAAAAACCGCTAAAAAAAATTACCCGATACCCGACCCGTT
** * *
11753427 TAAAAAGTGATTCTCGTTTTTTTGCCCAAACC-CTCCTATTTTCAGGTGACTCTTCGGGTCAAGC
131 TAAAAAACGAATCTCATTTTTTTGCCCAAACCTCTCCTATTTTCAGGTGACTCTTCGGGTCAAGC
11753491 CAATC-AAGTCTAATTTTAGATAATAG
196 CAATCGAA-TCTAATTTTAGATAATAG
* * *
11753517 CGAAATGCTAGCAAAACAGTGGTAAAACAACACCAAAACAATGAAAACAACAGTAG-TTTTTTTG
1 CGAAATGCCAACAAAACAGTGGCAAAACAACACCAAAACAATGAAAACAACAGTAGCTTTTTTTG
* *
11753581 ACAAATTCGAGACAGGCAAGGCCAAAAAAAACCGCTAAAAAAATTTACCCGATACCCGACCCGTT
66 ACAAATTCAAGACAGGCAAGGCCAAAAAAAACCGCTAAAAAAAATTACCCGATACCCGACCCGTT
*
11753646 TAAAAAACGAATCTCATTTTTTTGCCCAAACCTCTCCTATTTTCAGGTGACTCTTCGGGTCAGGC
131 TAAAAAACGAATCTCATTTTTTTGCCCAAACCTCTCCTATTTTCAGGTGACTCTTCGGGTCAAGC
11753711 CAATCGAATCTAATT
196 CAATCGAATCTAATT
11753726 CTTGGTAATT
Statistics
Matches: 187, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
219 91 0.49
220 94 0.50
221 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (221 bp):
CGAAATGCCAACAAAACAGTGGCAAAACAACACCAAAACAATGAAAACAACAGTAGCTTTTTTTG
ACAAATTCAAGACAGGCAAGGCCAAAAAAAACCGCTAAAAAAAATTACCCGATACCCGACCCGTT
TAAAAAACGAATCTCATTTTTTTGCCCAAACCTCTCCTATTTTCAGGTGACTCTTCGGGTCAAGC
CAATCGAATCTAATTTTAGATAATAG
Found at i:11763962 original size:29 final size:30
Alignment explanation
Indices: 11763896--11763962 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
11763886 TAAAAAAATA
* ** *
11763896 TTAAATATTAAATTAAAAATAATATGATCTT
1 TTAAA-ATTAAATAAAAAATAATATGAGATC
*
11763927 TTTAAATTAAA-AAAAAATAATATGAGATC
1 TTAAAATTAAATAAAAAATAATATGAGATC
11763956 TTAAAAT
1 TTAAAAT
11763963 ATGTTTGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 20 0.67
30 6 0.20
31 4 0.13
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (30 bp):
TTAAAATTAAATAAAAAATAATATGAGATC
Found at i:11778564 original size:26 final size:26
Alignment explanation
Indices: 11778534--11778585 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
11778524 GGTTTTCTTG
11778534 CTTCACATCCACAGCAGAAATAGCAT
1 CTTCACATCCACAGCAGAAATAGCAT
11778560 CTTCACATCCACAGCAGAAATAGCAT
1 CTTCACATCCACAGCAGAAATAGCAT
11778586 TTGAAGCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (26 bp):
CTTCACATCCACAGCAGAAATAGCAT
Found at i:11778781 original size:11 final size:11
Alignment explanation
Indices: 11778740--11778780 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
11778730 ATAATTTTAT
*
11778740 ATTTAAAAATA
1 ATTTTAAAATA
*
11778751 ATTTTAAATTA
1 ATTTTAAAATA
11778762 ATTTTAAAAT-
1 ATTTTAAAATA
11778772 ATTTTAAAA
1 ATTTTAAAA
11778781 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:11779292 original size:16 final size:16
Alignment explanation
Indices: 11779271--11779320 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 16
11779261 TAACCTTATA
11779271 AATAATATAAAACTTT
1 AATAATATAAAACTTT
11779287 AATAATGTATAAAA-TATT
1 AATAA--TATAAAACT-TT
11779305 -AT-ATATAAAACTTT
1 AATAATATAAAACTTT
11779319 AA
1 AA
11779321 ACTTTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
14 9 0.31
15 2 0.07
16 6 0.21
17 3 0.10
18 9 0.31
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (16 bp):
AATAATATAAAACTTT
Found at i:11787020 original size:52 final size:52
Alignment explanation
Indices: 11786887--11787061 Score: 174
Period size: 52 Copynumber: 3.4 Consensus size: 52
11786877 TGACTAAGTA
* * * * * ** *
11786887 TCATCGTGAGTAAATGAATCTTTTACGAATTACGAGGTCCGATGACTCTGTG
1 TCATCGTGAGTATATGAATCCTTCATGGATTATAAGGTCCGGTGACTCTGTG
* *
11786939 TCATCGTGAGTATATGGATCCTTTATGGATT-TAAAGGTCCGGTGACTCTGTG
1 TCATCGTGAGTATATGAATCCTTCATGGATTAT-AAGGTCCGGTGACTCTGTG
* * * * *
11786991 TCATCGTGAGTATACGAAT-CTCTCGTGGATTATAAGGTCTGGTGGCTATGTG
1 TCATCGTGAGTATATGAATCCT-TCATGGATTATAAGGTCCGGTGACTCTGTG
*
11787043 TCATCGTGAATATATGAAT
1 TCATCGTGAGTATATGAAT
11787062 GAAGTGAAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
51 2 0.02
52 100 0.97
53 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
TCATCGTGAGTATATGAATCCTTCATGGATTATAAGGTCCGGTGACTCTGTG
Found at i:11796682 original size:18 final size:18
Alignment explanation
Indices: 11796650--11796701 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
11796640 CTGGAATGAG
11796650 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
11796666 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
11796684 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
11796702 TAACTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:11810765 original size:2 final size:2
Alignment explanation
Indices: 11810758--11810783 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11810748 GAACATACTC
11810758 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11810784 GATCCTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11814916 original size:18 final size:19
Alignment explanation
Indices: 11814883--11814918 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11814873 TTACAGGAGT
11814883 TGAAACAGAAAAAAGAAAG
1 TGAAACAGAAAAAAGAAAG
*
11814902 TGAAA-AGAGAAAAGAAA
1 TGAAACAGAAAAAAGAAA
11814919 AACCTTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.06
Consensus pattern (19 bp):
TGAAACAGAAAAAAGAAAG
Found at i:11815195 original size:27 final size:26
Alignment explanation
Indices: 11815165--11815237 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
11815155 AATTTATTTT
*
11815165 ATATTTATAAAATTATTATAAATATTA
1 ATATTAATAAAATTATTA-AAATATTA
*
11815192 ATATTAATTAAATTATTAAAATATTA
1 ATATTAATAAAATTATTAAAATATTA
11815218 ATCATATAA-AAAA-TATTAAA
1 AT-AT-TAATAAAATTATTAAA
11815238 TAAAACTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 17 0.41
27 21 0.51
28 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATTAATAAAATTATTAAAATATTA
Found at i:11815234 original size:26 final size:24
Alignment explanation
Indices: 11815173--11815237 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 24
11815163 TTATATTTAT
11815173 AAAATTATTATAAATATTAATATTA
1 AAAATTATTA-AAATATTAATATTA
11815198 ATTAAATTATTAAAATATTAATCATATA
1 A--AAATTATTAAAATATTAAT-AT-TA
*
11815226 AAAAATATTAAA
1 AAAATTATTAAA
11815238 TAAAACTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
25 1 0.03
26 20 0.57
27 11 0.31
28 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATTATTAAAATATTAATATTA
Found at i:11815454 original size:16 final size:16
Alignment explanation
Indices: 11815429--11815462 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11815419 TCGGTACGTG
11815429 TTTTTATTATTT-TAT
1 TTTTTATTATTTGTAT
11815444 TTTTATATTATTTGTAT
1 TTTT-TATTATTTGTAT
11815461 TT
1 TT
11815463 ACGTAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTATTATTTGTAT
Found at i:11815561 original size:154 final size:154
Alignment explanation
Indices: 11815281--11815587 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 154
11815271 ATTTGAATTT
11815281 TTATTTTATTTTTATATTATTTGTATCTACGTAATCCTACTCACATCAGCTTCTAAACATCATCA
1 TTATTTTATTTTTATATTATTTGTATCTACGTAATCCTACTCACATCAGCTTCTAAACATCATCA
11815346 TGACCTAATAGATATTTATAATTTATAACAAGACTAATAGATATTGTTTGTATGTACATACATAC
66 TGACCTAATAGATATTTATAATTTATAACAAGACTAATAGATATTGTTTGTATGTACATACATAC
11815411 CAAATGGTTCGGTACGTGTTTTTA
131 CAAATGGTTCGGTACGTGTTTTTA
* * *
11815435 TTATTTTATTTTTATATTATTTGTATTTACGTAATCTTACTCACATCAGTTTCTAAACATCATCA
1 TTATTTTATTTTTATATTATTTGTATCTACGTAATCCTACTCACATCAGCTTCTAAACATCATCA
* *
11815500 TGACCTAATAGGTATTTATAATTTATAACAAGACTAATAGATATTGTTTTTATGTACATACATAC
66 TGACCTAATAGATATTTATAATTTATAACAAGACTAATAGATATTGTTTGTATGTACATACATAC
11815565 CAAATGGTTCGGTACGTGTTTTT
131 CAAATGGTTCGGTACGTGTTTTT
11815588 TTTAGGGTAA
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 148 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (154 bp):
TTATTTTATTTTTATATTATTTGTATCTACGTAATCCTACTCACATCAGCTTCTAAACATCATCA
TGACCTAATAGATATTTATAATTTATAACAAGACTAATAGATATTGTTTGTATGTACATACATAC
CAAATGGTTCGGTACGTGTTTTTA
Found at i:11819070 original size:16 final size:16
Alignment explanation
Indices: 11819049--11819088 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
11819039 CGTTTGGTTC
11819049 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
11819065 GCTGTAATGGAATAGG
1 GCTGTAATGGAATAGA
11819081 GCTGTAAT
1 GCTGTAAT
11819089 CAGTATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:11822293 original size:24 final size:24
Alignment explanation
Indices: 11822261--11822327 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
11822251 CGTTATTCTG
11822261 ATTCTGGGCTCGTAAGAGCAAACC
1 ATTCTGGGCTCGTAAGAGCAAACC
* *
11822285 ATTCTGGGCTCGTGAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCAAACC
* *
11822309 -TATCTCGGCTCGTATGAGC
1 AT-TCTGGGCTCGTAAGAGC
11822328 TAATTTTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCAAACC
Found at i:11838045 original size:90 final size:90
Alignment explanation
Indices: 11837892--11838071 Score: 288
Period size: 90 Copynumber: 2.0 Consensus size: 90
11837882 CAAGTTCCTA
*
11837892 ACTAAGAGGATCGTGGTGAAAGCCAAATGGTCTTTATGAAGGGTCTCTTGTGATGGCCTTATTTG
1 ACTAAGAGGATCGTGGTGAAAGCCAAATGGTCTTTATGAAGGGTCTCTTGTAATGGCCTTATTTG
*
11837957 ATTTGTTCGAGACTAATTAGGGGGT
66 ATTTGTTCAAGACTAATTAGGGGGT
* * * * *
11837982 ACTAAGAGGATCGTGGTGAAGGCGAAATGGTCTTTATTAAGGGTTTCTTGTAATGGTCTTATTTG
1 ACTAAGAGGATCGTGGTGAAAGCCAAATGGTCTTTATGAAGGGTCTCTTGTAATGGCCTTATTTG
*
11838047 ATTTGTTCAAGACTAATTGGGGGGT
66 ATTTGTTCAAGACTAATTAGGGGGT
11838072 TTAATGAGGC
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (90 bp):
ACTAAGAGGATCGTGGTGAAAGCCAAATGGTCTTTATGAAGGGTCTCTTGTAATGGCCTTATTTG
ATTTGTTCAAGACTAATTAGGGGGT
Found at i:11842926 original size:5 final size:5
Alignment explanation
Indices: 11842916--11842945 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
11842906 CATTGTCGAC
11842916 CCCCG CCCCG CCCCG CCCCG CCCCG CCCCG
1 CCCCG CCCCG CCCCG CCCCG CCCCG CCCCG
11842946 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.80, G:0.20, T:0.00
Consensus pattern (5 bp):
CCCCG
Done.