Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 208 of 295
Found at i:66464604 original size:36 final size:36
Alignment explanation
Indices: 66464509--66464613 Score: 99
Period size: 36 Copynumber: 3.0 Consensus size: 36
66464499 TTAATCACTT
*
66464509 TAACAA-T-ATCATTCAGTAAC-GATCATTTATTCAG
1 TAACAATTAATCATTCAATAACAG-TCATTTATTCAG
* * * *
66464543 TAATAATTAGTCATTTAGTAACAGTCATTTATTCAG
1 TAACAATTAATCATTCAATAACAGTCATTTATTCAG
* * * *
66464579 TAACAGTTAATTATTCAATAGCAGTCAGTTATTCA
1 TAACAATTAATCATTCAATAACAGTCATTTATTCA
66464614 ATACCTTTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 5 0.09
35 1 0.02
36 50 0.88
37 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (36 bp):
TAACAATTAATCATTCAATAACAGTCATTTATTCAG
Found at i:66466137 original size:13 final size:15
Alignment explanation
Indices: 66466111--66466143 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
66466101 CATTTACTTT
66466111 ATATATATTATAATA
1 ATATATATTATAATA
66466126 ATATA-ATT-TAATA
1 ATATATATTATAATA
66466139 ATATA
1 ATATA
66466144 CTTATCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 3 0.17
15 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATTATAATA
Found at i:66466292 original size:14 final size:15
Alignment explanation
Indices: 66466260--66466305 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
66466250 ACTTTATTTA
66466260 ATTAATATAAAATAAT
1 ATTAATAT-AAATAAT
66466276 ATTAATAT-AATAAT
1 ATTAATATAAATAAT
*
66466290 ATTTACT-TAAATAAT
1 A-TTAATATAAATAAT
66466305 A
1 A
66466306 AGTAAATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.30
15 11 0.41
16 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAATATAAATAAT
Found at i:66466637 original size:17 final size:18
Alignment explanation
Indices: 66466615--66466649 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
66466605 GAATTGGGCC
66466615 GTGTGGG-CCACACGGGT
1 GTGTGGGACCACACGGGT
*
66466632 GTGTGGGACCACATGGGT
1 GTGTGGGACCACACGGGT
66466650 AGTCCACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.20, G:0.46, T:0.20
Consensus pattern (18 bp):
GTGTGGGACCACACGGGT
Found at i:66469401 original size:27 final size:27
Alignment explanation
Indices: 66469371--66469548 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
66469361 ATATTGAGTC
* * * *
66469371 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
66469398 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
66469425 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
66469453 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
66469480 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
66469507 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
66469534 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66469549 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:66469510 original size:82 final size:81
Alignment explanation
Indices: 66469392--66469547 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
66469382 TGCTATATAA
* *
66469392 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
66469457 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
66469474 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
66469538 CACTTAGTGC
65 CACTTAGTGC
66469548 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:66470116 original size:13 final size:13
Alignment explanation
Indices: 66470098--66470122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66470088 TACTAAATTT
66470098 TCATGGATTCAAG
1 TCATGGATTCAAG
66470111 TCATGGATTCAA
1 TCATGGATTCAA
66470123 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:66475392 original size:38 final size:38
Alignment explanation
Indices: 66475321--66475509 Score: 193
Period size: 38 Copynumber: 4.9 Consensus size: 38
66475311 ATTTGATGTG
* *
66475321 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGAATTA
*
66475361 TATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGCAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG-AATTA
* *
66475399 TATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
* * * *
66475437 TATCTGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
* * * *
66475475 TATCTGAGCTTAAAGTCCCGCAGGTTTTGTGCTGG
1 TATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGG
66475510 TGACTAGATT
Statistics
Matches: 130, Mismatches: 14, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
37 2 0.02
38 90 0.69
39 13 0.10
40 25 0.19
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
Found at i:66475430 original size:76 final size:77
Alignment explanation
Indices: 66475328--66475509 Score: 215
Period size: 76 Copynumber: 2.4 Consensus size: 77
66475318 GTGTATCCGG
* * * * *
66475328 GCTTAAAGACCCGCAGGCTATATGCTGGAATTATATCCGGGTTAAATCCCGTAGGCTTCGTGCTG
1 GCTTAAAGTCCCGCAGGCT-TGTGCTGGAATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTG
66475393 GCAATATATC-CA
65 GCAATATATCTCA
* * *
66475405 GGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTATATCTGGGTTAAATCCCGCAGGCCTAGTGCTG
1 GCTTAAAGTCCCGCAGGCTT-GTGCTGGAATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTG
* * *
66475469 GTATTATATCTGA
65 GCAATATATCTCA
*
66475482 GCTTAAAGTCCCGCAGGTTTTGTGCTGG
1 GCTTAAAGTCCCGCAGG-CTTGTGCTGG
66475510 TGACTAGATT
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
75 1 0.01
76 56 0.64
77 13 0.15
78 16 0.18
79 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (77 bp):
GCTTAAAGTCCCGCAGGCTTGTGCTGGAATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGG
CAATATATCTCA
Found at i:66478070 original size:15 final size:15
Alignment explanation
Indices: 66478050--66478097 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
66478040 TCAAAGATGG
66478050 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
66478065 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
66478079 GTTTATGGATATAAA
1 GTTTATGGATATGAA
66478094 GTTT
1 GTTT
66478098 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:66478084 original size:14 final size:14
Alignment explanation
Indices: 66478044--66478087 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
66478034 AAGGATTCAA
66478044 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
66478058 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
66478073 AGATGGGTTTATGG
1 AGATGGGTTTATGG
66478087 A
1 A
66478088 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:66478113 original size:29 final size:29
Alignment explanation
Indices: 66478044--66478103 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
66478034 AAGGATTCAA
*
66478044 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
66478073 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
66478102 AG
1 AG
66478104 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:66481626 original size:18 final size:18
Alignment explanation
Indices: 66481605--66481654 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
66481595 AAACTCTTTT
66481605 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
66481623 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
66481641 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
66481655 TTTGTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:66481655 original size:24 final size:24
Alignment explanation
Indices: 66481580--66481657 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
66481570 CTTGTTCACA
*
66481580 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
66481604 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
66481628 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
66481652 TTCTTT
1 TTCTTT
66481658 GTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:66482762 original size:11 final size:11
Alignment explanation
Indices: 66482746--66482771 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
66482736 TTGTTTGAAA
66482746 TTTTTTTTCGT
1 TTTTTTTTCGT
66482757 TTTTTTTTCGT
1 TTTTTTTTCGT
66482768 TTTT
1 TTTT
66482772 AATGAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCGT
Found at i:66487377 original size:38 final size:38
Alignment explanation
Indices: 66487306--66487425 Score: 145
Period size: 38 Copynumber: 3.1 Consensus size: 38
66487296 ATTTGATGTG
* *
66487306 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGAATTA
*
66487346 TATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG-AATTA
* *
66487384 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
66487422 TATC
1 TATC
66487426 TGAGCTTAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
37 2 0.03
38 54 0.76
39 7 0.10
40 8 0.11
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
Found at i:66487456 original size:40 final size:38
Alignment explanation
Indices: 66487306--66487457 Score: 135
Period size: 38 Copynumber: 3.9 Consensus size: 38
66487296 ATTTGATGTG
* * * *
66487306 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGG-AATTA
1 TATCC-GGCTTAAA-TCCCACAGGCTTTGTGCTGGTAA-TA
* ** *
66487346 TATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAATA
1 TATCCGGCTTAAATCCCACAGGCTTTGTGCTGGTAATA
* * *
66487384 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTATTA
1 TATCCGGCTTAAATCCCACAGGCTTTGTGCTGGTAATA
* *
66487422 TATCTGAGCTTAAAGTCCCACAGGTTTTGTGCTGGT
1 TATCCG-GCTTAAA-TCCCACAGGCTTTGTGCTGGT
66487458 GACTAGATTC
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
38 57 0.59
39 15 0.16
40 24 0.25
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (38 bp):
TATCCGGCTTAAATCCCACAGGCTTTGTGCTGGTAATA
Found at i:66488733 original size:55 final size:54
Alignment explanation
Indices: 66488624--66488805 Score: 215
Period size: 55 Copynumber: 3.4 Consensus size: 54
66488614 TTAGTTTACC
* * * * *
66488624 AAATTACCAAAATA-CCCTCGATTAGCAAAATTACCGAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCCTAGTTTGTA
66488678 AAATTACCAAAATACCCCTAGTTTGTAAAATTTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAA-TTACCAAAATACCCCTAGTTTGTA
* * * * * *
66488733 AAATTACCAAAATACACCTAGTTTGTGAAATTACTAAAATA-CGCTCGACTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAG-TTTGTA
*
66488787 AAATTACCAAAGTACCCCT
1 AAATTACCAAAATACCCCT
66488806 GATTTACAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 4 0.04
54 53 0.47
55 55 0.49
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTA
Found at i:66488757 original size:82 final size:82
Alignment explanation
Indices: 66488624--66488858 Score: 221
Period size: 82 Copynumber: 2.9 Consensus size: 82
66488614 TTAGTTTACC
* * * *
66488624 AAATTACCAAAATA-CCCTCGATTAGCAAAATTACCGAAATACCCCTGGTTTGTAAAATTACCAA
1 AAATTACCAAAATACCCCTAGATTAGCAAAATTACCAAAATACACCTAGTTTGTAAAATTACCAA
*
66488688 AATACCCCTAG-TTTGTA
66 AATA-CCCTAGACTTGTA
* * * *
66488705 AAATTTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACACCTAGTTTGTGAAATTACTA
1 AAA-TTACCAAAATACCCCTAGATTAGCAAAATTACCAAAATACACCTAGTTTGTAAAATTACCA
* *
66488769 AAATACGCTCGACTTGTA
65 AAATACCCTAGACTTGTA
* * *** * **
66488787 AAATTACCAAAGTACCCCT-GATTTA-CAGAATTACCATTTTAC-CCTCAATTTACAAAATTACC
1 AAATTACCAAAATACCCCTAGA-TTAGCAAAATTACCAAAATACACCT-AGTTTGTAAAATTACC
66488849 AAAATACCCT
64 AAAATACCCT
66488859 TGTAGGGTAG
Statistics
Matches: 124, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
80 4 0.03
81 54 0.44
82 61 0.49
83 5 0.04
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (82 bp):
AAATTACCAAAATACCCCTAGATTAGCAAAATTACCAAAATACACCTAGTTTGTAAAATTACCAA
AATACCCTAGACTTGTA
Found at i:66488858 original size:27 final size:28
Alignment explanation
Indices: 66488624--66488858 Score: 180
Period size: 27 Copynumber: 8.6 Consensus size: 28
66488614 TTAGTTTACC
* * *
66488624 AAATTACCAAAATACCCTC-GATTAGCA
1 AAATTACCAAAATACCCTCTAATTTGTA
* **
66488651 AAATTACCGAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTCTAATTTGTA
*
66488678 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCTAATTTGTA
*
66488705 AAATTTACCAAAATACCC-CTAGTTTGTA
1 AAA-TTACCAAAATACCCTCTAATTTGTA
* * *
66488733 AAATTACCAAAATACAC-CTAGTTTGTG
1 AAATTACCAAAATACCCTCTAATTTGTA
* * * *
66488760 AAATTACTAAAATACGCTC-GACTTGTA
1 AAATTACCAAAATACCCTCTAATTTGTA
* * **
66488787 AAATTACCAAAGTACCC-CTGATTTACA
1 AAATTACCAAAATACCCTCTAATTTGTA
* *** **
66488814 GAATTACCATTTTACCCTC-AATTTACA
1 AAATTACCAAAATACCCTCTAATTTGTA
66488841 AAATTACCAAAATACCCT
1 AAATTACCAAAATACCCT
66488859 TGTAGGGTAG
Statistics
Matches: 174, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
26 2 0.01
27 143 0.82
28 29 0.17
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (28 bp):
AAATTACCAAAATACCCTCTAATTTGTA
Found at i:66488909 original size:27 final size:27
Alignment explanation
Indices: 66488850--66488911 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
66488840 AAAATTACCA
* *
66488850 AAATACCCTTGTAGGGTAGAAATTTTG
1 AAATACCCCTGTAGGGTAGAAATTCTG
66488877 AAATACCCCTGTAGGGTAG-AATTACTG
1 AAATACCCCTGTAGGGTAGAAATT-CTG
*
66488904 AGATACCC
1 AAATACCC
66488912 TTTAAGGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAAATTCTG
Found at i:66489560 original size:27 final size:27
Alignment explanation
Indices: 66489530--66489664 Score: 166
Period size: 27 Copynumber: 5.0 Consensus size: 27
66489520 ATTCTGTTAA
* *
66489530 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
*
66489557 GTGGCTATGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
66489584 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* * *
66489611 GTGGCTCTGCCACAATATATGTATCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* * *
66489638 GTGACTCTGTCACAATATCTG-TTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
66489664 G
1 G
66489665 AAGCCATGCT
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 12 0.12
27 78 0.80
28 7 0.07
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:66489791 original size:6 final size:6
Alignment explanation
Indices: 66489782--66489902 Score: 61
Period size: 6 Copynumber: 19.8 Consensus size: 6
66489772 TTGCATTCAC
* * * *
66489782 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTTTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * * * *
66489832 ATTTTG ATTTTG ATTTTG ATT-TG ATTTTG ATTCTG -TCACCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
* *
66489880 ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
66489903 AGTTCTAATA
Statistics
Matches: 89, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
5 9 0.10
6 69 0.78
7 8 0.09
8 3 0.03
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTCTG
Found at i:66489839 original size:25 final size:25
Alignment explanation
Indices: 66489785--66489846 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
66489775 CATTCACATT
* * *
66489785 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTTTGATTCTGTCACCTAATA
*
66489810 CTGATTTTGATTCTGTCACCTAATT
1 CTGATTTTGATTCTGTCACCTAATA
*
66489835 TTGATTTTGATT
1 CTGATTTTGATT
66489847 TTGATTTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (25 bp):
CTGATTTTGATTCTGTCACCTAATA
Found at i:66489856 original size:11 final size:11
Alignment explanation
Indices: 66489832--66489863 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
66489822 CTGTCACCTA
66489832 ATTTTGATTTTG
1 ATTTTGA-TTTG
66489844 ATTTTGATTTG
1 ATTTTGATTTG
66489855 ATTTTGATT
1 ATTTTGATT
66489864 CTGTCACCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.66
Consensus pattern (11 bp):
ATTTTGATTTG
Found at i:66498224 original size:14 final size:15
Alignment explanation
Indices: 66498192--66498233 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
66498182 ATATGCAAAT
*
66498192 AAAAGAATTACTAGA
1 AAAAGAATTAATAGA
*
66498207 AAAAGGATTAATAGA
1 AAAAGAATTAATAGA
66498222 AAAA-AA-TAATAG
1 AAAAGAATTAATAG
66498234 TCTACATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 6 0.25
14 1 0.04
15 17 0.71
ACGTcount: A:0.64, C:0.02, G:0.14, T:0.19
Consensus pattern (15 bp):
AAAAGAATTAATAGA
Found at i:66502029 original size:16 final size:16
Alignment explanation
Indices: 66502016--66502047 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
66502006 GTGATTTTTT
66502016 AAATAATTATTTTTAA
1 AAATAATTATTTTTAA
66502032 AAATAATTATTTTTAA
1 AAATAATTATTTTTAA
66502048 GGATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATAATTATTTTTAA
Found at i:66502030 original size:14 final size:14
Alignment explanation
Indices: 66502011--66502047 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
66502001 TAGGTGTGAT
66502011 TTTTTAAATAATTA
1 TTTTTAAATAATTA
66502025 TTTTTAAAAATAATTA
1 TTTTT--AAATAATTA
66502041 TTTTTAA
1 TTTTTAA
66502048 GGATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
16 14 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTAAATAATTA
Found at i:66504615 original size:20 final size:21
Alignment explanation
Indices: 66504576--66504618 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
66504566 AATTTGTAAC
66504576 TTAAAAAAAAACTTACATATA
1 TTAAAAAAAAACTTACATATA
* *
66504597 TTAATAAAAAA-TTATATATA
1 TTAAAAAAAAACTTACATATA
66504617 TT
1 TT
66504619 TCAGATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAAAAAAAAACTTACATATA
Found at i:66505823 original size:12 final size:12
Alignment explanation
Indices: 66505806--66505834 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
66505796 AACAACCTTC
66505806 ACATAAGGCTTT
1 ACATAAGGCTTT
66505818 ACATAAGGCTTT
1 ACATAAGGCTTT
66505830 ACATA
1 ACATA
66505835 GGTAATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (12 bp):
ACATAAGGCTTT
Found at i:66506796 original size:43 final size:44
Alignment explanation
Indices: 66506735--66506923 Score: 217
Period size: 43 Copynumber: 4.4 Consensus size: 44
66506725 AAACCACCAT
* * *
66506735 TATAGAATGTGACCTTTAGCGGCACTTTCTCT-ACTAACGCTGC
1 TATAGAACGTGACCTTTAGCGGCGCTTTCTCTCACAAACGCTGC
* * *
66506778 TATAGAACGTGACCTTTAGCGGCGCTTT-TCTGACAAATGCCGC
1 TATAGAACGTGACCTTTAGCGGCGCTTTCTCTCACAAACGCTGC
* * * * *
66506821 AATAGAACATGACCTTTAGCGACGCTTT-TCTCACAAACACTGT
1 TATAGAACGTGACCTTTAGCGGCGCTTTCTCTCACAAACGCTGC
* *
66506864 TATAGAACATGACCTTTAGCGGCGCTTTAC-CT-ACAAACGCTAC
1 TATAGAACGTGACCTTTAGCGGCGCTTT-CTCTCACAAACGCTGC
66506907 TATAGAACGTGACCTTT
1 TATAGAACGTGACCTTT
66506924 TGTGGCACTT
Statistics
Matches: 124, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 3 0.02
43 119 0.96
44 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
TATAGAACGTGACCTTTAGCGGCGCTTTCTCTCACAAACGCTGC
Found at i:66507121 original size:19 final size:19
Alignment explanation
Indices: 66507099--66507143 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
66507089 AACCAAAAAT
*
66507099 AACAAATACAAATCCAACC
1 AACAAATACAAAGCCAACC
*
66507118 AACAAATACAAAGCCAGCC
1 AACAAATACAAAGCCAACC
66507137 AA-AAATA
1 AACAAATA
66507144 GAAAATCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.60, C:0.27, G:0.04, T:0.09
Consensus pattern (19 bp):
AACAAATACAAAGCCAACC
Found at i:66513006 original size:9 final size:9
Alignment explanation
Indices: 66512932--66513020 Score: 76
Period size: 9 Copynumber: 10.1 Consensus size: 9
66512922 TATGTATTAA
*
66512932 GTAAGTTAA
1 GTAAGTTAT
*
66512941 GTAAGTTTT
1 GTAAGTTAT
*
66512950 GTAAGTTTT
1 GTAAGTTAT
66512959 GTAAGTTAT
1 GTAAGTTAT
* *
66512968 GATATGATAT
1 G-TAAGTTAT
* *
66512978 AT-ATTTAT
1 GTAAGTTAT
66512986 GT-A-TTAT
1 GTAAGTTAT
*
66512993 GTAAGTTTT
1 GTAAGTTAT
66513002 GTAAGTTAT
1 GTAAGTTAT
66513011 GTAAGTTAT
1 GTAAGTTAT
66513020 G
1 G
66513021 ATATGATATA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
7 6 0.09
8 6 0.09
9 47 0.72
10 6 0.09
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:66513417 original size:160 final size:161
Alignment explanation
Indices: 66513056--66513490 Score: 658
Period size: 160 Copynumber: 2.7 Consensus size: 161
66513046 TAAATATTAT
66513056 TTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGTATAAAAAGTTGA
1 TTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGTATAAAAAGTTGA
* * * *
66513121 AAACTGTATAAGACGAAATGTCAACTTTGTTCCATAAAAAAATAAAAATAAAAATAAAATTTGAC
66 AAACCGTATAAGATGAAATGTCAACTTTGTTCCAT---GAAA-AAAAATAAAAATAAAAATTGAC
*
66513186 AATGCAGAAAATCACATGGAAAAAAAATTGTTTTAA
127 AATGCAGAAAATCACATGG-AAAAAAATTATTTTAA
* *
66513222 TTAAATAATATTTAAATAAATTAATCTAAATTATATTATTTAAAAAATTGTGTATAAAAAGTTGA
1 TTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGTATAAAAAGTTGA
* * **
66513287 AAACCGTATAAGATGGAAATGTCAACTTTGATCCATGGAAAAAAATAAAAATAAAAATTGATGAT
66 AAACCGTATAAGAT-GAAATGTCAACTTTGTTCCATGAAAAAAAATAAAAATAAAAATTGACAAT
*
66513352 GTAGAAAATCACAT-G-AAAAAATTATTTTAA
130 GCAGAAAATCACATGGAAAAAAATTATTTTAA
** *
66513382 TTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAATTTTGTGTATAAACAGTTGA
1 TTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGTATAAAAAGTTGA
*
66513447 AAACCGTATAAGATGAAATGTCAACTTTGTTCTATGAAAAAAAA
66 AAACCGTATAAGATGAAATGTCAACTTTGTTCCATGAAAAAAAA
66513491 AAGATTGAAC
Statistics
Matches: 248, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
159 27 0.11
160 88 0.35
162 1 0.00
163 35 0.14
164 2 0.01
166 75 0.30
167 20 0.08
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.33
Consensus pattern (161 bp):
TTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAAATTGTGTATAAAAAGTTGA
AAACCGTATAAGATGAAATGTCAACTTTGTTCCATGAAAAAAAATAAAAATAAAAATTGACAATG
CAGAAAATCACATGGAAAAAAATTATTTTAA
Found at i:66514139 original size:32 final size:32
Alignment explanation
Indices: 66514103--66514167 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
66514093 TGTATGCATT
66514103 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
66514135 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
66514167 T
1 T
66514168 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:66518751 original size:7 final size:7
Alignment explanation
Indices: 66518739--66518894 Score: 86
Period size: 7 Copynumber: 21.9 Consensus size: 7
66518729 TTTGATCTTT
66518739 CCTAAAC
1 CCTAAAC
66518746 CCTAAA-
1 CCTAAAC
66518752 CCTCAAAC
1 CCT-AAAC
*
66518760 CATAAAC
1 CCTAAAC
*
66518767 TCTAAAC
1 CCTAAAC
* *
66518774 CATAAAT
1 CCTAAAC
66518781 CCTAAAC
1 CCTAAAC
*
66518788 CTTAAAC
1 CCTAAAC
66518795 CCTAAAC
1 CCTAAAC
66518802 CC-AAA-
1 CCTAAAC
66518807 CCTCAAGAC
1 CCT-AA-AC
66518816 CCTAAATC
1 CCTAAA-C
*
66518824 CC-AATC
1 CCTAAAC
*
66518830 TCTAAAC
1 CCTAAAC
66518837 CCATAAAC
1 CC-TAAAC
*
66518845 CTCAAAAC
1 C-CTAAAC
*
66518853 CATAAAC
1 CCTAAAC
* *
66518860 TCAAAACC
1 CCTAAA-C
66518868 CCTAAAC
1 CCTAAAC
**
66518875 TTTAAAC
1 CCTAAAC
**
66518882 TATAAAC
1 CCTAAAC
66518889 CCTAAA
1 CCTAAA
66518895 ATACTTAGAT
Statistics
Matches: 111, Mismatches: 27, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
5 2 0.02
6 8 0.07
7 73 0.66
8 24 0.22
9 4 0.04
ACGTcount: A:0.46, C:0.35, G:0.01, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:66518873 original size:15 final size:15
Alignment explanation
Indices: 66518833--66518875 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
66518823 CCCAATCTCT
66518833 AAACCCATAAACCTCA
1 AAACCCATAAA-CTCA
66518849 AAA-CCATAAACTCA
1 AAACCCATAAACTCA
*
66518863 AAACCCCTAAACT
1 AAACCCATAAACT
66518876 TTAAACTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 15 0.60
16 3 0.12
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACCCATAAACTCA
Found at i:66521593 original size:37 final size:37
Alignment explanation
Indices: 66521543--66521621 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
66521533 TTATTACGAA
* * *
66521543 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
66521580 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
66521617 GTCTT
1 GTCTT
66521622 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:66521818 original size:47 final size:47
Alignment explanation
Indices: 66521740--66522397 Score: 1048
Period size: 47 Copynumber: 13.7 Consensus size: 47
66521730 CCCTTCGGGA
* * * * * *
66521740 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
66521787 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66521834 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66521881 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66521928 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
66521977 CTTACCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522026 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66522075 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522124 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522171 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66522220 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522269 CTTATCACATATATACACTTTCACATTCATCACATCCGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66522316 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
66522363 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
66522398 AGAATCCTAA
Statistics
Matches: 583, Mismatches: 23, Indels: 10
0.95 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 300 0.51
49 282 0.48
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:66521961 original size:49 final size:49
Alignment explanation
Indices: 66521740--66522376 Score: 1059
Period size: 49 Copynumber: 13.3 Consensus size: 49
66521730 CCCTTCGGGA
* * * * *
66521740 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
66521787 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66521834 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66521881 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66521928 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
66521977 CTTACCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522026 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66522075 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522124 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522171 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66522220 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
66522269 CTTATCAC--ATATATACACTTTCACATTCATCACATCCGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66522316 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
66522363 CTTATCACATATAT
1 CTTATCACATATAT
66522377 GCATGTTCAC
Statistics
Matches: 562, Mismatches: 20, Indels: 14
0.94 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 275 0.49
49 286 0.51
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:66522035 original size:145 final size:143
Alignment explanation
Indices: 66521740--66522376 Score: 1080
Period size: 145 Copynumber: 4.4 Consensus size: 143
66521730 CCCTTCGGGA
* * * * * * * *
66521740 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
66521803 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66521868 TCGGCCATTAGGC
131 TCGGCCATTAGGC
66521881 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
66521946 ACTTTCACATTCATCACATCGGCCATTAGGCCTTACCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
*
66522011 CATTGGCCATTAGGC
129 CATCGGCCATTAGGC
*
66522026 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
66522091 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
66522156 CATCGGCCATTCGGC
129 CATCGGCCATTAGGC
*
66522171 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
66522236 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
66522301 CATCCGCCATTAGGC
129 CATCGGCCATTAGGC
66522316 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
66522377 GCATGTTCAC
Statistics
Matches: 473, Mismatches: 17, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
141 47 0.10
143 98 0.21
145 234 0.49
147 94 0.20
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:66527870 original size:46 final size:46
Alignment explanation
Indices: 66527820--66527918 Score: 162
Period size: 46 Copynumber: 2.2 Consensus size: 46
66527810 CAAGATTGTG
*
66527820 TTAATTTTATTTGAATTAATTTATTAAACTATAACAAATGCTTGAC
1 TTAATTTTATTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
* * *
66527866 TTAATTTTGTTTGTATTAATTTATTAAACTATCACAAAGGCTTGAC
1 TTAATTTTATTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
66527912 TTAATTT
1 TTAATTT
66527919 AAAATTTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.47
Consensus pattern (46 bp):
TTAATTTTATTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
Found at i:66539444 original size:46 final size:46
Alignment explanation
Indices: 66539394--66539492 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
66539384 CAAGATTGTG
*
66539394 TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAATGCTTGAC
1 TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
* *
66539440 TTAATTTTGTTTGCATTAATTTATTAAACTATCACAAAGGCTTGAC
1 TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
66539486 TTAATTT
1 TTAATTT
66539493 ATAATTTTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (46 bp):
TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
Found at i:66548274 original size:43 final size:43
Alignment explanation
Indices: 66548226--66548350 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
66548216 ATAGAGATGT
*
66548226 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT-TGA
1 GATTACATGTAAGACCATGTCTGGGATA-TGGCATTGTATATGA
* * * * * *
66548269 GATTACGTGTAAGACCCTGTATTGGATAGTGGCATCG-ATATGT
1 GATTACATGTAAGACCATGTCTGGGATA-TGGCATTGTATATGA
* * *
66548312 GATAACATGTAAGACCATATCTGGGATATGGCACTGTAT
1 GATTACATGTAAGACCATGTCTGGGATATGGCATTGTAT
66548351 GAGTTATATG
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
42 8 0.12
43 56 0.88
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGATATGGCATTGTATATGA
Found at i:66551854 original size:46 final size:46
Alignment explanation
Indices: 66551798--66551973 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
66551788 TATTTGGGCA
66551798 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
66551844 TCTGAACTCGTTGAGTTGAGTCCGAGTT---TGA-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
* *
66551889 CATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
66551937 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
66551974 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 11, Indels: 22
0.77 0.08 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
45 1 0.01
46 61 0.56
47 25 0.23
48 1 0.01
50 7 0.06
51 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:66551953 original size:93 final size:93
Alignment explanation
Indices: 66551794--66551964 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
66551784 AGGATATTTG
* *
66551794 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
66551859 TTGAGTCCGAGTTTGAGAGATGTAACTA
66 TTGAGTCCGAGTTTGAGAGATGTAACTA
* * *
66551887 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
*
66551952 TTGAGTCTGAGTT
66 TTGAGTCCGAGTT
66551965 CACTTATGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
TTGAGTCCGAGTTTGAGAGATGTAACTA
Found at i:66554711 original size:15 final size:15
Alignment explanation
Indices: 66554691--66554759 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
66554681 GTATCTTGGG
66554691 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
66554706 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
66554721 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
66554736 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
66554751 TTTCTTTAT
1 TTTCTTTAT
66554760 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:66554760 original size:30 final size:30
Alignment explanation
Indices: 66554682--66554769 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
66554672 CATAATATCG
* * * *
66554682 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
66554712 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
66554742 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
66554770 TATTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:66557203 original size:46 final size:45
Alignment explanation
Indices: 66557150--66557325 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
66557140 TATTTGGGCA
66557150 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
66557196 TCCGAACTTGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
66557243 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
66557289 CCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
66557326 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.62
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:66557310 original size:93 final size:93
Alignment explanation
Indices: 66557146--66557317 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
66557136 AGGATATTTG
* * *
66557146 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTTGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
66557211 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TCGAGTCCGAGTTCGAGAGATGTAACTA
* *
66557239 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
66557304 TCGAGTCCGAGTTC
66 TCGAGTCCGAGTTC
66557318 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TCGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:66559879 original size:26 final size:26
Alignment explanation
Indices: 66559850--66559957 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
66559840 TGGTACAAAT
66559850 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
66559876 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
66559902 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
66559928 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
66559954 TGAT
1 TGAT
66559958 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:66561595 original size:27 final size:27
Alignment explanation
Indices: 66561557--66561697 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
66561547 AGGAAGCGTC
66561557 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
66561584 CTGGTGGCTATGCCAC-ATATATCTG-T
1 CTGGTGGCTATGCCACAAT-TATCTGAT
66561610 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTATGCCACAATTATCTGAT
* * * *
66561638 CTAGTGGTTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
*
66561665 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
66561692 CTGGTG
1 CTGGTG
66561698 ACTTCGTCAC
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
26 11 0.11
27 85 0.85
28 4 0.04
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:66561619 original size:54 final size:54
Alignment explanation
Indices: 66561554--66561697 Score: 227
Period size: 54 Copynumber: 2.7 Consensus size: 54
66561544 TGGAGGAAGC
66561554 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTATGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTATGCCACATATATCT
* * *
66561608 GTCCTGGTGGCTATGCCACAATTATCTGATCTAGTGGTTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTATGCCACATATATCT
* *
66561662 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
66561698 ACTTCGTCAC
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 6 0.07
54 77 0.93
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTATGCCACATATATCT
Found at i:66561708 original size:27 final size:26
Alignment explanation
Indices: 66561557--66561715 Score: 131
Period size: 27 Copynumber: 5.9 Consensus size: 26
66561547 AGGAAGCGTC
* * *
66561557 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGACTCTGCCACAA-TATCTGTT
* * *
66561584 CTGGTGGCTATGCCACATATATCTGTC
1 CTGGTGACTCTGCCACA-ATATCTGTT
* * *
66561611 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGACTCTGCCACAA-TATCTGTT
* **
66561638 CTAGTGGTTCTGCCACATATATCTGTT
1 CTGGTGACTCTGCCACA-ATATCTGTT
*
66561665 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGACTCTGCCACAATATCTGT-T
*
66561692 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGACTCT-GCCACAATATCTG
66561716 GCAGCCTCGC
Statistics
Matches: 115, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.09
27 103 0.90
28 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (26 bp):
CTGGTGACTCTGCCACAATATCTGTT
Found at i:66561709 original size:81 final size:80
Alignment explanation
Indices: 66561567--66561715 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 80
66561557 CTGGTGGCTA
*
66561567 TGCCACAATTATCTGATCTGGTGGCTATGCCACATATATCTGTCCTGGTGGCTATGCCACAATTA
1 TGCCACAATTATCTGATCTGGTGGCTATGCCACATATATCTGTCCTGGTGACTATGCCACAA-TA
66561632 TCTGATCTAGTGGTTC
65 TCTGATCTAGTGGTTC
* * * *
66561648 TGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT-TCGTCACAA
1 TGCCACAAT-TATCTGATCTGGTGGCTATGCCACATATATCTGT-CCTGGTGACTAT-GCCACAA
66561710 TATCTG
63 TATCTG
66561716 GCAGCCTCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
80 17 0.28
81 43 0.72
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (80 bp):
TGCCACAATTATCTGATCTGGTGGCTATGCCACATATATCTGTCCTGGTGACTATGCCACAATAT
CTGATCTAGTGGTTC
Found at i:66563959 original size:290 final size:288
Alignment explanation
Indices: 66563406--66563984 Score: 1045
Period size: 290 Copynumber: 2.0 Consensus size: 288
66563396 TGCTATAATG
66563406 AGTGGCAATCGATGTTTGCGACTAGTTACACCAACAATAAACAATATTTGTTTTAGTTTTTTAAG
1 AGTGGCAATCGATGTTTGCGACTAGTTACACCAACAATAAACAATATTTGTTTTAGTTTTTTAAG
**
66563471 TGTCACATATTTTCATTTTTCATATTTTAAAAATCAATTTTTATTTTTTTAACCTGTTGGGGATA
66 TGTCACATATTTTCATTTTTCATATTTTAAAAATCAATTTTTATTTTTTTAACCTGTTGGAAATA
66563536 AACTCGATTAAATAACGAATAAGTAAAATAATAAAGAAATCGAAAAAATCAAACACAAATATTTT
131 AACTCGATTAAATAACGAATAAGTAAAATAATAAAGAAATCGAAAAAATCAAACACAAATATTTT
66563601 ACGTGAAAAAAAACTCTTCAAAGAAGATAAAAAACCATGGGTAAATATAATTTCACTATAACAAA
196 ACGTGAAAAAAAACTCTTCAAAGAAGATAAAAAACCATGGGTAAATATAATTTCACTATAAC--A
66563666 AAAAAATGAAGAGTACAAAGATGGAGATAA
259 AAAAAATGAAGAGTACAAAGATGGAGATAA
* *
66563696 AGTGGCAATCGATGTTTGCTACTAGTTACACCAACACTAAACAATATTTGTTTTAGTTTTTTAAG
1 AGTGGCAATCGATGTTTGCGACTAGTTACACCAACAATAAACAATATTTGTTTTAGTTTTTTAAG
66563761 TGTCACATATTTTCATTTTTCATATTTTAAAAATCAATTTTTATTTTTTTAACCTGTTGGAAATA
66 TGTCACATATTTTCATTTTTCATATTTTAAAAATCAATTTTTATTTTTTTAACCTGTTGGAAATA
* *
66563826 AACTCGATTAAATAACGAATAAGTAAAATAATAAAGAAATCGAAAAGATCGAACACAAATATTTT
131 AACTCGATTAAATAACGAATAAGTAAAATAATAAAGAAATCGAAAAAATCAAACACAAATATTTT
66563891 ACGTG-AAAAAAACATCTTCAAAGAAGAT-AAAAACCATGGGTAAATATAATTTCACTATAACGA
196 ACGTGAAAAAAAAC-TCTTCAAAGAAGATAAAAAACCATGGGTAAATATAATTTCACTATAAC-A
*
66563954 AAAAAATGAAGAGTACAAAGATTGAGATAA
259 AAAAAATGAAGAGTACAAAGATGGAGATAA
66563984 A
1 A
66563985 ATTAAACCCC
Statistics
Matches: 280, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
288 31 0.11
289 41 0.15
290 208 0.74
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (288 bp):
AGTGGCAATCGATGTTTGCGACTAGTTACACCAACAATAAACAATATTTGTTTTAGTTTTTTAAG
TGTCACATATTTTCATTTTTCATATTTTAAAAATCAATTTTTATTTTTTTAACCTGTTGGAAATA
AACTCGATTAAATAACGAATAAGTAAAATAATAAAGAAATCGAAAAAATCAAACACAAATATTTT
ACGTGAAAAAAAACTCTTCAAAGAAGATAAAAAACCATGGGTAAATATAATTTCACTATAACAAA
AAAATGAAGAGTACAAAGATGGAGATAA
Found at i:66565399 original size:14 final size:13
Alignment explanation
Indices: 66565382--66565416 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
66565372 CTGTTTTTGC
66565382 TTTCTTTCTTTTTT
1 TTTCTTT-TTTTTT
66565396 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
66565409 TGTTCTTT
1 T-TTCTTT
66565417 GGGGTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:66574569 original size:35 final size:35
Alignment explanation
Indices: 66574523--66574593 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
66574513 TAATAAACAC
*
66574523 TTAATCAAAATTGTACCTTTTTGATACGTCTAGGA
1 TTAATCAAAATTATACCTTTTTGATACGTCTAGGA
66574558 TTAATCAAAATTATACCTTTTTGATACGTCTAGGA
1 TTAATCAAAATTATACCTTTTTGATACGTCTAGGA
66574593 T
1 T
66574594 GAACGCTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (35 bp):
TTAATCAAAATTATACCTTTTTGATACGTCTAGGA
Found at i:66586925 original size:40 final size:40
Alignment explanation
Indices: 66586881--66587142 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
66586871 GCTCCTCGTT
* *
66586881 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
66586921 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
66586961 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
66587000 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
66587039 CAAATGCCTTC-GGACTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
66587078 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
66587119 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
66587143 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:66592273 original size:13 final size:13
Alignment explanation
Indices: 66592255--66592280 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66592245 TGATAAATAA
66592255 AAATAGAAGTAGC
1 AAATAGAAGTAGC
66592268 AAATAGAAGTAGC
1 AAATAGAAGTAGC
66592281 TTTTTTAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
AAATAGAAGTAGC
Found at i:66596804 original size:3 final size:3
Alignment explanation
Indices: 66596796--66596824 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
66596786 TGACTTAAAA
66596796 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
66596825 AGAGCTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:66597941 original size:21 final size:22
Alignment explanation
Indices: 66597900--66597946 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
66597890 CACATTTCTT
66597900 TTTTGTCTATCTTTTTGTTTTG
1 TTTTGTCTATCTTTTTGTTTTG
* *
66597922 TTTTGTCT-TGTTTTTTTTTTG
1 TTTTGTCTATCTTTTTGTTTTG
66597943 TTTT
1 TTTT
66597947 TACATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.02, C:0.06, G:0.13, T:0.79
Consensus pattern (22 bp):
TTTTGTCTATCTTTTTGTTTTG
Found at i:66597947 original size:22 final size:23
Alignment explanation
Indices: 66597899--66597947 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
66597889 TCACATTTCT
66597899 TTTTTGTCTATCTTTTTGTTTTG
1 TTTTTGTCTATCTTTTTGTTTTG
* *
66597922 -TTTTGTCT-TGTTTTTTTTTTG
1 TTTTTGTCTATCTTTTTGTTTTG
66597943 TTTTT
1 TTTTT
66597948 ACATTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.02, C:0.06, G:0.12, T:0.80
Consensus pattern (23 bp):
TTTTTGTCTATCTTTTTGTTTTG
Found at i:66598169 original size:26 final size:26
Alignment explanation
Indices: 66598121--66598173 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
66598111 ATAGAGGGAA
*
66598121 TTAAATTATCAAAAAATGTCAATTTT
1 TTAAATTATCAAAAAATGACAATTTT
*
66598147 TTAAATTATCAGAATAA-GACAATTTT
1 TTAAATTATCA-AAAAATGACAATTTT
66598173 T
1 T
66598174 AGAATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (26 bp):
TTAAATTATCAAAAAATGACAATTTT
Found at i:66600502 original size:27 final size:27
Alignment explanation
Indices: 66600472--66600649 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
66600462 ATATTGAGCC
* *
66600472 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
66600499 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
66600526 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
66600554 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
66600581 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
66600608 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
66600635 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66600650 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:66600584 original size:55 final size:54
Alignment explanation
Indices: 66600472--66600649 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
66600462 ATATTGAGCC
* * * * *
66600472 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
66600526 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
66600581 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
66600635 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66600650 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:66617326 original size:19 final size:19
Alignment explanation
Indices: 66617302--66617341 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66617292 AGCTCCCATG
66617302 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
66617321 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
66617340 TA
1 TA
66617342 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:66618606 original size:14 final size:14
Alignment explanation
Indices: 66618589--66618630 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
66618579 ACCGACCAAA
*
66618589 TTGTTCATACCATT
1 TTGTTCCTACCATT
*
66618603 TTGTTCCTACCCTT
1 TTGTTCCTACCATT
*
66618617 TCGTTCCTACCATT
1 TTGTTCCTACCATT
66618631 CCATTCGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (14 bp):
TTGTTCCTACCATT
Found at i:66618777 original size:18 final size:17
Alignment explanation
Indices: 66618754--66618839 Score: 63
Period size: 18 Copynumber: 5.1 Consensus size: 17
66618744 TCGTATCACA
66618754 TTTTCTTTTTCATTCTCT
1 TTTTCTTTTTCATT-TCT
*
66618772 TTTTCTTTCTCTATTTCT
1 TTTTCTTTTTC-ATTTCT
** *
66618790 TTTTCACTTTCGTTTTCT
1 TTTTCTTTTTC-ATTTCT
*
66618808 TTTTC--TTTCTTTTC-
1 TTTTCTTTTTCATTTCT
*
66618822 TCTTCTTTTT-ATTTCT
1 TTTTCTTTTTCATTTCT
66618838 TT
1 TT
66618840 ACAACTTGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.07
15 9 0.16
16 8 0.15
18 31 0.56
19 3 0.05
ACGTcount: A:0.05, C:0.21, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTCTTTTTCATTTCT
Found at i:66618778 original size:6 final size:6
Alignment explanation
Indices: 66618754--66618815 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
66618744 TCGTATCACA
* * * * * * *
66618754 TTTTCT TTTTCA TTCTCT TTTTCT TTCTCT ATTTCT TTTTCA CTTTCG
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
66618802 TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TT
66618816 CTTTTCTCTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTCT
Found at i:66619805 original size:34 final size:34
Alignment explanation
Indices: 66619740--66619806 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
66619730 TACAACAAAA
* **
66619740 AATCTCAACACATGAATTTTTTTTGAATTTTTTT
1 AATCCCAACACATGAATTTTTTTAAAATTTTTTT
*
66619774 AATCCCAATACATGAA-TTTTTTAAAATTTTTTT
1 AATCCCAACACATGAATTTTTTTAAAATTTTTTT
66619807 CACTACATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (34 bp):
AATCCCAACACATGAATTTTTTTAAAATTTTTTT
Found at i:66620038 original size:14 final size:14
Alignment explanation
Indices: 66620021--66620060 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
66620011 CGAATGGAAT
*
66620021 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
66620035 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
66620049 GATATGAACAAA
1 GGTAGGAACAAA
66620061 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:66626284 original size:72 final size:73
Alignment explanation
Indices: 66626201--66626348 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
66626191 TTTAATGCTA
* * *
66626201 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
66626264 TAAATGCCG
65 TAAATGCCG
* * * * * *
66626273 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
66626338 AAATGCCG
66 AAATGCCG
66626346 TCC
1 TCC
66626349 ATGTACCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.46
73 29 0.45
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:66626556 original size:16 final size:16
Alignment explanation
Indices: 66626535--66626566 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
66626525 CATTCTGCAT
66626535 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
66626551 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
66626567 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:66629268 original size:30 final size:30
Alignment explanation
Indices: 66629234--66629330 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
66629224 AGCTCACTCC
66629234 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
66629264 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
66629294 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
66629324 TAGCTCA
1 TAGCTCA
66629331 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:66631070 original size:12 final size:12
Alignment explanation
Indices: 66631052--66631111 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
66631042 AAGAAATTCA
66631052 GAAAAAAAAATTC
1 GAAAAAAAAA-TC
66631065 --AAAAAAAATC
1 GAAAAAAAAATC
*
66631075 GAAAAAAAAA-G
1 GAAAAAAAAATC
66631086 GAAAAAAAAAGT-
1 GAAAAAAAAA-TC
*
66631098 GACAAAAAAATC
1 GAAAAAAAAATC
66631110 GA
1 GA
66631112 GTTAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 2 0.05
11 19 0.47
12 19 0.47
ACGTcount: A:0.73, C:0.07, G:0.12, T:0.08
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:66632079 original size:37 final size:37
Alignment explanation
Indices: 66632028--66632098 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
66632018 CATTCTTGTA
66632028 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
66632065 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
66632099 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:66632098 original size:6 final size:6
Alignment explanation
Indices: 66632038--66632087 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
66632028 AAGAGAAAAC
*
66632038 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
66632087 A
1 A
66632088 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:66632180 original size:11 final size:12
Alignment explanation
Indices: 66632148--66632178 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66632138 TTGAGAGAAC
66632148 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66632160 TTGAAAAAGCCT
1 TTGAAAAAGCCT
66632172 TTGAAAA
1 TTGAAAA
66632179 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:66634393 original size:30 final size:30
Alignment explanation
Indices: 66634359--66634455 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
66634349 AGCTCACTCC
66634359 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
66634389 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
66634419 CAGCTCAACTTTAGCTCACGAGCTGAAA-CT
1 TAGCTCAACTTTAGCTCACGAGCT-AAACCT
66634449 TAGCTCA
1 TAGCTCA
66634456 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 1 0.02
30 49 0.96
31 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:66635384 original size:22 final size:20
Alignment explanation
Indices: 66635352--66635400 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
66635342 GCCGAATTTA
66635352 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
66635375 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
66635395 TGAACA
1 TGAACA
66635401 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:66636539 original size:10 final size:11
Alignment explanation
Indices: 66636518--66636543 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
66636508 AAAAAAAAAA
66636518 TTTTGAATTTT
1 TTTTGAATTTT
66636529 TTTTGAATTTT
1 TTTTGAATTTT
66636540 TTTT
1 TTTT
66636544 CAAATTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTGAATTTT
Found at i:66637804 original size:72 final size:73
Alignment explanation
Indices: 66637721--66637868 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
66637711 TTTAATGCTA
* * *
66637721 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
66637784 TAAATGCCG
65 TAAATGCCG
* * * * * *
66637793 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
66637858 AAATGCCG
66 AAATGCCG
66637866 TCC
1 TCC
66637869 ATGTACCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.46
73 29 0.45
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:66638076 original size:16 final size:16
Alignment explanation
Indices: 66638055--66638086 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
66638045 CATTCTACAT
*
66638055 TTAAACAACATCAGCA
1 TTAAACAACAGCAGCA
66638071 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
66638087 AAACACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.25, G:0.09, T:0.16
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:66639845 original size:7 final size:7
Alignment explanation
Indices: 66639833--66639869 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
66639823 ATTTGTAAAG
66639833 GACTTTT
1 GACTTTT
66639840 GACTTTT
1 GACTTTT
66639847 GACTTTT
1 GACTTTT
66639854 GACTTTT
1 GACTTTT
66639861 GACTTTT
1 GACTTTT
66639868 GA
1 GA
66639870 TCATTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (7 bp):
GACTTTT
Found at i:66641312 original size:11 final size:10
Alignment explanation
Indices: 66641296--66641356 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 10
66641286 CATAAATCAC
*
66641296 TTTTTTTCGA
1 TTTTTTTTGA
66641306 TTTTTTTT-A
1 TTTTTTTTGA
*
66641315 TTTTCTTTGAA
1 TTTTTTTTG-A
66641326 TTTTTTTTTGAA
1 -TTTTTTTTG-A
66641338 TTTTTTTTTTGA
1 --TTTTTTTTGA
66641350 TTTTTTT
1 TTTTTTT
66641357 AACTTGTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
9 8 0.18
10 14 0.32
11 1 0.02
12 11 0.25
13 10 0.23
ACGTcount: A:0.11, C:0.03, G:0.07, T:0.79
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:66641313 original size:12 final size:11
Alignment explanation
Indices: 66641296--66641356 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
66641286 CATAAATCAC
*
66641296 TTTTTTTCGA-
1 TTTTTTTTGAT
66641306 TTTTTTTT-A-
1 TTTTTTTTGAT
*
66641315 TTTTCTTTGAAT
1 TTTTTTTTG-AT
66641327 TTTTTTTTGAATT
1 TTTTTTTTG-A-T
66641340 TTTTTTTTGAT
1 TTTTTTTTGAT
66641351 TTTTTT
1 TTTTTT
66641357 AACTTGTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.18
10 7 0.16
11 8 0.18
12 11 0.25
13 10 0.23
ACGTcount: A:0.11, C:0.03, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:66641331 original size:13 final size:12
Alignment explanation
Indices: 66641315--66641356 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
66641305 ATTTTTTTTA
*
66641315 TTTTCTTTGAAT
1 TTTTTTTTGAAT
66641327 TTTTTTTTGAATT
1 TTTTTTTTGAA-T
66641340 TTTTTTTTG-AT
1 TTTTTTTTGAAT
66641351 TTTTTT
1 TTTTTT
66641357 AACTTGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 7 0.25
12 11 0.39
13 10 0.36
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:66641752 original size:14 final size:14
Alignment explanation
Indices: 66641735--66641774 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
66641725 CGAATGGAAT
*
66641735 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
66641749 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
66641763 GATATGAACAAA
1 GGTAGGAACAAA
66641775 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:66646051 original size:20 final size:19
Alignment explanation
Indices: 66646028--66646092 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
66646018 AAGCTCAAAC
66646028 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
66646048 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
66646068 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
66646088 GAGCT
1 GAGCT
66646093 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:66651041 original size:18 final size:18
Alignment explanation
Indices: 66651020--66651054 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
66651010 TTTTTCTTTT
66651020 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
66651038 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
66651055 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:66651995 original size:24 final size:25
Alignment explanation
Indices: 66651951--66652012 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 25
66651941 TTTAACTTGA
*
66651951 TTTTTTTTTTGGTCACCTTTTTTT-
1 TTTTTTTTTTGCTCACCTTTTTTTC
*
66651975 TTTTTTTTTTGCTCGA-TTTTTTTTCAC
1 TTTTTTTTTTGCTC-ACCTTTTTTT--C
66652002 TTTTTTTTTTG
1 TTTTTTTTTTG
66652013 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 20 0.62
25 1 0.03
27 11 0.34
ACGTcount: A:0.05, C:0.11, G:0.08, T:0.76
Consensus pattern (25 bp):
TTTTTTTTTTGCTCACCTTTTTTTC
Found at i:66652007 original size:13 final size:13
Alignment explanation
Indices: 66651991--66652065 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
66651981 TTTTGCTCGA
66651991 TTTTTTTTCACTT
1 TTTTTTTTCACTT
* *
66652004 TTTTTTTTGAATTT
1 TTTTTTTT-CACTT
*
66652018 TTTTTTTTCAATCAAT
1 TTTTTTTTC-A-C-TT
*
66652034 TTTTTTTTCGAATT
1 TTTTTTTTC-ACTT
*
66652048 TTTTTTTTGA-TT
1 TTTTTTTTCACTT
66652060 TTTTTT
1 TTTTTT
66652066 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
12 8 0.16
13 9 0.18
14 21 0.43
16 11 0.22
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCACTT
Found at i:66652063 original size:14 final size:14
Alignment explanation
Indices: 66651991--66652065 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 14
66651981 TTTTGCTCGA
66651991 TTTTTTTTC-ACT-T
1 TTTTTTTTCGA-TAT
*
66652004 TTTTTTTT-GAATTT
1 TTTTTTTTCG-ATAT
*
66652018 TTTTTTTTCAATCAAT
1 TTTTTTTTCGAT--AT
66652034 TTTTTTTTCGA-AT
1 TTTTTTTTCGATAT
*
66652047 TTTTTTTTTGAT-T
1 TTTTTTTTCGATAT
66652060 TTTTTT
1 TTTTTT
66652066 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
13 28 0.55
14 12 0.24
16 11 0.22
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCGATAT
Found at i:66653973 original size:33 final size:33
Alignment explanation
Indices: 66653935--66653997 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
66653925 GATTACTCAC
66653935 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
66653968 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
66653998 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:66654024 original size:14 final size:14
Alignment explanation
Indices: 66654000--66654053 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
66653990 TCTCTTTCAA
*
66654000 TTTCTTTTTTCTCTT
1 TTTC-TTTTTCTCAT
*
66654015 TTTCTTTTTC-AAT
1 TTTCTTTTTCTCAT
66654028 TTTC-TTTTCTTCAT
1 TTTCTTTTTC-TCAT
66654042 TTTCTTTTTCTC
1 TTTCTTTTTCTC
66654054 TCACTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 5 0.15
13 5 0.15
14 14 0.42
15 9 0.27
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTTTTCTCAT
Found at i:66654024 original size:27 final size:27
Alignment explanation
Indices: 66653994--66654119 Score: 96
Period size: 27 Copynumber: 4.6 Consensus size: 27
66653984 TCAAGCTCTC
66653994 TTTCAATTTCTTTTTTCTCTTTTTCTT
1 TTTCAATTTCTTTTTTCTCTTTTTCTT
* *
66654021 TTTCAATTT-TCTTTTCTTCATTTTCTT
1 TTTCAATTTCTTTTTTC-TCTTTTTCTT
** ** *
66654048 TTTCTCTCACTTTTTCGATTTCTTTTTCTT
1 TTTCAATTTCTTTTT---TCTCTTTTTCTT
* *
66654078 TTGCAATTTC-TTTTTCT-TTTTGTTTT
1 TTTCAATTTCTTTTTTCTCTTTT-TCTT
66654104 CTTTCAATTTCTTTTT
1 -TTTCAATTTCTTTTT
66654120 CAATCTCTTT
Statistics
Matches: 74, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
25 4 0.05
26 11 0.15
27 32 0.43
28 8 0.11
29 4 0.05
30 14 0.19
31 1 0.01
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTCAATTTCTTTTTTCTCTTTTTCTT
Found at i:66654050 original size:15 final size:15
Alignment explanation
Indices: 66653995--66654052 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
66653985 CAAGCTCTCT
*
66653995 TTCAATTTCTTTTT-
1 TTCATTTTCTTTTTC
*
66654009 TCTCTTTTTCTTTTTC
1 T-TCATTTTCTTTTTC
*
66654025 --AATTTTC-TTTTC
1 TTCATTTTCTTTTTC
66654037 TTCATTTTCTTTTTC
1 TTCATTTTCTTTTTC
66654052 T
1 T
66654053 CTCACTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
12 5 0.15
13 5 0.15
14 7 0.21
15 17 0.50
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCATTTTCTTTTTC
Found at i:66654078 original size:18 final size:18
Alignment explanation
Indices: 66654011--66654098 Score: 77
Period size: 18 Copynumber: 4.7 Consensus size: 18
66654001 TTCTTTTTTC
66654011 TCTTTTTCTTTTTCAATTT
1 TCTTTTTCTTTTTCAA-TT
* **
66654030 TCTTTTCTTCATTTTCTTTT
1 TC-TTT-TTCTTTTTCAATT
* ** *
66654050 TCTCTCACTTTTTCGATT
1 TCTTTTTCTTTTTCAATT
*
66654068 TCTTTTTCTTTTGCAATT
1 TCTTTTTCTTTTTCAATT
66654086 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
66654099 GTTTTCTTTC
Statistics
Matches: 52, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
18 33 0.63
19 4 0.08
20 7 0.13
21 8 0.15
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.70
Consensus pattern (18 bp):
TCTTTTTCTTTTTCAATT
Found at i:66654120 original size:6 final size:6
Alignment explanation
Indices: 66654006--66654107 Score: 62
Period size: 6 Copynumber: 16.5 Consensus size: 6
66653996 TCAATTTCTT
* * * **
66654006 TTTTCTC TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC
1 TTTT-TC TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC
** * ** *
66654058 TTTTTC GATTTC TTTTTC TTTTGC AATTTC TTTTTC TTTTT- GTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
66654105 TTT
1 TTT
66654108 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
5 4 0.06
6 49 0.71
7 13 0.19
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:66656816 original size:20 final size:19
Alignment explanation
Indices: 66656793--66656857 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
66656783 AAGCTCAAAC
66656793 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
66656813 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
66656833 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
66656853 GAGCT
1 GAGCT
66656858 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:66660180 original size:20 final size:20
Alignment explanation
Indices: 66660157--66660210 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
66660147 AGTTTTTCCC
*
66660157 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
66660177 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
66660197 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
66660211 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:66660192 original size:30 final size:30
Alignment explanation
Indices: 66660157--66660230 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
66660147 AGTTTTTCCC
66660157 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
66660187 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
66660217 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
66660231 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:66660220 original size:20 final size:20
Alignment explanation
Indices: 66660157--66660221 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
66660147 AGTTTTTCCC
* * * *
66660157 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
66660177 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
66660196 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
66660217 AGCTC
1 AGCTC
66660222 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:66663586 original size:22 final size:22
Alignment explanation
Indices: 66663556--66663599 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
66663546 TTTGGTATTT
66663556 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
66663578 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
66663600 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:66665224 original size:23 final size:22
Alignment explanation
Indices: 66665172--66665224 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
66665162 TCCACGTCTT
*
66665172 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
66665194 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
66665217 TTTCTTTT
1 TTTCTTTT
66665225 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:66666525 original size:39 final size:40
Alignment explanation
Indices: 66666480--66666563 Score: 145
Period size: 39 Copynumber: 2.1 Consensus size: 40
66666470 ACCCGCTGAA
66666480 TCTTTTTTTAAATTTTTATTGAATTTCATA-TTTTTTATT
1 TCTTTTTTTAAATTTTTATTGAATTTCATATTTTTTTATT
*
66666519 TCTTTTTTTAAATTTTTATTGAATTTCGTATTTTTTTATT
1 TCTTTTTTTAAATTTTTATTGAATTTCATATTTTTTTATT
66666559 T-TTTT
1 TCTTTT
66666564 GACTTTTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 33 0.77
40 10 0.23
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (40 bp):
TCTTTTTTTAAATTTTTATTGAATTTCATATTTTTTTATT
Found at i:66666534 original size:20 final size:20
Alignment explanation
Indices: 66666480--66666538 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
66666470 ACCCGCTGAA
66666480 TCTTTTTTTAAATTTTTATT
1 TCTTTTTTTAAATTTTTATT
*** ** *
66666500 GAATTTCAT-ATTTTTTATT
1 TCTTTTTTTAAATTTTTATT
66666519 TCTTTTTTTAAATTTTTATT
1 TCTTTTTTTAAATTTTTATT
66666539 GAATTTCGTA
Statistics
Matches: 26, Mismatches: 12, Indels: 2
0.65 0.30 0.05
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (20 bp):
TCTTTTTTTAAATTTTTATT
Found at i:66667359 original size:20 final size:20
Alignment explanation
Indices: 66667313--66667359 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
66667303 AGCTCGTTTC
*
66667313 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
66667333 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
66667353 CAGCTCA
1 CAGCTCA
66667360 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:66669972 original size:50 final size:50
Alignment explanation
Indices: 66669849--66669976 Score: 161
Period size: 50 Copynumber: 2.6 Consensus size: 50
66669839 TTGGTACGCA
* ** *
66669849 TAGTAGCCTGCACTTAGTACTACACATG-CGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTCGACCAACCATCCGATACACG
* * *
66669898 TAGTAGCCTGCACTTAGTACTACACACGTC-ACCTAACCGTCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTCGACC-AACCATCCGATACACG
*
66669948 TAGTAGCCTGCACTTTGTACTACACACGT
1 TAGTAGCCTGCACTTAGTACTACACACGT
66669977 GATCGAAGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 30 0.43
50 39 0.57
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTCGACCAACCATCCGATACACG
Found at i:66672038 original size:49 final size:50
Alignment explanation
Indices: 66671928--66672056 Score: 179
Period size: 49 Copynumber: 2.6 Consensus size: 50
66671918 GATCGTATCA
* * *
66671928 AGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAAGTACGCATAGT
1 AGCCTGCACTTAGTACTACACATGTGA-CCAAGTTATCAAGTACACATAGT
* * *
66671979 AGCCTGCACTTAGTACTACACATGCGACCAA-TTATCTAGTACACGTAGT
1 AGCCTGCACTTAGTACTACACATGTGACCAAGTTATCAAGTACACATAGT
*
66672028 AGCCTACACTTAGTACTACACATGTGACC
1 AGCCTGCACTTAGTACTACACATGTGACC
66672057 TCACAATAGC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
49 42 0.60
50 3 0.04
51 25 0.36
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
AGCCTGCACTTAGTACTACACATGTGACCAAGTTATCAAGTACACATAGT
Found at i:66672738 original size:30 final size:30
Alignment explanation
Indices: 66672704--66672763 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
66672694 CTTTAATACG
*
66672704 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGACAAAATTACAC-TTTTGCCCCTA
* *
66672734 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
66672764 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:66674604 original size:14 final size:14
Alignment explanation
Indices: 66674585--66674629 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66674575 AACTCATCTT
*
66674585 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
66674599 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
66674612 AATTTAATTTAATG
1 AGTTTAATTTAATG
66674626 AGTT
1 AGTT
66674630 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:66675641 original size:29 final size:29
Alignment explanation
Indices: 66675608--66675667 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
66675598 ATAACCAAAC
*
66675608 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
66675637 CTACATAAACTTCATATTCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
66675666 CT
1 CT
66675668 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:66675910 original size:29 final size:30
Alignment explanation
Indices: 66675877--66675935 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
66675867 CTTTAATACG
66675877 AACTTTGGCA-AAATAC-CATTTTGCCCCTA
1 AACTTTGGCATAAATACAC-TTTTGCCCCTA
* *
66675906 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCATAAATACACTTTTGCCCCTA
66675936 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 16 0.62
31 1 0.04
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.36
Consensus pattern (30 bp):
AACTTTGGCATAAATACACTTTTGCCCCTA
Found at i:66677748 original size:23 final size:21
Alignment explanation
Indices: 66677705--66677748 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
66677695 AGGGCTAGTC
*
66677705 GAATGGTCTTTTAAAGGAGCT
1 GAATGGTCTTTTAAAGAAGCT
*
66677726 GAATGGTCACTTTTAATGAAGCT
1 GAATGGT--CTTTTAAAGAAGCT
66677749 AATAATGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (21 bp):
GAATGGTCTTTTAAAGAAGCT
Found at i:66682100 original size:18 final size:18
Alignment explanation
Indices: 66682062--66682103 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
66682052 AAATCGAAAG
* **
66682062 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
66682080 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
66682098 AAAAGA
1 AAAAGA
66682104 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:66689510 original size:18 final size:19
Alignment explanation
Indices: 66689487--66689534 Score: 73
Period size: 17 Copynumber: 2.6 Consensus size: 19
66689477 AGAGTGAATG
66689487 TGAAAAAAGAAAAG-AAAA
1 TGAAAAAAGAAAAGAAAAA
66689505 TG-AAAAAGAAAAGAAAAA
1 TGAAAAAAGAAAAGAAAAA
66689523 TGAGAAAAAGAA
1 TGA-AAAAAGAA
66689535 TGCAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.41
18 8 0.30
20 8 0.30
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (19 bp):
TGAAAAAAGAAAAGAAAAA
Found at i:66691026 original size:30 final size:30
Alignment explanation
Indices: 66690992--66691088 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66690982 TAAACTAAAA
* *
66690992 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * *
66691022 TGAGCTAAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
66691052 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
66691082 TGAGCTA
1 TGAGCTA
66691089 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 49 0.94
31 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:66694824 original size:18 final size:18
Alignment explanation
Indices: 66694803--66694837 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
66694793 TTTTTCTTTT
66694803 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
66694821 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
66694838 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Done.