Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_pilon, whole genome shotgun sequence
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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 17
Found at i:991060 original size:13 final size:13
Alignment explanation
Indices: 991029--991070 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
991019 TCATATATAG
991029 TTTTGAAAACATA
1 TTTTGAAAACATA
991042 TTTTTTGAAAACATA
1 --TTTTGAAAACATA
*
991057 TTTTAAAAACATA
1 TTTTGAAAACATA
991070 T
1 T
991071 ATATAGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (13 bp):
TTTTGAAAACATA
Found at i:991072 original size:15 final size:15
Alignment explanation
Indices: 991023--991072 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
991013 TTAAAATCAT
991023 ATATAGTTTTGAAAAC
1 ATATA-TTTTGAAAAC
*
991039 ATATTTTTTGAAAAC
1 ATATATTTTGAAAAC
*
991054 --ATATTTTAAAAAC
1 ATATATTTTGAAAAC
991067 ATATAT
1 ATATAT
991073 ATAGTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 11 0.38
15 14 0.48
16 4 0.14
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
ATATATTTTGAAAAC
Found at i:991139 original size:17 final size:17
Alignment explanation
Indices: 991119--991153 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
991109 AATATATAAA
*
991119 TTTTGAAAACATATTAT
1 TTTTGAAAACATAATAT
991136 TTTTGAAAACATAATAT
1 TTTTGAAAACATAATAT
991153 T
1 T
991154 ATAAAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (17 bp):
TTTTGAAAACATAATAT
Found at i:992416 original size:4 final size:4
Alignment explanation
Indices: 992409--992468 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
992399 TTAAATTTAA
* *
992409 ATTT ATTTT ATTT ATTT A-AT ATTT ATTTT ATTTT ATTTT AATT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT A-TTT A-TTT A-TTT ATTT ATTT
992456 ATTT ACTTT ATTT
1 ATTT A-TTT ATTT
992469 TAACCCTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
3 2 0.04
4 24 0.50
5 22 0.46
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:992423 original size:9 final size:9
Alignment explanation
Indices: 992409--992468 Score: 68
Period size: 9 Copynumber: 6.4 Consensus size: 9
992399 TTAAATTTAA
992409 ATTTATTTT
1 ATTTATTTT
992418 ATTTATTTAAT
1 ATTTATTT--T
992429 ATTTATTTT
1 ATTTATTTT
992438 ATTTTATTTT
1 A-TTTATTTT
*
992448 AATTA-TTT
1 ATTTATTTT
*
992456 ATTTACTTT
1 ATTTATTTT
992465 ATTT
1 ATTT
992469 TAACCCTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
8 7 0.16
9 20 0.44
10 9 0.20
11 9 0.20
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTATTTT
Found at i:992425 original size:25 final size:25
Alignment explanation
Indices: 992379--992470 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
992369 TTTTCCTTTT
** *
992379 TTTAATTTAATTCAATTAATTTAA-A
1 TTTAATTT-ATTTTATTTATTTAATA
992404 TTTAAATTTATTTTATTTATTTAATA
1 TTT-AATTTATTTTATTTATTTAATA
* * *
992430 TTTATTTTATTTTATTTTAATTATTTA
1 TTTAATTTATTTTA-TTTATTTA-ATA
*
992457 TTTACTTTATTTTA
1 TTTAATTTATTTTA
992471 ACCCTAATGC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 25 0.45
26 16 0.29
27 15 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTAATTTATTTTATTTATTTAATA
Found at i:1001433 original size:22 final size:22
Alignment explanation
Indices: 1001407--1001466 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
1001397 TTAGTGCAGA
1001407 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
1001429 GGGAACCGATTCCCCC-TGTAG
1 GGGAATCGATACCCCCTTGAAG
1001450 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
1001467 GAGGGTTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:1003009 original size:18 final size:19
Alignment explanation
Indices: 1002983--1003035 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
1002973 CGATGATGAG
*
1002983 CAAGAACAACAC-GAGGAA
1 CAAGAACAACACAGAAGAA
*
1003001 CAAGCACAAC-CAGAAGAA
1 CAAGAACAACACAGAAGAA
*
1003019 CAAGTACAACA-AGAAGA
1 CAAGAACAACACAGAAGA
1003036 TCAAATGCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.57, C:0.23, G:0.19, T:0.02
Consensus pattern (19 bp):
CAAGAACAACACAGAAGAA
Found at i:1005491 original size:16 final size:16
Alignment explanation
Indices: 1005462--1005501 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1005452 TTAAATAAAG
1005462 AAAA-TAAAAATGCAT
1 AAAATTAAAAATGCAT
* *
1005477 AAATTTAAAAGTGCAT
1 AAAATTAAAAATGCAT
1005493 AAAATTAAA
1 AAAATTAAA
1005502 TATCAGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (16 bp):
AAAATTAAAAATGCAT
Found at i:1005590 original size:31 final size:30
Alignment explanation
Indices: 1005528--1005597 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
1005518 CAATAAAAAT
* **
1005528 AAAATGTTAGTAGTTAGTAATTAGCGGTTAG
1 AAAA-GTTAGTAGTTAGAAATTAGCAATTAG
* *
1005559 AAAGGTTAGTTGTTAGAAAATTAGCAATTAG
1 AAAAGTTAGTAGTTAG-AAATTAGCAATTAG
1005590 AAAAGTTA
1 AAAAGTTA
1005598 ACAGTTAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAAGTTAGTAGTTAGAAATTAGCAATTAG
Found at i:1005883 original size:127 final size:129
Alignment explanation
Indices: 1005704--1005984 Score: 376
Period size: 127 Copynumber: 2.2 Consensus size: 129
1005694 AAATAAAATA
* * * *
1005704 AATAAAA-AAAAGTTAGTGGGTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCC-GAATC
1 AATAAAATAAAAGTTAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAG-ATC
* * * *
1005767 G-GATCACCATAAGGTCG-ATTCAAATATTAGAAACAATAAATAAAT-A-AACAATTGTTAGAGT
65 GAG-TCACCACAAGATCGAATT-AAATATTAGAAACAATAAATAAATAATAACAATGGTTAAAGT
*
1005828 GC
128 AC
*
1005830 AATAAAATAAAAGTCAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAGATCG
1 AATAAAATAAAAGTTAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAGATCG
*
1005895 AGTCACCACAAGATCGAATTGAATATTAGAAACAATAAATAAATAAATAACAATGGTTAAAGTAC
66 AGTCACCACAAGATCGAATTAAATATTAGAAACAATAAATAAAT-AATAACAATGGTTAAAGTAC
*
1005960 AATAAAATAAAAATTAGTAGTTAGC
1 AATAAAATAAAAGTTAGTAGTTAGC
1005985 TTGAAATAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
126 7 0.05
127 85 0.63
128 5 0.04
129 1 0.01
130 37 0.27
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.23
Consensus pattern (129 bp):
AATAAAATAAAAGTTAGTAGTTAGCAGAGTCCGAACCATAACAATGTGAATCATACCCCAGATCG
AGTCACCACAAGATCGAATTAAATATTAGAAACAATAAATAAATAATAACAATGGTTAAAGTAC
Found at i:1008880 original size:33 final size:33
Alignment explanation
Indices: 1008831--1008905 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1008821 GATTGAATTG
* * *
1008831 TTGTTTCCTATCGACTTAATCGCTAAGTAATCT
1 TTGTTTCTTATAGACTTAATCGCTAAGTAATCA
1008864 TTGTTTCTTATAGACTTAATCGCTAAGTAATCA
1 TTGTTTCTTATAGACTTAATCGCTAAGTAATCA
1008897 TTGTTTCTT
1 TTGTTTCTT
1008906 TTTGTTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (33 bp):
TTGTTTCTTATAGACTTAATCGCTAAGTAATCA
Found at i:1025040 original size:56 final size:55
Alignment explanation
Indices: 1024973--1025077 Score: 165
Period size: 56 Copynumber: 1.9 Consensus size: 55
1024963 TTTTAGGCAC
* * *
1024973 TTGCCATGGTGAGTGCAAATGATTGCCATGGCATTTTTTTGGTGTAGAAAAGGTAA
1 TTGCCATGGTGAGTGCAAATGAATGCCATGACATTTTTGT-GTGTAGAAAAGGTAA
*
1025029 TTGCCATGGTGAGTGCAAATGAATGCCGTGACATTTTTGTGTGTAGAAA
1 TTGCCATGGTGAGTGCAAATGAATGCCATGACATTTTTGTGTGTAGAAA
1025078 TGATATTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 9 0.20
56 36 0.80
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (55 bp):
TTGCCATGGTGAGTGCAAATGAATGCCATGACATTTTTGTGTGTAGAAAAGGTAA
Found at i:1026153 original size:13 final size:13
Alignment explanation
Indices: 1026135--1026165 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1026125 TTGTTCATAA
1026135 CATCATAACTCAC
1 CATCATAACTCAC
*
1026148 CATCATAACTTAC
1 CATCATAACTCAC
1026161 CATCA
1 CATCA
1026166 CATCTCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (13 bp):
CATCATAACTCAC
Found at i:1030754 original size:30 final size:30
Alignment explanation
Indices: 1030720--1030794 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
1030710 AAATGGATTT
* * *
1030720 AGTTTAGTGATCAAATTATAAGATTTTG-AA
1 AGTTTAGTGACCAAAGTATAA-ACTTTGAAA
*
1030750 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAAA
*
1030780 AGTTTAGGGACCAAA
1 AGTTTAGTGACCAAA
1030795 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAAA
Found at i:1032014 original size:9 final size:9
Alignment explanation
Indices: 1031976--1032019 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
1031966 ATTCCAGTAC
1031976 TGGAATTTCT
1 TGGAATTT-T
*
1031986 T-GAATTTA
1 TGGAATTTT
1031994 TGGAATTTT
1 TGGAATTTT
1032003 TGGAATTTT
1 TGGAATTTT
*
1032012 TGGTATTT
1 TGGAATTT
1032020 AAAATTTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 1 0.03
9 28 0.93
10 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.20, T:0.55
Consensus pattern (9 bp):
TGGAATTTT
Found at i:1033110 original size:31 final size:31
Alignment explanation
Indices: 1033072--1033286 Score: 308
Period size: 31 Copynumber: 6.9 Consensus size: 31
1033062 GAGTCGAGGG
* **
1033072 TTACCTATGTTATTCGGGTTATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* *
1033103 TTACCTATGTTTTTCGGGAGATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
1033134 TTACCTATGTTCTTCGGGACATATGGACA-T
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
1033164 GTTACCTATGTTCTTCGGGATATATGGACAGT
1 -TTACCTATGTTCTTCGGGACATATGGACAGT
1033196 TTACCTATGTTCTTCGGGACATATGGACA-T
1 TTACCTATGTTCTTCGGGACATATGGACAGT
** *
1033226 GTTACCTATGTTCTTCGGGACATATGGGTAGA
1 -TTACCTATGTTCTTCGGGACATATGGACAGT
*
1033258 TTACCTATGTTCTTTGGGACATATGGACA
1 TTACCTATGTTCTTCGGGACATATGGACA
1033287 TATTATTATA
Statistics
Matches: 167, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
30 2 0.01
31 164 0.98
32 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:1033390 original size:30 final size:30
Alignment explanation
Indices: 1033356--1033416 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1033346 CCTTAAGTTC
* *
1033356 TCAGTAATGTACATGGGCTTATAAAAGATA
1 TCAGTAATATACATGGGCCTATAAAAGATA
* *
1033386 TCAGTACTATATATGGGCCTATAAAAGATA
1 TCAGTAATATACATGGGCCTATAAAAGATA
1033416 T
1 T
1033417 TAAAAGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (30 bp):
TCAGTAATATACATGGGCCTATAAAAGATA
Found at i:1033432 original size:30 final size:30
Alignment explanation
Indices: 1033365--1033432 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
1033355 CTCAGTAATG
* **
1033365 TACATGGGCTTATAAAAGATATCAGTACTA
1 TACATGGGCCTATAAAAGATATCAAAACTA
* * *
1033395 TATATGGGCCTATAAAAGATATTAAAAGTA
1 TACATGGGCCTATAAAAGATATCAAAACTA
1033425 TACATGGG
1 TACATGGG
1033433 ATAGTACATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (30 bp):
TACATGGGCCTATAAAAGATATCAAAACTA
Found at i:1033570 original size:6 final size:6
Alignment explanation
Indices: 1033559--1033659 Score: 62
Period size: 6 Copynumber: 16.8 Consensus size: 6
1033549 AATGTATTAC
* * * *
1033559 ATGATA ATGATA TTGATG TTGATA ATGATA GA-GATC ATGATA ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA
* * * * * * * *
1033607 TTGATG TTGATA ATGATA GA-GATC ATGATA ACGATA TTGATG TTGATA
1 ATGATA ATGATA ATGATA -ATGATA ATGATA ATGATA ATGATA ATGATA
1033655 ATGAT
1 ATGAT
1033660 GCTATTTATG
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
5 2 0.03
6 69 0.95
7 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.37
Consensus pattern (6 bp):
ATGATA
Found at i:1033583 original size:18 final size:18
Alignment explanation
Indices: 1033560--1033659 Score: 119
Period size: 18 Copynumber: 5.6 Consensus size: 18
1033550 ATGTATTACA
1033560 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
** **
1033578 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
1033596 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
** **
1033614 TGATAATGATAGAGATCA
1 TGATAATGATATTGATGT
*
1033632 TGATAACGATATTGATGT
1 TGATAATGATATTGATGT
1033650 TGATAATGAT
1 TGATAATGAT
1033660 GCTATTTATG
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:1033598 original size:36 final size:36
Alignment explanation
Indices: 1033558--1033659 Score: 195
Period size: 36 Copynumber: 2.8 Consensus size: 36
1033548 AAATGTATTA
1033558 CATGATAATGATATTGATGTTGATAATGATAGAGAT
1 CATGATAATGATATTGATGTTGATAATGATAGAGAT
1033594 CATGATAATGATATTGATGTTGATAATGATAGAGAT
1 CATGATAATGATATTGATGTTGATAATGATAGAGAT
*
1033630 CATGATAACGATATTGATGTTGATAATGAT
1 CATGATAATGATATTGATGTTGATAATGAT
1033660 GCTATTTATG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (36 bp):
CATGATAATGATATTGATGTTGATAATGATAGAGAT
Found at i:1036116 original size:64 final size:64
Alignment explanation
Indices: 1036030--1036239 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
1036020 TGCACTAAGA
* * * *
1036030 GTGCACCGATGCATCAAGTGCATTTGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGG-TT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGATT
** *
1036093 CGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGA
1 -GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGA
*
1036157 AT
63 TT
* ** *
1036159 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGGAT
1036222 T
64 T
*
1036223 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
1036240 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGATT
Found at i:1036164 original size:19 final size:19
Alignment explanation
Indices: 1036140--1036178 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1036130 AAAATCCTCA
* *
1036140 GTGCATCGGTGCATGGAAT
1 GTGCATCGATGCATGAAAT
1036159 GTGCATCGATGCATGAAAT
1 GTGCATCGATGCATGAAAT
1036178 G
1 G
1036179 CATTCGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (19 bp):
GTGCATCGATGCATGAAAT
Found at i:1044740 original size:19 final size:19
Alignment explanation
Indices: 1044716--1044755 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1044706 AAAATCCTCA
* *
1044716 GTGCATCGGTGCATGGAAT
1 GTGCATCGATGCATGAAAT
1044735 GTGCATCGATGCATGAAAT
1 GTGCATCGATGCATGAAAT
1044754 GT
1 GT
1044756 ATTCGATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
GTGCATCGATGCATGAAAT
Found at i:1044804 original size:65 final size:64
Alignment explanation
Indices: 1044650--1044806 Score: 178
Period size: 65 Copynumber: 2.4 Consensus size: 64
1044640 GTGCACTAAG
*
1044650 AGTGCATCGATGCATGG-CTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 AGTGCATCGATGCATGGAATGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CT
1044714 C
64 C
* * * **
1044715 AGTGCATCGGTGCATGGAAT-GTGCATCGATGCATGAAATGTATTCGATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGAATGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTC
*
1044777 ATGGTGCATCGATGCATGGATTGGTGCATC
1 A--GTGCATCGATGCATGGAATGGTGCATC
1044807 ACTCTGAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 22 0.28
65 50 0.63
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCATGGAATGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTC
Found at i:1047810 original size:64 final size:62
Alignment explanation
Indices: 1047734--1047924 Score: 181
Period size: 64 Copynumber: 3.0 Consensus size: 62
1047724 TGCATAAATA
1047734 CCATGCATCGATGCA-TCATGGATAAATTGAAACATCGAATGCATTCTATGCACCGATGCACTCT
1 CCATGCATCGATGCACTC-TGGATAAATTGAAACATCGAATGCATT-TATGCA-CGATGCACTCT
* * * * * * *
1047798 CCATGCATCGATGCACTCT-AATTTAATTAAAACATTGAATGCATTTGATGCATGGTGCAC-CAG
1 CCATGCATCGATGCACTCTGGA-TAAATTGAAACATCGAATGCATTT-ATGCACGATGCACTC-T
* * ** *
1047861 CCATGCATCGATGCACTCGGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTCT
1 CCATGCATCGATGCACTCTGGATAAATTGAAACATCGAATGCA-TTTATGCA-CGATGCACTCT
1047925 TAGTGCACCG
Statistics
Matches: 100, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
62 1 0.01
63 47 0.47
64 49 0.49
65 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (62 bp):
CCATGCATCGATGCACTCTGGATAAATTGAAACATCGAATGCATTTATGCACGATGCACTCT
Found at i:1055414 original size:64 final size:65
Alignment explanation
Indices: 1055306--1055491 Score: 186
Period size: 64 Copynumber: 2.9 Consensus size: 65
1055296 TGCATAAATA
* *
1055306 CCATGCATCGATGCA-TCAATGGATAAATTGAAACATCGAATGCATTCT-ATGCACCGATGCACT
1 CCATGCATCGATGCACTC-ATGGATAAATTAAAACATCGAATGCATT-TGATGCACCGATACAC-
*
1055369 C-T
63 CAG
* *
1055371 CCATGCATCGATGCACTC-T-GATTTAATTAAAACATCGAATGCATTTGATGCATCGATACACCA
1 CCATGCATCGATGCACTCATGGA-TAAATTAAAACATCGAATGCATTTGATGCACCGATACACCA
1055434 G
65 G
* * ** * * *
1055435 CCATGCATCGATGCACTC-GGGCTATTTTGAAACATCGAATGCACTTGATGCATCGAT
1 CCATGCATCGATGCACTCATGGATAAATTAAAACATCGAATGCATTTGATGCACCGAT
1055492 GCACTCTTAG
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
63 4 0.04
64 82 0.79
65 16 0.15
66 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (65 bp):
CCATGCATCGATGCACTCATGGATAAATTAAAACATCGAATGCATTTGATGCACCGATACACCAG
Found at i:1057909 original size:31 final size:31
Alignment explanation
Indices: 1057873--1058123 Score: 367
Period size: 31 Copynumber: 8.1 Consensus size: 31
1057863 GAGTCGAGGG
* * *
1057873 TTACCTATGTTCTTCGGGATATATGGATAGG
1 TTACCTATGTTCTTCGGGACATATGGACAGA
** *
1057904 TTACCTATGTTCTTCATGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* * * *
1057935 TTACCTAAGCTCTTCGGGCCATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
1057966 TTACCTATGTTCTTTGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
1057997 TTACCTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
1058028 TTACCTGTGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
1058059 TTACCTATGTTCTTCGGAACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
1058090 TTACCTATGTTCTTCGGGACATATGGACAAA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
1058121 TTA
1 TTA
1058124 TTATACGAGT
Statistics
Matches: 195, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 195 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:1058222 original size:30 final size:31
Alignment explanation
Indices: 1058186--1058266 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 31
1058176 TACCTTAAGT
* *
1058186 TATCAGTAATGTACATGGGCT-TATAAAAGA
1 TATCAGTAATATACATGGGCTCTAAAAAAGA
* *
1058216 TATCAGTACTATATATGGG-TCTAAAAAAGA
1 TATCAGTAATATACATGGGCTCTAAAAAAGA
**
1058246 TATCAAAAATATACATGGGCT
1 TATCAGTAATATACATGGGCT
1058267 AGTACATGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (31 bp):
TATCAGTAATATACATGGGCTCTAAAAAAGA
Found at i:1058415 original size:18 final size:17
Alignment explanation
Indices: 1058392--1058497 Score: 63
Period size: 18 Copynumber: 5.6 Consensus size: 17
1058382 ATGTATTACA
1058392 TGATAATGATATTGACGT
1 TGATAATGATATTGA-GT
1058410 TGATAATGATAATGATAGAGAT
1 TGATAATGAT-AT--T-GAG-T
1058432 CGTGATAATGATATTGATGT
1 --TGATAATGATATTGA-GT
1058452 TGATAATGATA--GAGAT
1 TGATAATGATATTGAG-T
* *
1058468 CATAATAACGATATTGATGT
1 --TGATAATGATATTGA-GT
1058488 TGATAATGAT
1 TGATAATGAT
1058498 GGTATTTATG
Statistics
Matches: 70, Mismatches: 4, Indels: 28
0.69 0.04 0.27
Matches are distributed among these distances:
15 1 0.01
16 3 0.04
18 38 0.54
19 2 0.03
20 6 0.09
21 5 0.07
22 3 0.04
23 2 0.03
24 10 0.14
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (17 bp):
TGATAATGATATTGAGT
Found at i:1058423 original size:24 final size:24
Alignment explanation
Indices: 1058391--1058455 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
1058381 AATGTATTAC
1058391 ATGATAATGATATTGA-CGTTGATA
1 ATGATAATGATATTGATCG-TGATA
**
1058415 ATGATAATGATAGAGATCGTGATA
1 ATGATAATGATATTGATCGTGATA
* *
1058439 ATGATATTGATGTTGAT
1 ATGATAATGATATTGAT
1058456 AATGATAGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 32 0.94
25 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (24 bp):
ATGATAATGATATTGATCGTGATA
Found at i:1058481 original size:36 final size:36
Alignment explanation
Indices: 1058416--1058497 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
1058406 ACGTTGATAA
* * *
1058416 TGATAATGATAGAGATCGTGATAATGATATTGATGT
1 TGATAATGATAGAGATCATAATAACGATATTGATGT
1058452 TGATAATGATAGAGATCATAATAACGATATTGATGT
1 TGATAATGATAGAGATCATAATAACGATATTGATGT
1058488 TGATAATGAT
1 TGATAATGAT
1058498 GGTATTTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (36 bp):
TGATAATGATAGAGATCATAATAACGATATTGATGT
Found at i:1063015 original size:6 final size:6
Alignment explanation
Indices: 1063006--1063030 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1062996 TACATTTTTA
1063006 TTTTGT TTTTGT TTTTGT TTTTGT T
1 TTTTGT TTTTGT TTTTGT TTTTGT T
1063031 ATTTTGATTG
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTGT
Found at i:1065717 original size:5 final size:5
Alignment explanation
Indices: 1065707--1065731 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1065697 TATCTTAGGA
1065707 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
1065732 CTCTAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:1068688 original size:69 final size:69
Alignment explanation
Indices: 1068606--1068744 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
1068596 TGAAACTCTA
*
1068606 TCCCACATGATTTTCTTGATTCTAAACTTTACCATGACATTTTTCTTTTGCTAACAACTATCCAT
1 TCCCACATGATTTTCTTGATTATAAACTTTACCATGACATTTTTCTTTTGCTAACAACTATCCAT
1068671 TGCT
66 TGCT
1068675 TCCCACATGATTTTCTTGATTATAAACTTTACCATGACATTTTTCTTTTGCTAACAACTATCCAT
1 TCCCACATGATTTTCTTGATTATAAACTTTACCATGACATTTTTCTTTTGCTAACAACTATCCAT
1068740 TGCT
66 TGCT
1068744 T
1 T
1068745 AAGGACAACC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (69 bp):
TCCCACATGATTTTCTTGATTATAAACTTTACCATGACATTTTTCTTTTGCTAACAACTATCCAT
TGCT
Found at i:1073217 original size:11 final size:11
Alignment explanation
Indices: 1073201--1073232 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1073191 TCACACCCTA
1073201 ATTTTCATTTG
1 ATTTTCATTTG
1073212 ATTTTCATTTG
1 ATTTTCATTTG
1073223 ATTTTCATTT
1 ATTTTCATTT
1073233 AATTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (11 bp):
ATTTTCATTTG
Found at i:1077391 original size:34 final size:33
Alignment explanation
Indices: 1077352--1077422 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
1077342 TTTTGTAAAG
* *
1077352 GGGAAAGGTTCTAGCTTAGCCTGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTG-AAAAACTA
* *
1077386 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
1077419 GGGA
1 GGGA
1077423 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
Found at i:1083325 original size:2 final size:2
Alignment explanation
Indices: 1083318--1083353 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1083308 CCAAATGTGA
1083318 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
1083354 TTCTTAGTCT
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:1083491 original size:2 final size:2
Alignment explanation
Indices: 1083401--1083475 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1083391 TGTTTAAGCT
1083401 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
1083443 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
1083476 GATAATTTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1086261 original size:2 final size:2
Alignment explanation
Indices: 1086254--1086279 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1086244 TCTGTTCTTT
1086254 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
1086280 CTTCTGTCTT
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):
TA
Found at i:1095795 original size:19 final size:16
Alignment explanation
Indices: 1095754--1095784 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1095744 TGAATGGGTT
1095754 AAAACATAATCTTTTA
1 AAAACATAATCTTTTA
1095770 AAAACATAATCTTTT
1 AAAACATAATCTTTT
1095785 GATAAAAACA
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:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAACATAATCTTTTA
Found at i:1098914 original size:21 final size:23
Alignment explanation
Indices: 1098866--1098918 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1098856 ACCCCTATAA
*
1098866 GGAACCGATTCCTCCTTTGAATG
1 GGAATCGATTCCTCCTTTGAATG
1098889 GGAATCGATTCCCTCC-TTG-A-G
1 GGAATCGATT-CCTCCTTTGAATG
1098910 GGAATCGAT
1 GGAATCGAT
1098919 ACCCCCACGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 10 0.36
22 1 0.04
23 12 0.43
24 5 0.18
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
GGAATCGATTCCTCCTTTGAATG
Found at i:1114059 original size:2 final size:2
Alignment explanation
Indices: 1114054--1114091 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1114044 TTTTCCTGTG
1114054 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
1114092 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1118654 original size:19 final size:21
Alignment explanation
Indices: 1118621--1118674 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
1118611 TAATTTTTTA
1118621 ATTTTTAATAAAAAAAT-ATT
1 ATTTTTAATAAAAAAATGATT
*
1118641 ATTTTTAAT-GAAAAATGATT
1 ATTTTTAATAAAAAAATGATT
1118661 -TTTTTAA-AAAAAAA
1 ATTTTTAATAAAAAAA
1118675 CTTAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
ATTTTTAATAAAAAAATGATT
Found at i:1120136 original size:26 final size:26
Alignment explanation
Indices: 1120106--1120180 Score: 150
Period size: 26 Copynumber: 2.9 Consensus size: 26
1120096 TTATTTTTTA
1120106 TTTTAAGAGTGGATTTAATTTATATG
1 TTTTAAGAGTGGATTTAATTTATATG
1120132 TTTTAAGAGTGGATTTAATTTATATG
1 TTTTAAGAGTGGATTTAATTTATATG
1120158 TTTTAAGAGTGGATTTAATTTAT
1 TTTTAAGAGTGGATTTAATTTAT
1120181 TTAAAATTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.51
Consensus pattern (26 bp):
TTTTAAGAGTGGATTTAATTTATATG
Found at i:1120402 original size:15 final size:14
Alignment explanation
Indices: 1120358--1120417 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
1120348 AAGTTATAAG
1120358 TTTAA-TTTATATAT
1 TTTAATTTTATAT-T
* *
1120372 TTTAATTTAATTTT
1 TTTAATTTTATATT
1120386 TTTATATTTTATATT
1 TTTA-ATTTTATATT
1120401 TTTAAATTTTAATATT
1 TTT-AATTTT-ATATT
1120417 T
1 T
1120418 CAGTTAAGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
14 10 0.26
15 21 0.55
16 7 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTAATTTTATATT
Found at i:1125557 original size:12 final size:10
Alignment explanation
Indices: 1125516--1125556 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1125506 TTTATCACAC
1125516 CAAATTCTCT
1 CAAATTCTCT
1125526 CAAATTCTCT
1 CAAATTCTCT
1125536 -AAATTTCTCT
1 CAAA-TTCTCT
*
1125546 CAAATACTCT
1 CAAATTCTCT
1125556 C
1 C
1125557 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1125597 original size:14 final size:14
Alignment explanation
Indices: 1125566--1125606 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1125556 CTTTTTAAGG
1125566 TATATTTTTA-TA-
1 TATATTTTTACTAT
1125578 -ATATTTTTACTAT
1 TATATTTTTACTAT
1125591 TATATTTTTACT-T
1 TATATTTTTACTAT
1125604 TAT
1 TAT
1125607 TTAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.35
12 2 0.08
13 4 0.15
14 11 0.42
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATTTTTACTAT
Found at i:1125820 original size:110 final size:111
Alignment explanation
Indices: 1125681--1125901 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
1125671 TGGAAATCAT
*
1125681 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * *
1125746 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
1125791 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1125856 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
1125902 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 33 0.32
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1131635 original size:49 final size:51
Alignment explanation
Indices: 1131531--1131637 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 51
1131521 TACAAAACGT
*
1131531 GGTACCTTCCCCGCGATATATAAAATTATGTCAGGAGTAAATGTATGTCGC
1 GGTACCTTCCCCGCGATATATAAAATTATGTCAGGAGTAAATGTATGTCAC
*
1131582 GGTACCTTCCCCGCGCTATATAAAATTAT-T-AGGAGTAAATGTATAGT-AC
1 GGTACCTTCCCCGCGATATATAAAATTATGTCAGGAGTAAATGTAT-GTCAC
1131631 GGTACCT
1 GGTACCT
1131638 GATCCACGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
49 22 0.42
50 3 0.06
51 28 0.53
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (51 bp):
GGTACCTTCCCCGCGATATATAAAATTATGTCAGGAGTAAATGTATGTCAC
Found at i:1131648 original size:49 final size:51
Alignment explanation
Indices: 1131547--1131650 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 51
1131537 TTCCCCGCGA
* ** *
1131547 TATATAAAATTATGTCAGGAGTAAATGTATGTCGCGGTACCTTCCCCGCGC
1 TATATAAAATTATGTCAGGAGTAAATGTATGTCACGGTACCTGACCCACGC
*
1131598 TATATAAAATTAT-T-AGGAGTAAATGTATAGT-ACGGTACCTGATCCACGC
1 TATATAAAATTATGTCAGGAGTAAATGTAT-GTCACGGTACCTGACCCACGC
1131647 TATA
1 TATA
1131651 CCCCTACGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 31 0.66
50 3 0.06
51 13 0.28
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (51 bp):
TATATAAAATTATGTCAGGAGTAAATGTATGTCACGGTACCTGACCCACGC
Found at i:1134578 original size:56 final size:55
Alignment explanation
Indices: 1134515--1134624 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 55
1134505 CGGGTCCACT
* * *
1134515 CCTATTCTTTCAGGGAGTATAGGACTTGAATTAATCTTTGGAAAATGAGTCTGCTC
1 CCTATTCTTTCAGGGAGTATAGGACTTGAA-CAATCTTCGGAAAACGAGTCTGCTC
* *
1134571 CCTATTCTTTCAGGGAGTATATGACTTGAACAATCTTCGGAAAACGGGTCTGCT
1 CCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGGAAAACGAGTCTGCT
1134625 TCACTACTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 20 0.41
56 29 0.59
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (55 bp):
CCTATTCTTTCAGGGAGTATAGGACTTGAACAATCTTCGGAAAACGAGTCTGCTC
Found at i:1146519 original size:20 final size:20
Alignment explanation
Indices: 1146494--1146549 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1146484 TTTTACAAAG
1146494 GGAGGTACCGATACACTCTT
1 GGAGGTACCGATACACTCTT
*
1146514 GGAGGTACCGATACATTCTT
1 GGAGGTACCGATACACTCTT
* *
1146534 GAAGGTATCGATACAC
1 GGAGGTACCGATACAC
1146550 CCCCAACTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (20 bp):
GGAGGTACCGATACACTCTT
Found at i:1154427 original size:12 final size:13
Alignment explanation
Indices: 1154397--1154438 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1154387 TAAGAGGGAG
*
1154397 TAATTTTCAAAAT
1 TAATTTTCAAAAA
1154410 TAA-TTTCAAAAA
1 TAATTTTCAAAAA
* *
1154422 TGATTTTCAAAGA
1 TAATTTTCAAAAA
1154435 TAAT
1 TAAT
1154439 CTTAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (13 bp):
TAATTTTCAAAAA
Found at i:1162600 original size:4 final size:4
Alignment explanation
Indices: 1162593--1162617 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1162583 TATTTATTTA
1162593 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
1162618 TGCTAATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1162614 original size:21 final size:20
Alignment explanation
Indices: 1162576--1162614 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1162566 TAATATTATA
* *
1162576 TAATTATTATTTATTTAAAT
1 TAATTATTAATTAATTAAAT
1162596 TAATTAATTAATTAATTAA
1 TAATT-ATTAATTAATTAA
1162615 TTATGCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTATTAATTAATTAAAT
Found at i:1164386 original size:42 final size:42
Alignment explanation
Indices: 1164334--1164434 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
1164324 AGCCCACAAT
* * *
1164334 TTCAGATGCTATCTCCGCAAGGGTATATGCCCAACCCATCAG
1 TTCATATGCTATCTCCGCAAGGGTATACGCCCAACCCACCAG
* * * *
1164376 TTCATATGCTATCTCCGCAGGGGTATACGCCTAGCTCACCAG
1 TTCATATGCTATCTCCGCAAGGGTATACGCCCAACCCACCAG
*
1164418 TTCATATGCCATCTCCG
1 TTCATATGCTATCTCCG
1164435 TAGGGTTACA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.27
Consensus pattern (42 bp):
TTCATATGCTATCTCCGCAAGGGTATACGCCCAACCCACCAG
Found at i:1164465 original size:21 final size:21
Alignment explanation
Indices: 1164436--1164493 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
1164426 CCATCTCCGT
1164436 AGGGTTACATTCCTAGCACAC
1 AGGGTTACATTCCTAGCACAC
* * * * *
1164457 AGGGGTACATACCCAGCCCGC
1 AGGGTTACATTCCTAGCACAC
*
1164478 AAGGTTACATTCCTAG
1 AGGGTTACATTCCTAG
1164494 TCCGTAGGGT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (21 bp):
AGGGTTACATTCCTAGCACAC
Found at i:1164504 original size:21 final size:21
Alignment explanation
Indices: 1164431--1164504 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
1164421 ATATGCCATC
*
1164431 TCCGTAGGGTTACATTCCTAG
1 TCCGCAGGGTTACATTCCTAG
* * * *
1164452 -CACACAGGGGTACATACCCAG
1 TC-CGCAGGGTTACATTCCTAG
* *
1164473 CCCGCAAGGTTACATTCCTAG
1 TCCGCAGGGTTACATTCCTAG
*
1164494 TCCGTAGGGTT
1 TCCGCAGGGTT
1164505 TTATGACACC
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (21 bp):
TCCGCAGGGTTACATTCCTAG
Found at i:1165023 original size:10 final size:10
Alignment explanation
Indices: 1165008--1165047 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1164998 CTTAATATAT
1165008 AATGTTTTTA
1 AATGTTTTTA
1165018 AATG--TTT-
1 AATGTTTTTA
1165025 AATGTTTGTTA
1 AATGTTT-TTA
1165036 AATGTTTTTA
1 AATGTTTTTA
1165046 AA
1 AA
1165048 ATGCAAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 4 0.15
8 3 0.12
9 1 0.04
10 11 0.42
11 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (10 bp):
AATGTTTTTA
Found at i:1165038 original size:18 final size:17
Alignment explanation
Indices: 1165007--1165042 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1164997 GCTTAATATA
1165007 TAATGTTTTTAAATGTT
1 TAATGTTTTTAAATGTT
1165024 TAATGTTTGTTAAATGTT
1 TAATGTTT-TTAAATGTT
1165042 T
1 T
1165043 TTAAAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (17 bp):
TAATGTTTTTAAATGTT
Found at i:1165085 original size:24 final size:23
Alignment explanation
Indices: 1165058--1165136 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
1165048 ATGCAAATCC
1165058 AAATTCAACTTAATATTCCAATTA
1 AAATTCAACTT-ATATTCCAATTA
* * * *
1165082 AAATTTAAAATTGTATTCGAAATTA
1 AAA-TTCAACTTATATTC-CAATTA
*
1165107 AAAGTC-ACTTCATATTCCAATTA
1 AAATTCAACTT-ATATTCCAATTA
*
1165130 AAGTTCA
1 AAATTCA
1165137 CAAAGAAAGT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
23 12 0.30
24 14 0.35
25 14 0.35
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (23 bp):
AAATTCAACTTATATTCCAATTA
Found at i:1165294 original size:20 final size:20
Alignment explanation
Indices: 1165266--1165304 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1165256 AAGTTTAAAT
1165266 AATAATTAATATATTCGAAG
1 AATAATTAATATATTCGAAG
*
1165286 AATATTTAATATATTCGAA
1 AATAATTAATATATTCGAA
1165305 TGACTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (20 bp):
AATAATTAATATATTCGAAG
Found at i:1168980 original size:13 final size:14
Alignment explanation
Indices: 1168952--1168985 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1168942 AACTTCTAAT
1168952 AACCCTAAACTATA
1 AACCCTAAACTATA
*
1168966 AACCTTAAACT-TA
1 AACCCTAAACTATA
1168979 AACCCTA
1 AACCCTA
1168986 CTTCAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCCTAAACTATA
Found at i:1172659 original size:20 final size:19
Alignment explanation
Indices: 1172612--1172650 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1172602 ATGACCAACA
*
1172612 AAATCGCAATGAGATCTCT
1 AAATCGCAACGAGATCTCT
*
1172631 AAATCGCAACGCGATCTCT
1 AAATCGCAACGAGATCTCT
1172650 A
1 A
1172651 GTATCGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGAGATCTCT
Found at i:1172704 original size:20 final size:21
Alignment explanation
Indices: 1172672--1172728 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
1172662 CAGTTTCCAG
**
1172672 ATTCGCAACGCGATTTTGAC-T
1 ATTCGCATTGCGATTTT-ACAT
*
1172693 A-TCGCGTTGCGA-TTTACAT
1 ATTCGCATTGCGATTTTACAT
1172712 ATTCGCATTGCGATTTT
1 ATTCGCATTGCGATTTT
1172729 CTAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 5 0.17
20 18 0.62
21 4 0.14
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTACAT
Found at i:1172777 original size:20 final size:20
Alignment explanation
Indices: 1172754--1172800 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1172744 GAATATGTAA
*
1172754 ATCGTAAAGCGATTCTGACT
1 ATCGCAAAGCGATTCTGACT
*
1172774 ATCGCAACGCGATTCTGACT
1 ATCGCAAAGCGATTCTGACT
1172794 ATCGCAA
1 ATCGCAA
1172801 CACTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAAAGCGATTCTGACT
Found at i:1172801 original size:20 final size:20
Alignment explanation
Indices: 1172762--1172801 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1172752 AAATCGTAAA
1172762 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
1172782 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
1172802 ACTGAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:1173646 original size:24 final size:24
Alignment explanation
Indices: 1173619--1173672 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1173609 GTATTCGAAA
1173619 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1173643 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1173667 TTTGAT
1 TTTGAT
1173673 GATGTTTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1173890 original size:14 final size:14
Alignment explanation
Indices: 1173861--1173897 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1173851 AGAAAAAGAA
1173861 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1173876 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1173890 GAAGAAAA
1 GAAGAAAA
1173898 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1175955 original size:18 final size:18
Alignment explanation
Indices: 1175932--1175966 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1175922 AGCAAAAGGC
* *
1175932 AATCAAATTCGCAATCAA
1 AATCAAAATCCCAATCAA
1175950 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1175967 CAACCAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1176159 original size:20 final size:20
Alignment explanation
Indices: 1176134--1176284 Score: 170
Period size: 20 Copynumber: 7.8 Consensus size: 20
1176124 TTACACATTC
*
1176134 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1176154 ATTTGACTATCACAATGC-A
1 ATTTGACTATCGCAACGCGA
*
1176173 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1176188 ATTCGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1176208 ATTTGACTGTCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1176228 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
1176248 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1176268 ATTTGACTATCTCAACG
1 ATTTGACTATCGCAACG
1176285 AGAAAATTGC
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
14 8 0.07
15 3 0.03
19 3 0.03
20 96 0.87
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1176385 original size:20 final size:20
Alignment explanation
Indices: 1176335--1176400 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
1176325 GACTTTCTTG
*
1176335 TTGCGATTTTTG-CTTTCGCA
1 TTGCGA-TTTTGACTTTAGCA
*
1176355 TTGCGATTTTGACTTTTGCA
1 TTGCGATTTTGACTTTAGCA
* *
1176375 TTGCGATTTTGAGTTTAGCG
1 TTGCGATTTTGACTTTAGCA
1176395 TTGCGA
1 TTGCGA
1176401 AAGTGTACCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.12
20 36 0.88
ACGTcount: A:0.14, C:0.15, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTGACTTTAGCA
Found at i:1176564 original size:67 final size:69
Alignment explanation
Indices: 1176452--1176629 Score: 199
Period size: 71 Copynumber: 2.6 Consensus size: 69
1176442 TATTGAAATC
*
1176452 AACAAATCAACTTTTACATTTTAATCAATTAAACAAGC---ACAAATAAGAA-TTA-TTTACACA
1 AACAAATCAACTTTTACA---TAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACA
1176512 TCAATTA
63 TCAATTA
* * *
1176519 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAA-AATAAGAA-T-TTATTTTACACA
1176583 TCAATTA
63 TCAATTA
* *
1176590 AACAAATCAACTTTTA-AGAATCAATTAAACAATCAAAAAA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAA
1176630 GTGTACCCCA
Statistics
Matches: 97, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
63 16 0.16
66 2 0.02
67 25 0.26
70 4 0.04
71 50 0.52
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (69 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACATCA
ATTA
Found at i:1177983 original size:42 final size:41
Alignment explanation
Indices: 1177921--1178014 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
1177911 CGTGTGAATC
*
1177921 GGGCTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAG
1 GGGCTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAG
* ** *
1177962 GGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAG
1 GGG-CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAG
1178004 GGGCTCTTGAA
1 GGGCTCTTGAA
1178015 TGATAGTAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 11 0.24
42 31 0.67
43 4 0.09
ACGTcount: A:0.20, C:0.17, G:0.40, T:0.22
Consensus pattern (41 bp):
GGGCTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAG
Found at i:1177984 original size:21 final size:21
Alignment explanation
Indices: 1177924--1177993 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
1177914 GTGAATCGGG
* *
1177924 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
1177945 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1177966 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
1177987 CTCTTGA
1 CTCTTGA
1177994 GGGATGATAG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1178542 original size:20 final size:20
Alignment explanation
Indices: 1178517--1178560 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1178507 AATAGTTTCT
1178517 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
1178537 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1178557 GAAA
1 GAAA
1178561 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1178570 original size:20 final size:19
Alignment explanation
Indices: 1178547--1178613 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 19
1178537 GAAACTTAAA
1178547 ATCGCAACGCGAAAATGACT
1 ATCGCAACGC-AAAATGACT
1178567 ATCGCAACGCAGAAATGACT
1 ATCGCAACGCA-AAATGACT
*
1178587 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCAAA-ATGACT
1178607 ATCGCAA
1 ATCGCAA
1178614 TGGGATAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCAAAATGACT
Found at i:1178644 original size:19 final size:20
Alignment explanation
Indices: 1178620--1178671 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1178610 GCAATGGGAT
*
1178620 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
* *
1178639 AATCGCAACACGAAACTTAA
1 AATCGCAACGCGAAACTAAA
1178659 AATCGCAACGCGA
1 AATCGCAACGCGA
1178672 TTCTGACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:1179537 original size:24 final size:24
Alignment explanation
Indices: 1179510--1179563 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1179500 GTATTCGAAA
1179510 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1179534 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1179558 TTTGAT
1 TTTGAT
1179564 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1179782 original size:14 final size:14
Alignment explanation
Indices: 1179753--1179789 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1179743 AGAAAAAGAA
1179753 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1179768 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1179782 GAAGAAAA
1 GAAGAAAA
1179790 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1182053 original size:20 final size:20
Alignment explanation
Indices: 1182028--1182178 Score: 188
Period size: 20 Copynumber: 7.8 Consensus size: 20
1182018 TTACACATTC
*
1182028 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1182048 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
1182067 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1182082 ATTCGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1182102 ATTTGACTGTCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1182122 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
1182142 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1182162 ATTTGACTATCTCAACG
1 ATTTGACTATCGCAACG
1182179 AGAAAATTGC
Statistics
Matches: 114, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
14 10 0.09
15 3 0.03
19 3 0.03
20 98 0.86
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1182079 original size:34 final size:37
Alignment explanation
Indices: 1182036--1182217 Score: 142
Period size: 40 Copynumber: 4.9 Consensus size: 37
1182026 TCATTTGAAT
1182036 ATCGCAACGCGAATTTGACTATCGCAACGC-AA-A-A
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATACA
* *
1182070 ATCGCAACGCGAATTCGACTATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA--T-ACA
* * **
1182110 GTCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA--T-ACA
* * *
1182150 ATCGCAACGGGAATTTGACTATCTCAACGAG-A-A-A
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATACA
* * * * *
1182184 ATTGCAAAGTGTATTAGACTATCGCAACGCGAAT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAAT
1182218 TGACTTTCTT
Statistics
Matches: 122, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
34 53 0.43
35 4 0.03
39 2 0.02
40 63 0.52
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (37 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATACA
Found at i:1182117 original size:54 final size:54
Alignment explanation
Indices: 1182035--1182222 Score: 200
Period size: 54 Copynumber: 3.4 Consensus size: 54
1182025 TTCATTTGAA
* *
1182035 TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTCGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGTGAATTAGAC
* * * *
1182089 TATCGCAACGCGAATTTGACTGTCGCAACGCGAATTTGACTATCGCAACGTGAATTTGAT
1 TATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-AATCGCAACGTGAATTAGAC
* * * * *
1182149 TATCGCAACGGGAATTTGACTATCTCAACG-AGAAAATTGCAAAGTGTATTAGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCA-AAAATCGCAACGTGAATTAGAC
1182203 TATCGCAACGCGAA-TTGACT
1 TATCGCAACGCGAATTTGACT
1182223 TTCTTGTTGT
Statistics
Matches: 112, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
53 6 0.05
54 57 0.51
55 3 0.03
58 1 0.01
59 2 0.02
60 43 0.38
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (54 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGTGAATTAGAC
Found at i:1182256 original size:20 final size:21
Alignment explanation
Indices: 1182233--1182294 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 21
1182223 TTCTTGTTGT
1182233 GATTTTTG-CTTTCGCATTGC
1 GATTTTTGACTTTCGCATTGC
*
1182253 GA-TTTTGACTTTTGCATTGC
1 GATTTTTGACTTTCGCATTGC
* *
1182273 GA-TTTTGAGTTTAGCATTGC
1 GATTTTTGACTTTCGCATTGC
1182293 GA
1 GA
1182295 AAGTGTACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 5 0.13
20 33 0.87
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.47
Consensus pattern (21 bp):
GATTTTTGACTTTCGCATTGC
Found at i:1182458 original size:67 final size:69
Alignment explanation
Indices: 1182346--1182524 Score: 201
Period size: 71 Copynumber: 2.6 Consensus size: 69
1182336 TATTGAAATC
*
1182346 AACAAATCAACTTTTACATTTTAATCAATTAAACAAGC---ACAAATAAGAA-TTA-TTTACACA
1 AACAAATCAACTTTTACA---TAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACA
1182406 TCAATTA
63 TCAATTA
* * *
1182413 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAA-AATAAGAA-T-TTATTTTACACA
1182477 TCAATTA
63 TCAATTA
* *
1182484 AACAAATCAACTTTTA-AGAATCAATTAAACAATCAAAAAAA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAA
1182525 TTGTACCCCA
Statistics
Matches: 98, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
63 16 0.16
66 2 0.02
67 25 0.26
70 5 0.05
71 50 0.51
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (69 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACATCA
ATTA
Found at i:1183868 original size:21 final size:21
Alignment explanation
Indices: 1183844--1183938 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
1183834 GGACCACTTC
1183844 AACGATGACAGGGGCCTCTTG
1 AACGATGACAGGGGCCTCTTG
* ** *
1183865 AACGGTGGGAGGGGACTCTTG
1 AACGATGACAGGGGCCTCTTG
** *
1183886 AGGGATGATAGGGG-CTCTTG
1 AACGATGACAGGGGCCTCTTG
* * *
1183906 AATGAT-AGTAGAGGCCTCTTG
1 AACGATGA-CAGGGGCCTCTTG
*
1183927 AATGATGACAGG
1 AACGATGACAGG
1183939 TGAGTCGGGC
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.02
20 15 0.26
21 40 0.70
22 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.22
Consensus pattern (21 bp):
AACGATGACAGGGGCCTCTTG
Found at i:1184436 original size:20 final size:20
Alignment explanation
Indices: 1184411--1184454 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1184401 AATAGTTTCT
1184411 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
1184431 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1184451 GAAA
1 GAAA
1184455 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1184464 original size:20 final size:20
Alignment explanation
Indices: 1184441--1184507 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
1184431 GAAACTTAAA
1184441 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1184461 ATCGCAACGC-AGAAATGACT
1 ATCGCAACGCGA-AAATGACT
**
1184481 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1184501 ATCGCAA
1 ATCGCAA
1184508 TGGGATAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1184538 original size:19 final size:20
Alignment explanation
Indices: 1184514--1184565 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1184504 GCAATGGGAT
*
1184514 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
* *
1184533 AATCGCAACACGAAACTTAA
1 AATCGCAACGCGAAACTAAA
1184553 AATCGCAACGCGA
1 AATCGCAACGCGA
1184566 TTCTGACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:1184581 original size:40 final size:39
Alignment explanation
Indices: 1184421--1184583 Score: 106
Period size: 40 Copynumber: 4.3 Consensus size: 39
1184411 GAAACTTAAA
*
1184421 ATCGCAACACGAAACTTAAAATCGCAACGCGAAAATGACT
1 ATCGCAACACGAAA-TTAAAATCGCAACGCGATAATGACT
* * ** *
1184461 ATCGCAACGCAGAAATGACTATCGCAACGCGA-ATTTGACT
1 ATCGCAACAC-GAAATTAAAATCGCAACGCGATA-ATGACT
* ** * * **
1184501 ATCGC-A-ATGGGA-T--AATCGCAATGCGA-AATAAAA
1 ATCGCAACACGAAATTAAAATCGCAACGCGATAATGACT
**
1184534 ATCGCAACACGAAACTTAAAATCGCAACGCGATTCTGACT
1 ATCGCAACACGAAA-TTAAAATCGCAACGCGATAATGACT
1184574 ATCGCAACAC
1 ATCGCAACAC
1184584 TGAATTTCAA
Statistics
Matches: 89, Mismatches: 25, Indels: 18
0.67 0.19 0.14
Matches are distributed among these distances:
33 7 0.08
34 13 0.15
35 3 0.03
37 3 0.03
39 14 0.16
40 45 0.51
41 4 0.04
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (39 bp):
ATCGCAACACGAAATTAAAATCGCAACGCGATAATGACT
Found at i:1185433 original size:24 final size:24
Alignment explanation
Indices: 1185406--1185459 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1185396 GTATTCGAAA
1185406 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1185430 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1185454 TTTGAT
1 TTTGAT
1185460 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1185642 original size:3 final size:3
Alignment explanation
Indices: 1185634--1185660 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1185624 ATATAACCCT
1185634 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1185661 ATCCCCGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1185681 original size:14 final size:14
Alignment explanation
Indices: 1185652--1185688 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1185642 AGAAGAAGAA
1185652 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1185667 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1185681 GAAGAAAA
1 GAAGAAAA
1185689 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1187748 original size:18 final size:18
Alignment explanation
Indices: 1187725--1187759 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1187715 AGCAAAAGGT
* *
1187725 AATCAAATTCGCAATCAA
1 AATCAAAATCCCAATCAA
1187743 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1187760 CAACCAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1187952 original size:20 final size:20
Alignment explanation
Indices: 1187927--1188063 Score: 202
Period size: 20 Copynumber: 6.8 Consensus size: 20
1187917 TTACACATTC
*
1187927 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1187947 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1187967 ATTCGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1187987 ATTTGACTGTCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1188007 ATTTGACTATCGTAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
1188027 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1188047 ATTTGACTATCTCAACG
1 ATTTGACTATCGCAACG
1188064 AGAAAATTGC
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1188137 original size:20 final size:20
Alignment explanation
Indices: 1188114--1188165 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1188104 GACTTTCTTG
* *
1188114 TTGCGATTTTGGCTTTCGCA
1 TTGCGATTTTGACTTTCACA
*
1188134 TTGCGATTTTGACTTTTACA
1 TTGCGATTTTGACTTTCACA
1188154 TTGCGATTTTGA
1 TTGCGATTTTGA
1188166 GTTTAGCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTGACTTTCACA
Found at i:1188177 original size:20 final size:20
Alignment explanation
Indices: 1188114--1188179 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
1188104 GACTTTCTTG
*
1188114 TTGCGATTTTG-GCTTTCGCA
1 TTGCGATTTTGAG-TTTAGCA
*
1188134 TTGCGATTTTGACTTTTA-CA
1 TTGCGATTTTGA-GTTTAGCA
*
1188154 TTGCGATTTTGAGTTTAGCG
1 TTGCGATTTTGAGTTTAGCA
1188174 TTGCGA
1 TTGCGA
1188180 AAGTGTACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.10
20 32 0.82
21 3 0.08
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTGAGTTTAGCA
Found at i:1188343 original size:67 final size:69
Alignment explanation
Indices: 1188231--1188409 Score: 201
Period size: 71 Copynumber: 2.6 Consensus size: 69
1188221 TATTGAAATC
*
1188231 AACAAATCAACTTTTACATTTTAATCAATTAAACAAGC---ACAAATAAGAA-TTA-TTTACACA
1 AACAAATCAACTTTTACA---TAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACA
1188291 TCAATTA
63 TCAATTA
* * *
1188298 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAA-AATAAGAA-T-TTATTTTACACA
1188362 TCAATTA
63 TCAATTA
* *
1188369 AACAAATCAACTTTTA-AGAATCAATTAAACAATCAAAAAAA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAA
1188410 GTGTACCCCA
Statistics
Matches: 98, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
63 16 0.16
66 2 0.02
67 25 0.26
70 5 0.05
71 50 0.51
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (69 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACATCA
ATTA
Found at i:1189763 original size:21 final size:21
Alignment explanation
Indices: 1189703--1189772 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
1189693 GTGAATCGGG
* *
1189703 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
1189724 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1189745 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
1189766 CTCTTGA
1 CTCTTGA
1189773 GGGATGATAT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1190322 original size:20 final size:20
Alignment explanation
Indices: 1190297--1190340 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1190287 AATAGTTTCT
1190297 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
1190317 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1190337 GAAA
1 GAAA
1190341 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1190350 original size:20 final size:20
Alignment explanation
Indices: 1190327--1190393 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
1190317 GAAACTTAAA
1190327 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1190347 ATCGCAACGC-AGAAATGACT
1 ATCGCAACGCGA-AAATGACT
**
1190367 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1190387 ATCGCAA
1 ATCGCAA
1190394 TGGGATAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1190468 original size:20 final size:20
Alignment explanation
Indices: 1190439--1190477 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1190429 CGAAACTAAA
* *
1190439 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCAATTTTCATT
1190459 TTCGCATTGCAATTTTCAT
1 TTCGCATTGCAATTTTCAT
1190478 GTTGCTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
TTCGCATTGCAATTTTCATT
Found at i:1190515 original size:33 final size:34
Alignment explanation
Indices: 1190443--1190518 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 34
1190433 ACTAAATTCG
*
1190443 CGTTGCGATTTTCATTTTCGCATTGCAATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCAATTATCA
* * * * *
1190477 TGTTGCTATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCAATTATCA
1190510 CGTTGCGAT
1 CGTTGCGAT
1190519 AGTCATTTCC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCAATTATCA
Found at i:1192495 original size:20 final size:20
Alignment explanation
Indices: 1192452--1192525 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1192442 GAAACTTAAA
**
1192452 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
1192472 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
1192492 ATCGTAACTCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
1192512 ATCGCAACGCGAAA
1 ATCGCAACACGAAA
1192526 CTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1192933 original size:22 final size:22
Alignment explanation
Indices: 1192906--1192958 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1192896 AGATAGACAG
1192906 ATTTCGCCGGAGATGGGGACGA
1 ATTTCGCCGGAGATGGGGACGA
* *
1192928 ATTTCGTCGGAGATGGGGACGG
1 ATTTCGCCGGAGATGGGGACGA
*
1192950 ATGTCGCCG
1 ATTTCGCCG
1192959 TAGAGAGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
ATTTCGCCGGAGATGGGGACGA
Found at i:1193506 original size:11 final size:11
Alignment explanation
Indices: 1193487--1193515 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1193477 TAATATTAAA
1193487 GTTAG-ATTAT
1 GTTAGTATTAT
1193497 GTTAGTATTAT
1 GTTAGTATTAT
1193508 GTTAGTAT
1 GTTAGTAT
1193516 GATACTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (11 bp):
GTTAGTATTAT
Found at i:1196616 original size:60 final size:60
Alignment explanation
Indices: 1196470--1196603 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
1196460 AATTGAAGAT
* * * *
1196470 AAAG-TACACAAATGATCCCT-CGACTATAGGGTACTGCTTTGTTTAGTCCCTCGACTATTA
1 AAAGTTACA-AAATGAT-CCTACGACTATAGAGTACTGCTTTGTTGAGTCCATCAACTATTA
* * **
1196530 AAAGTTATAAAATGATCCTATGACTATAGAGTGTTGCTTTGTTGAGTCCATCAACTATTA
1 AAAGTTACAAAATGATCCTACGACTATAGAGTACTGCTTTGTTGAGTCCATCAACTATTA
1196590 AAAGTTACAAAATG
1 AAAGTTACAAAATG
1196604 GTCACCCGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 57 0.90
61 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCTACGACTATAGAGTACTGCTTTGTTGAGTCCATCAACTATTA
Found at i:1196907 original size:60 final size:60
Alignment explanation
Indices: 1196827--1196940 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
1196817 GTCAGGTGAC
* * * *
1196827 CATTTTGTAACTCTTAATAGT-TGAGGGACTTAACAAAGTAACATTATATAGTCGAAGGAT
1 CATTTTATAACTCTTAATAGTCTAAGGG-CTTAACAAAATAACATCATATAGTCGAAGGAT
* * *
1196887 CATTTTATAACTTTTAATAGTCTAAGGGCTTAATAAAATAACATCCTATAGTCG
1 CATTTTATAACTCTTAATAGTCTAAGGGCTTAACAAAATAACATCATATAGTCG
1196941 GTTGATCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 41 0.89
61 5 0.11
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (60 bp):
CATTTTATAACTCTTAATAGTCTAAGGGCTTAACAAAATAACATCATATAGTCGAAGGAT
Found at i:1196948 original size:60 final size:59
Alignment explanation
Indices: 1196814--1196951 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 59
1196804 AACATAATGA
* * * * *
1196814 ATAGTCAGGTGACCATTTTGTAACTCTTAATAGTTGAGGGACTTAACAAAGTAACATTAT
1 ATAGTC-GGTGATCATTTTATAACTCTTAATAGTTAAGGGACTTAACAAAATAACATCAT
* * *
1196874 ATAGTCGAAG-GATCATTTTATAACTTTTAATAGTCTAAGGG-CTTAATAAAATAACATCCT
1 ATAGTCG--GTGATCATTTTATAACTCTTAATAGT-TAAGGGACTTAACAAAATAACATCAT
1196934 ATAGTCGGTTGATCATTT
1 ATAGTCGG-TGATCATTT
1196952 GTGTATCTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
58 1 0.02
59 1 0.02
60 57 0.88
61 6 0.09
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (59 bp):
ATAGTCGGTGATCATTTTATAACTCTTAATAGTTAAGGGACTTAACAAAATAACATCAT
Found at i:1202998 original size:18 final size:18
Alignment explanation
Indices: 1202975--1203015 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1202965 TTGTAATCAA
1202975 TGGATCTTCGGGTCAAAT
1 TGGATCTTCGGGTCAAAT
1202993 TGGATCTTCGGGTCAAAT
1 TGGATCTTCGGGTCAAAT
1203011 TGGAT
1 TGGAT
1203016 TAGGGTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (18 bp):
TGGATCTTCGGGTCAAAT
Found at i:1203178 original size:3 final size:3
Alignment explanation
Indices: 1203170--1203216 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1203160 ACATTAAGTC
1203170 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1203217 CAAGAAAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1203311 original size:2 final size:2
Alignment explanation
Indices: 1203263--1203292 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1203253 GTAGGTCAAG
1203263 TA TA -A 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 T
1203293 TATTAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1205333 original size:28 final size:28
Alignment explanation
Indices: 1205301--1205359 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1205291 TACCGTAGCA
* *
1205301 TGTGAATCTGTGGCTTTTTATTAATGTT
1 TGTGAATATGTGGCTTTTTATTAACGTT
1205329 TGTGAATATGTGGCTTTTTATTAACGTT
1 TGTGAATATGTGGCTTTTTATTAACGTT
1205357 TGT
1 TGT
1205360 TTTTATTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.07, G:0.22, T:0.53
Consensus pattern (28 bp):
TGTGAATATGTGGCTTTTTATTAACGTT
Found at i:1206439 original size:16 final size:16
Alignment explanation
Indices: 1206402--1206440 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1206392 TTGTACCCAT
*
1206402 CGTTAAAAACTTAACG
1 CGTTTAAAACTTAACG
* *
1206418 CATTTAAAACTTAATG
1 CGTTTAAAACTTAACG
1206434 CGTTTAA
1 CGTTTAA
1206441 TACCTAAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (16 bp):
CGTTTAAAACTTAACG
Found at i:1207926 original size:34 final size:35
Alignment explanation
Indices: 1207878--1207945 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
1207868 GTTCGTGTTA
*
1207878 ATACGATTATTTGTTATTGTTAATAATAATATTTG
1 ATACGATTATTTGTTATTGATAATAATAATATTTG
*
1207913 ATAC-ATTATTTGTTATTGATAATATTAATATTT
1 ATACGATTATTTGTTATTGATAATAATAATATTT
1207946 TTGTTTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (35 bp):
ATACGATTATTTGTTATTGATAATAATAATATTTG
Found at i:1210821 original size:2 final size:2
Alignment explanation
Indices: 1210814--1210844 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1210804 CTGCAAGTGA
1210814 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 A
1210845 GTTTGTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1214220 original size:25 final size:23
Alignment explanation
Indices: 1214192--1214263 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
1214182 TAAAATTCAT
1214192 AATATTTTACATATATTAACTTAAA
1 AATATTTT--ATATATTAACTTAAA
1214217 AATATATTT-TATATTAACTTATTAA
1 AATAT-TTTATATATTAACTTA--AA
1214242 ATATATTTTAT-TATTAACTTAA
1 A-ATATTTTATATATTAACTTAA
1214264 TTAAAAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
23 13 0.31
25 21 0.50
26 8 0.19
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTTTATATATTAACTTAAA
Found at i:1214230 original size:23 final size:23
Alignment explanation
Indices: 1214203--1214263 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
1214193 ATATTTTACA
1214203 TATATTAACTTAAAAATATATTT
1 TATATTAACTTAAAAATATATTT
*
1214226 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA-AAAATATATTT
1214250 TATTATTAACTTAA
1 TA-TATTAACTTAA
1214264 TTAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 12 0.35
24 12 0.35
25 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATTAACTTAAAAATATATTT
Done.