Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 173 of 206
Found at i:52779616 original size:22 final size:22
Alignment explanation
Indices: 52779591--52779634 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52779581 TCAACTTTTA
*
52779591 ACACAAACATTCAATTATATTG
1 ACACAAACAATCAATTATATTG
* *
52779613 ACACAACCAATCAATTCTATTG
1 ACACAAACAATCAATTATATTG
52779635 GCATAGTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (22 bp):
ACACAAACAATCAATTATATTG
Found at i:52783160 original size:13 final size:14
Alignment explanation
Indices: 52783142--52783171 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52783132 AAGCCTAAGA
52783142 AAAGAA-AAAGACT
1 AAAGAATAAAGACT
52783155 AAAGAATAAAGACT
1 AAAGAATAAAGACT
52783169 AAA
1 AAA
52783172 TCTAACAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (14 bp):
AAAGAATAAAGACT
Found at i:52784971 original size:132 final size:132
Alignment explanation
Indices: 52784734--52785002 Score: 511
Period size: 132 Copynumber: 2.0 Consensus size: 132
52784724 CTTTCAATTG
*
52784734 ATTTGCTCATTTCTAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
1 ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
52784799 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
66 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
52784864 AT
131 AT
52784866 ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
1 ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
* *
52784931 TGTATTATGATTTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
66 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
52784996 AT
131 AT
52784998 ATTTG
1 ATTTG
52785003 TTTTCATTTT
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 134 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (132 bp):
ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
AT
Found at i:52790003 original size:3 final size:3
Alignment explanation
Indices: 52789995--52790035 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
52789985 TTTTTTAAGT
* *
52789995 TTA TTA TTA TTA TTA TTA TTA TTA TACA GTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
52790036 ACTTTTACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.97
4 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:52790158 original size:2 final size:2
Alignment explanation
Indices: 52790153--52790208 Score: 71
Period size: 2 Copynumber: 28.0 Consensus size: 2
52790143 CTTAGTTTTT
*
52790153 TA TA TA TA GTT TA TA TA TA TA TA T- TA GT- 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
52790195 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
52790209 AATTTACATT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52790263 original size:26 final size:26
Alignment explanation
Indices: 52790215--52790264 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
52790205 TATAAATTTA
*
52790215 CATTTTATAATACATATACATTTTTC
1 CATTTTATAATACATACACATTTTTC
* *
52790241 CATTTTATAATTCATACATATTTT
1 CATTTTATAATACATACACATTTT
52790265 CACATACATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (26 bp):
CATTTTATAATACATACACATTTTTC
Found at i:52790653 original size:18 final size:20
Alignment explanation
Indices: 52790613--52790653 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
52790603 ACCATTCATC
* *
52790613 AAGGTTATTTTCTTGATTTA
1 AAGGTTATTTTCTTGAATAA
52790633 AAGGTT-TTTT-TTGAATAA
1 AAGGTTATTTTCTTGAATAA
52790651 AAG
1 AAG
52790654 CATTATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (20 bp):
AAGGTTATTTTCTTGAATAA
Found at i:52792784 original size:11 final size:11
Alignment explanation
Indices: 52792738--52792805 Score: 68
Period size: 11 Copynumber: 6.2 Consensus size: 11
52792728 TAAATCATTT
*
52792738 CTCTC-AATTT
1 CTCTCAAATTC
52792748 CTCTCTAATATT-
1 CTCTC-AA-ATTC
52792760 CTCTCAAATTC
1 CTCTCAAATTC
* *
52792771 CTCCCAATTTC
1 CTCTCAAATTC
*
52792782 CTCTCAAGTTC
1 CTCTCAAATTC
52792793 CTCTCAAATTC
1 CTCTCAAATTC
52792804 CT
1 CT
52792806 ATTTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
10 8 0.16
11 32 0.65
12 6 0.12
13 3 0.06
ACGTcount: A:0.22, C:0.35, G:0.01, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:52792857 original size:29 final size:28
Alignment explanation
Indices: 52792810--52792865 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
52792800 ATTCCTATTT
*
52792810 AAAAAAGTTTTAATTTTTTAATTATTTTTA
1 AAAAAAGTTTTAATATTTT-ATT-TTTTTA
52792840 AAAAAAGTTTTAA-ATTTTATTTTTTT
1 AAAAAAGTTTTAATATTTTATTTTTTT
52792866 GAATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 3 0.12
29 4 0.16
30 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
AAAAAAGTTTTAATATTTTATTTTTTTA
Found at i:52793989 original size:7 final size:7
Alignment explanation
Indices: 52793979--52794010 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
52793969 TTAGTATTTA
52793979 GTATTAT
1 GTATTAT
52793986 GTATTAT
1 GTATTAT
52793993 GTATTAT
1 GTATTAT
52794000 GTATTAT
1 GTATTAT
52794007 GTAT
1 GTAT
52794011 ATAACTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:52793989 original size:14 final size:15
Alignment explanation
Indices: 52793972--52794010 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
52793962 TTGGTATTTA
52793972 GTATTTA-GTATTAT
1 GTATTTATGTATTAT
52793986 GTA-TTATGTATTAT
1 GTATTTATGTATTAT
52794000 GTA-TTATGTAT
1 GTATTTATGTAT
52794011 ATAACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 3 0.12
14 21 0.88
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (15 bp):
GTATTTATGTATTAT
Found at i:52794674 original size:18 final size:18
Alignment explanation
Indices: 52794651--52794694 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52794641 ATGCCAGGTG
* * *
52794651 TGTATCGTAGCCCTTTTA
1 TGTATCCTAACCCTTATA
52794669 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
52794687 TGTTTCCT
1 TGTATCCT
52794695 TTTTTTAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:52795169 original size:34 final size:34
Alignment explanation
Indices: 52795121--52795217 Score: 185
Period size: 34 Copynumber: 2.9 Consensus size: 34
52795111 GAATATTTTG
*
52795121 ATATTATTTGATGTAATAAAATAGAAATTCTTCT
1 ATATTATTTCATGTAATAAAATAGAAATTCTTCT
52795155 ATATTATTTCATGTAATAAAATAGAAATTCTTCT
1 ATATTATTTCATGTAATAAAATAGAAATTCTTCT
52795189 ATATTATTTCATGTAATAAAATAGAAATT
1 ATATTATTTCATGTAATAAAATAGAAATT
52795218 TACTTTTACA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (34 bp):
ATATTATTTCATGTAATAAAATAGAAATTCTTCT
Found at i:52796482 original size:126 final size:126
Alignment explanation
Indices: 52796257--52796672 Score: 663
Period size: 126 Copynumber: 3.3 Consensus size: 126
52796247 CAAACATGCA
* * * * * *
52796257 CTACTGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAATACT-TCTACTGACAAACCATCCT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAACTTCTTTCAGTACTAT-TGCTGACAAAGCATCCT
* * * *
52796321 GCTTAAAGCTTTTTTAACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCATGAG
65 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTTAGGAG
*
52796383 CTACTGTAGCAAAAGCGCGTCCACGTGGGAACTTCTTTCAGTACTATTGTTGACAAAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAACTTCTTTCAGTACTATTGCTGACAAAGCATCCTG
* *
52796448 CTTAAAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTTAGGAG
66 CTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTTAGGAG
*
52796509 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAACTTCTTTCAGTACTATTGCTGACAAAGCATCCTG
*
52796574 CTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTATTCAAAATTATTTTTTTAGGAG
66 CTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTTAGGAG
* *
52796635 CTACTGTAGCAAAAGCGCGTCTACGTGAGAACTTCTTT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAACTTCTTT
52796673 AAATTAACAA
Statistics
Matches: 268, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
126 267 1.00
127 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAACTTCTTTCAGTACTATTGCTGACAAAGCATCCTG
CTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTTAGGAG
Found at i:52796853 original size:96 final size:95
Alignment explanation
Indices: 52796711--52797044 Score: 336
Period size: 96 Copynumber: 3.4 Consensus size: 95
52796701 CCTCAACCAC
* *
52796711 AAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCATAATCTAATTTTTTA
1 AAACCCTAATTTATTT-AATTTTTTCTTAAAAACCCTAAACACTAAACC-TAATCTAATTTTTTA
52796776 AAAATTTATAATTAATTTACTCAAGTAACCCT
64 AAAATTTATAATTAATTTACTCAAGTAACCCT
* * * *
52796808 GAACCCTAATTTATTTAATTTTTTCATAAAAACCCTTAACTCTAAACCCTAATCTAATTTTTTTT
1 AAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAA-CCTAATCTAA--TTTTTT
* * *
52796873 AAAAA-TT-TAATTAAATTACTTAAGTAACCTT
63 AAAAATTTATAATTAATTTACTCAAGTAACCCT
* ** * * *
52796904 AAACCCTAATTTAATT-ATTTTTTCTTAAAAAACAATAAACACGAAACCTAATCCAA-TTTTGAA
1 AAACCCTAATTTATTTAATTTTTTCTT-AAAAACCCTAAACACTAAACCTAATCTAATTTTTTAA
* *
52796967 AAATTTATAATTAATTTAATTGACAAACCATAAACCCT
65 AAATTTATAATTAATTT-ACT--C-AA--GT-AACCCT
* *
52797005 AATCCCTTATTTATTTAATTTTTTCTCT-AAAACCCTAAAC
1 AAACCCTAATTTATTTAATTTTTTCT-TAAAAACCCTAAAC
52797045 TTAAAAATAT
Statistics
Matches: 193, Mismatches: 29, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
92 9 0.05
93 2 0.01
94 9 0.05
95 20 0.10
96 82 0.42
97 19 0.10
98 13 0.07
100 1 0.01
101 28 0.15
102 9 0.05
103 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (95 bp):
AAACCCTAATTTATTTAATTTTTTCTTAAAAACCCTAAACACTAAACCTAATCTAATTTTTTAAA
AATTTATAATTAATTTACTCAAGTAACCCT
Found at i:52799410 original size:6 final size:6
Alignment explanation
Indices: 52799399--52799427 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52799389 AGGCAGATAT
52799399 GGCGGA GGCGGA GGCGGA GGCGGA GGCGG
1 GGCGGA GGCGGA GGCGGA GGCGGA GGCGG
52799428 CGGTGCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.17, G:0.69, T:0.00
Consensus pattern (6 bp):
GGCGGA
Found at i:52802517 original size:12 final size:12
Alignment explanation
Indices: 52802502--52802559 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
52802492 TAGGATGATT
52802502 TTTATTTTAATA
1 TTTATTTTAATA
52802514 TTTATTTTTAATCA
1 TTTA-TTTTAAT-A
*
52802528 TTTTATTTAAATA
1 -TTTATTTTAATA
*
52802541 -TTATTTTAAAA
1 TTTATTTTAATA
*
52802552 TATATTTT
1 TTTATTTT
52802560 TTAAGAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 9 0.24
12 10 0.26
13 8 0.21
14 7 0.18
15 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATTTTAATA
Found at i:52806119 original size:4 final size:4
Alignment explanation
Indices: 52806102--52806139 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
52806092 CAAATTATTT
52806102 TTAA TTATA TTAA TTAA TTAA TTAA TTAA TTAAA TTAA
1 TTAA TTA-A TTAA TTAA TTAA TTAA TTAA TT-AA TTAA
52806140 CATATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:52810730 original size:51 final size:50
Alignment explanation
Indices: 52810654--52810816 Score: 235
Period size: 51 Copynumber: 3.3 Consensus size: 50
52810644 ACTTCTAACC
* *
52810654 AGTGAAAAGTGATAAGTGGTAGCTTTAGCTACGCTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGA-TAGTGACA
*
52810705 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT-AGTGACA
* *
52810756 AGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATC----AGGGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATAGTGACA
52810802 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
52810817 ATGTGATCCG
Statistics
Matches: 104, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
46 20 0.19
50 1 0.01
51 83 0.80
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATAGTGACA
Found at i:52811968 original size:14 final size:14
Alignment explanation
Indices: 52811949--52811977 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52811939 CTGTTTCGTC
52811949 ATCGAATACGGGTT
1 ATCGAATACGGGTT
52811963 ATCGAATACGGGTT
1 ATCGAATACGGGTT
52811977 A
1 A
52811978 GGGGTGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (14 bp):
ATCGAATACGGGTT
Found at i:52818547 original size:18 final size:18
Alignment explanation
Indices: 52818524--52818559 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52818514 GCCTAGCACA
52818524 CGGGCATGTGGTCTGGCC
1 CGGGCATGTGGTCTGGCC
52818542 CGGGCATGTGGTCTGGCC
1 CGGGCATGTGGTCTGGCC
52818560 GTGTGACCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.28, G:0.44, T:0.22
Consensus pattern (18 bp):
CGGGCATGTGGTCTGGCC
Found at i:52819197 original size:2 final size:2
Alignment explanation
Indices: 52819192--52819217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52819182 TATAAAAGTG
52819192 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
52819218 AAAAGGCATG
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:52819675 original size:16 final size:16
Alignment explanation
Indices: 52819654--52819687 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52819644 TAAATAAATT
*
52819654 AAAATAATAGACAATA
1 AAAATAAAAGACAATA
*
52819670 AAAATAAAAGATAATA
1 AAAATAAAAGACAATA
52819686 AA
1 AA
52819688 TCACGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAAAAGACAATA
Found at i:52820867 original size:16 final size:17
Alignment explanation
Indices: 52820846--52820877 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52820836 ATCGATATTG
52820846 GATCGATA-CTTAGTTT
1 GATCGATACCTTAGTTT
52820862 GATCGATACCTTAGTT
1 GATCGATACCTTAGTT
52820878 GAATTTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (17 bp):
GATCGATACCTTAGTTT
Found at i:52823803 original size:48 final size:48
Alignment explanation
Indices: 52823738--52823856 Score: 150
Period size: 48 Copynumber: 2.4 Consensus size: 48
52823728 AAAATAATGT
*
52823738 TATTTTAATAGATTTAATATTAAATTAAATTTAATATTTATCTTAATAG-
1 TATTTTATTA-ATTTAATATTAAATTAAATTTAATATTTATCTT-ATAGA
* *
52823787 TATTTTATTAATTTAATATTAAATTTAATTTAATGTTTATCTTATAGA
1 TATTTTATTAATTTAATATTAAATTAAATTTAATATTTATCTTATAGA
52823835 TAAATATTCTATTAATTTAATA
1 T--AT-TT-TATTAATTTAATA
52823857 ATATTTAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
47 4 0.06
48 32 0.52
49 9 0.15
50 2 0.03
51 2 0.03
52 13 0.21
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (48 bp):
TATTTTATTAATTTAATATTAAATTAAATTTAATATTTATCTTATAGA
Found at i:52823816 original size:17 final size:17
Alignment explanation
Indices: 52823749--52823820 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
52823739 ATTTTAATAG
*
52823749 ATTTAATATTAAATTAA
1 ATTTAATATTAAATTTA
*
52823766 ATTTAATATT-TATCTTA
1 ATTTAATATTAAAT-TTA
* **
52823783 A--TAGTATTTTA-TTA
1 ATTTAATATTAAATTTA
52823797 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
52823814 ATTTAAT
1 ATTTAAT
52823821 GTTTATCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.09
15 6 0.14
16 11 0.25
17 23 0.52
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:52831038 original size:24 final size:24
Alignment explanation
Indices: 52831011--52831095 Score: 99
Period size: 24 Copynumber: 3.6 Consensus size: 24
52831001 GGTGGCAATG
52831011 GAAAACTTTATCCTTATGTTATAT
1 GAAAACTTTATCCTTATGTTATAT
52831035 GAAATA-TAAATTAT--TTAT-TTATA-
1 GAAA-ACT---TTATCCTTATGTTATAT
52831058 GAAAACTTTATCCTTATGTTATAT
1 GAAAACTTTATCCTTATGTTATAT
52831082 GAAAACTTTATCCT
1 GAAAACTTTATCCT
52831096 AATTGTTGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
20 4 0.08
22 5 0.10
23 10 0.19
24 24 0.46
25 5 0.10
27 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.45
Consensus pattern (24 bp):
GAAAACTTTATCCTTATGTTATAT
Found at i:52831258 original size:159 final size:160
Alignment explanation
Indices: 52830933--52831242 Score: 464
Period size: 159 Copynumber: 1.9 Consensus size: 160
52830923 TCTAAAGGCA
52830933 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTTAAAGACGCAAATAAGACCAAAATTCAAGATA
1 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTTAAAGACGCAAATAAGACCAAAATTCAAGATA
*
52830998 GTGGGTGGCAATGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTATAGAAAA
66 GTGGGTGGCAATGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAAGAAAA
*** ** * * ** *
52831063 CTTTATCCTTATGTTATATGAAAACTTTAT
131 AGGTAAACTTATATAATACCAAAACTATAT
*
52831093 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTTAAAGATGC-AATAAGACCAAAATTCAAGATA
1 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTTAAAGACGCAAATAAGACCAAAATTCAAGATA
52831157 GTGGGTGGCAATGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAATGTTA
66 GTGGGTGGCAATGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAA-G--A
52831222 AAAAGGTAAAC-TA-ATAATACC
128 AAAAGGTAAACTTATATAATACC
52831243 TTAATATATG
Statistics
Matches: 136, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
159 81 0.60
160 46 0.34
161 2 0.01
162 7 0.05
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (160 bp):
CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTTAAAGACGCAAATAAGACCAAAATTCAAGATA
GTGGGTGGCAATGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAAGAAAA
AGGTAAACTTATATAATACCAAAACTATAT
Found at i:52832555 original size:2 final size:2
Alignment explanation
Indices: 52832548--52832576 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52832538 TAATAGTAGA
52832548 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 A
52832577 GACACGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52835892 original size:15 final size:16
Alignment explanation
Indices: 52835874--52835907 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52835864 AAATTAAATT
52835874 AATTAA-CTAAATGAA
1 AATTAACCTAAATGAA
*
52835889 AATTAACCTAAATGCA
1 AATTAACCTAAATGAA
52835905 AAT
1 AAT
52835908 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGAA
Found at i:52840613 original size:42 final size:43
Alignment explanation
Indices: 52840519--52840685 Score: 216
Period size: 43 Copynumber: 3.9 Consensus size: 43
52840509 TATTGAATAA
* ** *
52840519 AAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTTTGATTATG
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTGAATATG
52840562 AAAGGGGTTGCTAAGTGCTGATTCC-CCGTATCACTGAATAT-
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTGAATATG
* * *
52840603 AAAGGTGGTTGCTAAGTGCTGATTCCACCGAATC-CTTAATTGTG
1 AAAGG-GGTTGCTAAGTGCTGATTCCACCGTATCACTGAA-TATG
*
52840647 AAAGGGGTTGCTATGTGCTGATTCC-CCGTATCACTGAAT
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTGAAT
52840686 TTATGGTGGA
Statistics
Matches: 109, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
41 5 0.05
42 44 0.40
43 55 0.50
44 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTGAATATG
Found at i:52840624 original size:85 final size:84
Alignment explanation
Indices: 52840512--52840685 Score: 276
Period size: 85 Copynumber: 2.1 Consensus size: 84
52840502 CAGAATATAT
* * *
52840512 TGAATAAAAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTTTGATTATGAAAGGGGTTGCTAAG
1 TGAATAAAAAGGGGTTGCTAAGTGCTGATCCCACCGAATCCTTAATTATGAAAGGGGTTGCTAAG
52840577 TGCTGATTCCCCGTATCAC
66 TGCTGATTCCCCGTATCAC
* * * *
52840596 TGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTGAAAGGGGTTGCTAT
1 TGAATAAAAAGG-GGTTGCTAAGTGCTGATCCCACCGAATCCTTAATTATGAAAGGGGTTGCTAA
52840661 GTGCTGATTCCCCGTATCAC
65 GTGCTGATTCCCCGTATCAC
52840681 TGAAT
1 TGAAT
52840686 TTATGGTGGA
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 11 0.13
85 71 0.87
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (84 bp):
TGAATAAAAAGGGGTTGCTAAGTGCTGATCCCACCGAATCCTTAATTATGAAAGGGGTTGCTAAG
TGCTGATTCCCCGTATCAC
Found at i:52843142 original size:23 final size:22
Alignment explanation
Indices: 52843099--52843144 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
52843089 TTTGTTTTTA
*
52843099 ACTTTAACTTTTATTTAAAAAC
1 ACTTTAACTTTTATATAAAAAC
* *
52843121 ACTTTAATTTGTTATATCAAAAC
1 ACTTTAACTT-TTATATAAAAAC
52843144 A
1 A
52843145 TATTATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (22 bp):
ACTTTAACTTTTATATAAAAAC
Found at i:52855105 original size:33 final size:33
Alignment explanation
Indices: 52855068--52855141 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
52855058 CTACTGAGAA
* * *
52855068 AGTAAACACAGAATAGAGATAA-TCCGTTGGGAT
1 AGTAAACACAGAACAGAG-TAAGTCCGTCGGGAG
*
52855101 AGTAAACACAGAACAGAGTAAGTTCGTCGGGAG
1 AGTAAACACAGAACAGAGTAAGTCCGTCGGGAG
52855134 AGTAAACA
1 AGTAAACA
52855142 TGAGGTGAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 3 0.08
33 33 0.92
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.18
Consensus pattern (33 bp):
AGTAAACACAGAACAGAGTAAGTCCGTCGGGAG
Found at i:52856725 original size:29 final size:29
Alignment explanation
Indices: 52856665--52856753 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
52856655 CATAACAAAA
* * *
52856665 CAACCACAAGGGCTTCCGCATATAACATATT
1 CAACCACAAGGGC-T-CACATATAATAGATT
*
52856696 CAACCACAAAGGCTCACATATAATAGATT
1 CAACCACAAGGGCTCACATATAATAGATT
** * *
52856725 CTGCCACTAGGGCTCACATATAATTGATT
1 CAACCACAAGGGCTCACATATAATAGATT
52856754 TCGCCACTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 36 0.73
30 1 0.02
31 12 0.24
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (29 bp):
CAACCACAAGGGCTCACATATAATAGATT
Found at i:52856759 original size:29 final size:29
Alignment explanation
Indices: 52856706--52856776 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
52856696 CAACCACAAA
52856706 GGCTCACATATAATAGATTCTGCCACTAG
1 GGCTCACATATAATAGATTCTGCCACTAG
*
52856735 GGCTCACATATAATTGATT-TCGCCACTAG
1 GGCTCACATATAATAGATTCT-GCCACTAG
52856764 GGC-CTACATATAA
1 GGCTC-ACATATAA
52856777 CTCAATGTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (29 bp):
GGCTCACATATAATAGATTCTGCCACTAG
Found at i:52864783 original size:25 final size:25
Alignment explanation
Indices: 52864691--52864803 Score: 104
Period size: 25 Copynumber: 4.5 Consensus size: 25
52864681 ATTCATGTAT
* * *
52864691 GCTCATACGAGCTATGAATCAGTAT
1 GCTCATACGAGCTATAAATCAGGAA
* *
52864716 GCTC-TCACGAGTTATGAATCAGGAA
1 GCTCAT-ACGAGCTATAAATCAGGAA
* * *
52864741 GCTCATACAAGCTGTAAATCGGGAA
1 GCTCATACGAGCTATAAATCAGGAA
*
52864766 GCTCATACGAGCTATAAAT-TGGAAA
1 GCTCATACGAGCTATAAATCAGG-AA
*
52864791 GCTCATACAAGCT
1 GCTCATACGAGCT
52864804 GTGGTGTCTC
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
24 3 0.04
25 69 0.95
26 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCAGGAA
Found at i:52872345 original size:24 final size:24
Alignment explanation
Indices: 52872299--52872351 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
52872289 TAATAATTGA
52872299 AATATTTTATAATTAATTATTTTT
1 AATATTTTATAATTAATTATTTTT
*
52872323 TATATTTT-TAATTGTAATT-TTTTT
1 AATATTTTATAA-T-TAATTATTTTT
52872347 AATAT
1 AATAT
52872352 AAAGATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 3 0.12
24 17 0.68
25 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
AATATTTTATAATTAATTATTTTT
Found at i:52873863 original size:19 final size:19
Alignment explanation
Indices: 52873839--52873880 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
52873829 ACTGGTTCAT
*
52873839 GAAAAAAAATTGAATTGTA
1 GAAAAAAAACTGAATTGTA
*
52873858 GAAAAAAAACTGATTTGTA
1 GAAAAAAAACTGAATTGTA
52873877 GAAA
1 GAAA
52873881 TGAAGGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (19 bp):
GAAAAAAAACTGAATTGTA
Found at i:52874358 original size:12 final size:12
Alignment explanation
Indices: 52874343--52874368 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52874333 TAGTTATATA
52874343 TATTTCTATAAT
1 TATTTCTATAAT
52874355 TATTTCTATAAT
1 TATTTCTATAAT
52874367 TA
1 TA
52874369 ATATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTCTATAAT
Found at i:52875337 original size:29 final size:28
Alignment explanation
Indices: 52875304--52875372 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
52875294 ATTTTATTAG
*
52875304 TTTTTAATAATTTTAAATTCTTTTCTAT-
1 TTTTT-ATAATTTTAAATTATTTTCTATA
52875332 TCTTTTATAAATTTTAAATTATTTTCTATA
1 T-TTTTAT-AATTTTAAATTATTTTCTATA
52875362 TTTTTATAATT
1 TTTTTATAATT
52875373 ATTTAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 7 0.19
29 29 0.78
30 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTTATAATTTTAAATTATTTTCTATA
Found at i:52875384 original size:29 final size:29
Alignment explanation
Indices: 52875312--52875384 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
52875302 AGTTTTTAAT
**
52875312 AATTTTAAATTCTTTTCTATTCTTTTATA
1 AATTTTAAATAATTTTCTATTCTTTTATA
*
52875341 AATTTTAAATTATTTTCTATAT-TTTTATA
1 AATTTTAAATAATTTTCTAT-TCTTTTATA
*
52875370 ATTATTTAAA-AATTT
1 AAT-TTTAAATAATTT
52875385 ATTTTGCCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 32 0.82
30 7 0.18
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (29 bp):
AATTTTAAATAATTTTCTATTCTTTTATA
Found at i:52876558 original size:21 final size:21
Alignment explanation
Indices: 52876528--52876596 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
52876518 ACTCACAAAG
* * *
52876528 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
52876548 AAAAAGAGAAGAAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
52876569 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
52876590 AAAAAGA
1 AAAAAGA
52876597 AACAAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.57, C:0.07, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:52876980 original size:18 final size:18
Alignment explanation
Indices: 52876957--52877000 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
52876947 TTGCGATCGG
52876957 ATCGATTCTTTTTAATGA
1 ATCGATTCTTTTTAATGA
52876975 ATCGATTCTTTTTAATGA
1 ATCGATTCTTTTTAATGA
52876993 ATCGATTC
1 ATCGATTC
52877001 AATACATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (18 bp):
ATCGATTCTTTTTAATGA
Found at i:52885206 original size:53 final size:53
Alignment explanation
Indices: 52885093--52885199 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
52885083 ACCTTGATAC
52885093 AGCTGGATCTTGGAGGCCTTCTAGTTGTTGTTCATGTGCTATAACTGGATCTT
1 AGCTGGATCTTGGAGGCCTTCTAGTTGTTGTTCATGTGCTATAACTGGATCTT
52885146 AGCTGGATCTTGGAGGCCTTCTAGTTGTTGTTCATGTGCTATAACTGGATCTT
1 AGCTGGATCTTGGAGGCCTTCTAGTTGTTGTTCATGTGCTATAACTGGATCTT
52885199 A
1 A
52885200 CATGGATGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (53 bp):
AGCTGGATCTTGGAGGCCTTCTAGTTGTTGTTCATGTGCTATAACTGGATCTT
Found at i:52894016 original size:25 final size:25
Alignment explanation
Indices: 52893988--52894065 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 25
52893978 AGTGTCTCGT
*
52893988 TATATGGCTCTCCGGAGCTTTTCGA
1 TATATGGCTCTCCAGAGCTTTTCGA
* *
52894013 TATATGGCTC-GCATGAGC-TTCCAGA
1 TATATGGCTCTCCA-GAGCTTTTC-GA
52894038 T-TAATGGCTCTCCAGAGCTTTTCGA
1 TAT-ATGGCTCTCCAGAGCTTTTCGA
52894063 TAT
1 TAT
52894066 TTGCTCACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
24 5 0.12
25 31 0.74
26 6 0.14
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (25 bp):
TATATGGCTCTCCAGAGCTTTTCGA
Found at i:52894050 original size:50 final size:48
Alignment explanation
Indices: 52893990--52894096 Score: 153
Period size: 50 Copynumber: 2.2 Consensus size: 48
52893980 TGTCTCGTTA
* *
52893990 TATGGCTCTCCGGAGCTTTTCGATATATGGCTCGCATGAGCTT-CCAGAT
1 TATGGCTCTCCAGAGCTTTTCGATAT-TGGCTCACATGAGCTTCCCA-AT
*
52894039 TAATGGCTCTCCAGAGCTTTTCGATATTTGCTCACATGAGCTTCCCAAT
1 T-ATGGCTCTCCAGAGCTTTTCGATATTGGCTCACATGAGCTTCCCAAT
52894088 TATGGCTCT
1 TATGGCTCT
52894097 TATGAGCTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
48 8 0.15
49 18 0.34
50 27 0.51
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.35
Consensus pattern (48 bp):
TATGGCTCTCCAGAGCTTTTCGATATTGGCTCACATGAGCTTCCCAAT
Found at i:52894120 original size:49 final size:50
Alignment explanation
Indices: 52893991--52894120 Score: 126
Period size: 49 Copynumber: 2.6 Consensus size: 50
52893981 GTCTCGTTAT
* ** *
52893991 ATGGCTCTCCGGAGCTTTTCGATATATG-GCTCGCATGAGCTTCCAGATTA
1 ATGGCTCTCCAGAGCTTCCCG-TATATGTGCTCACATGAGCTTCCAGATTA
** *
52894041 ATGGCTCTCCAGAGCTTTTCG-ATATTTGCTCACATGAGCTTCCCA-ATT-
1 ATGGCTCTCCAGAGCTTCCCGTATATGTGCTCACATGAGCTT-CCAGATTA
*
52894089 ATGGCTCT-TATGAGCTTCCCGTATATGTGCTC
1 ATGGCTCTCCA-GAGCTTCCCGTATATGTGCTC
52894121 GAACGAGCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
47 1 0.01
48 20 0.29
49 25 0.36
50 23 0.33
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (50 bp):
ATGGCTCTCCAGAGCTTCCCGTATATGTGCTCACATGAGCTTCCAGATTA
Found at i:52898254 original size:51 final size:50
Alignment explanation
Indices: 52898123--52898260 Score: 152
Period size: 50 Copynumber: 2.7 Consensus size: 50
52898113 GTGAAGTTGC
* *
52898123 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGG
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAAATGG
* * * * * * *
52898173 TAGGTTACATGTGTAGTATTGTGTGCAGGCTGCTATGCGTACCG-GATAGCT
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAAAT-G-G
* *
52898224 TCGGTCACGTGTGTAGTACTATGTGTAGGCTACTATG
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTATG
52898261 TGAATCGAGT
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
49 2 0.03
50 38 0.54
51 30 0.43
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (50 bp):
TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAAATGG
Found at i:52901118 original size:8 final size:9
Alignment explanation
Indices: 52901064--52901126 Score: 51
Period size: 8 Copynumber: 7.2 Consensus size: 9
52901054 AATGATCATT
52901064 TTTTTATAA
1 TTTTTATAA
*
52901073 -TTTTAAAA
1 TTTTTATAA
52901081 TTTGTTATAA
1 TTT-TTATAA
**
52901091 CATTTAT-A
1 TTTTTATAA
*
52901099 TTTTTATGA
1 TTTTTATAA
52901108 TTTTTA-AA
1 TTTTTATAA
*
52901116 TTTTTTTAA
1 TTTTTATAA
52901125 TT
1 TT
52901127 AGTTTTATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
8 19 0.45
9 17 0.40
10 6 0.14
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52903525 original size:41 final size:41
Alignment explanation
Indices: 52903480--52903588 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 41
52903470 CTGGTGAATT
52903480 ATATCAGGCTTTATGCCTAGCAGGCTTCGTGCCGGTGTACC
1 ATATCAGGCTTTATGCCTAGCAGGCTTCGTGCCGGTGTACC
** *
52903521 ATATCAGGCTTTATGCCTAGCAGGCTTCGTGTTGGTGTATC
1 ATATCAGGCTTTATGCCTAGCAGGCTTCGTGCCGGTGTACC
* * *
52903562 ATATCTA-GCTTTGTGACTAGAAGGCTT
1 ATATC-AGGCTTTATGCCTAGCAGGCTT
52903589 TATGTCGATG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 60 0.98
42 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (41 bp):
ATATCAGGCTTTATGCCTAGCAGGCTTCGTGCCGGTGTACC
Found at i:52912609 original size:20 final size:20
Alignment explanation
Indices: 52912584--52912623 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52912574 ACAACATTGA
*
52912584 ATAGTTAATCTTTAGGGATT
1 ATAGTTAATCTTTAGAGATT
* *
52912604 ATAGTTGATTTTTAGAGATT
1 ATAGTTAATCTTTAGAGATT
52912624 CTAATTAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (20 bp):
ATAGTTAATCTTTAGAGATT
Found at i:52914716 original size:21 final size:20
Alignment explanation
Indices: 52914685--52914741 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
52914675 TTCTCAATCC
52914685 AATATACATTTCAATATCACAAT
1 AATAT-CATTTCAAT-TCA-AAT
52914708 AAT-TCATTT-AATTCAAAT
1 AATATCATTTCAATTCAAAT
*
52914726 CATATCATTTGCAATT
1 AATATCATTT-CAATT
52914742 TCCATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 9 0.30
20 3 0.10
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (20 bp):
AATATCATTTCAATTCAAAT
Found at i:52915260 original size:35 final size:35
Alignment explanation
Indices: 52915214--52915283 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
52915204 CAACATGAGT
*
52915214 TAATTCATAAACCATTTCTGACATTGCTACATACC
1 TAATTCATAAACCATTTCTAACATTGCTACATACC
52915249 TAATTCATAAACCATTTCTAACATTGCTACATACC
1 TAATTCATAAACCATTTCTAACATTGCTACATACC
52915284 AAATCGTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (35 bp):
TAATTCATAAACCATTTCTAACATTGCTACATACC
Found at i:52916237 original size:23 final size:22
Alignment explanation
Indices: 52916194--52916237 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52916184 TTCCAAGTCG
52916194 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
52916217 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52916238 TTATGGCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:52916279 original size:16 final size:16
Alignment explanation
Indices: 52916258--52916311 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
52916248 TTTAGTTCGC
52916258 TGTAATGGAATACAGG
1 TGTAATGGAATACAGG
* * *
52916274 TGTAATGGAGTAGAGC
1 TGTAATGGAATACAGG
* *
52916290 TGTAAAGGAATATAGG
1 TGTAATGGAATACAGG
*
52916306 CGTAAT
1 TGTAAT
52916312 AGTAATTCAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATACAGG
Found at i:52916760 original size:13 final size:12
Alignment explanation
Indices: 52916736--52916776 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
52916726 TATAATACTA
52916736 TAAAATATAATT
1 TAAAATATAATT
52916748 TAAAATAATAATT
1 TAAAAT-ATAATT
*
52916761 ATTAAATATAATT
1 -TAAAATATAATT
52916774 TAA
1 TAA
52916777 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:52916807 original size:17 final size:18
Alignment explanation
Indices: 52916646--52916799 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
52916636 TTATTATTAA
52916646 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
52916664 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
* ****
52916682 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
*
52916701 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
52916719 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* * *
52916735 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
*
52916754 A-ATAA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
52916766 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
52916784 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
52916800 TTCTTAATAT
Statistics
Matches: 97, Mismatches: 25, Indels: 28
0.65 0.17 0.19
Matches are distributed among these distances:
12 1 0.01
13 6 0.06
14 2 0.02
15 4 0.04
16 8 0.08
17 15 0.15
18 42 0.43
19 13 0.13
20 3 0.03
21 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:52916876 original size:119 final size:120
Alignment explanation
Indices: 52916544--52916983 Score: 796
Period size: 119 Copynumber: 3.7 Consensus size: 120
52916534 TTATTATTAA
* *
52916544 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTCTATGAATTTACTGAAATCATAATATAT
1 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
*
52916609 AATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
66 AATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
52916664 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
52916729 AATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
66 AATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
* *
52916784 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
52916848 AATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
66 AATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
* *
52916903 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
52916967 AATACTATAAAA-ATAAT
66 AATACTATAAAATATAAT
52916984 ATATAATCTA
Statistics
Matches: 315, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
118 5 0.02
119 169 0.54
120 141 0.45
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (120 bp):
ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
AATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
Found at i:52916879 original size:13 final size:12
Alignment explanation
Indices: 52916855--52916895 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
52916845 TATAATACTA
52916855 TAAAATATAATT
1 TAAAATATAATT
52916867 TAAAATAATAATT
1 TAAAAT-ATAATT
*
52916880 ATTAAATATAATT
1 -TAAAATATAATT
52916893 TAA
1 TAA
52916896 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:52918433 original size:49 final size:49
Alignment explanation
Indices: 52918358--52918461 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
52918348 AGAAAAAAAC
* * * *
52918358 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATAACATGAATCAAAAGCTCAACACTTTATA
52918407 AAATTAAAATTAAGTTCAATAACATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATAACATGAATCAAAAGCTCAACACTTTATA
52918456 AAATTA
1 AAATTA
52918462 TAACACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATAACATGAATCAAAAGCTCAACACTTTATA
Found at i:52920852 original size:16 final size:16
Alignment explanation
Indices: 52920813--52920846 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
52920803 AATAAATTAG
52920813 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
52920829 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
52920845 AA
1 AA
52920847 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:52921442 original size:15 final size:15
Alignment explanation
Indices: 52921422--52921459 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
52921412 TATCATTTTC
*
52921422 TCAAACATGCCATAG
1 TCAAACACGCCATAG
52921437 TCAAACACGCCATAG
1 TCAAACACGCCATAG
52921452 TCAAACAC
1 TCAAACAC
52921460 TTTACAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (15 bp):
TCAAACACGCCATAG
Found at i:52922026 original size:21 final size:20
Alignment explanation
Indices: 52921996--52922043 Score: 87
Period size: 21 Copynumber: 2.4 Consensus size: 20
52921986 TAATCCATAA
52921996 ACAGAAAACATCAACTTAAT
1 ACAGAAAACATCAACTTAAT
52922016 ACAGACAAACATCAACTTAAT
1 ACAGA-AAACATCAACTTAAT
52922037 ACAGAAA
1 ACAGAAA
52922044 CCAAAACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.56, C:0.21, G:0.06, T:0.17
Consensus pattern (20 bp):
ACAGAAAACATCAACTTAAT
Found at i:52923018 original size:17 final size:18
Alignment explanation
Indices: 52922998--52923038 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
52922988 AAATAGAGAA
52922998 AAGAAAAAAAACGT-GAG
1 AAGAAAAAAAACGTAGAG
*
52923015 AAGAAAAGAAACGTACGAG
1 AAGAAAAAAAACGTA-GAG
52923034 AAGAA
1 AAGAA
52923039 GAAGCAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.63, C:0.07, G:0.24, T:0.05
Consensus pattern (18 bp):
AAGAAAAAAAACGTAGAG
Found at i:52923548 original size:50 final size:49
Alignment explanation
Indices: 52923413--52923606 Score: 201
Period size: 50 Copynumber: 3.9 Consensus size: 49
52923403 CAATGATGTT
* * *
52923413 CGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCA--AACATC
* * *
52923464 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACATAGTAGCCTACACATAGTACTACACACGTGA-CCAAAC-ATC
* * * * * *
52923515 TGGTAC-CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTC
1 CGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCAAACA-TC
* * *
52923564 CGGTACACGTAGTAGCCTGCACAAAGTACTACACACGTGACCA
1 CGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCA
52923607 TCACTTTCAC
Statistics
Matches: 118, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 10 0.08
50 62 0.53
51 43 0.36
52 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (49 bp):
CGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCAAACATC
Found at i:52923601 original size:100 final size:100
Alignment explanation
Indices: 52923420--52923603 Score: 289
Period size: 100 Copynumber: 1.8 Consensus size: 100
52923410 GTTCGGTTCA
*
52923420 CATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTACA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTACA
*
52923485 CATAGTACTACACACGTGATCGAAACTATCTGGTAC
65 CAAAGTACTACACACGTGATCGAAACTATCTGGTAC
* * * *
52923521 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTACA
52923585 CAAAGTACTACACACGTGA
65 CAAAGTACTACACACGTGA
52923604 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
99 4 0.05
100 39 0.51
101 33 0.43
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (100 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTACAC
AAAGTACTACACACGTGATCGAAACTATCTGGTAC
Found at i:52929774 original size:14 final size:15
Alignment explanation
Indices: 52929752--52929828 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
52929742 CAATCAAACA
52929752 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
52929766 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
52929781 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
52929801 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
52929815 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
52929829 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:52929793 original size:20 final size:20
Alignment explanation
Indices: 52929768--52929807 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52929758 AATATTTTCC
*
52929768 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
52929788 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
52929808 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:52929813 original size:34 final size:35
Alignment explanation
Indices: 52929756--52929822 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
52929746 CAAACACCAG
*
52929756 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
52929791 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
52929823 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:52929829 original size:14 final size:14
Alignment explanation
Indices: 52929791--52929830 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52929781 ACAGAAAAGT
*
52929791 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
52929805 AAATCATTTTACGG
1 AAAACATTTTACAG
52929819 AAAACATTTTAC
1 AAAACATTTTAC
52929831 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:52933464 original size:75 final size:75
Alignment explanation
Indices: 52933323--52933464 Score: 162
Period size: 75 Copynumber: 1.9 Consensus size: 75
52933313 GTACATGCTG
* * * ** *
52933323 CTCATACAAGCATGTAACCGGGAAGCTCCTTCGAGCCATATAACGGGAAACTTATGTGAGCTAAG
1 CTCATACAAGCATGTAACCGGGAAGCTCCTTCGAGACAAATAACGGGAAACTCATAAGAGCCAAG
52933388 TAACGGGGAA
66 TAACGGGGAA
* * * *
52933398 CTCATACTAGC-TGTATATCGGGAAGCT-CTTGCGAGACAAATATCGGGAAGCTCATAAGAGCCA
1 CTCATACAAGCATGTA-ACCGGGAAGCTCCTT-CGAGACAAATAACGGGAAACTCATAAGAGCCA
52933461 AGTA
64 AGTA
52933465 TTGGGAAGCT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
74 7 0.13
75 48 0.87
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (75 bp):
CTCATACAAGCATGTAACCGGGAAGCTCCTTCGAGACAAATAACGGGAAACTCATAAGAGCCAAG
TAACGGGGAA
Found at i:52941025 original size:25 final size:25
Alignment explanation
Indices: 52940996--52941066 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
52940986 TACTAGCTGT
* *
52940996 ATATCGGGAAGCTCTTGCGAGACAA
1 ATATCGGGAAGCTCATGAGAGACAA
* *
52941021 ATATCGAGAAGCTCATGAGAGCCAA
1 ATATCGGGAAGCTCATGAGAGACAA
* *
52941046 GTATCGGGAAGCTCAAGAGAG
1 ATATCGGGAAGCTCATGAGAG
52941067 TTGTGGTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (25 bp):
ATATCGGGAAGCTCATGAGAGACAA
Found at i:52947358 original size:43 final size:43
Alignment explanation
Indices: 52947310--52947481 Score: 299
Period size: 43 Copynumber: 4.0 Consensus size: 43
52947300 CGCTAAAGAA
** *
52947310 GCTAAAGAACATGTTCTTTAGCGGCGCTTTTTACACAAACGCC
1 GCTAAAGCTCATGTTCTTTAGCGGCGCTTTCTACACAAACGCC
*
52947353 GCTAAAGCTCATGTTCTTTAGCGACGCTTTCTACACAAACGCC
1 GCTAAAGCTCATGTTCTTTAGCGGCGCTTTCTACACAAACGCC
52947396 GCTAAAGCTCATGTTCTTTAGCGGCGCTTTCTACACAAACGCC
1 GCTAAAGCTCATGTTCTTTAGCGGCGCTTTCTACACAAACGCC
*
52947439 GCTAAAGCTCATGTTCTTTAGCGGCGCTTTTTACACAAACGCC
1 GCTAAAGCTCATGTTCTTTAGCGGCGCTTTCTACACAAACGCC
52947482 ACTATTTGTT
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 123 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (43 bp):
GCTAAAGCTCATGTTCTTTAGCGGCGCTTTCTACACAAACGCC
Found at i:52947831 original size:21 final size:21
Alignment explanation
Indices: 52947805--52947875 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
52947795 TTCTGCTCTG
*
52947805 CTCTGCTTCTCTCGTTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
*
52947826 CTCTGCTTCTCTCACTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
* * *
52947847 CTCTGTTTCCCTCGCTGCCGC
1 CTCTGCTTCTCTCGCTGCAGC
52947868 CTCTGCTT
1 CTCTGCTT
52947876 TAAGTTGTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.04, C:0.42, G:0.17, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCAGC
Found at i:52953735 original size:24 final size:24
Alignment explanation
Indices: 52953705--52953779 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
52953695 GTATTATCAC
52953705 GTAAGTTATTATGTAGGATATTAT
1 GTAAGTTATTATGTAGGATATTAT
* * *
52953729 GTAAG---TTAGGTAAG-T-TTTT
1 GTAAGTTATTATGTAGGATATTAT
52953748 GTAAGTTATTATGTAGGATATTAT
1 GTAAGTTATTATGTAGGATATTAT
52953772 GTAAGTTA
1 GTAAGTTA
52953780 GGATATTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 8 0.20
20 1 0.03
21 7 0.17
22 7 0.17
23 1 0.03
24 16 0.40
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (24 bp):
GTAAGTTATTATGTAGGATATTAT
Found at i:52955469 original size:6 final size:6
Alignment explanation
Indices: 52955458--52955510 Score: 63
Period size: 6 Copynumber: 8.3 Consensus size: 6
52955448 ACACATGTTA
52955458 AATAAC AATAAC AAATAAC AAATAAC AATAAC AATGAGA- AATAAC AATAAC
1 AATAAC AATAAC -AATAAC -AATAAC AATAAC AAT-A-AC AATAAC AATAAC
52955509 AA
1 AA
52955511 ATAAACAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 1 0.02
6 24 0.56
7 17 0.40
8 1 0.02
ACGTcount: A:0.68, C:0.13, G:0.04, T:0.15
Consensus pattern (6 bp):
AATAAC
Found at i:52955475 original size:13 final size:13
Alignment explanation
Indices: 52955457--52955514 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
52955447 TACACATGTT
52955457 AAATAACAATAAC
1 AAATAACAATAAC
52955470 AAATAACAAATAAC
1 AAATAAC-AATAAC
* *
52955484 -AATAACAATGAG
1 AAATAACAATAAC
52955496 AAATAACAATAAC
1 AAATAACAATAAC
52955509 AAATAA
1 AAATAA
52955515 ACAGTTCTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 4 0.10
13 29 0.74
14 6 0.15
ACGTcount: A:0.69, C:0.12, G:0.03, T:0.16
Consensus pattern (13 bp):
AAATAACAATAAC
Found at i:52958297 original size:23 final size:22
Alignment explanation
Indices: 52958224--52958299 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 22
52958214 TAAACCATAA
52958224 ACTATAAAAGCCTTAAACTACAT
1 ACTATAAAA-CCTTAAACTACAT
*
52958247 ACTATAGTAAACATTAAACCTTA-A-
1 ACTATA--AAACCTTAAA-C-TACAT
52958271 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAA-CCTTAAACTACAT
52958294 ACTATA
1 ACTATA
52958300 GCCCTTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
21 2 0.05
22 5 0.11
23 18 0.41
24 12 0.27
25 5 0.11
26 2 0.05
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.28
Consensus pattern (22 bp):
ACTATAAAACCTTAAACTACAT
Found at i:52958644 original size:24 final size:21
Alignment explanation
Indices: 52958600--52958649 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 21
52958590 CTTCTAATTT
52958600 TAATTAATATAAATAAATAAA
1 TAATTAATATAAATAAATAAA
**
52958621 TCAATTAAATAATAAATAGGTAAA
1 T-AATT-AAT-ATAAATAAATAAA
52958645 TAATT
1 TAATT
52958650 TTTTTGCGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 4 0.17
23 7 0.29
24 12 0.50
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (21 bp):
TAATTAATATAAATAAATAAA
Found at i:52958759 original size:41 final size:41
Alignment explanation
Indices: 52958690--52958974 Score: 387
Period size: 41 Copynumber: 6.9 Consensus size: 41
52958680 AAATGAATAG
* ** * * *
52958690 CATTAGCGGCGTTTTTAAAAAAAGCGCCGCTAAAGGCCTGAGA
1 CATTAGCGGCGCTTACATAAAAA-CGCCGCTAAAGCCCAGA-A
* *
52958733 -ATTAGCGGCGCAT-CAATAAAAACGCCGCTAAATCCCAGAA
1 CATTAGCGGCGCTTAC-ATAAAAACGCCGCTAAAGCCCAGAA
*
52958773 CATTAGCGGCGCTTACTTAAAAACGCCGCTAAAAGCCCAGAA
1 CATTAGCGGCGCTTACATAAAAACGCCGCT-AAAGCCCAGAA
*
52958815 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCGGAA
1 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAA
* *
52958856 CATTAGCGGCGCTTAAATAAAAATGCCGCTAAAGCCCAGAA
1 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAA
*
52958897 CATTAGCGACGCTTACATAAAAACGCCGCTAAAGTCCC-GAA
1 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAG-CCCAGAA
52958938 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCC
1 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCC
52958975 CCGAAAAGTC
Statistics
Matches: 218, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
40 4 0.02
41 154 0.71
42 60 0.28
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (41 bp):
CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAA
Found at i:52958972 original size:82 final size:83
Alignment explanation
Indices: 52958690--52958974 Score: 391
Period size: 83 Copynumber: 3.4 Consensus size: 83
52958680 AAATGAATAG
* ** * * * *
52958690 CATTAGCGGCGTTTTTAAAAAAAGCGCCGCTAAAGGCCTGAGA-ATTAGCGGCGCAT-CAATAAA
1 CATTAGCGGCGCTTACATAAAAA-CGCCGCTAAAGCCCAGA-ACATTAGCGGCGCTTAC-ATAAA
52958753 AACGCCGCTAAA-TCCCAGAA
63 AACGCCGCTAAAGTCCCAGAA
*
52958773 CATTAGCGGCGCTTACTTAAAAACGCCGCTAAAAGCCCAGAACATTAGCGGCGCTTACATAAAAA
1 CATTAGCGGCGCTTACATAAAAACGCCGCT-AAAGCCCAGAACATTAGCGGCGCTTACATAAAAA
*
52958838 CGCCGCTAAAG-CCCGGAA
65 CGCCGCTAAAGTCCCAGAA
* * *
52958856 CATTAGCGGCGCTTAAATAAAAATGCCGCTAAAGCCCAGAACATTAGCGACGCTTACATAAAAAC
1 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAAC
52958921 GCCGCTAAAGTCCC-GAA
66 GCCGCTAAAGTCCCAGAA
52958938 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCC
1 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCC
52958975 CCGAAAAGTC
Statistics
Matches: 182, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
82 90 0.49
83 91 0.50
84 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (83 bp):
CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAAC
GCCGCTAAAGTCCCAGAA
Found at i:52978406 original size:19 final size:19
Alignment explanation
Indices: 52978348--52978407 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
52978338 CGGAAATTGA
* *
52978348 TTTCTAGAAAATGAATTACT
1 TTTCTGGAAAATGATTTA-T
* * *
52978368 TTTCTGGAATA-GCTAATAT
1 TTTCTGGAAAATGAT-TTAT
52978387 TTTCTGGAAAATGATTTAT
1 TTTCTGGAAAATGATTTAT
52978406 TT
1 TT
52978408 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (19 bp):
TTTCTGGAAAATGATTTAT
Found at i:52983353 original size:3 final size:3
Alignment explanation
Indices: 52983345--52983423 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
52983335 AAAGGAAAGG
* * * * *
52983345 AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AGG AGG CGC AGA AGGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA
* * *
52983391 AGA AAA AGGA AAA AG- AGA AGG AGA AGA AGA AGA
1 AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
52983424 GGGAGGGAAG
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.03
3 53 0.88
4 5 0.08
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52983488 original size:20 final size:20
Alignment explanation
Indices: 52983463--52983500 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52983453 AAGGAAAGGT
52983463 ATTTTTTTTATATTATTTTA
1 ATTTTTTTTATATTATTTTA
*
52983483 ATTTTTTTTGTATTATTT
1 ATTTTTTTTATATTATTT
52983501 GTGTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (20 bp):
ATTTTTTTTATATTATTTTA
Found at i:52983713 original size:44 final size:45
Alignment explanation
Indices: 52983624--52983710 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
52983614 TTGTAATGAG
52983624 TTTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAAATA
1 TTTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAAATA
52983669 TTTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAA
1 TTTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAA
52983711 TATGTTTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (45 bp):
TTTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAAATA
Found at i:52984015 original size:161 final size:163
Alignment explanation
Indices: 52983828--52984248 Score: 703
Period size: 162 Copynumber: 2.6 Consensus size: 163
52983818 NNNNNNNNNN
52983828 ATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTT
1 ATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTT
*
52983893 TTGAAAGTAATAAAATCCGGGAAAA-AAGAAAAATACGAAC-AAAGGGCC-AAAATAAGGGTTTT
66 TTGAAAGTAATAAAATCC--GAAAATAAGAAAAATACGAACAAAAGGACCAAAAATAAGGGTTTT
52983955 TTTACTAAATTTATAT-AAAAAACACACTAAATTA
129 TTTACTAAATTTATATAAAAAAACACACTAAATTA
*
52983989 ATATATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATAC-AAAAATAGTATA-TTT
1 ATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTT
* *
52984052 TTGTAAAGTAATAAAATCCGAAAATAAGAAAAAAACGAACAAAAGGACCAAAAATAATGGTTTTT
66 TTG-AAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAAGGACCAAAAATAAGGGTTTTT
52984117 TTACTAAATTTATATAAAAAAACACACTAAATTA
130 TTACTAAATTTATATAAAAAAACACACTAAATTA
*
52984151 ATACATTTCAAACATTATGTACTAAAATAATATGAAATAATAAAATACG-AAAATAGTATATTTT
1 ATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTT
* *
52984215 TTTAAAGTAATAAAATTCGAAAATAAGAAAAATA
66 TTGAAAGTAATAAAATCCGAAAATAAGAAAAATA
52984249 TATTAAAATT
Statistics
Matches: 244, Mismatches: 9, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
158 5 0.02
159 20 0.08
160 34 0.14
161 76 0.31
162 104 0.43
163 5 0.02
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (163 bp):
ATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTT
TTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAAGGACCAAAAATAAGGGTTTTTT
TACTAAATTTATATAAAAAAACACACTAAATTA
Found at i:52989605 original size:76 final size:76
Alignment explanation
Indices: 52989525--52989666 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 76
52989515 ATAATAGTTT
52989525 ACTAAAAATAATACTAACTAACAATAATAATTAGGG-TTTTACTAAAAATAATAACTAACAATAA
1 ACTAAAAATAATACTAACTAA-AATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAA
52989589 TATAGTGTAAAA
65 TATAGTGTAAAA
* * *** *
52989601 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTTACTAATCCTAATAACTAACCATAAT
1 ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
52989666 A
66 A
52989667 ATACTAGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 14 0.24
76 45 0.76
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
ATAGTGTAAAA
Found at i:52990015 original size:20 final size:20
Alignment explanation
Indices: 52989982--52990035 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
52989972 CTCATCCTCC
*
52989982 TTCTTT-TTCCCCTTTCCTT
1 TTCTTTCTTCTCCTTTCCTT
*
52990001 TTCTTTCTTCTCCTTTTCTT
1 TTCTTTCTTCTCCTTTCCTT
52990021 TTCTTTCTTCTCCTT
1 TTCTTTCTTCTCCTT
52990036 CAGCTGAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTTCTTCTCCTTTCCTT
Found at i:52990382 original size:6 final size:6
Alignment explanation
Indices: 52990345--52990413 Score: 66
Period size: 6 Copynumber: 10.5 Consensus size: 6
52990335 TCTACTTTGG
* *
52990345 TTTTAA TATTTAA TTTTACA TTTCAA TTTTTTTA TTTTAA TTTTAA TTTTAA
1 TTTTAA T-TTTAA TTTTA-A TTTTAA --TTTTAA TTTTAA TTTTAA TTTTAA
52990397 TATTTAA TTTTATA TTT
1 T-TTTAA TTTTA-A TTT
52990414 GAGTTTAGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
6 28 0.53
7 21 0.40
8 4 0.08
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:52990388 original size:13 final size:13
Alignment explanation
Indices: 52990345--52990413 Score: 61
Period size: 13 Copynumber: 5.2 Consensus size: 13
52990335 TCTACTTTGG
52990345 TTTTAATATTTAA-
1 TTTTAAT-TTTAAT
*
52990358 TTTTACATTTCAATT
1 TTTTA-ATTTTAA-T
*
52990373 TTTTTATTTTAA-
1 TTTTAATTTTAAT
52990385 TTTTAATTTTAAT
1 TTTTAATTTTAAT
*
52990398 ATTTAATTTTATAT
1 TTTTAATTTTA-AT
52990412 TT
1 TT
52990414 GAGTTTAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 11 0.24
13 19 0.42
14 11 0.24
15 4 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:52990392 original size:20 final size:20
Alignment explanation
Indices: 52990345--52990413 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
52990335 TCTACTTTGG
52990345 TTTTAATA-TTTAATTTTACA
1 TTTTAATATTTTAATTTTA-A
* * *
52990365 TTTCAATTTTTTTATTTTAA
1 TTTTAATATTTTAATTTTAA
52990385 TTTT-A-ATTTTAATATTTAA
1 TTTTAATATTTTAAT-TTTAA
52990404 TTTT-ATATTT
1 TTTTAATATTT
52990414 GAGTTTAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 6 0.15
19 11 0.28
20 14 0.35
21 9 0.22
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATATTTTAATTTTAA
Found at i:52991472 original size:27 final size:26
Alignment explanation
Indices: 52991442--52991501 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
52991432 TAATCACTTC
* *
52991442 ATATAACTAATTCCATATAACTGATTT
1 ATATAACTAATTCCACAT-ACTCATTT
* *
52991469 ATATAA-TCATTTCACATACTCATTT
1 ATATAACTAATTCCACATACTCATTT
52991494 ATATAACT
1 ATATAACT
52991502 CTTTCGTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 13 0.46
26 9 0.32
27 6 0.21
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATAACTAATTCCACATACTCATTT
Found at i:52991474 original size:13 final size:13
Alignment explanation
Indices: 52991442--52991502 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
52991432 TAATCACTTC
* *
52991442 ATATAACTAATTCC
1 ATATAACTCATT-T
*
52991456 ATATAACTGATTT
1 ATATAACTCATTT
52991469 ATATAA-TCATTT
1 ATATAACTCATTT
*
52991481 CACAT-ACTCATTT
1 -ATATAACTCATTT
52991494 ATATAACTC
1 ATATAACTC
52991503 TTTCGTATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 9 0.23
13 19 0.49
14 11 0.28
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (13 bp):
ATATAACTCATTT
Found at i:52991532 original size:26 final size:26
Alignment explanation
Indices: 52991503--52991584 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
52991493 TATATAACTC
* *
52991503 TTTCGTATACCCATCTCATTTTACCA
1 TTTCGTATAACCATTTCATTTTACCA
* * *
52991529 TTTCGTTTAACCATTTCATATAACCA
1 TTTCGTATAACCATTTCATTTTACCA
52991555 TTTCG-AGTAACCATTTCATTTTACACA
1 TTTCGTA-TAACCATTTCATTTTAC-CA
52991582 TTT
1 TTT
52991585 AACACGTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 41 0.89
27 5 0.11
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (26 bp):
TTTCGTATAACCATTTCATTTTACCA
Found at i:52991541 original size:13 final size:13
Alignment explanation
Indices: 52991525--52991571 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
52991515 ATCTCATTTT
*
52991525 ACCATTTCGTTTA
1 ACCATTTCGTATA
*
52991538 ACCATTTCATATA
1 ACCATTTCGTATA
52991551 ACCATTTCG-AGTA
1 ACCATTTCGTA-TA
52991564 ACCATTTC
1 ACCATTTC
52991572 ATTTTACACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 1 0.03
13 29 0.97
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (13 bp):
ACCATTTCGTATA
Found at i:52996198 original size:9 final size:9
Alignment explanation
Indices: 52996187--52996262 Score: 64
Period size: 9 Copynumber: 8.2 Consensus size: 9
52996177 TTAATTAATT
*
52996187 TTTTAAAAT
1 TTTTAAAAA
52996196 TTTTAAAAA
1 TTTTAAAAA
*
52996205 -ATTAAAAA
1 TTTTAAAAA
52996213 TTATTAAAAA
1 TT-TTAAAAA
*
52996223 TATTAAAAA
1 TTTTAAAAA
* *
52996232 GTATTAAAATC
1 -TTTTAAAA-A
*
52996243 TTTTTAAAA
1 TTTTAAAAA
52996252 TTTTAAAAA
1 TTTTAAAAA
52996261 TT
1 TT
52996263 AATTAAACGT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
8 7 0.13
9 25 0.46
10 22 0.41
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:52996214 original size:18 final size:19
Alignment explanation
Indices: 52996191--52996240 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
52996181 TTAATTTTTT
*
52996191 AAAATTTTTAAAAA-ATTA
1 AAAATTATTAAAAATATTA
52996209 AAAATTATTAAAAATATTA
1 AAAATTATTAAAAATATTA
*
52996228 AAAAGTATTAAAA
1 AAAATTATTAAAA
52996241 TCTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTATTAAAAATATTA
Found at i:52996976 original size:61 final size:60
Alignment explanation
Indices: 52996872--52997015 Score: 148
Period size: 61 Copynumber: 2.4 Consensus size: 60
52996862 TAAAAAGTAT
* * * * *
52996872 AATGAGAATTTTTAAAAA-TTTGAGGAGACCTAATTAAAGTTTTCTAAAA-ACTTCAATGGAGA
1 AATGAAAATTTTTAAAAATTTTG-GG-G-CCTAATTAAAATTTTC-AAAAGAATTCAAGGGAAA
*
52996934 AATGAAAATTTTTAAAAAATTTTGGGGCTTAATTAAAATTTTCAAAAGAATTCAAGGGAAA
1 AATGAAAATTTTT-AAAAATTTTGGGGCCTAATTAAAATTTTCAAAAGAATTCAAGGGAAA
* * *
52996995 AATTAAAATTTCTCAAAATTT
1 AATGAAAATTTTTAAAAATTT
52997016 GTTGGGGCAA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
60 11 0.16
61 35 0.50
62 13 0.19
63 7 0.10
64 4 0.06
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (60 bp):
AATGAAAATTTTTAAAAATTTTGGGGCCTAATTAAAATTTTCAAAAGAATTCAAGGGAAA
Found at i:53000210 original size:371 final size:369
Alignment explanation
Indices: 52999387--53006546 Score: 4548
Period size: 372 Copynumber: 19.0 Consensus size: 369
52999377 GAAGAGAAAA
* * * *
52999387 GAAATTGC-AGAAATCCTCACTCACCAGAAGAGAAAAC-CTCTCACGAACCACCCTTAGCAAAAT
1 GAAATTGCTA-AAATCCTCACTCGCTAGAAGAGTAAACGC-CTCACGAACCACCCCTAGCAAAAT
* *
52999450 CACAACTAATGAAACAAAAAGACCTTCCAAAGATATCAAAACAACCACCCTAAAATGAAACTAAC
64 CACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAAC
* ** * * **
52999515 AAATTATAC-T---TGAGGATTTTAATAACACCAATGCAGTTTAAATGATGGCACAATAGAAGAT
129 GAATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGAT
* * * **
52999576 AGGTTGGCAATGAAGAAACAATAGCAAGAGA-TAACAACAGGGGAAAATGATAACAAATGTAAAA
194 AGGTCGGCAATGAAGAAACAATAGCAAGAGACGAA-AACAGGGGAATATGGCAACAAATGTAAAA
* * * *
52999640 GAAACAAAAGAATAATGAAACAGAAATAAAGAAGAAGAAAAAAATAACGTCAGAGGAACAGAAAA
258 GAAACGAAAGAA-AATAAAACAGAAAGAAAGAAGAA-AAAAAAATAACGTTAGAGGAACA-AAAA
* * * *
52999705 TAGGACAAAAGAGATGGAAGTAGTGGAAAGAGAAGAACATAAAAAATTGGG
320 TTGGA-AAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
* * * * * **
52999756 GAAATTGCTAAAATCATCACTCTCCAGAAGAGTAAACACCTTACGAACCACCTTTAGCAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* ** *
52999821 TAACTAACAAAACCAAAAGACCTTCCAAAGATACCAAGACAACCACCCTAAAATGAAACTAACGA
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
*
52999886 ATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAACAGAAGATAG
131 ATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATAG
* ** * *
52999951 ATCGATAATGAAGAAGCAATATCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGAA
196 GTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGAA
* * * * *
53000016 ACGAAAGCAAAATGAAATA-AAAAAAAGAAGAAAAAGAAAATAAAGTTAGAGGAACAGAAAGTTG
261 ACGAAAG-AAAATAAAACAGAAAGAAAGAAGAAAAA-AAAATAACGTTAGAGGAACA-AAAATTG
*
53000080 GAAAAAGAAATGGAAGTAGTGGAAAAAGAGGAACATAAAAAATTTGG
323 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
* * * *
53000127 GAAATTGCTAAAACCCTCACTCGCTAGAAAAGTAAACGCCTTACGAACCACCCCTAGAAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* * *
53000192 -ACACTAATGAAACCAAAAGTCCTTCCAAAGATAGCAAAACAACCACCCTAAAATGAAACTAACG
66 CA-ACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACG
* * * * * * * * * *
53000256 AATTATACATACTTGAAGATTTTAAAAACACCGATGCAGTCAAAATGGCAGCACAACAGAATATA
130 AATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATA
* * ** *
53000321 GGTCGGCAATGAAGAAACAGTAGCAAGAGGCGTCAACAGGGGAATATGACAACAAATGTAAAAGA
195 GGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGA
* * * * * * * *
53000386 AACAAAAGAAAACAAAGCAAAAAGAAAAAAAGAAGAAAAAAATAACATCAGAGGAA-AAAAATAG
260 AACGAAAGAAAATAAAACAGAAAG-AAAGAAGAA-AAAAAAATAACGTTAGAGGAACAAAAATTG
*
53000450 GAAAAAGAAATGGAAGTAGTGGAAAGAGAAGAACATAAAAAATTTGGG
323 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
* *
53000498 GAAATTGCTAAAATCCTCACTCGCTAGAAGACTAAACGCCTCACGAACCA-CTCTAGCAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* ** * * * * *
53000562 CAACTAATGAAAGCAAAAGACCTTTTAAAGATATCAAGTCAACCACTCTAAAACGAAATTAATGA
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
* * *
53000627 ATTATACTTACCT-AATGATTTTAAGAACACCAATGCAGTCTAAATGGTGGCA-AAGTAGAAGAT
131 ATTATACTTACCTGAAT-ATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAA-TAGAAGAT
* * * * * *
53000690 AAGTTGACAATGAAGAAACAATAGCAAGAGACGATAACAGGGGAATATGGAAATAAATGTAAAAG
194 AGGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAG
* *
53000755 AAACGAAAGAAATATAAAACAGAATGGAAGAAGAAGAAAAAAAATAACGTTAGAGGAACTAAAAA
259 AAACGAAAGAAA-ATAAAACAGAAAGAAAGAAG-A-AAAAAAAATAACGTTAGAGGAAC-AAAAA
53000820 TTGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
320 TTGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
* *
53000870 GAAAATTACTAAAATCCTCACTCGCTAGAAGAGTAAACGTCTCACGAACCACCCCTAGCAAAATC
1 G-AAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATC
53000935 ACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAA-GAAAACTAAC
65 ACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATG-AAACTAAC
* * *
53000999 TAATTATACTTACCT-AATGATTTTAAGAACACCAACACAGTCTAAATGGCGGCACAATAGAAGA
129 GAATTATACTTACCTGAAT-ATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGA
*** * *
53001063 TAGGTCGGCAATGAAGAAACAATAGCAAGAGAC-AACAACAAAAGAATATAGCAACAAATGTAAT
193 TAGGTCGGCAATGAAGAAACAATAGCAAGAGACGAA-AACAGGGGAATATGGCAACAAATGTAAA
* * * * *
53001127 AGAAACGAAGGAAAAATGAAACAGAAAGGAAA-AAGAAGAAAAAATGACGTTAGAGGAAGAAAAA
257 AGAAACGAAAG-AAAATAAAACAGAAA-GAAAGAAGAAAAAAAAATAACGTTAGAGGAACAAAAA
* * * * * * *
53001191 ATGAGAAAACA-AAATGAAAGTAGTAGAAAGAGAGAAATATAAAAAAAATAGG
320 TTG-GAAAA-AGAAATGGAAGTAGTGGAAAGAGAGGAACAT-AAAAAATTTGG
* * * * * *
53001243 AAAATTGCAAAAATCCTCACTCGCCAGAAGAGTAAATGCCTTACGAACCACCCCTAACAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
*
53001308 CAACTAATGAAACCAAAAGACCTCCCAAAGATATCAAGACAACCACCCTAAAA-GAAAACTAACG
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATG-AAACTAACG
* * * * *
53001372 AATTATACTTACCTGAAGATTTTAATAGCACCAACCCAGTCTACATGGCGGCACAATAGAAAATA
130 AATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATA
* * * * *
53001437 GGTCGGTAACGAAGAAACAGTAGCAAGAGACGATAATAGGGGAATATGGCAACAAATGTAAAA-A
195 GGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGA
*
53001501 AAC-AGAAGAAAATAAAACAGAAAGAAAGAAG-AAAAAAAATAACGTTAGAGGAACAAAAAATGG
260 AACGA-AAGAAAATAAAACAGAAAGAAAGAAGAAAAAAAAATAACGTTAGAGGAAC-AAAAATTG
* * *
53001564 GAAAAGGAAATGAAAGTAGTGGAAAGAGAGGAACATAAAAATTTTGGG
323 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
* * *
53001612 GAAATT-CTAAAATCCTTACTCGCTAGAAGAGTAAACGCCTCACGAACCA-ACCTAGAAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* * * ***
53001675 CAACTAATGAAACCAAAAGACCTTCCAAAGATATTAAGATAACCACCTTAAAATG-AA-TATTTT
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTA-ACG
* * *** * * *
53001738 AA-TA-AC--ACC--AACGTAGTCT-A-AATGGCAA--CAGAAC-AAAAGGCAGGTCGGCAAT-G
130 AATTATACTTACCTGAA--TATTTTAATAACACCAACGCAG-TCTAAATGGC-GG-C-ACAATAG
** * * * * * * ** * * *
53001791 AAGCA-ACAAT-AGTAA-G-AGACGACAATAGGGGAATATGGC-AAAA-AATGTAA-A-AGAAAC
189 AAG-ATA-GGTCGGCAATGAAGA-AACAATA--GCAAGA-GACGAAAACAGGGGAATATGGCAAC
* * * * * *
53001848 GAAA-GAAAAATAAA--ACAG-AAA-G-----G-AAG-AAGAAG--AAGAAGATAACGTTAGAGG
248 -AAATGTAAAAGAAACGAAAGAAAATAAAACAGAAAGAAAGAAGAAAAAAAAATAACGTTAGAGG
*
53001899 AACATAAAA-TGGTAAAAAGAAATGGAAGTAGTGGAAAGAGAAGAACATAAAAAATTTGGG
312 AACA-AAAATTGG-AAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
* *
53001959 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACACCTCACGAACCACCCCTAGCAAAATTA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
** * * *
53002024 CAACTAATGAAAGGAAAAGACCTTTCAAAGATATTAAGACAACCACCCTAAAA-GAGTACTAACG
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGA-AACTAACG
* * *
53002088 AATTATACTTACCT-AATAATTTTAAGAACACCAACACAGTCTAAATGGCCGCACAATAGAAGAT
130 AATTATACTTACCTGAAT-ATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGAT
* * * * * ** * ** * **
53002152 A--TCAAGACAACCACCCTAAAAGAAA-ACTAGCGAATTATAC-TTACCAGAAGATTTTAATAAC
194 AGGTC--GGC-A--A---T-GAAGAAACAATAGC-AA-GAGACGAAAACAGGGGA--AT-ATGGC
* * * **
53002213 ACCAATGCAGTCTAAATAGCAGCAC-AACAGAAGATAGGTCGGCAACGAAGAAACAGTAGCAAGA
245 AACAA---A-TGTAAA-AG-A-AACGAA-AGAA-A-A--T--AAAAC--AG-AA-AG-A--AAG-
* * * * *** **
53002277 AACGACAACAGGAGAATATGGCAACAAATGTAAAAGAAACGAAAGAA-AACAAAACAGAAA-AAA
288 AA-GA-AA-A--A-AAAAT---AAC----GTTAGAGGAAC-AAA-AATTGGAAAA-AGAAATGGA
* ** * ** * **
53002340 AGAAGAAG-AAGAAAATAACGTTAGAGGAACCGAAACTGG
337 AGTAGTGGAAAGAGAGGAAC-ATA-A--AA---AATTTGG
** * ** * * * ** * **** *** *
53002379 GAAAAAGAAATGAAGAAATGGAATTAGTGGAAAGAGAGGAACATAAAAAATTTGGGAA--A---A
1 GAAATTG--CT--A-AAAT--CCTCACTCGCTAGA-A-G-A-GTAAACGCCTCACGAACCACCCC
* * ** * ** *** * * *
53002439 TTGCTAAAATC-CTAACTCACTAGAAAAGTAAACG-CC-TCACGAACCACCCCTAGCAAAATCAA
55 TAGC-AAAATCAC-AACT-AAT-G-AAACCAAAAGACCTTC-C-AAAGATATCAAG-ACAA-CCA
* * * * * * * * *
53002501 CACT--AATGAAACCAA--AA-GA-CCTT-CC-AAAGATATCAA-GACAACC-AC-CA---TAAA
111 CCCTAAAATGAAACTAACGAATTATACTTACCTGAATATTTTAATAAC-ACCAACGCAGTCTAAA
* * * ** * * * * *
53002552 ----AG-AAAAGTAACGAATTATACTTACCTGAAGATTTTAATAACACCAACACAGTCTAA-ATG
175 TGGCGGCACAA-T-A-GAA-GATAGGT--CGGCA-A--TGAAGAA-A-C-A-ATAG-C-AAGA--
** * ** * * *
53002611 GTGGCACAACAGAAG-ATAGGTCGGCAATAAA-G-AAACAGTAGCAA-GAGACGACAATAGGGGA
223 GACG-AAAACAGGGGAATA--T-GGCAACAAATGTAAA-AG-A--AACGA-AAGAAAATA----A
* * *
53002672 ATATGGCAACAAATGTAAAAGAAACAAAAGAAAACATAACATAAATAAAGAAGAAGAA-AATAAA
275 A-A---C-AGAAA-G--AAAG-AAGAAAA-AAAA-ATAACGT---T--AG-AG--GAACAA-AAA
* * * * *
53002736 GTCAGAGGAACAAA-AAATGGGAAAAAGAAATGG-AAGTAGTGGAAACAGAGGAACGTAAAAGAT
320 -T---TGGAA-AAAGAAAT-GG---AAGTAGTGGAAAG-AGAGG-AAC------A--TAAAAAAT
53002799 TTGGG
366 TT-GG
* * * * *
53002804 GAAATTGCTGAAATACTCACTCGCCA-AAGAGTAAAAGCCTCATGAACCACCCCTAGCAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* * * * * * * *
53002868 CAACTAAAGAAAGCAAAATACCTTCCAAAGATTTAAAAACAACCACCCTAAAACGAAACTAATGA
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
* * *
53002933 ATTATACTTACCTGAAAATTTTAATAATAACACCAACGCAGTCTAAATGGTGGCACAAAAGAAGA
131 ATTATACTTACCTGAATA-TTT--TAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGA
* * ** * *
53002998 TAAGTCGGCAATGAAGAAACAATAGCAAGAGACGACAACAAAGGAATATGACAACAAATTTAAAA
193 TAGGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAA
** * * *
53003063 GAAATAAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACGTTAGAGGAAAAGAAAA
258 GAAACGAAAG-AAAATAAAACAGAAAGAAAGAAGAA-AAAAAAATAACGTTAGAGGAACA-AAAA
* *
53003128 TGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAAGAACATAAAAAATTTGCG
320 TTGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTG-G
* * * * * *
53003179 AAAATTGCTAAAATCCTCACTTGCCAGAAAATTAAACGCCTCACGAACCACCCTTAGCAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* * *
53003244 -ACACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACTACTCTAAAATGAAACTAACT
66 CA-ACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACG
* ** ** * *
53003308 AATTATACTTACCTGAAGATTTTAATAACACTGACGCAGTCTAAATGGCAACACAACAGAATATA
130 AATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATA
* * * ** * * *
53003373 GGTCGGTAATGAAGAGACAATAGTAAGAGACGTCAATAGGAGAATATGGAAACAAATGTAAAAGA
195 GGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGA
* ** * * * *
53003438 AACAAAAGAAAACGAAACTAG-AAGAAAGAAGAAGAAAAAATAACATTAGAGGAACCGAGAA-TG
260 AACGAAAGAAAATAAAAC-AGAAAGAAAGAAGAAAAAAAAATAACGTTAGAGGAA-CAAAAATTG
* * *
53003501 AGAAAAAGAAATTGAAGTAGTGGAAAGAGAAGAAAATAAAAAATTTGG
323 -GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
* * * * * * *
53003549 AGAAATTGCTAAAATCCTCATTCGCCAAAAGATTAAACGCCTTATGAACC-TCCCTAGCAAAATC
1 -GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATC
* * * *
53003613 ACAACTAATGAAAGCAAAAGACCTTCCAATGATATCAAGACAACCATCCTAAAACGAAACTAACG
65 ACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACG
* *
53003678 AATTATACTTACCT-AATGATTTTAAGAACACCAACACAGTCTAAATGGCGGCACAATAGAAGAT
130 AATTATACTTACCTGAAT-ATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGAT
* ** * ** *
53003742 AGGTCGGCAATAAAGAAACAATAGTGAGAGACGACAACAAAGGAATATAGCAACAAATGTAAAAG
194 AGGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAG
* * * * * * * **
53003807 AAACGAAGGAAAAATGAGACAAAAAGGAAGAAGAAGAAAAAATAACATTAGAGGAACATAAAAGG
259 AAACGAAAG-AAAATAAAACAGAAAGAAAGAAGAAAAAAAAATAACGTTAGAGGAACA-AAAATT
* *
53003872 GGAAAAAGAAATAGAAGTTGTGGAAAGAGAGGAACATAAAAAATTTGGG
322 GGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
* * * * *
53003921 GAAATTCCTAAAATCCTCATTCGCCAGAAGAGTAAACACCTCACGAACCA-CCCTA-AAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
** ** * * * * *
53003984 GTACTAATGAAAGTAAAAGGCCTTCCAAAGATATCAAGATAACCATCCTAAAACGAAACTAACAA
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
* * * * *
53004049 ATTATACTTACTTG-ATGATTTTAATAACACCAACACAGTCAAAATGGTGGCACAATAGAAGATT
131 ATTATACTTACCTGAAT-ATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATA
* * *
53004113 GATCGACAATGAAGAAACAATAGCAAGAGACGACAACAGGGGAATATGGCAACAAATGTAAAAGA
195 GGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGA
* * * * * * *
53004178 AACAAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAGAGAACGTTAGACGAACATAAAATG
260 AACGAAAG-AAAATAAAACAGAAAGAAAGAAGAA-AAAAAAATAACGTTAGAGGAACA-AAAATT
* * * * * *
53004243 GGAGAAAGAAATGGAAGCAATGGAAAGAGAGAAATATAAAAAATTCGG
322 GGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
* * * * *
53004291 GAAAATTGCTAAAATCTTTACTCACTAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATC
1 G-AAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATC
* *
53004356 ACAACTAATGAAACCAAAAGACCTTTCAACGATATCAAGACAACCACCCTAAAA-GAAAACTAAC
65 ACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATG-AAACTAAC
* * * * *
53004420 GAATTATACTTACCAGAAGATTTTAATAACACCAACGTAGTCTAAATGTCGCCACAATAGAAGAT
129 GAATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGAT
* * *
53004485 AGGTCGGCAATGAAGAAACAGTAGCAAGAGACGATAACAAGGGAATATGGCAACAAATGTAAAAG
194 AGGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAG
* ** * *
53004550 AAACAAAAGAAAACGAAACAGAAAGAAAGAAG-----AAAATAACGTCAGAGGAACAAAAAATGG
259 AAACGAAAGAAAATAAAACAGAAAGAAAGAAGAAAAAAAAATAACGTTAGAGGAAC-AAAAATTG
* *
53004610 GAAACAGAAATGGAAGTAGTGGAAAGAGAGGAACGTAAAAAATTTGG
323 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
* ** ** * *** * **** * * ** * ** * * *
53004657 GTAAATT-TTAGGA-GGT-ATTTTTTTG--GA-TAATTTTCTAAAGTTCAAATCCAACCCAAAT-
1 G-AAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATC
* ** * * * * * * *
53004715 ACCACTAGATGGGTGACACATGAGGA-TTTAGCAAAAATAATTCCATTTTTAG-TAA-CA-ACT-
65 ACAACTA-AT--GAAAC-CA-AAAGACCTT-CCAAAGAT-A-T-CA-----AGACAACCACCCTA
* * * * ** ** * *** * * *
53004775 -AATGAAACCAAAAGACCTTTCAAAGATATCAAGACAACCACCATAA-AACAAAACTAACGAATT
116 AAATGAAA-CTAACGA--ATT-ATACTTA-CCTG--AA-TATTTTAATAAC---ACCAACGCAGT
* ** ** * * * * * * * * *
53004838 ATACTTACCTGAAGATTTTGATA-ACACCGACGCAGTCTAAATGACAG-CACAATAG-AAGATAG
170 CTAAATGGCGGCACA-ATAGA-AGATA-GGTCG--G-C--AATGA-AGAAACAATAGCAAG--AG
* * *** *
53004900 CTCGACAATAAAGAAACAATAGTAAGAGACGAAAACAGGTGAATATGACAACAAATGTAAAAGAA
224 -ACGA-AA-ACAG-GGGAATA-T--G-G-C---AAC-----AA-ATG--TA-AAA-G--AAA---
* * *
53004965 ACGAAAGAAAAATGAAACAGAAAGAAAGAAAAAGAAAAAAATAACGTTAGAGGAACAAAAAATGG
262 -CGAAAG-AAAATAAAACAGAAAGAAAGAAGAA-AAAAAAATAACGTTAGAGGAAC-AAAAATTG
*
53005030 GAAAAAGAAATGGAAGTAGTGAAAAGAGAGGAACATAAAAAATTTGGG
323 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
* * * *
53005078 GAAATTGCTAAAATCTTCACTCGTTAGAAGAGTAAATGCCTCACGAACCACCTCTAGCAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* * * **
53005143 CAACTAATAAAACCAAAAGGCCTTCCAAAGATATCAAGAAAACCACCCTAAAATGAAACTAATAA
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
* * * * * * *
53005208 ATTATATTTACCTGAAGATTTTAATAACACCGACGTAGTCTAAATGGCGGCATAACAGAAAATAG
131 ATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATAG
* * * * *
53005273 GTTGGCAATGAA-AGGACGATAGCAAGAGACGAGAAGAGGGGAATATGGCAACAAATGTAAAAGA
196 GTCGGCAATGAAGA-AACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGA
** * * *** *
53005337 AATAAAAGAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACAACAGAGGAACAGAAAATGG
260 AACGAAAGAAAATAAAACAGAAAGAAAGAAGAA-AAAAAAATAACGTTAGAGGAACA-AAAATTG
53005402 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGG
323 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
* * * * * *
53005450 GAAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAATGCCTCACAAACCACCTCTAGTAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* * * *
53005515 CAATTAATAAAACCAAAAGACCTTCTAAAGATATCAAGACAACCACCCTAAAATGAAACTAACAA
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
* * ** * * *
53005580 ATTATACTTACTTGAAGATTTTAATAACACCGGCGTAGTCTAAATGGTGGCACAACAGAAGATAG
131 ATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATAG
* * *
53005645 GTTGGTAATGAAGAAATAATAGC-A-AGA-G--AAC--------A---C-A-AAA-GTAAAAGAA
196 GTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGAA
* * * * * *
53005691 ACGAAAGAAAAATGAGACAGAAAGAAAGAAGAAGAAGAAAATAACATTAAAGGAACAAAAAATGG
261 ACGAAAG-AAAATAAAACAGAAAGAAAGAAGAA-AAAAAAATAACGTTAGAGGAAC-AAAAATTG
* *
53005756 GAAAAAGAAATGGAAGTAGTGGAAATAGAGGAATATAAAAAATTTGGG
323 GAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
* * * * * *
53005804 GAAATTGCTAAAATCTTCACTCACCAGAAGAGTAAATGCCTCACGAACCAGCCTTAGCAAAATCA
1 GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
* * *
53005869 CAACTAATGAAATCAAAAGACCTTCCAATGATATCATGACAACCACCCTAAAATGAAACTAACGA
66 CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
* * * * * * *
53005934 ATTATTCTTACCTGAAGATTTTAAGAACACCAACGTAGTCTAAATGTCGGTACAATAGAAGATGG
131 ATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATAG
* * * * * *
53005999 GTAGGCAATGAAGTAATAGTAGCAAGAGACGACAATAGGGGAATATGGCAACAAATGTAAAAGAA
196 GTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGAA
* * * * * *
53006064 ACAAAAGAAAATGAAACAAAAAGAAAGAAGAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGG
261 ACGAAAGAAAATAAAACAGAAAGAAAGAAGAA-AAAAAAATAACGTTAGAGGAAC-AAAAATTGG
* * *
53006129 AAAACGTAATGGAAGTAGTGGAAAGAGAGGAACGTAAAAAATTTGG
324 AAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
* * * * *
53006175 GAAAATTACTGAAATACTCACTCG-TCAGAAGAGTAAACACCTCATGAACCACCCCTAGCAAAAT
1 G-AAATTGCTAAAATCCTCACTCGCT-AGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAAT
* * * * * * * *
53006239 -----C-----AAACCAAAATACCTTCCAAAGATTTAAAAACAACCAGCCTAGAACGAAGCTAAC
64 CACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAAC
* * * *
53006294 GAATTATACTTACC-GAAAGAGTTTATTAATTACACCAATGCAGTCTAAATGGTGGCACAATAGA
129 GAATTATACTTACCTG-AATA--TT-TTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGA
* * * * * *
53006358 AGATAAGTCGGCAATGAATAAACAATAGCAAGAGACGACAACAAGGGAATATGACAATAAATGTA
190 AGATAGGTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTA
* * * * *
53006423 AAAGAAATGAAAGAAAA-ACGAAACAGAAAGAAAGAAGAAGAAAAAATAACGTCAAATGAACAGA
255 AAAGAAACGAAAGAAAATA--AAACAGAAAGAAAGAAGAAAAAAAAATAACGTTAGAGGAACA-A
* * *
53006487 AAA-TGGAAAAAAGAAATGAAAGTAATGGAAAGAGAGGAACGTAAAAAATTTGGG
317 AAATTGG-AAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTT-GG
53006541 GAAATT
1 GAAATT
53006547 TTAGGAGGTA
Statistics
Matches: 5368, Mismatches: 993, Indels: 864
0.74 0.14 0.12
Matches are distributed among these distances:
346 3 0.00
347 73 0.01
348 48 0.01
349 62 0.01
350 4 0.00
351 4 0.00
352 2 0.00
353 16 0.00
354 295 0.05
355 11 0.00
356 18 0.00
357 6 0.00
358 30 0.01
359 26 0.00
360 39 0.01
361 18 0.00
362 75 0.01
363 15 0.00
364 17 0.00
365 179 0.03
366 93 0.02
367 75 0.01
368 54 0.01
369 192 0.04
370 671 0.12
371 723 0.13
372 838 0.16
373 527 0.10
374 210 0.04
375 49 0.01
376 103 0.02
377 20 0.00
378 6 0.00
379 6 0.00
380 4 0.00
381 2 0.00
382 1 0.00
383 9 0.00
384 23 0.00
385 8 0.00
386 3 0.00
387 6 0.00
388 10 0.00
389 7 0.00
390 1 0.00
391 4 0.00
392 7 0.00
393 5 0.00
394 5 0.00
395 2 0.00
396 2 0.00
397 7 0.00
398 3 0.00
399 10 0.00
400 12 0.00
401 10 0.00
402 13 0.00
403 7 0.00
404 6 0.00
405 4 0.00
406 4 0.00
407 4 0.00
408 9 0.00
409 19 0.00
410 3 0.00
411 8 0.00
412 22 0.00
413 27 0.01
414 70 0.01
415 41 0.01
416 41 0.01
417 43 0.01
418 34 0.01
419 22 0.00
420 98 0.02
421 25 0.00
422 19 0.00
423 27 0.01
424 29 0.01
425 19 0.00
426 27 0.01
427 28 0.01
428 10 0.00
429 11 0.00
430 25 0.00
431 15 0.00
432 6 0.00
433 3 0.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (369 bp):
GAAATTGCTAAAATCCTCACTCGCTAGAAGAGTAAACGCCTCACGAACCACCCCTAGCAAAATCA
CAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACGA
ATTATACTTACCTGAATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAATAGAAGATAG
GTCGGCAATGAAGAAACAATAGCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGAA
ACGAAAGAAAATAAAACAGAAAGAAAGAAGAAAAAAAAATAACGTTAGAGGAACAAAAATTGGAA
AAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGG
Found at i:53002215 original size:96 final size:96
Alignment explanation
Indices: 53002051--53002248 Score: 274
Period size: 96 Copynumber: 2.1 Consensus size: 96
53002041 AGACCTTTCA
* **
53002051 AAGATATTAAGACAACCACCCTAAAAGAGTACTAACGAATTATACTTACCTAATAATTTTAAGAA
1 AAGATATCAAGACAACCACCCTAAAAGAAAACTAACGAATTATACTTACCTAATAATTTTAAGAA
* * *
53002116 CACCAACACAGTCTAAATGGCCGCACAATAG
66 CACCAACACAGTCTAAATAGCAGCACAACAG
* *
53002147 AAGATATCAAGACAACCACCCTAAAAGAAAACTAGCGAATTATACTTACC-AGA-AGATTTTAAT
1 AAGATATCAAGACAACCACCCTAAAAGAAAACTAACGAATTATACTTACCTA-ATA-ATTTTAAG
**
53002210 AACACCAATGCAGTCTAAATAGCAGCACAACAG
64 AACACCAACACAGTCTAAATAGCAGCACAACAG
53002243 AAGATA
1 AAGATA
53002249 GGTCGGCAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
95 2 0.02
96 88 0.98
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.20
Consensus pattern (96 bp):
AAGATATCAAGACAACCACCCTAAAAGAAAACTAACGAATTATACTTACCTAATAATTTTAAGAA
CACCAACACAGTCTAAATAGCAGCACAACAG
Found at i:53004197 original size:16 final size:16
Alignment explanation
Indices: 53004172--53004211 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
53004162 CAACAAATGT
53004172 AAAAGAAACA-AAAGA
1 AAAAGAAACAGAAAGA
53004187 AAAATGAAACAGAAAGA
1 AAAA-GAAACAGAAAGA
53004204 AAGAAGAA
1 AA-AAGAA
53004212 GAAGAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 10 0.45
18 2 0.09
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAAACAGAAAGA
Found at i:53004556 original size:15 final size:15
Alignment explanation
Indices: 53004545--53004577 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
53004535 CAACAAATGT
53004545 AAAA-GAAACAAAAG
1 AAAACGAAACAAAAG
53004559 AAAACGAAACAGAAAG
1 AAAACGAAACA-AAAG
53004575 AAA
1 AAA
53004578 GAAGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAACGAAACAAAAG
Found at i:53004989 original size:17 final size:15
Alignment explanation
Indices: 53004958--53004991 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
53004948 CAACAAATGT
53004958 AAAAGAAACGAAAGA
1 AAAAGAAACGAAAGA
53004973 AAAATGAAACAGAAAGA
1 AAAA-GAAAC-GAAAGA
53004990 AA
1 AA
53004992 GAAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.74, C:0.06, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAAGAAACGAAAGA
Found at i:53004993 original size:21 final size:21
Alignment explanation
Indices: 53004952--53005002 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
53004942 ATATGACAAC
53004952 AAATGTAAAAGAAACGAAAGAA
1 AAATG-AAAAGAAACGAAAGAA
53004974 AAATGAAACAGAAA-GAAAGAA
1 AAATGAAA-AGAAACGAAAGAA
53004995 AAA-GAAAA
1 AAATGAAAA
53005003 AAATAACGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.04
20 4 0.14
21 13 0.46
22 10 0.36
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.06
Consensus pattern (21 bp):
AAATGAAAAGAAACGAAAGAA
Found at i:53005996 original size:354 final size:353
Alignment explanation
Indices: 53005321--53006546 Score: 1249
Period size: 354 Copynumber: 3.4 Consensus size: 353
53005311 GGGAATATGG
* * *
53005321 CAACAAATGTAAAAGAAATAAAAGAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACAACA
1 CAACAAAAGTAAAAGAAACAAAAGAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATCA
*
53005386 GAGGAACAGAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGG
66 GAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGG
* * *
53005451 AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAATGCCTCACAAACCACCTCTAGTAAAATCAC
131 AAATTGCTAAAAT-CTCACTCGCCAGAAGAGTAAATGCCTCACGAACCACCT-TAGCAAAATCAC
* *
53005516 AATTAATAAAACCAAAAGACCTTCTAAAGATATCAAGACAACCACCCTAAAATGAAACTAACAAA
194 AACTAATAAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACAAA
* * **
53005581 TTATACTTACTTGAAGATTTTAATAACACCGGCGTAGTCTAAATGGTGGCACAACAGAAGATAGG
259 TTATACTTACCTGAAGATTTTAAGAACACCAACGTAGTCTAAATGGTGGCACAACAGAAGATAGG
* *
53005646 TTGGTAATGAAGAAATAATAGCAAGAGA-A
324 TAGGCAATGAAGAAATAATAGCAAGAGACA
* * *
53005675 C-ACAAAAGTAAAAGAAACGAAAGAAAAATGAGACAGAAAGAAAGAAGAAGAAGAAAATAACATT
1 CAACAAAAGTAAAAGAAACAAAAG-AAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATC
* * *
53005739 AAAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAATAGAGGAATATAAAAAATTTGGG
65 AGAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGG
*
53005804 GAAATTGCTAAAATCTTCACTCACCAGAAGAGTAAATGCCTCACGAACCAGCCTTAGCAAAATCA
130 GAAATTGCTAAAATC-TCACTCGCCAGAAGAGTAAATGCCTCACGAACCA-CCTTAGCAAAATCA
* * * * *
53005869 CAACTAATGAAATCAAAAGACCTTCCAATGATATCATGACAACCACCCTAAAATGAAACTAACGA
193 CAACTAATAAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACAA
* * * *
53005934 ATTATTCTTACCTGAAGATTTTAAGAACACCAACGTAGTCTAAAT-GTCGGTACAATAGAAGATG
258 ATTATACTTACCTGAAGATTTTAAGAACACCAACGTAGTCTAAATGGT-GGCACAACAGAAGATA
* *
53005998 GGTAGGCAATGAAGTAATAGTAGCAAGAGACGA
322 GGTAGGCAATGAAGAAATAATAGCAAGAGAC-A
*
53006031 CAATAGGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAATGAAACAAAAAGAAAGAAGAA
1 C---------A-A---C-A-AAA-GTAAAAGAAACAAAAGAAAATGAAACAGAAAGAAAGAAGAA
* * *
53006096 GAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAACGTAATGGAAGTAGTGGAAAGAGAGGAA
50 GAAGAAAATAACATCAGAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAA
* * * * * ** *
53006161 CGTAAAAAATTTGGGAAAATTACTGAAATACTCACTCGTCAGAAGAGTAAACACCTCATGAACCA
115 CATAAAAAATTTGGGGAAATTGCTAAAAT-CTCACTCGCCAGAAGAGTAAATGCCTCACGAACCA
* * * * * *
53006226 CCCCTAGCAAAAT-----C-----AAACCAAAATACCTTCCAAAGATTTAAAAACAACCAGCCTA
179 -CCTTAGCAAAATCACAACTAATAAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTA
* * * * ** * *
53006281 GAACGAAGCTAACGAATTATACTTACC-GAAAGAGTTTATTAATTACACCAATGCAGTCTAAATG
243 AAATGAAACTAACAAATTATACTTACCTG-AAGA--TT-TTAAGAACACCAACGTAGTCTAAATG
* * * * *
53006345 GTGGCACAATAGAAGATAAGTCGGCAATGAATAAACAATAGCAAGAGACGACAA
304 GTGGCACAACAGAAGATAGGTAGGCAATGAAGAAATAATAGC-A-AGA-GAC-A
** *
53006399 CAAGGGAATATGACAATAAATGTAAAAGAAATGAAAGAAAAACGAAACAGAAAGAAAGAAGAAGA
1 C--------A--AC-A-AAA-GTAAAAGAAACAAAAG-AAAATGAAACAGAAAGAAAGAAGAAGA
* * * * * * * *
53006464 A-AAAATAACGTCAAATGAACAGAAAATGGAAAAAAGAAATGAAAGTAATGGAAAGAGAGGAACG
52 AGAAAATAACATCAGAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACA
53006528 TAAAAAATTTGGGGAAATT
117 TAAAAAATTTGGGGAAATT
53006547 TTAGGAGGTA
Statistics
Matches: 739, Mismatches: 99, Indels: 57
0.83 0.11 0.06
Matches are distributed among these distances:
353 22 0.03
354 291 0.39
355 3 0.00
356 2 0.00
361 1 0.00
362 60 0.08
364 2 0.00
365 147 0.20
366 29 0.04
367 9 0.01
368 6 0.01
370 1 0.00
371 1 0.00
372 149 0.20
373 16 0.02
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.17
Consensus pattern (353 bp):
CAACAAAAGTAAAAGAAACAAAAGAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATCA
GAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGG
AAATTGCTAAAATCTCACTCGCCAGAAGAGTAAATGCCTCACGAACCACCTTAGCAAAATCACAA
CTAATAAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAATGAAACTAACAAATT
ATACTTACCTGAAGATTTTAAGAACACCAACGTAGTCTAAATGGTGGCACAACAGAAGATAGGTA
GGCAATGAAGAAATAATAGCAAGAGACA
Found at i:53006068 original size:15 final size:15
Alignment explanation
Indices: 53006057--53006089 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
53006047 CAACAAATGT
53006057 AAAA-GAAACAAAAG
1 AAAATGAAACAAAAG
53006071 AAAATGAAACAAAAAG
1 AAAATGAAAC-AAAAG
53006087 AAA
1 AAA
53006090 GAAGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 5 0.29
16 8 0.47
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAATGAAACAAAAG
Found at i:53006197 original size:726 final size:732
Alignment explanation
Indices: 52999388--53006546 Score: 4743
Period size: 726 Copynumber: 9.5 Consensus size: 732
52999378 AAGAGAAAAG
* * *
52999388 AAATTGC-AGAAATCCTCACTCACCAGAAGAGAAAAC-CTCTCACGAACCACCCTTAGCAAAATC
1 AAATTGCTA-AAATCCTCACTCGCCAAAAGAGTAAACGC-CTCACGAACCACCC-TAGCAAAATC
* * * *
52999451 ACAACTAATGAAACAAAAAGACCTTCCAAAGATATCAAAACAACCACCCTAAAATGAAACTAACA
63 ACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACG
* * * * *
52999516 AATTATAC-T---TGAGGATTTTAATAACACCAATGCAGTTTAAATGATGGCACAATAGAAGATA
128 AATTATACTTACCTGAAGATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATA
* * *
52999577 GGTTGGCAATGAAGAAACAATAGCAAGAGATAACAACAGGGGAAAATGATAACAAATGTAAAAGA
193 GGTCGGCAATGAAGAAACAATAGCAAGAG------AC----G-AAACGACAACAAATGTAAAAGA
* * * * * * * *
52999642 AACAAAAGAATAATGAAACAGAAATAAAGAAGAAGAAAAAAATAACGTCAGAGGAACAGAAAATA
247 AACGAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAATG
* *
52999707 GGACAAAAGAGATGGAAGTAGTGGAAAGAGAAGAACATAAAAAA-TTGGGGAAATTGCTAAAATC
312 GGA-AAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATC
* * ** * * ** * **
52999771 ATCACTCTCCAGAAGAGTAAACACCTTACGAACCACCTTTAGCAAAATCATAACTAACAAAACCA
376 TTCACTCGCCAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCA
*
52999836 AAAGACCTTCCAAAGATACCAAGACAACCACCCTAAAATGAAACTAACGAATTATACTTACCTGA
441 AAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAA-GAAACTAACGAATTATACTTACCTGA
* * * * **
52999901 ATATTTTAATAACACCAACGCAGTCTAAATGGCGGCACAACAGAAGATAGATCGATAATGAAGAA
505 AGATTTTAATAACACCAACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTCGGCAATGAAGAA
* * * * * *
52999966 GCAATATCAAGAGACGAAAACAGGGGAATATGGCAACAAATGTAAAAGAAACGAAAGCAAAATGA
570 ACAGTAGCAAGAGACGACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAG-AAAATGA
* * * * * * *
53000031 AATAAAAA-AAAGAAGAAAAAGAAAATAAAGTTAGAGGAACAGAAAGTTGGAAAAAGAAATGGAA
634 AACAAAAAGAAAGAAGAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAATGGAA
*
53000095 GTAGTGGAAAAAGAGGAACATAAAAAATTTGGG-
699 GTAGTGGAAAGAGAGGAACATAAAAAATTTGGGA
* * * *
53000128 AAATTGCTAAAACCCTCACTCGCTAGAAA-AGTAAACGCCTTACGAACCACCCCTAGAAAAATCA
1 AAATTGCTAAAATCCTCACTCGCCA-AAAGAGTAAACGCCTCACGAACCA-CCCTAGCAAAATCA
* * * *
53000192 -ACACTAATGAAACCAAAAGTCCTTCCAAAGATAGCAAAACAACCACCCTAAAATGAAACTAACG
64 CA-ACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACG
* * * * * * ** *
53000256 AATTATACATACTTGAAGATTTTAAAAACACCGATGCAGTCAAAATGGCAGCACAACAGAATATA
128 AATTATACTTACCTGAAGATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATA
* *
53000321 GGTCGGCAATGAAGAAACAGTAGCAAGAGGCGTCAACAGGGGAATATGACAACAAATGTAAAAGA
193 GGTCGGCAATGAAGAAACAATAGCAAGA---G---AC----GAA-ACGACAACAAATGTAAAAGA
* * * * * *
53000386 AACAAAAGAAAACA--AAGCAAAAAGAAAAAAAGAAGAAAAAAATAACATCAGAGG-A-AAAAAA
247 AACGAAAGAAAA-ATGAAACAGAAAG-AAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAA
* *
53000447 TAGGAAAAAGAAATGGAAGTAGTGGAAAGAGAAGAACATAAAAAATTTGGGGAAATTGCTAAAAT
310 TGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAAT
* * * * * * *
53000512 CCTCACTCGCTAGAAGACTAAACGCCTCACGAACCA-CTCTAGCAAAATCACAACTAATGAAAGC
375 CTTCACTCGCCAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACC
** * * * *
53000576 AAAAGACCTTTTAAAGATATCAAGTCAACCACTCTAAAACGAAATTAATGAATTATACTTACCT-
440 AAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAA-GAAACTAACGAATTATACTTACCTG
* * * * *
53000640 AATGATTTTAAGAACACCAATGCAGTCTAAATGGT-GGCA-AAGTAGAAGATAAGTTGACAATGA
504 AA-GATTTTAATAACACCAACGCAGTCTAAAT-GTCGGCACAA-TAGAAGATAGGTCGGCAATGA
* * * * * *
53000703 AGAAACAATAGCAAGAGACGATAACAGGGGAATATGGAAATAAATGTAAAAGAAACGAAAGAAAT
566 AGAAACAGTAGCAAGAGACGACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAA-
* * * * * * * *
53000768 ATAAAACAGAATGGAAGAAGAAGAAAAAAAATAACGTTAGAGGAACTAAAAATTGGAAAAAGAAA
630 ATGAAACAAAAAGAAAGAAGAAG-AAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAA
53000833 TGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGA
694 TGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGA
* * * *
53000872 AAATTACTAAAATCCTCACTCGCTAGAAGAGTAAACGTCTCACGAACCACCCCTAGCAAAATCAC
1 AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAACGCCTCACGAACCA-CCCTAGCAAAATCAC
*
53000937 AACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAA-GAAAACTAACTA
65 AACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACG-AAACTAACGA
* * * *
53001001 ATTATACTTACCT-AATGATTTTAAGAACACCAACACAGTCTAAATGGCGGCACAATAGAAGATA
129 ATTATACTTACCTGAA-GATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATA
* *
53001065 GGTCGGCAATGAAGAAACAATAGCAAGAGACAACAACAAAAGAATATAGCAACAAATGTAATAGA
193 GGTCGGCAATGAAGAAACAATAGCAAGAGACGA-AAC----G-----A-CAACAAATGTAAAAGA
* * * *
53001130 AACGAAGGAAAAATGAAACAGAAAGGAAA-AAGAAGAA-AAAATGACGTTAGAGGAAGAAAAAAT
247 AACGAAAGAAAAATGAAACAGAAA-GAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAAT
* * * * * ** * * *
53001193 GAGAAAACA-AAATGAAAGTAGTAGAAAGAGAGAAATATAAAAAAAATAGGAAAATTGCAAAAAT
311 GGGAAAA-AGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAAT
* * * *
53001257 CCTCACTCGCCAGAAGAGTAAATGCCTTACGAACCACCCCTAACAAAATCACAACTAATGAAACC
375 CTTCACTCGCCAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACC
*
53001322 AAAAGACCTCCCAAAGATATCAAGACAACCACCCTAAAAGAAAACTAACGAATTATACTTACCTG
440 AAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAAG-AAACTAACGAATTATACTTACCTG
* * * * * * *
53001387 AAGATTTTAATAGCACCAACCCAGTCTACATGGCGGCACAATAGAAAATAGGTCGGTAACGAAGA
504 AAGATTTTAATAACACCAACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTCGGCAATGAAGA
* * * * *
53001452 AACAGTAGCAAGAGACGATAATAGGGGAATATGGCAACAAATGTAAAA-AAACAGAAGAAAATAA
569 AACAGTAGCAAGAGACGACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAATGA
* * * *
53001516 AACAGAAAGAAAGAAGAA-AA-AAAATAACGTTAGAGGAACAAAAAATGGGAAAAGGAAATGAAA
634 AACAAAAAGAAAGAAGAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAATGGAA
* *
53001579 GTAGTGGAAAGAGAGGAACATAAAAATTTTGGGG
699 GTAGTGGAAAGAGAGGAACATAAAAAATTTGGGA
* * * * *
53001613 AAATT-CTAAAATCCTTACTCGCTAGAAGAGTAAACGCCTCACGAACCAACCTAGAAAAATCACA
1 AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAACGCCTCACGAACCACCCTAGCAAAATCACA
* *
53001677 ACTAATGAAACCAAAAGACCTTCCAAAGATATTAAGATAACCA-CCT----------T-----A-
66 ACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACGAAT
* * *** * * **
53001725 -A-A---A--TGAATATTTTAATAACACCAACGTAGTCTAAATGGCAACAGAACAAAAGGCAGGT
131 TATACTTACCTGAAGATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATAGGT
* * * *
53001783 CGGCAATGAAGCAACAATAGTAAGAGACGACAATAGGGGAATATGGCAAAAAATGTAAAAGAAAC
196 CGGCAATGAAGAAACAATAGCAAGAGACG--AA-A--CG---A---CAACAAATGTAAAAGAAAC
* * * * * *
53001848 GAAAGAAAAATAAAACAGAAAGGAAGAAGAAGAAGAAGATAACGTTAGAGGAACATAAAATGGTA
250 GAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAATGGGA
* *
53001913 AAAAGAAATGGAAGTAGTGGAAAGAGAAGAACATAAAAAATTTGGGGAAATTGCTAAAATCCTCA
315 AAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATCTTCA
* ** * * **
53001978 CTCGCTAGAAGAGTAAACACCTCACGAACCACCCCTAGCAAAATTACAACTAATGAAAGGAAAAG
380 CTCGCCAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCAAAAG
* * * *
53002043 ACCTTTCAAAGATATTAAGACAACCACCCTAAAAGAGTACTAACGAATTATACTTACCT-AATAA
445 ACCTTCCAAAGATATCAAGACAACCACCCTAAAAGA-AACTAACGAATTATACTTACCTGAA-GA
* * * * *
53002107 TTTTAAGAACACCAACACAGTCTAAATGGCCGCACAATAGAAGATA--TCAAGACAACCACCCTA
508 TTTTAATAACACCAACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTC--GGC-A--A---T-
* * * * * * * **** ** * *
53002170 AAAGAAA-ACTAGCGAATTATACTTACCAGAAGATTTTAATAACACCAATGCAGTCTAAATAGCA
564 GAAGAAACAGTAGC-AA-GAGAC-GACAACAAGGGAAT-ATGGCAACAA---A-TGTAAA-AG-A
* * * *** * * * * * **
53002234 GCACAACAGAAGATAGGTCGGCAACGAAGAAA-CAGTAGCAAGAAACGACAACAG-GAGAATATG
619 -AACAAAAGAA-A-ATG-AAACAA-AAAGAAAGAAGAAG-AAGAAA--ATAAC-GTCAGAGGA--
* * * * * **** * *** *
53002297 GCAACAAAT--GTAAAAGAAACGAAAG-AAAACAAA-ACA-GAA-A-AAAAGAAGAAGAAGA
673 ACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAA-AATTTG-GGA
* * ** * ** * * ** * * *
53002352 AAATAACGTTAGAGGAA-CCGAAACTGGGAAAAAGAAATGAAGAAATGGAATTAGTGGAA--A-G
1 AAAT--TGCTA-A--AATCC-TCACTCGCCAAAAG--A-G--TAAA-CGCCTCA--CGAACCACC
** * * * * * * * * * * * *
53002413 AGAGGAACATAAAAAAT-TTGGGAAAATTGCTAAAA-TCCTAACTCACTAGAAAAGTAAACGCCT
52 CTAGCAAAATCACAACTAAT--G-AAA---CCAAAAGACCT-TC-CA-AAG-ATA-TCAA-G---
* ** * * * *
53002476 CACGAACCACCCCTAGCAAAATC-AACACTAATGAAACCAAAAGACCTT-CC-AAAGATATCAA-
102 -AC-AACCA-CCCT---AAAA-CGAA-ACTAACG--A--ATTATA-CTTACCTGAAGATTTTAAT
* * *** * * ** *
53002537 GACAACC-AC-CA---TAAA-AG-AAAAGTAAC-GAATTATACTTAC--C--TGAAGATTTTAAT
154 AAC-ACCAACGCAGTCTAAATGGTGGCA-CAACAGAA-GATAGGT-CGGCAATGAAGA----AAC
* * * * * *
53002590 AACACCAACACAGTCTAAATGGTGGCACAACAGAAGATAGGTCGGCAATAAAGAAACAGTAGCAA
211 AATAGC-A-AGAGACGAAA----CG-ACAAC--AA-AT--GT-----A-AAAGAAAC-G-A--AA
** * * *
53002655 GAGACGACAATAGGGGAATATGGCAACAAATGTAA-AAGAA-ACAAAAGAAAACATAACATAAAT
254 GA-A--A-AAT----GAA-ACAGAAAGAAA-G-AAGAAGAAGA-AAAT--------AACAT---T
* * * * *
53002718 AAAGAAGAAGAAAATAAAGTCAGAGGAACAAA-AAATGGGAAAAAGAAATGG-AAGTAGTGGAAA
296 --AGAGGAA-CAAA-AAA-T--G-GGAA-AAAGAAAT-GG---AAGTAGTGGAAAG-AGAGG-AA
* * ** *** * *
53002781 CAGAGGAACGTAAAAGATTTGGGGAAATTGCTGAAATAC-TCACTCGCCA-AAGAGTAAAAGCCT
346 CATA-AAAAAT-TTG------GGGAAATTGCTAAAAT-CTTCACTCGCCAGAAGAGTAAATGCCT
* * * * * *
53002844 CATGAACCACCCCTAGCAAAATCACAACTAAAGAAAGCAAAATACCTTCCAAAGATTTAAAAACA
402 CATGAACCACCCCTAGCAAAATCACAACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACA
* *
53002909 ACCACCCTAAAACGAAACTAATGAATTATACTTACCTGAAAATTTTAATAATAACACCAACGCAG
467 ACCACCCTAAAA-GAAACTAACGAATTATACTTACCTGAAGA-TTT--TAATAACACCAACGCAG
* * *
53002974 TCTAAATGGT-GGCACAAAAGAAGATAAGTCGGCAATGAAGAAACAATAGCAAGAGACGACAACA
528 TCTAAAT-GTCGGCACAATAGAAGATAGGTCGGCAATGAAGAAACAGTAGCAAGAGACGACAACA
* * * * *
53003038 AAGGAATATGACAACAAATTTAAAAGAAATAAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAG
592 AGGGAATATGGCAACAAATGTAAAAGAAACAAAAG-AAAATGAAACAAAAAGAAAGAAGAAGAAG
* *
53003103 AAAATAACGTTAGAGGAA-AAGAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAAGAACAT
656 AAAATAACGTCAGAGGAACAA-AAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACAT
*
53003167 AAAAAATTTGCGA
720 AAAAAATTTGGGA
* *
53003180 AAATTGCTAAAATCCTCACTTGCCAGAAA-ATTAAACGCCTCACGAACCACCCTTAGCAAAATCA
1 AAATTGCTAAAATCCTCACTCGCCA-AAAGAGTAAACGCCTCACGAACCACCC-TAGCAAAATCA
* * * *
53003244 -ACACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACTACTCTAAAATGAAACTAACT
64 CA-ACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACG
** *** *
53003308 AATTATACTTACCTGAAGATTTTAATAACACTGACGCAGTCTAAATGGCAACACAACAGAATATA
128 AATTATACTTACCTGAAGATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATA
* * * * *
53003373 GGTCGGTAATGAAGAGACAATAGTAAGAGACGTCAATAGGAGAATATGGAAACAAATGTAAAAGA
193 GGTCGGCAATGAAGAAACAATAGCAAGAGACG--AA-A--CG---A---CAACAAATGTAAAAGA
* * ** *
53003438 AACAAAAG-AAAACGAAACTAG-AAGAAAGAAGAAGAA-AAAATAACATTAGAGGAACCGAGAAT
247 AACGAAAGAAAAATGAAAC-AGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAAT
* * * * *
53003500 GAGAAAAAGAAATTGAAGTAGTGGAAAGAGAAGAAAATAAAAAATTTGGAGAAATTGCTAAAATC
311 GGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATC
* * * * * * * *
53003565 CTCATTCGCCAAAAGATTAAACGCCTTATGAACC-TCCCTAGCAAAATCACAACTAATGAAAGCA
376 TTCACTCGCCAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCA
* *
53003629 AAAGACCTTCCAATGATATCAAGACAACCATCCTAAAACGAAACTAACGAATTATACTTACCT-A
441 AAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAA-GAAACTAACGAATTATACTTACCTGA
* * * *
53003693 ATGATTTTAAGAACACCAACACAGTCTAAATGGCGGCACAATAGAAGATAGGTCGGCAATAAAGA
505 A-GATTTTAATAACACCAACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTCGGCAATGAAGA
* ** * * * *
53003758 AACAATAGTGAGAGACGACAACAAAGGAATATAGCAACAAATGTAAAAGAAACGAAGGAAAAATG
569 AACAGTAGCAAGAGACGACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAG-AAAATG
* * * * * * *
53003823 AGACAAAAAGGAAGAAGAAGAA-AAAATAACATTAGAGGAACATAAAAGGGGAAAAAGAAATAGA
633 AAACAAAAAGAAAGAAGAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAATGGA
* *
53003887 AGTTGTGGAAAGAGAGGAACATAAAAAATTTGGGG
698 AGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGA
* * * * * **
53003922 AAATTCCTAAAATCCTCATTCGCCAGAAGAGTAAACACCTCACGAACCACCCTA-AAAAATCAGT
1 AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAACGCCTCACGAACCACCCTAGCAAAATCACA
** * * * *
53003986 ACTAATGAAAGTAAAAGGCCTTCCAAAGATATCAAGATAACCATCCTAAAACGAAACTAACAAAT
66 ACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACGAAT
* * * * * * *
53004051 TATACTTACTTGATGATTTTAATAACACCAACACAGTCAAAATGGTGGCACAATAGAAGATTGAT
131 TATACTTACCTGAAGATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATAGGT
*
53004116 CGACAATGAAGAAACAATAGCAAGAGACGACAACAGGGGAATATGGCAACAAATGTAAAAGAAAC
196 CGGCAATGAAGAAACAATAGCAAGAGACGA-AAC----G---A---CAACAAATGTAAAAGAAAC
* * * * * *
53004181 AAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAGAGAACGTTAGACGAACATAAAATGGGA
250 GAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAATGGGA
* * * * * * * *
53004246 GAAAGAAATGGAAGCAATGGAAAGAGAGAAATATAAAAAATTCGGGAAAATTGCTAAAATCTTTA
315 AAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATCTTCA
* *
53004311 CTCACTAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCAAAAG
380 CTCGCCAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCAAAAG
* * *
53004376 ACCTTTCAACGATATCAAGACAACCACCCTAAAAGAAAACTAACGAATTATACTTACCAGAAGAT
445 ACCTTCCAAAGATATCAAGACAACCACCCTAAAAG-AAACTAACGAATTATACTTACCTGAAGAT
* *
53004441 TTTAATAACACCAACGTAGTCTAAATGTCGCCACAATAGAAGATAGGTCGGCAATGAAGAAACAG
509 TTTAATAACACCAACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTCGGCAATGAAGAAACAG
* *
53004506 TAGCAAGAGACGATAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAACGAAAC--
574 TAGCAAGAGACGACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAATGAAACAA
*
53004569 --AGAAAG-A-AAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAACAGAAATGGAAGTAGT
639 AAAGAAAGAAGAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGT
* *
53004630 GGAAAGAGAGGAACGTAAAAAATTTGGGT
704 GGAAAGAGAGGAACATAAAAAATTTGGGA
* * * *** * ** * * * **
53004659 AAATT-TTAGGAGGTAT-TTTTTTGGATAATTTTCTAA-AGTTCAAA-TCC-AACCCAAATACCA
1 AAATTGCTA--A--AATCCTCACTCGCCAA------AAGAG-T-AAACGCCTCA-CGAACCACC-
*** * * * * * ** * * *
53004719 CTAG-ATGGGTGAC-ACATGAGGATTTAGCAAAA-ATAATTCCATTTTTAGTAACAACTAATGA-
52 CTAGCA-AAATCACAAC-TAATGA--AACCAAAAGA-CCTTCCA----AAG--ATATC-AA-GAC
* * * * ** * * *
53004780 AACCAAAAGACCTTTCAAAGATATC-AAGAC-AACCACCATAAAACAAAACT-AACGAATTATAC
104 AACC-----ACC---CTAA-A-A-CGAA-ACTAACGA--ATTATACTTACCTGAA-G-ATTTTAA
* * * * ** ** * * * **
53004842 TTAC-CTGAA-G-ATTTTGATAACACCGACGCAGTCTAA-ATGACAGCACA-ATAGAAGATAGCT
153 TAACAC-CAACGCA--GT-CTAA-ATGGTGGCA--C-AACA-GA-AG-ATAGGTCG-GCA-A--T
*
53004902 CGACAATAAAGAAACAATAGTAAGAGACGAAAACAGGTGAATATGACAACAAATGTAAAAGAAAC
203 -G------AAGAAACAATAGCAAGAGACG-AAAC----------GACAACAAATGTAAAAGAAAC
* * *
53004967 GAAAGAAAAATGAAACAGAAAGAAAGAAAAAGAAAAAAATAACGTTAGAGGAACAAAAAATGGGA
250 GAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAATGGGA
*
53005032 AAAAGAAATGGAAGTAGTGAAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATCTTCA
315 AAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATCTTCA
** * * *
53005097 CTCGTTAGAAGAGTAAATGCCTCACGAACCACCTCTAGCAAAATCACAACTAATAAAACCAAAAG
380 CTCGCCAGAAGAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCAAAAG
* * ** *
53005162 GCCTTCCAAAGATATCAAGAAAACCACCCTAAAATGAAACTAATAAATTATATTTACCTGAAGAT
445 ACCTTCCAAAGATATCAAGACAACCACCCTAAAA-GAAACTAACGAATTATACTTACCTGAAGAT
* * * * * * * *
53005227 TTTAATAACACCGACGTAGTCTAAATGGCGGCATAACAGAAAATAGGTTGGCAATGAA-AGGAC-
509 TTTAATAACACCAACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTCGGCAATGAAGA-AACA
* * * *
53005290 GATAGCAAGAGACGAGAAGAGGGGAATATGGCAACAAATGTAAAAGAAATAAAAGAAAATGAAAC
573 G-TAGCAAGAGACGACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAATGAAAC
* ** *
53005355 AGAAAGAAAGAAGAAGAAGAAAATAACAACAGAGGAACAGAAAATGGGAAAAAGAAATGGAAGTA
637 AAAAAGAAAGAAGAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAATGGAAGTA
*
53005420 GTGGAAAGAGAGGAACATAAAAAATTTGGGG
702 GTGGAAAGAGAGGAACATAAAAAATTTGGGA
* * *
53005451 AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAATGCCTCACAAACCACCTCTAGTAAAATCAC
1 AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAACGCCTCACGAACCACC-CTAGCAAAATCAC
* * * * *
53005516 AATTAATAAAACCAAAAGACCTTCTAAAGATATCAAGACAACCACCCTAAAATGAAACTAACAAA
65 AACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACGAA
* ** *
53005581 TTATACTTACTTGAAGATTTTAATAACACCGGCGTAGTCTAAATGGTGGCACAACAGAAGATAGG
130 TTATACTTACCTGAAGATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATAGG
* * *
53005646 TTGGTAATGAAGAAATAATAGC-A-AGA-G-AAC-AC-A-AAA-GTAAAAGAAACGAAAGAAAAA
195 TCGGCAATGAAGAAACAATAGCAAGAGACGAAACGACAACAAATGTAAAAGAAACGAAAGAAAAA
* *
53005703 TGAGACAGAAAGAAAGAAGAAGAAGAAAATAACATTAAAGGAACAAAAAATGGGAAAAAGAAATG
260 TGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAATGGGAAAAAGAAATG
* * *
53005768 GAAGTAGTGGAAATAGAGGAATATAAAAAATTTGGGGAAATTGCTAAAATCTTCACTCACCAGAA
325 GAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATCTTCACTCGCCAGAA
* * * * *
53005833 GAGTAAATGCCTCACGAACCAGCCTTAGCAAAATCACAACTAATGAAATCAAAAGACCTTCCAAT
390 GAGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCAAAAGACCTTCCAAA
* * *
53005898 GATATCATGACAACCACCCTAAAATGAAACTAACGAATTATTCTTACCTGAAGATTTTAAGAACA
455 GATATCAAGACAACCACCCTAAAA-GAAACTAACGAATTATACTTACCTGAAGATTTTAATAACA
* * * * * *
53005963 CCAACGTAGTCTAAATGTCGGTACAATAGAAGATGGGTAGGCAATGAAGTAATAGTAGCAAGAGA
519 CCAACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTCGGCAATGAAGAAACAGTAGCAAGAGA
* *
53006028 CGACAATAGGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAATGAAACAAAAAGAAAGAA
584 CGACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAATGAAACAAAAAGAAAGAA
* *
53006093 GAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAACGTAATGGAAGTAGTGGAAAGAGAG
649 GAAGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAG
*
53006158 GAACGTAAAAAATTTGGGA
714 GAACATAAAAAATTTGGGA
* * * * * * *
53006177 AAATTACTGAAATACTCACTCGTCAGAAGAGTAAACACCTCATGAACCACCCCTAGCAAAAT---
1 AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAACGCCTCACGAACCA-CCCTAGCAAAATCAC
* * * * * * *
53006239 --C-----AAACCAAAATACCTTCCAAAGATTTAAAAACAACCAGCCTAGAACGAAGCTAACGAA
65 AACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACGAA
* * *
53006297 TTATACTTACC-GAAAGAGTTTATTAATTACACCAATGCAGTCTAAATGGTGGCACAATAGAAGA
130 TTATACTTACCTG-AAGA--TT-TTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGA
* * *
53006361 TAAGTCGGCAATGAATAAACAATAGCAAGAGACGACAACAAGGGAATATGACAATAAATGTAAAA
191 TAGGTCGGCAATGAAGAAACAATAGCAAGAGACGA-AAC----------GACAACAAATGTAAAA
* * * * * * *
53006426 GAAATGAAAGAAAAACGAAACAGAAAGAAAGAAGAAGAA-AAAATAACGTCAAATGAACAGAAAA
245 GAAACGAAAGAAAAATGAAACAGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAA
* * * *
53006490 TGGAAAAAAGAAATGAAAGTAATGGAAAGAGAGGAACGTAAAAAATTTGGGGAAATT
310 TGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATT
53006547 TTAGGAGGTA
Statistics
Matches: 5081, Mismatches: 900, Indels: 879
0.74 0.13 0.13
Matches are distributed among these distances:
713 3 0.00
714 5 0.00
715 118 0.02
716 293 0.06
717 4 0.00
718 2 0.00
719 58 0.01
720 2 0.00
721 4 0.00
722 6 0.00
723 9 0.00
724 6 0.00
725 5 0.00
726 501 0.10
727 6 0.00
728 2 0.00
729 3 0.00
730 5 0.00
731 1 0.00
733 1 0.00
734 9 0.00
735 4 0.00
736 9 0.00
737 158 0.03
738 65 0.01
739 72 0.01
740 343 0.07
741 345 0.07
742 312 0.06
743 427 0.08
744 393 0.08
745 151 0.03
746 289 0.06
747 31 0.01
748 1 0.00
749 12 0.00
750 13 0.00
751 6 0.00
752 4 0.00
753 8 0.00
754 8 0.00
755 22 0.00
756 15 0.00
757 8 0.00
758 8 0.00
759 10 0.00
760 7 0.00
761 5 0.00
762 10 0.00
763 12 0.00
764 10 0.00
765 19 0.00
766 8 0.00
767 12 0.00
768 9 0.00
769 11 0.00
770 10 0.00
771 5 0.00
773 2 0.00
774 6 0.00
775 11 0.00
776 6 0.00
777 1 0.00
778 7 0.00
779 8 0.00
780 7 0.00
781 5 0.00
782 10 0.00
783 4 0.00
784 21 0.00
785 9 0.00
786 383 0.08
787 2 0.00
788 9 0.00
789 3 0.00
790 23 0.00
791 12 0.00
792 98 0.02
793 9 0.00
794 15 0.00
795 7 0.00
796 14 0.00
797 15 0.00
798 3 0.00
799 17 0.00
800 12 0.00
801 12 0.00
802 13 0.00
803 15 0.00
804 5 0.00
805 11 0.00
806 1 0.00
807 3 0.00
809 1 0.00
810 3 0.00
811 4 0.00
812 9 0.00
813 10 0.00
814 8 0.00
815 6 0.00
817 7 0.00
818 5 0.00
819 9 0.00
820 1 0.00
821 5 0.00
822 2 0.00
823 11 0.00
824 7 0.00
825 22 0.00
826 13 0.00
827 16 0.00
828 18 0.00
829 7 0.00
830 10 0.00
831 4 0.00
832 9 0.00
833 10 0.00
834 1 0.00
835 3 0.00
836 10 0.00
837 13 0.00
838 9 0.00
839 3 0.00
840 8 0.00
841 6 0.00
844 103 0.02
845 31 0.01
846 2 0.00
847 38 0.01
848 1 0.00
849 2 0.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (732 bp):
AAATTGCTAAAATCCTCACTCGCCAAAAGAGTAAACGCCTCACGAACCACCCTAGCAAAATCACA
ACTAATGAAACCAAAAGACCTTCCAAAGATATCAAGACAACCACCCTAAAACGAAACTAACGAAT
TATACTTACCTGAAGATTTTAATAACACCAACGCAGTCTAAATGGTGGCACAACAGAAGATAGGT
CGGCAATGAAGAAACAATAGCAAGAGACGAAACGACAACAAATGTAAAAGAAACGAAAGAAAAAT
GAAACAGAAAGAAAGAAGAAGAAGAAAATAACATTAGAGGAACAAAAAATGGGAAAAAGAAATGG
AAGTAGTGGAAAGAGAGGAACATAAAAAATTTGGGGAAATTGCTAAAATCTTCACTCGCCAGAAG
AGTAAATGCCTCATGAACCACCCCTAGCAAAATCACAACTAATGAAACCAAAAGACCTTCCAAAG
ATATCAAGACAACCACCCTAAAAGAAACTAACGAATTATACTTACCTGAAGATTTTAATAACACC
AACGCAGTCTAAATGTCGGCACAATAGAAGATAGGTCGGCAATGAAGAAACAGTAGCAAGAGACG
ACAACAAGGGAATATGGCAACAAATGTAAAAGAAACAAAAGAAAATGAAACAAAAAGAAAGAAGA
AGAAGAAAATAACGTCAGAGGAACAAAAAATGGGAAAAAGAAATGGAAGTAGTGGAAAGAGAGGA
ACATAAAAAATTTGGGA
Found at i:53008857 original size:18 final size:18
Alignment explanation
Indices: 53008831--53008870 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53008821 GTGAAATATT
* *
53008831 AAGTGAAGTGTTTTATGA
1 AAGTAAAGTGTTATATGA
53008849 AAGTAAAGTGTTATATGA
1 AAGTAAAGTGTTATATGA
53008867 AAGT
1 AAGT
53008871 GAATTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (18 bp):
AAGTAAAGTGTTATATGA
Found at i:53019802 original size:112 final size:112
Alignment explanation
Indices: 53019605--53019831 Score: 364
Period size: 112 Copynumber: 2.0 Consensus size: 112
53019595 AAAGTAGAAT
* *
53019605 TAGAACTCGTACCTTTATAATATTGTGATGCACCAAATGGACGAGATTAACGTTACTGAAAATGT
1 TAGAACTCGTACCTCTATAATATTGTGATGCACCAAATGGACGAGATTAACATTACTGAAAATGT
* * *
53019670 TGCATTGGCTATTGAAACGTTCAAGCCATCCACAAACTGCACCATGG
66 TGCATTAGCTATTGAAACGTTCAAGCCATCCAAAAACTACACCATGG
* * ** *
53019717 TAGAACTTGTACCTCTATAATTTTGTGATGCACCAAATGGACGAGATTAACATTTTTGAATATGT
1 TAGAACTCGTACCTCTATAATATTGTGATGCACCAAATGGACGAGATTAACATTACTGAAAATGT
53019782 TGCATTAGCTATTGAAACGTTCAAGCCATCCAAAAACTACACCATGG
66 TGCATTAGCTATTGAAACGTTCAAGCCATCCAAAAACTACACCATGG
53019829 TAG
1 TAG
53019832 TCTCTTCATC
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (112 bp):
TAGAACTCGTACCTCTATAATATTGTGATGCACCAAATGGACGAGATTAACATTACTGAAAATGT
TGCATTAGCTATTGAAACGTTCAAGCCATCCAAAAACTACACCATGG
Found at i:53026062 original size:29 final size:30
Alignment explanation
Indices: 53025990--53026053 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
53025980 ATTATTTTAA
*
53025990 TTAT-TTAATATT-AATTTAATTGTAATAT
1 TTATCTTAATATTAAATTAAATTGTAATAT
*
53026018 TTATCTTAATATTAAATTAAATT-TAATGT
1 TTATCTTAATATTAAATTAAATTGTAATAT
53026047 TTATCTT
1 TTATCTT
53026054 GTATTTAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 4 0.12
29 20 0.62
30 8 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (30 bp):
TTATCTTAATATTAAATTAAATTGTAATAT
Found at i:53029937 original size:25 final size:25
Alignment explanation
Indices: 53029878--53029937 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
53029868 AAGGTTACCG
53029878 ATTTCAGCTCGTATGAGCTTATCGAT
1 ATTT-AGCTCGTATGAGCTTATCGAT
* *
53029904 ACTCT-GCTCGTATGAGCTTATCGTT
1 A-TTTAGCTCGTATGAGCTTATCGAT
53029929 ATTTAGCTC
1 ATTTAGCTC
53029938 AGAGGAGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.07
25 24 0.83
26 1 0.03
27 2 0.07
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (25 bp):
ATTTAGCTCGTATGAGCTTATCGAT
Found at i:53033181 original size:42 final size:40
Alignment explanation
Indices: 53033134--53033293 Score: 124
Period size: 42 Copynumber: 3.8 Consensus size: 40
53033124 CAATCATATA
* **
53033134 AAGCTCGCATGGGGAGCTTTGCTGACATTCAACTTGTCACTT
1 AAGCTCGCA--GGGAGCTTCGCTGACACACAACTTGTCACTT
* *
53033176 AAGCTCACGCAGGGAGCTTCGCTGACACACAACTTTTCCCTT
1 AAGCT--CGCAGGGAGCTTCGCTGACACACAACTTGTCACTT
* ** * *
53033218 AAGCTCATGTAGGGAGCTTCATTGATACACAACTTATCAC-T
1 AAGCTC--GCAGGGAGCTTCGCTGACACACAACTTGTCACTT
* * *
53033259 AAGCTCACGAGGGGAGCTTCACTGATACACAACTT
1 AAGCTCGC-A-GGGAGCTTCGCTGACACACAACTT
53033294 ATAAAACCGT
Statistics
Matches: 98, Mismatches: 14, Indels: 13
0.78 0.11 0.10
Matches are distributed among these distances:
40 2 0.02
41 30 0.31
42 62 0.63
44 4 0.04
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
AAGCTCGCAGGGAGCTTCGCTGACACACAACTTGTCACTT
Found at i:53033274 original size:41 final size:42
Alignment explanation
Indices: 53033163--53033295 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 42
53033153 TGCTGACATT
* * *
53033163 CAACTTGTCACTTAAGCTCACGCAGGGAGCTTCGCTGACACA
1 CAACTTATCACTTAAGCTCACGCAGGGAGCTTCACTGATACA
* * * * *
53033205 CAACTTTTCCCTTAAGCTCATGTAGGGAGCTTCATTGATACA
1 CAACTTATCACTTAAGCTCACGCAGGGAGCTTCACTGATACA
53033247 CAACTTATCAC-TAAGCTCACG-AGGGGAGCTTCACTGATACA
1 CAACTTATCACTTAAGCTCACGCA-GGGAGCTTCACTGATACA
53033288 CAACTTAT
1 CAACTTAT
53033296 AAAACCGTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 1 0.01
41 34 0.43
42 44 0.56
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (42 bp):
CAACTTATCACTTAAGCTCACGCAGGGAGCTTCACTGATACA
Found at i:53034902 original size:15 final size:16
Alignment explanation
Indices: 53034877--53034906 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53034867 CAGATTGTCT
53034877 AATATAGCTAAAATAC
1 AATATAGCTAAAATAC
53034893 AATA-AGCTAAAATA
1 AATATAGCTAAAATA
53034907 AAAATAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (16 bp):
AATATAGCTAAAATAC
Found at i:53039748 original size:17 final size:16
Alignment explanation
Indices: 53039728--53039761 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53039718 TTTTGTTTCA
53039728 CATTACTTTTTTCTTTT
1 CATTACTTTTTT-TTTT
*
53039745 CATTTCTTTTTTTTTT
1 CATTACTTTTTTTTTT
53039761 C
1 C
53039762 CAGAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (16 bp):
CATTACTTTTTTTTTT
Found at i:53041139 original size:30 final size:30
Alignment explanation
Indices: 53041075--53041139 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
53041065 TACATGGCTG
* * *
53041075 TGTGAGTAGGCCATGTGTGGCACACGACCG
1 TGTGAGTAAGCCATGTGTGACACACGACCA
*
53041105 TGTGAGTAAGCCGTGTGTGACACAC-AGCCA
1 TGTGAGTAAGCCATGTGTGACACACGA-CCA
53041135 TGTGA
1 TGTGA
53041140 CATCCCTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.23, C:0.22, G:0.34, T:0.22
Consensus pattern (30 bp):
TGTGAGTAAGCCATGTGTGACACACGACCA
Found at i:53044474 original size:13 final size:13
Alignment explanation
Indices: 53044456--53044480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53044446 ACCGAAAGAG
53044456 TAGTTTAATGTTT
1 TAGTTTAATGTTT
53044469 TAGTTTAATGTT
1 TAGTTTAATGTT
53044481 GTCGTGCTTT
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
TAGTTTAATGTTT
Found at i:53052444 original size:50 final size:50
Alignment explanation
Indices: 53052328--53052623 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
53052318 GATAATAACA
* ** * *
53052328 TGCCAACGCCATGT-CCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * * ** *
53052376 TACCAATGCCATATCCCAGATATGGCCTTACTTGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
53052426 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * *
53052476 TGGCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
53052526 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
*
53052581 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53052624 TTACACAAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
48 11 0.05
49 25 0.12
50 123 0.61
53 2 0.01
55 1 0.00
56 40 0.20
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:53055250 original size:27 final size:28
Alignment explanation
Indices: 53055180--53055240 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
53055170 TATTGCACTG
* * *
53055180 CACTGATATTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTACTGGGCTAAGGCCCA
*
53055208 CATTGTTACTGTACTGGGCTAAGG-CCA
1 CACTGTTACTGTACTGGGCTAAGGCCCA
53055235 CACTGT
1 CACTGT
53055241 ACTATTACTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTACTGGGCTAAGGCCCA
Done.