Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 89 of 230
Found at i:24890625 original size:21 final size:21
Alignment explanation
Indices: 24890580--24890642 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24890570 TTTGAACCAT
* *
24890580 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
24890602 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
24890623 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
24890643 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:24896121 original size:21 final size:21
Alignment explanation
Indices: 24896095--24896157 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24896085 TTGGTATTTG
24896095 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
24896116 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24896137 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
24896158 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:24896834 original size:30 final size:30
Alignment explanation
Indices: 24896800--24896895 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
24896790 GCTCACTCCT
24896800 AGCTCATA-TTTAGCTCACGAGCTAAACCTA
1 AGCTCA-ACTTTAGCTCACGAGCTAAACCTA
* * * * * * *
24896830 AGCTCAACTTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAACCTA
* *
24896860 AGCTCAACTTTAGCTCACGAGCTAAAACTT
1 AGCTCAACTTTAGCTCACGAGCTAAACCTA
24896890 AGCTCA
1 AGCTCA
24896896 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAACCTA
Found at i:24898644 original size:14 final size:14
Alignment explanation
Indices: 24898625--24898656 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
24898615 TTGGAGTAAC
24898625 AAAAAAAATC-AAA
1 AAAAAAAATCGAAA
24898638 AAAAAAAATCGAAA
1 AAAAAAAATCGAAA
24898652 AAAAA
1 AAAAA
24898657 TTGATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAAAAATCGAAA
Found at i:24898680 original size:13 final size:13
Alignment explanation
Indices: 24898625--24898683 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
24898615 TTGGAGTAAC
24898625 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
*
24898637 AAAAAAAAATCGAA
1 AAAAAAAATTC-AA
* *
24898651 AAAAAATTGATT-GA
1 AAAAAA--AATTCAA
24898665 AAAAAAAATTCAA
1 AAAAAAAATTCAA
24898678 AAAAAA
1 AAAAAA
24898684 GTGAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
12 11 0.30
13 9 0.24
14 15 0.41
16 2 0.05
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:24898691 original size:12 final size:12
Alignment explanation
Indices: 24898662--24898744 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 12
24898652 AAAAATTGAT
24898662 TGAAAAAAAAA-
1 TGAAAAAAAAAG
**
24898673 TTCAAAAAAAAG
1 TGAAAAAAAAAG
*
24898685 TGAAAAAAAATCG
1 TGAAAAAAAA-AG
* *
24898698 AGCAAAAAAAAGG
1 TG-AAAAAAAAAG
24898711 TGACCAAAAAATCAAG
1 TGA--AAAAAA--AAG
*
24898727 TTAAAAAAAAAG
1 TGAAAAAAAAAG
24898739 TGAAAA
1 TGAAAA
24898745 GTCTTGCGAG
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
11 9 0.17
12 17 0.31
13 4 0.07
14 20 0.37
16 4 0.07
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.12
Consensus pattern (12 bp):
TGAAAAAAAAAG
Found at i:24898694 original size:27 final size:27
Alignment explanation
Indices: 24898635--24898694 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
24898625 AAAAAAAATC
* *
24898635 AAAAAAAAAAATCGAAAAAAAATTGATT
1 AAAAAAAAAAATCGAAAAAAAAGTGA-A
* *
24898663 GAAAAAAAAATTC-AAAAAAAAGTGAA
1 AAAAAAAAAAATCGAAAAAAAAGTGAA
24898689 AAAAAA
1 AAAAAA
24898695 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 11 0.41
28 11 0.41
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.13
Consensus pattern (27 bp):
AAAAAAAAAAATCGAAAAAAAAGTGAA
Found at i:24898732 original size:28 final size:25
Alignment explanation
Indices: 24898675--24898744 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
24898665 AAAAAAAATT
*
24898675 CAAAAAAAAGTGAAAAAAAATCGAG
1 CAAAAAAAAGTGAAAAAAAATCAAG
*
24898700 CAAAAAAAAGGTGACCAAAAAATCAAG
1 CAAAAAAAA-GTGA-AAAAAAATCAAG
*
24898727 TTAAAAAAAAAGTGAAAA
1 --CAAAAAAAAGTGAAAA
24898745 GTCTTGCGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 9 0.24
26 4 0.11
27 12 0.32
28 4 0.11
29 8 0.22
ACGTcount: A:0.67, C:0.09, G:0.14, T:0.10
Consensus pattern (25 bp):
CAAAAAAAAGTGAAAAAAAATCAAG
Found at i:24899794 original size:17 final size:18
Alignment explanation
Indices: 24899762--24899795 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24899752 AAAAGAGAGT
*
24899762 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
24899780 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
24899796 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:24905047 original size:6 final size:6
Alignment explanation
Indices: 24905027--24905076 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
24905017 AAGAGAAAAC
*
24905027 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
24905076 A
1 A
24905077 TAAAAGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:24905057 original size:21 final size:21
Alignment explanation
Indices: 24905027--24905086 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
24905017 AAGAGAAAAC
24905027 AAAGAAAAGAAAAGAAAAAGAA
1 AAAG-AAAGAAAAGAAAAAGAA
* *
24905049 AAAGCAAGAGAAGAAAAAGAA
1 AAAGAAAGAAAAGAAAAAGAA
* *
24905070 AATGAAATAAAAGAAAA
1 AAAGAAAGAAAAGAAAA
24905087 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAGAAAGAAAAGAAAAAGAA
Found at i:24905057 original size:26 final size:25
Alignment explanation
Indices: 24905027--24905088 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
24905017 AAGAGAAAAC
24905027 AAAGAAAAGAAAAGAAAAAGAAA-A
1 AAAGAAAAGAAAAGAAAAAGAAATA
* *
24905051 AGCAAGAGAAGAAAAAGAAAATGAAATA
1 A--AAGAAAAG-AAAAGAAAAAGAAATA
24905079 AAAGAAAAGA
1 AAAGAAAAGA
24905089 GAGGCAAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.03
25 1 0.03
26 14 0.45
27 13 0.42
28 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (25 bp):
AAAGAAAAGAAAAGAAAAAGAAATA
Found at i:24905168 original size:11 final size:12
Alignment explanation
Indices: 24905136--24905166 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
24905126 TTGAGAGAAC
24905136 TTGAAAAAGCCT
1 TTGAAAAAGCCT
24905148 TTGAAAAAGCCT
1 TTGAAAAAGCCT
24905160 TTGAAAA
1 TTGAAAA
24905167 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:24907380 original size:30 final size:30
Alignment explanation
Indices: 24907346--24907442 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
24907336 AGCTCACTTC
24907346 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
24907376 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
24907406 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
24907436 TAGCTCA
1 TAGCTCA
24907443 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:24910648 original size:11 final size:11
Alignment explanation
Indices: 24910600--24910664 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
24910590 TTGGAGTAAC
24910600 AAAAAAA-TC-
1 AAAAAAATTCA
24910609 AAAAAAATTCGA
1 AAAAAAATTC-A
*
24910621 AAAAAATTTATTGA
1 AAAAAA---ATTCA
24910635 AAAAAAATTCA
1 AAAAAAATTCA
* *
24910646 AAAAAAAGTGA
1 AAAAAAATTCA
24910657 AAAAAAAT
1 AAAAAAAT
24910665 CGAGCAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
9 7 0.16
10 2 0.04
11 20 0.44
12 6 0.13
14 7 0.16
15 3 0.07
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.18
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:24913201 original size:55 final size:54
Alignment explanation
Indices: 24913106--24913255 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
24913096 CTACTTTGTT
* ** * *
24913106 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
24913160 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
24913215 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
24913256 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:24913218 original size:27 final size:27
Alignment explanation
Indices: 24913078--24913255 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
24913068 TAAATTGTAC
24913078 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
24913105 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
24913131 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
24913159 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
24913187 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
24913214 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
24913241 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
24913256 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:24913219 original size:82 final size:81
Alignment explanation
Indices: 24913079--24913234 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
24913069 AAATTGTACA
* * * *
24913079 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
24913144 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
24913160 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
24913223 TGTGCGAGTTGA
63 TGTGCGAATTGA
24913235 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:24921211 original size:55 final size:54
Alignment explanation
Indices: 24921116--24921265 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
24921106 CTACTTTGTT
* ** * *
24921116 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
24921170 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
24921225 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
24921266 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:24921228 original size:27 final size:27
Alignment explanation
Indices: 24921088--24921265 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
24921078 TAAATTGTAC
24921088 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
24921115 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
24921141 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
24921169 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
24921197 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
24921224 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
24921251 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
24921266 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:24921229 original size:82 final size:81
Alignment explanation
Indices: 24921089--24921244 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
24921079 AAATTGTACA
* * * *
24921089 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
24921154 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
24921170 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
24921233 TGTGCGAGTTGA
63 TGTGCGAATTGA
24921245 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:24924138 original size:25 final size:25
Alignment explanation
Indices: 24924085--24924141 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
24924075 AAGCTCTTTC
* *
24924085 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCAAGA
* * *
24924110 GAGCCATGTAACGGGAAGCTTAAGA
1 GAGCCATATAACAGGAAGCTCAAGA
24924135 GAGCCAT
1 GAGCCAT
24924142 TATTGGGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCAAGA
Found at i:24925688 original size:16 final size:16
Alignment explanation
Indices: 24925663--24925748 Score: 52
Period size: 17 Copynumber: 5.1 Consensus size: 16
24925653 TTTTATATAT
24925663 ATTTTTATAT-TTTTA
1 ATTTTTATATATTTTA
*
24925678 ATTTATTATATATTTTT
1 ATTT-TTATATATTTTA
*
24925695 ATGCTTCTTACAATATTTT-
1 AT--TT-TTA-TATATTTTA
**
24925714 A-TAATATATATTTTAA
1 ATTTTTATATATTTT-A
24925730 ATTTTTATATACTTTTA
1 ATTTTTATATA-TTTTA
24925747 AT
1 AT
24925749 AAATTTGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
14 7 0.13
15 6 0.11
16 8 0.15
17 16 0.30
18 4 0.07
19 6 0.11
20 7 0.13
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (16 bp):
ATTTTTATATATTTTA
Found at i:24925764 original size:17 final size:17
Alignment explanation
Indices: 24925742--24925780 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
24925732 TTTTATATAC
* **
24925742 TTTTAATAAATTTGTAT
1 TTTTAAAAAATTCATAT
24925759 TTTTAAAAAATTCATAT
1 TTTTAAAAAATTCATAT
24925776 TTTTA
1 TTTTA
24925781 CAATTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTAAAAAATTCATAT
Found at i:24925876 original size:19 final size:20
Alignment explanation
Indices: 24925852--24925897 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
24925842 AATTTTTTGC
24925852 AATTTTTTATCATTTAT-AT
1 AATTTTTTATCATTTATAAT
24925871 AATTTTTTATCATTTATAAT
1 AATTTTTTATCATTTATAAT
24925891 AATTTTT
1 AATTTTT
24925898 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTTTTATCATTTATAAT
Found at i:24926916 original size:23 final size:23
Alignment explanation
Indices: 24926888--24926932 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
24926878 GTTCAAAATT
*
24926888 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
24926911 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
24926933 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:24927002 original size:14 final size:14
Alignment explanation
Indices: 24926979--24927008 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24926969 AATGAATTGG
*
24926979 ATAATTTATAATAA
1 ATAATATATAATAA
24926993 ATAATATATAATAA
1 ATAATATATAATAA
24927007 AT
1 AT
24927009 TTGAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATATAATAA
Found at i:24927019 original size:24 final size:24
Alignment explanation
Indices: 24926981--24927232 Score: 150
Period size: 24 Copynumber: 10.8 Consensus size: 24
24926971 TGAATTGGAT
* *
24926981 AATTTATAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
24927006 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
24927030 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
24927050 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
24927075 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
24927099 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
24927120 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** ** *
24927144 AATTTAAAATAATGTTA-ACAATG
1 AATTTAAAATAATAATATATGATA
24927167 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* * *
24927190 AATTAAAAATAATAAAACATGATA
1 AATTTAAAATAATAATATATGATA
*
24927214 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
24927233 CAATACACTT
Statistics
Matches: 172, Mismatches: 39, Indels: 33
0.70 0.16 0.14
Matches are distributed among these distances:
20 5 0.03
21 13 0.08
22 16 0.09
23 51 0.30
24 75 0.44
25 12 0.07
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:24927077 original size:69 final size:69
Alignment explanation
Indices: 24927003--24927264 Score: 194
Period size: 69 Copynumber: 3.8 Consensus size: 69
24926993 ATAATATATA
* * *
24927003 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TGA-AATAGAT
*
24927064 CATACGTG
63 -ATACATG
** * *
24927072 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
24927137 CATG
66 CATG
** * * * * **
24927141 ATAAATTTAAAATAATGTTA-ACAATGAATTTAAAATAATAATATTGATAAATTAAAAATA-ATA
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGATAAATTTGAAATAGAT-
*
24927204 AAACATG
63 ATACATG
* * * * * * *
24927211 ATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAATTT
1 ATAAATTTAAAATAATAATACATAATAAATTTA-AAAATATTAATGATAAATTT
24927265 AATAATAGTA
Statistics
Matches: 154, Mismatches: 30, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
68 9 0.06
69 69 0.45
70 67 0.44
71 9 0.06
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
CATG
Found at i:24927249 original size:70 final size:68
Alignment explanation
Indices: 24927070--24927272 Score: 176
Period size: 70 Copynumber: 2.9 Consensus size: 68
24927060 TAATCATACG
* * * * * **
24927070 TGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATA
1 TGATAAATCTAAAATAATAATATACAAT-AATTTAATAATAATAATGATAAATTAAAAATAGATA
*
24927135 TACA
65 AACA
* ** *
24927139 TGATAAATTTAAAATAATGTTA-ACAATGAATTTAAAATAATAATATTGATAAATTAAAAATA-A
1 TGATAAATCTAAAATAATAATATACAAT-AATTT--AATAATAATAATGATAAATTAAAAATAGA
24927202 TAAAACA
63 T-AAACA
* * * *
24927209 TGATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAATTTAATAATAG
1 TGATAAATCTAAAATAATAATATACAATA-ATTTA-ATAATAATAATGA-TAAATTAAAAATAG
24927273 TAAGTATAAA
Statistics
Matches: 106, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
68 9 0.08
69 21 0.20
70 57 0.54
71 19 0.18
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (68 bp):
TGATAAATCTAAAATAATAATATACAATAATTTAATAATAATAATGATAAATTAAAAATAGATAA
ACA
Found at i:24928088 original size:22 final size:22
Alignment explanation
Indices: 24928063--24928110 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
24928053 TATAAATTAA
24928063 ATCTT-TAAGATTACAAAATCTT
1 ATCTTCTAAGATTAC-AAATCTT
* *
24928085 ATCTTCTAAGATTGCATATCTT
1 ATCTTCTAAGATTACAAATCTT
24928107 ATCT
1 ATCT
24928111 AAGATTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (22 bp):
ATCTTCTAAGATTACAAATCTT
Found at i:24928450 original size:44 final size:45
Alignment explanation
Indices: 24928399--24928493 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 45
24928389 AGGCTCACTT
* *
24928399 TCTTCAACCTACTCCATTGCAACTTCAGGGAGATAAGATT-GATA
1 TCTTCAACCGACTCCACTGCAACTTCAGGGAGATAAGATTGGATA
* * * *
24928443 TCTTCAACCGGCTCCACTGTAACTTCAGGGAGATAAGGTTGGTTA
1 TCTTCAACCGACTCCACTGCAACTTCAGGGAGATAAGATTGGATA
24928488 TCTTCA
1 TCTTCA
24928494 GTCTTTAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 35 0.80
45 9 0.20
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
TCTTCAACCGACTCCACTGCAACTTCAGGGAGATAAGATTGGATA
Found at i:24928939 original size:169 final size:167
Alignment explanation
Indices: 24928643--24929134 Score: 617
Period size: 169 Copynumber: 2.9 Consensus size: 167
24928633 TTTTTCAATT
* * * * *
24928643 TTAACGCCAAGGAGATGAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAACACCAGGGAA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
* ** ** *
24928708 ACCAGATTTTCTACCTTTAGCCTTAATCAATTCCACTGTAATGCAAAAGAGATAGGATTCGCTGC
66 ACAAGATTCACTACCTTTAG-CTTAATCTGTTCCACTATAATGC-AAAGAGATAGGATTCGCTGC
24928773 CCACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
129 CCACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
** * * * *
24928812 TTAATGCCAGGGATATAAGATTCGCTGCCCT-ATGCTCTAATCTGCTCCGCTGCAACGCTAGGGA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCA-GCTTTAATCTGCTCCGCTGCAACACCAGGGA
* *
24928876 AACAAGATTCGCTACCTTTAGCTTCAATCTGTTCCACTATAATGTCAAAGAGTTAGGATTCGCTG
65 AACAAGATTCACTACCTTTAGCTT-AATCTGTTCCACTATAATG-CAAAGAGATAGGATTCGCTG
* * ** * *
24928941 TCCGCAGCTTTAATCTACTCAACCTCAGCTATTCCAAGTC
128 CCCACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
* * * *
24928981 TTAACACCAGGGAGATAAGATTCGCTGCGCTCAGCTTTAGTTTACTCCGCTGCAACACCAGGGAA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
* * *
24929046 ATAAGATTCACTACCTTTAGCTTTAATCTGTTCCACTATAAGGCCAAATAGATAGGATTCGCTGC
66 ACAAGATTCACTACCTTTAGC-TTAATCTGTTCCACTATAATG-CAAAGAGATAGGATTCGCTGC
*
24929111 CCACAGTTTTAATCCGCTCCACTT
129 CCACAGCTTTAATCCGCTCCACTT
24929135 TAGCATTAAC
Statistics
Matches: 273, Mismatches: 45, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
168 4 0.01
169 265 0.97
170 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (167 bp):
TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
ACAAGATTCACTACCTTTAGCTTAATCTGTTCCACTATAATGCAAAGAGATAGGATTCGCTGCCC
ACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
Found at i:24929418 original size:45 final size:46
Alignment explanation
Indices: 24929367--24929502 Score: 159
Period size: 45 Copynumber: 3.0 Consensus size: 46
24929357 CGTCGTTTTT
* * *
24929367 GATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCTATCTTCA
1 GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
* ** **
24929413 G-TCTGCTCCGCTACCAATACAGGAAGACAAGATCTAATATCTTC-
1 GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
* * *
24929457 GATCTACTTCACTGTCAATACAGGAAGATAAGATCTGCTATCTTCA
1 GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
24929503 ATTCACTCTA
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
44 1 0.01
45 70 0.97
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (46 bp):
GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
Found at i:24930817 original size:6 final size:6
Alignment explanation
Indices: 24930778--24930808 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
24930768 TTTTTTTCCA
24930778 TCATTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
24930809 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:24934246 original size:8 final size:8
Alignment explanation
Indices: 24934233--24934259 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
24934223 AGTTGATTAA
24934233 TTAATGTC
1 TTAATGTC
24934241 TTAATGTC
1 TTAATGTC
24934249 TTAATGTC
1 TTAATGTC
24934257 TTA
1 TTA
24934260 CTTTAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (8 bp):
TTAATGTC
Found at i:24934844 original size:23 final size:23
Alignment explanation
Indices: 24934816--24934860 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
24934806 ATTCAAAATT
*
24934816 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
24934839 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
24934861 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:24935035 original size:24 final size:24
Alignment explanation
Indices: 24934973--24935160 Score: 124
Period size: 24 Copynumber: 8.0 Consensus size: 24
24934963 AAAAATTTTG
* *
24934973 ATGAT-AATTCTAGAATAATCATAT
1 ATGATAAATT-TAAAATAATAATAT
* * *
24934997 GTGAT-AATTCCAAAATAATAGTAT
1 ATGATAAATT-TAAAATAATAATAT
* *
24935021 ATAATAAATTT-AAA-AATATTA-
1 ATGATAAATTTAAAATAATAATAT
* *
24935042 ATGATAAATTTGAAATAGAT-ATAC
1 ATGATAAATTTAAAATA-ATAATAT
**
24935066 ATGATAAATTTAAAATAATGTTA-
1 ATGATAAATTTAAAATAATAATAT
** *
24935089 ACAATGAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAATAATAT
* *
24935113 -TGATAAA-TTACAAATAATAAAAC
1 ATGATAAATTTA-AAATAATAATAT
*
24935136 ATGATAAATCTAAAATAATAATAT
1 ATGATAAATTTAAAATAATAATAT
24935160 A
1 A
24935161 CAATACACTT
Statistics
Matches: 128, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
21 10 0.08
22 12 0.09
23 40 0.31
24 60 0.47
25 6 0.05
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (24 bp):
ATGATAAATTTAAAATAATAATAT
Found at i:24935177 original size:70 final size:66
Alignment explanation
Indices: 24934998--24935199 Score: 174
Period size: 70 Copynumber: 2.9 Consensus size: 66
24934988 TAATCATATG
* * * * *
24934998 TGATAATTCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGAT-
1 TGATAAATCTAAAATAATAATATACAAT-AATTTAATAATATTAATGATAAA-TT-AAATA-ATA
*
24935062 ATACA
62 AAACA
* ** * *
24935067 TGATAAATTTAAAATAATGTTA-ACAATGAATTTAAAATAATAATATTGATAAATTACAAATAAT
1 TGATAAATCTAAAATAATAATATACAAT-AATTT--AATAATATTAATGATAAATT--AAATAAT
24935131 AAAACA
61 AAAACA
* *
24935137 TGATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAATTAAATAATA
1 TGATAAATCTAAAATAATAATATACAATA-ATTTA-ATAATATTAATGATAAATTAAATAATA
24935200 GTAAGTATAA
Statistics
Matches: 107, Mismatches: 19, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
68 17 0.16
69 22 0.21
70 60 0.56
71 8 0.07
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (66 bp):
TGATAAATCTAAAATAATAATATACAATAATTTAATAATATTAATGATAAATTAAATAATAAAAC
A
Found at i:24937013 original size:20 final size:20
Alignment explanation
Indices: 24936962--24937018 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
24936952 TTAATAATTT
* * *
24936962 ATAAGCCTAATGTATTATAG
1 ATAAGTCTAATATATTAGAG
*
24936982 AT-AGATCCAATATATTAGAG
1 ATAAG-TCTAATATATTAGAG
*
24937002 ATAAGTCTAATACATTA
1 ATAAGTCTAATATATTA
24937019 CATAAGCCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (20 bp):
ATAAGTCTAATATATTAGAG
Found at i:24937222 original size:21 final size:22
Alignment explanation
Indices: 24937176--24937222 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
24937166 AATGTAAGGT
*
24937176 TTGTTATTATGTTTTAATTTAG
1 TTGTTATTATGTGTTAATTTAG
24937198 -TGTTATTATTGTGTT-ATTT-G
1 TTGTTATTA-TGTGTTAATTTAG
24937218 TTGTT
1 TTGTT
24937223 TTAAATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (22 bp):
TTGTTATTATGTGTTAATTTAG
Found at i:24942900 original size:36 final size:36
Alignment explanation
Indices: 24942829--24942900 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
24942819 TCGGAAAAGC
* *
24942829 TGTTTTTACATATATTAATAAATTTATATTTTAAAT
1 TGTTTTTACATATATTAACAAATTTATATTATAAAT
24942865 TGTTTTTACATATA-TAACAATGATTTAT-TTATAAAT
1 TGTTTTTACATATATTAACAA--ATTTATATTATAAAT
24942901 AAATAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 5 0.16
36 21 0.66
37 6 0.19
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (36 bp):
TGTTTTTACATATATTAACAAATTTATATTATAAAT
Found at i:24944138 original size:32 final size:32
Alignment explanation
Indices: 24944102--24944191 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
24944092 CAATTATTTC
24944102 AATATCCAACAAGCTTAAAACATAATAAATTA
1 AATATCCAACAAGCTTAAAACATAATAAATTA
*
24944134 AATATCCAACAAGCTTAAAACATAATAAATTC
1 AATATCCAACAAGCTTAAAACATAATAAATTA
*
24944166 AATATCTAACAAGCTTAAAACATAAT
1 AATATCCAACAAGCTTAAAACATAAT
24944192 CAATATCTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (32 bp):
AATATCCAACAAGCTTAAAACATAATAAATTA
Found at i:24944198 original size:27 final size:30
Alignment explanation
Indices: 24944099--24944204 Score: 128
Period size: 32 Copynumber: 3.5 Consensus size: 30
24944089 TGTCAATTAT
24944099 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
*
24944131 TTAAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
*
24944163 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCCAACAAGCTTAAAACAATAAA
*
24944191 -TCAATATCTAACAA
1 TTCAATATCCAACAA
24944205 ATTCAAGACA
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
27 14 0.20
28 2 0.03
29 2 0.03
32 53 0.75
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCCAACAAGCTTAAAACAATAAA
Found at i:24944215 original size:27 final size:27
Alignment explanation
Indices: 24944164--24944218 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
24944154 CATAATAAAT
*
24944164 TCAATATCTAACAAGCTTAAAACATAA
1 TCAATATCTAACAAGATTAAAACATAA
*
24944191 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
24944218 T
1 T
24944219 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:24944226 original size:59 final size:62
Alignment explanation
Indices: 24944097--24944236 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 62
24944087 ATTGTCAATT
*
24944097 ATTTCAATATCCAACAAGCTTAAAACATAATAAATTAAATATCCAACAAGCTTAAAACATAATA
1 ATTTCAATATCCAACAAGCTTAAAAC--AATAAATTAAATATCCAACAAGATTAAAACATAATA
* * * * *
24944161 AATTCAATATCTAACAAGCTTAAAAC-AT-AA-TCAATATCTAACAA-ATTCAAGACATAATA
1 ATTTCAATATCCAACAAGCTTAAAACAATAAATTAAATATCCAACAAGATT-AAAACATAATA
*
24944220 ATTTCAAAATCCAACAA
1 ATTTCAATATCCAACAA
24944237 ACTAAAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.03
59 36 0.55
60 2 0.03
61 2 0.03
64 24 0.36
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (62 bp):
ATTTCAATATCCAACAAGCTTAAAACAATAAATTAAATATCCAACAAGATTAAAACATAATA
Found at i:24947374 original size:17 final size:17
Alignment explanation
Indices: 24947352--24947404 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
24947342 TCTTCAACAG
24947352 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
*
24947369 ACAGAT--TAAA--CAA
1 ACAGATGCAAAATCCAA
*
24947382 ACAGATGCAAAATCTAA
1 ACAGATGCAAAATCCAA
24947399 ACAGAT
1 ACAGAT
24947405 TCTTCAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 9 0.31
15 6 0.21
17 14 0.48
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (17 bp):
ACAGATGCAAAATCCAA
Found at i:24947386 original size:30 final size:30
Alignment explanation
Indices: 24947347--24947405 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
24947337 AAGATTCTTC
*
24947347 AACAGACAGATGCAAAATCCAAACAGATTA
1 AACAAACAGATGCAAAATCCAAACAGATTA
*
24947377 AACAAACAGATGCAAAATCTAAACAGATT
1 AACAAACAGATGCAAAATCCAAACAGATT
24947406 CTTCAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (30 bp):
AACAAACAGATGCAAAATCCAAACAGATTA
Found at i:24948028 original size:9 final size:8
Alignment explanation
Indices: 24947951--24948086 Score: 69
Period size: 8 Copynumber: 15.6 Consensus size: 8
24947941 TAAACTTATA
24947951 AAAAGATAT
1 AAAA-ATAT
*
24947960 AAAAATCCT
1 AAAAAT-AT
*
24947969 AGAAAATAA
1 A-AAAATAT
24947978 AAAAATATT
1 AAAAATA-T
24947987 AGAGATAATAT
1 A-A-A-AATAT
**
24947998 AAACTTAT
1 AAAAATAT
24948006 AAAAATAT
1 AAAAATAT
24948014 AAAAAAATCAT
1 --AAAAAT-AT
24948025 AAAAATAT
1 AAAAATAT
24948033 AAAAACTTAT
1 AAAAA--TAT
24948043 AAAAATA-
1 AAAAATAT
*
24948050 ATAAAT-T
1 AAAAATAT
24948057 AAAAATAT
1 AAAAATAT
* * *
24948065 ATAATTAC
1 AAAAATAT
24948073 AAAAATTAT
1 AAAAA-TAT
24948082 AAAAA
1 AAAAA
24948087 AAATCATTTA
Statistics
Matches: 97, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
7 10 0.10
8 35 0.36
9 22 0.23
10 21 0.22
11 5 0.05
12 4 0.04
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:24948051 original size:56 final size:56
Alignment explanation
Indices: 24947919--24948052 Score: 157
Period size: 56 Copynumber: 2.4 Consensus size: 56
24947909 TTTAAAATTT
* * *
24947919 TATAAAATATTA-AAAAATTATATAAACTTATAAAAAGATATAAAAATCCTAGAAAA
1 TATAAAA-ATTATAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAGAAAA
* * * *
24947975 TA-AAAAAATATTAGAGATAATATAAACTTATAAAAATATAAAAAAATCATA-AAAA
1 TATAAAAATTA-TAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAGAAAA
24948030 TATAAAAACTTATAAAAATAATA
1 TATAAAAA-TTATAAAAATAATA
24948053 AATTAAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
54 3 0.05
55 10 0.16
56 49 0.77
57 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (56 bp):
TATAAAAATTATAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAGAAAA
Found at i:24948068 original size:18 final size:17
Alignment explanation
Indices: 24948005--24948065 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 17
24947995 TATAAACTTA
*
24948005 TAAAAATATAAAAAAAT
1 TAAAAATATAAATAAAT
*
24948022 CATAAAAATATAAA-AACT
1 --TAAAAATATAAATAAAT
24948040 TATAAAA-AT-AATAAAT
1 TA-AAAATATAAATAAAT
24948056 TAAAAATATA
1 TAAAAATATA
24948066 TAATTACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 4 0.11
18 3 0.08
19 12 0.33
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAATATAAATAAAT
Found at i:24948084 original size:30 final size:32
Alignment explanation
Indices: 24948024--24948084 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
24948014 AAAAAAATCA
*
24948024 TAAAAATATAAAAACTTATAAAAATAATAAAT
1 TAAAAATATAAAAACTTACAAAAATAATAAAT
* *
24948056 TAAAAATAT-ATAA-TTACAAAAATTATAAA
1 TAAAAATATAAAAACTTACAAAAATAATAAA
24948085 AAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 3 0.12
32 9 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (32 bp):
TAAAAATATAAAAACTTACAAAAATAATAAAT
Found at i:24952790 original size:29 final size:27
Alignment explanation
Indices: 24952758--24952859 Score: 75
Period size: 30 Copynumber: 3.6 Consensus size: 27
24952748 TATTGTACCA
24952758 TTTATAAGTTTTTATGGTTTTATATAAT
1 TTTATAAGTTTTTAT-GTTTTATATAAT
* *
24952786 TTT-TAAAATATTTTGAT-TTTTAAAATTAAT
1 TTTAT-AAGT-TTTT-ATGTTTT-ATA-TAAT
*
24952816 TTTATAAGTTTTTATGAATTTTTTATAAGT
1 TTTATAAGTTTTTATG--TTTTATATAA-T
24952846 TTTATAA-TTTTTAT
1 TTTATAAGTTTTTAT
24952860 AAGTATACAT
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
27 1 0.02
28 12 0.20
29 20 0.34
30 21 0.36
31 5 0.08
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (27 bp):
TTTATAAGTTTTTATGTTTTATATAAT
Found at i:24952839 original size:21 final size:19
Alignment explanation
Indices: 24952758--24952863 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 19
24952748 TATTGTACCA
**
24952758 TTTATAAGTTTTTATGGTT
1 TTTATAAGTTTTTATAATT
* *
24952777 TTATATAA-TTTTTAAAATA
1 TT-TATAAGTTTTTATAATT
* *
24952796 TTT-TGA-TTTTTAAAATTAAT
1 TTTATAAGTTTTTATAA-T--T
24952816 TTTATAAGTTTTTATGAATTT
1 TTTATAAGTTTTTAT-AA-TT
24952837 TTTATAAG-TTTTATAATT
1 TTTATAAGTTTTTATAATT
24952855 TTTATAAGT
1 TTTATAAGT
24952864 ATACATAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
17 11 0.15
18 12 0.17
19 13 0.18
20 14 0.20
21 11 0.15
22 6 0.08
23 4 0.06
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTATAAGTTTTTATAATT
Found at i:24952848 original size:9 final size:9
Alignment explanation
Indices: 24952815--24952863 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
24952805 TTAAAATTAA
24952815 TTTTATAAG
1 TTTTATAAG
*
24952824 TTTTTATGAATT
1 -TTTTAT-AA-G
24952836 TTTTATAAG
1 TTTTATAAG
*
24952845 TTTTATAAT
1 TTTTATAAG
24952854 TTTTATAAG
1 TTTTATAAG
24952863 T
1 T
24952864 ATACATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 17 0.52
10 8 0.24
11 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (9 bp):
TTTTATAAG
Found at i:24952912 original size:18 final size:19
Alignment explanation
Indices: 24952874--24952927 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 19
24952864 ATACATAAAA
24952874 TTTAAATATTTTTATTAAT
1 TTTAAATATTTTTATTAAT
24952893 TTTAAATAGTTTTTA-T-AT
1 TTTAAATA-TTTTTATTAAT
24952911 TTT-AATGATTTTTATTA
1 TTTAAAT-ATTTTTATTA
24952928 GAAAATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.29
18 7 0.23
19 9 0.29
20 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTAAATATTTTTATTAAT
Found at i:24971753 original size:13 final size:13
Alignment explanation
Indices: 24971737--24971761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24971727 TTTACTTTTT
24971737 CTTAGTTAATTTA
1 CTTAGTTAATTTA
24971750 CTTAGTTAATTT
1 CTTAGTTAATTT
24971762 TTAGTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
CTTAGTTAATTTA
Found at i:24976324 original size:25 final size:25
Alignment explanation
Indices: 24976290--24976339 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
24976280 CTGACTTTGT
24976290 TATCTTAGACTTTGAAGTAGATAAA
1 TATCTTAGACTTTGAAGTAGATAAA
24976315 TATCTTAGACTTTGAAGTAGATAAA
1 TATCTTAGACTTTGAAGTAGATAAA
24976340 GAGGTACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (25 bp):
TATCTTAGACTTTGAAGTAGATAAA
Found at i:24979068 original size:21 final size:20
Alignment explanation
Indices: 24979042--24979080 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
24979032 GTTTTGATGA
24979042 AGGTATAGATACCTTAGGCCT
1 AGGTATAGATACC-TAGGCCT
*
24979063 AGGTATCGATACCTAGGC
1 AGGTATAGATACCTAGGC
24979081 TTATATTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
AGGTATAGATACCTAGGCCT
Found at i:24979929 original size:28 final size:30
Alignment explanation
Indices: 24979897--24979978 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 30
24979887 GGAAATAATG
24979897 ATAAGCACCAAAGTGCAAATTAATA-A-CA
1 ATAAGCACCAAAGTGCAAATTAATACAGCA
* **
24979925 ATAAGCATCAAAGTGCAAATTTTTACAGCA
1 ATAAGCACCAAAGTGCAAATTAATACAGCA
** *
24979955 ATAAGCACCATTGTGCAAAATAAT
1 ATAAGCACCAAAGTGCAAATTAAT
24979979 TCGATAAGCG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
28 22 0.51
29 1 0.02
30 20 0.47
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (30 bp):
ATAAGCACCAAAGTGCAAATTAATACAGCA
Found at i:24982691 original size:15 final size:16
Alignment explanation
Indices: 24982671--24982700 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24982661 TAACAACTAA
24982671 TATATAA-ATATATTT
1 TATATAATATATATTT
24982686 TATATAATATATATT
1 TATATAATATATATT
24982701 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:24984292 original size:3 final size:3
Alignment explanation
Indices: 24984284--24984309 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
24984274 TGAGGATCCT
24984284 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
24984310 TCCTACAGTG
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24991947 original size:33 final size:33
Alignment explanation
Indices: 24991895--24991958 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
24991885 AACAAGCAGT
* * *
24991895 GACAGTCTGGGCCTGAGCCCTATTCAGTAACAG
1 GACAGTCTGGACCTGAGCCCAATACAGTAACAG
* *
24991928 GACAGTGTGGACCTTAGCCCAATACAGTAAC
1 GACAGTCTGGACCTGAGCCCAATACAGTAAC
24991959 GGTGTGGGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (33 bp):
GACAGTCTGGACCTGAGCCCAATACAGTAACAG
Found at i:24992528 original size:26 final size:27
Alignment explanation
Indices: 24992312--24992527 Score: 250
Period size: 27 Copynumber: 8.1 Consensus size: 27
24992302 TATAACAGTT
24992312 ATTTTA-CCTATGAGGGTATTTTAGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
24992338 ATTTTACCCTAT-AGAGGTATTTT-GATC
1 ATTTTACCCTATGAG-GGTATTTTAG-TC
* *
24992365 ATTTTACCCTATGAGGGTATTTAAGTT
1 ATTTTACCCTATGAGGGTATTTTAGTC
24992392 ATTTTACCCTAT-AGGGGTATTTTAGTC
1 ATTTTACCCTATGA-GGGTATTTTAGTC
* * *
24992419 ATTTTACCATATGAGAGTATTTCAGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
* **
24992446 ATTTTATCCTA--AGGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
24992471 ATTTTACCCTATGAGGGTATTTT-GATC
1 ATTTTACCCTATGAGGGTATTTTAG-TC
* *
24992498 A-TTTAACCTATGAGGGTATTTTGGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
24992524 ATTT
1 ATTT
24992528 ATTAACCTCT
Statistics
Matches: 164, Mismatches: 14, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
25 22 0.13
26 34 0.21
27 104 0.63
28 4 0.02
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTATGAGGGTATTTTAGTC
Found at i:24992774 original size:19 final size:17
Alignment explanation
Indices: 24992733--24992775 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
24992723 CATCCGTGTG
24992733 GGGCCCACAAGCCCTTT
1 GGGCCCACAAGCCCTTT
* *
24992750 GAGCCCACACTGCCCATTT
1 GGGCCCACA-AGCCC-TTT
24992769 GGGCCCA
1 GGGCCCA
24992776 ACGTGGCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.16
Consensus pattern (17 bp):
GGGCCCACAAGCCCTTT
Found at i:24995370 original size:25 final size:25
Alignment explanation
Indices: 24995328--24995390 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
24995318 TTAAGTGTTT
* *
24995328 TCAGTATAGT-CTATCTATAGTAGTC
1 TCAGTATA-TACTACCTATAGCAGTC
*
24995353 TCAGTATATACTACCTATAGCAGTT
1 TCAGTATATACTACCTATAGCAGTC
*
24995378 TCAGGATATACTA
1 TCAGTATATACTA
24995391 TCAAAGACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (25 bp):
TCAGTATATACTACCTATAGCAGTC
Found at i:24995754 original size:18 final size:19
Alignment explanation
Indices: 24995733--24995771 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
24995723 TTTCAAAACA
24995733 TTATTC-ATTTACAAAT-TT
1 TTATTCAATTT-CAAATGTT
24995751 TTATTCAATTTCAAATGTT
1 TTATTCAATTTCAAATGTT
24995770 TT
1 TT
24995772 CTTATTACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTCAATTTCAAATGTT
Found at i:25001196 original size:30 final size:30
Alignment explanation
Indices: 25001153--25001212 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
25001143 GAGACAGTTT
* *
25001153 GAAAGCAGTTTCAGATCGACAGAAATCTTA
1 GAAAGAAGATTCAGATCGACAGAAATCTTA
25001183 GAAAGAAGATTCAGATCGACAGAAATCTTA
1 GAAAGAAGATTCAGATCGACAGAAATCTTA
25001213 TTGGGATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (30 bp):
GAAAGAAGATTCAGATCGACAGAAATCTTA
Found at i:25002584 original size:16 final size:16
Alignment explanation
Indices: 25002563--25002594 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25002553 ATATTAGGGG
25002563 CAAAAGTGTAAATTTT
1 CAAAAGTGTAAATTTT
*
25002579 CAAAAGTGTGAATTTT
1 CAAAAGTGTAAATTTT
25002595 GGATTGAATT
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:0.06, G:0.16, T:0.38
Consensus pattern (16 bp):
CAAAAGTGTAAATTTT
Found at i:25006657 original size:42 final size:43
Alignment explanation
Indices: 25006596--25006704 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 43
25006586 AATTTGAGAT
* *
25006596 TTACGTGTATGACCATGTCTGGGACATTGACATCG-TATATGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
* * * *
25006638 TTACGTGTAAGACCCTGTCTTGGACAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
*
25006681 TTACATGTAA-ACCATGTCTGGGAC
1 TTACGTGTAAGACCATGTCTGGGAC
25006705 GTTGGCATTG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 42 0.74
43 15 0.26
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
Found at i:25006711 original size:42 final size:42
Alignment explanation
Indices: 25006557--25006712 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 42
25006547 TGAGATATAG
* * * * *
25006557 TGTAAGACCACGTCTGGGACGTTAGCATC-AATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGTATAT--GA-TTACA
* * * *
25006601 TGTATGACCATGTCTGGGACATTGACATCGTATATGATTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGTATATGATTACA
* * *
25006643 TGTAAGACCCTGTCTTGGACAG-TGGCATCGTTATTTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTTGGCATCG-TATATGATTACA
25006686 TGTAA-ACCATGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
25006713 TGTAGGAGCT
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 47 0.51
43 17 0.18
44 24 0.26
45 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGTATATGATTACA
Found at i:25013457 original size:13 final size:13
Alignment explanation
Indices: 25013439--25013463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25013429 GAATTAAAAT
25013439 GTGTGAAAATTTC
1 GTGTGAAAATTTC
25013452 GTGTGAAAATTT
1 GTGTGAAAATTT
25013464 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:25014636 original size:42 final size:43
Alignment explanation
Indices: 25014570--25014672 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 43
25014560 GATTTGAGAT
* * *
25014570 TTACGTGTAAGATCATGTCAAGGACATTGGCATCG-TATATGA
1 TTACGTGTAAGACCATATCAAGGACAGTGGCATCGTTATATGA
* * * *
25014612 TTACGTGTAAGACCCTATCTAGGACAGTGGCATTGTTATTTGA
1 TTACGTGTAAGACCATATCAAGGACAGTGGCATCGTTATATGA
* *
25014655 TTACATGTAAGATCATAT
1 TTACGTGTAAGACCATAT
25014673 TTGGGACGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 29 0.58
43 21 0.42
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (43 bp):
TTACGTGTAAGACCATATCAAGGACAGTGGCATCGTTATATGA
Found at i:25014686 original size:43 final size:42
Alignment explanation
Indices: 25014529--25014692 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 42
25014519 ATATGAGAAT
* **
25014529 CGTGTAAGACCACGTCTAGGACGTTGGCATTG-ATTTGAGATTTA
1 CGTGTAAGATCATATCTAGGACGTTGGCATTGTATTT--GA-TTA
* * * * *
25014573 CGTGTAAGATCATGTCAAGGACATTGGCATCGTATATGATTA
1 CGTGTAAGATCATATCTAGGACGTTGGCATTGTATTTGATTA
* *
25014615 CGTGTAAGACCCTATCTAGGACAG-TGGCATTGTTATTTGATTA
1 CGTGTAAGATCATATCTAGGAC-GTTGGCATTG-TATTTGATTA
* * *
25014658 CATGTAAGATCATATTTGGGACGTTGGCATTGTAT
1 CGTGTAAGATCATATCTAGGACGTTGGCATTGTAT
25014693 GAGCTTTTTG
Statistics
Matches: 98, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
42 32 0.33
43 36 0.37
44 27 0.28
45 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (42 bp):
CGTGTAAGATCATATCTAGGACGTTGGCATTGTATTTGATTA
Found at i:25017896 original size:21 final size:21
Alignment explanation
Indices: 25017867--25017908 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25017857 ACGGAAATTG
*
25017867 AAAAGGTAAGACATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
* *
25017888 AAAATGTAACCCATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
25017909 TGTTTTGGAG
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:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAGGTAACACATTTTCCCT
Found at i:25021700 original size:27 final size:27
Alignment explanation
Indices: 25021678--25021850 Score: 211
Period size: 27 Copynumber: 6.4 Consensus size: 27
25021668 AAGTATAACA
* *
25021678 GTCATTTTACCTTATGGGGGTATTTAG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
25021705 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
25021732 ATCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
25021759 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
25021786 GTTATTTTACCATATGAGAGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
25021813 GCCATTTTACCTTATGGGAGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
25021840 GTCATTTTACC
1 GTCATTTTACC
25021851 TATTTTGGGA
Statistics
Matches: 126, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:25025216 original size:27 final size:27
Alignment explanation
Indices: 25025159--25025329 Score: 256
Period size: 27 Copynumber: 6.4 Consensus size: 27
25025149 GGGTATAATA
25025159 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
25025185 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
25025212 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
25025239 GTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
25025266 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
25025292 GTCATTTTACCTTATGGGAGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
25025319 GTCATTTTACC
1 GTCATTTTACC
25025330 TATTTTGGGG
Statistics
Matches: 130, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
26 38 0.29
27 92 0.71
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:25025216 original size:53 final size:53
Alignment explanation
Indices: 25025159--25025329 Score: 288
Period size: 53 Copynumber: 3.2 Consensus size: 53
25025149 GGGTATAATA
* *
25025159 GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
**
25025212 GTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
*
25025266 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGAGTATTTTG
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
25025319 GTCATTTTACC
1 GTCATTTTACC
25025330 TATTTTGGGG
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 61 0.55
54 49 0.45
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.44
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
Found at i:25031045 original size:41 final size:41
Alignment explanation
Indices: 25030852--25031034 Score: 287
Period size: 41 Copynumber: 4.5 Consensus size: 41
25030842 GATAATTTAG
25030852 ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTCAA
1 ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTCAA
25030893 ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTCAA
1 ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTCAA
* *
25030934 ACTTTACGTCTAGAAGGCTTGATGCTGAG-GAAATGTTTCAG
1 ACTTTACGTCTAGCAGGCTTGATGCTG-GTGAAATGTTTCAA
* * * **
25030975 ACTTTACGTCTAGCAAGCTTGATGCCGGTGAAATATTTCGT
1 ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTCAA
25031016 ACTTTACGTCTAGCAGGCT
1 ACTTTACGTCTAGCAGGCT
25031035 AATTGTCGGT
Statistics
Matches: 131, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 1 0.01
41 129 0.98
42 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTCAA
Found at i:25032107 original size:23 final size:22
Alignment explanation
Indices: 25032072--25032117 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
25032062 TGCTTACTTA
* *
25032072 TATTTATTTAAATTCATATATT
1 TATTTATTAAAATGCATATATT
25032094 TATTGTATTAAAATGCATATATT
1 TATT-TATTAAAATGCATATATT
25032117 T
1 T
25032118 TGATTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
TATTTATTAAAATGCATATATT
Found at i:25034168 original size:41 final size:40
Alignment explanation
Indices: 25034101--25034180 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
25034091 AATACCGACC
*
25034101 TTTTCATTGATATCTTATTTGTATATCGTCCTTTTCAACA
1 TTTTCATTGATATCTTATTTGGATATCGTCCTTTTCAACA
25034141 TTTTCATTTGATATCCTT-TTTGGATATCGTCCTTTTCAAC
1 TTTTCA-TTGATAT-CTTATTTGGATATCGTCCTTTTCAAC
25034181 CTATTATTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 6 0.16
41 28 0.76
42 3 0.08
ACGTcount: A:0.20, C:0.19, G:0.09, T:0.53
Consensus pattern (40 bp):
TTTTCATTGATATCTTATTTGGATATCGTCCTTTTCAACA
Found at i:25034353 original size:70 final size:70
Alignment explanation
Indices: 25034237--25034373 Score: 195
Period size: 70 Copynumber: 2.0 Consensus size: 70
25034227 TTCACCTGGC
* * **
25034237 GCTAGTCGGATAAACCAATGATAGGTGTGCTCTTTACTAGTCGGATAAACAT-ACAACATCTTGT
1 GCTAGTCGGATAAACCAAGGATAGGTGTGCCCTGCACTAGTCGGATAAAC-TGACAACATCTTGT
25034301 GCCAAT
65 GCCAAT
* * *
25034307 GCTAGTCGGATAAACCGAGGATAGGTGTGCCCTGCAGTAGTTGGATAAACTGACAACATCTTGTG
1 GCTAGTCGGATAAACCAAGGATAGGTGTGCCCTGCACTAGTCGGATAAACTGACAACATCTTGTG
25034372 CC
66 CC
25034374 CAGTTCTAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 1 0.02
70 58 0.98
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (70 bp):
GCTAGTCGGATAAACCAAGGATAGGTGTGCCCTGCACTAGTCGGATAAACTGACAACATCTTGTG
CCAAT
Found at i:25037411 original size:37 final size:36
Alignment explanation
Indices: 25037370--25037447 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 36
25037360 TTATTGATTA
*
25037370 GATTAGCTTTTAGGAGCGATTGGCGTGTTATCGAG-TG
1 GATTAGCTCTTAGGAGCGATTGGCGTGTT-TC-AGTTG
*
25037407 GATTAGCTCTTATGAGCGATTGGCGTGTTTCAGTTG
1 GATTAGCTCTTAGGAGCGATTGGCGTGTTTCAGTTG
25037443 GATTA
1 GATTA
25037448 CTTGTGTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 2 0.05
36 9 0.24
37 27 0.71
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.37
Consensus pattern (36 bp):
GATTAGCTCTTAGGAGCGATTGGCGTGTTTCAGTTG
Found at i:25041151 original size:36 final size:36
Alignment explanation
Indices: 25041111--25041179 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
25041101 ATGTCATTCA
*
25041111 ATGGTTTAGCATTTGTTGTGAATCATCAAATGTGTG
1 ATGGTTTAGCATTTGTTGCGAATCATCAAATGTGTG
25041147 ATGGTTTAGCATTTGTTGCGAATCATCAAATGT
1 ATGGTTTAGCATTTGTTGCGAATCATCAAATGT
25041180 ACACTGTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (36 bp):
ATGGTTTAGCATTTGTTGCGAATCATCAAATGTGTG
Found at i:25049552 original size:6 final size:6
Alignment explanation
Indices: 25049543--25049567 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25049533 TAAAGATGAA
25049543 GAGAGG GAGAGG GAGAGG GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG G
25049568 GGTTAGGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:25051443 original size:18 final size:18
Alignment explanation
Indices: 25051420--25051454 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25051410 GGCTTAGTAC
25051420 CCAAAC-TAAAGCCCAAAA
1 CCAAACTTAAA-CCCAAAA
25051438 CCAAACTTAAACCCAAA
1 CCAAACTTAAACCCAAA
25051455 CCTACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.34, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAACTTAAACCCAAAA
Found at i:25061075 original size:44 final size:43
Alignment explanation
Indices: 25061025--25061137 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 43
25061015 AAGGGTGAGA
*
25061025 AGTAAAATTTTAAGGGGAAAATAAAAAGTTTGGGGGGTTGATA-G
1 AGTAAAATTTT-AGGGGAAAGTAAAAAGTTTGGGGGGTTGA-AGG
*** *
25061069 AGTAAAATTTTAGAGGGAAAGTAAATTTTTTTGGGGGTTGAAGG
1 AGTAAAATTTTAG-GGGAAAGTAAAAAGTTTGGGGGGTTGAAGG
* *
25061113 AGTAAATTTTTGGGGGGAAAGTAAA
1 AGTAAAATTTT-AGGGGAAAGTAAA
25061138 GAGGTTCGGG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.05
44 55 0.93
45 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (43 bp):
AGTAAAATTTTAGGGGAAAGTAAAAAGTTTGGGGGGTTGAAGG
Found at i:25061137 original size:19 final size:19
Alignment explanation
Indices: 25061069--25061137 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 19
25061059 GGGTTGATAG
* * *
25061069 AGTAAAATTTTAGAGGGAA
1 AGTAAATTTTTGGGGGGAA
25061088 AGTAAATTTTTTTGGGGGTTGAA
1 AGTAAA--TTTTTGGGGG--GAA
25061111 GGAGTAAATTTTTGGGGGGAA
1 --AGTAAATTTTTGGGGGGAA
25061132 AGTAAA
1 AGTAAA
25061138 GAGGTTCGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
19 12 0.29
21 10 0.24
23 13 0.32
25 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (19 bp):
AGTAAATTTTTGGGGGGAA
Found at i:25062759 original size:20 final size:20
Alignment explanation
Indices: 25062734--25062775 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
25062724 TTTATGTTAG
25062734 TATATATTTATAATTGAAAA
1 TATATATTTATAATTGAAAA
*
25062754 TATATATTTATAGTTGAAAA
1 TATATATTTATAATTGAAAA
25062774 TA
1 TA
25062776 AGTTATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TATATATTTATAATTGAAAA
Found at i:25062810 original size:3 final size:3
Alignment explanation
Indices: 25062802--25062853 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
25062792 TGTTGCTAAA
* * *
25062802 TAT TAT TAT GAT TAT TAT TAT CAT TAT TAT TAC TACT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT
25062848 TAT TAT
1 TAT TAT
25062854 GGTAATTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.85
4 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:25067095 original size:37 final size:37
Alignment explanation
Indices: 25067045--25067123 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
25067035 TTATTACGAA
* *
25067045 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
25067082 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
25067119 GTCTT
1 GTCTT
25067124 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:25067320 original size:47 final size:47
Alignment explanation
Indices: 25067242--25067893 Score: 1040
Period size: 47 Copynumber: 14.1 Consensus size: 47
25067232 CCCTTCGGGA
* * * * * * *
25067242 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
25067289 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
25067336 CTTATCACATATATACATTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
25067383 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25067430 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25067477 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25067524 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
25067571 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
25067618 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
25067665 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
25067712 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25067761 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25067808 CTTATCACATATATACACTTTCACA-T--T--CAT--G----T-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25067843 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25067890 CTTA
1 CTTA
25067894 CTATCATTTC
Statistics
Matches: 568, Mismatches: 23, Indels: 28
0.92 0.04 0.05
Matches are distributed among these distances:
35 28 0.05
36 2 0.00
38 1 0.00
40 4 0.01
42 4 0.01
44 1 0.00
46 2 0.00
47 481 0.85
49 45 0.08
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:25067833 original size:16 final size:16
Alignment explanation
Indices: 25067812--25067868 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
25067802 TTAGGCCTTA
25067812 TCACATATATACACTT
1 TCACATATATACACTT
* *
25067828 TCACATTCATGTGGC-CTT
1 TCACA-T-ATAT-ACACTT
25067846 ATCACATATATACACTT
1 -TCACATATATACACTT
25067863 TCACAT
1 TCACAT
25067869 TCATCACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 12 0.38
17 7 0.22
18 7 0.22
19 6 0.19
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (16 bp):
TCACATATATACACTT
Found at i:25067845 original size:35 final size:35
Alignment explanation
Indices: 25067805--25067872 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
25067795 TCGGCCATTA
25067805 GGCCTTATCACATATATACACTTTCACATTCATGT
1 GGCCTTATCACATATATACACTTTCACATTCATGT
25067840 GGCCTTATCACATATATACACTTTCACATTCAT
1 GGCCTTATCACATATATACACTTTCACATTCAT
25067873 CACATCGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.37
Consensus pattern (35 bp):
GGCCTTATCACATATATACACTTTCACATTCATGT
Found at i:25076214 original size:139 final size:141
Alignment explanation
Indices: 25076018--25076319 Score: 410
Period size: 139 Copynumber: 2.2 Consensus size: 141
25076008 GATCCGTCAC
* * * *
25076018 CTTGGGTTGCCCGGCAACAATGACGATATACATTTACATAATACCATCTCAGATTGCCCAACAAC
1 CTTGGGTTGCCTGGCAACGATGACGATATACATGTACATAATACCACCTCAGATTGCCCAACAAC
* * * *
25076083 GATGGCATTCTCAATCTGATTAATCTGTCA-CCTTGGTTTCCCGACAAAGATGACACACCGAGTA
66 GATGGCATTCTCAATCTGATTAATCTGTCACCCTGGGCTACCCGACAAAGATGACACACCAAGTA
25076147 CAATCTACCAT
131 CAATCTACCAT
* * * *
25076158 TTTGGG-TGCCTGGCAACGATGACGCTATACATGTACATAATACCACCTCAGGTTGCCCGACAAC
1 CTTGGGTTGCCTGGCAACGATGACGATATACATGTACATAATACCACCTCAGATTGCCCAACAAC
* * * * * *
25076222 GATGGCTTTCTCAATCTGATTAATTTGTCACCCTGGGCTACCCGACCAAGATGACTCACTAATTA
66 GATGGCATTCTCAATCTGATTAATCTGTCACCCTGGGCTACCCGACAAAGATGACACACCAAGTA
25076287 CAATCTACCAT
131 CAATCTACCAT
* *
25076298 CCTGGGTTGCCTAGCAACGATG
1 CTTGGGTTGCCTGGCAACGATG
25076320 GTTATCAATC
Statistics
Matches: 139, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
139 79 0.57
140 46 0.33
141 14 0.10
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (141 bp):
CTTGGGTTGCCTGGCAACGATGACGATATACATGTACATAATACCACCTCAGATTGCCCAACAAC
GATGGCATTCTCAATCTGATTAATCTGTCACCCTGGGCTACCCGACAAAGATGACACACCAAGTA
CAATCTACCAT
Found at i:25080740 original size:19 final size:19
Alignment explanation
Indices: 25080714--25080752 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
25080704 AAATATAGAG
*
25080714 AAATTTGAGAG-AAATAAT
1 AAATTTGAAAGAAAATAAT
25080732 AAATATTGAAAGAAAATAAT
1 AAAT-TTGAAAGAAAATAAT
25080752 A
1 A
25080753 GGGGGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (19 bp):
AAATTTGAAAGAAAATAAT
Found at i:25083367 original size:27 final size:27
Alignment explanation
Indices: 25083336--25083390 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
25083326 AATGATCAAA
25083336 TCTGAAACACATTTTAGCAATGAATAG
1 TCTGAAACACATTTTAGCAATGAATAG
25083363 TCTGAAACACATTTTAGCAATGAATAG
1 TCTGAAACACATTTTAGCAATGAATAG
25083390 T
1 T
25083391 TACACAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (27 bp):
TCTGAAACACATTTTAGCAATGAATAG
Found at i:25085217 original size:45 final size:45
Alignment explanation
Indices: 25085153--25085327 Score: 235
Period size: 45 Copynumber: 3.9 Consensus size: 45
25085143 CTTTCCTTTC
** * * *
25085153 TGGCTGTGCAGCCTTTTTGGAATGACTCTCATCAGGAACAGTCTT
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
* ** * *
25085198 TGGCTGTGCTGCCTTTTTGGATTGACTCTCATCAGGTATACTTTT
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
25085243 TGGCTGTGCAGCCTTTTCAG-ATCGACTCTCATCAGGTATACTCTT
1 TGGCTGTGCAGCCTTTTCAGAAT-GACTCTCATCAGGTATACTCTT
*
25085288 TGGCTGAGCAGCCTTTTCAGAATGACTCTCATCAGGTATA
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATA
25085328 GACCCACTTG
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.01
45 113 0.97
46 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (45 bp):
TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
Found at i:25086112 original size:47 final size:48
Alignment explanation
Indices: 25086055--25086150 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 48
25086045 ATTAAGGAGA
25086055 ATAAAGCAGTTATAACTTC-A-AAGAAGACATAACAGATTTTATTAAGC
1 ATAAAGCAGTTATAACTTCAAGAAGAAGACATAACAGATTTTA-TAAGC
* * *
25086102 ATAAATCAGTTGTAACTTCAATGAAGAAGGCATAACAGATTTTATAAGC
1 ATAAAGCAGTTATAACTTCAA-GAAGAAGACATAACAGATTTTATAAGC
25086151 CAACAACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 17 0.40
48 1 0.02
49 5 0.12
50 20 0.47
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (48 bp):
ATAAAGCAGTTATAACTTCAAGAAGAAGACATAACAGATTTTATAAGC
Found at i:25088182 original size:94 final size:94
Alignment explanation
Indices: 25088019--25088211 Score: 350
Period size: 94 Copynumber: 2.1 Consensus size: 94
25088009 AAAAAGCATC
*
25088019 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGTACCTAAAATAC
1 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAC
*
25088084 TAAGACAATCAGTCAGTTGTAGCATGATT
66 TAAGACAATCAGTCAGTGGTAGCATGATT
* *
25088113 CACTAACGTGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAT
1 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAC
25088178 TAAGACAATCAGTCAGTGGTAGCATGATT
66 TAAGACAATCAGTCAGTGGTAGCATGATT
25088207 CACTA
1 CACTA
25088212 GTCACGAAAC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (94 bp):
CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAC
TAAGACAATCAGTCAGTGGTAGCATGATT
Found at i:25093474 original size:24 final size:23
Alignment explanation
Indices: 25093432--25093491 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 23
25093422 ATTAAATTAT
25093432 AAATTTATTTATTAAATTATAAAATA
1 AAATTTA--TATTAAATTAT-AAATA
*
25093458 AAATTTATATTACATTATAAATA
1 AAATTTATATTAAATTATAAATA
25093481 AAATTTCATAT
1 AAATTT-ATAT
25093492 AATTATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 11 0.34
24 14 0.44
26 7 0.22
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATTTATATTAAATTATAAATA
Found at i:25094164 original size:13 final size:12
Alignment explanation
Indices: 25094128--25094169 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
25094118 ATCATATTTG
*
25094128 ATTTTTATATCA
1 ATTTTTATATAA
25094140 ATTTTT-TATAA
1 ATTTTTATATAA
25094151 ATTTATTATATAAA
1 ATTT-TTATAT-AA
25094165 ATTTT
1 ATTTT
25094170 CATCCATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.31
12 8 0.31
13 4 0.15
14 6 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTTTATATAA
Found at i:25094331 original size:14 final size:14
Alignment explanation
Indices: 25094311--25094349 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
25094301 TTATTTCATT
*
25094311 AAAAATGATTTCTG
1 AAAAATGATTTCTA
*
25094325 GAAAATGATTTCTA
1 AAAAATGATTTCTA
25094339 AAAAATGATTT
1 AAAAATGATTT
25094350 ACTTTTCTGG
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:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (14 bp):
AAAAATGATTTCTA
Found at i:25094830 original size:19 final size:19
Alignment explanation
Indices: 25094792--25094830 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
25094782 TTATACTACA
**
25094792 AAATATTTATAATTGTAAT
1 AAATATTTATAATTAAAAT
*
25094811 AAATATTTATTATTAAAAT
1 AAATATTTATAATTAAAAT
25094830 A
1 A
25094831 TTAATGTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAATATTTATAATTAAAAT
Found at i:25094896 original size:16 final size:16
Alignment explanation
Indices: 25094865--25094901 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
25094855 ATGTGAATAA
25094865 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
25094881 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
25094897 TATTA
1 TATTA
25094902 AAATAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:25094953 original size:22 final size:21
Alignment explanation
Indices: 25094913--25094965 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
25094903 AATAAGATTG
*
25094913 AAATATTAAA-TAATTTATTA
1 AAATAATAAATTAATTTATTA
25094933 AAATAATAAATTATATTTATTA
1 AAATAATAAATTA-ATTTATTA
* *
25094955 TATTAATAAAT
1 AAATAATAAAT
25094966 ATGAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
21 2 0.07
22 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAATAAATTAATTTATTA
Found at i:25113039 original size:106 final size:106
Alignment explanation
Indices: 25112883--25113077 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 106
25112873 ATCCAAGGAA
*
25112883 ACAAAGAGAGTTAACACGAGCATAACAACAATAATTCCACTACAATGTAATCGAACCAAATATCA
1 ACAAAGAGAGTTAACACGAGCATAACAACAATAATACCACTACAATGTAATCGAACCAAATATCA
*
25112948 TAAAACTTGTACTCTGATTGGTTGATCTGATATCGGAGAAC
66 TAAAACTTGTACTCTGATCGGTTGATCTGATATCGGAGAAC
** ** * * * *
25112989 ACAAAGAGAGTTAACACGAGCATGTCAACGGTGAA-ACCACTGCAATGTAATTGAGCCAAATTTC
1 ACAAAGAGAGTTAACACGAGCATAACAACAAT-AATACCACTACAATGTAATCGAACCAAATATC
*
25113053 ATAAAATTTGTACTCTGATCGGTTG
65 ATAAAACTTGTACTCTGATCGGTTG
25113078 TTGCGACAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 75 0.97
107 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (106 bp):
ACAAAGAGAGTTAACACGAGCATAACAACAATAATACCACTACAATGTAATCGAACCAAATATCA
TAAAACTTGTACTCTGATCGGTTGATCTGATATCGGAGAAC
Found at i:25115690 original size:19 final size:19
Alignment explanation
Indices: 25115666--25115776 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
25115656 AATCATATCT
*
25115666 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
**
25115685 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
25115704 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
25115723 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
25115742 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
25115761 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
25115777 CCTGAAGATT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:25115713 original size:38 final size:38
Alignment explanation
Indices: 25115666--25115769 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
25115656 AATCATATCT
*
25115666 TCTAAGATTGTATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
25115704 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
25115742 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
25115770 GCATATCCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:25120017 original size:11 final size:11
Alignment explanation
Indices: 25120001--25120031 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
25119991 TTTAAGGTGA
25120001 GTAATGTAATT
1 GTAATGTAATT
25120012 GTAATGTAATT
1 GTAATGTAATT
*
25120023 GAAATGTAA
1 GTAATGTAA
25120032 AATGTTACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (11 bp):
GTAATGTAATT
Found at i:25123402 original size:16 final size:16
Alignment explanation
Indices: 25123381--25123413 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25123371 AGTCCTTGTA
25123381 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
25123397 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
25123413 A
1 A
25123414 ACAAAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:25129994 original size:43 final size:43
Alignment explanation
Indices: 25129947--25130071 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
25129937 TGTAATCTCG
*
25129947 TATCGATGCCAATAGCCCAGCCATGGTCTTACACGAAATCACA
1 TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
* * * *
25129990 TATCGATGTCAAT-GTCCCAGACATGGTCTTACATGAATTCTCA
1 TATCGATGCCAATAG-CCCAGACATGGTCTTACACGAAATCACA
* * * *
25130033 TATCGATGCC-ATATCCCAAATATGGTCTTACACGTAATC
1 TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATC
25130072 TCGGTAACCC
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 23 0.34
43 45 0.66
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
Found at i:25137354 original size:24 final size:24
Alignment explanation
Indices: 25137316--25137362 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25137306 AGACTGTGTG
*
25137316 CATTTTAAAATTTGGTTTTATTTT
1 CATTTTAAAATTTGGGTTTATTTT
25137340 CATTTATAAAA-TTGGGTTTATTT
1 CATTT-TAAAATTTGGGTTTATTT
25137363 AGGTTTGCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (24 bp):
CATTTTAAAATTTGGGTTTATTTT
Found at i:25151515 original size:87 final size:87
Alignment explanation
Indices: 25151367--25152570 Score: 1952
Period size: 87 Copynumber: 13.9 Consensus size: 87
25151357 AAGATAGCAG
25151367 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25151432 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* * **
25151454 ATCCTATCTCCCTAAGCAATAGTGGAGTGGATCAAAGACGGCGAATCTCATCTTCTGCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25151519 GGGAAACAAATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
*
25151541 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAAGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25151606 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* *
25151628 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACAGCGAATCTCATCTTCCTCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25151693 AGGAAACAGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* *
25151715 ATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25151780 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* * * *
25151802 ATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAATATGGCGAATCTCATCTTCCCTAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25151867 GGGAAACAGATTTAGAACATTA
66 GGGAAACAGATTTAGACCATTA
* * * *
25151889 ATCCCATCTCCCTAAGCAATAGTGGAGCGTATCGAAGACTGCGAATCTCATCTTCCTCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25151954 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* * *
25151976 ATTCTATCTCCCTAAGAAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCACAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
25152041 GGGAAACAGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* *
25152063 ATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAATACGGCGAATCTCATCTTCCCCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25152128 GGGAAACAGATTTATACCATTA
66 GGGAAACAGATTTAGACCATTA
*
25152150 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGTGAATCTCATCTTCCCCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25152215 GGGAAACATATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* *
25152237 ATCCCATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCACAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25152302 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* * *
25152324 ATCCTATCTCCCTAAGCAATAGTAGAGCGGATCGAAAACGGCGAATCTCATCTTCCCTAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
25152389 -GG-----GATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* * *
25152405 ATCCCATCTCCCTAAACAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
25152470 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* * * *
25152492 ATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCAAATCTCATATTCCCCAGGAATA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
25152557 GGGAAACAGATTTA
66 GGGAAACAGATTTA
25152571 AGCCACAAAT
Statistics
Matches: 1027, Mismatches: 84, Indels: 12
0.91 0.07 0.01
Matches are distributed among these distances:
81 73 0.07
82 2 0.00
86 2 0.00
87 950 0.93
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (87 bp):
ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
GGGAAACAGATTTAGACCATTA
Found at i:25156511 original size:22 final size:21
Alignment explanation
Indices: 25156467--25156511 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
25156457 ACTAAAATTG
*
25156467 AATTATAATTTTTTATATATT
1 AATTATAATTTTTTAGATATT
* *
25156488 AATTTTAATTTTTTTAGATTTT
1 AATTATAA-TTTTTTAGATATT
25156510 AA
1 AA
25156512 AAGGGGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTATAATTTTTTAGATATT
Found at i:25158844 original size:46 final size:44
Alignment explanation
Indices: 25158740--25158847 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
25158730 TGTCTTTAAC
** * * *
25158740 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
25158784 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
25158830 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
25158848 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:25159181 original size:4 final size:4
Alignment explanation
Indices: 25159172--25159203 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
25159162 CCTTTTTCTT
25159172 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
25159204 CTTCCTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:25159285 original size:15 final size:16
Alignment explanation
Indices: 25159253--25159299 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
25159243 GTTTCGTCTC
* *
25159253 TTCTATTCTGTTTCTT
1 TTCTATTCTTTTTTTT
25159269 TTCT-TTCTTTTTTTT
1 TTCTATTCTTTTTTTT
25159284 TTCTATTCTTTCTTTT
1 TTCTATTCTTT-TTTT
25159300 GTTTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 13 0.48
16 10 0.37
17 4 0.15
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (16 bp):
TTCTATTCTTTTTTTT
Found at i:25159286 original size:20 final size:21
Alignment explanation
Indices: 25159263--25159304 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
25159253 TTCTATTCTG
*
25159263 TTTCTTTTCTTTCTTTT-TTT
1 TTTCTATTCTTTCTTTTGTTT
25159283 TTTCTATTCTTTCTTTTGTTT
1 TTTCTATTCTTTCTTTTGTTT
25159304 T
1 T
25159305 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTCTATTCTTTCTTTTGTTT
Found at i:25159321 original size:5 final size:5
Alignment explanation
Indices: 25159308--25159380 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
25159298 TTGTTTTATG
25159308 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
25159356 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
25159381 TTTTTAACAC
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Done.