Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 166 of 276
Found at i:54443735 original size:30 final size:29
Alignment explanation
Indices: 54443686--54443746 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
54443676 CAAGTAGCCG
*
54443686 AAGCTAGTTAAACCGCACACTTAGTGCCA
1 AAGCTAGTTAAACCACACACTTAGTGCCA
*
54443715 AAGCTAGTTTAAATCACACACTTAGTGCCA
1 AAGCTAG-TTAAACCACACACTTAGTGCCA
54443745 AA
1 AA
54443747 ACTTCCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (29 bp):
AAGCTAGTTAAACCACACACTTAGTGCCA
Found at i:54453519 original size:119 final size:122
Alignment explanation
Indices: 54453341--54453605 Score: 353
Period size: 119 Copynumber: 2.2 Consensus size: 122
54453331 TCGAATGATG
* * *
54453341 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCTGAAGGGATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
* *
54453405 TGTGCGAGATACTAATTCCGGGCTAAG-CCCGAATGCATTTGTGCGAGTTACTA-AA
66 TGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* * * * **
54453460 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
54453523 TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
65 TTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
54453581 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54453606 AACGATTAGC
Statistics
Matches: 127, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
118 1 0.01
119 69 0.54
120 55 0.43
121 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (122 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:54453619 original size:40 final size:40
Alignment explanation
Indices: 54453341--54453605 Score: 340
Period size: 40 Copynumber: 6.7 Consensus size: 40
54453331 TCGAATGATG
* * * * *
54453341 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * * * *
54453381 TCCGGACTAAGAT-CTGAAGGGATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54453421 TCCGGGCTAAG-CCCGAATGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
54453460 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
54453500 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
54453540 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
54453581 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
54453606 AACGATTAGC
Statistics
Matches: 201, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
39 32 0.16
40 159 0.79
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54453623 original size:120 final size:118
Alignment explanation
Indices: 54453396--54453638 Score: 328
Period size: 120 Copynumber: 2.0 Consensus size: 118
54453386 ACTAAGATCT
* * *
54453396 GAAGGGATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAATGCATTTGTGCGAGTTACTAAAT
1 GAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAAT
* ** *
54453461 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCC
66 CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAATCC-GGTTAAATCCC
* *
54453515 GAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 GAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-A
* * *
54453580 A-CCGGGCTATGTCCCGAAGGCATTTGAACGA-TTAGCTATATCCGGTTAAATTCC
64 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTA-CTAAATCCGGTTAAATCCC
54453634 GAAGG
1 GAAGG
54453639 TACGTGATTT
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
119 49 0.45
120 58 0.53
121 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (118 bp):
GAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAAT
CCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAATCCGGTTAAATCCC
Found at i:54459772 original size:24 final size:24
Alignment explanation
Indices: 54459727--54459772 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
54459717 ATATACAATG
* * *
54459727 CAATCATTCTTTAATTCATTCATT
1 CAATCAATCATTAATACATTCATT
*
54459751 CAATCAATCATTAATACTTTCA
1 CAATCAATCATTAATACATTCA
54459773 ACATTCTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (24 bp):
CAATCAATCATTAATACATTCATT
Found at i:54466327 original size:13 final size:13
Alignment explanation
Indices: 54466297--54466321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54466287 CTAAATCATA
54466297 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
54466310 ATTTTAGTAAAA
1 ATTTTAGTAAAA
54466322 CTTTTTTTTT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:54466776 original size:21 final size:21
Alignment explanation
Indices: 54466751--54466792 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54466741 GCATGAATTA
54466751 ATTAT-TTGTATTTATTAAAAT
1 ATTATATT-TATTTATTAAAAT
*
54466772 ATTATATTTATTTATTTAAAT
1 ATTATATTTATTTATTAAAAT
54466793 TTTTTATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTATATTTATTTATTAAAAT
Found at i:54466895 original size:73 final size:75
Alignment explanation
Indices: 54466761--54466909 Score: 230
Period size: 73 Copynumber: 2.0 Consensus size: 75
54466751 ATTATTTGTA
**
54466761 TTTATTAAAATATTATATTTATTTATTTAAATTTTTTATACAAAAACTTTTGGTATTTAATAATT
1 TTTATTAAAATATTATATTTATTTATTTAAATTTTTTATACAAAAACTTTCAGTATTTAATAATT
54466826 AGAATCACTT
66 AGAATCACTT
* * * *
54466836 TTTATTAGAATGTTATATTTA-TTATTTAAATTTTTTGTA-TAAAACTTTCAGTATTTAATAATT
1 TTTATTAAAATATTATATTTATTTATTTAAATTTTTTATACAAAAACTTTCAGTATTTAATAATT
54466899 AGAATCACTT
66 AGAATCACTT
54466909 T
1 T
54466910 AAGAAACCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 32 0.47
74 17 0.25
75 19 0.28
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.52
Consensus pattern (75 bp):
TTTATTAAAATATTATATTTATTTATTTAAATTTTTTATACAAAAACTTTCAGTATTTAATAATT
AGAATCACTT
Found at i:54467238 original size:6 final size:6
Alignment explanation
Indices: 54467227--54467258 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
54467217 TAAAGTATTG
54467227 TAATTA TAATTA TAATTA TAATTA TAA-TA TAA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAA
54467259 CTGTATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATTA
Found at i:54473334 original size:93 final size:93
Alignment explanation
Indices: 54473222--54473393 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54473212 CGCCCATAAG
* *
54473222 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54473287 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54473315 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54473380 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54473394 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54473390 original size:46 final size:46
Alignment explanation
Indices: 54473215--54473390 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54473205 TGTAACCCGC
* * *
54473215 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
54473261 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54473311 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54473354 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54473391 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54477608 original size:40 final size:40
Alignment explanation
Indices: 54477553--54477777 Score: 299
Period size: 40 Copynumber: 5.6 Consensus size: 40
54477543 TATTCGGATG
54477553 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
54477593 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
54477636 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
54477676 ATTTCCGGGCTAAGACCCGAAGGCATGTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
54477716 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
54477756 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
54477778 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 14 0.09
40 111 0.68
41 1 0.01
43 37 0.23
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:54477696 original size:83 final size:80
Alignment explanation
Indices: 54477557--54477777 Score: 286
Period size: 83 Copynumber: 2.7 Consensus size: 80
54477547 CGGATGATAT
* * *
54477557 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
*
54477622 TGCGAGTAGTTGCTATAC
66 TGC--G-AGTTACTATAC
* *
54477640 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATTTCCGGGCTAAGACCCGAAGGCATGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
*
54477705 TGCGAGTTACTATAT
66 TGCGAGTTACTATAC
* * *
54477720 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTG-CGATATCC-GGCTAA-ATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGA-CCCGAAGG
54477778 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
78 1 0.01
79 14 0.11
80 44 0.35
81 3 0.02
83 63 0.50
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCATGTG
TGCGAGTTACTATAC
Found at i:54479958 original size:40 final size:40
Alignment explanation
Indices: 54479903--54480127 Score: 265
Period size: 40 Copynumber: 5.6 Consensus size: 40
54479893 TATTCGGATG
54479903 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
54479943 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTG-CA--AGTTACT
* * * *
54479986 ATACCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
54480026 ATTTCCGGGCTAAGACCCGAAGGC-TTGTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATT-TGTGCAAGTTACT
* * * *
54480066 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
54480106 ATCTCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
54480128 TACTGTAACG
Statistics
Matches: 158, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
39 16 0.10
40 104 0.66
41 3 0.02
43 35 0.22
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:54480046 original size:83 final size:80
Alignment explanation
Indices: 54479907--54480097 Score: 274
Period size: 83 Copynumber: 2.4 Consensus size: 80
54479897 CGGATGATAT
* *
54479907 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGC--TTG
*
54479972 TGTGAGTAGTTGCTATAC
64 TGTGAG-AGTTACTATAC
* * *
54479990 CCGGGCTAAGTCCCGAAGACATTTGTGCTAGTGACTATTTCCGGGCTAAGACCCGAAGGCTTGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCTTGTG
* *
54480055 TGCGAGTTACTATAT
66 TGAGAGTTACTATAC
*
54480070 CCGGGTTAAGTCCCGAAGGCATTTGTGC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC
54480098 GAGTTGCGAT
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 35 0.36
81 8 0.08
83 55 0.56
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCTTGTG
TGAGAGTTACTATAC
Found at i:54490337 original size:25 final size:23
Alignment explanation
Indices: 54490286--54490337 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
54490276 ATTTACACAT
* *
54490286 TTTAAAAAATATATATTATTTTA
1 TTTAAAAAATATAAATTATTTAA
54490309 -TTAAAAAATAATAAATATATTTAA
1 TTTAAAAAAT-ATAAAT-TATTTAA
54490333 TTTAA
1 TTTAA
54490338 TTTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 9 0.38
23 5 0.21
24 6 0.25
25 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAAAAATATAAATTATTTAA
Found at i:54490515 original size:3 final size:3
Alignment explanation
Indices: 54490507--54490533 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54490497 TTTTAAAACC
54490507 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
54490534 TAAAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54491023 original size:14 final size:15
Alignment explanation
Indices: 54491006--54491039 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54490996 AAAAGCCTAT
*
54491006 AAATAAAA-TTATAA
1 AAATAAAATTTACAA
54491020 AAATAAAATTTACAA
1 AAATAAAATTTACAA
54491035 AAATA
1 AAATA
54491040 TGATAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAAATTTACAA
Found at i:54491135 original size:14 final size:14
Alignment explanation
Indices: 54491103--54491136 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54491093 AAAAAAATGG
54491103 TAAAAATTATTTTA
1 TAAAAATTATTTTA
* *
54491117 AAAAAATTATTTTT
1 TAAAAATTATTTTA
54491131 TAAAAA
1 TAAAAA
54491137 AAGTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAAATTATTTTA
Found at i:54491143 original size:27 final size:27
Alignment explanation
Indices: 54491113--54491164 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54491103 TAAAAATTAT
54491113 TTTAAAA-AAATTATTTTTTAAAAAAAG
1 TTTAAAATAAATT-TTTTTTAAAAAAAG
* *
54491140 TTTAAAATGAATTTTTTTTATAAAA
1 TTTAAAATAAATTTTTTTTAAAAAA
54491165 TTCTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTAAAATAAATTTTTTTTAAAAAAAG
Found at i:54491257 original size:20 final size:18
Alignment explanation
Indices: 54491214--54491259 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
54491204 GAAACTTAAT
54491214 AGTTTTTATAACATTTTA
1 AGTTTTTATAACATTTTA
* *
54491232 AATTTTTATATATCATTTTG
1 AGTTTTTATA-A-CATTTTA
54491252 AGTTTTTA
1 AGTTTTTA
54491260 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.39
19 1 0.04
20 13 0.57
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (18 bp):
AGTTTTTATAACATTTTA
Found at i:54491633 original size:31 final size:30
Alignment explanation
Indices: 54491563--54491633 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
54491553 TTTTTTATTT
*
54491563 TTTAATAATTATATATTATACTGATTAAAATG
1 TTTAA-AATTATATATAATAC-GATTAAAATG
**
54491595 TAAAAAATTATATATAATAC-ATTAAAAATG
1 TTTAAAATTATATATAATACGATT-AAAATG
54491625 CTTTAAAAT
1 -TTTAAAAT
54491634 AAAAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 3 0.09
30 6 0.19
31 20 0.62
32 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (30 bp):
TTTAAAATTATATATAATACGATTAAAATG
Found at i:54492003 original size:18 final size:17
Alignment explanation
Indices: 54491976--54492009 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54491966 ATTTTTCCAA
54491976 TTTCTTTATATATTTAT
1 TTTCTTTATATATTTAT
*
54491993 TTTCATTTATATTTTTA
1 TTTC-TTTATATATTTA
54492010 ATGTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTTATATATTTAT
Found at i:54494747 original size:46 final size:46
Alignment explanation
Indices: 54494697--54494872 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
54494687 TGGTTGAGCA
54494697 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54494743 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54494788 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54494836 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54494873 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54494853 original size:93 final size:93
Alignment explanation
Indices: 54494694--54494864 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54494684 GGATGGTTGA
* *
54494694 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54494759 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54494787 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54494852 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54494865 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54500282 original size:15 final size:15
Alignment explanation
Indices: 54500262--54500317 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
54500252 GTATCTTCGG
54500262 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
54500277 TTTCTTTATTTTGGA
1 TTTCTTTATTCTGGA
*
54500292 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
54500307 TTTCGTTATTC
1 TTTCTTTATTC
54500318 AGTTTCCTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 1 0.03
15 31 0.91
16 2 0.06
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:54505076 original size:43 final size:42
Alignment explanation
Indices: 54504989--54505100 Score: 161
Period size: 43 Copynumber: 2.6 Consensus size: 42
54504979 TGAGTTTACG
**
54504989 TGTAAGACCATATCTGGGATATGGCATCCATATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCCATATGAGATCCCA
* * * *
54505031 TGTAAGACCATAGCTGGGCTATTGGCATCGATCTGAGATCCCA
1 TGTAAGACCATATCTGGGATA-TGGCATCCATATGAGATCCCA
54505074 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
54505101 TGGTATGGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 25 0.41
43 36 0.59
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCCATATGAGATCCCA
Found at i:54508332 original size:36 final size:36
Alignment explanation
Indices: 54508285--54508357 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
54508275 CAGGGCACTT
54508285 AATCAAGGAACACACTCTTGAGCCACATATCGTATA
1 AATCAAGGAACACACTCTTGAGCCACATATCGTATA
54508321 AATCAAGGAACACACTCTTGAGCCACATATCGTATA
1 AATCAAGGAACACACTCTTGAGCCACATATCGTATA
54508357 A
1 A
54508358 CAGGATTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.22
Consensus pattern (36 bp):
AATCAAGGAACACACTCTTGAGCCACATATCGTATA
Found at i:54513547 original size:27 final size:27
Alignment explanation
Indices: 54513485--54513596 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
54513475 AGCATGGCTG
* * *
54513485 CCAGAACAGATAA-TGTGACAGGGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* * *
54513511 CTAGATACAGATAATCGTGGCAAAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
54513539 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
54513566 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
54513593 CCAG
1 CCAG
54513597 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.10
27 49 0.69
28 15 0.21
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:54513576 original size:54 final size:54
Alignment explanation
Indices: 54513485--54513596 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
54513475 AGCATGGCTG
* * * *
54513485 CCAGAACAGATAATGTGACAGGGTCACTAGATACAGATAATCGTGGCAAAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAAAGCCA
* * *
54513539 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAAAGCCA
54513593 CCAG
1 CCAG
54513597 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.68
55 16 0.32
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAAAGCCA
Found at i:54515836 original size:79 final size:79
Alignment explanation
Indices: 54515705--54515861 Score: 287
Period size: 79 Copynumber: 2.0 Consensus size: 79
54515695 CGTGAATCTT
*
54515705 GTCCAACTCTGGAGGTAATTCCAACTGATAAGCTACTGGGCCTACTCGCTTCAAAACCCGATAAG
1 GTCCAACTCTGGAGGTAATTCCAACTGATAAGCTACTAGGCCTACTCGCTTCAAAACCCGATAAG
54515770 GCCCAATGAACCGC
66 GCCCAATGAACCGC
* *
54515784 GTCCAACTCTGGAGGTAATTCCAACTGATAAGCTACTAGTCCTACTCGCTTCAGAACCCGATAAG
1 GTCCAACTCTGGAGGTAATTCCAACTGATAAGCTACTAGGCCTACTCGCTTCAAAACCCGATAAG
54515849 GCCCAATGAACCG
66 GCCCAATGAACCG
54515862 AGGACTCAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (79 bp):
GTCCAACTCTGGAGGTAATTCCAACTGATAAGCTACTAGGCCTACTCGCTTCAAAACCCGATAAG
GCCCAATGAACCGC
Found at i:54521361 original size:27 final size:26
Alignment explanation
Indices: 54521326--54521437 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
54521316 AGCATGGCTG
* *
54521326 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
54521352 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
54521380 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
54521407 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
54521434 CCAG
1 CCAG
54521438 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:54521418 original size:54 final size:54
Alignment explanation
Indices: 54521326--54521437 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
54521316 AGCATGGCTG
* *
54521326 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
54521380 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
54521434 CCAG
1 CCAG
54521438 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:54532093 original size:37 final size:38
Alignment explanation
Indices: 54531992--54532094 Score: 133
Period size: 37 Copynumber: 2.8 Consensus size: 38
54531982 TTTGAGTACG
*
54531992 TGTAAGACCATAG-CTGGGCTATGGCATCGTAATGACA
1 TGTAAGACCATAGTCTGGGCTATGGCATTGTAATGACA
* *
54532029 TGTAAGACCATAGT-TGGGCTATGGCATTGTGAT-CCTA
1 TGTAAGACCATAGTCTGGGCTATGGCATTGTAATGAC-A
*
54532066 TGTAAGACCAT-GTCTGGGATATGGCATTG
1 TGTAAGACCATAGTCTGGGCTATGGCATTG
54532095 GCATCAATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
36 3 0.05
37 56 0.95
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (38 bp):
TGTAAGACCATAGTCTGGGCTATGGCATTGTAATGACA
Found at i:54532109 original size:48 final size:48
Alignment explanation
Indices: 54532056--54532301 Score: 307
Period size: 48 Copynumber: 5.1 Consensus size: 48
54532046 GCTATGGCAT
*
54532056 TGTGATCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCAATA
1 TGTGATCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCGATA
* *
54532104 TGTGATCCCATGTAAGACCATGTCTGGGAGATGGCATTGGCATCGATA
1 TGTGATCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCGATA
* * * * *
54532152 TGTGATCCTATGTAAGACCATATTTGGGATATGACGTTGGCATCAATA
1 TGTGATCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCGATA
* * * *
54532200 TGTGATTTCGTA--TAAAACCATGTCTAGGAGATGGCATTGGCATCGATA
1 TGTGA--TCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCGATA
** * * *
54532248 TGCAATCCTATGTAAGACCATATCTGGGATATGACGTTGGCATCGATA
1 TGTGATCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCGATA
54532296 TGTGAT
1 TGTGAT
54532302 TTCGTATAAA
Statistics
Matches: 164, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
46 4 0.02
48 156 0.95
50 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (48 bp):
TGTGATCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCGATA
Found at i:54532220 original size:96 final size:96
Alignment explanation
Indices: 54532056--54532332 Score: 421
Period size: 96 Copynumber: 2.9 Consensus size: 96
54532046 GCTATGGCAT
* * * ** * * *
54532056 TGTGATCCTATGTAAGACCATGTCTGGGATATGGCATTGGCATCAATATGTGATCCCATGTAAGA
1 TGTGATCCTATGTAAGACCATATCTGGGATATGACGTTGGCATCAATATGTGATTTCGTATAAAA
54532121 CCATGTCTGGGAGATGGCATTGGCATCGATA
66 CCATGTCTGGGAGATGGCATTGGCATCGATA
*
54532152 TGTGATCCTATGTAAGACCATATTTGGGATATGACGTTGGCATCAATATGTGATTTCGTATAAAA
1 TGTGATCCTATGTAAGACCATATCTGGGATATGACGTTGGCATCAATATGTGATTTCGTATAAAA
*
54532217 CCATGTCTAGGAGATGGCATTGGCATCGATA
66 CCATGTCTGGGAGATGGCATTGGCATCGATA
** *
54532248 TGCAATCCTATGTAAGACCATATCTGGGATATGACGTTGGCATCGATATGTGATTTCGTATAAAA
1 TGTGATCCTATGTAAGACCATATCTGGGATATGACGTTGGCATCAATATGTGATTTCGTATAAAA
54532313 CCATGTCTGGG-GCATGGCAT
66 CCATGTCTGGGAG-ATGGCAT
54532333 CGATATGAGA
Statistics
Matches: 165, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
95 1 0.01
96 164 0.99
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (96 bp):
TGTGATCCTATGTAAGACCATATCTGGGATATGACGTTGGCATCAATATGTGATTTCGTATAAAA
CCATGTCTGGGAGATGGCATTGGCATCGATA
Found at i:54532316 original size:48 final size:48
Alignment explanation
Indices: 54532068--54532332 Score: 252
Period size: 48 Copynumber: 5.5 Consensus size: 48
54532058 TGATCCTATG
* * *
54532068 TAAGACCATGTCTGGGATATGGCATTGGCATCAATATGTGA-TCCCATG
1 TAAGACCATGTCTGGGATATGGCATTGGCATCGATATGTGATTTCC-TA
*
54532116 TAAGACCATGTCTGGGAGATGGCATTGGCATCGATATGTGA--TCCTA
1 TAAGACCATGTCTGGGATATGGCATTGGCATCGATATGTGATTTCCTA
* * * * * *
54532162 TGTAAGACCATATTTGGGATATGACGTTGGCATCAATATGTGATTTCGTA
1 --TAAGACCATGTCTGGGATATGGCATTGGCATCGATATGTGATTTCCTA
* * * * *
54532212 TAAAACCATGTCTAGGAGATGGCATTGGCATCGATATG-CA-ATCCTA
1 TAAGACCATGTCTGGGATATGGCATTGGCATCGATATGTGATTTCCTA
* * * *
54532258 TGTAAGACCATATCTGGGATATGACGTTGGCATCGATATGTGATTTCGTA
1 --TAAGACCATGTCTGGGATATGGCATTGGCATCGATATGTGATTTCCTA
* **
54532308 TAAAACCATGTCTGGGGCATGGCAT
1 TAAGACCATGTCTGGGATATGGCAT
54532333 CGATATGAGA
Statistics
Matches: 172, Mismatches: 37, Indels: 16
0.76 0.16 0.07
Matches are distributed among these distances:
46 5 0.03
47 3 0.02
48 155 0.90
49 1 0.01
50 8 0.05
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (48 bp):
TAAGACCATGTCTGGGATATGGCATTGGCATCGATATGTGATTTCCTA
Found at i:54535573 original size:60 final size:60
Alignment explanation
Indices: 54535446--54535584 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
54535436 ATCAGAGTTA
* * *
54535446 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTAAAGTATCAGGGTAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTAAAGTATCAGGATAT
* * * *
54535507 ACTGGGCCTAGCCCATATCAGTATCAATCTTGGCCGTAGCCCTATTACAAGT-TGA-GATAT
1 ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTA-AAGTATCAGGATAT
* *
54535567 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTAGCCCATAT
54535585 TAACACAGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 50 0.75
61 13 0.19
62 4 0.06
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (60 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTAAAGTATCAGGATAT
Found at i:54540151 original size:28 final size:28
Alignment explanation
Indices: 54540119--54540217 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
54540109 ATAGTAAGTC
*
54540119 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
54540147 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
54540175 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
54540204 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54540218 CAATCTCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 45 0.71
29 18 0.29
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54545187 original size:16 final size:16
Alignment explanation
Indices: 54545161--54545200 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
54545151 TTAAGAAATA
*
54545161 ATAATTATTATGTTAAT
1 ATAA-TATTATATTAAT
*
54545178 ATTATATTATATTAAT
1 ATAATATTATATTAAT
54545194 ATAATAT
1 ATAATAT
54545201 AATAAACATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATAATATTATATTAAT
Found at i:54556536 original size:43 final size:42
Alignment explanation
Indices: 54556455--54556536 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 42
54556445 TTGGGACATC
* * *
54556455 GGCATCGTATTTGATTTCATGTAAGACTCTGTCTGGGACAGA
1 GGCATCGTATTTGATTACATGTAAGACTCCGTCCGGGACAGA
54556497 GGCATCG-ATATTGAATTACATGTAAGAC-CACGTCCGGGAC
1 GGCATCGTAT-TTG-ATTACATGTAAGACTC-CGTCCGGGAC
54556537 GTCGGCATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 2 0.06
42 11 0.32
43 21 0.62
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (42 bp):
GGCATCGTATTTGATTACATGTAAGACTCCGTCCGGGACAGA
Found at i:54556536 original size:85 final size:85
Alignment explanation
Indices: 54556389--54556544 Score: 192
Period size: 85 Copynumber: 1.8 Consensus size: 85
54556379 TGAGACATCG
* * * **
54556389 TGTAAGATCGTGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTTTGGGACAT
1 TGTAAGATCGTGTCTGGGACACAGGCATCGATTGAGATTTACATATAAGACCACGTCCGGGACAT
54556454 CGGCATCGTATTTGATTTCA
66 CGGCATCGTATTTGATTTCA
* *
54556474 TGTAAGACTC-TGTCTGGGACAGAGGCATCGATATTGA-A-TTACATGTAAGACCACGTCCGGGA
1 TGTAAGA-TCGTGTCTGGGACACAGGCATCG--ATTGAGATTTACATATAAGACCACGTCCGGGA
*
54556536 CGTCGGCAT
63 CATCGGCAT
54556545 TGTACTTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
85 52 0.87
86 3 0.05
87 5 0.08
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (85 bp):
TGTAAGATCGTGTCTGGGACACAGGCATCGATTGAGATTTACATATAAGACCACGTCCGGGACAT
CGGCATCGTATTTGATTTCA
Found at i:54556544 original size:43 final size:42
Alignment explanation
Indices: 54556447--54556544 Score: 94
Period size: 43 Copynumber: 2.3 Consensus size: 42
54556437 GACCATGTTT
* * * *
54556447 GGGACATCGGCATCGTATTTGATTTCATGTAAGACTCTGTCT
1 GGGACGTCGGCATCGTATTTGATTACATGTAAGACTCCGTCC
*
54556489 GGGACAG-AGGCATCG-ATATTGAATTACATGTAAGAC-CACGTCC
1 GGGAC-GTCGGCATCGTAT-TTG-ATTACATGTAAGACTC-CGTCC
54556532 GGGACGTCGGCAT
1 GGGACGTCGGCAT
54556545 TGTACTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
41 2 0.04
42 17 0.38
43 26 0.58
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (42 bp):
GGGACGTCGGCATCGTATTTGATTACATGTAAGACTCCGTCC
Found at i:54560184 original size:67 final size:67
Alignment explanation
Indices: 54560071--54560198 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
54560061 ATTCAGACCG
**
54560071 TATTTAGATAAATTTGTTGTAGTATTCCTTGATGATATTTTAATTTATTCACGTGATTAATCTAC
1 TATTTAGATAAATTTACTGTAGTATTCCTTGATGATATTTTAATTTATTCACGTGATTAATCTAC
54560136 CT
66 CT
*
54560138 TATTTAGATAAATTTACTGTAGTATTCCTTGATGATATTTTGATTTATTCACGTGATTAAT
1 TATTTAGATAAATTTACTGTAGTATTCCTTGATGATATTTTAATTTATTCACGTGATTAAT
54560199 TTGAGCATGC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (67 bp):
TATTTAGATAAATTTACTGTAGTATTCCTTGATGATATTTTAATTTATTCACGTGATTAATCTAC
CT
Found at i:54562293 original size:27 final size:27
Alignment explanation
Indices: 54562263--54562440 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54562253 ATATTGAGTC
* * * *
54562263 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54562290 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54562317 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54562345 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54562372 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54562399 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54562426 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54562441 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:54562402 original size:82 final size:81
Alignment explanation
Indices: 54562284--54562439 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54562274 TGCTATATAA
* *
54562284 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54562349 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54562366 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54562430 CACTTAGTGC
65 CACTTAGTGC
54562440 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:54570483 original size:27 final size:27
Alignment explanation
Indices: 54570453--54570630 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54570443 ATATTGAGTC
* * * *
54570453 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54570480 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54570507 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54570535 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54570562 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54570589 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54570616 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54570631 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:54570592 original size:82 final size:81
Alignment explanation
Indices: 54570474--54570629 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54570464 TGCTATATAA
* *
54570474 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54570539 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54570556 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54570620 CACTTAGTGC
65 CACTTAGTGC
54570630 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:54573814 original size:42 final size:43
Alignment explanation
Indices: 54573754--54573864 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
54573744 GATTTACGTA
* *
54573754 TAAGACCATGTCTGGGACATCGACATCG-TATCT-AATTTCGTG
1 TAAGACCATGTCTGGGACATCGACATCGATAT-TGAATTACATG
* * *
54573796 TAATACCCTGTCTGGGACATAGACATCGATATTGAATTACATG
1 TAAGACCATGTCTGGGACATCGACATCGATATTGAATTACATG
* *
54573839 TAAGACCATGTCCGGGACGTCGACAT
1 TAAGACCATGTCTGGGACATCGACAT
54573865 TGTACTTGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
42 26 0.46
43 31 0.54
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATCGACATCGATATTGAATTACATG
Found at i:54588305 original size:20 final size:21
Alignment explanation
Indices: 54588280--54588328 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
54588270 GAGGCAAAGC
54588280 ACACGCC-TGTGTGCTTAGGG
1 ACACGCCTTGTGTGCTTAGGG
54588300 ACACGCCTTTGTGTGCTTAGGG
1 ACACGCC-TTGTGTGCTTAGGG
54588322 ACACGCC
1 ACACGCC
54588329 CATGTCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.26
22 20 0.74
ACGTcount: A:0.16, C:0.29, G:0.31, T:0.24
Consensus pattern (21 bp):
ACACGCCTTGTGTGCTTAGGG
Found at i:54591167 original size:39 final size:40
Alignment explanation
Indices: 54591072--54591294 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
54591062 TTGAATGATG
*
54591072 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
54591110 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
54591151 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54591190 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
54591229 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
54591268 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54591295 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54591258 original size:79 final size:81
Alignment explanation
Indices: 54591072--54591294 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
54591062 TTGAATGATG
* * *
54591072 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
54591134 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
54591151 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
54591212 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
54591229 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
54591293 TG
66 TG
54591295 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:54591316 original size:79 final size:79
Alignment explanation
Indices: 54591072--54591327 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
54591062 TTGAATGATG
* * * *
54591072 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
54591133 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
54591151 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
54591215 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
54591229 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
54591292 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
54591309 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54591328 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:54599557 original size:23 final size:23
Alignment explanation
Indices: 54599530--54599582 Score: 99
Period size: 22 Copynumber: 2.3 Consensus size: 23
54599520 TATAACTTGG
54599530 AAAATTTTTAAAATTTTGTAAAA
1 AAAATTTTTAAAATTTTGTAAAA
54599553 AAAA-TTTTAAAATTTTGTAAAA
1 AAAATTTTTAAAATTTTGTAAAA
54599575 AAAATTTT
1 AAAATTTT
54599583 GAGTTCCCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AAAATTTTTAAAATTTTGTAAAA
Found at i:54600906 original size:22 final size:23
Alignment explanation
Indices: 54600855--54600906 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
54600845 GTCTAAATTC
* *
54600855 TTCTTCTCAAAATCGTTAATAAT
1 TTCTTTTCAAAAACGTTAATAAT
54600878 TTCTTTTCAAAAACGTTAAT-AT
1 TTCTTTTCAAAAACGTTAATAAT
*
54600900 TTTTTTT
1 TTCTTTT
54600907 ACATTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (23 bp):
TTCTTTTCAAAAACGTTAATAAT
Found at i:54602952 original size:21 final size:20
Alignment explanation
Indices: 54602912--54602950 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54602902 GATACCTGAT
54602912 AAAAGGTATCGATATTTTTG
1 AAAAGGTATCGATATTTTTG
*
54602932 AAAAGGTATTGATATTTTT
1 AAAAGGTATCGATATTTTT
54602951 TGTGATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (20 bp):
AAAAGGTATCGATATTTTTG
Found at i:54606666 original size:30 final size:31
Alignment explanation
Indices: 54606626--54606690 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
54606616 TTTTTGAACT
* *
54606626 TTTTCCAAAAT-TTTCGAAGTGTTCAAAAT-A
1 TTTTCCAAAATGTTTAGAAGTCTT-AAAATGA
*
54606656 TTTTCTAAAATGTTTAGAAGTCTTAAAATGA
1 TTTTCCAAAATGTTTAGAAGTCTTAAAATGA
54606687 TTTT
1 TTTT
54606691 TATGCTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (31 bp):
TTTTCCAAAATGTTTAGAAGTCTTAAAATGA
Found at i:54615775 original size:31 final size:31
Alignment explanation
Indices: 54615722--54615786 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
54615712 TAAATATTTT
*
54615722 AAAAATTATTAGAAATAGTAAAAGATTGTACA
1 AAAAATTATTAGAAATAGTAAAAAATTGTA-A
*
54615754 AAAAATTATTA-AAAGT-TTAAAAAATTGTAA
1 AAAAATTATTAGAAA-TAGTAAAAAATTGTAA
54615784 AAA
1 AAA
54615787 TTGTTGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.13
31 14 0.47
32 12 0.40
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (31 bp):
AAAAATTATTAGAAATAGTAAAAAATTGTAA
Found at i:54616574 original size:12 final size:12
Alignment explanation
Indices: 54616547--54616584 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54616537 TATTTTTATA
*
54616547 TTTTATAATTTC
1 TTTTATAATTTT
54616559 TTTTATAATTTT
1 TTTTATAATTTT
*
54616571 TTTTGT-ATTTT
1 TTTTATAATTTT
54616582 TTT
1 TTT
54616585 CATTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:54616841 original size:3 final size:3
Alignment explanation
Indices: 54616833--54616858 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54616823 AAATACTAAC
54616833 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
54616859 AACTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:54618225 original size:22 final size:24
Alignment explanation
Indices: 54618200--54618252 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
54618190 ATATAATTTC
54618200 ATTTTAATCT-TT-TAAAAATTAT
1 ATTTTAATCTATTGTAAAAATTAT
*
54618222 ATTTTTA-CTATTGTAAAAATTAT
1 ATTTTAATCTATTGTAAAAATTAT
*
54618245 AATTTAAT
1 ATTTTAAT
54618253 TTTAACCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 8 0.32
23 15 0.60
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTTAATCTATTGTAAAAATTAT
Found at i:54628086 original size:49 final size:50
Alignment explanation
Indices: 54628009--54628106 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 50
54627999 TCCATATAGA
* * *
54628009 ACTATACTTCTTTTATTTTACATTGATTAGAATAAGGTTTT-TCAACCTT
1 ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTCTCAACCTT
54628058 ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTCTCAACCT
1 ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTCTCAACCT
54628107 ATAAATAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 38 0.84
50 7 0.16
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (50 bp):
ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTCTCAACCTT
Found at i:54628234 original size:17 final size:17
Alignment explanation
Indices: 54628212--54628245 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54628202 TCCACGTAAA
54628212 ATCTGTGTATTATTATT
1 ATCTGTGTATTATTATT
54628229 ATCTGTGTATTATTATT
1 ATCTGTGTATTATTATT
54628246 TTTCTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
ATCTGTGTATTATTATT
Found at i:54632001 original size:15 final size:15
Alignment explanation
Indices: 54631981--54632010 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54631971 CAAGTTGTCC
54631981 TATACATGCCATTAT
1 TATACATGCCATTAT
54631996 TATACATGCCATTAT
1 TATACATGCCATTAT
54632011 ACCAAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
TATACATGCCATTAT
Found at i:54637343 original size:85 final size:85
Alignment explanation
Indices: 54636970--54637334 Score: 714
Period size: 85 Copynumber: 4.3 Consensus size: 85
54636960 CTTACCAATT
54636970 CCATA-TCCTAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTT
1 CCATATTCC-AGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTT
54637034 ACACGAAGTCTCATATTGATG
65 ACACGAAGTCTCATATTGATG
54637055 CCATATTCCAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTA
1 CCATATTCCAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTA
54637120 CACGAAGTCTCATATTGATG
66 CACGAAGTCTCATATTGATG
54637140 CCATATTCCAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTA
1 CCATATTCCAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTA
54637205 CACGAAGTCTCATATTGATG
66 CACGAAGTCTCATATTGATG
54637225 CCATATTCCAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTA
1 CCATATTCCAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTA
54637290 CACGAAGTCTCATATTGATG
66 CACGAAGTCTCATATTGATG
54637310 CCATATTCCAGATATGGTCTTACAT
1 CCATATTCCAGATATGGTCTTACAT
54637335 GTAATCTCAA
Statistics
Matches: 279, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
85 276 0.99
86 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (85 bp):
CCATATTCCAGATATGGTCTTACATAGGATCTCATATCAATGCCAATAGCCCAGCTATGGTCTTA
CACGAAGTCTCATATTGATG
Found at i:54641129 original size:48 final size:48
Alignment explanation
Indices: 54640826--54641145 Score: 263
Period size: 48 Copynumber: 6.7 Consensus size: 48
54640816 GAAAATTGTA
* * *
54640826 GATGCCATGTCCTAGACATGGTCTTACACTGGCT-TACATGTCGA-GGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATATC-ATGGCC
* * *
54640874 AATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATCTCAAT-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC-ATGGCC
* *
54640922 GATCCCATGTCCCAGACATGGTCTTACACTAGCTCTGATAAT-ATGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCATGGCC
* * * * * * * ** **
54640970 GTTGCCATGTCCTAGACATGGTCGTACGCTAGCGCACCTAAAAACGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCATGGCC
* * * *
54641018 GATGCCATGTCCC-GAACATGGTCTTACACTGGCTCTCATAACATTGCT
1 GATGCCATGTCCCAG-ACATGGTCTTACACTAGCTCTCATATCATGGCC
* * * * * *
54641066 GATGCCATGTTCCAAACATGGTCTTATACTGGCTCTCATATCGTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCATGGCC
* * * *
54641114 GATGCCATGTCCCAAATATGGCCTTATACTAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAG
54641146 TACACATATC
Statistics
Matches: 222, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
47 4 0.02
48 216 0.97
49 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCATGGCC
Found at i:54642273 original size:17 final size:17
Alignment explanation
Indices: 54642251--54642283 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54642241 TCATATAATC
54642251 ATGATA-TAAAACATAAA
1 ATGATATTAAAA-ATAAA
54642268 ATGATATTAAAAATAA
1 ATGATATTAAAAATAA
54642284 TTTCTCTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (17 bp):
ATGATATTAAAAATAAA
Found at i:54644720 original size:20 final size:20
Alignment explanation
Indices: 54644687--54644730 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
54644677 AAAGAAAAGT
* *
54644687 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAATAAGG
54644707 AAATGCAAAT-GAAAATAAGG
1 AAATGC-AATGGAAAATAAGG
54644727 AAAT
1 AAAT
54644731 TTGAAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (20 bp):
AAATGCAATGGAAAATAAGG
Found at i:54649323 original size:20 final size:20
Alignment explanation
Indices: 54649290--54649333 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
54649280 AAAGAAAAGT
* *
54649290 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAATAAGG
54649310 AAATGCAAAT-GAAAATAAGG
1 AAATGC-AATGGAAAATAAGG
54649330 AAAT
1 AAAT
54649334 TTGAAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (20 bp):
AAATGCAATGGAAAATAAGG
Found at i:54656928 original size:155 final size:152
Alignment explanation
Indices: 54656680--54656986 Score: 443
Period size: 155 Copynumber: 2.0 Consensus size: 152
54656670 TTTCCTCCTC
* * * ** *
54656680 CTTCTGTTCCTTATCTTCCTTCTCCTTTTTCATCCACTTCTTTTCCTGAATCTCAATCAAGGTAA
1 CTTCCGTTCCTTATCTTCCTTCTCCTTCTTCATCCACTCCCCTTCCTAAATCTCAATCAAGGTAA
* *
54656745 CTTTTTTATGCTTTATTTAATCTGCCTTTACTTCATTCAATTCCTTTTAAATCTTCTTCTTCCCT
66 CTTTTTTATACTTTATTTAATCTACCTTTACTTCATTCAATTCCTTTTAAATCTTCTTCTT-CC-
*
54656810 TTTTTTTTTGGTTGAAGAATCTGTT
129 -TTTTTTTTCGTTGAAGAATCTGTT
* * *
54656835 CTTCCGTTCTTTATCTTCCTTCTTCTTCTTCATCCACTCCCCTTCCTAAATCTCAATTAAGGTAA
1 CTTCCGTTCCTTATCTTCCTTCTCCTTCTTCATCCACTCCCCTTCCTAAATCTCAATCAAGGTAA
* * *
54656900 CTTTTTTATACTTTATTTAGTCTACCTTTATTTCATTCAATTTCTTTTAAATCTTCTTCTTCCTT
66 CTTTTTTATACTTTATTTAATCTACCTTTACTTCATTCAATTCCTTTTAAATCTTCTTCTTCCTT
*
54656965 TTTTTTCGTTGAAGTATCTGTT
131 TTTTTTCGTTGAAGAATCTGTT
54656987 TGGATTTTAC
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
152 22 0.16
154 2 0.01
155 112 0.82
ACGTcount: A:0.17, C:0.24, G:0.06, T:0.52
Consensus pattern (152 bp):
CTTCCGTTCCTTATCTTCCTTCTCCTTCTTCATCCACTCCCCTTCCTAAATCTCAATCAAGGTAA
CTTTTTTATACTTTATTTAATCTACCTTTACTTCATTCAATTCCTTTTAAATCTTCTTCTTCCTT
TTTTTTCGTTGAAGAATCTGTT
Found at i:54665375 original size:32 final size:32
Alignment explanation
Indices: 54665338--54665419 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
54665328 TTGAAATTAG
*
54665338 TTTGTTGGATTTTGAAATTATTATG-TCTTAAA
1 TTTGTTGGATATTGAAATTATTATGCT-TTAAA
* * *
54665370 TTTGTTAGATATTGAATTTATTATGCTTTAAG
1 TTTGTTGGATATTGAAATTATTATGCTTTAAA
*
54665402 CTTGTTGGATATTGAAAT
1 TTTGTTGGATATTGAAAT
54665420 GATTGACAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 41 0.98
33 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (32 bp):
TTTGTTGGATATTGAAATTATTATGCTTTAAA
Found at i:54666841 original size:19 final size:20
Alignment explanation
Indices: 54666817--54666858 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
54666807 CAAACATCAC
54666817 AAAAGTAAATCA-CTTCCAG
1 AAAAGTAAATCATCTTCCAG
*
54666836 AAAAGTAAATCATTTTCCAG
1 AAAAGTAAATCATCTTCCAG
54666856 AAA
1 AAA
54666859 CTATTTTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (20 bp):
AAAAGTAAATCATCTTCCAG
Found at i:54670130 original size:20 final size:20
Alignment explanation
Indices: 54670095--54670135 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54670085 GAAAGTGTAT
* *
54670095 ACAGAGGCATCAAAGTGCAA
1 ACAGAGGCACCAAAGTACAA
*
54670115 ACAGAGGCACCGAAGTACAA
1 ACAGAGGCACCAAAGTACAA
54670135 A
1 A
54670136 TCATGTACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.22, G:0.24, T:0.07
Consensus pattern (20 bp):
ACAGAGGCACCAAAGTACAA
Found at i:54674189 original size:15 final size:15
Alignment explanation
Indices: 54674169--54674198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54674159 TTCACTATTA
*
54674169 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
54674184 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
54674199 GCATACATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:54677034 original size:28 final size:30
Alignment explanation
Indices: 54677003--54677070 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
54676993 TTTTCGCCCT
*
54677003 ATTTTGTTACCATTTT-A-CAATTACGTTA
1 ATTTTGTTACCATTTTAAGAAATTACGTTA
* **
54677031 ATTTTATTATTATTTTAAAGAAATTACGTTA
1 ATTTTGTTACCATTTT-AAGAAATTACGTTA
54677062 ATTTTGTTA
1 ATTTTGTTA
54677071 TTATTTTAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 13 0.41
30 1 0.03
31 18 0.56
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.53
Consensus pattern (30 bp):
ATTTTGTTACCATTTTAAGAAATTACGTTA
Found at i:54679349 original size:33 final size:33
Alignment explanation
Indices: 54679307--54679373 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
54679297 TATAGGAGAA
54679307 ATCACATGTGAAGGGT-CGAATCAATACCGTCGT
1 ATCACATGTGAAGGGTCCG-ATCAATACCGTCGT
54679340 ATCACATGTGAAGGGTCCGATCAATACCGTCGT
1 ATCACATGTGAAGGGTCCGATCAATACCGTCGT
54679373 A
1 A
54679374 ACATCAATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (33 bp):
ATCACATGTGAAGGGTCCGATCAATACCGTCGT
Found at i:54683611 original size:21 final size:23
Alignment explanation
Indices: 54683581--54683622 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
54683571 TTCTCCAAAA
*
54683581 CCATCCTACTATTC-CTTTCTTC
1 CCATCCTACTACTCTCTTTCTTC
54683603 CCAT-CTACTACTCTCTTTCT
1 CCATCCTACTACTCTCTTTCT
54683623 CACCATCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.45
Consensus pattern (23 bp):
CCATCCTACTACTCTCTTTCTTC
Found at i:54683628 original size:22 final size:22
Alignment explanation
Indices: 54683580--54683629 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
54683570 CTTCTCCAAA
*
54683580 ACCATCCTACTATTCCTTTCTTC
1 ACCAT-CTACTACTCCTTTCTTC
54683603 -CCATCTACTACTCTCTTTC-TC
1 ACCATCTACTACTC-CTTTCTTC
54683624 ACCATC
1 ACCATC
54683630 ACTTTTGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40
Consensus pattern (22 bp):
ACCATCTACTACTCCTTTCTTC
Found at i:54684661 original size:24 final size:24
Alignment explanation
Indices: 54684631--54684676 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54684621 TATAATGTGA
* * *
54684631 AAATGACCTTTTTGCCCCTAGGTG
1 AAATGACCATTATACCCCTAGGTG
54684655 AAATGACCATTATACCCCTAGG
1 AAATGACCATTATACCCCTAGG
54684677 GTTATGTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (24 bp):
AAATGACCATTATACCCCTAGGTG
Found at i:54684732 original size:10 final size:10
Alignment explanation
Indices: 54684717--54684755 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
54684707 TTCTTTTGTA
54684717 CATGATATGC
1 CATGATATGC
54684727 CATGATATGC
1 CATGATATGC
54684737 ACATGATATGC
1 -CATGATATGC
54684748 CATGATAT
1 CATGATAT
54684756 ATTCACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:54684741 original size:21 final size:21
Alignment explanation
Indices: 54684716--54684755 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54684706 CTTCTTTTGT
54684716 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
54684737 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
54684756 ATTCACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:54684836 original size:25 final size:25
Alignment explanation
Indices: 54684802--54684871 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
54684792 AGGAAGTGCT
*
54684802 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
54684827 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
54684852 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54684872 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:54684884 original size:24 final size:24
Alignment explanation
Indices: 54684801--54684907 Score: 108
Period size: 25 Copynumber: 4.2 Consensus size: 24
54684791 GAGGAAGTGC
*
54684801 TAAAAGGGCTTTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
54684826 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
54684850 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
**
54684874 TAAAAGAGGCTAGGCCTCCAGTTATAT
1 TAAAAG-GGCTTTGCC-CCAGTT-TAT
54684901 TATAAAG
1 TA-AAAG
54684908 CAGCTATGCT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.07
24 11 0.16
25 44 0.63
26 1 0.01
27 5 0.07
28 4 0.06
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:54684895 original size:50 final size:50
Alignment explanation
Indices: 54684802--54684896 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
54684792 AGGAAGTGCT
**
54684802 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
**
54684852 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
54684897 ATATTATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 24 0.62
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:54689366 original size:24 final size:24
Alignment explanation
Indices: 54689336--54689381 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54689326 TATAATGTGA
* * *
54689336 AAATGACCTTTTTGCCCCTAGGTG
1 AAATGACCATTATACCCCTAGGTG
54689360 AAATGACCATTATACCCCTAGG
1 AAATGACCATTATACCCCTAGG
54689382 GTTATGTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (24 bp):
AAATGACCATTATACCCCTAGGTG
Found at i:54689437 original size:10 final size:10
Alignment explanation
Indices: 54689422--54689460 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
54689412 TTCTTTTGTA
54689422 CATGATATGC
1 CATGATATGC
54689432 CATGATATGC
1 CATGATATGC
54689442 ACATGATATGC
1 -CATGATATGC
54689453 CATGATAT
1 CATGATAT
54689461 ATTCACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:54689446 original size:21 final size:21
Alignment explanation
Indices: 54689421--54689460 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54689411 CTTCTTTTGT
54689421 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
54689442 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
54689461 ATTCACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:54689564 original size:24 final size:24
Alignment explanation
Indices: 54689506--54689578 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
54689496 GAGGAAGTGC
54689506 TAAAAG-GGCTTTGCCCCAGTTTAT
1 TAAAAGAGGCTTTGCCCCAG-TTAT
*
54689530 CAAAA-AGGGCTTTGCCCCAGTTAT
1 TAAAAGA-GGCTTTGCCCCAGTTAT
**
54689554 TAAAAGAGGCTAGGCCTCCAGTTAT
1 TAAAAGAGGCTTTGCC-CCAGTTAT
54689579 ATTATAAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
TAAAAGAGGCTTTGCCCCAGTTAT
Found at i:54706029 original size:16 final size:16
Alignment explanation
Indices: 54706008--54706039 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54705998 AGAAACTAAT
54706008 TCAGGGCCTAGAACAC
1 TCAGGGCCTAGAACAC
54706024 TCAGGGCCTAGAACAC
1 TCAGGGCCTAGAACAC
54706040 GCCGCTTGCC
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:0.31, C:0.31, G:0.25, T:0.12
Consensus pattern (16 bp):
TCAGGGCCTAGAACAC
Found at i:54715259 original size:18 final size:18
Alignment explanation
Indices: 54715232--54715282 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
54715222 TTGGGATATT
54715232 TGGG-CCACACGGGCATA
1 TGGGCCCACACGGGCATA
54715249 TGGGCCCACACGGGCATA
1 TGGGCCCACACGGGCATA
* *
54715267 TAGGCCCACATGGGCA
1 TGGGCCCACACGGGCA
54715283 CACATTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.24, C:0.31, G:0.33, T:0.12
Consensus pattern (18 bp):
TGGGCCCACACGGGCATA
Found at i:54722203 original size:87 final size:87
Alignment explanation
Indices: 54722096--54722338 Score: 256
Period size: 87 Copynumber: 2.8 Consensus size: 87
54722086 GTACAAACAT
* * * * *
54722096 GTTGCAGACTAAACTACCAGATCAGATAATAGTACGCAGCAAAGCTGACATACATGTGGTACAGT
1 GTTGCAG-TTAAACTGCCAGATCAGATAATAGTATGCAGCAAAGCTGACGTACAAGTGGTACAGT
*** *
54722161 GTGGGAAA-CTGCTGTAAAG-TCAA
65 GCAAGAAATC-ACTGTAAAGAT-AA
** ** ** **
54722184 GTTTTAGTTAAACTGCCAGATCAGATAATAGTATATAGCAAATTTGACGTACAAGCAGTACAGTG
1 GTTGCAGTTAAACTGCCAGATCAGATAATAGTATGCAGCAAAGCTGACGTACAAGTGGTACAGTG
* **
54722249 CAATAAATCACTGTACTGATAA
66 CAAGAAATCACTGTAAAGATAA
*
54722271 GTTGCAGTTAAACTGCCAAATCAGATAATAGTATGCAGCAAAGCTGACGTACAAGTGGTACAGTG
1 GTTGCAGTTAAACTGCCAGATCAGATAATAGTATGCAGCAAAGCTGACGTACAAGTGGTACAGTG
54722336 CAA
66 CAA
54722339 CCTATAAGTT
Statistics
Matches: 124, Mismatches: 29, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
87 117 0.94
88 7 0.06
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (87 bp):
GTTGCAGTTAAACTGCCAGATCAGATAATAGTATGCAGCAAAGCTGACGTACAAGTGGTACAGTG
CAAGAAATCACTGTAAAGATAA
Found at i:54722533 original size:14 final size:14
Alignment explanation
Indices: 54722514--54722542 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54722504 GCTCACTGGG
54722514 TTCAAAATTAGATA
1 TTCAAAATTAGATA
54722528 TTCAAAATTAGATA
1 TTCAAAATTAGATA
54722542 T
1 T
54722543 CTCGCACAAC
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:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
TTCAAAATTAGATA
Found at i:54725080 original size:40 final size:40
Alignment explanation
Indices: 54724938--54725120 Score: 221
Period size: 40 Copynumber: 4.5 Consensus size: 40
54724928 TCAATATCTA
* **
54724938 GCACACTAAGTGCCTATACATAGCCAAAGCTAT-TATAATCTC
1 GCACACTAAGTGCC-ATATATAGCCAAAGCTATCTCGAA--TC
* *
54724980 GCACACTAAGTGCCTTACATAGCCAAAGCTATCTCG-ATC
1 GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGAATC
54725019 TTGCACACTAAGTGCCA-ATATAGCCAAAGCTAT-TCCGAATC
1 --GCACACTAAGTGCCATATATAGCCAAAGCTATCT-CGAATC
* *
54725060 GCACACTAAGTGCCATATATAGCCGAAGATATCTCGAATC
1 GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGAATC
54725100 GCACACTAAGTGCCATATATA
1 GCACACTAAGTGCCATATATA
54725121 TATCTGAGTC
Statistics
Matches: 127, Mismatches: 7, Indels: 16
0.85 0.05 0.11
Matches are distributed among these distances:
39 18 0.14
40 58 0.46
41 36 0.28
42 15 0.12
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (40 bp):
GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGAATC
Found at i:54732391 original size:46 final size:46
Alignment explanation
Indices: 54732324--54732542 Score: 302
Period size: 46 Copynumber: 4.7 Consensus size: 46
54732314 AACCCGCCCC
* * *
54732324 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
54732370 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
54732418 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54732463 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54732509 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54732543 TGCTCAACCA
Statistics
Matches: 153, Mismatches: 11, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 1 0.01
45 2 0.01
46 107 0.70
47 29 0.19
48 2 0.01
49 1 0.01
50 3 0.02
51 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54732997 original size:30 final size:30
Alignment explanation
Indices: 54732963--54733022 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54732953 ATTTAATACG
54732963 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
54732993 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
54733023 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:54736928 original size:40 final size:40
Alignment explanation
Indices: 54736786--54736971 Score: 160
Period size: 40 Copynumber: 4.6 Consensus size: 40
54736776 ACTCGATATC
* * * **
54736786 TCGCGCACTAAGTGCCTATACATAGCCTAAGCTATT-ATAA
1 TCGCACACTAAGTGCC-ATATATAGCCGAAGCTATTCCGAA
* * * * * **
54736826 TCTCACACACTAAGTGCCTTACATATCCGAAGCTATCTCAGTC
1 --TCGCACACTAAGTGCCATATATAGCCGAAGCTAT-TCCGAA
* *
54736869 TCGCACACTTAGTGTCATATATAGCCGAAGCTATTCCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATTCCGAA
*
54736909 TCGTACACTAAGTGCCATATATAGCCGAAGCTA-TCTCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATTC-CGAA
* *
54736949 CCGCACACTGAGTGCCATATATA
1 TCGCACACTAAGTGCCATATATA
54736972 TATCTGAGTC
Statistics
Matches: 118, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
39 2 0.02
40 57 0.48
41 43 0.36
42 15 0.13
43 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATTCCGAA
Found at i:54742136 original size:49 final size:51
Alignment explanation
Indices: 54742013--54742250 Score: 254
Period size: 51 Copynumber: 4.7 Consensus size: 51
54742003 TATTGTGAGG
* *
54742013 TCACCTGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTCGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCGACAACTTCGA
* * * * ** *
54742064 TCACGTGCGTAGTACTAAATGCAGGCTACTACGTGTAC-CGGATTA-TT-GG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACTC-GACAACTTCGA
* *
54742113 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTCGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCGACAACTTCGA
* * * * * *
54742164 TCACGTGCGTAGTACTAAATGCAGGCTACTACGTGTAC-CGGATAA-TT-GG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACTC-GACAACTTCGA
*
54742213 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTAC
54742251 CAGATAGCTT
Statistics
Matches: 152, Mismatches: 30, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
49 70 0.46
50 9 0.06
51 73 0.48
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (51 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCGACAACTTCGA
Found at i:54742191 original size:100 final size:100
Alignment explanation
Indices: 54742011--54742250 Score: 453
Period size: 100 Copynumber: 2.4 Consensus size: 100
54742001 TCTATTGTGA
*
54742011 GGTCACCTGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTCGATCACGTGCGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTCGATCACGTGCGTAG
*
54742076 TACTAAATGCAGGCTACTACGTGTACCGGATTATT
66 TACTAAATGCAGGCTACTACGTGTACCGGATAATT
*
54742111 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTCGATCACGTGCGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTCGATCACGTGCGTAG
54742176 TACTAAATGCAGGCTACTACGTGTACCGGATAATT
66 TACTAAATGCAGGCTACTACGTGTACCGGATAATT
54742211 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTAC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTAC
54742251 CAGATAGCTT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 136 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (100 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTCGATCACGTGCGTAG
TACTAAATGCAGGCTACTACGTGTACCGGATAATT
Found at i:54742251 original size:49 final size:50
Alignment explanation
Indices: 54742011--54742256 Score: 266
Period size: 49 Copynumber: 4.9 Consensus size: 50
54742001 TCTATTGTGA
* *
54742011 GGTCACCTGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTAC-CGATAACTTC
* * * * * * *
54742062 GATCACGTGCGTAGTACTAAATGCAGGCTACTACGTGTACCGGATTA-TT-
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC-GATAACTTC
* *
54742111 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGACAACTTC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTAC-CGATAACTTC
* * * * * *
54742162 GATCACGTGCGTAGTACTAAATGCAGGCTACTACGTGTACCGGATAA-TT-
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC-GATAACTTC
54742211 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC-GATA
54742257 GCTTTGGCTA
Statistics
Matches: 158, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
49 75 0.47
50 9 0.06
51 74 0.47
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGATAACTTC
Found at i:54745691 original size:42 final size:42
Alignment explanation
Indices: 54745635--54745753 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 42
54745625 ATACTCGAAT
* * * *
54745635 TCTCACACACTAAGTGCCAAAACATAGTCGAAGCTATTTTAA
1 TCTCGCACACTAAGTGCCAAAACATAGCCGAAGCTATCTCAA
* ***
54745677 TCTCGCACATTAAGTGCC-TTTCATAGCCGAAGCTATCTCAA
1 TCTCGCACACTAAGTGCCAAAACATAGCCGAAGCTATCTCAA
* * * *
54745718 TCTCGCACACTAAATGCC-ACATATAGCCTAAGCTAT
1 TCTCGCACACTAAGTGCCAAAACATAGCCGAAGCTAT
54745754 TTCGAATCAC
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
41 46 0.74
42 16 0.26
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (42 bp):
TCTCGCACACTAAGTGCCAAAACATAGCCGAAGCTATCTCAA
Found at i:54745802 original size:21 final size:21
Alignment explanation
Indices: 54745778--54745820 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
54745768 GAAGTGCCAT
54745778 ATATATATTCGAATCGTCGTC
1 ATATATATTCGAATCGTCGTC
54745799 ATATATATTCGAATCGTCGTC
1 ATATATATTCGAATCGTCGTC
54745820 A
1 A
54745821 AACGTGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (21 bp):
ATATATATTCGAATCGTCGTC
Found at i:54758379 original size:29 final size:29
Alignment explanation
Indices: 54758291--54758379 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
54758281 AATTGTCAAA
* *
54758291 GATTACAGTTCTAGGTACTATGTACCGAT
1 GATTATAGTTCCAGGTACTATGTACCGAT
* * * * *
54758320 G-TT-TCAGTTCCAGGCACTCTGTGCTGGT
1 GATTAT-AGTTCCAGGTACTATGTACCGAT
*
54758348 GATTATAGTTCCATGTACTATGTACCGAT
1 GATTATAGTTCCAGGTACTATGTACCGAT
54758377 GAT
1 GAT
54758380 GGATATCATA
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
28 20 0.45
29 23 0.52
30 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (29 bp):
GATTATAGTTCCAGGTACTATGTACCGAT
Found at i:54771304 original size:40 final size:40
Alignment explanation
Indices: 54771190--54771306 Score: 175
Period size: 40 Copynumber: 3.0 Consensus size: 40
54771180 TGATAACCGA
*
54771190 GCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-TAACCAG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-TCCAG
* *
54771229 GCTATGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCAG
*
54771269 GCTAAGTTCCGAAGGCATTTGTGCGAGTTACTAGTTCC
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCC
54771307 NNNNNNNNNN
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
39 5 0.07
40 65 0.92
41 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCAG
Found at i:54772936 original size:14 final size:15
Alignment explanation
Indices: 54772909--54772946 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
54772899 ATAGATTGCT
54772909 AATGGTTGATGTTTG
1 AATGGTTGATGTTTG
*
54772924 AATGGTT-ATGTTTT
1 AATGGTTGATGTTTG
*
54772938 AATGTTTGA
1 AATGGTTGA
54772947 ATCGTGGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (15 bp):
AATGGTTGATGTTTG
Found at i:54781060 original size:16 final size:16
Alignment explanation
Indices: 54781039--54781070 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54781029 ATTAACCAAA
54781039 ATATATAATATATTTT
1 ATATATAATATATTTT
54781055 ATATATAATATATTTT
1 ATATATAATATATTTT
54781071 TTGAACTAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATATAATATATTTT
Found at i:54782942 original size:31 final size:28
Alignment explanation
Indices: 54782874--54782943 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
54782864 AACTTAAATA
*
54782874 TAAATTTGATACTTAAATTTATTTTCTTC
1 TAAA-TTGATACTTAAAGTTATTTTCTTC
54782903 TAAATTGATACTTAAAAGGTTATTTT-TGTC
1 TAAATTGATACTT-AAA-GTTATTTTCT-TC
54782933 TCAAATTGATA
1 T-AAATTGATA
54782944 TTCAAATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 9 0.25
29 8 0.22
30 10 0.28
31 9 0.25
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (28 bp):
TAAATTGATACTTAAAGTTATTTTCTTC
Found at i:54783085 original size:15 final size:15
Alignment explanation
Indices: 54783058--54783101 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
54783048 TAAAATATAT
54783058 TTAAAAATATAAAAAA
1 TTAAAAAT-TAAAAAA
54783074 TTAAAAATT-AAAAA
1 TTAAAAATTAAAAAA
54783088 TTATAAAATTAAAA
1 TTA-AAAATTAAAA
54783102 TTAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.31
15 7 0.27
16 11 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAAATTAAAAAA
Found at i:54783096 original size:8 final size:7
Alignment explanation
Indices: 54783058--54783107 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
54783048 TAAAATATAT
54783058 TTAAAAA
1 TTAAAAA
54783065 TATAAAAAA
1 T-T-AAAAA
54783074 TTAAAAA
1 TTAAAAA
54783081 TTAAAAA
1 TTAAAAA
54783088 TTATAAAA
1 TTA-AAAA
54783096 TT-AAAA
1 TTAAAAA
54783102 TTAAAA
1 TTAAAA
54783108 TATATTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.15
7 19 0.49
8 8 0.21
9 6 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:54785300 original size:18 final size:18
Alignment explanation
Indices: 54785277--54785311 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54785267 TTGTTTACAT
*
54785277 AAATGTAAATATCATTTG
1 AAATGTAAACATCATTTG
*
54785295 AAATGTGAACATCATTT
1 AAATGTAAACATCATTT
54785312 ATCGTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (18 bp):
AAATGTAAACATCATTTG
Found at i:54790598 original size:39 final size:40
Alignment explanation
Indices: 54790503--54790764 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
54790493 TTGAATGATG
*
54790503 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
54790541 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
54790582 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
54790621 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54790660 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
54790699 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
54790738 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54790765 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54794388 original size:23 final size:22
Alignment explanation
Indices: 54794362--54794406 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54794352 ACGCAGAGNC
54794362 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
54794385 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
54794407 AAGATTGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:54794409 original size:19 final size:19
Alignment explanation
Indices: 54794385--54794529 Score: 239
Period size: 19 Copynumber: 7.9 Consensus size: 19
54794375 AATCATATCT
54794385 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54794404 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
54794422 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
54794439 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54794458 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
54794476 TCTAAGATTG--TATTATA
1 TCTAAGATTGCATATCATA
54794493 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54794512 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
54794530 TGAAGATTAT
Statistics
Matches: 118, Mismatches: 2, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
17 31 0.26
18 32 0.27
19 55 0.47
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54794461 original size:54 final size:54
Alignment explanation
Indices: 54794385--54794529 Score: 272
Period size: 54 Copynumber: 2.7 Consensus size: 54
54794375 AATCATATCT
54794385 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
*
54794439 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATTATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
54794493 TCTAAGATTGCATATCATATCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCATATCTAAGATTGCA-ATCAT
54794530 TGAAGATTAT
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
54 84 0.94
55 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (54 bp):
TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
Found at i:54794511 original size:73 final size:72
Alignment explanation
Indices: 54794378--54794530 Score: 240
Period size: 73 Copynumber: 2.1 Consensus size: 72
54794368 ATTACAAAAT
54794378 CATATC-TTCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATATCT
1 CATATCATTCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATATCT
54794442 AAGATTG
66 AAGATTG
* *
54794449 CATATCATATCTAAGATTGCA-ATCATATCTAAGATTG-TATTATATCTAAGATTGCATATCATA
1 CATATCAT-TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTG--TATCATA
54794512 TCTAAGATTG
63 TCTAAGATTG
54794522 CATATCATT
1 CATATCATT
54794531 GAAGATTATA
Statistics
Matches: 76, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
71 21 0.28
72 18 0.24
73 37 0.49
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (72 bp):
CATATCATTCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATATCT
AAGATTG
Found at i:54794537 original size:36 final size:38
Alignment explanation
Indices: 54794378--54794529 Score: 239
Period size: 35 Copynumber: 4.2 Consensus size: 38
54794368 ATTACAAAAT
54794378 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
54794414 CA-ATCATATCTAAGATTG--TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
54794449 CATATCATATCTAAGATTGCA-ATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
*
54794486 --TATTATATCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
54794522 CATATCAT
1 CATATCAT
54794530 TGAAGATTAT
Statistics
Matches: 106, Mismatches: 2, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
35 40 0.38
36 35 0.33
37 26 0.25
38 5 0.05
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGATTG
Found at i:54795192 original size:78 final size:78
Alignment explanation
Indices: 54795002--54795300 Score: 413
Period size: 78 Copynumber: 3.8 Consensus size: 78
54794992 ATGTAAACAC
*
54795002 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCTGTT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAATC----
*
54795067 ATCTTGGATCTGCTTCA
62 ATCTTGAATCTGCTTCA
* * * *
54795084 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATACAAAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAATCATC
54795148 TTGAATCTGCTTCA
65 TTGAATCTGCTTCA
* * *
54795162 ATGAAGGTCAGATCTACTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAATCATCT
*
54795227 T-AGATCTACTTCA
66 TGA-ATCTGCTTCA
* * *
54795240 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTCCGTTGAATATAGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAATC
54795301 TGTTTCTTCG
Statistics
Matches: 194, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
77 3 0.02
78 136 0.70
82 53 0.27
83 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAATCATCT
TGAATCTGCTTCA
Found at i:54795293 original size:156 final size:157
Alignment explanation
Indices: 54795002--54795300 Score: 467
Period size: 156 Copynumber: 1.9 Consensus size: 157
54794992 ATGTAAACAC
*
54795002 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCTGTT
1 ATGAAGGTCAGATCTACTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATC---T
* * * *
54795067 ATCTTGGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATACA
63 ATCTTAGATCTACTTCAATGAAGGTCCAATCTGCTATGTCTTCGATCTACTCTCCGTCGAATACA
54795132 AAGATGCCAAATCATCTTGAATCTGCTTCA
128 AAGATGCCAAATCATCTTGAATCTGCTTCA
*
54795162 ATGAAGGTCAGATCTACTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATC-ATC
1 ATGAAGGTCAGATCTACTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCTATC
* * *
54795226 TTAGATCTACTTCAATGAAGGT-CAGATCTGCTATGTCTTCGATCTACTCTCCGTTGAATATAGA
66 TTAGATCTACTTCAATGAAGGTCCA-ATCTGCTATGTCTTCGATCTACTCTCCGTCGAATACAAA
54795290 GATGCCAAATC
130 GATGCCAAATC
54795301 TGTTTCTTCG
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
155 2 0.02
156 68 0.53
160 59 0.46
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (157 bp):
ATGAAGGTCAGATCTACTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCTATC
TTAGATCTACTTCAATGAAGGTCCAATCTGCTATGTCTTCGATCTACTCTCCGTCGAATACAAAG
ATGCCAAATCATCTTGAATCTGCTTCA
Found at i:54795432 original size:87 final size:89
Alignment explanation
Indices: 54795333--54795494 Score: 222
Period size: 89 Copynumber: 1.8 Consensus size: 89
54795323 ACAGTACAGA
* * *
54795333 GATGCCAAATCATCTTAGATCTATTTC-AAG-GTAAACA-CGTGAAAGCCAGATCTGCTATGTCT
1 GATGCCAAATCATCTTAGATCTAATTCGAAGTGAAAACATC-CGAAAGCCAGATCTGCTATGTCT
54795395 TCGATCTGCTCCTTGTCAACGTAAG
65 TCGATCTGCTCCTTGTCAACGTAAG
* * * **
54795420 GATGCCAAATCATCTTGGATCTAATTCGATGTGAAAACATCCGAAGGTTAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTAATTCGAAGTGAAAACATCCGAAAGCCAGATCTGCTATGTCTT
54795485 CGATCTGCTC
66 CGATCTGCTC
54795495 TCCGTCGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 25 0.39
88 2 0.03
89 36 0.56
90 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (89 bp):
GATGCCAAATCATCTTAGATCTAATTCGAAGTGAAAACATCCGAAAGCCAGATCTGCTATGTCTT
CGATCTGCTCCTTGTCAACGTAAG
Found at i:54803941 original size:22 final size:21
Alignment explanation
Indices: 54803916--54803963 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
54803906 TACAAATTAA
*
54803916 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAAATT-CAAAATCAT
* *
54803938 ATCTTCTAAAATTGAATATCAT
1 ATC-TCTAAAATTCAAAATCAT
54803960 ATCT
1 ATCT
54803964 AAGATTGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 13 0.59
23 8 0.36
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (21 bp):
ATCTCTAAAATTCAAAATCAT
Found at i:54803970 original size:19 final size:19
Alignment explanation
Indices: 54803942--54804032 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
54803932 AATCATATCT
* *
54803942 TCTAAAATTGAATATCATA
1 TCTAAGATTGCATATCATA
54803961 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
54803979 TCTAATATTG--TATCATA
1 TCTAAGATTGCATATCATA
54803996 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54804015 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
54804033 TGAAGATTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
17 15 0.23
18 15 0.23
19 35 0.54
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Done.