Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 167 of 172
Found at i:49449885 original size:24 final size:24
Alignment explanation
Indices: 49449833--49449888 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
49449823 GATTAAAAAG
49449833 TATACATAAATATTTGGTAATAATA
1 TATA-ATAAATATTTGGTAATAATA
* *
49449858 -ATAATACAATA-TTGGTGATATTA
1 TATAATA-AATATTTGGTAATAATA
49449881 TATAATAA
1 TATAATAA
49449889 TAGTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (24 bp):
TATAATAAATATTTGGTAATAATA
Found at i:49450191 original size:31 final size:29
Alignment explanation
Indices: 49450120--49450193 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
49450110 AATAAACACC
49450120 AAAAAATA-ATTTTAAAAATAAAAAAAAT
1 AAAAAATATATTTTAAAAATAAAAAAAAT
* *
49450148 AAAAAA-AGTATTTTAAAAATAATTTAAAATT
1 AAAAAATA-TATTTTAAAAATAA--AAAAAAT
49450179 AAAAAATATATTTTA
1 AAAAAATATATTTTA
49450194 TTAAATTCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 1 0.03
28 6 0.15
29 13 0.33
31 18 0.46
32 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAAAATATATTTTAAAAATAAAAAAAAT
Found at i:49457565 original size:20 final size:21
Alignment explanation
Indices: 49457537--49457580 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
49457527 TATGTATTAT
*
49457537 AAATTACATAATATA-TACAA
1 AAATAACATAATATATTACAA
49457557 AAATAACATAATATATTACAA
1 AAATAACATAATATATTACAA
49457578 AAA
1 AAA
49457581 AACTTAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAACATAATATATTACAA
Found at i:49462093 original size:20 final size:20
Alignment explanation
Indices: 49462068--49462105 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49462058 GCTTTTATCT
49462068 AATATATTGTTT-AAATTTGA
1 AATATA-TGTTTGAAATTTGA
49462088 AATATATGTTTGAAATTT
1 AATATATGTTTGAAATTT
49462106 TATCTAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
AATATATGTTTGAAATTTGA
Found at i:49463034 original size:7 final size:7
Alignment explanation
Indices: 49463002--49463031 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
49462992 GGAGTGGGGT
49463002 AAACTTA
1 AAACTTA
49463009 AAACTTA
1 AAACTTA
49463016 AAACTTA
1 AAACTTA
*
49463023 AATCTTA
1 AAACTTA
49463030 AA
1 AA
49463032 TCTATATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (7 bp):
AAACTTA
Found at i:49470166 original size:17 final size:19
Alignment explanation
Indices: 49470132--49470168 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
49470122 TTGTATTATG
*
49470132 TTTTAAAGATATATTATTT
1 TTTTAAAGATATAATATTT
49470151 TTTTAAA-AT-TAATATTT
1 TTTTAAAGATATAATATTT
49470168 T
1 T
49470169 AGATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTAAAGATATAATATTT
Found at i:49478523 original size:16 final size:17
Alignment explanation
Indices: 49478488--49478525 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
49478478 ATTAAACCCG
*
49478488 AATAACCCAGAACCCCA
1 AATAACCCAGAACCCAA
*
49478505 AATAACCCA-AACCGAA
1 AATAACCCAGAACCCAA
49478521 AATAA
1 AATAA
49478526 TTGGACCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.55, C:0.32, G:0.05, T:0.08
Consensus pattern (17 bp):
AATAACCCAGAACCCAA
Found at i:49495714 original size:49 final size:49
Alignment explanation
Indices: 49495657--49495760 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
49495647 TCATGTGTTA
* * * *
49495657 TAATTTTATTAAGTGTTGAGCTTTTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
*
49495706 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
49495755 TAATTT
1 TAATTT
49495761 GTTTTTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:49497260 original size:21 final size:18
Alignment explanation
Indices: 49497214--49497257 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
49497204 ATATTAAGAA
49497214 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
49497232 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
*
49497250 TATTATTA
1 TTTTATTA
49497258 TTATTTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:49497270 original size:26 final size:28
Alignment explanation
Indices: 49497223--49497278 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
49497213 ATTTTATTAA
*
49497223 ATTATATATTTTTATTAAATTATATATT
1 ATTATATATTATTATTAAATTATATATT
* *
49497251 ATTAT-TATTATT-TTAGATTATATTTT
1 ATTATATATTATTATTAAATTATATATT
49497277 AT
1 AT
49497279 AGTATTGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.56
27 6 0.24
28 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTATATATTATTATTAAATTATATATT
Found at i:49497276 original size:120 final size:120
Alignment explanation
Indices: 49497144--49498214 Score: 1740
Period size: 120 Copynumber: 9.0 Consensus size: 120
49497134 AAGTAGATTA
*
49497144 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATGAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
49497209 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATATT-ATTATTATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATAT-TTAATAATAATTATTT
* * * *
49497264 TAGATTATATTTTATAGTATTGTTTATTATGATTATAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
49497329 AAGAATTTTATTAAATTATATATTTTTAATAAATTATA-TTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
*
49497383 TAAATTATATTTTATAGTGTTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
49497448 AAGAATTTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATTATTA-TT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* * *
49497501 TAGATTATATTTTATACTATTAT-TATTACGA-TTTAGTAAATTCATATAA-AATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
49497563 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATAATTAATT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
*
49497618 TAAATTATATTTTATAATATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
49497680 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATAATTAATT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
*
49497735 TAAATTATATTTTATAGTA-T-TATATTATGAATTTAGTAAATTC---TAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
49497795 AAGAATTTTATTAAATTATATATTTTTACTAAATTATATTTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATA-TTTAATAATAATTATTT
*
49497851 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
49497916 AAGAATTTTATTAAATTATATATTGTTATTAAATTATATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* * **
49497971 TAAATTATATTTTATAGTATTACATATTATGATTTTATTAAATTTGTATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
49498036 AAGAATTTTATTAAATTATATATTTGTATTAAATTATATTTAATAATAATTATGT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* *
49498091 TAAATTATATTTTATAGTATTTTATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
49498156 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
49498211 TAAA
1 TAAA
49498215 ATGTGATTAA
Statistics
Matches: 891, Mismatches: 47, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
115 111 0.12
116 83 0.09
117 117 0.13
118 67 0.08
119 117 0.13
120 343 0.38
121 53 0.06
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (120 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
Found at i:49497472 original size:17 final size:17
Alignment explanation
Indices: 49497452--49497485 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49497442 AATATTAAGA
49497452 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
49497469 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
49497486 TTAATAATTA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:49497620 original size:26 final size:26
Alignment explanation
Indices: 49497591--49497746 Score: 82
Period size: 26 Copynumber: 5.5 Consensus size: 26
49497581 TATATTTTTA
49497591 TTAAATTATATTTAAAAATAATTAAT
1 TTAAATTATATTTAAAAATAATTAAT
49497617 TTAAATTATATTTTATAATATTATATATTATGAT
1 TTAAATTATA-TTTA-AA-A--ATA-ATTA--AT
* * * * *
49497651 TT-TAGTAAATTCTAAGAATATTTAAT
1 TTAAATTATATT-TAAAAATAATTAAT
* * **
49497677 ATTAAGAATTTTA-TTAAATTATATATTTTT
1 -TT-A-AATTATATTTAAA-AATA-ATTAAT
49497707 ATTAAATTATATTTAAAAATAATTAAT
1 -TTAAATTATATTTAAAAATAATTAAT
49497734 TTAAATTATATTT
1 TTAAATTATATTT
49497747 TATAGTATTA
Statistics
Matches: 96, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
26 25 0.26
27 10 0.10
28 17 0.18
29 14 0.15
30 9 0.09
31 4 0.04
32 7 0.07
33 6 0.06
34 4 0.04
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (26 bp):
TTAAATTATATTTAAAAATAATTAAT
Found at i:49497698 original size:51 final size:51
Alignment explanation
Indices: 49497643--49497813 Score: 146
Period size: 57 Copynumber: 3.1 Consensus size: 51
49497633 AATATTATAT
49497643 ATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAA
* * * * * *
49497694 ATTATATATTTTTATTAAATTATATTTAAAAATAATTAAT-TTAAATTATATTTTATAGTATTA
1 ATTAT-GA-TTTTAGT-AA--AT-TCTAAGAATATTTAATATT-AA-GA-ATTTTAT--TA--A
*
49497757 TATTATGAATTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAA
1 -ATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAA
49497809 ATTAT
1 ATTAT
49497814 ATATTTTTAC
Statistics
Matches: 92, Mismatches: 13, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
51 10 0.11
52 2 0.02
53 6 0.07
54 4 0.04
56 11 0.12
57 16 0.17
58 16 0.17
59 11 0.12
61 4 0.04
62 5 0.05
63 2 0.02
64 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (51 bp):
ATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:49498065 original size:18 final size:17
Alignment explanation
Indices: 49498040--49498074 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
49498030 AATATTAAGA
49498040 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
49498057 ATTTGTATTAAATTATAT
1 ATTT-TATTAAATTATAT
49498075 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:49498435 original size:45 final size:44
Alignment explanation
Indices: 49498352--49498447 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
49498342 ATTACAACAT
*
49498352 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
*
49498396 CATTACATTCAACCAAACA-ATTGAATTACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTC
49498441 CATTACA
1 CATTACA
49498448 GCTCTATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.44
45 26 0.54
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.30
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
Found at i:49498452 original size:16 final size:16
Alignment explanation
Indices: 49498433--49498465 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
49498423 ACTATTACGC
49498433 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
49498449 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
49498465 C
1 C
49498466 GAACCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:49500080 original size:21 final size:22
Alignment explanation
Indices: 49500038--49500084 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
49500028 ATTATATAAA
*
49500038 TTTTATATTTATATTAATATAT
1 TTTTATAGTTATATTAATATAT
49500060 TTTTATAGTTAGT-TTAA-ATAT
1 TTTTATAGTTA-TATTAATATAT
49500081 TTTT
1 TTTT
49500085 TAAAACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 14 0.61
23 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTATAGTTATATTAATATAT
Found at i:49521292 original size:28 final size:26
Alignment explanation
Indices: 49521234--49521293 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
49521224 AAGATAACCA
* * *
49521234 AAACCCAATGCTCAATCTAATAAATT
1 AAACCCAATGCCCAATCCAATAAACT
49521260 AAACCCAATGCCCAATACACAATAAACT
1 AAACCCAATGCCCAAT-C-CAATAAACT
49521288 AAACCC
1 AAACCC
49521294 TAGCCCGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.52
27 1 0.03
28 13 0.45
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.18
Consensus pattern (26 bp):
AAACCCAATGCCCAATCCAATAAACT
Found at i:49530013 original size:30 final size:30
Alignment explanation
Indices: 49529977--49530035 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
49529967 TAGGACATAT
* *
49529977 GCCCATGTGCTAGGTCGTGTGTCACACACG
1 GCCCATGTGCTAGGCCGTGTGCCACACACG
49530007 GCCCATGTGCTAGGCCGTGTGCCACACAC
1 GCCCATGTGCTAGGCCGTGTGCCACACAC
49530036 AGCTGAGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.34, G:0.29, T:0.20
Consensus pattern (30 bp):
GCCCATGTGCTAGGCCGTGTGCCACACACG
Found at i:49550768 original size:24 final size:24
Alignment explanation
Indices: 49550740--49550794 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
49550730 TAATATTGAT
*
49550740 CTTTTATAAATAATAAATACTTTTA
1 CTTTTA-AAATAATAAATAATTTTA
* *
49550765 -TTTTGAACATAATAATTAATTTTA
1 CTTTT-AAAATAATAAATAATTTTA
49550789 CTTTTA
1 CTTTTA
49550795 CATAGGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (24 bp):
CTTTTAAAATAATAAATAATTTTA
Found at i:49561853 original size:28 final size:27
Alignment explanation
Indices: 49561821--49561876 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
49561811 TCTCTCAACA
49561821 AAAAT-TACATAAAAATTTTCAGAAATTT
1 AAAATATACATAAAAA-TTTCA-AAATTT
**
49561849 AAAATATTTATAAAAATTTCAAAATTT
1 AAAATATACATAAAAATTTCAAAATTT
49561876 A
1 A
49561877 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.28
28 10 0.40
29 8 0.32
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAATATACATAAAAATTTCAAAATTT
Found at i:49561877 original size:18 final size:19
Alignment explanation
Indices: 49561843--49561878 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49561833 AAATTTTCAG
49561843 AAATTTAAAATATTTATAA
1 AAATTTAAAATATTTATAA
*
49561862 AAATTTCAAA-ATTTATA
1 AAATTTAAAATATTTATA
49561879 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTAAAATATTTATAA
Found at i:49564211 original size:4 final size:4
Alignment explanation
Indices: 49564204--49564229 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
49564194 AAGGTAATGA
49564204 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
49564230 TGCTTGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:49565118 original size:22 final size:25
Alignment explanation
Indices: 49565073--49565123 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 25
49565063 AACATATAAT
49565073 AATATAATAATATGTAAATATTAAA
1 AATATAATAATATGTAAATATTAAA
* *
49565098 AATAT-AT-ATAT-TAAATTTTAAT
1 AATATAATAATATGTAAATATTAAA
49565120 AATA
1 AATA
49565124 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 4 0.17
24 2 0.08
25 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AATATAATAATATGTAAATATTAAA
Found at i:49574640 original size:3 final size:3
Alignment explanation
Indices: 49574632--49574670 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
49574622 TGATTCACCG
* * *
49574632 TCA TCA TCA CCA TCA TCA TCG TCA TCG TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
49574671 CTTTCTCGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:49590469 original size:21 final size:21
Alignment explanation
Indices: 49590443--49590483 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49590433 AGACGAGCAA
* *
49590443 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
49590464 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
49590484 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:49594149 original size:26 final size:26
Alignment explanation
Indices: 49594120--49594172 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
49594110 TATGTGAATG
*
49594120 TTGAAATGGTGGGTTTACTATAAAGT
1 TTGAAATGATGGGTTTACTATAAAGT
49594146 TTGAAATGATGGGTTTACTATAAAGT
1 TTGAAATGATGGGTTTACTATAAAGT
49594172 T
1 T
49594173 GAATTTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.40
Consensus pattern (26 bp):
TTGAAATGATGGGTTTACTATAAAGT
Found at i:49595009 original size:4 final size:4
Alignment explanation
Indices: 49595000--49595048 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
49594990 TATCTAGTGG
49595000 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
49595048 T
1 T
49595049 ATTCAAGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:49598249 original size:29 final size:31
Alignment explanation
Indices: 49598202--49598270 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
49598192 ATGGGAAAAG
*
49598202 TTTGATTTAATGTGTAATTTTATACAT-AAAT
1 TTTGATTT-ATGTGCAATTTTATACATGAAAT
*
49598233 TTTGATTT-TGTGCAATTTTATATATGAAAT
1 TTTGATTTATGTGCAATTTTATACATGAAAT
*
49598263 TTTAATTT
1 TTTGATTT
49598271 GATCTAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 15 0.44
30 11 0.32
31 8 0.24
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTGATTTATGTGCAATTTTATACATGAAAT
Found at i:49600920 original size:23 final size:24
Alignment explanation
Indices: 49600894--49600938 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
49600884 TAGGAATACC
*
49600894 TCATCTAA-ATATT-TTAGTATTTA
1 TCATATAACATATTGTTA-TATTTA
49600917 TCATATAACATATTGTTATATT
1 TCATATAACATATTGTTATATT
49600939 CTTCTATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 9 0.47
25 3 0.16
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (24 bp):
TCATATAACATATTGTTATATTTA
Found at i:49601984 original size:17 final size:17
Alignment explanation
Indices: 49601962--49601996 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
49601952 ACTAATACAT
*
49601962 AAAAGAATAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
49601979 AAAAGAAGAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
49601996 A
1 A
49601997 GAGACCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAAAAGAAAC
Found at i:49603722 original size:43 final size:43
Alignment explanation
Indices: 49603657--49603750 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
49603647 CAACTATGGT
49603657 CTTA-CACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCA
1 CTTATCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCA
* *
49603699 CTTGTCACTGATCAGGTAAGTGTAGCTAAGCTACCACTTATCA
1 CTTATCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCA
49603742 CTTATCACT
1 CTTATCACT
49603751 TGTCACTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 3 0.06
43 45 0.94
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (43 bp):
CTTATCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCA
Found at i:49603745 original size:7 final size:7
Alignment explanation
Indices: 49603733--49603769 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
49603723 GCTAAGCTAC
49603733 CACTTAT
1 CACTTAT
49603740 CACTTAT
1 CACTTAT
*
49603747 CACTTGT
1 CACTTAT
49603754 CACTTAT
1 CACTTAT
*
49603761 CACTGAT
1 CACTTAT
49603768 CA
1 CA
49603770 GATAAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (7 bp):
CACTTAT
Found at i:49603778 original size:57 final size:58
Alignment explanation
Indices: 49603690--49603813 Score: 178
Period size: 57 Copynumber: 2.2 Consensus size: 58
49603680 GCTAAGCTAC
* * *
49603690 CACTTATCACTTGTCACTGATCAGGTAAGTGTAGCT-AAGCTACCACTTATCACTTAT
1 CACTTATCACTTATCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTAT
* * *
49603747 CACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAATTACCACTTATCACTTGT
1 CACTTATCACTTATCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTAT
*
49603805 CACTGATCA
1 CACTTATCA
49603814 GAAGTACTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
57 33 0.57
58 25 0.43
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (58 bp):
CACTTATCACTTATCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTAT
Found at i:49605858 original size:46 final size:42
Alignment explanation
Indices: 49605805--49605906 Score: 134
Period size: 44 Copynumber: 2.4 Consensus size: 42
49605795 GCTTTGCCGA
* *
49605805 TCAGGCACTTTATGTGTCATACATCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCAT--ATCAGGCACCTCATGTGTCGT-T
*
49605850 CTCAGGCACTTTATGTGTCGTATCAGGCACCTCATGTGTCGTT
1 -TCAGGCACTTTATGTGTCATATCAGGCACCTCATGTGTCGTT
49605893 TCAGGCAC-TTATGT
1 TCAGGCACTTTATGT
49605907 ATCGTATGCT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
41 6 0.11
42 8 0.15
43 1 0.02
44 19 0.36
46 19 0.36
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (42 bp):
TCAGGCACTTTATGTGTCATATCAGGCACCTCATGTGTCGTT
Found at i:49605877 original size:21 final size:21
Alignment explanation
Indices: 49605804--49605913 Score: 132
Period size: 23 Copynumber: 5.1 Consensus size: 21
49605794 GGCTTTGCCG
*
49605804 ATCAGGCACTTTATGTGTCAT
1 ATCAGGCACTTTATGTGTCGT
49605825 ACATCAGGCACTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
49605848 ATCTCAGGCACTTTATGTGTCGT
1 A--TCAGGCACTTTATGTGTCGT
* *
49605871 ATCAGGCACCTCATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* *
49605892 TTCAGGCAC-TTATGTATCGT
1 ATCAGGCACTTTATGTGTCGT
49605912 AT
1 AT
49605914 GCTGATCAGG
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.13
21 27 0.35
23 41 0.53
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:49608931 original size:35 final size:35
Alignment explanation
Indices: 49608891--49608959 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
49608881 AATCACACAA
49608891 AGTTCAATTCCCAGGAAAGAGAGGTGGATCACATT
1 AGTTCAATTCCCAGGAAAGAGAGGTGGATCACATT
49608926 AGTTCAATTCCCAGGAAAGAGAGGTGGATCACAT
1 AGTTCAATTCCCAGGAAAGAGAGGTGGATCACAT
49608960 GGATCTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (35 bp):
AGTTCAATTCCCAGGAAAGAGAGGTGGATCACATT
Found at i:49611362 original size:21 final size:21
Alignment explanation
Indices: 49611336--49611376 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49611326 ATCTGCTCAA
* *
49611336 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
49611357 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
49611377 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:49622022 original size:48 final size:48
Alignment explanation
Indices: 49621940--49622033 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
49621930 TTTCTTGGCT
* * *
49621940 TAAAAATGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
49621988 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
49622034 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:49624528 original size:48 final size:48
Alignment explanation
Indices: 49624446--49624539 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
49624436 TTTCTTGGCT
* * *
49624446 TAAAAATGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
49624494 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
49624540 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:49629332 original size:22 final size:23
Alignment explanation
Indices: 49629294--49629337 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
49629284 ATAATTTGTC
*
49629294 ATTATTTTGTATAATGTGAATTA
1 ATTAGTTTGTATAATGTGAATTA
49629317 ATTAGTTTG-ATAATGTGAATT
1 ATTAGTTTGTATAATGTGAATT
49629338 TGTCAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (23 bp):
ATTAGTTTGTATAATGTGAATTA
Found at i:49632299 original size:27 final size:27
Alignment explanation
Indices: 49632268--49632331 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
49632258 AGTGGTCTAT
* *
49632268 ATATAATTTTTTAATAAATTAAAAGGC
1 ATATAATTTTTTAATAAATTAAAAAGA
* * *
49632295 ATATAA--ATTTATTAAATTAAAAATA
1 ATATAATTTTTTAATAAATTAAAAAGA
49632320 ATATAATTTTTT
1 ATATAATTTTTT
49632332 TTCAAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
25 20 0.69
27 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATAATTTTTTAATAAATTAAAAAGA
Found at i:49637111 original size:91 final size:89
Alignment explanation
Indices: 49637057--49637418 Score: 435
Period size: 91 Copynumber: 4.0 Consensus size: 89
49637047 TGATTTTAGT
* *
49637057 AAATTCATGTAAGAAAATTTATTAGTAAGAATTTTGTGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATT--ATTATAT
*
49637122 TTAATAATAATAATTTTTAATTATAC
64 TTAATAATAATAATTTATAATTATAC
* *
49637148 AAATTCGTATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAAATATAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATT--ATTATAT
*
49637213 TTAATAATAATTATTT-TAAATTATAC
64 TTAATAATAATAATTTAT-AATTATAC
* **
49637239 AATTTTGTATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATT--ATTATAT
* *
49637304 TTAGTAATAAAAATTT-TAAATTATAC
64 TTAATAATAATAATTTAT-AATTATAC
* * * * * *
49637330 AAATTCATATAAGAATATTTATTACTAAAAAATTTATTAAATTATATATTTTTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATT--ATTATAT
*
49637395 TTAATAAAAACTAA-TTA-AATTATA
64 TTAATAATAA-TAATTTATAATTATA
49637419 TTTTATAGTA
Statistics
Matches: 245, Mismatches: 23, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
90 8 0.03
91 235 0.96
92 2 0.01
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (89 bp):
AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTATTATATTT
AATAATAATAATTTATAATTATAC
Found at i:49637215 original size:47 final size:46
Alignment explanation
Indices: 49637073--49637397 Score: 214
Period size: 47 Copynumber: 7.1 Consensus size: 46
49637063 ATGTAAGAAA
*
49637073 ATTTATTAGTAAGAATTTTGTGAAATTATATATTATTATTAAATTAT
1 ATTTATTAGTAAGAATTTT-TGAAATTATATATTATTATTAAAATAT
* * * * * *
49637120 ATTTAATAATAATAATTTTT--AATTATACA-AATTCGTATAAGAA-A-
1 ATTTATTAGTAAGAATTTTTGAAATTATATATTATT-AT-TAA-AATAT
49637164 ATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAAATAT
1 ATTTATTAGTAAGAATTTT-TGAAATTATATATTATTATTAAAATAT
* * * *
49637211 ATTTA--A-TAATAATTATTTTAAATTATACAATT-TTGTATAAGAA-A-
1 ATTTATTAGTAAGAATT-TTTGAAATTATA-TATTATTAT-TAA-AATAT
*
49637255 ATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTAT
1 ATTTATTAGTAAGAATTTT-TGAAATTATATATTATTATTAAAATAT
* * * * * *
49637302 ATTTAGTAATAA-AAATTTT-AAATTATACA-AATTCATATAAGA-AT
1 ATTTATTAGTAAGAATTTTTGAAATTATATATTATT-AT-TAAAATAT
* * * *
49637346 ATTTATTACTAAAAAATTTATT-AAATTATATATTTTTATTAAATTAT
1 ATTTATTAGT-AAGAATTT-TTGAAATTATATATTATTATTAAAATAT
49637393 ATTTA
1 ATTTA
49637398 ATAAAAACTA
Statistics
Matches: 214, Mismatches: 37, Indels: 54
0.70 0.12 0.18
Matches are distributed among these distances:
43 6 0.03
44 70 0.33
45 24 0.11
46 30 0.14
47 79 0.37
48 5 0.02
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (46 bp):
ATTTATTAGTAAGAATTTTTGAAATTATATATTATTATTAAAATAT
Found at i:49637359 original size:44 final size:43
Alignment explanation
Indices: 49637118--49637375 Score: 144
Period size: 44 Copynumber: 5.7 Consensus size: 43
49637108 TTATTAAATT
* * * *
49637118 ATATTTAATAATAATAATTTTTAATTATACAAATTCGTATAAGA
1 ATATTTATTAATAAAAATTTTAAATTATACAAATT-ATATAAGA
* * * * * *
49637162 AAATTTATTAGTAAGAATTTTATGAAATTATATATTATTAT-TAAAA
1 ATATTTATTAATAA-AAATTT-T-AAATTATACA-AATTATATAAGA
* ** * *
49637208 TATATTTAATAATAATTATTTTAAATTATACAATTTTGTATAAGA
1 -ATATTTATTAATAAAAATTTTAAATTATACAA-ATTATATAAGA
* * * * *
49637253 AAATTTATTAGTAAGAATTTTATGAAATTATATATTATTAT-TAA-A
1 ATATTTATTAATAA-AAATTT-T-AAATTATACA-AATTATATAAGA
*
49637298 TTATATTTAGTAATAAAAATTTTAAATTATACAAATTCATATAAGA
1 --ATATTTATTAATAAAAATTTTAAATTATACAAATT-ATATAAGA
*
49637344 ATATTTATTACTAAAAAATTTATTAAATTATA
1 ATATTTATTAAT-AAAAA-TT-TTAAATTATA
49637376 TATTTTTATT
Statistics
Matches: 156, Mismatches: 39, Indels: 35
0.68 0.17 0.15
Matches are distributed among these distances:
43 3 0.02
44 55 0.35
45 22 0.14
46 20 0.13
47 53 0.34
48 3 0.02
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (43 bp):
ATATTTATTAATAAAAATTTTAAATTATACAAATTATATAAGA
Found at i:49637374 original size:182 final size:181
Alignment explanation
Indices: 49637066--49637418 Score: 562
Period size: 182 Copynumber: 1.9 Consensus size: 181
49637056 TAAATTCATG
*
49637066 TAAGAAAATTTATTAGTAAGAATTTTGTGAAATTATATATTATTATTAAATTATATTTAATAATA
1 TAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATA
* * * * * *
49637131 ATAATTTTTAATTATACAAATTCGTATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATA
66 AAAATTTTAAATTATACAAATTCATATAAGAAAATTTATTACTAAAAAATTTATGAAATTATATA
* * *
49637196 TTATTATTAAAATATATTTAATAATAATTATTTTAAATTATACAATTTTGTA
131 TTATTATTAAAATATATTTAATAAAAACTA-ATTAAATTATACAATTTTGTA
*
49637248 TAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATATTTAGTAATA
1 TAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATA
* *
49637313 AAAATTTTAAATTATACAAATTCATATAAGAATATTTATTACTAAAAAATTTATTAAATTATATA
66 AAAATTTTAAATTATACAAATTCATATAAGAAAATTTATTACTAAAAAATTTATGAAATTATATA
* *
49637378 TTTTTATTAAATTATATTTAATAAAAACTAATTAAATTATA
131 TTATTATTAAAATATATTTAATAAAAACTAATTAAATTATA
49637419 TTTTATAGTA
Statistics
Matches: 156, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
181 10 0.06
182 146 0.94
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (181 bp):
TAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATA
AAAATTTTAAATTATACAAATTCATATAAGAAAATTTATTACTAAAAAATTTATGAAATTATATA
TTATTATTAAAATATATTTAATAAAAACTAATTAAATTATACAATTTTGTA
Found at i:49637457 original size:119 final size:121
Alignment explanation
Indices: 49637330--49637549 Score: 383
Period size: 120 Copynumber: 1.8 Consensus size: 121
49637320 TAAATTATAC
* *
49637330 AAATTCATATAAGAATATTTATTACTAAAAAA-TTTATTAAATTATATATTTTTATTAAATTATA
1 AAATTCATATAAGAATATTTATGACTAAAAAATTTTATGAAATTATATATTTTTATTAAATTATA
49637394 TTTAATAAA-AACTAA-TTAAATTATATTTTATAGTATTATATAATATGATTTTGGT
66 TTTAATAAATAA-TAATTTAAATTATATTTTATAGTATTATATAATATGATTTTGGT
49637449 AAATTCATATAAGAATATTTATGACTAAAAAATTTTATGAAATTATATATTTTTATTAAATTATA
1 AAATTCATATAAGAATATTTATGACTAAAAAATTTTATGAAATTATATATTTTTATTAAATTATA
49637514 TTTAATAAATAATAATTTTAAATTATATTTTATAGT
66 TTTAATAAATAATAA-TTTAAATTATATTTTATAGT
49637550 TGTTGACACC
Statistics
Matches: 95, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
119 31 0.33
120 43 0.45
121 2 0.02
122 19 0.20
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (121 bp):
AAATTCATATAAGAATATTTATGACTAAAAAATTTTATGAAATTATATATTTTTATTAAATTATA
TTTAATAAATAATAATTTAAATTATATTTTATAGTATTATATAATATGATTTTGGT
Found at i:49639051 original size:3 final size:3
Alignment explanation
Indices: 49639040--49639103 Score: 92
Period size: 3 Copynumber: 21.3 Consensus size: 3
49639030 CAATAATACC
* * * *
49639040 AAT ACT AAT AAT AGT AAA AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49639088 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
49639104 GCAAAAGTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49639599 original size:12 final size:12
Alignment explanation
Indices: 49639582--49639609 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
49639572 GGCTCCAGTC
49639582 GCCGTCCGTCGT
1 GCCGTCCGTCGT
49639594 GCCGTCCGTCGT
1 GCCGTCCGTCGT
49639606 GCCG
1 GCCG
49639610 GCGTTGCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.36, T:0.21
Consensus pattern (12 bp):
GCCGTCCGTCGT
Found at i:49640675 original size:174 final size:174
Alignment explanation
Indices: 49640414--49641471 Score: 1947
Period size: 174 Copynumber: 6.1 Consensus size: 174
49640404 TTTAGAGAGG
* * * *
49640414 TAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCTA
1 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
*
49640479 TTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
66 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
49640544 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
131 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
* * * * * * *
49640588 CAAGATCTGCATTTCTTCGGTCT-GTTCCACTGTAATCTCAGGGAAATAATACCTGATGCGATCT
1 TAAGATCTGCAATTCTTCGGTCTACTT-CGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCT
49640652 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGA
65 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGA
49640717 GATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
130 GATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
49640762 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
49640827 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
66 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
49640892 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
131 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
* * *
49640936 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAATCTCAGGGAAATAATACCTGATGCGATCTA
1 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
49641001 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
66 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
49641066 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
131 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
49641110 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
49641175 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
66 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
49641240 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
131 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
49641284 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
49641349 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
66 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
*
49641414 ATAGGATTATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
131 ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
*
49641458 TAAGATCTGAAATT
1 TAAGATCTGCAATT
49641472 TCCAACCTAT
Statistics
Matches: 857, Mismatches: 25, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
173 1 0.00
174 854 1.00
175 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (174 bp):
TAAGATCTGCAATTCTTCGGTCTACTTCGCTGTAACCTCAGGGAGATAAGACCTGATGCGATCTA
CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAG
ATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
Found at i:49642137 original size:53 final size:53
Alignment explanation
Indices: 49642074--49642179 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
49642064 ACAAAATTTG
49642074 TACCATCATTCTCCCACTACAATCCAAGGGTAGAAATATGGTTTTTCCTCAAT
1 TACCATCATTCTCCCACTACAATCCAAGGGTAGAAATATGGTTTTTCCTCAAT
49642127 TACCATCATTCTCCCACTACAATCCAAGGGTAGAAATATGGTTTTTCCTCAAT
1 TACCATCATTCTCCCACTACAATCCAAGGGTAGAAATATGGTTTTTCCTCAAT
49642180 CCTCTTTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (53 bp):
TACCATCATTCTCCCACTACAATCCAAGGGTAGAAATATGGTTTTTCCTCAAT
Found at i:49643943 original size:9 final size:9
Alignment explanation
Indices: 49643931--49643960 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
49643921 CTATTTTGAC
49643931 TTTGATTTT
1 TTTGATTTT
49643940 TTTGATTTTT
1 TTTGA-TTTT
49643950 TTTGATTTT
1 TTTGATTTT
49643959 TT
1 TT
49643961 GAATTCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTGATTTT
Found at i:49643951 original size:10 final size:10
Alignment explanation
Indices: 49643931--49643960 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
49643921 CTATTTTGAC
49643931 TTTGA-TTTT
1 TTTGATTTTT
49643940 TTTGATTTTT
1 TTTGATTTTT
49643950 TTTGATTTTT
1 TTTGATTTTT
49643960 T
1 T
49643961 GAATTCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (10 bp):
TTTGATTTTT
Found at i:49648878 original size:38 final size:37
Alignment explanation
Indices: 49648843--49648915 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
49648833 TATATATACT
49648843 TATAAAAATAA-AAATAT-GTATATGTATATAGATATA
1 TATAAAAA-AAGAAATATAGTATATGTATATAGATATA
*
49648879 TATAAAAAAAGAAATATGAGTATATGTATATATATAT
1 TATAAAAAAAGAAATAT-AGTATATGTATATAGATAT
49648916 TAAACAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 2 0.06
36 14 0.42
38 17 0.52
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (37 bp):
TATAAAAAAAGAAATATAGTATATGTATATAGATATA
Found at i:49648915 original size:36 final size:34
Alignment explanation
Indices: 49648832--49648919 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 34
49648822 ATACATATAA
49648832 ATATATATACTTATAAAAATAAAAATATGTATATGT
1 ATATATATA--TATAAAAATAAAAATATGTATATGT
49648868 ATATAGATATATATAAAAA-AAGAAATATGAGTATATGT
1 ATAT--ATATATATAAAAATAA-AAATAT--GTATATGT
49648906 ATATATATAT-TAAA
1 ATATATATATATAAA
49648920 CAAATTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
35 6 0.13
36 24 0.51
38 17 0.36
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (34 bp):
ATATATATATATAAAAATAAAAATATGTATATGT
Found at i:49649057 original size:3 final size:3
Alignment explanation
Indices: 49649046--49649103 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
49649036 CAATAATACC
* * * *
49649046 AAT ACT AAT AAT AGT AAA AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49649094 AAT AAT AAT A
1 AAT AAT AAT A
49649104 GCAAAAGTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49649595 original size:12 final size:12
Alignment explanation
Indices: 49649578--49649605 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
49649568 GGCTCCAGTC
49649578 GCCGTCCGTCGT
1 GCCGTCCGTCGT
49649590 GCCGTCCGTCGT
1 GCCGTCCGTCGT
49649602 GCCG
1 GCCG
49649606 GCGTTGCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.36, T:0.21
Consensus pattern (12 bp):
GCCGTCCGTCGT
Found at i:49650239 original size:24 final size:22
Alignment explanation
Indices: 49650211--49650289 Score: 63
Period size: 27 Copynumber: 3.4 Consensus size: 22
49650201 ATTATATATT
49650211 TTTATTAAATTATATTTAATAA
1 TTTATTAAATTATATTTAATAA
* *
49650233 TAATTATGTTAAAATATGATTAAATAA
1 T--TTA--TTAAATTAT-ATTTAATAA
*
49650260 TTTATT-ATTTATA-TTAATAA
1 TTTATTAAATTATATTTAATAA
49650280 TCTTATTAAA
1 T-TTATTAAA
49650290 ATTTAATAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
20 7 0.16
21 6 0.14
22 6 0.14
23 2 0.05
24 3 0.07
25 3 0.07
26 8 0.18
27 9 0.20
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTATTAAATTATATTTAATAA
Found at i:49650486 original size:16 final size:16
Alignment explanation
Indices: 49650467--49650512 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
49650457 CTATTATGCC
**
49650467 TCTATTCCATTACGTA
1 TCTATTCCATTACACA
*
49650483 TCTATTCCATTACACC
1 TCTATTCCATTACACA
49650499 TCTATTCCATTACA
1 TCTATTCCATTACA
49650513 GCGAACCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.41
Consensus pattern (16 bp):
TCTATTCCATTACACA
Found at i:49658020 original size:21 final size:20
Alignment explanation
Indices: 49657994--49658066 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
49657984 ACATATATGT
49657994 ATAATAATGATGAAAATAATA
1 ATAATAAT-ATGAAAATAATA
49658015 ATAATAATAGTGAAAATAAATA
1 ATAATAATA-TGAAAAT-AATA
49658037 AT-ATAATAAT-AAATATAATA
1 ATAATAAT-ATGAAA-ATAATA
* *
49658057 GTAACAATAT
1 ATAATAATAT
49658067 TAGTAATATG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.24
21 27 0.60
22 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAATAATATGAAAATAATA
Found at i:49658038 original size:16 final size:15
Alignment explanation
Indices: 49658009--49658051 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
49657999 AATGATGAAA
49658009 ATAATAAT-AATAAT
1 ATAATAATAAATAAT
49658023 AGTGAA-AATAAATAAT
1 A-T-AATAATAAATAAT
49658039 ATAATAATAAATA
1 ATAATAATAAATA
49658052 TAATAGTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 13 0.52
16 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:49659400 original size:53 final size:53
Alignment explanation
Indices: 49659320--49659430 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 53
49659310 GCTACCCCTC
* *
49659320 TTTGCTCATTATCGTATAACGAGAATAGAGCAAATACATAAAGAGAGGTCAAT
1 TTTGCTCATTATCGTATAACGAGAATAGAGCAAAGACATAAAGAGAGGCCAAT
*
49659373 TTTGCTCATTATCGTATAACGGGAATAGAGCAAAGACATAAAGAGAGGCCAAT
1 TTTGCTCATTATCGTATAACGAGAATAGAGCAAAGACATAAAGAGAGGCCAAT
49659426 TTTGC
1 TTTGC
49659431 CTGGTCTTGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (53 bp):
TTTGCTCATTATCGTATAACGAGAATAGAGCAAAGACATAAAGAGAGGCCAAT
Found at i:49660226 original size:75 final size:72
Alignment explanation
Indices: 49660007--49660239 Score: 292
Period size: 73 Copynumber: 3.2 Consensus size: 72
49659997 ATAAATTGAA
** * * *
49660007 AAAAACATTAATTGAGAATACCTCAGCGTGCCTCGAGGCTCAACTCACCTCTTGCAATATGAGTT
1 AAAAACAGAAATTGAAAAGACCTCAGCGTGCCT-GAGGCTCAACTCACCTCTCGCAATATGAGTT
49660072 GA--TTTG
65 GATTTTTG
** *
49660078 ATGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCGATATGA
1 AAAAACAGAAATTGAAAAGACCTCAGC--GT--GCCTGAGGCTCAACTCACCTCTCGCAATATGA
49660142 GTTGATTTTTG
62 GTTGATTTTTG
*
49660153 ACAAACAGAAATTGAAAAGACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAAGACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
49660218 GATTTTTTTG
65 GA--TTTTTG
49660228 AAAAACAGAAAT
1 AAAAACAGAAAT
49660240 CAAAAGGCTT
Statistics
Matches: 140, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
71 22 0.16
72 2 0.01
73 67 0.48
75 49 0.35
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (72 bp):
AAAAACAGAAATTGAAAAGACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTG
Found at i:49660353 original size:235 final size:234
Alignment explanation
Indices: 49659913--49660385 Score: 564
Period size: 235 Copynumber: 2.0 Consensus size: 234
49659903 GAAAACAGAA
* * * * * *
49659913 TTTGCCAAACAAATTTGAAAATACCTCGGCATGTGACCTGAGGTTCAACTCACCTCTCGTAATAT
1 TTTGACAAACAAAATTGAAAAGACCTCAGCA-GTGACCTGAGGCTCAACTCACCTCTCGCAATAT
** * *
49659978 GAGTTGATTCTTGAAAAGTATAAATTGAAAAAAACATTAATTGAGAATACCTCAGCGTGCCTCGA
65 GAGTTGATTCTTGAAAAACAGAAATTGAAAAAAACATTAATTGAAAATACCTCAGCGTGCCTCGA
* * ** *
49660043 GGCTCAACTCACCTCTTGCAATATGAGTTGATTTGATGAACAGAAATTGAAAAGACCTCAGCATG
130 GGCTCAACTCACCTCTCGCAATATGAGTTGAATTGAAAAACAAAAATTGAAAAGACCTCAGCA-G
* * *
49660108 TGAGCCGAGGCTCAACTCACCTCTCGCGATATGAGTTGATT
194 TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
*
49660149 TTTGACAAACAGAAATTGAAAAGACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTTGACAAACA-AAATTGAAAAGACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
* * ** *
49660213 GAGTTGATTTTTTTGAAAAACAGAAA-T-CAAAAGGC-TTAATTGAAAATACCTCGGCGTGTGTC
65 GAGTTGA--TTCTTGAAAAACAGAAATTGAAAAAAACATTAATTGAAAATACCTCAGC--GTG-C
*
49660275 CT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATT-AAAACACAAAAATTGAAAATACCT
125 CTCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-AATTGAAAA-ACAAAAATTGAAAAGACCT
* *
49660338 CAGC-GTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATT
188 CAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
49660384 TT
1 TT
49660386 GAAAAAGTAG
Statistics
Matches: 202, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
234 18 0.09
235 81 0.40
236 47 0.23
237 56 0.28
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (234 bp):
TTTGACAAACAAAATTGAAAAGACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTCTTGAAAAACAGAAATTGAAAAAAACATTAATTGAAAATACCTCAGCGTGCCTCGAG
GCTCAACTCACCTCTCGCAATATGAGTTGAATTGAAAAACAAAAATTGAAAAGACCTCAGCAGTG
ACCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
Found at i:49660374 original size:162 final size:163
Alignment explanation
Indices: 49660087--49660385 Score: 433
Period size: 162 Copynumber: 1.8 Consensus size: 163
49660077 GATGAACAGA
* **
49660087 AATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCGATATGAGTTGATTTTT
1 AATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATT
* * * * *
49660152 GACAAACAGAAATTGAAAAGACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
66 GAAAAACAAAAATTGAAAAGACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGC
49660217 TGATTTTTTTGAAAAACAGAAATCAAAAGGCTT
131 TGATTTTTTTGAAAAACAGAAATCAAAAGGCTT
* * * *
49660250 AATTGAAAATACCTCGGCGTGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-AAT
1 AATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATAAT
* *
49660313 T-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGA
65 TGAAAA-ACAAAAATTGAAAAGACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
49660377 GCTGATTTT
129 GCTGATTTT
49660386 GAAAAAGTAG
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
161 3 0.03
162 65 0.54
163 52 0.43
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (163 bp):
AATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATT
GAAAAACAAAAATTGAAAAGACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGC
TGATTTTTTTGAAAAACAGAAATCAAAAGGCTT
Found at i:49660703 original size:75 final size:75
Alignment explanation
Indices: 49660529--49660865 Score: 430
Period size: 75 Copynumber: 4.5 Consensus size: 75
49660519 AGTGTGTAAT
* * *
49660529 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAATACT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
* **
49660594 TCAGCATGTGAA
66 TCA--ACGTGTC
* *
49660606 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTGAAAACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
49660671 TCAACGTGTC
66 TCAACGTGTC
* ** * * * *
49660681 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA---ATTTTGAAAACAGAAATTGGAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
*
49660743 TCAGCGTGTC
66 TCAACGTGTC
** *
49660753 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTT-AACAACAGAAATTGAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAA-AACAGAAATTGAAAATAC
*
49660817 CTCAGCGTGTC
65 CTCAACGTGTC
*
49660828 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
49660866 GAAAAACAAA
Statistics
Matches: 233, Mismatches: 23, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
72 65 0.28
74 2 0.01
75 103 0.44
77 63 0.27
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (75 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
TCAACGTGTC
Found at i:49660775 original size:147 final size:148
Alignment explanation
Indices: 49660529--49660883 Score: 441
Period size: 147 Copynumber: 2.4 Consensus size: 148
49660519 AGTGTGTAAT
* * * *
49660529 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAATACT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---ATTTTGAAAACAGAAATTGAAAATACC
49660594 TCAGCATGTGAACTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTGAA-AACAAA
63 TCAGCA-GTGAACTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTT-AACAACAAA
49660658 AATTGAAAATACCTCAACGTGTC
126 AATTGAAAATACCTCAACGTGTC
* ** * * *
49660681 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGGAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCA
** ** * *
49660746 GC-GTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTG
66 GCAGTGAACTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTAACAACAAAAATTG
* *
49660810 AAATTACCTCAGCGTGTC
131 AAAATACCTCAACGTGTC
* *
49660828 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-A-TTTGAAAAACAAAAATT-AAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAAA
49660884 GGCTTAACTC
Statistics
Matches: 175, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
145 6 0.03
146 14 0.08
147 98 0.56
149 27 0.15
152 30 0.17
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (148 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCA
GCAGTGAACTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTAACAACAAAAATTG
AAAATACCTCAACGTGTC
Found at i:49661031 original size:71 final size:70
Alignment explanation
Indices: 49660883--49661058 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
49660873 AAAAATTAAA
* * * * * * **
49660883 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG
49660947 CCCCG
66 CCCCG
*
49660952 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAAAAAAAACTAAAAATACCTCAACGT
* **
49661017 GTCTTG
65 GCCCCG
49661023 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
49661059 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 26 0.28
70 6 0.07
71 60 0.65
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:49673412 original size:15 final size:15
Alignment explanation
Indices: 49673392--49673431 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
49673382 ACATATATGT
49673392 ATAATAAT-GATGAAA
1 ATAATAATAG-TGAAA
49673407 ATAATAATAGTGAAA
1 ATAATAATAGTGAAA
49673422 ATAAATAATA
1 AT-AATAATA
49673432 TAATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
ATAATAATAGTGAAA
Found at i:49675622 original size:13 final size:13
Alignment explanation
Indices: 49675604--49675630 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49675594 CAACCCCTCG
49675604 ACAATAATATAAC
1 ACAATAATATAAC
49675617 ACAATAATATAAC
1 ACAATAATATAAC
49675630 A
1 A
49675631 TAGGAAAGAA
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:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (13 bp):
ACAATAATATAAC
Found at i:49676115 original size:15 final size:15
Alignment explanation
Indices: 49676091--49676146 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
49676081 ATTTTGAATT
*
49676091 TTTTTTATTTTAAAA
1 TTTTTAATTTTAAAA
* *
49676106 TTTTTAATTTTTATA
1 TTTTTAATTTTAAAA
**
49676121 TTTCAAATTTTAAAA
1 TTTTTAATTTTAAAA
49676136 --TTTAATTTTAA
1 TTTTTAATTTTAA
49676147 TTATTAGTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.28
15 23 0.72
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAATTTTAAAA
Found at i:49676118 original size:21 final size:21
Alignment explanation
Indices: 49676092--49676146 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
49676082 TTTTGAATTT
*
49676092 TTTTTATTTTAAAATTTTTAA
1 TTTTTATTTTAAAATTTTAAA
*
49676113 TTTTTATATTTCAAATTTTAAA
1 TTTTTAT-TTTAAAATTTTAAA
* *
49676135 ATTTAATTTTAA
1 TTTTTATTTTAA
49676147 TTATTAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATTTTAAAATTTTAAA
Found at i:49676330 original size:26 final size:28
Alignment explanation
Indices: 49676262--49676329 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
49676252 ATAAAAAACA
*
49676262 ACCAAAATGT-TATAACTTTTTTTATTT
1 ACCAAAATATATATAACTTTTTTTATTT
*
49676289 ACCAAAATATATATAATTTTTTTTATTT
1 ACCAAAATATATATAACTTTTTTTATTT
**
49676317 ATGAAAATATATA
1 ACCAAAATATATA
49676330 AAAAAACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (28 bp):
ACCAAAATATATATAACTTTTTTTATTT
Found at i:49676481 original size:4 final size:4
Alignment explanation
Indices: 49676472--49676618 Score: 117
Period size: 4 Copynumber: 36.0 Consensus size: 4
49676462 GAAGGAGAGG
*
49676472 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA
* * * *
49676522 G-AA -AAA GAAG GAAA GAAAA GGGAA G-GA GAAGA GAAA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
*
49676570 G-AA G-AA GAAAA GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA
1 GAAA GAAA G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
49676615 GAAA
1 GAAA
49676619 ATGAAAGGAG
Statistics
Matches: 119, Mismatches: 11, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
3 15 0.13
4 76 0.64
5 23 0.19
6 5 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:49676602 original size:45 final size:45
Alignment explanation
Indices: 49676515--49676647 Score: 140
Period size: 45 Copynumber: 3.1 Consensus size: 45
49676505 AAAGGAGAGG
* * *
49676515 AAAGAAAGAAA-AAGAAGGAAAGAAAAGG-GAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAA-GAGAAAAGAAAA
*
49676559 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAG-A-AG-AAA-AAAG
1 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAAGAAAA
* *
49676600 AAAGAAAG-AAGGA-AAGAAAATGAAAGGAGAAGAGAAAA-AAAA
1 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAAGAAAA
49676642 AAAGAA
1 AAAGAA
49676648 GAAGAGGGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
39 15 0.19
40 5 0.06
41 13 0.17
42 14 0.18
43 2 0.03
44 11 0.14
45 16 0.21
46 1 0.01
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.01
Consensus pattern (45 bp):
AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAAGAAAA
Found at i:49676632 original size:16 final size:15
Alignment explanation
Indices: 49676563--49676632 Score: 64
Period size: 16 Copynumber: 5.0 Consensus size: 15
49676553 AGAAAAAAAG
*
49676563 AAAGAAAGAAGAAGA
1 AAAGAAAGGAGAAGA
49676578 AAAGGAAAGGAGAAG-
1 AAA-GAAAGGAGAAGA
49676593 AAA-AAA-GA-AAG-
1 AAAGAAAGGAGAAGA
49676604 AAAG-AAGGA-AAGA
1 AAAGAAAGGAGAAGA
49676617 AAATGAAAGGAGAAGA
1 AAA-GAAAGGAGAAGA
49676633 GAAAAAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
11 8 0.17
12 7 0.15
13 6 0.13
14 1 0.02
15 11 0.23
16 14 0.30
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (15 bp):
AAAGAAAGGAGAAGA
Found at i:49676634 original size:79 final size:77
Alignment explanation
Indices: 49676463--49676652 Score: 246
Period size: 79 Copynumber: 2.5 Consensus size: 77
49676453 GGGGGACCAG
* * *
49676463 AAGGAGAGG-GAA-AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAA
1 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAG-AAGAAAGAAAGAAAGGAGAAGAAAGAAAGAAA
49676526 AAGAAGGAAAGAA
65 AAGAAGGAAAGAA
*
49676539 AAGGGAAGGAGAAGAGAAAAAAAGAAAGAAAGAAG-AAGAAAAGGAAAGGAGAAGAAA-AAAGAA
1 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAAG-AAA-GAAAGGAGAAGAAAGAAAG-A
49676602 AGAAAGAAGGAAAGAA
63 A-AAAGAAGGAAAGAA
* *
49676618 AATGAAAGGAGAAGAGAAAAAAAAAAAG-AAGAAGA
1 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGA
49676653 GGGAAGGAAG
Statistics
Matches: 100, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
76 10 0.10
77 13 0.13
78 38 0.38
79 39 0.39
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (77 bp):
AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAAGAAAGAAAGGAGAAGAAAGAAAGAAAA
AGAAGGAAAGAA
Found at i:49676636 original size:34 final size:33
Alignment explanation
Indices: 49676494--49676677 Score: 94
Period size: 33 Copynumber: 5.5 Consensus size: 33
49676484 GAAAGAAAGA
* * * *
49676494 AAGAAAGAAAG-A-AAGGAGAGGAAAGAAAGAAA
1 AAGAAAGAAAGAAGAAGAAAAGGAAAG-GAGAAG
* ** * *
49676526 AAGAAGGAAAGAA-AAGGGAAGGAGAAGAGAAAAA
1 AAGAAAGAAAGAAGAAGAAAAGGA-AAG-GAGAAG
49676560 AAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAG
1 AAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAG
*
49676593 AAAAAAGAAAGAAAGAAGGAAAGAAAATGAAAGGAGAAG
1 ----AAGAAAGAAAGAA-G-AAGAAAAGGAAAGGAGAAG
* * * * *
49676632 -AGAAAAAAAAAAAGAAGAAGAGGGAAGGA-AGG
1 AAG-AAAGAAAGAAGAAGAAAAGGAAAGGAGAAG
49676664 AA-AAA-AAAGAAGAA
1 AAGAAAGAAAGAAGAA
49676678 AAGAAATGGT
Statistics
Matches: 123, Mismatches: 18, Indels: 24
0.75 0.11 0.15
Matches are distributed among these distances:
30 8 0.07
31 3 0.02
32 12 0.10
33 26 0.21
34 26 0.21
35 16 0.13
37 13 0.11
38 1 0.01
39 18 0.15
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (33 bp):
AAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAG
Found at i:49676638 original size:78 final size:77
Alignment explanation
Indices: 49676463--49676679 Score: 236
Period size: 79 Copynumber: 2.8 Consensus size: 77
49676453 GGGGGACCAG
* *
49676463 AAGGAGAGG-GAA-AGAAAGAAAGAAAGAAAGAAAGAA-AGAAAGAAAGGAGAGGAAAGAAAGAA
1 AAGGAAAGGAGAAGAGAAA-AAAGAAAGAAAG-AAGAAGAGAAAGAAAGGAGAAGAAAGAAAGAA
49676525 AAAGAAGGAAAGAA
64 AAAGAAGGAAAGAA
*
49676539 AAGGGAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGA-AAAGGAAAGGAGAAGAAA-AAAGAA
1 AAGGAAAGGAGAAGAG-AAAAAAGAAAGAAAGAAGAAGAGAAA-GAAAGGAGAAGAAAGAAAG-A
49676602 AGAAAGAAGGAAAGAA
63 A-AAAGAAGGAAAGAA
* * * * *
49676618 AATGAAAGGAGAAGAG-AAAAA-AAA-AAAGAAGAAGAGGGAAGGAAGGAAAAAAAAG-AAGAAA
1 AAGGAAAGGAGAAGAGAAAAAAGAAAGAAAGAAGAAGA-GAAAGAAAGGAGAAGAAAGAAAGAAA
49676679 A
65 A
49676680 GAAATGGTAA
Statistics
Matches: 122, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
74 2 0.02
75 13 0.11
76 24 0.20
77 22 0.18
78 30 0.25
79 31 0.25
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.00
Consensus pattern (77 bp):
AAGGAAAGGAGAAGAGAAAAAAGAAAGAAAGAAGAAGAGAAAGAAAGGAGAAGAAAGAAAGAAAA
AGAAGGAAAGAA
Found at i:49677467 original size:77 final size:78
Alignment explanation
Indices: 49677318--49677463 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 78
49677308 TATTTCGGGT
* *
49677318 TTTTTACCAAAATATTACAAAAAAATAAAAAAAAATACGAAAATATTATAAACTTTTTTTATTTA
1 TTTTTACAAAAATATTACAAAAAAATAAAAAAAAATACCAAAATATTATAAACTTTTTTTATTTA
49677383 CCAAAATAATGGG
66 CCAAAATAATGGG
* * *
49677396 TTTTTACAAAAATATTA-AAAATAA-AAATAAAAATAACCAAAATGTTAT-AA-TTTTTTTATTT
1 TTTTTACAAAAATATTACAAAAAAATAAAAAAAAAT-ACCAAAATATTATAAACTTTTTTTATTT
49677457 ACCAAAA
65 ACCAAAA
49677464 AATATATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
75 18 0.29
76 11 0.18
77 17 0.27
78 16 0.26
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (78 bp):
TTTTTACAAAAATATTACAAAAAAATAAAAAAAAATACCAAAATATTATAAACTTTTTTTATTTA
CCAAAATAATGGG
Found at i:49677914 original size:15 final size:15
Alignment explanation
Indices: 49677894--49677925 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
49677884 TGATCGGCTA
49677894 ATAAATTTAGAAATT
1 ATAAATTTAGAAATT
49677909 ATAAATTTAGAAATT
1 ATAAATTTAGAAATT
49677924 AT
1 AT
49677926 GATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
ATAAATTTAGAAATT
Found at i:49681645 original size:18 final size:18
Alignment explanation
Indices: 49681619--49681663 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
49681609 ATCCCAATGA
*
49681619 TCGCTACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
49681637 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
49681655 TCACCACCA
1 TCGCCACCA
49681664 ACCATGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.49, G:0.04, T:0.31
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:49682836 original size:27 final size:27
Alignment explanation
Indices: 49682764--49682837 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
49682754 AATACGAGTA
49682764 GTGCCGCCAAT--CAGTATGGCACCATTG
1 GTGCCGCCAATGCCA-T-TGGCACCATTG
* *
49682791 GTGCCGCTAATGGCATTGGCACCATTG
1 GTGCCGCCAATGCCATTGGCACCATTG
*
49682818 GTGCCGCCAATGCCTTTGGC
1 GTGCCGCCAATGCCATTGGC
49682838 GTGACCAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 38 0.93
28 1 0.02
29 2 0.05
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (27 bp):
GTGCCGCCAATGCCATTGGCACCATTG
Found at i:49682926 original size:23 final size:23
Alignment explanation
Indices: 49682897--49682940 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
49682887 TTTTGTTTTT
49682897 TATATATTTTGGTAAATAAAATA
1 TATATATTTTGGTAAATAAAATA
49682920 TATATATTTTGGTAAATAAAA
1 TATATATTTTGGTAAATAAAA
49682941 AAAAGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
TATATATTTTGGTAAATAAAATA
Found at i:49690894 original size:33 final size:33
Alignment explanation
Indices: 49690825--49690922 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
49690815 CTATACCCAT
* * *
49690825 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
49690862 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
49690895 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
49690923 ATACATATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:49691323 original size:41 final size:41
Alignment explanation
Indices: 49691139--49691335 Score: 299
Period size: 41 Copynumber: 4.8 Consensus size: 41
49691129 ACTGGCTCTT
*
49691139 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
49691180 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
49691221 AGCCTGCTAGACTTATAGCCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
49691262 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCGTTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
49691303 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
49691336 TAACGATAAA
Statistics
Matches: 145, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 136 0.94
42 2 0.01
43 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:49696121 original size:55 final size:55
Alignment explanation
Indices: 49696038--49696149 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
49696028 GTACAAGTAG
*
49696038 AGTAAAATATATTATCAATATATCAAATATTCACTCAAACAAGAACAGAAGTTAA
1 AGTAAAATACATTATCAATATATCAAATATTCACTCAAACAAGAACAGAAGTTAA
* *
49696093 AGTAAAGTACATTATCAATATATCAAATATTCACTCAAATAAGAACAGAAGTTAA
1 AGTAAAATACATTATCAATATATCAAATATTCACTCAAACAAGAACAGAAGTTAA
49696148 AG
1 AG
49696150 AGTTAAGACT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (55 bp):
AGTAAAATACATTATCAATATATCAAATATTCACTCAAACAAGAACAGAAGTTAA
Found at i:49698883 original size:5 final size:5
Alignment explanation
Indices: 49698866--49698903 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
49698856 TATAATTACC
* *
49698866 AATAT TATAT AATTT AATAT AATAT AATAT AAT-T AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
49698904 AAAAATGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
AATAT
Found at i:49700847 original size:22 final size:22
Alignment explanation
Indices: 49700822--49700913 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
49700812 AAATTCAATA
* *
49700822 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
49700844 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
49700866 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
49700888 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
49700910 TCAA
1 TCAA
49700914 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:49700929 original size:52 final size:51
Alignment explanation
Indices: 49700863--49700965 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
49700853 TTCAAAATTT
* * *
49700863 CTCTCAATTCCCTT-CAAAATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
49700915 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
49700966 TCCATACTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:49700954 original size:21 final size:22
Alignment explanation
Indices: 49700915--49700956 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
49700905 TTCTCTCAAA
49700915 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
49700937 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
49700957 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:49701053 original size:29 final size:29
Alignment explanation
Indices: 49700998--49701053 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
49700988 ATTAAATTTC
49700998 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
*
49701027 ATTTTTTTAA-ATAATTTTAAAATTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTT
49701054 AATATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:49701061 original size:29 final size:29
Alignment explanation
Indices: 49700998--49701061 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
49700988 ATTAAATTTC
*
49700998 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
49701027 ATTTTTTTAA-ATAATTTTAAAATTTTTA
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
49701055 ATATTTT
1 ATTTTTT
49701062 CAACAATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTA
Found at i:49703441 original size:28 final size:28
Alignment explanation
Indices: 49703359--49703779 Score: 367
Period size: 28 Copynumber: 15.5 Consensus size: 28
49703349 AATTAAAAAC
*
49703359 CCTAAATTAATTAAATTAAAAACCCTAAA
1 CCTAACTTAATTAAATTAAAAACCCT-AA
*
49703388 CCCT-ACTTAATTAAA--AACCCTAACCCTAA
1 -CCTAACTTAATTAAATTAA---AAACCCTAA
*
49703417 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
* * *
49703445 CCTTATTTTATTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
* *
49703473 CCTAACCTACTTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
*
49703501 CCTAACCTAATTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
**
49703529 CCTTATTTTAATTAAATTAAAAACCCTAA
1 CC-TAACTTAATTAAATTAAAAACCCTAA
49703558 CCT-AC----TT-AATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
49703580 --T---TTAATTAAATTAAAAACCCTAAA
1 CCTAACTTAATTAAATTAAAAACCCT-AA
*
49703604 CCCT-ACTTAATTAAA--AACCCTAACCCTAA
1 -CCTAACTTAATTAAATTAA---AAACCCTAA
*
49703633 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
*
49703661 CCTAACCTAATTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
**
49703689 CCTTATTTTAATTAAATTAAAAACCCTAA
1 CC-TAACTTAATTAAATTAAAAACCCTAA
*
49703718 CC---C-TACTT-AATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
49703741 --T---TTAATTAAATTAAAAACCCTAAA
1 CCTAACTTAATTAAATTAAAAACCCT-AA
49703765 CCCT-ACTTAATTAAA
1 -CCTAACTTAATTAAA
49703780 AACCCTAATT
Statistics
Matches: 329, Mismatches: 28, Indels: 69
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.00
22 21 0.06
23 43 0.13
24 8 0.02
27 6 0.02
28 129 0.39
29 102 0.31
30 15 0.05
31 4 0.01
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (28 bp):
CCTAACTTAATTAAATTAAAAACCCTAA
Found at i:49703611 original size:216 final size:206
Alignment explanation
Indices: 49703327--49703794 Score: 704
Period size: 216 Copynumber: 2.2 Consensus size: 206
49703317 ACATTATTTG
*
49703327 ATTAAAAACCCTAACCTTACTTAATTAAAAACCCTAAATTAATTAAATTAAAAACCCTAAACCCT
1 ATTAAAAACCCTAACC-TACTTAATTAAAAACCCTAATTTAATTAAATTAAAAACCCTAAACCCT
* ** *
49703392 ACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCTTATTTTATT
65 ACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCTAACCTAATT
*
49703457 AAATTAAAAACCCTAACC-TAACCTACTTAAATTAAAAACCCTAACCTAACCTAATTAAATTAAA
130 AAATTAAAAACCCTAACCTTAACCTAATTAAATTAAAAACCCTAA-C---CCTAATT-AATTAAA
49703521 AACCCTAACCTTATTTTAATTAA
190 AACCCT-A----A-TTTAATTAA
49703544 ATTAAAAACCCTAACCTACTTAATTAAAAACCCTAATTTAATTAAATTAAAAACCCTAAACCCTA
1 ATTAAAAACCCTAACCTACTTAATTAAAAACCCTAATTTAATTAAATTAAAAACCCTAAACCCTA
49703609 CTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCTAACCTAATTA
66 CTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCTAACCTAATTA
*** *
49703674 AATTAAAAACCCTAACCTTATTTTAATTAAATTAAAAACCCTAACCCTACTTAATTAAAAACCCT
131 AATTAAAAACCCTAACCTTAACCTAATTAAATTAAAAACCCTAACCCTAATTAATTAAAAACCCT
49703739 AATTTAATTAA
196 AATTTAATTAA
*
49703750 ATTAAAAACCCTAAACCCTACTTAATTAAAAACCCTAATTAAATT
1 ATTAAAAACCCT-AA-CCTACTTAATTAAAAACCCTAATTTAATT
49703795 GTAGTTTTAC
Statistics
Matches: 237, Mismatches: 11, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
206 21 0.09
207 3 0.01
208 28 0.12
211 1 0.00
212 13 0.05
213 6 0.03
216 127 0.54
217 38 0.16
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.30
Consensus pattern (206 bp):
ATTAAAAACCCTAACCTACTTAATTAAAAACCCTAATTTAATTAAATTAAAAACCCTAAACCCTA
CTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCTAACCTAATTA
AATTAAAAACCCTAACCTTAACCTAATTAAATTAAAAACCCTAACCCTAATTAATTAAAAACCCT
AATTTAATTAA
Found at i:49703629 original size:23 final size:23
Alignment explanation
Indices: 49703327--49703631 Score: 130
Period size: 23 Copynumber: 11.8 Consensus size: 23
49703317 ACATTATTTG
*
49703327 ATTAAAAACCCTAACCTTACTTA
1 ATTAAAAACCCTAACCCTACTTA
** *
49703350 ATTAAAAACCCTAA-ATTAATTAA
1 ATTAAAAACCCTAACCCTACTT-A
49703373 ATTAAAAACCCTAAACCCTACTTA
1 ATTAAAAACCCT-AACCCTACTTA
*
49703397 ATTAAAAACCCTAACCCTAACCTA
1 ATTAAAAACCCTAACCCT-ACTTA
****
49703421 ATTTAATTAAATTAAAAACCCTAACCTTA
1 A-TTAA--AAA-CCCTAACCCT-A-CTTA
49703450 TTTTATTAAATTAAAAACCCTAACCTAACCTACTTAA
1 ----ATT-----AAAAACCCTAA-C---CCTACTT-A
*
49703487 ATTAAAAACCCTAACCTAACCTAATTAA
1 ATTAAAAACCCTAA-C---CCTACTT-A
* *
49703515 ATTAAAAACCCTAACCTTATTTTAATTAA
1 ATTAAAAACCCTAACC-----CTACTT-A
49703544 ATTAAAAACCCTAA-CCTACTTA
1 ATTAAAAACCCTAACCCTACTTA
** *
49703566 ATTAAAAACCCTAA-TTTAATTAA
1 ATTAAAAACCCTAACCCTACTT-A
49703589 ATTAAAAACCCTAAACCCTACTTA
1 ATTAAAAACCCT-AACCCTACTTA
49703613 ATTAAAAACCCTAACCCTA
1 ATTAAAAACCCTAACCCTA
49703632 ACCTAATTTA
Statistics
Matches: 226, Mismatches: 25, Indels: 62
0.72 0.08 0.20
Matches are distributed among these distances:
22 24 0.11
23 57 0.25
24 36 0.16
25 12 0.05
27 4 0.02
28 47 0.21
29 24 0.11
32 2 0.01
33 4 0.02
34 2 0.01
35 4 0.02
36 3 0.01
37 4 0.02
38 3 0.01
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAAAAACCCTAACCCTACTTA
Found at i:49703639 original size:24 final size:22
Alignment explanation
Indices: 49703543--49703628 Score: 118
Period size: 22 Copynumber: 3.8 Consensus size: 22
49703533 ATTTTAATTA
49703543 AATTAAAAACCCTAACCTACTT
1 AATTAAAAACCCTAACCTACTT
** *
49703565 AATTAAAAACCCTAATTTAATT
1 AATTAAAAACCCTAACCTACTT
49703587 AAATTAAAAACCCTAAACCCTACTT
1 -AATTAAAAACCCT-AA-CCTACTT
49703612 AATTAAAAACCCTAACC
1 AATTAAAAACCCTAACC
49703629 CTAACCTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 21 0.38
23 15 0.27
24 15 0.27
25 4 0.07
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (22 bp):
AATTAAAAACCCTAACCTACTT
Found at i:49703660 original size:23 final size:24
Alignment explanation
Indices: 49703633--49703787 Score: 129
Period size: 23 Copynumber: 6.2 Consensus size: 24
49703623 CTAACCCTAA
49703633 CCTAA-TTTAATTAAATTAAAAAC
1 CCTAACTTTAATTAAATTAAAAAC
*
49703656 CCTAACCTAACCTAATTAAATTAAAAAC
1 CCTAA-CT---TTAATTAAATTAAAAAC
49703684 CCTAACCTTATTTTAATTAAATTAAAAAC
1 CCTAA-C----TTTAATTAAATTAAAAAC
** *
49703713 CCTAACCCTACTT-AATTAAAAAC
1 CCTAACTTTAATTAAATTAAAAAC
49703736 CCTAA-TTTAATTAAATTAAAAAC
1 CCTAACTTTAATTAAATTAAAAAC
** *
49703759 CCTAAACCCTACTT-AATTAAAAAC
1 CCT-AACTTTAATTAAATTAAAAAC
49703783 CCTAA
1 CCTAA
49703788 TTAAATTGTA
Statistics
Matches: 109, Mismatches: 11, Indels: 24
0.76 0.08 0.17
Matches are distributed among these distances:
22 4 0.04
23 35 0.32
24 19 0.17
25 5 0.05
28 24 0.22
29 21 0.19
32 1 0.01
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (24 bp):
CCTAACTTTAATTAAATTAAAAAC
Found at i:49703738 original size:17 final size:18
Alignment explanation
Indices: 49703716--49703750 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49703706 TAAAAACCCT
49703716 AACCCT-ACTTAATTAAA
1 AACCCTAACTTAATTAAA
*
49703733 AACCCTAATTTAATTAAA
1 AACCCTAACTTAATTAAA
49703751 TTAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AACCCTAACTTAATTAAA
Found at i:49707220 original size:125 final size:124
Alignment explanation
Indices: 49706955--49707235 Score: 334
Period size: 125 Copynumber: 2.3 Consensus size: 124
49706945 CCACGAGGGC
* *
49706955 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTCACACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * * * * **
49707020 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAACATCCTGGTATCA
66 AAATCGCATCCACGAGGCCACGACTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
* * *
49707079 GCGATTTTATATTATTTCCTCAGAAAACGTCAAAAAAAAATTATTT-CTCACATGACC-ACTGTA
1 GCGATTTCACACTATTTCCTCAG-AAACGTC-AAAAAAAATTATTTCCT-ACATGACCAACTGTA
* * * *
49707142 GCGAAATCGCATCCTCGAGGCCACTACTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
63 GCGAAATCGCATCCACGAGGCCACGACTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
* *
49707204 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTCACACTATTT-CCTCAGAAACGTCAA
49707236 CTCGAAAAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
123 2 0.02
124 26 0.20
125 81 0.61
126 23 0.17
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (124 bp):
GCGATTTCACACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCATCCACGAGGCCACGACTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
Found at i:49708134 original size:29 final size:29
Alignment explanation
Indices: 49708099--49708162 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
49708089 TTTGATAAAT
49708099 TAAAAATTAAGTATTAAAAATATAAGTTA
1 TAAAAATTAAGTATTAAAAATATAAGTTA
* * *
49708128 TGAAAATTAATTATTAAAAATTTAAGTTA
1 TAAAAATTAAGTATTAAAAATATAAGTTA
49708157 TAAAAA
1 TAAAAA
49708163 AATTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (29 bp):
TAAAAATTAAGTATTAAAAATATAAGTTA
Found at i:49708162 original size:16 final size:15
Alignment explanation
Indices: 49708097--49708168 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 15
49708087 TATTTGATAA
49708097 ATTAAAAATTAAG-T
1 ATTAAAAATTAAGTT
49708111 ATTAAAAATATAAGTT
1 ATTAAAAAT-TAAGTT
*
49708127 A-TGAAAATTAA-TT
1 ATTAAAAATTAAGTT
49708140 ATTAAAAATTTAAGTT
1 ATTAAAAA-TTAAGTT
*
49708156 ATAAAAAAATTAA
1 AT-TAAAAATTAA
49708169 AATAAAATAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.06
14 17 0.35
15 14 0.29
16 10 0.20
17 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (15 bp):
ATTAAAAATTAAGTT
Found at i:49718422 original size:11 final size:11
Alignment explanation
Indices: 49718408--49718495 Score: 69
Period size: 11 Copynumber: 8.4 Consensus size: 11
49718398 ACAAAAATTA
49718408 AAAAGTATTTT
1 AAAAGTATTTT
*
49718419 AAAAATATTTT
1 AAAAGTATTTT
49718430 AAAAGTATTTTT
1 AAAAGTA-TTTT
**
49718442 AAAA--A-AAT
1 AAAAGTATTTT
*
49718450 AAAAATATTTT
1 AAAAGTATTTT
***
49718461 AAAA-T-TAAA
1 AAAAGTATTTT
49718470 AAAAGTATTTT
1 AAAAGTATTTT
49718481 AAAAGTATTTT
1 AAAAGTATTTT
49718492 AAAA
1 AAAA
49718496 TTTAAAAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
8 5 0.08
9 5 0.08
10 4 0.07
11 37 0.63
12 8 0.14
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:49718423 original size:20 final size:20
Alignment explanation
Indices: 49718400--49718484 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
49718390 AAATTAAAAC
49718400 AAAAATTAAAAAGTATTTTA
1 AAAAATTAAAAAGTATTTTA
*
49718420 AAAATATTTTAAAAGTATTTTTA
1 AAAA-A-TTAAAAAGTA-TTTTA
*
49718443 AAAAAATAAAAA-TATTTT-
1 AAAAATTAAAAAGTATTTTA
49718461 -AAAATTAAAAAAAGTATTTTA
1 AAAAATT--AAAAAGTATTTTA
49718482 AAA
1 AAA
49718485 GTATTTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
17 5 0.09
19 9 0.17
20 12 0.23
21 6 0.11
22 12 0.23
23 9 0.17
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
AAAAATTAAAAAGTATTTTA
Found at i:49720508 original size:11 final size:11
Alignment explanation
Indices: 49720492--49720539 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
49720482 GGTGACGAAG
*
49720492 AAATAAAAGGA
1 AAATAAAAAGA
49720503 AAATAAAAAGA
1 AAATAAAAAGA
49720514 AAAGTTAAAAAGA
1 AAA--TAAAAAGA
*
49720527 AACT-AAAAGA
1 AAATAAAAAGA
49720537 AAA
1 AAA
49720540 AGAAACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
13 10 0.31
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.10
Consensus pattern (11 bp):
AAATAAAAAGA
Found at i:49720528 original size:24 final size:23
Alignment explanation
Indices: 49720495--49720539 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
49720485 GACGAAGAAA
*
49720495 TAAAAGGAAAATAAAAAGAAAAGT
1 TAAAAAGAAAAT-AAAAGAAAAGT
*
49720519 TAAAAAGAAACTAAAAGAAAA
1 TAAAAAGAAAATAAAAGAAAA
49720540 AGAAACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.11
Consensus pattern (23 bp):
TAAAAAGAAAATAAAAGAAAAGT
Found at i:49725742 original size:24 final size:23
Alignment explanation
Indices: 49725715--49725759 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
49725705 ATTTTTGATT
49725715 ATTTTTAGTGTTTAAATTTTTAAA
1 ATTTTTAGT-TTTAAATTTTTAAA
*
49725739 ATTTTTAGTTTTGAATTTTTA
1 ATTTTTAGTTTTAAATTTTTA
49725760 GTCATGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
ATTTTTAGTTTTAAATTTTTAAA
Found at i:49727592 original size:117 final size:118
Alignment explanation
Indices: 49727319--49728115 Score: 990
Period size: 117 Copynumber: 6.7 Consensus size: 118
49727309 GTCTTCTTCT
* * * * *
49727319 TCTTCTAGTAATCTTGCTGGTGGATTGTTTCCTTCGTCGTCACTAGGTGGTTTCTCACCGGCGAA
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCC-T--TCGTCACTAGGTGGTTTCTCGCCGGCGAA
* * *
49727384 TGGACTCTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCGCCGATGACCCCAATG
63 TGGACTCTCTTCCTCAACG--TGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
* ** * *
49727442 CCTGCTAGTAATCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * *
49727507 ACTCTCTTCCTCAACGT-CTTGTAGTAATCGTTCCTCACGGATGAGCTCAATG
66 ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
* * *
49727559 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCATCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * * * *
49727624 ACTTTCTTCCTCGACGTCTGCTTGTAGTAACCGTTTTTCACCCATGACCTCAATG
66 ACTCTCTTCCTCAACG--TGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
*
49727679 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCAAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* ** * *
49727744 ACTCTTTTCCTCAACGT-CTTGTAGTTTTCGTTTCTCACCAATGACCTTAATG
66 ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
*
49727796 TCTTTTAGTAATCTTTCCGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * **
49727861 ACTTTCTTCCTCAACAT-CTTGTAGTTTTCGTTTCTCACCGATGACCTCAATG
66 ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
* *
49727913 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGCGGTTTCTCTCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
** *
49727978 ACTCTCTTCCTCGACATC-TGCTTGTAGTTTTCGTTTTCGTTTCTCACCGATGACCTCAATT
66 ACTCTCTTCCTC-A-A-CGTGCTTGTA------GTAATCGTTTCTCACCGATGACCTCAATG
* * * * * * *
49728039 TCTTTTAGTAATCTTTCTGGGGGCTTATCTCCTTCGTCACTAGGTGGTTTCTCACCAGCAAACGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
*
49728104 ACTTTCTTCCTC
66 ACTCTCTTCCTC
49728116 GACATTCTCT
Statistics
Matches: 599, Mismatches: 62, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
117 315 0.53
118 3 0.01
119 3 0.01
120 156 0.26
122 1 0.00
123 25 0.04
126 96 0.16
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (118 bp):
TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
Found at i:49727798 original size:237 final size:237
Alignment explanation
Indices: 49727319--49728118 Score: 1077
Period size: 237 Copynumber: 3.3 Consensus size: 237
49727309 GTCTTCTTCT
* * * * *
49727319 TCTTCTAGTAATCTTGCTGGTGGATTGTTTCCTTCGTCGTCACTAGGTGGTTTCTCACCGGCGAA
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCC-T--TCGTCACTAGGTGGTTTCTCACCGGCGAA
* * * * **
49727384 TGGACTCTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCGCCGATGACCCCAATGCCTGCTA
63 TGGACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTA
* *
49727449 GTAATCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCT
128 GTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCT
** * * *
49727514 TCCTCAACGTCTTGTAGTAATCGTTCCTCACGGATGAGCTCAATG
193 TCCTCAACGTCTTGTAGTTTTCGTTTCTCACCGATGACCTCAATG
* *
49727559 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCATCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCACCGGCGAATGG
* * *
49727624 ACTTTCTTCCTCGACGTCTGCTTGTAGTAACCGTTTTTCACCCATGACCTCAATGTCTTTTAGTA
66 ACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
* *
49727689 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCAAATGGACTCTTTTCC
131 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCC
* *
49727754 TCAACGTCTTGTAGTTTTCGTTTCTCACCAATGACCTTAATG
196 TCAACGTCTTGTAGTTTTCGTTTCTCACCGATGACCTCAATG
* * * *
49727796 TCTTTTAGTAATCTTTCCGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCACCGGCGAATGG
* * **
49727861 ACTTTCTTCCTCAAC--AT-CTTGTAGTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
66 ACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
* *
49727923 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGCGGTTTCTCTCCGGCGAATGGACTCTCTTCC
131 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCC
*
49727988 TCGACATC-TGCTTGTAGTTTTCGTTTTCGTTTCTCACCGATGACCTCAATT
196 TC-A-A-CGT-CTTGTA------GTTTTCGTTTCTCACCGATGACCTCAATG
* * * *
49728039 TCTTTTAGTAATCTTTCTGGGGGCTTATCTCCTTCGTCACTAGGTGGTTTCTCACCAGCAAACGG
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCACCGGCGAATGG
49728104 ACTTTCTTCCTCGAC
66 ACTTTCTTCCTCGAC
49728119 ATTCTCTTCC
Statistics
Matches: 496, Mismatches: 54, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
234 103 0.21
235 2 0.00
236 2 0.00
237 264 0.53
239 1 0.00
240 27 0.05
243 97 0.20
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (237 bp):
TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCACCGGCGAATGG
ACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCC
TCAACGTCTTGTAGTTTTCGTTTCTCACCGATGACCTCAATG
Found at i:49728112 original size:126 final size:126
Alignment explanation
Indices: 49727884--49728120 Score: 384
Period size: 126 Copynumber: 1.9 Consensus size: 126
49727874 ACATCTTGTA
*
49727884 GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCG
1 GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTATCTCCTTCG
* * * *
49727949 TCACTAGGCGGTTTCTCTCCGGCGAATGGACTCTCTTCCTCGACATCTGCTTGTAGTTTTC
66 TCACTAGGCGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACATCTGCTTGTAGTTTTC
* * *
49728010 GTTTTCGTTTCTCACCGATGACCTCAATTTCTTTTAGTAATCTTTCTGGGGGCTTATCTCCTTCG
1 GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTATCTCCTTCG
* *
49728075 TCACTAGGTGGTTTCTCACCAGCAAACGGACTTTCTTCCTCGACAT
66 TCACTAGGCGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACAT
49728121 TCTCTTCCAA
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 101 1.00
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (126 bp):
GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTATCTCCTTCG
TCACTAGGCGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACATCTGCTTGTAGTTTTC
Found at i:49728818 original size:20 final size:20
Alignment explanation
Indices: 49728780--49728818 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49728770 CATTTTAATT
*
49728780 TTTTTTATTTTAATTAGATA
1 TTTTTTATTTTAATAAGATA
*
49728800 TTTTTTATTTTTATAAGAT
1 TTTTTTATTTTAATAAGAT
49728819 TTTATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTTATTTTAATAAGATA
Found at i:49732855 original size:27 final size:27
Alignment explanation
Indices: 49732795--49732861 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
49732785 GAGGGTCTAC
* *
49732795 CACAGGCGACACCAAAGGTGCCAATGG
1 CACAGGCGGCACCAAAAGTGCCAATGG
* * * *
49732822 CAGAGGCGGTACCAAAAGTGCCATTGT
1 CACAGGCGGCACCAAAAGTGCCAATGG
49732849 CACAGGCGGCACC
1 CACAGGCGGCACC
49732862 CCAACCTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.30, T:0.10
Consensus pattern (27 bp):
CACAGGCGGCACCAAAAGTGCCAATGG
Found at i:49732940 original size:18 final size:18
Alignment explanation
Indices: 49732905--49732986 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 18
49732895 TGCACGAAGG
*
49732905 AGAAGAAAGG-AAAGGAGA
1 AGAA-AAAGGAAAAAGAGA
49732923 AGAAAAAGGAAAAAGAGA
1 AGAAAAAGGAAAAAGAGA
* * *
49732941 AGGAGAA-GAAGAAGAG-
1 AGAAAAAGGAAAAAGAGA
*
49732957 AGAGGAAAGGAAAAAG-GA
1 AGA-AAAAGGAAAAAGAGA
*
49732975 AGAAAAAAGAAA
1 AGAAAAAGGAAA
49732987 GGGAAAACAT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
16 2 0.04
17 23 0.46
18 25 0.50
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
AGAAAAAGGAAAAAGAGA
Found at i:49732941 original size:15 final size:17
Alignment explanation
Indices: 49732904--49732979 Score: 56
Period size: 17 Copynumber: 4.5 Consensus size: 17
49732894 CTGCACGAAG
*
49732904 GAGAAGAAAGGAAAGGA
1 GAGAAGAAAGGAAAGAA
49732921 GAAGAA-AAAGGAAA-AA
1 G-AGAAGAAAGGAAAGAA
49732937 GAGAAGGAGAA-G-AAGAA
1 GAGAA-GA-AAGGAAAGAA
49732954 GAGAGAGGAAAGGAAA-AA
1 GAGA-A-GAAAGGAAAGAA
49732972 G-GAAGAAA
1 GAGAAGAAA
49732980 AAAGAAAGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
15 8 0.16
16 5 0.10
17 21 0.42
18 14 0.28
19 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
GAGAAGAAAGGAAAGAA
Found at i:49732963 original size:30 final size:28
Alignment explanation
Indices: 49732907--49732964 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
49732897 CACGAAGGAG
*
49732907 AAGAAAGGAAAGGAGAAGAAAAAGGAAA
1 AAGAAAGGAAAGAAGAAGAAAAAGGAAA
* *
49732935 AAGAGAAGGAGAAGAAGAAGAGAGAGGAAA
1 AAGA-AAGGA-AAGAAGAAGAAAAAGGAAA
49732965 GGAAAAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 16 0.64
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (28 bp):
AAGAAAGGAAAGAAGAAGAAAAAGGAAA
Found at i:49738227 original size:51 final size:51
Alignment explanation
Indices: 49738150--49738285 Score: 209
Period size: 51 Copynumber: 2.6 Consensus size: 51
49738140 ACTCCCTTAC
* * * *
49738150 TTCCCTTGCTGCTGCTGATGGCTCCCCTGTTTCAGCCATTGAAGATGATTCT
1 TTCCCTT-TTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGATTCT
* *
49738202 TTCCCTTTTGTTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGATTCT
49738253 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCA
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCA
49738286 CTCCCCTGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 70 0.91
52 7 0.09
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.39
Consensus pattern (51 bp):
TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGATTCT
Found at i:49738290 original size:13 final size:13
Alignment explanation
Indices: 49738272--49738298 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49738262 GCTGATGATG
49738272 ACTCCCCTGTTTC
1 ACTCCCCTGTTTC
49738285 ACTCCCCTGTTTC
1 ACTCCCCTGTTTC
49738298 A
1 A
49738299 GCCATAGAAG
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:0.11, C:0.44, G:0.07, T:0.37
Consensus pattern (13 bp):
ACTCCCCTGTTTC
Found at i:49738322 original size:64 final size:64
Alignment explanation
Indices: 49738221--49738349 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
49738211 GTTGATGATG
49738221 ACTCCCCTGTTTCAGCCATAGAAGATGGTTCTTTCCCTTTTGCTGATGATGACTCCCCTGTTTC
1 ACTCCCCTGTTTCAGCCATAGAAGATGGTTCTTTCCCTTTTGCTGATGATGACTCCCCTGTTTC
*
49738285 ACTCCCCTGTTTCAGCCATAGAAGATGGTTCTTTCCCTTTTGCTGATGATGACTCCTCTGTTTC
1 ACTCCCCTGTTTCAGCCATAGAAGATGGTTCTTTCCCTTTTGCTGATGATGACTCCCCTGTTTC
49738349 A
1 A
49738350 GCCATTGAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (64 bp):
ACTCCCCTGTTTCAGCCATAGAAGATGGTTCTTTCCCTTTTGCTGATGATGACTCCCCTGTTTC
Found at i:49740553 original size:24 final size:24
Alignment explanation
Indices: 49740525--49740576 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
49740515 TTAGTAAGTC
* *
49740525 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
49740549 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
49740573 AAAT
1 AAAT
49740577 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Done.