Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 14 of 17
Found at i:1990039 original size:2 final size:2
Alignment explanation
Indices: 1990032--1990078 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1990022 TTATAAAATT
1990032 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1990074 TA TA T
1 TA TA T
1990079 TGAAAATTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1990953 original size:2 final size:2
Alignment explanation
Indices: 1990946--1990979 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1990936 ATGGTTGGAA
*
1990946 TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1990980 AAAGAGAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:1991884 original size:15 final size:16
Alignment explanation
Indices: 1991864--1991901 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1991854 ATAAAATTAG
1991864 ATTTTTTATT-TTATT
1 ATTTTTTATTGTTATT
*
1991879 ATTTTTT-TTGTTTTT
1 ATTTTTTATTGTTATT
1991894 ATTTTTTA
1 ATTTTTTA
1991902 AAATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
ATTTTTTATTGTTATT
Found at i:1991926 original size:8 final size:8
Alignment explanation
Indices: 1991864--1991995 Score: 60
Period size: 8 Copynumber: 16.2 Consensus size: 8
1991854 ATAAAATTAG
1991864 ATTTTTT-
1 ATTTTTTA
1991871 ATTTTATT-
1 ATTTT-TTA
1991879 ATTTTTT-
1 ATTTTTTA
*
1991886 -TTGTTTTT
1 ATT-TTTTA
1991894 ATTTTTTAAA
1 ATTTTTT--A
1991904 ATTTTTTA
1 ATTTTTTA
**
1991912 A-AATTTA
1 ATTTTTTA
1991919 ATTTTTTAGA
1 ATTTTTT--A
*
1991929 ATATTTTTG
1 AT-TTTTTA
1991938 ATTTTTTGA
1 ATTTTTT-A
*
1991947 TTTTTTTA
1 ATTTTTTA
* *
1991955 CTTTTTGA
1 ATTTTTTA
*
1991963 ATTTTTGA
1 ATTTTTTA
*
1991971 ATTTTTAA
1 ATTTTTTA
1991979 ATTTTTT-
1 ATTTTTTA
*
1991986 ATTATTTA
1 ATTTTTTA
1991994 AT
1 AT
1991996 ATAAAAGTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.02
7 22 0.22
8 50 0.51
9 10 0.10
10 10 0.10
11 5 0.05
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.70
Consensus pattern (8 bp):
ATTTTTTA
Found at i:1991983 original size:24 final size:24
Alignment explanation
Indices: 1991931--1991984 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1991921 TTTTTAGAAT
* * *
1991931 ATTTTTGATTTTTTGATTTTTTTA
1 ATTTTTGAATTTTTGAATTTTTAA
*
1991955 CTTTTTGAATTTTTGAATTTTTAA
1 ATTTTTGAATTTTTGAATTTTTAA
1991979 ATTTTT
1 ATTTTT
1991985 TATTATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.70
Consensus pattern (24 bp):
ATTTTTGAATTTTTGAATTTTTAA
Found at i:1993308 original size:22 final size:21
Alignment explanation
Indices: 1993283--1993335 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1993273 TATAATGATT
1993283 CTTTTCTTA-ATTGATAATAACA
1 CTTTT-TTATATTGAT-ATAACA
* *
1993305 CTTTTTTATATTTATATGACA
1 CTTTTTTATATTGATATAACA
*
1993326 CTTTTATATA
1 CTTTTTTATA
1993336 AACTTTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (21 bp):
CTTTTTTATATTGATATAACA
Found at i:1995283 original size:2 final size:2
Alignment explanation
Indices: 1995276--1995314 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1995266 ACACATTGTG
1995276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1995315 CACACACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1998921 original size:2 final size:2
Alignment explanation
Indices: 1998914--1998938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1998904 TACTTGTATG
1998914 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1998939 TCAACAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1999983 original size:16 final size:16
Alignment explanation
Indices: 1999964--1999994 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1999954 AATTATATTT
1999964 AATATTTAATTTTTTA
1 AATATTTAATTTTTTA
1999980 AATATTTAATTTTTT
1 AATATTTAATTTTTT
1999995 TATCAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATATTTAATTTTTTA
Found at i:2006080 original size:20 final size:20
Alignment explanation
Indices: 2006054--2006108 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2006044 AAAAAGATAG
* *
2006054 AATGTATCGATTCATTCATA
1 AATGTATCGATACATTCAAA
* *
2006074 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
2006094 AATGTATCGATACAT
1 AATGTATCGATACAT
2006109 CTGGGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:2008636 original size:2 final size:2
Alignment explanation
Indices: 2008622--2008658 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
2008612 TTCTATTGTT
2008622 TA TA TA -A TCA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
2008659 TATTGAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2008904 original size:2 final size:2
Alignment explanation
Indices: 2008897--2008924 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2008887 CATTTACATA
2008897 AT 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 AT
2008925 TCCATCTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2009703 original size:2 final size:2
Alignment explanation
Indices: 2009691--2009734 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
2009681 ATAAAATTAG
* *
2009691 TA TA T- TA TA TA TA TA TA TA TA TG TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2009732 TA T
1 TA T
2009735 TGCCTCTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2012343 original size:2 final size:2
Alignment explanation
Indices: 2012336--2012363 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2012326 AAACATAGAA
2012336 AT 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 AT
2012364 GTACATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2013167 original size:2 final size:2
Alignment explanation
Indices: 2013160--2013221 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
2013150 TACTATTGTG
* *
2013160 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2013202 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
2013222 GCTCTGTAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2016158 original size:1 final size:1
Alignment explanation
Indices: 2016152--2016177 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2016142 CAACCATATG
2016152 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2016178 CTTAATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2020866 original size:2 final size:2
Alignment explanation
Indices: 2020859--2020894 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2020849 TATCAATTAC
2020859 AT AT AT AT AT 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 AT AT AT AT AT
2020895 TGTCATTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2024456 original size:19 final size:22
Alignment explanation
Indices: 2024434--2024478 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2024424 ATAAAATATA
2024434 AAATTA-TTTT-T-AAAAATTT
1 AAATTATTTTTATCAAAAATTT
2024453 AAATTATTTTTATCAAAAATTT
1 AAATTATTTTTATCAAAAATTT
2024475 AAAT
1 AAAT
2024479 ATTATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 1 0.04
22 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTATTTTTATCAAAAATTT
Found at i:2024529 original size:29 final size:31
Alignment explanation
Indices: 2024480--2024538 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
2024470 AATTTAAATA
2024480 TTATAATATATTATTTATTTA-TATCAAATTG
1 TTATAATATATTATTTATTTATTAT-AAATTG
*
2024511 TTATTATA-ATTATTT-TTTATTATAAATT
1 TTATAATATATTATTTATTTATTATAAATT
2024539 TATTTTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 9 0.35
30 10 0.38
31 7 0.27
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (31 bp):
TTATAATATATTATTTATTTATTATAAATTG
Found at i:2024530 original size:16 final size:16
Alignment explanation
Indices: 2024511--2024557 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2024501 TATCAAATTG
2024511 TTATTATAATTATTTT
1 TTATTATAATTATTTT
*
2024527 TTATTATAAATT-TATT
1 TTATTAT-AATTATTTT
*
2024543 TTATTCTAATATATT
1 TTATTATAAT-TATT
2024558 AAATGAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 5 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTATAATTATTTT
Found at i:2025116 original size:2 final size:2
Alignment explanation
Indices: 2025111--2025138 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2025101 TATATATATA
2025111 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2025139 AACCATGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2029217 original size:12 final size:12
Alignment explanation
Indices: 2029202--2029231 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2029192 CTTTAATTAA
*
2029202 ATATTCGTAAAT
1 ATATTCGTAAAC
2029214 ATATTCGTAAAC
1 ATATTCGTAAAC
2029226 ATATTC
1 ATATTC
2029232 ATTTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (12 bp):
ATATTCGTAAAC
Found at i:2029363 original size:29 final size:26
Alignment explanation
Indices: 2029304--2029384 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
2029294 TATTTTAGAA
*
2029304 ATATAA-TA-TAATATA-AAAAAATT
1 ATATAATTATTAATATATAAAAATTT
2029327 ATATAATTATTTATATATATAAAAATTT
1 ATATAATTA-TTA-ATATATAAAAATTT
* *
2029355 ATATAAATTATTAATATGTTAAAATTT
1 ATAT-AATTATTAATATATAAAAATTT
2029382 ATA
1 ATA
2029385 ACAAAATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
23 6 0.12
24 2 0.04
26 2 0.04
27 20 0.41
28 14 0.29
29 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (26 bp):
ATATAATTATTAATATATAAAAATTT
Found at i:2029377 original size:28 final size:28
Alignment explanation
Indices: 2029307--2029384 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
2029297 TTTAGAAATA
*
2029307 TAATATAATATAAAAAAATTATATAATTAT
1 TAATAT-ATAT-AAAAATTTATATAATTAT
*
2029337 TTATATATATAAAAATTTATATAAATTAT
1 TAATATATATAAAAATTTATAT-AATTAT
*
2029366 TAATATGT-T-AAAATTTATA
1 TAATATATATAAAAATTTATA
2029385 ACAAAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
27 10 0.23
28 12 0.28
29 16 0.37
30 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
TAATATATATAAAAATTTATATAATTAT
Found at i:2030679 original size:4 final size:4
Alignment explanation
Indices: 2030670--2030696 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2030660 ACACGTGGCT
2030670 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2030697 TTGGCTGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2030818 original size:16 final size:16
Alignment explanation
Indices: 2030799--2030829 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2030789 ATTTTTTTAT
*
2030799 TTTTATATTTATATTA
1 TTTTATATATATATTA
2030815 TTTTATATATATATT
1 TTTTATATATATATT
2030830 TAAAATATTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATATATATATTA
Found at i:2030838 original size:22 final size:22
Alignment explanation
Indices: 2030793--2030843 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2030783 CGAGAAATTT
* * * *
2030793 TTTTATTTTTATATTTATATTA
1 TTTTATATATATATTTAAAATA
2030815 TTTTATATATATATTTAAAATA
1 TTTTATATATATATTTAAAATA
*
2030837 TTATATA
1 TTTTATA
2030844 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTATATATATATTTAAAATA
Found at i:2030854 original size:16 final size:16
Alignment explanation
Indices: 2030835--2030866 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2030825 ATATTTAAAA
*
2030835 TATTATATAAATTTTT
1 TATTATAAAAATTTTT
2030851 TATTATAAAAATTTTT
1 TATTATAAAAATTTTT
2030867 GTTATTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATAAAAATTTTT
Found at i:2030915 original size:6 final size:6
Alignment explanation
Indices: 2030898--2031004 Score: 73
Period size: 6 Copynumber: 18.0 Consensus size: 6
2030888 GTATATTTTA
* * *
2030898 TATATT TTTATT TATA-T TATGTT TAT-TT TAT-TT TTTATAT TAT-TT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATAT-T TATATT
* *
2030943 T-TATT TA-ATT TTTATAT TATATT TATATTT TATATT AATTTATT TATATT
1 TATATT TATATT TATAT-T TATATT TATA-TT TATATT --TATATT TATATT
*
2030993 TATTTT TATATT
1 TATATT TATATT
2031005 AATTTATTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.01
5 22 0.28
6 38 0.47
7 14 0.17
8 5 0.06
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (6 bp):
TATATT
Found at i:2030929 original size:26 final size:25
Alignment explanation
Indices: 2030893--2031040 Score: 124
Period size: 26 Copynumber: 5.6 Consensus size: 25
2030883 TTTATGTATA
2030893 TTTTATA-TATTTTTATTTATATTAT
1 TTTTATATTA-TTTTATTTATATTAT
* *
2030918 GTTTATTTTA-TTT-TTTATATTAT
1 TTTTATATTATTTTATTTATATTAT
2030941 TTTTAT-TTAATTTTTATATTATATTTAT
1 TTTTATATT-A-TTTTAT-TTATA-TTAT
*
2030969 ATTTTATATTAATTTATTTATATTTAT
1 -TTTTATATTATTTTATTTATA-TTAT
*
2030996 TTTTATATTAATTTATTTATATATCAT
1 TTTTATATTATTTTATTTATAT-T-AT
*
2031023 GTTATATATTAATTTTAT
1 -TTTTATATT-ATTTTAT
2031041 ATTACTTTTA
Statistics
Matches: 104, Mismatches: 6, Indels: 22
0.79 0.05 0.17
Matches are distributed among these distances:
22 2 0.02
23 16 0.15
24 3 0.03
25 9 0.09
26 25 0.24
27 17 0.16
28 17 0.16
29 13 0.12
30 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (25 bp):
TTTTATATTATTTTATTTATATTAT
Found at i:2030943 original size:11 final size:11
Alignment explanation
Indices: 2030891--2031051 Score: 105
Period size: 11 Copynumber: 13.8 Consensus size: 11
2030881 GTTTTATGTA
2030891 TATTTTATATAT
1 TATTTT-TATAT
*
2030903 TTTTATTTATAT
1 TATT-TTTATAT
* *
2030915 TATGTTTATTT
1 TATTTTTATAT
2030926 TATTTTTTATAT
1 TA-TTTTTATAT
2030938 TATTTTTAT-T
1 TATTTTTATAT
2030948 TAATTTTTATAT
1 T-ATTTTTATAT
*
2030960 TATATTTATAT
1 TATTTTTATAT
2030971 T-TTATATTA-AT
1 TATT-T-TTATAT
*
2030982 T-TATTTATATT
1 TATTTTTATA-T
2030993 TATTTTTATAT
1 TATTTTTATAT
2031004 TAATTTATTTATAT
1 T-A-TT-TTTATAT
*
2031018 ATCATGTTATATAT
1 -T-AT-TTTTATAT
*
2031032 TAATTTTATAT
1 TATTTTTATAT
*
2031043 TACTTTTAT
1 TATTTTTAT
2031052 TTAATTTCAT
Statistics
Matches: 120, Mismatches: 15, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
9 3 0.03
10 5 0.04
11 57 0.47
12 33 0.28
13 5 0.04
14 14 0.12
15 3 0.03
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:2030959 original size:66 final size:65
Alignment explanation
Indices: 2030889--2031058 Score: 163
Period size: 66 Copynumber: 2.6 Consensus size: 65
2030879 TTGTTTTATG
* * *
2030889 TATATTTTATATAT-TTTTAT-TTATATTATGTTTAT-TTTATTTTTTATATTATTTTTATTTAA
1 TATATTATATATATATTTTATATTA-ATT-TATTTATATTTA-TTTTTATATTA-ATTTATTTAA
2030951 TTTT
62 TTTT
* *
2030955 TATATTATATTTATATTTTATATTAATTTATTTATATTTATTTTTATATTAATTTATTT-ATATA
1 TATATTATATATATATTTTATATTAATTTATTTATATTTATTTTTATATTAATTTATTTAAT-TT
2031019 T
65 T
* * *
2031020 CATGTTATATAT-TAATTTTATATTACTTTTATTTA-ATTT
1 TATATTATATATAT-ATTTTATATTA-ATTTATTTATATTT
2031059 CATGATATAT
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
64 3 0.03
65 33 0.37
66 37 0.42
67 13 0.15
68 3 0.03
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (65 bp):
TATATTATATATATATTTTATATTAATTTATTTATATTTATTTTTATATTAATTTATTTAATTTT
Found at i:2030968 original size:45 final size:43
Alignment explanation
Indices: 2030900--2031017 Score: 89
Period size: 40 Copynumber: 3.0 Consensus size: 43
2030890 ATATTTTATA
* *
2030900 TATTTTTAT-TTATA-TTATGTTTAT-TTTATTT-TTTATA-T
1 TATTTTTATATTATATTTATTTTTATATTAATTTATTTATATT
* *
2030938 TATTTTTAT-TTA-ATTT-TTATATTATATTTATAT-TTTATA-T
1 TATTTTTATATTATATTTATT-T-TTATATTAATTTATTTATATT
*
2030978 TA-ATTTAT-TTATATTTATTTTTATATTAATTTATTTATAT
1 TATTTTTATATTATATTTATTTTTATATTAATTTATTTATAT
2031018 ATCATGTTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
37 2 0.03
38 15 0.22
39 22 0.33
40 26 0.39
41 2 0.03
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (43 bp):
TATTTTTATATTATATTTATTTTTATATTAATTTATTTATATT
Found at i:2030971 original size:77 final size:83
Alignment explanation
Indices: 2030889--2031044 Score: 202
Period size: 77 Copynumber: 2.0 Consensus size: 83
2030879 TTGTTTTATG
* * *
2030889 TATATTTTATA-TATTTTTATTTATA-TTATGTTTAT-TTTATTT-TTTATAT-T-AT-TTTTAT
1 TATATTTTATATTA-ATTTATTTATATTTATGTTTATATTAATTTATTTATATATCATGTTATAT
2030947 -TTAATTTTTATATTATATT
65 ATTAA-TTTTATATTATATT
*
2030966 TATATTTTATATTAATTTATTTATATTTATTTTTATATTAATTTATTTATATATCATGTTATATA
1 TATATTTTATATTAATTTATTTATATTTATGTTTATATTAATTTATTTATATATCATGTTATATA
2031031 TTAATTTTATATTA
66 TTAATTTTATATTA
2031045 CTTTTATTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
77 21 0.31
78 11 0.16
79 6 0.09
80 7 0.10
81 1 0.01
82 2 0.03
83 15 0.22
84 4 0.06
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (83 bp):
TATATTTTATATTAATTTATTTATATTTATGTTTATATTAATTTATTTATATATCATGTTATATA
TTAATTTTATATTATATT
Found at i:2031009 original size:16 final size:16
Alignment explanation
Indices: 2030945--2031019 Score: 72
Period size: 18 Copynumber: 4.9 Consensus size: 16
2030935 TATTATTTTT
2030945 ATTTAATTTTTATATTA
1 ATTT-ATTTTTATATTA
2030962 TATTTATATTTTATATTA
1 -ATTTAT-TTTTATATTA
2030980 ATTTA---TT-TA-T-
1 ATTTATTTTTATATTA
2030990 ATTTATTTTTATATTA
1 ATTTATTTTTATATTA
*
2031006 ATTTATTTATATAT
1 ATTTATTTTTATAT
2031020 CATGTTATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
10 5 0.10
11 1 0.02
12 2 0.04
13 4 0.08
14 2 0.04
15 1 0.02
16 13 0.27
17 7 0.14
18 14 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATTTTTATATTA
Found at i:2031039 original size:39 final size:39
Alignment explanation
Indices: 2030986--2031070 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
2030976 ATTAATTTAT
*
2030986 TTATAT-TTATTTTTATATTA-ATTTATTTATATATCATG
1 TTATATATTAATTTTATATTACATTTATTTA-ATATCATG
* *
2031024 TTATATATTAATTTTATATTACTTTTATTTAATTTCATG
1 TTATATATTAATTTTATATTACATTTATTTAATATCATG
*
2031063 ATATATAT
1 TTATATAT
2031071 ATATCAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 6 0.15
39 27 0.66
40 8 0.20
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (39 bp):
TTATATATTAATTTTATATTACATTTATTTAATATCATG
Found at i:2031639 original size:13 final size:13
Alignment explanation
Indices: 2031621--2031654 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2031611 TTGTTTTATT
*
2031621 TTATTTTTAAATA
1 TTATTTTAAAATA
2031634 TTATTTTAAAATA
1 TTATTTTAAAATA
*
2031647 TTAGTTTA
1 TTATTTTA
2031655 TACATTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTATTTTAAAATA
Found at i:2033752 original size:16 final size:16
Alignment explanation
Indices: 2033718--2033760 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2033708 ACCCTAATTA
*
2033718 TCATTTGATCTTTTCTT
1 TCATTT-ATTTTTTCTT
* *
2033735 TCCTTTATTTTTTTTT
1 TCATTTATTTTTTCTT
2033751 TCATTTATTT
1 TCATTTATTT
2033761 GATCCTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72
Consensus pattern (16 bp):
TCATTTATTTTTTCTT
Found at i:2039044 original size:14 final size:14
Alignment explanation
Indices: 2039025--2039054 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2039015 TAAGTCTCCT
2039025 ATCCGTTACATAAC
1 ATCCGTTACATAAC
2039039 ATCCGTTACATAAC
1 ATCCGTTACATAAC
2039053 AT
1 AT
2039055 TAGATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (14 bp):
ATCCGTTACATAAC
Found at i:2039981 original size:2 final size:2
Alignment explanation
Indices: 2039976--2040011 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2039966 TGCGATATCC
*
2039976 CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2040012 ATTTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2040322 original size:3 final size:3
Alignment explanation
Indices: 2040303--2040351 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
2040293 ATTTTAGTCA
*
2040303 ATT ATTT ATT AATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT
1 ATT A-TT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2040350 AT
1 AT
2040352 CCTTTGTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2045693 original size:2 final size:2
Alignment explanation
Indices: 2045686--2045728 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2045676 ATTACCATTG
2045686 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
2045728 A
1 A
2045729 AATAAGAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2045876 original size:17 final size:17
Alignment explanation
Indices: 2045856--2045904 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
2045846 AATAATATTC
2045856 ATTAAATATCTAAATTT
1 ATTAAATATCTAAATTT
*
2045873 ATTAAATATTTAAATTT
1 ATTAAATATCTAAATTT
* *
2045890 AATATATATCTAAAT
1 ATTAAATATCTAAAT
2045905 CTGTTTTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAAATATCTAAATTT
Found at i:2047684 original size:4 final size:4
Alignment explanation
Indices: 2047675--2047699 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2047665 AATCAGTGCG
2047675 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2047700 TTGATGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2048107 original size:41 final size:41
Alignment explanation
Indices: 2048030--2048108 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
2048020 TCGGCTCTCT
* *
2048030 TAACTCTTTTGCTCTTTCTTTGCCTTCGTAAGCATTTGCTG
1 TAACTCTTTTGATCTTTCTTTGCCTTCGTAAACATTTGCTG
* *
2048071 TAACTC-TTTGATCTTTCTTTTCCTTCTTAAAACATTTG
1 TAACTCTTTTGATCTTTCTTTGCCTTCGT-AAACATTTG
2048109 TGTTGATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 19 0.58
41 14 0.42
ACGTcount: A:0.16, C:0.23, G:0.10, T:0.51
Consensus pattern (41 bp):
TAACTCTTTTGATCTTTCTTTGCCTTCGTAAACATTTGCTG
Found at i:2050212 original size:25 final size:26
Alignment explanation
Indices: 2050156--2050217 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
2050146 TATTTATCAT
* *
2050156 TAATTTTAATTTTATTATTATCATAAA
1 TAATTTT-ATTTTAATATTATCAAAAA
2050183 TAATTTTATTTTAAT-TTAT-AAAAA
1 TAATTTTATTTTAATATTATCAAAAA
2050207 TGAATTTTATT
1 T-AATTTTATT
2050218 ATCCATTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 5 0.16
25 13 0.41
26 7 0.22
27 7 0.22
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
TAATTTTATTTTAATATTATCAAAAA
Found at i:2060743 original size:18 final size:17
Alignment explanation
Indices: 2060716--2060749 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2060706 TAATGTGTTA
2060716 TTTTAAATTTATTATAT
1 TTTTAAATTTATTATAT
*
2060733 TTTTAAAATTTTTTATA
1 TTTT-AAATTTATTATA
2060750 AAAATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAATTTATTATAT
Found at i:2060826 original size:21 final size:21
Alignment explanation
Indices: 2060776--2060841 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
2060766 TATTAAATTG
2060776 ATTA-ATA-AAATATATATTTT
1 ATTAGATATAAATATAT-TTTT
* *
2060796 CTAAGCATATAAATATATTTTT
1 ATTAG-ATATAAATATATTTTT
** *
2060818 ATTAGATATGCATATATATTT
1 ATTAGATATAAATATATTTTT
2060839 ATT
1 ATT
2060842 TATAAATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.06
21 16 0.44
22 10 0.28
23 8 0.22
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTAGATATAAATATATTTTT
Found at i:2061044 original size:13 final size:14
Alignment explanation
Indices: 2061026--2061054 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2061016 AAATGATAAA
2061026 AATTTT-AAAAATT
1 AATTTTAAAAAATT
2061039 AATTTTAAAAAATT
1 AATTTTAAAAAATT
2061053 AA
1 AA
2061055 ATGAGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTTAAAAAATT
Found at i:2062477 original size:19 final size:20
Alignment explanation
Indices: 2062444--2062494 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2062434 TTAAATAGTA
*
2062444 ATAATTAATAATAAAATA-TT
1 ATAA-TAATATTAAAATACTT
2062464 ATAATAATATT-AAATACTT
1 ATAATAATATTAAAATACTT
*
2062483 AAAATAATATTA
1 ATAATAATATTA
2062495 TTTATCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 18 0.67
20 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATAATATTAAAATACTT
Found at i:2062496 original size:22 final size:22
Alignment explanation
Indices: 2062464--2062535 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
2062454 ATAAAATATT
*
2062464 ATAATAATATTAAATACTTAAA
1 ATAATATTATTAAATACTTAAA
*
2062486 ATAATATTATT-TAT-CATTAAA
1 ATAATATTATTAAATAC-TTAAA
*
2062507 TATTAAT-TTA-TAAATATTTAAA
1 -A-TAATATTATTAAATACTTAAA
2062529 ATAATAT
1 ATAATAT
2062536 AATACTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
20 5 0.12
21 10 0.25
22 21 0.52
23 4 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATATTATTAAATACTTAAA
Found at i:2062556 original size:43 final size:42
Alignment explanation
Indices: 2062474--2062556 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 42
2062464 ATAATAATAT
* *
2062474 TAAATACTTAAAATAATATTATTTATCATTAAATATTAATTTA
1 TAAATACTTAAAATAATATTACTTAT-ATAAAATATTAATTTA
* *
2062517 TAAATATTTAAAATAATATAATACTTAT-TAAAATCTTAAT
1 TAAATACTTAAAATAATAT--TACTTATATAAAATATTAAT
2062557 AGTTTATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 28 0.82
45 6 0.18
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (42 bp):
TAAATACTTAAAATAATATTACTTATATAAAATATTAATTTA
Found at i:2062638 original size:24 final size:25
Alignment explanation
Indices: 2062611--2062657 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2062601 ACATTTATTT
*
2062611 ATTATTAAA-ATAGTAATAAAAAAC
1 ATTATTAAATAAAGTAATAAAAAAC
*
2062635 ATTATTAAATAAAGTATTAAAAA
1 ATTATTAAATAAAGTAATAAAAA
2062658 TACTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (25 bp):
ATTATTAAATAAAGTAATAAAAAAC
Found at i:2063480 original size:19 final size:19
Alignment explanation
Indices: 2063456--2063496 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2063446 AAAGTTGTCA
2063456 ATGTTAATTTGATTAGTAT
1 ATGTTAATTTGATTAGTAT
2063475 ATGTTAATTTGATTAGTAT
1 ATGTTAATTTGATTAGTAT
2063494 ATG
1 ATG
2063497 ATATATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (19 bp):
ATGTTAATTTGATTAGTAT
Found at i:2064192 original size:31 final size:29
Alignment explanation
Indices: 2064122--2064195 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
2064112 CTTTTTTTAA
* * *
2064122 ATATCTCAAATAAATTTTAATTTTTAATTT
1 ATATCT-AAATAAATATTAATTGTTAATTC
*
2064152 ATATTTAAATAAATAATTAATTCGTTAATTC
1 ATATCTAAATAAAT-ATTAATT-GTTAATTC
2064183 ATATCTAAATAAA
1 ATATCTAAATAAA
2064196 CGATCAACCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 8 0.22
30 11 0.30
31 18 0.49
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATCTAAATAAATATTAATTGTTAATTC
Found at i:2065336 original size:27 final size:27
Alignment explanation
Indices: 2065289--2065340 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2065279 CTAATTTGAC
*
2065289 AAGCCCAATAGTTTAGCCTTGTTTTAT
1 AAGCCCAATAGTCTAGCCTTGTTTTAT
*
2065316 AAGCCCAACT-GTCTAGTCTTGTTTT
1 AAGCCCAA-TAGTCTAGCCTTGTTTT
2065341 TCTTTGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (27 bp):
AAGCCCAATAGTCTAGCCTTGTTTTAT
Found at i:2065903 original size:2 final size:2
Alignment explanation
Indices: 2065896--2065924 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2065886 CGGTTGTTAA
2065896 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2065925 GAATGCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2066255 original size:2 final size:2
Alignment explanation
Indices: 2066248--2066273 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2066238 TCATGAGAAG
2066248 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
2066274 CATTAAAATG
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:2072097 original size:53 final size:53
Alignment explanation
Indices: 2072028--2072134 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 53
2072018 AACAAATCAC
* * *
2072028 ATGATAATGCTAATAACATTATCCTCTACCAAT-CCTTCATCATGTTTGCAATT
1 ATGATAATGCTAATAACATTATCCCCTACCAATCCCTT-ATCATATCTGCAATT
*
2072081 ATGATAATGCTGATAACATTATCCCCTACCAATCCCTTATCATATCTGCAATT
1 ATGATAATGCTAATAACATTATCCCCTACCAATCCCTTATCATATCTGCAATT
2072134 A
1 A
2072135 AAGGTAGTCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 45 0.92
54 4 0.08
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (53 bp):
ATGATAATGCTAATAACATTATCCCCTACCAATCCCTTATCATATCTGCAATT
Found at i:2072659 original size:27 final size:27
Alignment explanation
Indices: 2072629--2072688 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2072619 AGTTAATATT
* *
2072629 TATTATAATGTTATTAAT-TTTTATTTA
1 TATTATAATGGTATTAATATTTT-TATA
* *
2072656 TATTATTATGGTGTTAATATTTTTATA
1 TATTATAATGGTATTAATATTTTTATA
2072683 TATTAT
1 TATTAT
2072689 TATTGTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.62
Consensus pattern (27 bp):
TATTATAATGGTATTAATATTTTTATA
Found at i:2072664 original size:30 final size:27
Alignment explanation
Indices: 2072624--2072699 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 27
2072614 ATTAAAGTTA
*
2072624 ATAT-TTATTATAATGTTATTAATTTTT
1 ATATATTATTATAATGTTAAT-ATTTTT
**
2072651 ATTTATATTATTATGGTGTTAATATTTTT
1 A--TATATTATTATAATGTTAATATTTTT
2072680 ATATATTATTAT--TGTTAATA
1 ATATATTATTATAATGTTAATA
2072700 ATATTACTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
25 8 0.19
27 12 0.28
29 10 0.23
30 13 0.30
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (27 bp):
ATATATTATTATAATGTTAATATTTTT
Found at i:2072695 original size:25 final size:27
Alignment explanation
Indices: 2072645--2072699 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
2072635 AATGTTATTA
2072645 ATTTTTATTTATATTATTATGGTGTTAAT
1 ATTTTTA-TTATATTATTAT-GTGTTAAT
2072674 ATTTTTA-TATATTATTAT-TGTTAAT
1 ATTTTTATTATATTATTATGTGTTAAT
2072699 A
1 A
2072700 ATATTACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 8 0.31
27 11 0.42
29 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (27 bp):
ATTTTTATTATATTATTATGTGTTAAT
Found at i:2072705 original size:18 final size:17
Alignment explanation
Indices: 2072680--2072761 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 17
2072670 TAATATTTTT
2072680 ATATATTATTATTGTTA
1 ATATATTATTATTGTTA
* *
2072697 ATAATATTACTATTGCTTC
1 AT-ATATTATTATTG-TTA
* *
2072716 ATTTATT-TATATTATT-
1 ATATATTAT-TATTGTTA
2072732 ATAT-TTATTATTGTTA
1 ATATATTATTATTGTTA
2072748 ATAATATTTATTAT
1 AT-ATA-TTATTAT
2072762 AATGGTAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
15 8 0.16
16 6 0.12
17 6 0.12
18 19 0.38
19 11 0.22
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (17 bp):
ATATATTATTATTGTTA
Found at i:2074021 original size:3 final size:3
Alignment explanation
Indices: 2074013--2074044 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2074003 CATTTAATAC
2074013 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2074045 AAATAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2074620 original size:21 final size:21
Alignment explanation
Indices: 2074573--2074614 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
2074563 AGATTGTCTC
2074573 AAAATAATAT-T-TTTATATT
1 AAAATAATATATGTTTATATT
2074592 AAAATAATATATGTTTAT-TT
1 AAAATAATATATGTTTATATT
2074612 AAA
1 AAA
2074615 TTTAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 6 0.29
21 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATAATATATGTTTATATT
Found at i:2075658 original size:14 final size:13
Alignment explanation
Indices: 2075639--2075672 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2075629 ATTTAATTTA
2075639 TTAATAATAAAATT
1 TTAATAATAAAA-T
*
2075653 TTAATAATATAAT
1 TTAATAATAAAAT
2075666 TTAATAA
1 TTAATAA
2075673 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATAATAAAAT
Found at i:2075670 original size:13 final size:14
Alignment explanation
Indices: 2075639--2075677 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
2075629 ATTTAATTTA
*
2075639 TTAATAATAAAATT
1 TTAATAATATAATT
2075653 TTAATAATATAA-T
1 TTAATAATATAATT
*
2075666 TTAATAAAATAA
1 TTAATAATATAA
2075678 AAAATTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATATAATT
Found at i:2077558 original size:95 final size:95
Alignment explanation
Indices: 2077442--2077632 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
2077432 CTAAAATCCC
2077442 TAATTTTTCATCCCAAATCCCCCAGGCCATCAAAAAGAGGTTTCAGGCTGATTATTGAAATCTGC
1 TAATTTTTCATCCCAAATCCCCCAGGCCATCAAAAAGAGGTTTCAGGCTGATTATTGAAATCTGC
2077507 CTTAGGATCATTCCACATAACAATTTACTA
66 CTTAGGATCATTCCACATAACAATTTACTA
*
2077537 TAATTTTTCATCCCAAATCCCCTAGGCCATCAAAAAGAGGTTTCAGGCTGATTATTGAAATCTGC
1 TAATTTTTCATCCCAAATCCCCCAGGCCATCAAAAAGAGGTTTCAGGCTGATTATTGAAATCTGC
2077602 CTTAGGATCATTCCACATAACAATTTACTA
66 CTTAGGATCATTCCACATAACAATTTACTA
2077632 T
1 T
2077633 GTGTGCTACC
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (95 bp):
TAATTTTTCATCCCAAATCCCCCAGGCCATCAAAAAGAGGTTTCAGGCTGATTATTGAAATCTGC
CTTAGGATCATTCCACATAACAATTTACTA
Found at i:2089123 original size:23 final size:22
Alignment explanation
Indices: 2089097--2089159 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
2089087 AATTTATTAT
2089097 ATTTTAAAATTTTATACTCAATA
1 ATTTTAAAATTTTATA-TCAATA
** **
2089120 ATTTTAAATATTAAATATTTATA
1 ATTTTAAA-ATTTTATATCAATA
2089143 ATTTTAAAATTTTATAT
1 ATTTTAAAATTTTATAT
2089160 TCATATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 7 0.21
23 20 0.61
24 6 0.18
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTAAAATTTTATATCAATA
Found at i:2089903 original size:23 final size:23
Alignment explanation
Indices: 2089868--2089928 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2089858 TATTTATTTT
* **
2089868 TTAATAAAATAAAAAATTTTAAA
1 TTAAAAAAATAAAAAATTAAAAA
* * *
2089891 TTAAAACATTAAAAAGTTAAAAA
1 TTAAAAAAATAAAAAATTAAAAA
2089914 TTAAAAAAATAAAAA
1 TTAAAAAAATAAAAA
2089929 TGTTACATGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
TTAAAAAAATAAAAAATTAAAAA
Found at i:2089917 original size:7 final size:7
Alignment explanation
Indices: 2089873--2089920 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
2089863 ATTTTTTAAT
*
2089873 AAAATAA
1 AAAATTA
*
2089880 AAAATTT
1 AAAATTA
*
2089887 TAAATTA
1 AAAATTA
2089894 AAACATTA
1 AAA-ATTA
2089902 AAAAGTTA
1 AAAA-TTA
2089910 AAAATTA
1 AAAATTA
2089917 AAAA
1 AAAA
2089921 AATAAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 20 0.59
8 14 0.41
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:2089921 original size:16 final size:16
Alignment explanation
Indices: 2089891--2089920 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2089881 AAATTTTAAA
2089891 TTAAAACATTAAAAAG
1 TTAAAACATTAAAAAG
2089907 TTAAAA-ATTAAAAA
1 TTAAAACATTAAAAA
2089921 AATAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (16 bp):
TTAAAACATTAAAAAG
Found at i:2090213 original size:66 final size:68
Alignment explanation
Indices: 2090136--2090264 Score: 172
Period size: 66 Copynumber: 1.9 Consensus size: 68
2090126 AATAAAAAAA
* * * *
2090136 TATACTATAAAAATTTAAACTCATGTAATCA-A-CCTAAAAATAAATTTAAATTTCTACAAATTG
1 TATACCATAAAAATATAAACTCATATAATCATATCCAAAAAATAAATTTAAATTTCTACAAATTG
2090199 AAT
66 AAT
* * * *
2090202 TATACCATAAAAATATAAACTTATATAATTATATCCAAAAAATATATTTAAATTTCTATAAAT
1 TATACCATAAAAATATAAACTCATATAATCATATCCAAAAAATAAATTTAAATTTCTACAAAT
2090265 AAAAATAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 26 0.49
67 1 0.02
68 26 0.49
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (68 bp):
TATACCATAAAAATATAAACTCATATAATCATATCCAAAAAATAAATTTAAATTTCTACAAATTG
AAT
Found at i:2090302 original size:74 final size:73
Alignment explanation
Indices: 2090104--2090354 Score: 195
Period size: 74 Copynumber: 3.6 Consensus size: 73
2090094 TGTAACTTTT
* * * * * * *
2090104 AAATAAAAATTTAACTTTTACAAAT-AAAA-AAA-TATACTATAAAAATTTAAACTCATGTAATC
1 AAATAATAATTAAACTTTTACAAATAAAAATAAATTATACCATAAAAATATAAAATTATATAATC
* *
2090166 -AACCTAA
66 AAATCAAA
* * *
2090173 AAATAA-ATTTAAA-TTTCTACAAAT-----TGAATTATACCATAAAAATATAAACTTATATAAT
1 AAATAATAATTAAACTTT-TACAAATAAAAATAAATTATACCATAAAAATATAAAATTATATAAT
* *
2090231 TATATCCAAA
65 CAAAT-CAAA
* * * *
2090241 AAAT-ATATTTAAA-TTTCTATAAATAAAAATAAATTATATCATCAAAAATTTAAAATTATATAA
1 AAATAATAATTAAACTTT-TACAAATAAAAATAAATTATACCAT-AAAAATATAAAATTATATAA
2090304 TCAAATCAAA
64 TCAAATCAAA
* *
2090314 AAATAATAATTAAACTTTTACAAATAAAGATAAATAATACC
1 AAATAATAATTAAACTTTTACAAATAAAAATAAATTATACC
2090355 GTGACCCTTA
Statistics
Matches: 145, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
65 2 0.01
66 25 0.17
67 5 0.03
68 36 0.25
69 6 0.04
73 19 0.13
74 49 0.34
75 3 0.02
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (73 bp):
AAATAATAATTAAACTTTTACAAATAAAAATAAATTATACCATAAAAATATAAAATTATATAATC
AAATCAAA
Found at i:2092751 original size:16 final size:16
Alignment explanation
Indices: 2092732--2092766 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2092722 AAAACAAAAA
2092732 GAGAGAGAAACAGAGG
1 GAGAGAGAAACAGAGG
* *
2092748 GAGAGAGAGAGAGAGG
1 GAGAGAGAAACAGAGG
2092764 GAG
1 GAG
2092767 GGAGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.51, T:0.00
Consensus pattern (16 bp):
GAGAGAGAAACAGAGG
Found at i:2092938 original size:3 final size:3
Alignment explanation
Indices: 2092932--2092961 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2092922 TATTAAAACT
2092932 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2092962 CGTCTTTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2093119 original size:13 final size:13
Alignment explanation
Indices: 2093090--2093145 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
2093080 TAATATTTTT
*
2093090 TATTTTTTAATATA
1 TATTTTTT-ATAAA
2093104 TATTTTTTATAAA
1 TATTTTTTATAAA
* *
2093117 TATTTATCA-AAA
1 TATTTTTTATAAA
*
2093129 TATTTTTTATAAT
1 TATTTTTTATAAA
2093142 TATT
1 TATT
2093146 GAGAAATCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
12 10 0.29
13 17 0.49
14 8 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTTTATAAA
Found at i:2093326 original size:6 final size:7
Alignment explanation
Indices: 2093305--2093330 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2093295 AATAAATATA
2093305 TTAATTT
1 TTAATTT
2093312 TTAATTT
1 TTAATTT
2093319 TTAATTT
1 TTAATTT
2093326 TTAAT
1 TTAAT
2093331 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTAATTT
Found at i:2093345 original size:19 final size:20
Alignment explanation
Indices: 2093321--2093358 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2093311 TTTAATTTTT
*
2093321 AATTTTTAA-TAAAATAAAA
1 AATTTTAAATTAAAATAAAA
2093340 AATTTTAAATTAAAATAAA
1 AATTTTAAATTAAAATAAA
2093359 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTTTAAATTAAAATAAAA
Found at i:2093649 original size:22 final size:22
Alignment explanation
Indices: 2093611--2093660 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2093601 GAATTAATCT
*
2093611 ATTT-TTATTTATAAAAGTTTAA
1 ATTTATTATTTATAAAAGTAT-A
*
2093633 ATTTATTATTT-TTAAAGTATA
1 ATTTATTATTTATAAAAGTATA
2093654 ATTTATT
1 ATTTATT
2093661 CTTATTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTATTATTTATAAAAGTATA
Found at i:2093776 original size:73 final size:72
Alignment explanation
Indices: 2093686--2094016 Score: 352
Period size: 73 Copynumber: 4.6 Consensus size: 72
2093676 AATTTAATTA
* *
2093686 AAGGTATTATTTATTTTTATTTATAGAAGTTTAAATTTGTTTTTAGGGTATGATTATATGAGTTT
1 AAGGTATAATTTATTTTTATTTATAGAAGTTTAAATTTGTTTTTA-GGTATGATTATATAAGTTT
*
2093751 AAATTTTA
65 AAATTTTT
* * * *
2093759 AATGTATAATTTATTTTTATTTTTAGAAGTTTAAATTTGTTTTT---TAT--TT-TACAAATTTA
1 AAGGTATAATTTATTTTTATTTATAGAAGTTTAAATTTGTTTTTAGGTATGATTATATAAGTTTA
2093818 AATTTTT
66 AATTTTT
* * * * * * ** *
2093825 AATGTGTTATTTATTTTTATTTGTAGGAGTTTAAATTTGTATTTTAAGTATGATTATAGGAGCTT
1 AAGGTATAATTTATTTTTATTTATAGAAGTTTAAATTTGT-TTTTAGGTATGATTATATAAGTTT
2093890 AAAGTTTTTT
65 AAA--TTTTT
* * * * *
2093900 AGGGTATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTT-GGATATAATTATATAAGTTT
1 AAGGTATAATTTATTTTTATTTATAGAAGTTTAAATTTGTTTTTAGG-TATGATTATATAAGTTT
2093964 AAATTTTT
65 AAATTTTT
* * *
2093972 AAGGTATAATTTATTTTTATTTATAAAAATTTAAATTTATTTTTA
1 AAGGTATAATTTATTTTTATTTATAGAAGTTTAAATTTGTTTTTA
2094017 TTTTTTTAGG
Statistics
Matches: 217, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
66 49 0.23
67 6 0.03
69 3 0.01
70 3 0.01
72 48 0.22
73 50 0.23
74 20 0.09
75 38 0.18
ACGTcount: A:0.33, C:0.01, G:0.11, T:0.55
Consensus pattern (72 bp):
AAGGTATAATTTATTTTTATTTATAGAAGTTTAAATTTGTTTTTAGGTATGATTATATAAGTTTA
AATTTTT
Found at i:2093795 original size:26 final size:26
Alignment explanation
Indices: 2093766--2093822 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2093756 TTAAATGTAT
* *
2093766 AATTTA-TTTTTATTTTTAGAAGTTTA
1 AATTTATTTTTTA-TTTTACAAATTTA
*
2093792 AATTTGTTTTTTATTTTACAAATTTA
1 AATTTATTTTTTATTTTACAAATTTA
2093818 AATTT
1 AATTT
2093823 TTAATGTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (26 bp):
AATTTATTTTTTATTTTACAAATTTA
Found at i:2093805 original size:33 final size:33
Alignment explanation
Indices: 2093768--2093870 Score: 100
Period size: 33 Copynumber: 3.1 Consensus size: 33
2093758 AAATGTATAA
2093768 TTTATTTTTATTTTTAGAAGTTTAAATTTGTTT
1 TTTATTTTTATTTTTAGAAGTTTAAATTTGTTT
* ** * * * *
2093801 TTTATTTTACAAATTTA-AATTTTTAATGTGTTA
1 TTTATTTT-TATTTTTAGAAGTTTAAATTTGTTT
* * *
2093834 TTTATTTTTATTTGTAGGAGTTTAAATTTGTAT
1 TTTATTTTTATTTTTAGAAGTTTAAATTTGTTT
2093867 TTTA
1 TTTA
2093871 AGTATGATTA
Statistics
Matches: 51, Mismatches: 17, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
32 4 0.08
33 42 0.82
34 5 0.10
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.62
Consensus pattern (33 bp):
TTTATTTTTATTTTTAGAAGTTTAAATTTGTTT
Found at i:2094202 original size:21 final size:21
Alignment explanation
Indices: 2094164--2094205 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2094154 ATCTGTTGAA
* **
2094164 ACTCCACCTGTTTTGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
2094185 ACTCCACCTGCTGCGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
2094206 TACTTGTCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (21 bp):
ACTCCACCTGCTGCGGAGTAT
Found at i:2096806 original size:26 final size:26
Alignment explanation
Indices: 2096767--2096816 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2096757 AAACAACATG
* *
2096767 CCACCATTTTTGACAAATAAAAAGAA
1 CCACCATATCTGACAAATAAAAAGAA
*
2096793 CCACCATATCTGACAAATATAAAG
1 CCACCATATCTGACAAATAAAAAG
2096817 GGTGGCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.22
Consensus pattern (26 bp):
CCACCATATCTGACAAATAAAAAGAA
Found at i:2096961 original size:13 final size:14
Alignment explanation
Indices: 2096932--2097011 Score: 53
Period size: 14 Copynumber: 5.8 Consensus size: 14
2096922 ATTTATTTTA
2096932 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
2096946 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
2096959 TTAATAAAAATAAAAAT
1 TTAAT---AATAAAAAT
* *
2096976 TT-ATAATTTATAAT
1 TTAATAA-TAAAAAT
2096990 TT-AT-ATAAAAA-
1 TTAATAATAAAAAT
*
2097001 TTAATACTAAA
1 TTAATAATAAA
2097012 TTCAATAACT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
11 2 0.04
12 6 0.12
13 16 0.31
14 17 0.33
16 5 0.10
17 6 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:2096991 original size:31 final size:32
Alignment explanation
Indices: 2096920--2097001 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
2096910 AGAGTTAACG
* *
2096920 TAATTTAT--TTTATTAATAATAAAAATTTAA
1 TAATTTATAATTTAATAAAAATAAAAATTTAA
2096950 TAA--TATAATTTAATAAAAATAAAAATTT-A
1 TAATTTATAATTTAATAAAAATAAAAATTTAA
2096979 TAATTTATAATTTATATAAAAAT
1 TAATTTATAATTTA-ATAAAAAT
2097002 TAATACTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
28 3 0.07
29 4 0.09
30 21 0.47
31 9 0.20
32 8 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TAATTTATAATTTAATAAAAATAAAAATTTAA
Found at i:2100094 original size:19 final size:20
Alignment explanation
Indices: 2100072--2100115 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
2100062 GCATTAACAT
2100072 ATATTTTTATAA-ATTTTAA
1 ATATTTTTATAATATTTTAA
*
2100091 ATATTTTTATAATTTTTTAA
1 ATATTTTTATAATATTTTAA
2100111 ATATT
1 ATATT
2100116 AAAATTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTTTATAATATTTTAA
Found at i:2100098 original size:20 final size:21
Alignment explanation
Indices: 2100065--2100115 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 21
2100055 ATTTTGTGCA
2100065 TTAACATATATTTTTATAA-ATT
1 TTAA-ATAT-TTTTTATAATATT
*
2100087 TTAAATA-TTTTTATAATTTT
1 TTAAATATTTTTTATAATATT
2100107 TTAAATATT
1 TTAAATATT
2100116 AAAATTAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.35
20 9 0.35
21 4 0.15
22 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAATATTTTTTATAATATT
Found at i:2103427 original size:2 final size:2
Alignment explanation
Indices: 2103420--2103452 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2103410 AGTGTTCATT
2103420 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2103453 TTTGGCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2105916 original size:29 final size:31
Alignment explanation
Indices: 2105859--2105918 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
2105849 TTTTGAACAA
2105859 AATAATATTTAATTTTTAATAAATTTTAATAT
1 AATAATATTTAATTTTTAATAAA-TTTAATAT
*
2105891 AATAATTTTTAATTTTTAA-AAA-TTAATA
1 AATAATATTTAATTTTTAATAAATTTAATA
2105919 ATTATAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.22
31 3 0.11
32 18 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AATAATATTTAATTTTTAATAAATTTAATAT
Found at i:2107577 original size:17 final size:17
Alignment explanation
Indices: 2107550--2107592 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2107540 ACAACGGGCC
*
2107550 TCTTAAATGTTGGTTTT
1 TCTTAAGTGTTGGTTTT
*
2107567 TCTTTAGTGTTGGTTTT
1 TCTTAAGTGTTGGTTTT
2107584 TCTTAAGTG
1 TCTTAAGTG
2107593 ATAGGCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.58
Consensus pattern (17 bp):
TCTTAAGTGTTGGTTTT
Found at i:2112467 original size:13 final size:13
Alignment explanation
Indices: 2112449--2112475 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2112439 CTCTTACTCA
2112449 TTACAAATGCTCT
1 TTACAAATGCTCT
2112462 TTACAAATGCTCT
1 TTACAAATGCTCT
2112475 T
1 T
2112476 AAGGCCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (13 bp):
TTACAAATGCTCT
Found at i:2113541 original size:29 final size:30
Alignment explanation
Indices: 2113480--2113555 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
2113470 CTTTATACGT
*
2113480 TTAAATATTTTTTTATATAAAATTAATATA
1 TTAAATATTTTTTTATATAAAATTAATACA
* *
2113510 TTAAATA-TTTTTTATATGAAATTAATGCA
1 TTAAATATTTTTTTATATAAAATTAATACA
*
2113539 TTATATTTATTTTTTTA
1 TTA-A-ATATTTTTTTA
2113556 AATACTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 22 0.56
30 8 0.21
31 2 0.05
32 7 0.18
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (30 bp):
TTAAATATTTTTTTATATAAAATTAATACA
Found at i:2115825 original size:38 final size:38
Alignment explanation
Indices: 2115752--2115826 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
2115742 AAATTAATTT
** **
2115752 TTTTTATAAAAAAAATTATAGTTTTGGATAAGAAAAAC
1 TTTTTATAAAAAAAATTATAACTTAAGATAAGAAAAAC
* *
2115790 TTTTTATAAATAAAATTATAACTTAAGATATGAAAAA
1 TTTTTATAAAAAAAATTATAACTTAAGATAAGAAAAA
2115827 AGATTGTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (38 bp):
TTTTTATAAAAAAAATTATAACTTAAGATAAGAAAAAC
Found at i:2116594 original size:8 final size:8
Alignment explanation
Indices: 2116581--2116627 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
2116571 TGCATGTATA
2116581 TATTTATG
1 TATTTATG
2116589 TATTTA--
1 TATTTATG
*
2116595 TATATATG
1 TATTTATG
2116603 TATTTATG
1 TATTTATG
2116611 TTTATTTATG
1 --TATTTATG
2116621 TATTTAT
1 TATTTAT
2116628 ATCTTTTCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
6 5 0.15
8 20 0.61
10 8 0.24
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (8 bp):
TATTTATG
Found at i:2116600 original size:18 final size:18
Alignment explanation
Indices: 2116577--2116629 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
2116567 ATCATGCATG
2116577 TATATATTTATGTA-TT-
1 TATATATTTATGTATTTA
2116593 TATATA--TATGTATTTA
1 TATATATTTATGTATTTA
* *
2116609 TGTTTATTTATGTATTTA
1 TATATATTTATGTATTTA
2116627 TAT
1 TAT
2116630 CTTTTCCGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.20
15 2 0.07
16 10 0.33
18 12 0.40
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (18 bp):
TATATATTTATGTATTTA
Found at i:2116602 original size:14 final size:14
Alignment explanation
Indices: 2116579--2116609 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2116569 CATGCATGTA
*
2116579 TATATTTATGTATT
1 TATATATATGTATT
2116593 TATATATATGTATT
1 TATATATATGTATT
2116607 TAT
1 TAT
2116610 GTTTATTTAT
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:0.06, T:0.61
Consensus pattern (14 bp):
TATATATATGTATT
Found at i:2116863 original size:2 final size:2
Alignment explanation
Indices: 2116856--2116899 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2116846 GTGTCAACAA
*
2116856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2116898 AT
1 AT
2116900 TTTAAATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2122173 original size:2 final size:2
Alignment explanation
Indices: 2122166--2122196 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2122156 TCATAGATAG
*
2122166 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2122197 GTTATCTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2122598 original size:14 final size:16
Alignment explanation
Indices: 2122579--2122611 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2122569 AAGTCACGGT
2122579 TAATT-AATTTTA-AA
1 TAATTAAATTTTATAA
2122593 TAATTAAATTTTATAA
1 TAATTAAATTTTATAA
2122609 TAA
1 TAA
2122612 ATCGAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTAAATTTTATAA
Found at i:2124070 original size:2 final size:2
Alignment explanation
Indices: 2124063--2124100 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2124053 GTATTGCTTC
*
2124063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2124101 GCTGAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2124772 original size:16 final size:15
Alignment explanation
Indices: 2124744--2124781 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2124734 TTAATAAACA
*
2124744 AAATTAAATATAAAT
1 AAATTAAAAATAAAT
2124759 AAATTCAAAAATAAAT
1 AAATT-AAAAATAAAT
2124775 -AATTAAA
1 AAATTAAA
2124782 TACAAACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAAAATAAAT
Found at i:2125331 original size:19 final size:19
Alignment explanation
Indices: 2125307--2125363 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
2125297 AGTTGGACTG
*
2125307 TTTATTCTGCTTTTATTTA
1 TTTATTCTGCTTTTATTGA
* *
2125326 TTTATT-T-ATTTTGAATTGG
1 TTTATTCTGCTTTT--ATTGA
2125345 TTTATTCTGCTTTTATTGA
1 TTTATTCTGCTTTTATTGA
2125364 ATTTGTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
17 4 0.14
18 1 0.03
19 19 0.66
20 1 0.03
21 4 0.14
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTATTCTGCTTTTATTGA
Found at i:2129503 original size:4 final size:4
Alignment explanation
Indices: 2129494--2129520 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2129484 ATAATCTTCA
2129494 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2129521 ACTGACGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2134553 original size:28 final size:28
Alignment explanation
Indices: 2134491--2134560 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
2134481 CCACCCACTT
*
2134491 ATTTGTCCAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
*
2134519 -TTTGTCAAAAATGGTGGTTTTCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT-TTTGTG
*
2134546 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
2134561 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:2135740 original size:27 final size:27
Alignment explanation
Indices: 2135709--2135777 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
2135699 AAATCACTCA
*
2135709 TTATTTGTCAAAAATTATAGTTACTTT
1 TTATTTGTCAAAAATGATAGTTACTTT
* * *
2135736 TTATTTGTAAAAAATGATGGTTTCTTT
1 TTATTTGTCAAAAATGATAGTTACTTT
*
2135763 TTATTTATCAAAAAT
1 TTATTTGTCAAAAAT
2135778 AGTGGCATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.51
Consensus pattern (27 bp):
TTATTTGTCAAAAATGATAGTTACTTT
Found at i:2141933 original size:34 final size:34
Alignment explanation
Indices: 2141887--2142037 Score: 198
Period size: 34 Copynumber: 4.5 Consensus size: 34
2141877 GTAAAAACCA
*
2141887 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2141921 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
2141955 CCATTTAATCAATAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2141989 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2142022 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2142038 TCTCCCACTT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
33 18 0.18
34 79 0.78
35 4 0.04
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2141996 original size:68 final size:67
Alignment explanation
Indices: 2141885--2142037 Score: 252
Period size: 68 Copynumber: 2.3 Consensus size: 67
2141875 TGGTAAAAAC
2141885 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
2141950 AT
66 AT
* * * * *
2141952 CACCCATTTAATCAATAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCA
1 CA-CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCA
2142017 AAT
65 AAT
2142020 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2142038 TCTCCCACTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
67 17 0.22
68 62 0.78
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
AT
Found at i:2146130 original size:19 final size:19
Alignment explanation
Indices: 2146103--2146165 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2146093 TCACGTGTAC
* *
2146103 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2146122 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2146141 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2146160 AGTACC
1 AGTACC
2146166 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2146517 original size:34 final size:34
Alignment explanation
Indices: 2146471--2146619 Score: 185
Period size: 34 Copynumber: 4.4 Consensus size: 34
2146461 GTAAAAACCA
*
2146471 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2146505 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
2146539 CCATTTAATCAATAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
2146573 CCATTTAGTCAACAATGATAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2146606 CCATTTAATCAACA
1 CCATTTAATCAACA
2146620 TGATTCCCCC
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
33 16 0.16
34 78 0.80
35 4 0.04
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2146580 original size:68 final size:67
Alignment explanation
Indices: 2146469--2146619 Score: 239
Period size: 68 Copynumber: 2.2 Consensus size: 67
2146459 TGGTAAAAAC
*
2146469 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGATAAACCACCAA
2146534 AT
66 AT
* * * * *
2146536 CACCCATTTAATCAATAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGATAAACTACCA
1 CA-CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGATAAACCACCA
2146601 AAT
65 AAT
2146604 CACCATTTAATCAACA
1 CACCATTTAATCAACA
2146620 TGATTCCCCC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
67 15 0.20
68 61 0.80
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGATAAACCACCAA
AT
Found at i:2147184 original size:2 final size:2
Alignment explanation
Indices: 2147179--2147228 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2147169 AAAAAAAACA
2147179 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2147221 AG AG AG AG
1 AG AG AG AG
2147229 GAGGGTTAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2147420 original size:3 final size:3
Alignment explanation
Indices: 2147412--2147454 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
2147402 ATTAAAACTA
*
2147412 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2147455 TGTCTTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2147655 original size:24 final size:26
Alignment explanation
Indices: 2147604--2147656 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
2147594 TTTATTTTTT
*
2147604 AATATATATTTTATAAATATTATCAA
1 AATATATATTTTATAAATATTATAAA
*
2147630 AATAT-TATTTTATAATTATTA-AAA
1 AATATATATTTTATAAATATTATAAA
2147654 AAT
1 AAT
2147657 CATCATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.20
25 15 0.60
26 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AATATATATTTTATAAATATTATAAA
Found at i:2147664 original size:25 final size:25
Alignment explanation
Indices: 2147607--2147664 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
2147597 ATTTTTTAAT
*
2147607 ATAT-ATTTTATAAATATTATCAAA
1 ATATCATTTTATAAATATTATAAAA
* *
2147631 ATATTATTTTATAATTATTA-AAAA
1 ATATCATTTTATAAATATTATAAAA
2147655 ATCATCATTT
1 AT-ATCATTT
2147665 AATATGACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (25 bp):
ATATCATTTTATAAATATTATAAAA
Found at i:2147785 original size:24 final size:24
Alignment explanation
Indices: 2147758--2147868 Score: 73
Period size: 24 Copynumber: 4.5 Consensus size: 24
2147748 TTCATTAAAA
2147758 AAATTTAAAAAATAAATTTTAACT
1 AAATTTAAAAAATAAATTTTAACT
* ** * *
2147782 AAATTTTAAAAATTCATGTTGAAAT
1 AAATTTAAAAAATAAAT-TTTAACT
* * * *
2147807 CAATTTATTAATTATTAATTTTTAA-T
1 AAATTTA--AA-AAATAAATTTTAACT
* *
2147833 AAA-ATAAAAAATAAAATTTAACT
1 AAATTTAAAAAATAAATTTTAACT
2147856 AAATTTAAAAAAT
1 AAATTTAAAAAAT
2147869 TTTGTATTGA
Statistics
Matches: 61, Mismatches: 20, Indels: 12
0.66 0.22 0.13
Matches are distributed among these distances:
22 9 0.15
23 6 0.10
24 22 0.36
25 12 0.20
26 3 0.05
27 6 0.10
28 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
AAATTTAAAAAATAAATTTTAACT
Found at i:2147841 original size:74 final size:76
Alignment explanation
Indices: 2147763--2147922 Score: 218
Period size: 74 Copynumber: 2.1 Consensus size: 76
2147753 TAAAAAAATT
* * * *
2147763 TAAAAAATAAATTTTAACTAAATTTTAAAAATTCATG-TTG-AAATCAATTTATTAATTATT-AA
1 TAAAAAATAAAATTTAACTAAATTTAAAAAATT-ATGATTGAAAATAAATATATTAATTATTGAA
2147825 TTTTTAATAAAA
65 TTTTTAATAAAA
*
2147837 TAAAAAATAAAATTTAACTAAATTTAAAAAATTTTGTATTGAAAAATAAATATATTAATTATTGA
1 TAAAAAATAAAATTTAACTAAATTTAAAAAATTATG-ATTG-AAAATAAATATATTAATTATTGA
*
2147902 TTTTTTAATAAAA
64 ATTTTTAATAAAA
2147915 TAAAAAAT
1 TAAAAAAT
2147923 CTTATATTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
73 2 0.03
74 31 0.41
75 3 0.04
77 18 0.24
78 21 0.28
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (76 bp):
TAAAAAATAAAATTTAACTAAATTTAAAAAATTATGATTGAAAATAAATATATTAATTATTGAAT
TTTTAATAAAA
Found at i:2148514 original size:2 final size:2
Alignment explanation
Indices: 2148507--2148547 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2148497 GGCTTTATCA
2148507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2148548 CTACTATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2149580 original size:2 final size:2
Alignment explanation
Indices: 2149569--2149604 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2149559 ATTTTTCTTT
2149569 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2149605 TTGAGGGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.