Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 194 of 202
Found at i:59143769 original size:22 final size:22
Alignment explanation
Indices: 59143741--59143787 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
59143731 TCCCCGAATC
*
59143741 ACTGATCGAAAAGGGGTTGCTA
1 ACTGATCGAAAAGGGATTGCTA
59143763 ACTGATCGAAAAGGGATTGCTA
1 ACTGATCGAAAAGGGATTGCTA
59143785 ACT
1 ACT
59143788 ACAGATTCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (22 bp):
ACTGATCGAAAAGGGATTGCTA
Found at i:59143803 original size:63 final size:63
Alignment explanation
Indices: 59143702--59143826 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
59143692 CCCGAATCAT
* * *
59143702 TGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAC
1 TGATCGAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAC
*
59143765 TGATCGAAAAGGGATTGCTAACTACAGATTCCCTGAATCACTGATCGAAAAGGGGTTGCTAA
1 TGATCGAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAA
59143827 TTGTAGATTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (63 bp):
TGATCGAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAC
Found at i:59143839 original size:104 final size:104
Alignment explanation
Indices: 59143659--59143867 Score: 337
Period size: 104 Copynumber: 2.0 Consensus size: 104
59143649 TCCCCGAATC
* * * *
59143659 ACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAAAAGGGGTTGCTAAG
1 ACTGATCAAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAG
59143724 TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
66 TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
* * *
59143763 ACTGATCGAAAAGGGATTGCTAACTACAGATTCCCTGAATCACTGATCGAAAAGGGGTTGCTAAT
1 ACTGATCAAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAG
* *
59143828 TGTAGATTCCCCGAATCATTGATCGAAAAGGGGTTGCTA
66 TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
59143867 A
1 A
59143868 GTGCAGATTC
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (104 bp):
ACTGATCAAAAAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTAAG
TGCAGATTCCCCGAATCACTGATCGAAAAGGGGTTGCTA
Found at i:59143848 original size:145 final size:145
Alignment explanation
Indices: 59143628--59143908 Score: 481
Period size: 145 Copynumber: 1.9 Consensus size: 145
59143618 CATTGAATGT
* * *
59143628 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
1 AAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
*
59143693 CCGAATCATTGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAGGGGT
66 CCGAATCATTGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAAGGGT
59143758 TGCTAACTGATCGAA
131 TGCTAACTGATCGAA
* * * *
59143773 AAGGGATTGCTAACTACAGATTCCCTGAATCACTGATCGAAAAGGGGTTGCTAATTGTAGATTCC
1 AAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
*
59143838 CCGAATCATTGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAAAAAGGGT
66 CCGAATCATTGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAAGGGT
59143903 TGCTAA
131 TGCTAA
59143909 GTGCAGATTC
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
145 127 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (145 bp):
AAGGGATTGCTAACTACAGATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCC
CCGAATCATTGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAAGGGT
TGCTAACTGATCGAA
Found at i:59144024 original size:15 final size:15
Alignment explanation
Indices: 59144004--59144034 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
59143994 CAGATTCCTC
59144004 GAGGGGTTGCTAAGT
1 GAGGGGTTGCTAAGT
59144019 GAGGGGTTGCTAAGT
1 GAGGGGTTGCTAAGT
59144034 G
1 G
59144035 CAGATTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.48, T:0.26
Consensus pattern (15 bp):
GAGGGGTTGCTAAGT
Found at i:59144024 original size:41 final size:41
Alignment explanation
Indices: 59143979--59144060 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
59143969 CTGATCAAAA
59143979 AGGGGTTGCTAAGTGCAGATTCCTCGAGGGGTTGCTAAGTG
1 AGGGGTTGCTAAGTGCAGATTCCTCGAGGGGTTGCTAAGTG
59144020 AGGGGTTGCTAAGTGCAGATTCCTCGAGGGGTTGCTAAGTG
1 AGGGGTTGCTAAGTGCAGATTCCTCGAGGGGTTGCTAAGTG
59144061 CTAATTCCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.15, G:0.39, T:0.27
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCAGATTCCTCGAGGGGTTGCTAAGTG
Found at i:59144024 original size:82 final size:81
Alignment explanation
Indices: 59143769--59144042 Score: 327
Period size: 82 Copynumber: 3.3 Consensus size: 81
59143759 GCTAACTGAT
* * * * * * *
59143769 CGAAAAGGGATTGCTAACTACAGATTCCCTGAATCACTGATCGAAAAGGGGTTGCTAATTGTAGA
1 CGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAAGGGTTGCTAAGTGCAGA
*
59143834 TTCCCCGAATCATTGA
66 TTCCCCGAAGCATTGA
*
59143850 TCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAAAAAGGGTTGCTAAGTGCAG
1 -CGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAAGGGTTGCTAAGTGCAG
* *
59143915 ATTCCCCTAATCATTGA
65 ATTCCCCGAAGCATTGA
*
59143932 TCGAAAAGGGGTTGCTAAGTGCAGATTCTCCGAATCACTGATC-AAAAAGGGGTTGCTAAGTGCA
1 -CGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAA-GGGTTGCTAAGTGCA
* * **
59143996 GATTCCTCGAGGGGTTG-
64 GATTCCCCGAAGCATTGA
* *
59144013 CTAAGTGAGGGGTTGCTAAGTGCAGATTCC
1 CGAA--AAGGGGTTGCTAAGTGCAGATTCC
59144043 TCGAGGGGTT
Statistics
Matches: 169, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
80 3 0.02
81 5 0.03
82 161 0.95
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (81 bp):
CGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAAAAAGGGTTGCTAAGTGCAGA
TTCCCCGAAGCATTGA
Found at i:59144026 original size:123 final size:123
Alignment explanation
Indices: 59143769--59144042 Score: 347
Period size: 123 Copynumber: 2.2 Consensus size: 123
59143759 GCTAACTGAT
* * * * *
59143769 CGAAAAGGGATTGCTAACTACAGATT-CCCTGAATCACTGATCGAAAAGGGGTTGCTAATTGTAG
1 CGAAAAGGGGTTGCTAAGTGCAGATTCCCCTGAATCACTGATCGAAAAGGGGTTGCTAAGTGCAG
* * *
59143833 ATTCCCCGAATCATTGATCGAAAAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGA
66 ATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAAGCATTGA
* *
59143891 TCGAAAAAGGGTTGCTAAGTGCAGATTCCCCT-AATCATTGATCGAAAAGGGGTTGCTAAGTGCA
1 -CGAAAAGGGGTTGCTAAGTGCAGATTCCCCTGAATCACTGATCGAAAAGGGGTTGCTAAGTGCA
* * * **
59143955 GATTCTCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCTCGAGGGGTTG-
65 GATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAAGCATTGA
* *
59144013 CTAAGTGAGGGGTTGCTAAGTGCAGATTCC
1 CGAA--AAGGGGTTGCTAAGTGCAGATTCC
59144043 TCGAGGGGTT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
121 3 0.02
123 123 0.95
124 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (123 bp):
CGAAAAGGGGTTGCTAAGTGCAGATTCCCCTGAATCACTGATCGAAAAGGGGTTGCTAAGTGCAG
ATTCCCCGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCCCGAAGCATTGA
Found at i:59146393 original size:15 final size:14
Alignment explanation
Indices: 59146359--59146394 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59146349 AATTTAGAGT
59146359 AAAT-AATAATTTA
1 AAATAAATAATTTA
59146372 AAATAAATAATTTA
1 AAATAAATAATTTA
59146386 AGAATAAAT
1 A-AATAAAT
59146395 CAAGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 10 0.48
15 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AAATAAATAATTTA
Found at i:59146508 original size:2 final size:2
Alignment explanation
Indices: 59146501--59146531 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59146491 AATTTTTGAG
59146501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59146532 GGAATCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59149615 original size:20 final size:20
Alignment explanation
Indices: 59149590--59149630 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
59149580 AAGGAGAGTG
59149590 TTGAGAAGAAAGTAGACAGT
1 TTGAGAAGAAAGTAGACAGT
59149610 TTGAGAAGAAAGTAGACAGT
1 TTGAGAAGAAAGTAGACAGT
59149630 T
1 T
59149631 AGCTGAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.29, T:0.22
Consensus pattern (20 bp):
TTGAGAAGAAAGTAGACAGT
Found at i:59150409 original size:14 final size:14
Alignment explanation
Indices: 59150390--59150418 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59150380 TGGGATTTGG
59150390 ATCACACAACTCTA
1 ATCACACAACTCTA
59150404 ATCACACAACTCTA
1 ATCACACAACTCTA
59150418 A
1 A
59150419 CAACATACAT
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:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
ATCACACAACTCTA
Found at i:59151580 original size:22 final size:23
Alignment explanation
Indices: 59151537--59151585 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
59151527 TAAAACAAGC
*
59151537 ATATATATAATAAATATTAAAATT
1 ATATATATAATAAATA-TAAAAAT
* *
59151561 ATATTTATATTAAATA-AAAAAT
1 ATATATATAATAAATATAAAAAT
59151583 ATA
1 ATA
59151586 AACTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
24 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATATATAATAAATATAAAAAT
Found at i:59151679 original size:17 final size:18
Alignment explanation
Indices: 59151652--59151685 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59151642 AAATTTATGT
*
59151652 AAATTATTATTTTTATTA
1 AAATTATTATTTATATTA
59151670 AAATTA-TATTTATATT
1 AAATTATTATTTATATT
59151686 GAATTATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTATTATTTATATTA
Found at i:59157378 original size:31 final size:29
Alignment explanation
Indices: 59157342--59157445 Score: 77
Period size: 31 Copynumber: 3.4 Consensus size: 29
59157332 TATATGTATT
59157342 TGAGGATCAAATTGATAGAATTTGTAAATA
1 TGAGGATCAAATTGATA-AATTTGTAAATA
* * *
59157372 TGGAGGATTAAATTTATTAAATTATTTAGAAT-
1 T-GAGGATCAAATTGA-TAAATT-TGTA-AATA
* *
59157404 T-AGGATCAAATTGATAAAATGTGTAAGTA
1 TGAGGATCAAATTGAT-AAATTTGTAAATA
*
59157433 TTGAGGATTAAAT
1 -TGAGGATCAAAT
59157446 GTGTTATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
28 2 0.04
29 4 0.07
30 17 0.30
31 25 0.44
32 6 0.11
33 3 0.05
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (29 bp):
TGAGGATCAAATTGATAAATTTGTAAATA
Found at i:59163777 original size:9 final size:9
Alignment explanation
Indices: 59163734--59163799 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
59163724 ATAGGAGGAT
59163734 ATTTTTTAA
1 ATTTTTTAA
* *
59163743 AATTTTAAA
1 ATTTTTTAA
**
59163752 TATTTTTTTGG
1 -A-TTTTTTAA
59163763 ATTTTTATAA
1 ATTTTT-TAA
59163773 ATTTTTT-A
1 ATTTTTTAA
*
59163781 CTTTTTTAA
1 ATTTTTTAA
59163790 ATTTTTTAA
1 ATTTTTTAA
59163799 A
1 A
59163800 ATTAATTAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
8 7 0.16
9 23 0.53
10 9 0.21
11 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:59163785 original size:17 final size:17
Alignment explanation
Indices: 59163765--59163797 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59163755 TTTTTTGGAT
59163765 TTTTATAAATTTTTTAC
1 TTTTATAAATTTTTTAC
*
59163782 TTTTTTAAATTTTTTA
1 TTTTATAAATTTTTTA
59163798 AAATTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATAAATTTTTTAC
Found at i:59164602 original size:16 final size:16
Alignment explanation
Indices: 59164581--59164614 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
59164571 TTTTCCTCTC
59164581 TTTTTTTAA-ATATTTA
1 TTTTTTTAACAT-TTTA
59164597 TTTTTTTAACATTTTA
1 TTTTTTTAACATTTTA
59164613 TT
1 TT
59164615 AGACCTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTAACATTTTA
Found at i:59167326 original size:13 final size:16
Alignment explanation
Indices: 59167296--59167327 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59167286 GTTGAACTAG
59167296 TTTTTACTATATATTT
1 TTTTTACTATATATTT
59167312 TTTTTACT-TA-ATTT
1 TTTTTACTATATATTT
59167326 TT
1 TT
59167328 AACAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTACTATATATTT
Found at i:59169376 original size:9 final size:10
Alignment explanation
Indices: 59169343--59169376 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
59169333 TGAAGGTAAT
59169343 AAATTTTATA
1 AAATTTTATA
59169353 AAATTTTATA
1 AAATTTTATA
59169363 AAATTTTA-A
1 AAATTTTATA
59169372 AAATT
1 AAATT
59169377 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATTTTATA
Found at i:59171520 original size:29 final size:33
Alignment explanation
Indices: 59171487--59171553 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
59171477 AAAATTAAGG
59171487 TTATAA-AAAAAT-TTAT-AAAAATAATA-ATA
1 TTATAAGAAAAATGTTATAAAAAATAATACATA
*
59171516 TTATAAGAATAATGTTATAAAAAATAATAGCATA
1 TTATAAGAAAAATGTTATAAAAAATAATA-CATA
59171550 TTAT
1 TTAT
59171554 GTATGTACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.19
30 5 0.16
31 4 0.12
32 10 0.31
34 7 0.22
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (33 bp):
TTATAAGAAAAATGTTATAAAAAATAATACATA
Found at i:59177860 original size:13 final size:13
Alignment explanation
Indices: 59177842--59177866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59177832 ACCAATACGA
59177842 CGTCGTTTTGAGT
1 CGTCGTTTTGAGT
59177855 CGTCGTTTTGAG
1 CGTCGTTTTGAG
59177867 CCTAAGCTTC
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:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (13 bp):
CGTCGTTTTGAGT
Found at i:59180034 original size:24 final size:23
Alignment explanation
Indices: 59179996--59180057 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
59179986 GGAAGAACCA
*
59179996 TATATCGGAAAGCTCAAGAGAGCT
1 TATATCGGGAAGCTCAAGAGAG-T
* * *
59180020 TATATCGGGATGCTCATGTGAGT
1 TATATCGGGAAGCTCAAGAGAGT
* *
59180043 TATAGCGGGACGCTC
1 TATATCGGGAAGCTC
59180058 TTACGATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (23 bp):
TATATCGGGAAGCTCAAGAGAGT
Found at i:59190187 original size:28 final size:28
Alignment explanation
Indices: 59190124--59190194 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
59190114 TTTAATAGCC
*
59190124 TATATTTTTATAATTTTAAAGAATTAAA
1 TATATTTTTATTATTTTAAAGAATTAAA
* *
59190152 TGAAATTTTTATTATTTTGAA-AATTAAA
1 T-ATATTTTTATTATTTTAAAGAATTAAA
59190180 -ATATATTTTATTATT
1 TATAT-TTTTATTATT
59190195 ACTAATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 3 0.08
27 10 0.27
28 8 0.22
29 16 0.43
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TATATTTTTATTATTTTAAAGAATTAAA
Found at i:59191344 original size:20 final size:20
Alignment explanation
Indices: 59191319--59191364 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
59191309 ATTTAAAGAA
59191319 AATTTTTAATCAACTCAATC
1 AATTTTTAATCAACTCAATC
* *
59191339 AATTTTTTATCAATTCAATC
1 AATTTTTAATCAACTCAATC
59191359 AATTTT
1 AATTTT
59191365 GCATCGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTTTAATCAACTCAATC
Found at i:59191378 original size:20 final size:20
Alignment explanation
Indices: 59191335--59191378 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
59191325 TAATCAACTC
** *
59191335 AATCAATTTTTTATCAATTC
1 AATCAATTTTGCATCAATTA
*
59191355 AATCAATTTTGCATCGATTA
1 AATCAATTTTGCATCAATTA
59191375 AATC
1 AATC
59191379 TTTTTTAGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (20 bp):
AATCAATTTTGCATCAATTA
Found at i:59192836 original size:24 final size:22
Alignment explanation
Indices: 59192809--59192855 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
59192799 TTTCTTTGAA
*
59192809 ATTTTTATGAACTTATTTATTTTT
1 ATTTTTATGAA-TTA-TAATTTTT
*
59192833 ATTTTTTTGAATTATAATTTTT
1 ATTTTTATGAATTATAATTTTT
59192855 A
1 A
59192856 AATTATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (22 bp):
ATTTTTATGAATTATAATTTTT
Found at i:59194969 original size:17 final size:18
Alignment explanation
Indices: 59194947--59194987 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
59194937 TTCAAAATGC
59194947 AATTAATTTAAA-TT-TTT
1 AATTAA-TTAAATTTATTT
59194964 AATTAATTAAATTTATTT
1 AATTAATTAAATTTATTT
59194982 AATTAA
1 AATTAA
59194988 AAACTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 8 0.36
18 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTAATTAAATTTATTT
Found at i:59195911 original size:23 final size:23
Alignment explanation
Indices: 59195885--59195937 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
59195875 TGGGCCAATC
*
59195885 ACTGTAATATCCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
59195908 ACTGTAATACCCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
*
59195931 ACAGTAA
1 ACTGTAA
59195938 GAAAGTAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (23 bp):
ACTGTAATACCCCGAAAATTACT
Found at i:59196521 original size:4 final size:4
Alignment explanation
Indices: 59196512--59196538 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
59196502 TATGAAGAGA
59196512 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
59196539 CTTTCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:59203520 original size:15 final size:16
Alignment explanation
Indices: 59203500--59203530 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
59203490 TAATTATAAA
59203500 AATATAAG-AGATATT
1 AATATAAGAAGATATT
59203515 AATATAAGAAGATATT
1 AATATAAGAAGATATT
59203531 TTTAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
AATATAAGAAGATATT
Found at i:59205013 original size:31 final size:31
Alignment explanation
Indices: 59204976--59205041 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
59204966 AACAACCCAA
*
59204976 TGACTTAAAT-AATAACTTTCGAATAGTTCAG
1 TGACTTAAATGAA-AACTTTCAAATAGTTCAG
*
59205007 TGACTTAAATGAAAACTTTTAAATAGTTCAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
59205038 TGAC
1 TGAC
59205042 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAG
Found at i:59213965 original size:89 final size:88
Alignment explanation
Indices: 59213852--59214146 Score: 256
Period size: 89 Copynumber: 3.3 Consensus size: 88
59213842 CATAGCAAGC
* * *
59213852 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCCTATCTCTCCGAAGTTGCAG
1 CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCTTATCTCTCCGAAGTTGCAG
59213917 TGGAGCAGACTGAAGATAGCGAAT
66 TGGAGCAGACT-AAGATAGCGAAT
* * * * * * * * **
59213941 CTTATTTTCCTGAAGTTTCAGTGGAACAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAA
1 CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAA---AT-TACT--AG-TCTTATCTCTCCGAA
* * * * *
59214006 GTTGTAGTAGAGCAGA-T--TATAGCAAAC
59 GTTGCAGTGGAGCAGACTAAGATAGCGAAT
* * * *
59214033 CTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTC-CCTGAAGTTGCA
1 CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCTTATCTCTCC-GAAGTTGCA
* *
59214097 GTGGAGTAAACTAAAGATAGCGAAT
65 GTGGAGCAGACT-AAGATAGCGAAT
59214122 CTTATATCCCTAAAGTTGCAGTGGA
1 CTTATATCCCTAAAGTTGCAGTGGA
59214147 ACGAATTGAA
Statistics
Matches: 158, Mismatches: 36, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
84 1 0.01
85 23 0.15
86 3 0.02
88 1 0.01
89 61 0.39
92 38 0.24
93 2 0.01
95 3 0.02
96 26 0.16
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (88 bp):
CTTATATCCCTAAAGTTGCAGTGGAGCAGGTTGAAATTACTAGTCTTATCTCTCCGAAGTTGCAG
TGGAGCAGACTAAGATAGCGAAT
Found at i:59214326 original size:44 final size:44
Alignment explanation
Indices: 59214209--59214564 Score: 207
Period size: 44 Copynumber: 7.9 Consensus size: 44
59214199 CTGATCATAG
* * * *
59214209 CAAACCTTATCTCCCTGAAA-TTGTAGTGGAGCAGACTGAAGATAA
1 CAAACCTTATCTCCCT-AAAGTTGCAGTGGAGCAGATTAAAG-CAA
* * * * *
59214254 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
* * * * **
59214298 CAAACCTTGTCTCCCTGAAGTTGAAGTGGAACA-AGTTAAAAATAAA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TT--AAAGCAA
* * * * *
59214344 CCAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATGGGCTA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTAA-A---GCAA
* * *
59214393 CAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGATTAAAGCCA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
* * *
59214437 TAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAG-ATA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCA-A
* * * * * * * * * *
59214481 CCAATCTCATCTCTCTGAAGTTGTAGTGGATCAAATTGAAGCTA
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
* * ** *
59214525 CTAATCC-CATCTCCCCGAAGTTGCAGTGGAGCGGATTAAA
1 C-AAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA
59214565 ACGATGAATC
Statistics
Matches: 237, Mismatches: 62, Indels: 25
0.73 0.19 0.08
Matches are distributed among these distances:
43 1 0.00
44 131 0.55
45 35 0.15
46 31 0.13
47 3 0.01
48 3 0.01
49 33 0.14
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (44 bp):
CAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCAA
Found at i:59214326 original size:89 final size:90
Alignment explanation
Indices: 59214209--59214470 Score: 232
Period size: 90 Copynumber: 2.9 Consensus size: 90
59214199 CTGATCATAG
* * * * * *
59214209 CAAACCTTATCTCCCTGAAATTGTAGTGGAGC-AGACTGAAGAT-AACCAATCTTATCTCTCTGA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAG-CTAAAAATAAACCAATCTTATCTCCCTAA
59214272 AGTTGCAGTGGAGCAGATTAAAGCCA
65 AGTTGCAGTGGAGCAGATTAAAGCCA
* * *
59214298 CAAACCTTGTCTCCCTGAAGTTGAAGTGGAACAAGTTAAAAATAAACCAATCTTATCTCCCTAAA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAGCTAAAAATAAACCAATCTTATCTCCCTAAA
* * *
59214363 GTTGCAGTGGAGTAGACTGAAGATGGGCTA
66 GTTGCAGTGGAGCAGA-TTAA-A---GCCA
* * * * * *
59214393 CAAATCTTATCTCCCTAAAATTGCAGTGGAGC-AGATTAAAGCCATAAA-C---CTTATCTCCCT
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAG-CTAAA--AATAAACCAATCTTATCTCCCT
59214453 AAAGTTGCAGTGGAGCAG
63 AAAGTTGCAGTGGAGCAG
59214471 GTTGAAGATA
Statistics
Matches: 143, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
89 33 0.23
90 36 0.25
91 3 0.02
92 1 0.01
93 28 0.20
94 2 0.01
95 34 0.24
96 1 0.01
97 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (90 bp):
CAAACCTTATCTCCCTGAAATTGAAGTGGAACAAGCTAAAAATAAACCAATCTTATCTCCCTAAA
GTTGCAGTGGAGCAGATTAAAGCCA
Found at i:59214328 original size:181 final size:182
Alignment explanation
Indices: 59213838--59214330 Score: 593
Period size: 181 Copynumber: 2.7 Consensus size: 182
59213828 GATGGATTGA
* * * * *
59213838 AGATCATAGCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATTACTAGTCCTATC
1 AGATCATAGCAAACCTTATCTCCCTGAAATTGCAGTGGAGCAGGTTGAAGATTACCAATCTTATC
* * * * *
59213902 TCTCCGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTTCCTGAAGTTTCAGTGGAA
66 TCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAA
** *
59213967 CAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTGTAGTAGAGC
131 CAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTACAATAGAGC
* *
59214019 AGATTATAGCAAACCTTATCTCCCT-AAAGTTACAGTGGAGCAGGTTGAAG-TTA-CAAGTCTTA
1 AGATCATAGCAAACCTTATCTCCCTGAAA-TTGCAGTGGAGCAGGTTGAAGATTACCAA-TCTTA
* * * *
59214081 TCTCCCTGAAGTTGCAGTGGAGTAAACTAAAGATAGCGAATCTTATATCCCTAAAGTTGCAGTGG
64 TCTCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGG
* * * *
59214146 AAC-GAATTGAAGTTATAAATTGTAGGTCTTATCTCTCTGAAGTTACAATAGAGC
129 AACAG-ATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTACAATAGAGC
* * ** *
59214200 TGATCATAGCAAACCTTATCTCCCTGAAATTGTAGTGGAGCAGACTGAAGATAACCAATCTTATC
1 AGATCATAGCAAACCTTATCTCCCTGAAATTGCAGTGGAGCAGGTTGAAGATTACCAATCTTATC
* ** * * * * *
59214265 TCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CAAACCTTGTCTCCCTGAAGTTGAAGTGGAA
66 TCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAA
59214329 CA
131 CA
59214331 AGTTAAAAAT
Statistics
Matches: 262, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
180 4 0.02
181 216 0.82
182 39 0.15
183 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (182 bp):
AGATCATAGCAAACCTTATCTCCCTGAAATTGCAGTGGAGCAGGTTGAAGATTACCAATCTTATC
TCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAA
CAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTAAAGTTACAATAGAGC
Found at i:59214369 original size:90 final size:89
Alignment explanation
Indices: 59214209--59214470 Score: 244
Period size: 95 Copynumber: 2.9 Consensus size: 89
59214199 CTGATCATAG
* * * * * *
59214209 CAAACCTTATCTCCCTGAAATTGTAGTGGAGCAGACTGAAGATAACCAATCTTATCTCTCTGAAG
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGACTAAAAATAACCAATCTTATCTCCCTAAAG
59214274 TTGCAGTGGAGCAGATTAAAGCCA
66 TTGCAGTGGAGCAGATTAAAGCCA
* * *
59214298 CAAACCTTGTCTCCCTGAAGTTGAAGTGGAACA-AGTTAAAAATAAACCAATCTTATCTCCCTAA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGA-CTAAAAAT-AACCAATCTTATCTCCCTAA
* * *
59214362 AGTTGCAGTGGAGTAGACTGAAGATGGGCTA
64 AGTTGCAGTGGAGCAGA-TTAA-A---GCCA
* * * * * * *
59214393 CAAATCTTATCTCCCTAAAATTGCAGTGGAGCAGATTAAAGCCAT-A--AACCTTATCTCCCTAA
1 CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGACTAAA--AATAACCAATCTTATCTCCCTAA
59214455 AGTTGCAGTGGAGCAG
64 AGTTGCAGTGGAGCAG
59214471 GTTGAAGATA
Statistics
Matches: 142, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
88 1 0.01
89 34 0.24
90 34 0.24
91 3 0.02
92 1 0.01
93 30 0.21
95 36 0.25
96 1 0.01
97 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (89 bp):
CAAACCTTATCTCCCTGAAATTGAAGTGGAACAGACTAAAAATAACCAATCTTATCTCCCTAAAG
TTGCAGTGGAGCAGATTAAAGCCA
Found at i:59214465 original size:139 final size:133
Alignment explanation
Indices: 59214214--59214564 Score: 364
Period size: 139 Copynumber: 2.6 Consensus size: 133
59214204 CATAGCAAAC
* * * *
59214214 CTTATCTCCCTGAAA-TTGTAGTGGAGCAGACTGAAGATAACCAATCTTATCTCTCTGAAGTTGC
1 CTTATCTCCCT-AAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATCTCCCTAAAATTGC
* *
59214278 AGTGGAGCAGATTAAAGCCACAAACCTTGTCTCCCTGAAGTTGAAGTGGAACAAGTTAAAAATAA
65 AGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGAAGTGGAACAAGTTAAAAAT--
59214343 ACCAAT
128 ACCAAT
* * *
59214349 CTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATGGGCTACAAATCTTATCTCCCTAAAAT
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGAT----AACAAATCTTATCTCCCTAAAAT
* * * * * *
59214414 TGCAGTGGAGCAGATTAAAGCCATAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGA
62 TGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGAAGTGGAACAAGTTAAAAA
59214479 TACCAAT
127 TACCAAT
* * * * * * * * ** ** *
59214486 CTCATCTCTCTGAAGTTGTAGTGGATCAAATTGAAGCT-ACTAATCCCATCTCCCCGAAGTTGCA
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATCTCCCTAAAATTGCA
*
59214550 GTGGAGCGGATTAAA
66 GTGGAGCAGATTAAA
59214565 ACGATGAATC
Statistics
Matches: 180, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
132 34 0.19
134 3 0.02
135 32 0.18
137 35 0.19
139 76 0.42
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (133 bp):
CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATCTCCCTAAAATTGCA
GTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGAAGTGGAACAAGTTAAAAATACC
AAT
Found at i:59222577 original size:118 final size:120
Alignment explanation
Indices: 59222437--59222678 Score: 434
Period size: 121 Copynumber: 2.0 Consensus size: 120
59222427 TGTTTGAATG
*
59222437 AATATGAACTTGAATTTTCATATAGTGTGTAC-AA-ATAGATTTTTTATGTCATTTTTCTTGTAT
1 AATATGAACTTGAATTTTCATATAGTGTGTACAAATATAGATTTTTTATGTCAATTTTCTTGTAT
59222500 GAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
66 GAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
*
59222555 AATATGAACTTGAATTTTCATATAGTGTGTACAAATTATAGATTTTTTATGTTAATTTTCTTGTA
1 AATATGAACTTGAATTTTCATATAGTGTGTACAAA-TATAGATTTTTTATGTCAATTTTCTTGTA
*
59222620 TGAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATATT
65 TGAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
59222676 AAT
1 AAT
59222679 GTCACATTAA
Statistics
Matches: 118, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
118 32 0.27
119 2 0.02
121 84 0.71
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (120 bp):
AATATGAACTTGAATTTTCATATAGTGTGTACAAATATAGATTTTTTATGTCAATTTTCTTGTAT
GAAGATAAACTTGTCTTTTTAAAGAAAATTGGGTATGAATTTCCTACCTTATAAT
Found at i:59222689 original size:11 final size:11
Alignment explanation
Indices: 59222673--59222698 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59222663 CCTACCTTAT
59222673 ATTAATGTCAC
1 ATTAATGTCAC
59222684 ATTAATGTCAC
1 ATTAATGTCAC
59222695 ATTA
1 ATTA
59222699 CTTAATTAGA
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:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (11 bp):
ATTAATGTCAC
Found at i:59225602 original size:14 final size:15
Alignment explanation
Indices: 59225578--59225618 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
59225568 TGGGATAGTG
59225578 TTTTATCTTTTTTA-T
1 TTTTAT-TTTTTTATT
59225593 TTTTA-TTTTTTATT
1 TTTTATTTTTTTATT
59225607 TTTTATTTTTTT
1 TTTTATTTTTTT
59225619 CAAATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.29
14 6 0.25
15 11 0.46
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTATTTTTTTATT
Found at i:59225617 original size:7 final size:7
Alignment explanation
Indices: 59225585--59225617 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
59225575 GTGTTTTATC
59225585 TTTTTTA
1 TTTTTTA
59225592 -TTTTTA
1 TTTTTTA
59225598 TTTTTTA
1 TTTTTTA
59225605 TTTTTTA
1 TTTTTTA
59225612 TTTTTT
1 TTTTTT
59225618 TCAAATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:59226383 original size:18 final size:18
Alignment explanation
Indices: 59226352--59226400 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
59226342 GGCCAATCTA
*
59226352 GGCGTGT-TGGCCACACG
1 GGCGTGTGTGCCCACACG
59226369 GGCGTGTGTGCCCACACG
1 GGCGTGTGTGCCCACACG
* * *
59226387 AGCATGTGGGCCCA
1 GGCGTGTGTGCCCA
59226401 TAATTCTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.14, C:0.31, G:0.39, T:0.16
Consensus pattern (18 bp):
GGCGTGTGTGCCCACACG
Found at i:59231604 original size:2 final size:2
Alignment explanation
Indices: 59231597--59231703 Score: 178
Period size: 2 Copynumber: 51.5 Consensus size: 2
59231587 GTTAGGTGAC
59231597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59231639 TA GTA GTA GTA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA -TA -TA -TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59231683 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
59231704 GCGTGTGTGT
Statistics
Matches: 104, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 93 0.89
3 11 0.11
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:59234084 original size:99 final size:99
Alignment explanation
Indices: 59233913--59234106 Score: 318
Period size: 99 Copynumber: 2.0 Consensus size: 99
59233903 TATATGTTTC
* * * *
59233913 GACAGCACATAGTAATTGAATGAGTGTAATAATTCTTAGGGTAGTAATTACACTCTCTTGTAATT
1 GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
*
59233978 ACAAAGAATTAG-AATTCCCTAGATGTGTTTTTTG
66 ACAAAGAATT-GTAATTCCCTAGACGTGTTTTTTG
59234012 GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
1 GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
*
59234077 ATAAAGAATTGTAATTCCCTAGACGTGTTT
66 ACAAAGAATTGTAATTCCCTAGACGTGTTT
59234107 AGCTAGCAGA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 1 0.01
99 87 0.99
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (99 bp):
GACAGAACAGAGTAATTGAATGAGTGTAATAATTATTAAGGTAGTAATTACACTCTCTTGTAATT
ACAAAGAATTGTAATTCCCTAGACGTGTTTTTTG
Found at i:59234217 original size:16 final size:17
Alignment explanation
Indices: 59234196--59234240 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
59234186 TATATTTTTA
59234196 AAAAAATAATTACTAT-
1 AAAAAATAATTACTATG
* *
59234212 AAAAAATTATTAGTATG
1 AAAAAATAATTACTATG
59234229 ATAAAAATAATT
1 A-AAAAATAATT
59234241 TCTGGACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 1 0.04
18 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAAAATAATTACTATG
Found at i:59236618 original size:57 final size:57
Alignment explanation
Indices: 59236503--59236649 Score: 197
Period size: 57 Copynumber: 2.5 Consensus size: 57
59236493 ATTGACGGTA
59236503 AAAAAGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAAGATCTAGCCCGGACGGGTGAT-C--T-CTGATATAGCCCTCCCGAAGAATATGTG-G
*
59236565 AAAAAGATCTAGCCCGGATGGGTGATCT-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCTCTGATATAGCCCTCCCGAAGAATATGTGG
* * *
59236621 AAAATGGATTTAGCCCGGACGGGTAATCT
1 AAAA-AGATCTAGCCCGGACGGGTGATCT
59236650 GAATTAGGGT
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
56 5 0.06
57 47 0.59
59 1 0.01
61 1 0.01
62 25 0.32
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCTCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:59236822 original size:67 final size:67
Alignment explanation
Indices: 59236714--59236848 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
59236704 GTAATTGTCG
*
59236714 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
59236779 TC
66 TC
* *
59236781 TTGCATGGGATTTAGCCTAGACTGGTAATCCTGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGGGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
59236846 TC
66 TC
59236848 T
1 T
59236849 AAATTGGAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (67 bp):
TTGCAGGGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
TC
Found at i:59239955 original size:11 final size:11
Alignment explanation
Indices: 59239939--59239963 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59239929 TCATTTACTA
59239939 AAAAAATGGAC
1 AAAAAATGGAC
59239950 AAAAAATGGAC
1 AAAAAATGGAC
59239961 AAA
1 AAA
59239964 TTAGTCCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAAAATGGAC
Found at i:59245495 original size:30 final size:30
Alignment explanation
Indices: 59245451--59245513 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
59245441 ACTTAACAAG
59245451 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
59245481 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
59245511 CAA
1 CAA
59245514 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:59256444 original size:32 final size:32
Alignment explanation
Indices: 59256408--59256487 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
59256398 AAATATTTTT
* **
59256408 CAGATCTATATCATGAAA-ATTATATCCATTAA
1 CAGATCTATAACATGAAAGA-TATATCCACAAA
* *
59256440 CAGATCTAAAACAT-AAAGATATATTCACAAA
1 CAGATCTATAACATGAAAGATATATCCACAAA
59256471 CAGATCTATAACATGAA
1 CAGATCTATAACATGAA
59256488 GTTATATACC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 25 0.62
32 15 0.38
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (32 bp):
CAGATCTATAACATGAAAGATATATCCACAAA
Found at i:59263455 original size:47 final size:47
Alignment explanation
Indices: 59263386--59263479 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
59263376 GATCGAACTA
59263386 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
1 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
*
59263433 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTGAATCC
1 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
59263480 GACATATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (47 bp):
AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
Found at i:59269723 original size:18 final size:18
Alignment explanation
Indices: 59269700--59269736 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
59269690 TACAATGATA
59269700 AAAAACCTTGCCTGCTAG
1 AAAAACCTTGCCTGCTAG
59269718 AAAAACCTTGCCTGCTAG
1 AAAAACCTTGCCTGCTAG
59269736 A
1 A
59269737 GTATCACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (18 bp):
AAAAACCTTGCCTGCTAG
Found at i:59278141 original size:6 final size:6
Alignment explanation
Indices: 59278130--59278156 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59278120 AGGTAGTTCC
59278130 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
59278157 TAATCTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:59297929 original size:26 final size:26
Alignment explanation
Indices: 59297894--59297961 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
59297884 GGTCCAACAA
59297894 TTAAGGCTTCAATTGGTAGGATTTAAG
1 TTAA-GCTTCAATTGGTAGGATTTAAG
59297921 TTAAGCTTCAATTGGTAGGATTTAAG
1 TTAAGCTTCAATTGGTAGGATTTAAG
59297947 TTAAGCTTCAATTGG
1 TTAAGCTTCAATTGG
59297962 GAGGTCATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (26 bp):
TTAAGCTTCAATTGGTAGGATTTAAG
Found at i:59299984 original size:28 final size:28
Alignment explanation
Indices: 59299953--59300009 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
59299943 TCTTGACTAG
*
59299953 AGCTTATTCAATTTTATGCTTTGGTTGA
1 AGCTTATTCAATTTTATGCTTCGGTTGA
59299981 AGCTTATTCAATTTTATGCTTCGGTTGA
1 AGCTTATTCAATTTTATGCTTCGGTTGA
59300009 A
1 A
59300010 AGCCAATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (28 bp):
AGCTTATTCAATTTTATGCTTCGGTTGA
Found at i:59306764 original size:10 final size:10
Alignment explanation
Indices: 59306749--59306776 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
59306739 TGAACACCAT
59306749 AAACAAAAGA
1 AAACAAAAGA
59306759 AAACAAAAGA
1 AAACAAAAGA
59306769 AAACAAAA
1 AAACAAAA
59306777 AAACAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (10 bp):
AAACAAAAGA
Found at i:59307232 original size:4 final size:4
Alignment explanation
Indices: 59307223--59307269 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
59307213 TCATCAAAGT
* * * *
59307223 TACA TACA TACA TACA CACA TACA TGCA TGCA TACA TATA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
59307270 GTATACATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:59310942 original size:94 final size:95
Alignment explanation
Indices: 59310781--59310969 Score: 353
Period size: 94 Copynumber: 2.0 Consensus size: 95
59310771 GGTCTAGGTT
59310781 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
1 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
59310846 CCAC-AAAACTAGGTAGGTTTATGACAACA
66 CCACAAAAACTAGGTAGGTTTATGACAACA
* *
59310875 TCTTCACTACTGGTGAAGAATCTAAGGGAAGACTAAGAACAATAATGTTGAAACTACATATAAAC
1 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
59310940 CCACAAAAACTAGGTAGGTTTATGACAACA
66 CCACAAAAACTAGGTAGGTTTATGACAACA
59310970 CAACAATACC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 67 0.73
95 25 0.27
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.23
Consensus pattern (95 bp):
TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
CCACAAAAACTAGGTAGGTTTATGACAACA
Found at i:59311212 original size:2 final size:2
Alignment explanation
Indices: 59311205--59311232 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59311195 CATTGTATGT
59311205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59311233 CATACACTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59327305 original size:13 final size:13
Alignment explanation
Indices: 59327287--59327316 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
59327277 GGCACTATTG
*
59327287 ACAAAATTGGGTC
1 ACAAAATTAGGTC
59327300 ACAAAATTAGGTC
1 ACAAAATTAGGTC
59327313 ACAA
1 ACAA
59327317 CATGGGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (13 bp):
ACAAAATTAGGTC
Found at i:59328880 original size:17 final size:17
Alignment explanation
Indices: 59328858--59328890 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
59328848 TATTTAATTT
59328858 TTATTT-ATAAATATATA
1 TTATTTAAT-AATATATA
59328875 TTATTTAATAATATAT
1 TTATTTAATAATATAT
59328891 TTGTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTAATAATATATA
Found at i:59335037 original size:9 final size:9
Alignment explanation
Indices: 59335023--59335059 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
59335013 TATAGTTTGA
59335023 TATTCGAAT
1 TATTCGAAT
59335032 TATTCGAAT
1 TATTCGAAT
* *
59335041 TATTTGAGT
1 TATTCGAAT
59335050 TATTCGAAT
1 TATTCGAAT
59335059 T
1 T
59335060 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:59335130 original size:9 final size:9
Alignment explanation
Indices: 59335113--59335143 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
59335103 TCGAGTTGAT
59335113 TCGAATAAC
1 TCGAATAAC
*
59335122 TCGATTAAC
1 TCGAATAAC
59335131 TCGAATAAC
1 TCGAATAAC
59335140 TCGA
1 TCGA
59335144 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:59337155 original size:10 final size:10
Alignment explanation
Indices: 59337140--59337164 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59337130 AGGCTTAATT
59337140 AAAAGAAATA
1 AAAAGAAATA
59337150 AAAAGAAATA
1 AAAAGAAATA
59337160 AAAAG
1 AAAAG
59337165 GATCTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAAGAAATA
Found at i:59338479 original size:2 final size:2
Alignment explanation
Indices: 59338472--59338542 Score: 92
Period size: 2 Copynumber: 36.0 Consensus size: 2
59338462 AATAAGCATG
* * *
59338472 TA TA TA TA TA TG TA TA TA TA TA -A TGC TA GA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
59338513 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59338543 AAAGTTATTG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
1 2 0.03
2 58 0.95
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:59339333 original size:83 final size:81
Alignment explanation
Indices: 59339207--59339429 Score: 313
Period size: 83 Copynumber: 2.7 Consensus size: 81
59339197 AGGCTAAGCG
*
59339207 CCTAGCAGGCTACGTGCCGATGA-TTGAATCGGGTATAAACCTAGCAGGCTATGTGCCGGTGATT
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTATAAACCTAGCAGGCTATGTGCCGGTGATT
* *
59339271 TGAATTGTGTTATAAA
66 TGAATCGGGTTATAAA
* *
59339287 CCTAGCAGGCCTATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGCTACGTGCCGGTGA
1 CCTAGCAGG-CTACGTGCCGGTGATTTGAATCGGG-TATAAACCTAGCAGGCTATGTGCCGGTGA
59339352 TTTGAATCGGGTTATAAA
64 TTTGAATCGGGTTATAAA
* * * ** *
59339370 CCTAGCAGGCTACGTGCCGGTGATCTGAATCAAGCTATAAGTCTAGCAGTCTATGTGCCG
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATC-GGGTATAAACCTAGCAGGCTATGTGCCG
59339430 TTGAATCTAT
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
80 9 0.07
81 12 0.10
82 51 0.40
83 54 0.43
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (81 bp):
CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTATAAACCTAGCAGGCTATGTGCCGGTGATT
TGAATCGGGTTATAAA
Found at i:59339429 original size:41 final size:41
Alignment explanation
Indices: 59339207--59339400 Score: 311
Period size: 41 Copynumber: 4.8 Consensus size: 41
59339197 AGGCTAAGCG
*
59339207 CCTAGCAGGCTACGTGCCGATGA-TTGAATCGGG-TATAAA
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
* * *
59339246 CCTAGCAGGCTATGTGCCGGTGATTTGAATTGTGTTATAAA
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
*
59339287 CCTAGCAGGCCTATGTGCCGGTGATTTGAATCGGGTTATAAA
1 CCTAGCAGG-CTACGTGCCGGTGATTTGAATCGGGTTATAAA
59339329 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
*
59339370 CCTAGCAGGCTACGTGCCGGTGATCTGAATC
1 CCTAGCAGGCTACGTGCCGGTGATTTGAATC
59339401 AAGCTATAAG
Statistics
Matches: 144, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
39 21 0.15
40 8 0.06
41 76 0.53
42 39 0.27
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (41 bp):
CCTAGCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAA
Found at i:59344129 original size:32 final size:32
Alignment explanation
Indices: 59344088--59344152 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
59344078 AAATCCTTAA
59344088 TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
1 TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
*
59344120 TGTTTTTGTTTTTCTAGAGCACTATTGTAGGT
1 TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
59344152 T
1 T
59344153 TGAAGGCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.17, C:0.09, G:0.22, T:0.52
Consensus pattern (32 bp):
TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
Found at i:59345067 original size:2 final size:2
Alignment explanation
Indices: 59345060--59345089 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59345050 ATATTCAATG
59345060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59345090 ATTATGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59347107 original size:21 final size:20
Alignment explanation
Indices: 59347081--59347135 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
59347071 TATAGAGATA
*
59347081 AAAAATGATATTAAATTTAT
1 AAAAATGATATTAAAGTTAT
59347101 AATAAAT-A-ATGTACAAGTT-T
1 AA-AAATGATAT-TA-AAGTTAT
59347121 AAAAATGATATTAAA
1 AAAAATGATATTAAA
59347136 AAATTACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
19 8 0.28
20 11 0.38
21 10 0.34
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAAATGATATTAAAGTTAT
Found at i:59350888 original size:18 final size:19
Alignment explanation
Indices: 59350865--59350906 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
59350855 AGTACAGGGA
59350865 CTAATAGAAAAT-TTT-AAC
1 CTAATA-AAAATCTTTGAAC
*
59350883 CTAATATAAATCTTTGAAC
1 CTAATAAAAATCTTTGAAC
59350902 CTAAT
1 CTAAT
59350907 TGCCGTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (19 bp):
CTAATAAAAATCTTTGAAC
Found at i:59358523 original size:27 final size:27
Alignment explanation
Indices: 59358493--59358552 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
59358483 ATAGGTGGTG
*
59358493 CCTATCC-AGTAGGCGCCACTGGTGACT
1 CCTATCCGA-TAGGCGCCACGGGTGACT
* * *
59358520 CCTATTCGATAGGTGCCTCGGGTGACT
1 CCTATCCGATAGGCGCCACGGGTGACT
59358547 CCTATC
1 CCTATC
59358553 AATAAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.32, G:0.25, T:0.27
Consensus pattern (27 bp):
CCTATCCGATAGGCGCCACGGGTGACT
Found at i:59358597 original size:16 final size:16
Alignment explanation
Indices: 59358576--59358612 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
59358566 AAATAAAAAT
59358576 AAAATTACATTACA-AA
1 AAAATTACATTA-ATAA
59358592 AAAATTACATTAATAA
1 AAAATTACATTAATAA
59358608 AAAAT
1 AAAAT
59358613 CACAAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATTACATTAATAA
Found at i:59358771 original size:99 final size:102
Alignment explanation
Indices: 59358589--59358840 Score: 314
Period size: 99 Copynumber: 2.5 Consensus size: 102
59358579 ATTACATTAC
* *
59358589 AAAAAAA-TTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACTT
1 AAAAAAATTTACAGTACTAAAAAATCACAAAACAC---A--AAACACTAACAATTTATATAACTT
* * *
59358653 AATCATAAATTATTAACAAAATAACTATAAAATTATTTTTAA
61 AATCATAAATAACTAACAAAATAACTATAAAAATATTTTTAA
* *
59358695 AAAAAAATTT-CATTACTAAAAAATCACAAATCACAAAACACTAACAATTTATA-AAC-TAATCA
1 AAAAAAATTTACAGTACTAAAAAATCACAAAACACAAAACACTAACAATTTATATAACTTAATCA
* **
59358757 TAAATAACTGACAAAATAACTATAAAAATATTTTTTT
66 TAAATAACTAACAAAATAACTATAAAAATATTTTTAA
* * *
59358794 AAAATATTTTACAGTACTAAAAAATCACAAAACACAAAAAACTAACA
1 AAAAAAATTTACAGTACTAAAAAATCACAAAACACAAAACACTAACA
59358841 TAAATTACTA
Statistics
Matches: 131, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
99 45 0.34
100 36 0.27
101 18 0.14
103 1 0.01
106 29 0.22
107 2 0.02
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.28
Consensus pattern (102 bp):
AAAAAAATTTACAGTACTAAAAAATCACAAAACACAAAACACTAACAATTTATATAACTTAATCA
TAAATAACTAACAAAATAACTATAAAAATATTTTTAA
Found at i:59358864 original size:12 final size:12
Alignment explanation
Indices: 59358827--59358870 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
59358817 ATCACAAAAC
59358827 ACAAAA-AACTA
1 ACAAAATAACTA
*
59358838 ACATAAATTACTA
1 ACA-AAATAACTA
*
59358851 ACAAAATAATTA
1 ACAAAATAACTA
59358863 ACAAAATA
1 ACAAAATA
59358871 GTTTTACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 3 0.11
12 18 0.64
13 7 0.25
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (12 bp):
ACAAAATAACTA
Found at i:59364053 original size:173 final size:173
Alignment explanation
Indices: 59363764--59364110 Score: 685
Period size: 173 Copynumber: 2.0 Consensus size: 173
59363754 GTTTAATCCA
59363764 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
1 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
59363829 CTATTGAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAATGC
66 CTATTGAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAATGC
59363894 TTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
131 TTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
59363937 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
1 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
*
59364002 CTATTGAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAATTAAAATGC
66 CTATTGAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAATGC
59364067 TTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
131 TTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
59364110 A
1 A
59364111 CGAATATAAT
Statistics
Matches: 173, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 173 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (173 bp):
AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
CTATTGAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAATGC
TTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
Found at i:59365315 original size:54 final size:54
Alignment explanation
Indices: 59365241--59365350 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
59365231 AAACCAAAAA
* *
59365241 TCCCAATATGAACAGTCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
1 TCCCAAAATGAACAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
*
59365295 TCCCAAAATGAATAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
1 TCCCAAAATGAACAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
59365349 TC
1 TC
59365351 GAAAACCAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.22
Consensus pattern (54 bp):
TCCCAAAATGAACAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
Found at i:59366913 original size:68 final size:68
Alignment explanation
Indices: 59366804--59366940 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
59366794 TCATTTTTCG
*
59366804 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTGTAGGGGCAAAATGGTAATTGTGCCTAAGATG
1 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
59366869 TGA
66 TGA
59366872 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
1 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
59366937 TGA
66 TGA
59366940 A
1 A
59366941 TTGGATTGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (68 bp):
AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
TGA
Found at i:59367512 original size:25 final size:24
Alignment explanation
Indices: 59367441--59367520 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 24
59367431 CCGTTATATA
* *
59367441 GCTCTTCGGAGCTTCCCGACTAAAG
1 GCTCTTCGGAGCTTCCC-AATAATG
**
59367466 GCTCTTTTATGAGCTTCCCAATTAATG
1 GCTC--TTCGGAGCTTCCCAA-TAATG
*
59367493 GCTCTTCGGAGCTTCCCAATATTG
1 GCTCTTCGGAGCTTCCCAATAATG
59367517 GCTC
1 GCTC
59367521 GCTTGAACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
24 8 0.18
25 17 0.38
26 1 0.02
27 19 0.42
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.33
Consensus pattern (24 bp):
GCTCTTCGGAGCTTCCCAATAATG
Found at i:59367602 original size:25 final size:24
Alignment explanation
Indices: 59367548--59367619 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
59367538 ATGTGCTCGT
* *
59367548 ATGAGGTTCCCATTAATGGCTCTC
1 ATGAGCTTCCCATTAATGGCTCAC
*
59367572 -TGGAGCTTCCCGTTACATGGCTCAC
1 AT-GAGCTTCCCATTA-ATGGCTCAC
59367597 ATGAGCTT-CCATTATATGGCTCA
1 ATGAGCTTCCCATTA-ATGGCTCA
59367620 AGAGATAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 24 0.60
25 14 0.35
26 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (24 bp):
ATGAGCTTCCCATTAATGGCTCAC
Found at i:59373285 original size:17 final size:17
Alignment explanation
Indices: 59373263--59373296 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59373253 TTAATATAAA
59373263 TAAATAAATTTCCCAAT
1 TAAATAAATTTCCCAAT
* *
59373280 TAAATAATTTTCTCAAT
1 TAAATAAATTTCCCAAT
59373297 GCAATTCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAAATTTCCCAAT
Found at i:59376151 original size:31 final size:28
Alignment explanation
Indices: 59376108--59376164 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
59376098 TCTCAAATGT
*
59376108 ACACAGCCATGTGAACCGCCCGTGTGGGG
1 ACACAGCCATGTG-ACCACCCGTGTGGGG
*
59376137 ACACACGCCAATGTGGCCACCCGTGTGG
1 ACACA-GCC-ATGTGACCACCCGTGTGG
59376165 TTACGAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 14 0.58
31 5 0.21
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.14
Consensus pattern (28 bp):
ACACAGCCATGTGACCACCCGTGTGGGG
Found at i:59376729 original size:11 final size:11
Alignment explanation
Indices: 59376713--59376752 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
59376703 CTCCCACAAC
59376713 TAAAATAAAAA
1 TAAAATAAAAA
*
59376724 TAAAATAGAAA
1 TAAAATAAAAA
59376735 TAAAATAATAAA
1 TAAAATAA-AAA
*
59376747 CAAAAT
1 TAAAAT
59376753 CTTCTATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:59379896 original size:19 final size:21
Alignment explanation
Indices: 59379860--59379900 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
59379850 TTCTTTGCTC
59379860 TTTTGCTTCGAGTTTGCTTTTG
1 TTTTGCTTCGAG-TTGCTTTTG
59379882 TTTTGCTTCG-G-TGCTTTTG
1 TTTTGCTTCGAGTTGCTTTTG
59379901 AGAATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.02, C:0.15, G:0.24, T:0.59
Consensus pattern (21 bp):
TTTTGCTTCGAGTTGCTTTTG
Found at i:59386237 original size:22 final size:22
Alignment explanation
Indices: 59386204--59386259 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
59386194 ATTTTGTATT
*
59386204 AATTTATCAAATTGAAC-TAAA
1 AATTTATTAAATTGAACTTAAA
* *
59386225 AATATTATTAAATTTATCTTAAA
1 AAT-TTATTAAATTGAACTTAAA
59386248 AATTTA-TAAATT
1 AATTTATTAAATT
59386260 TTATAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.30
22 14 0.47
23 7 0.23
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTATTAAATTGAACTTAAA
Found at i:59386762 original size:22 final size:23
Alignment explanation
Indices: 59386737--59386782 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
59386727 TTTAAACATC
59386737 AATTACAAAA-TTAAAATAAAAA
1 AATTACAAAAGTTAAAATAAAAA
* *
59386759 AATTTCAAAAGGTTAAAATGAAAA
1 AATTACAAAA-GTTAAAATAAAAA
59386783 TTTACTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (23 bp):
AATTACAAAAGTTAAAATAAAAA
Found at i:59388014 original size:2 final size:2
Alignment explanation
Indices: 59388007--59388032 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59387997 ATGTAGGTTC
59388007 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59388033 TCCCCTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59395867 original size:50 final size:50
Alignment explanation
Indices: 59395805--59396595 Score: 633
Period size: 50 Copynumber: 15.8 Consensus size: 50
59395795 TAATTAACTA
* * **
59395805 CAATGTCGGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
59395855 CAATATCGGGGAAGCCAGATTCACCGTTGTAGCTTCAAT-TCGTTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCT-TTTTAATTG
* * * *
59395905 CACCT-CCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTG
1 CA-ATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
59395955 CAATGCCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * * **
59396005 CACCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * *
59396055 CAATGTC-GGGAAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTCACTG
1 CAATGTCAGGG-AAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * **
59396105 CACTG-CTAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTC-AGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * *
59396155 CAATGTC-GGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTG
1 CAATGTCAGGG-AAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * **
59396205 CACTG-CTAGGGAAGTAAGATTCATCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTC-AGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
59396255 CAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * * ** *
59396305 CACCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** ** *
59396355 CAATGTCGGGGAAGCAATATTCACCATTGTAGCTTCAATATGCTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * ** * * *
59396405 CACCGCCAGGGAAGTAAGATTTGCCATTGT-GAATTCAACCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAG-CTTCAATCTTTTTAATTG
* * * ** * *
59396455 CAATGTCAGGGAAGCAAGATTCACTGGTGTAGCTTCAATCTGTTCCACTA
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * * *
59396505 CACCGCCAAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
*
59396555 CAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCT
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCT
59396596 GTTCCACTAC
Statistics
Matches: 567, Mismatches: 160, Indels: 28
0.75 0.21 0.04
Matches are distributed among these distances:
49 11 0.02
50 545 0.96
51 11 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (50 bp):
CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
Found at i:59395939 original size:100 final size:100
Alignment explanation
Indices: 59395813--59396659 Score: 1246
Period size: 100 Copynumber: 8.5 Consensus size: 100
59395803 TACAATGTCG
* * *
59395813 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCCAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
59395878 CCGTTGTAGCTTCAAT-TCGTTCCACTGCACCTCCA
66 CCGTTGTAGCTTCAATCT-GTTCCACTGCACCGCCA
* * * *
59395913 GGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
59395978 CCGTTGTAGCTTCAATCTATTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
*
59396013 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGAAAGCAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
59396078 CCGTTGTAGCTTCAATCTGTTTCACTGCACTGCTA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
59396113 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGAAAGTAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
59396178 CCGTTGTAGCTTCAATCTGTTTCACTGCACTGCTA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
** *
59396213 GGGAAGTAAGATTCATCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
59396278 CCATTGTAGCTTCAATCTGTTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* *
59396313 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAATATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
59396378 CCATTGTAGCTTCAATATGCTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * ** * *
59396413 GGGAAGTAAGATTTGCCATTGTGAATTCAACCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
59396478 CTGGTGTAGCTTCAATCTGTTCCACTACACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * *
59396513 AGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
59396578 CCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
59396613 GAGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTTTAATTGCAAT
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATC-TTTTTAATTGCAAT
59396660 CTCAGGGGTA
Statistics
Matches: 680, Mismatches: 65, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
100 665 0.98
101 15 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
Found at i:59396832 original size:15 final size:15
Alignment explanation
Indices: 59396792--59396832 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
59396782 TAACTAGATG
59396792 TGTATGAATGATATT
1 TGTATGAATGATATT
*
59396807 TGCATTGAATGATATT
1 TGTA-TGAATGATATT
59396823 TGTATGAATG
1 TGTATGAATG
59396833 CAAAATGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:59397610 original size:13 final size:13
Alignment explanation
Indices: 59397576--59397602 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59397566 TTCGTTCTTC
59397576 TTTTCTTTTTATT
1 TTTTCTTTTTATT
59397589 TTTTCTTTTTATT
1 TTTTCTTTTTATT
59397602 T
1 T
59397603 CTTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTTATT
Found at i:59398068 original size:5 final size:5
Alignment explanation
Indices: 59398042--59398087 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
59398032 CCCGGTAGAG
*
59398042 GTTTT -TTTT CTTTT -TTTCT GTTTT GTTTT GTTTT GTTTT GTTTT GT
1 GTTTT GTTTT GTTTT GTTT-T GTTTT GTTTT GTTTT GTTTT GTTTT GT
59398088 GCCTCCACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 7 0.18
5 28 0.74
6 3 0.08
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:59400827 original size:24 final size:25
Alignment explanation
Indices: 59400800--59400852 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
59400790 AGCCTTTTCG
*
59400800 TGAAATTTAATACAAATG-ATGCAA
1 TGAAATGTAATACAAATGCATGCAA
* *
59400824 TGAAATGTAATACAGATGCATGGAA
1 TGAAATGTAATACAAATGCATGCAA
59400849 TGAA
1 TGAA
59400853 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATACAAATGCATGCAA
Found at i:59402465 original size:50 final size:50
Alignment explanation
Indices: 59402350--59402598 Score: 300
Period size: 50 Copynumber: 4.8 Consensus size: 50
59402340 GATAATAACA
* * ** * *
59402350 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
59402401 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
59402451 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
59402501 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
59402556 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
59402599 TTACCCAAAT
Statistics
Matches: 172, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
50 94 0.55
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:59402536 original size:100 final size:104
Alignment explanation
Indices: 59402349--59402598 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 104
59402339 TGATAATAAC
* ** * *
59402349 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
59402414 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
*
59402451 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
59402515 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
*
59402556 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
59402599 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
100 48 0.36
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 41 0.31
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:59402714 original size:13 final size:13
Alignment explanation
Indices: 59402693--59402723 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
59402683 GCTTAGATCA
*
59402693 TCATCAAATAAAT
1 TCATAAAATAAAT
59402706 TCATAAAATAAAT
1 TCATAAAATAAAT
59402719 TCATA
1 TCATA
59402724 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:59402968 original size:29 final size:30
Alignment explanation
Indices: 59402936--59402992 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
59402926 CCTCGACTCT
59402936 AACTTTT-CAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
59402965 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
59402993 AAGGCTCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:59408541 original size:25 final size:25
Alignment explanation
Indices: 59408481--59408641 Score: 177
Period size: 25 Copynumber: 6.6 Consensus size: 25
59408471 ATGTAACAGA
*
59408481 AAGCTCATAAGAGCC-ATAAT-GGG
1 AAGCTCATAAGAGCCAATTATCGGG
59408504 AAGCTCATAAGAGCCAATTATCGGG
1 AAGCTCATAAGAGCCAATTATCGGG
*
59408529 AAGCTC-TAGAGAGCCAATTATTGGG
1 AAGCTCATA-AGAGCCAATTATCGGG
* * *
59408554 AAGCTCATACGAGCC-ATAAACGGG
1 AAGCTCATAAGAGCCAATTATCGGG
* * *
59408578 AAGCTCATAAGAGCTAAATAACGGG
1 AAGCTCATAAGAGCCAATTATCGGG
* *
59408603 AAGCTCATGAGAGCCTATTATCGGG
1 AAGCTCATAAGAGCCAATTATCGGG
* *
59408628 ACGCTCGTAAGAGC
1 AAGCTCATAAGAGC
59408642 TATGGTGTGT
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
23 15 0.13
24 25 0.22
25 73 0.63
26 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
AAGCTCATAAGAGCCAATTATCGGG
Found at i:59408607 original size:74 final size:73
Alignment explanation
Indices: 59408481--59408641 Score: 216
Period size: 74 Copynumber: 2.2 Consensus size: 73
59408471 ATGTAACAGA
* * *
59408481 AAGCTCATAAGAGCCATAATGGGAAGCTCATAAGAGCCAATTATCGGGAAGCTC-TAGAGAGCCA
1 AAGCTCATAAGAGCCATAACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCAT-GAGAGCCA
*
59408545 ATTATTGGG
65 ATTATCGGG
* * *
59408554 AAGCTCATACGAGCCATAAACGGGAAGCTCATAAGAGCTAAATAACGGGAAGCTCATGAGAGCCT
1 AAGCTCATAAGAGCCAT-AACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCA
59408619 ATTATCGGG
65 ATTATCGGG
* *
59408628 ACGCTCGTAAGAGC
1 AAGCTCATAAGAGC
59408642 TATGGTGTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
73 16 0.21
74 59 0.78
75 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (73 bp):
AAGCTCATAAGAGCCATAACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCAA
TTATCGGG
Found at i:59419453 original size:19 final size:19
Alignment explanation
Indices: 59419429--59419468 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
59419419 GGTACTTAAA
*
59419429 AACTTTGAATCAAAGATAT
1 AACTTTGAAGCAAAGATAT
59419448 AACTTTGAAGCAAAGATAT
1 AACTTTGAAGCAAAGATAT
59419467 AA
1 AA
59419469 TAACATGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (19 bp):
AACTTTGAAGCAAAGATAT
Found at i:59419806 original size:15 final size:15
Alignment explanation
Indices: 59419781--59419815 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
59419771 GACTCTATTT
*
59419781 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
59419795 TAATTAATATTAAGA
1 TAATTAATATTAAGA
59419810 TAATTA
1 TAATTA
59419816 TTAAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:59419831 original size:18 final size:18
Alignment explanation
Indices: 59419810--59419853 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
59419800 AATATTAAGA
59419810 TAATTATTAAG-TATTATT
1 TAATT-TTAAGATATTATT
* *
59419828 TAATTTTAGGATTTTATT
1 TAATTTTAAGATATTATT
59419846 TAATTTTA
1 TAATTTTA
59419854 TTTAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
TAATTTTAAGATATTATT
Found at i:59419853 original size:10 final size:10
Alignment explanation
Indices: 59419838--59419867 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
59419828 TAATTTTAGG
59419838 ATTTTATTTA
1 ATTTTATTTA
59419848 ATTTTATTTA
1 ATTTTATTTA
59419858 ATTTTATTTA
1 ATTTTATTTA
59419868 TCTTCAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTATTTA
Found at i:59422615 original size:3 final size:3
Alignment explanation
Indices: 59422609--59422639 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59422599 TCTCCAACTC
59422609 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
59422640 GCTTTATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:59428854 original size:69 final size:69
Alignment explanation
Indices: 59428772--59428911 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
59428762 GATCTACATG
59428772 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
1 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
59428837 TGTA
66 TGTA
59428841 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
1 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
59428906 TGTA
66 TGTA
59428910 AA
1 AA
59428912 ATTACTTAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (69 bp):
AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
TGTA
Found at i:59448592 original size:24 final size:24
Alignment explanation
Indices: 59448563--59448624 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
59448553 TCAAAGAAGT
*
59448563 TGATAGTAATAGTGCAAGCTATGA
1 TGATAGTAATAGTGCAAACTATGA
59448587 TGATAGTAATAGTGCAAACTATGA
1 TGATAGTAATAGTGCAAACTATGA
*
59448611 TGATAGTGATAGTG
1 TGATAGTAATAGTG
59448625 AACTTTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (24 bp):
TGATAGTAATAGTGCAAACTATGA
Found at i:59453933 original size:26 final size:26
Alignment explanation
Indices: 59453897--59453950 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
59453887 TTCATCTCTC
59453897 CTAGGTATTTAGAAAATTAGTTAATG
1 CTAGGTATTTAGAAAATTAGTTAATG
*
59453923 CTAGGTATTTAGAAAATTAGTTCATG
1 CTAGGTATTTAGAAAATTAGTTAATG
59453949 CT
1 CT
59453951 TGAAAATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (26 bp):
CTAGGTATTTAGAAAATTAGTTAATG
Found at i:59467015 original size:13 final size:13
Alignment explanation
Indices: 59466997--59467022 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59466987 GAATTTTTAA
59466997 GAATCGTTAACAC
1 GAATCGTTAACAC
59467010 GAATCGTTAACAC
1 GAATCGTTAACAC
59467023 TTTTAAAAAT
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:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
GAATCGTTAACAC
Found at i:59468143 original size:11 final size:12
Alignment explanation
Indices: 59468126--59468170 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
59468116 GATTGTTTGA
59468126 ATATTTTATTAT
1 ATATTTTATTAT
59468138 -TATTTTATTAT
1 ATATTTTATTAT
*
59468149 AGATATTTATT-T
1 ATAT-TTTATTAT
59468161 ATATTTTATT
1 ATATTTTATT
59468171 TAATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 17 0.59
12 6 0.21
13 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:59472789 original size:17 final size:19
Alignment explanation
Indices: 59472761--59472809 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
59472751 TAAAAAGGAA
*
59472761 ATAATAAGTAAATAAATA-
1 ATAATAAATAAATAAATAC
59472779 A-AATAAATAAAT-AATAC
1 ATAATAAATAAATAAATAC
59472796 ATAA-AAATAAATAA
1 ATAATAAATAAATAA
59472810 CCTAGACAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAATAAATAAATAAATAC
Found at i:59474295 original size:51 final size:49
Alignment explanation
Indices: 59474240--59474496 Score: 236
Period size: 51 Copynumber: 5.3 Consensus size: 49
59474230 CCACTACAAT
*
59474240 TTCAGGGAGATAAGACTTGTAACTTGTAGCTTCT-ATCTGTTCCACTGAAAC
1 TTCAGGGAAATAAGA-TTGT-ACTTGTAGCTT-TAATCTGTTCCACTGAAAC
*
59474291 TTCAGGGAAATAAGA---T--TTGTAGCTTTAATCTGTTCCA-TTACAAC
1 TTCAGGGAAATAAGATTGTACTTGTAGCTTTAATCTGTTCCACTGA-AAC
* * *
59474335 TTCAGGGAGATAAGATTTGTGACTTGTAGCTTTAATCTGTTCTACTGCAAC
1 TTCAGGGAAATAAGA-TTGT-ACTTGTAGCTTTAATCTGTTCCACTGAAAC
* * * *
59474386 TTCAGGGAAATAAGATT-TGC--ATA--TTCAATCTG-TCCACTGTAAC
1 TTCAGGGAAATAAGATTGTACTTGTAGCTTTAATCTGTTCCACTGAAAC
* *
59474429 TTCAAGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACT-ACAAC
1 TTCAGGGAAATAAGA-TTGT-ACTTGTAGCTTTAATCTGTTCCACTGA-AAC
59474480 TTCAGGGAAATAAGATT
1 TTCAGGGAAATAAGATT
59474497 TTCTATCTTC
Statistics
Matches: 167, Mismatches: 20, Indels: 39
0.74 0.09 0.17
Matches are distributed among these distances:
43 25 0.15
44 46 0.28
45 1 0.01
46 3 0.02
47 1 0.01
48 4 0.02
49 1 0.01
50 12 0.07
51 73 0.44
52 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (49 bp):
TTCAGGGAAATAAGATTGTACTTGTAGCTTTAATCTGTTCCACTGAAAC
Found at i:59474538 original size:45 final size:45
Alignment explanation
Indices: 59474269--59474666 Score: 301
Period size: 45 Copynumber: 8.6 Consensus size: 45
59474259 TAACTTGTAG
* * * *
59474269 CTTCTATCTGTTCCACTGAAACTTCAGGGAA-ATAAGATTTG-TAG
1 CTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTTGCTAT
* * * * * *
59474313 CTTTAATCTGTTCCATTACAACTTCAGGGAGATAAGATTTGTGACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA-TT-TG-C---TAT
* * *
59474364 CTTTAATCTGTTCTACTGCAACTTCAGGGAA-ATAAGATTTGC-AT
1 CTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTTGCTAT
* * *
59474408 ATTCAATCTG-TCCACTGTAACTTCAAGG-AGATAAGATTTGTAACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTC-AGGAAGATAAGATTTG---C---TAT
* * * *
59474458 CTTTAATCTGTTCCACTACAACTTCAGGGAA-ATAAGATTTTCTAT
1 CTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTTGCTAT
* **
59474503 CTTCAATTTGCTCCACTGCAACTTCAGGAAGATAAGATTCACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
* * * *
59474548 CTTCAATTTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAC
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
* *
59474593 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
*
59474638 CTTCAATC--CATCCCACTGCAACTTTAGGA
1 CTTCAATCTGC-T-CCACTGCAACTTCAGGA
59474667 GTATGAGTAA
Statistics
Matches: 290, Mismatches: 40, Indels: 47
0.77 0.11 0.12
Matches are distributed among these distances:
42 1 0.00
43 28 0.10
44 42 0.14
45 141 0.49
46 3 0.01
48 2 0.01
49 2 0.01
50 12 0.04
51 55 0.19
52 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
Found at i:59474605 original size:90 final size:92
Alignment explanation
Indices: 59474209--59474631 Score: 435
Period size: 95 Copynumber: 4.5 Consensus size: 92
59474199 ATAGGTATAG
* * * * * *
59474209 GATTTGTTGCTTCAATCTTCTCCACTACAATTTCAGGGAGATAAGACTTGTAACTTGTAGCTTCT
1 GATTTGCTACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAAC-T-TAGCTTCA
* *
59474274 ATCTGTTCCACTGAAACTTCAGGGAAATAA
63 ATCTGTTCTACTGCAACTTCAGGGAAATAA
* * * * * *
59474304 GATTTG-TAGCTTTAATCTGTTCCATTACAACTTCAGGGAGATAAGATTTGTGACTTGTAGCTTT
1 GATTTGCTA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAAC-T-TAGCTTC
59474368 AATCTGTTCTACTGCAACTTCAGGGAAATAA
62 AATCTGTTCTACTGCAACTTCAGGGAAATAA
* * *
59474399 GATTTGCATA-TTCAATCTG-TCCACTGTAACTTCAAGGAGATAAGATTTGTAACTTGTAGCTTT
1 GATTTGC-TACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAAC-T-TAGCTTC
* *
59474462 AATCTGTTCCACTACAACTTCAGGGAAATAA
62 AATCTGTTCTACTGCAACTTCAGGGAAATAA
* * * * *
59474493 GATTTTCTATCTTCAATTTGCTCCACTGCAACTTCAGGAAGATAAGA-T-TCAC-TATCTTCAAT
1 GATTTGCTA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAACTTAGCTTCAAT
* * *
59474555 TTGCTCTACTGCAACTTCAGGGAGATAA
65 CTGTTCTACTGCAACTTCAGGGAAATAA
*
59474583 GATTTGCTACCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 GATTTGCTA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
59474632 TGCTATCTTC
Statistics
Matches: 283, Mismatches: 38, Indels: 18
0.83 0.11 0.05
Matches are distributed among these distances:
90 73 0.26
91 1 0.00
93 5 0.02
94 76 0.27
95 103 0.36
96 23 0.08
97 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (92 bp):
GATTTGCTACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAACTTAGCTTCAATC
TGTTCTACTGCAACTTCAGGGAAATAA
Found at i:59474656 original size:90 final size:91
Alignment explanation
Indices: 59474171--59474661 Score: 406
Period size: 95 Copynumber: 5.3 Consensus size: 91
59474161 CTTCTTTAAG
* ** * * * * * *
59474171 TAGCTTCATTCTAACCCACTGCAACTTCATAGG-TATAGGATTTGTTGCTTCAATCTTCTCCACT
1 TAGCTTCAATCTGTCCCACTGCAACTTCA-GGGAAATAAGATTTGCTACTTCAATCTGCTCCACT
* * *
59474235 ACAATTTCAGGGAGATAAGACTTGTAACTT
65 GCAACTTCAGGGAGATAAGA-TT-TGAC-T
* * * * * *
59474265 GTAGCTTCTATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTG-TAGCTTTAATCTGTTCCAT
1 -TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGCTA-CTTCAATCTGCTCCAC
*
59474329 TACAACTTCAGGGAGATAAGATTTGTGACTT
64 TGCAACTTCAGGGAGATAAGA-TT-TGAC-T
* * *
59474360 GTAGCTTTAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCATA-TTCAATCTG-TCCAC
1 -TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGC-TACTTCAATCTGCTCCAC
* *
59474423 TGTAACTTCAAGGAGATAAGATTTGTAACTT
64 TGCAACTTCAGGGAGATAAGATTTG--AC-T
* * * * *
59474454 GTAGCTTTAATCTGTTCCACTACAACTTCAGGGAAATAAGATTTTCTATCTTCAATTTGCTCCAC
1 -TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGCTA-CTTCAATCTGCTCCAC
* *
59474519 TGCAACTTCAGGAAGATAAGA-TTCAC-
64 TGCAACTTCAGGGAGATAAGATTTGACT
* * * * *
59474545 TATCTTCAATTTG-CTCTACTGCAACTTCAGGGAGATAAGATTTGCTACCTTTAATCTGCTCCAC
1 TAGCTTCAATCTGTC-CCACTGCAACTTCAGGGAAATAAGATTTGCTA-CTTCAATCTGCTCCAC
59474609 TGCAACTTCAGGGAGATAAGATTTG-C-
64 TGCAACTTCAGGGAGATAAGATTTGACT
* **
59474635 TATCTTCAATCCATCCCACTGCAACTT
1 TAGCTTCAATCTGTCCCACTGCAACTT
59474662 TAGGAGTATG
Statistics
Matches: 333, Mismatches: 51, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
90 94 0.28
91 3 0.01
92 2 0.01
93 6 0.02
94 72 0.22
95 131 0.39
96 23 0.07
97 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (91 bp):
TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGCTACTTCAATCTGCTCCACTG
CAACTTCAGGGAGATAAGATTTGACT
Found at i:59481991 original size:3 final size:3
Alignment explanation
Indices: 59481985--59482028 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
59481975 AATAAAAACC
59481985 ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
59482029 GGAAGTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:59483865 original size:19 final size:19
Alignment explanation
Indices: 59483841--59483877 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59483831 TATAACCATT
59483841 AAATATTTGTAATTTTAAA
1 AAATATTTGTAATTTTAAA
* *
59483860 AAATATTTTTATTTTTAA
1 AAATATTTGTAATTTTAA
59483878 TTAATGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
AAATATTTGTAATTTTAAA
Found at i:59487369 original size:2 final size:2
Alignment explanation
Indices: 59487362--59487388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59487352 AGGTTAATAG
59487362 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59487389 GGATTTGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59501586 original size:31 final size:33
Alignment explanation
Indices: 59501527--59501592 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
59501517 GGCAAATTAC
59501527 AAGAGTAATTGAATCCTAATAAAAACTC-TTAA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTAA
59501559 AAGAGTAATTGAATCCTAAT-AAAACTCTTTAA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTAA
59501591 AA
1 AA
59501593 TTATCTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 7 0.21
32 26 0.79
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (33 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTAA
Found at i:59502052 original size:17 final size:17
Alignment explanation
Indices: 59502030--59502062 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
59502020 AAAGGAAGAA
59502030 AACATACTGAAAGCCAC
1 AACATACTGAAAGCCAC
59502047 AACATACTGAAAGCCA
1 AACATACTGAAAGCCA
59502063 AGTCTTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.27, G:0.12, T:0.12
Consensus pattern (17 bp):
AACATACTGAAAGCCAC
Done.