Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 44 of 120
Found at i:12162455 original size:4 final size:4
Alignment explanation
Indices: 12162446--12162615 Score: 50
Period size: 4 Copynumber: 40.5 Consensus size: 4
12162436 AGATAATTTC
* *
12162446 AATA AATA AA-A AATA AATA AGA-A ACATAA AATA AA-A AA-C AACA AATA
1 AATA AATA AATA AATA AATA A-ATA A-AT-A AATA AATA AATA AATA AATA
* * * * *
12162493 AATA AAGCA CATA AAAA CAATA AAGA AATAA AATTA AATA AA-A ACAGGA
1 AATA AA-TA AATA AATA -AATA AATA AAT-A AA-TA AATA AATA A-A-TA
* *
12162542 ATATA AATA ACAT- AA-A AATA AAT- AACA AATA AATA AATA AAGGGA
1 A-ATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA AA--TA
*
12162587 CAATA AATAA AATA ATTCA AATA AATA AA
1 -AATA AAT-A AATA AAT-A AATA AATA AA
12162616 ACATGAGATC
Statistics
Matches: 125, Mismatches: 20, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
3 15 0.12
4 75 0.60
5 26 0.21
6 7 0.06
7 2 0.02
ACGTcount: A:0.71, C:0.06, G:0.05, T:0.18
Consensus pattern (4 bp):
AATA
Found at i:12162562 original size:15 final size:15
Alignment explanation
Indices: 12162544--12162581 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
12162534 AAACAGGAAT
12162544 ATAAATAACATAA-AA
1 ATAAATAACA-AATAA
12162559 ATAAATAACAAATAA
1 ATAAATAACAAATAA
12162574 ATAAATAA
1 ATAAATAA
12162582 AGGGACAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAATAACAAATAA
Found at i:12162696 original size:29 final size:30
Alignment explanation
Indices: 12162626--12162696 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
12162616 ACATGAGATC
* *
12162626 AAATTAAATAAAATAAAAATAGTAGGGTCT
1 AAATTAAATAAAATAAAAATAATAGGGTCA
* *
12162656 AAATTTAA-AAAATAGAAATAA-ATGGGT-A
1 AAATTAAATAAAATAAAAATAATA-GGGTCA
12162684 AAATTAAATAAAA
1 AAATTAAATAAAA
12162697 GACTAAATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 8 0.24
29 19 0.56
30 7 0.21
ACGTcount: A:0.62, C:0.01, G:0.11, T:0.25
Consensus pattern (30 bp):
AAATTAAATAAAATAAAAATAATAGGGTCA
Found at i:12162779 original size:15 final size:16
Alignment explanation
Indices: 12162753--12162782 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12162743 AAAAACAAAC
12162753 TAAAATTAAAATAAAT
1 TAAAATTAAAATAAAT
12162769 TAAAA-TAAAATAAA
1 TAAAATTAAAATAAA
12162783 AATTTCAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATTAAAATAAAT
Found at i:12171561 original size:13 final size:13
Alignment explanation
Indices: 12171545--12171569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12171535 TTAAATCAAA
12171545 TTTTTAAAAATAC
1 TTTTTAAAAATAC
12171558 TTTTTAAAAATA
1 TTTTTAAAAATA
12171570 ATGCTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAATAC
Found at i:12182845 original size:50 final size:50
Alignment explanation
Indices: 12182729--12182868 Score: 158
Period size: 50 Copynumber: 2.8 Consensus size: 50
12182719 TACATCTTTT
* *
12182729 AATTATGACATGCATTATGTAACTCT-CATGATTAGTTAAGTTTCCATCATA
1 AATTATGACATGCATTATGTAACT-TACATG-TTAGTTAAATATCCATCATA
* * * **
12182780 AATAATGACAAGCATTAAGTAACTTACATGTTAGTTAAATATGTATCATA
1 AATTATGACATGCATTATGTAACTTACATGTTAGTTAAATATCCATCATA
* *
12182830 AATTAT-ATCATGCATTATGTAACTCACATGTCAGTTAAA
1 AATTATGA-CATGCATTATGTAACTTACATGTTAGTTAAA
12182869 GTTTGCATAA
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 49 0.65
51 25 0.33
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (50 bp):
AATTATGACATGCATTATGTAACTTACATGTTAGTTAAATATCCATCATA
Found at i:12184011 original size:25 final size:25
Alignment explanation
Indices: 12183973--12184027 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12183963 TGAAAAAATT
12183973 AAAAAAAAACTCAAAAAAATTA-AA
1 AAAAAAAAACTCAAAAAAATTAGAA
* * *
12183997 GAAAAAGAAATTCAAAAATATTAGAA
1 -AAAAAAAAACTCAAAAAAATTAGAA
12184023 AAAAA
1 AAAAA
12184028 CAAAGGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (25 bp):
AAAAAAAAACTCAAAAAAATTAGAA
Found at i:12184060 original size:23 final size:23
Alignment explanation
Indices: 12184034--12184078 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12184024 AAAACAAAGG
*
12184034 AAATTCAAATTTAAAAAAGAAAA
1 AAATTCAAATTAAAAAAAGAAAA
*
12184057 AAATTCGAATTAAAAAAAGAAA
1 AAATTCAAATTAAAAAAAGAAA
12184079 GATTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (23 bp):
AAATTCAAATTAAAAAAAGAAAA
Found at i:12187112 original size:51 final size:50
Alignment explanation
Indices: 12187034--12187141 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 50
12187024 GAAAGTCATA
* * * * * * *
12187034 CATTATGTAATTTTGATGTTAGCTAAGTAAGGATCATAAATAATGACATG
1 CATTATGTAAATCTCATGTTAGCTAAGTAAGCATAAAAAATAATAACATG
**
12187084 CATTATGTAAATCTCATGATTAGCTAAGTCTGCATAAAAAATAATAACATG
1 CATTATGTAAATCTCATG-TTAGCTAAGTAAGCATAAAAAATAATAACATG
12187135 CATTATG
1 CATTATG
12187142 CAACTTACGT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
50 15 0.31
51 33 0.69
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (50 bp):
CATTATGTAAATCTCATGTTAGCTAAGTAAGCATAAAAAATAATAACATG
Found at i:12187542 original size:21 final size:21
Alignment explanation
Indices: 12187513--12187556 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
12187503 AGGCCAATTC
*
12187513 AAGACAAGGTG-ACTCTTCAA
1 AAGACAAGGGGAACTCTTCAA
12187533 AAGACCAAGGGGAAACTCTTCAA
1 AAGA-CAAGGGG-AACTCTTCAA
12187556 A
1 A
12187557 TGCAAATCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
23 10 0.50
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (21 bp):
AAGACAAGGGGAACTCTTCAA
Found at i:12187691 original size:36 final size:36
Alignment explanation
Indices: 12187628--12187705 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
12187618 ATAAAGTGGA
*
12187628 GACCTTTAAGCTACCTAAGGACTAATGAAAAGACAT
1 GACCTTTAAGCTACCTAAGGACAAATGAAAAGACAT
* * *
12187664 GACCTTTCATCTACTCTAA-GACAAATGAAGAGACAT
1 GACCTTTAAGCTAC-CTAAGGACAAATGAAAAGACAT
12187700 G-CCTTT
1 GACCTTT
12187706 TGAGCTAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 5 0.14
36 28 0.76
37 4 0.11
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (36 bp):
GACCTTTAAGCTACCTAAGGACAAATGAAAAGACAT
Found at i:12190131 original size:35 final size:35
Alignment explanation
Indices: 12190048--12190135 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
12190038 TACACGATTA
* *
12190048 ACCATCCAGCACACCAGATACTCATAAGAGCTACT
1 ACCATCAAGCACACCAAATACTCATAAGAGCTACT
** * *
12190083 ACCATTGAGCACACCAAATGCTCATAAGAGCTAGT
1 ACCATCAAGCACACCAAATACTCATAAGAGCTACT
*
12190118 ACCATCAAACACACCAAA
1 ACCATCAAGCACACCAAA
12190136 AACACTGTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (35 bp):
ACCATCAAGCACACCAAATACTCATAAGAGCTACT
Found at i:12191844 original size:18 final size:18
Alignment explanation
Indices: 12191806--12191844 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12191796 GTTTATCGAA
*
12191806 TTTCCTTATCTATTTCCT
1 TTTCCTTATCTATTTCAT
* *
12191824 TTTCTTTATCTATTTTAT
1 TTTCCTTATCTATTTCAT
12191842 TTT
1 TTT
12191845 ATGTTCCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCCTTATCTATTTCAT
Found at i:12194749 original size:21 final size:20
Alignment explanation
Indices: 12194721--12194759 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12194711 TAAATCATGT
12194721 ATCAAATTTCGAA-TATATGA
1 ATCAAATTTC-AATTATATGA
12194741 ATCACAATTTCAATTATAT
1 ATCA-AATTTCAATTATAT
12194760 TTTCATGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCAAATTTCAATTATATGA
Found at i:12201602 original size:20 final size:20
Alignment explanation
Indices: 12201572--12201628 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
12201562 ATTAGCATGA
*
12201572 TTTATATTAAGTTTAAATAG-G
1 TTTA-ATTAAGATTAAA-AGTG
12201593 TTTAATTAAGATTAAAAGTG
1 TTTAATTAAGATTAAAAGTG
*
12201613 ATTAATTAAGACTTAA
1 TTTAATTAAGA-TTAA
12201629 TGATGAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 22 0.69
21 8 0.25
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (20 bp):
TTTAATTAAGATTAAAAGTG
Found at i:12203084 original size:51 final size:51
Alignment explanation
Indices: 12203006--12203198 Score: 287
Period size: 51 Copynumber: 3.8 Consensus size: 51
12202996 CTCTTGTATT
* * *
12203006 CATATAAGAATTCATATACTCACGATGACACTTAGTCATCGGACCTATAGTC
1 CATA-AAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTATAATC
*
12203058 CATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTCTAATC
1 CATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTATAATC
* * * * *
12203109 CGTAAAAGATTCATTTACTCACGATGACACTTAGTTATTGGACCTTTAATC
1 CATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTATAATC
*
12203160 CGTAAAGGATTCATTTACTCACGATGACACTTAGTCATC
1 CATAAAGGATTCATTTACTCACGATGACACTTAGTCATC
12203199 AGACTCTTTC
Statistics
Matches: 129, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 125 0.97
52 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (51 bp):
CATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTATAATC
Found at i:12206509 original size:12 final size:11
Alignment explanation
Indices: 12206481--12206532 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
12206471 CAAAATTTTC
12206481 TTTCTTTTCTT
1 TTTCTTTTCTT
*
12206492 TCTCTTTCTCTT
1 TTTCTTT-TCTT
12206504 TTTCTTATTACTT
1 TTTCTT-TT-CTT
*
12206517 TGTTTTTTTCTT
1 T-TTCTTTTCTT
12206529 TTTC
1 TTTC
12206533 AAATGAGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 8 0.24
12 14 0.42
13 7 0.21
14 4 0.12
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:12220720 original size:51 final size:51
Alignment explanation
Indices: 12220663--12220921 Score: 304
Period size: 51 Copynumber: 5.1 Consensus size: 51
12220653 AAATTTGAGT
* *
12220663 TGACTATTTAGCAGTCTTCGAGCCGGTGATTTTTAGCAGGCTTTGAGTCGG
1 TGACTATTTAGCAGGCTTCGAGCCGGTGATTTTTAGCAGGCTTTGAGTCAG
** * *
12220714 TGACTATTTAATAGGCTTCGAGCCGATGATTTTTAGCAGCCTTTGAGTCAG
1 TGACTATTTAGCAGGCTTCGAGCCGGTGATTTTTAGCAGGCTTTGAGTCAG
* * * * * * * *
12220765 TGACTATTTAACAAGCTTCTAGCTGGTGACTTTTAGCACGCTTTGAGCCAA
1 TGACTATTTAGCAGGCTTCGAGCCGGTGATTTTTAGCAGGCTTTGAGTCAG
* * * * *
12220816 AGACTAATTAGCAGGCTTCGAGCCGCTGATTGTTAGCAAGCTTTGAG-CGAG
1 TGACTATTTAGCAGGCTTCGAGCCGGTGATTTTTAGCAGGCTTTGAGTC-AG
* *
12220867 TGACTATTTAGCAGGCTTCGAGCTGGTGATTATTTAGCAGGCTTTGAGCCAG
1 TGACTATTTAGCAGGCTTCGAGCCGGTGATT-TTTAGCAGGCTTTGAGTCAG
12220919 TGA
1 TGA
12220922 ATGCTTAGTA
Statistics
Matches: 172, Mismatches: 33, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
50 1 0.01
51 151 0.88
52 19 0.11
53 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (51 bp):
TGACTATTTAGCAGGCTTCGAGCCGGTGATTTTTAGCAGGCTTTGAGTCAG
Found at i:12220915 original size:26 final size:26
Alignment explanation
Indices: 12220663--12220921 Score: 199
Period size: 26 Copynumber: 10.1 Consensus size: 26
12220653 AAATTTGAGT
* *
12220663 TGACTATTTAGCAGTCTTCGAGCCGG
1 TGACTATTTAGCAGGCTTTGAGCCGG
* *
12220689 TGA-TTTTTAGCAGGCTTTGAGTCGG
1 TGACTATTTAGCAGGCTTTGAGCCGG
** * *
12220714 TGACTATTTAATAGGCTTCGAGCCGA
1 TGACTATTTAGCAGGCTTTGAGCCGG
* * * *
12220740 TGA-TTTTTAGCAGCCTTTGAGTCAG
1 TGACTATTTAGCAGGCTTTGAGCCGG
* * *
12220765 TGACTATTTAACAAGCTTCT-AGCTGG
1 TGACTATTTAGCAGGCTT-TGAGCCGG
* **
12220791 TGACT-TTTAGCACGCTTTGAGCCAA
1 TGACTATTTAGCAGGCTTTGAGCCGG
* * * *
12220816 AGACTAATTAGCAGGCTTCGAGCCGC
1 TGACTATTTAGCAGGCTTTGAGCCGG
*
12220842 TGA-T-TGTTAGCAAGCTTTGAG-CGAG
1 TGACTAT-TTAGCAGGCTTTGAGCCG-G
* *
12220867 TGACTATTTAGCAGGCTTCGAGCTGG
1 TGACTATTTAGCAGGCTTTGAGCCGG
* *
12220893 TGATTATTTAGCAGGCTTTGAGCCAG
1 TGACTATTTAGCAGGCTTTGAGCCGG
12220919 TGA
1 TGA
12220922 ATGCTTAGTA
Statistics
Matches: 175, Mismatches: 48, Indels: 20
0.72 0.20 0.08
Matches are distributed among these distances:
24 3 0.02
25 72 0.41
26 97 0.55
27 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (26 bp):
TGACTATTTAGCAGGCTTTGAGCCGG
Found at i:12227950 original size:26 final size:25
Alignment explanation
Indices: 12227888--12228057 Score: 126
Period size: 25 Copynumber: 6.7 Consensus size: 25
12227878 AGTCAGTGAC
* * ** *
12227888 TTTAGTAGGCTTTAAGCTAGTGATT
1 TTTAGAAGGCTTTGAGCCGGTGATA
12227913 TTTAGCAA-GCTTTGAGCCGGTGACTA
1 TTTAG-AAGGCTTTGAGCCGGTGA-TA
* * *
12227939 TTTAGAAGGCTTCGAGCCGATGATG
1 TTTAGAAGGCTTTGAGCCGGTGATA
* * *
12227964 TTTTGAAGGCTTTGAGCCGATGAACA
1 TTTAGAAGGCTTTGAGCCGGTG-ATA
* * *
12227990 TTTAGCAGGCTATGAGCCGGTGATT
1 TTTAGAAGGCTTTGAGCCGGTGATA
* * *
12228015 TTTTGCAGGCTTTGACCCGGTGATTA
1 TTTAGAAGGCTTTGAGCCGGTGA-TA
* *
12228041 ATTAGCAGGCTTTGAGC
1 TTTAGAAGGCTTTGAGC
12228058 TGGCATTGAC
Statistics
Matches: 115, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
25 61 0.53
26 54 0.47
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (25 bp):
TTTAGAAGGCTTTGAGCCGGTGATA
Found at i:12227976 original size:51 final size:50
Alignment explanation
Indices: 12227921--12228057 Score: 159
Period size: 51 Copynumber: 2.7 Consensus size: 50
12227911 TTTTTAGCAA
*
12227921 GCTTTGAGCCGGTGACTATTTAGAAGGCTTCGAGCCGATGATGTTTTGAAG
1 GCTTTGAGCCGGTGACTATTTAGCAGGCTT-GAGCCGATGATGTTTTGAAG
* * * *
12227972 GCTTTGAGCCGATGAAC-ATTTAGCAGGCTATGAGCCGGTGATTTTTTGCAG
1 GCTTTGAGCCGGTG-ACTATTTAGCAGGCT-TGAGCCGATGATGTTTTGAAG
* * *
12228023 GCTTTGACCCGGTGATTAATTAGCAGGCTTTGAGC
1 GCTTTGAGCCGGTGACTATTTAGCAGGC-TTGAGC
12228058 TGGCATTGAC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
50 1 0.01
51 68 0.93
52 4 0.05
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (50 bp):
GCTTTGAGCCGGTGACTATTTAGCAGGCTTGAGCCGATGATGTTTTGAAG
Found at i:12228076 original size:37 final size:37
Alignment explanation
Indices: 12228026--12228097 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
12228016 TTTGCAGGCT
12228026 TTGACCCGGTGATTAATTAGCAGGCTTTGAGCTGGCA
1 TTGACCCGGTGATTAATTAGCAGGCTTTGAGCTGGCA
*
12228063 TTGACCCGGTGATTATTTAGCAGGCTTTGAGCTGG
1 TTGACCCGGTGATTAATTAGCAGGCTTTGAGCTGG
12228098 TCAATGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (37 bp):
TTGACCCGGTGATTAATTAGCAGGCTTTGAGCTGGCA
Found at i:12228928 original size:24 final size:24
Alignment explanation
Indices: 12228896--12228952 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
12228886 AACTAGGTTG
12228896 CACATGGTCTATGACACAGGCTGT
1 CACATGGTCTATGACACAGGCTGT
*
12228920 CACAGGGTCTATGACACAGGCTGT
1 CACATGGTCTATGACACAGGCTGT
12228944 CACATGGTC
1 CACATGGTC
12228953 GTCTGTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (24 bp):
CACATGGTCTATGACACAGGCTGT
Found at i:12239179 original size:8 final size:8
Alignment explanation
Indices: 12239166--12239194 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12239156 TACAGTAGTC
12239166 AAGTGGTT
1 AAGTGGTT
12239174 AAGTGGTT
1 AAGTGGTT
12239182 AAGTGGTT
1 AAGTGGTT
12239190 AAGTG
1 AAGTG
12239195 CTCATTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (8 bp):
AAGTGGTT
Found at i:12240944 original size:47 final size:48
Alignment explanation
Indices: 12240867--12240979 Score: 156
Period size: 47 Copynumber: 2.4 Consensus size: 48
12240857 TGAAAGTATG
* * *
12240867 TGACAGTTTATCTGCAAAAGTTGTGGCTTGTTCACGAAGTGTT-TCAA
1 TGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACCAAGTGTTATCAA
* * * *
12240914 TGGCAGTATATCTGCATAAGTGGTGGCTTGTCCACCAAGTGTTATCAG
1 TGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACCAAGTGTTATCAA
12240962 TGACAGTTTATCTGCAAA
1 TGACAGTTTATCTGCAAA
12240980 TTAGAGGTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 37 0.67
48 18 0.33
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (48 bp):
TGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACCAAGTGTTATCAA
Found at i:12247380 original size:15 final size:15
Alignment explanation
Indices: 12247359--12247415 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
12247349 ACACGAATAA
12247359 TGCGAGCATGGACCT
1 TGCGAGCATGGACCT
* * ***
12247374 TGAGAGCTTGGAAGA
1 TGCGAGCATGGACCT
12247389 TGCGAGCATGGACCT
1 TGCGAGCATGGACCT
*
12247404 TGCGAGCTTGGA
1 TGCGAGCATGGA
12247416 AGATGCGAAC
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (15 bp):
TGCGAGCATGGACCT
Found at i:12247392 original size:30 final size:30
Alignment explanation
Indices: 12247358--12247423 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
12247348 AACACGAATA
12247358 ATGCGAGCATGGACCTTGAGAGCTTGGAAG
1 ATGCGAGCATGGACCTTGAGAGCTTGGAAG
*
12247388 ATGCGAGCATGGACCTTGCGAGCTTGGAAG
1 ATGCGAGCATGGACCTTGAGAGCTTGGAAG
12247418 ATGCGA
1 ATGCGA
12247424 ACACTGGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (30 bp):
ATGCGAGCATGGACCTTGAGAGCTTGGAAG
Found at i:12247422 original size:15 final size:15
Alignment explanation
Indices: 12247377--12247423 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
12247367 TGGACCTTGA
12247377 GAGCTTGGAAGATGC
1 GAGCTTGGAAGATGC
* ***
12247392 GAGCATGGACCTTGC
1 GAGCTTGGAAGATGC
12247407 GAGCTTGGAAGATGC
1 GAGCTTGGAAGATGC
12247422 GA
1 GA
12247424 ACACTGGTGT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.38, T:0.19
Consensus pattern (15 bp):
GAGCTTGGAAGATGC
Found at i:12249196 original size:16 final size:17
Alignment explanation
Indices: 12249175--12249206 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12249165 ACTTCGAGCG
12249175 AGCAAAGAGTG-GAAAA
1 AGCAAAGAGTGCGAAAA
12249191 AGCAAAGAGTGCGAAA
1 AGCAAAGAGTGCGAAA
12249207 GAGCTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.09, G:0.31, T:0.06
Consensus pattern (17 bp):
AGCAAAGAGTGCGAAAA
Found at i:12250625 original size:32 final size:32
Alignment explanation
Indices: 12250589--12250652 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
12250579 AATCGTGGAG
*
12250589 AATGAGTAGCAATGCAAAAACATTTTTCACAC
1 AATGAGTAGCAACGCAAAAACATTTTTCACAC
*
12250621 AATGAGTAGCAACGCGAAAACATTTTTCACAC
1 AATGAGTAGCAACGCAAAAACATTTTTCACAC
12250653 GCATTGTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (32 bp):
AATGAGTAGCAACGCAAAAACATTTTTCACAC
Found at i:12251360 original size:18 final size:17
Alignment explanation
Indices: 12251337--12251370 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12251327 TCAAACACCT
12251337 TGTCTTCCTTATTCTTTG
1 TGTCTT-CTTATTCTTTG
*
12251355 TGTCTTTTTATTCTTT
1 TGTCTTCTTATTCTTT
12251371 TAAGCCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.18, G:0.09, T:0.68
Consensus pattern (17 bp):
TGTCTTCTTATTCTTTG
Found at i:12264788 original size:30 final size:30
Alignment explanation
Indices: 12264754--12264836 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 30
12264744 TTAATATAAC
*
12264754 ATTTGGTACCTGAACTTGATATTTTTCCTA
1 ATTTGGTACCTGAACTTGATATTTTTCCCA
* *
12264784 ATTTGGTACCTAAACTT--T-TTTTACCCA
1 ATTTGGTACCTGAACTTGATATTTTTCCCA
* * *
12264811 ATTTGATACTTGAACTTGACATTTTT
1 ATTTGGTACCTGAACTTGATATTTTT
12264837 TTCTAATTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 21 0.50
28 1 0.02
30 20 0.48
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (30 bp):
ATTTGGTACCTGAACTTGATATTTTTCCCA
Found at i:12264813 original size:27 final size:29
Alignment explanation
Indices: 12264754--12264815 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
12264744 TTAATATAAC
* * *
12264754 ATTTGGTACCTGAACTTGATATTTTTCCTA
1 ATTTGGTACCTAAACTT-ATATTTTACCCA
12264784 ATTTGGTACCTAAACTT-T-TTTTACCCA
1 ATTTGGTACCTAAACTTATATTTTACCCA
12264811 ATTTG
1 ATTTG
12264816 ATACTTGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 12 0.41
28 1 0.03
30 16 0.55
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (29 bp):
ATTTGGTACCTAAACTTATATTTTACCCA
Found at i:12264825 original size:57 final size:58
Alignment explanation
Indices: 12264754--12264864 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
12264744 TTAATATAAC
* * *
12264754 ATTTGGTACCTGAACTTGATA-TTTTTCCTAATTTGG-TACCTAAACTTTTTTTACCCA
1 ATTTGATACCTGAACTTGACATTTTTTCCTAA-TTGGACACCTAAACTTTTTTTACCCA
* * *
12264811 ATTTGATACTTGAACTTGACATTTTTTTCTAATTGGACACCTAAGCTTTTTTTA
1 ATTTGATACCTGAACTTGACATTTTTTCCTAATTGGACACCTAAACTTTTTTTA
12264865 GATTCAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 22 0.48
58 24 0.52
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (58 bp):
ATTTGATACCTGAACTTGACATTTTTTCCTAATTGGACACCTAAACTTTTTTTACCCA
Found at i:12265123 original size:32 final size:31
Alignment explanation
Indices: 12265085--12265152 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
12265075 GGACCCCAAA
*
12265085 AAGTTTAAGTACCAACTTTAGAAAAAAGTGTC
1 AAGTTTAAGTACCAA-ATTAGAAAAAAGTGTC
* * *
12265117 AAGTTTAGGTATCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
12265148 AAGTT
1 AAGTT
12265153 CATGTACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
Found at i:12265548 original size:21 final size:21
Alignment explanation
Indices: 12265522--12265564 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12265512 AAAAACTGAA
12265522 ATTCTTGATCAATGGAGGAAC
1 ATTCTTGATCAATGGAGGAAC
12265543 ATTCTTGATCAATGGAGGAAC
1 ATTCTTGATCAATGGAGGAAC
12265564 A
1 A
12265565 ATATCACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (21 bp):
ATTCTTGATCAATGGAGGAAC
Found at i:12266119 original size:21 final size:19
Alignment explanation
Indices: 12266082--12266130 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
12266072 TTCATTTTTA
*
12266082 ATAAAAATATATAAAAGTTT
1 ATAAAAATACATAAAAG-TT
*
12266102 ATAAAAATACATGCAAAGTT
1 ATAAAAATACAT-AAAAGTT
*
12266122 ATGAAAATA
1 ATAAAAATA
12266131 TTCATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (19 bp):
ATAAAAATACATAAAAGTT
Found at i:12266215 original size:20 final size:20
Alignment explanation
Indices: 12266191--12266234 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12266181 ATTTATTAAT
*
12266191 TAAATTAACAAT-TTAAAAA
1 TAAAATAACAATATTAAAAA
* *
12266210 TAAAATAATAATATTATAAA
1 TAAAATAACAATATTAAAAA
12266230 TAAAA
1 TAAAA
12266235 ACATTTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATAACAATATTAAAAA
Found at i:12269995 original size:79 final size:79
Alignment explanation
Indices: 12269878--12270270 Score: 549
Period size: 79 Copynumber: 5.0 Consensus size: 79
12269868 TACTTTTATA
* * * * *
12269878 GCTTTAATTTGCCTCATGGTCAGGATAAGAGATCAGATGGTCTTCAATCTGCCCTCTAGTTAGGG
1 GCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTCAATCTGCCCTCTAGTTAGGG
12269943 TAAAAGATTGGATT
66 TAAAAGATTGGATT
* * *
12269957 GCTTCAATATGCCCCATGGTCGAGGTAAGAGATCAGATGGTCTTTAATCTGCCCTCTAGTTAGGG
1 GCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTCAATCTGCCCTCTAGTTAGGG
12270022 TAAAAGATTGGATT
66 TAAAAGATTGGATT
* * * * *
12270036 GCTTCAATTTACCTCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCTTCTAGTTAGGG
1 GCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTCAATCTGCCCTCTAGTTAGGG
12270101 TAAAAGATTGGATT
66 TAAAAGATTGGATT
* * *
12270115 GCTTCAATCTGCCCCATGGTCGGGGTAAGAG-TCCGGATGGTCTTCAATTTGCCCTCTTGTTAGG
1 GCTTCAATCTGCCCCATGGTCGGGGTAAGAGAT-CAGATGGTCTTCAATCTGCCCTCTAGTTAGG
12270179 GTAAAAGATTGGAATT
65 GTAAAAGATTGG-ATT
* * * * *
12270195 --TTACAATCTGCCCCATGGTTGGGGTAAGAGATCAGATGTTTTTTAATTTGCCCTCTAGTTAGG
1 GCTT-CAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTCAATCTGCCCTCTAGTTAGG
12270258 GTAAAAGATTGGA
65 GTAAAAGATTGGA
12270271 GGTTGTAACT
Statistics
Matches: 284, Mismatches: 26, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
78 4 0.01
79 276 0.97
80 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (79 bp):
GCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTCAATCTGCCCTCTAGTTAGGG
TAAAAGATTGGATT
Found at i:12270010 original size:40 final size:40
Alignment explanation
Indices: 12269887--12270232 Score: 173
Period size: 39 Copynumber: 8.8 Consensus size: 40
12269877 AGCTTTAATT
* *
12269887 TGCCTCATGGTC-AGGATAAGAGATCAGATGGTCTTCAATC
1 TGCCCCATGGTCGAGG-TAAGAGATCGGATGGTCTTCAATC
* * * * * *
12269927 TGCCCTC-TAGT-TAGGGTAAAAGATTGGATTG-CTTCAATA
1 TGCCC-CATGGTCGA-GGTAAGAGATCGGATGGTCTTCAATC
* *
12269966 TGCCCCATGGTCGAGGTAAGAGATCAGATGGTCTTTAATC
1 TGCCCCATGGTCGAGGTAAGAGATCGGATGGTCTTCAATC
* * * * * *
12270006 TGCCCTC-TAGT-TAGGGTAAAAGATTGGATTG-CTTCAATT
1 TGCCC-CATGGTCGA-GGTAAGAGATCGGATGGTCTTCAATC
* * *
12270045 TACCTCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATC
1 TGCCCCATGGTCGAGGTAAGAGATCGGATGGTCTTCAATC
* * * * * *
12270085 TGCCTTC-TAGT-TAGGGTAAAAGATTGGATTG-CTTCAATC
1 TGCC-CCATGGTCGA-GGTAAGAGATCGGATGGTCTTCAATC
* *
12270124 TGCCCCATGGTCGGGGTAAGAG-TCCGGATGGTCTTCAATT
1 TGCCCCATGGTCGAGGTAAGAGAT-CGGATGGTCTTCAATC
* * * * *
12270164 TGCCCTCTTGTTAG-GGTAAAAGATTGGAAT--T-TTACAATC
1 TGCCC-CATGGTCGAGGTAAGAGATCGG-ATGGTCTT-CAATC
* * *
12270203 TGCCCCATGGTTGGGGTAAGAGATCAGATG
1 TGCCCCATGGTCGAGGTAAGAGATCGGATG
12270233 TTTTTTAATT
Statistics
Matches: 224, Mismatches: 59, Indels: 47
0.68 0.18 0.14
Matches are distributed among these distances:
38 13 0.06
39 102 0.46
40 95 0.42
41 14 0.06
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (40 bp):
TGCCCCATGGTCGAGGTAAGAGATCGGATGGTCTTCAATC
Found at i:12280161 original size:68 final size:68
Alignment explanation
Indices: 12280052--12280202 Score: 257
Period size: 68 Copynumber: 2.2 Consensus size: 68
12280042 AGAGTTCATG
*
12280052 AATGATTTTAAACCTCGAAGTAAATAAGTACTTGAGGAACTTTTGAGAACTACACAAAGCCCTAT
1 AATGATTTTAAACCTCGAAGTAAATAAGTACTCGAGGAACTTTTGAGAACTACACAAAGCCCTAT
*
12280117 AGT
66 AAT
* *
12280120 AATGATTTTAAACCTTGAAGTAAATAAGTACTCGAGGAACTTTTGAGAACTACACAAAGCCTTAT
1 AATGATTTTAAACCTCGAAGTAAATAAGTACTCGAGGAACTTTTGAGAACTACACAAAGCCCTAT
12280185 AAT
66 AAT
12280188 AATGATTTTATAACC
1 AATGATTTTA-AACC
12280203 AACTCTTAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
68 74 0.95
69 4 0.05
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (68 bp):
AATGATTTTAAACCTCGAAGTAAATAAGTACTCGAGGAACTTTTGAGAACTACACAAAGCCCTAT
AAT
Found at i:12283951 original size:7 final size:7
Alignment explanation
Indices: 12283939--12283963 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12283929 GCCATAGCCA
12283939 CTCTCTT
1 CTCTCTT
12283946 CTCTCTT
1 CTCTCTT
12283953 CTCTCTT
1 CTCTCTT
12283960 CTCT
1 CTCT
12283964 GTGATTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
CTCTCTT
Found at i:12297566 original size:28 final size:28
Alignment explanation
Indices: 12297526--12297583 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12297516 TCTCAAGGAG
12297526 ATAAACAATCTTCTTGATACAGTTCAGT
1 ATAAACAATCTTCTTGATACAGTTCAGT
*
12297554 ATAAATAATCTTCTTGATACAGTTCAGT
1 ATAAACAATCTTCTTGATACAGTTCAGT
12297582 AT
1 AT
12297584 TTTAAAGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (28 bp):
ATAAACAATCTTCTTGATACAGTTCAGT
Found at i:12330162 original size:66 final size:68
Alignment explanation
Indices: 12330053--12330187 Score: 177
Period size: 66 Copynumber: 2.0 Consensus size: 68
12330043 GGGAAATAAA
* * * **
12330053 GAGAGTGTTAGCTTTACGCTTCACTTTTGGGACATTTTCGACTCTATGA-TTGT-TTTGGTGTGT
1 GAGAGTGTTAGCTATACACTTCACTTGTGGGACATTTTCGACTCTATGAGTCATATTTGGTGTGT
12330116 TTG
66 TTG
* *
12330119 GAGAGTGTTGGCTATATACTTCACTTGTGGGACATGTTT-GACTCTATGAGTCATATTTGGTGTG
1 GAGAGTGTTAGCTATACACTTCACTTGTGGGACAT-TTTCGACTCTATGAGTCATATTTGGTGTG
12330183 TTTG
65 TTTG
12330187 G
1 G
12330188 GGATCCGCGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 40 0.68
67 5 0.08
68 14 0.24
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (68 bp):
GAGAGTGTTAGCTATACACTTCACTTGTGGGACATTTTCGACTCTATGAGTCATATTTGGTGTGT
TTG
Found at i:12330294 original size:23 final size:23
Alignment explanation
Indices: 12330268--12330446 Score: 268
Period size: 23 Copynumber: 7.8 Consensus size: 23
12330258 TAAATTATCA
* *
12330268 TTAAATATTAACGTGATTTATAC
1 TTAAATATTAATGTGATTTATGC
* *
12330291 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
*
12330314 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
12330337 TTAAATATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
12330360 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
12330383 TTAAATATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
12330406 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
*
12330429 TTAAATATTCATGTGATT
1 TTAAATATTAATGTGATT
12330447 AAATGTGATA
Statistics
Matches: 139, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 139 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Found at i:12330454 original size:10 final size:10
Alignment explanation
Indices: 12330439--12330486 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
12330429 TTAAATATTC
12330439 ATGTGATTAA
1 ATGTGATTAA
*
12330449 ATGTGATAAA
1 ATGTGATTAA
*
12330459 ATGTGACTAA
1 ATGTGATTAA
12330469 ATGTGATTAA
1 ATGTGATTAA
12330479 TATGTGAT
1 -ATGTGAT
12330487 GTGATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:12330531 original size:58 final size:61
Alignment explanation
Indices: 12330466--12330645 Score: 168
Period size: 68 Copynumber: 2.9 Consensus size: 61
12330456 AAAATGTGAC
** * *
12330466 TAAATGTGATTAATATGTGATGTGATAAATTTTGAAATATTTATGTGACTAATGTCATTAAATGT
1 TAAATGTGATTAATATGTGATGTGATAAATGCTAAAATATTCATGTGACTAATG----TAAA-GT
12330531 GA
61 -A
12330533 CTAAATGTGATTAATATGTGATGTGATAAATGCTAAAATATTCATGTGACTAATGT-AA-T-
1 -TAAATGTGATTAATATGTGATGTGATAAATGCTAAAATATTCATGTGACTAATGTAAAGTA
* * * * * * * *
12330592 TAAATGTGATTAATATGCGTTGTGTTAAACGCTTAAGTACTCATGTGATTAATG
1 TAAATGTGATTAATATGTGATGTGATAAATGCTAAAATATTCATGTGACTAATG
12330646 CGATTAATGT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
58 46 0.46
61 1 0.01
63 2 0.02
64 1 0.01
68 50 0.50
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (61 bp):
TAAATGTGATTAATATGTGATGTGATAAATGCTAAAATATTCATGTGACTAATGTAAAGTA
Found at i:12330532 original size:19 final size:21
Alignment explanation
Indices: 12330507--12330553 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
12330497 TTGAAATATT
12330507 TATGTGACT-AATGTCATTAA
1 TATGTGACTAAATGTCATTAA
*
12330527 -ATGTGACTAAATGTGATTAA
1 TATGTGACTAAATGTCATTAA
12330547 TATGTGA
1 TATGTGA
12330554 TGTGATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 10 0.42
21 6 0.25
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.38
Consensus pattern (21 bp):
TATGTGACTAAATGTCATTAA
Found at i:12330541 original size:68 final size:68
Alignment explanation
Indices: 12330425--12330600 Score: 262
Period size: 68 Copynumber: 2.6 Consensus size: 68
12330415 AATATGATTT
* * * *
12330425 ATGCTTAAATATTCATGTGATTAAATGTGATAAAATGTGACTAAATGTGATTAATATGTGATGTG
1 ATGCTAAAATATTCATGTGACT-AATGTAATTAAATGTGACTAAATGTGATTAATATGTGATGTG
12330490 ATAA
65 ATAA
** * * *
12330494 ATTTTGAAATATTTATGTGACTAATGTCATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
1 ATGCTAAAATATTCATGTGACTAATGTAATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
12330559 TAA
66 TAA
12330562 ATGCTAAAATATTCATGTGACTAATGTAATTAAATGTGA
1 ATGCTAAAATATTCATGTGACTAATGTAATTAAATGTGA
12330601 TTAATATGCG
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
68 78 0.82
69 17 0.18
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (68 bp):
ATGCTAAAATATTCATGTGACTAATGTAATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
TAA
Found at i:12330553 original size:11 final size:10
Alignment explanation
Indices: 12330516--12330554 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
12330506 TTATGTGACT
*
12330516 AATGTCATTA
1 AATGTGATTA
*
12330526 AATGTGACTA
1 AATGTGATTA
12330536 AATGTGATTA
1 AATGTGATTA
12330546 ATATGTGAT
1 A-ATGTGAT
12330555 GTGATAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (10 bp):
AATGTGATTA
Found at i:12330652 original size:58 final size:58
Alignment explanation
Indices: 12330534--12330656 Score: 149
Period size: 58 Copynumber: 2.1 Consensus size: 58
12330524 TAAATGTGAC
* * * *
12330534 TAAATGTGATTAATATGTGATGTGATAAATGCTAAAATATTCATGTGACTAATGTAAT
1 TAAATGTGATTAATATGCGATGTGATAAACGCTAAAATACTCATGTGACTAATGCAAT
* * * * * *
12330592 TAAATGTGATTAATATGCGTTGTGTTAAACGCTTAAGTACTCATGTGATTAATGCGAT
1 TAAATGTGATTAATATGCGATGTGATAAACGCTAAAATACTCATGTGACTAATGCAAT
12330650 T-AATGTG
1 TAAATGTG
12330657 TAAAAGAATG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 6 0.11
58 49 0.89
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (58 bp):
TAAATGTGATTAATATGCGATGTGATAAACGCTAAAATACTCATGTGACTAATGCAAT
Found at i:12333326 original size:15 final size:15
Alignment explanation
Indices: 12333306--12333335 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12333296 AATCGTATAG
*
12333306 AGGAAAGGTCTCGAA
1 AGGAAAGGCCTCGAA
12333321 AGGAAAGGCCTCGAA
1 AGGAAAGGCCTCGAA
12333336 GAACCCCAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.33, T:0.10
Consensus pattern (15 bp):
AGGAAAGGCCTCGAA
Found at i:12345784 original size:23 final size:21
Alignment explanation
Indices: 12345747--12345806 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 21
12345737 CAAAGAAAAC
12345747 AGAAAAATAGAAAGAAAAGAA
1 AGAAAAATAGAAAGAAAAGAA
* * *
12345768 AGAGAAAATAAGCAAGAGAGGAA
1 AGA-AAAAT-AGAAAGAAAAGAA
* *
12345791 AGAAAAAGAAAAAGAA
1 AGAAAAATAGAAAGAA
12345807 GAATCGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 8 0.27
22 9 0.30
23 13 0.43
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.03
Consensus pattern (21 bp):
AGAAAAATAGAAAGAAAAGAA
Found at i:12349398 original size:24 final size:24
Alignment explanation
Indices: 12349386--12349464 Score: 158
Period size: 24 Copynumber: 3.3 Consensus size: 24
12349376 AATAATCTAG
12349386 ATTGAAACAAATAAACAGAGTTTA
1 ATTGAAACAAATAAACAGAGTTTA
12349410 ATTGAAACAAATAAACAGAGTTTA
1 ATTGAAACAAATAAACAGAGTTTA
12349434 ATTGAAACAAATAAACAGAGTTTA
1 ATTGAAACAAATAAACAGAGTTTA
12349458 ATTGAAA
1 ATTGAAA
12349465 GATTATTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (24 bp):
ATTGAAACAAATAAACAGAGTTTA
Found at i:12351995 original size:12 final size:13
Alignment explanation
Indices: 12351976--12352013 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
12351966 TATAGATACG
12351976 ATTTTATTTATTT
1 ATTTTATTTATTT
12351989 A-TTTATTTATTTT
1 ATTTTATTTA-TTT
*
12352002 ATTTTCTTTATT
1 ATTTTATTTATT
12352014 GTTTATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 8 0.36
13 7 0.32
14 7 0.32
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:12352018 original size:21 final size:22
Alignment explanation
Indices: 12351976--12352027 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
12351966 TATAGATACG
12351976 ATTTTA-TTTATTTATTTATTT
1 ATTTTATTTTATTTATTTATTT
* *
12351997 ATTTTATTTTCTTTA-TTGTTT
1 ATTTTATTTTATTTATTTATTT
*
12352018 ATTTGATTTT
1 ATTTTATTTT
12352028 GGTTTATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (22 bp):
ATTTTATTTTATTTATTTATTT
Found at i:12356783 original size:19 final size:22
Alignment explanation
Indices: 12356742--12356784 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
12356732 CAGCAAATGA
12356742 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTATTAAAATTATT
12356764 TTTTAAAA-TA-T-AAATTATT
1 TTTTAAAATTATTAAAATTATT
12356783 TT
1 TT
12356785 AAATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 2 0.10
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTATT
Found at i:12356796 original size:30 final size:29
Alignment explanation
Indices: 12356745--12356846 Score: 152
Period size: 29 Copynumber: 3.4 Consensus size: 29
12356735 CAAATGATTT
12356745 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
*
12356774 T-AAATTATTTTAAATTATTTTTTAAAATA
1 TAAAATTA-TTAAAATTATTTTTTAAAATA
*
12356803 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
12356834 TAAAATTATTAAA
1 TAAAATTATTAAA
12356847 TAATTTTAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
28 6 0.09
29 30 0.45
30 16 0.24
31 14 0.21
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:12356853 original size:30 final size:29
Alignment explanation
Indices: 12356745--12356853 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 29
12356735 CAAATGATTT
*
12356745 TAAAATTATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
*
12356774 T-AAATTATTTTAAATTA-TTTTTTAAAATA
1 TAAAATTA--TTAAATAATTTTTTTAAAATA
* *
12356803 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
12356834 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
12356854 AATTTCCAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
28 8 0.12
29 20 0.29
30 30 0.43
31 11 0.16
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:12357459 original size:7 final size:7
Alignment explanation
Indices: 12357449--12357480 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
12357439 CAAAACTCAA
12357449 AAATCTT
1 AAATCTT
12357456 AAATCTT
1 AAATCTT
12357463 AAATCTT
1 AAATCTT
12357470 AAATCTT
1 AAATCTT
12357477 AAAT
1 AAAT
12357481 TTTGTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATCTT
Found at i:12362131 original size:30 final size:30
Alignment explanation
Indices: 12362097--12362158 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
12362087 TAATAATGGT
*
12362097 AAAATTATACTTTAA-CCTCCAAAAATTATA
1 AAAATT-TAATTTAATCCTCCAAAAATTATA
**
12362127 AAAATTTAATTTAATCCTTTAAAAATTATA
1 AAAATTTAATTTAATCCTCCAAAAATTATA
12362157 AA
1 AA
12362159 GATATAGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAATTTAATTTAATCCTCCAAAAATTATA
Found at i:12362655 original size:29 final size:29
Alignment explanation
Indices: 12362601--12362657 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12362591 CGGATTTTTT
*
12362601 TTATAAAAGTAACCTAAATTTTTAATTAA
1 TTATAAAAGTAACCTAAATTTATAATTAA
12362630 TTATGAAAA-TAACCT-AATTTAATAATTA
1 TTAT-AAAAGTAACCTAAATTT-ATAATTA
12362658 TGTACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 16 0.64
30 4 0.16
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (29 bp):
TTATAAAAGTAACCTAAATTTATAATTAA
Found at i:12369071 original size:41 final size:41
Alignment explanation
Indices: 12369026--12369109 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
12369016 TAAACACAAT
12369026 TTAACAAGGGTAAAAATGACATTTCCAATATTTTGGGAGAC
1 TTAACAAGGGTAAAAATGACATTTCCAATATTTTGGGAGAC
* *
12369067 TTAACAAGGGTAAAAATGGCATTTCTAATATTTTGGGAGAC
1 TTAACAAGGGTAAAAATGACATTTCCAATATTTTGGGAGAC
12369108 TT
1 TT
12369110 CTACCTGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (41 bp):
TTAACAAGGGTAAAAATGACATTTCCAATATTTTGGGAGAC
Found at i:12370001 original size:52 final size:52
Alignment explanation
Indices: 12369923--12370058 Score: 202
Period size: 52 Copynumber: 2.6 Consensus size: 52
12369913 ATTTTATTTA
**
12369923 ATACTCACGATGACACATAGTCATCGGACCTCT-TGTTCCATAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCT-TATAATCCATAAAGGAATCAT
* *
12369975 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCATAAAGGAATCAT
* *
12370027 ATACTCACGATGACATATAGTCATCGAACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
12370059 TTTGCATTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 1 0.01
52 76 0.99
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCCATAAAGGAATCAT
Found at i:12377181 original size:52 final size:52
Alignment explanation
Indices: 12377098--12377232 Score: 189
Period size: 52 Copynumber: 2.6 Consensus size: 52
12377088 ATTTCATTTA
* * * **
12377098 ATACACACGATGACTCATAGTCATCGGACCTCTTGTTCCGTAAAGAAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGAAATCAT
* * *
12377150 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGAAATCAT
*
12377202 ATACTCACAATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
12377233 TTTTACATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGAAATCAT
Found at i:12379730 original size:25 final size:23
Alignment explanation
Indices: 12379701--12379766 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
12379691 TGAAAAATAA
12379701 ATCTCTCT-ATTTTTCATATTTGTT
1 ATCTCT-TAATTTTTCATATTT-TT
* *
12379725 ACTCTCTTTCATTTCTCATATTTTT
1 A-TCTC-TTAATTTTTCATATTTTT
12379750 AT-TCTTAATTTTTCATA
1 ATCTCTTAATTTTTCATA
12379767 AAACATTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 11 0.31
23 2 0.06
24 2 0.06
25 8 0.22
26 13 0.36
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.61
Consensus pattern (23 bp):
ATCTCTTAATTTTTCATATTTTT
Found at i:12380448 original size:31 final size:31
Alignment explanation
Indices: 12380391--12380474 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
12380381 AATTTAATTA
* * * *
12380391 AAAAGTTATAATTTGA-TCATTAAACTATTT
1 AAAAGTTTTAATTTAAGTTATTGAACTATTT
* **
12380421 AAAATTTTTTGTTTAAGTTATTGAACTATTT
1 AAAAGTTTTAATTTAAGTTATTGAACTATTT
12380452 AAAAGTTTTAATTTAAGTTATTG
1 AAAAGTTTTAATTTAAGTTATTG
12380475 GCTATTAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
30 11 0.26
31 32 0.74
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.49
Consensus pattern (31 bp):
AAAAGTTTTAATTTAAGTTATTGAACTATTT
Found at i:12381234 original size:16 final size:16
Alignment explanation
Indices: 12381192--12381243 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
12381182 TTTTTATTTT
*
12381192 TTTAAAAATATTT-ATA
1 TTTAATAAT-TTTAATA
12381208 TTATAAT-ATTTTAATA
1 TT-TAATAATTTTAATA
12381224 TTTAATAATTTTATATA
1 TTTAATAATTTTA-ATA
12381241 TTT
1 TTT
12381244 TTTATTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 7 0.23
16 15 0.48
17 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATAATTTTAATA
Found at i:12389539 original size:19 final size:17
Alignment explanation
Indices: 12389515--12389553 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
12389505 CTTTTTCTTT
*
12389515 TTCTCTTGCTTCTTCTCTC
1 TTCTCTT-CTTCCTC-CTC
12389534 TTCTCTTCTTCCTCCTC
1 TTCTCTTCTTCCTCCTC
12389551 TTC
1 TTC
12389554 GTCAACACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 6 0.32
19 7 0.37
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (17 bp):
TTCTCTTCTTCCTCCTC
Found at i:12396151 original size:79 final size:78
Alignment explanation
Indices: 12396061--12396218 Score: 235
Period size: 79 Copynumber: 2.0 Consensus size: 78
12396051 CAATGAGTCA
* *
12396061 TGTCTCTTCATTAGGATCTAATGTAGTTAAAAAGGCATGGCATTTCTCCTTAATGAAGACTTATT
1 TGTCTCTTCATTAGGATCTAATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGACTTA-T
**
12396126 GTATTCTTAATGTG
65 GTAACCTTAATGTG
* * * *
12396140 TGTCTCTTCATTGGGATCTGATGTAGCTGAAAAGGCATGATATTTCTCCTTAATGAAGACTTATG
1 TGTCTCTTCATTAGGATCTAATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGACTTATG
12396205 TAACCTTAATGTG
66 TAACCTTAATGTG
12396218 T
1 T
12396219 TTATTGGTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 14 0.20
79 57 0.80
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (78 bp):
TGTCTCTTCATTAGGATCTAATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGACTTATG
TAACCTTAATGTG
Found at i:12400914 original size:7 final size:6
Alignment explanation
Indices: 12400852--12400919 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
12400842 TACCACAACC
* * ** **
12400852 TCTTTT TCTTGT TCTTTT ATTTTTT TCTTTT TCACTT TCACTT TCTTTT
1 TCTTTT TCTTTT TCTTTT -TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
12400901 TCTTTT TCTATTT T-TTTT T
1 TCTTTT TCT-TTT TCTTTT T
12400920 GCATTCTCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
5 4 0.08
6 39 0.75
7 9 0.17
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.76
Consensus pattern (6 bp):
TCTTTT
Found at i:12402520 original size:15 final size:16
Alignment explanation
Indices: 12402487--12402521 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
12402477 CTTGGTGATC
12402487 TTCCCTTTCGAGGCCT
1 TTCCCTTTCGAGGCCT
*
12402503 TTCCCTTT-GAGTCCT
1 TTCCCTTTCGAGGCCT
12402518 TTCC
1 TTCC
12402522 TCCACTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.06, C:0.37, G:0.14, T:0.43
Consensus pattern (16 bp):
TTCCCTTTCGAGGCCT
Found at i:12403846 original size:79 final size:78
Alignment explanation
Indices: 12403747--12403901 Score: 249
Period size: 79 Copynumber: 2.0 Consensus size: 78
12403737 AATGAGTCAT
*
12403747 GTCTCTTTATTAGGATCTGATGTAGTTGAAAAGGCATGACATTTCTCCTTAATGAAGACTTATTG
1 GTCTCTTTATTAGGATCTGATGTAGCTGAAAAGGCATGACATTTCTCCTTAATGAAGACTTA-TG
*
12403812 TATCCTTAATGTAA
65 TAACCTTAATGTAA
**
12403826 GTCT-TTTCATTAGGATCTGATGTAGCTGAAAAGGCATGGTATTTCTCCTTAATGAAGACTTATG
1 GTCTCTTT-ATTAGGATCTGATGTAGCTGAAAAGGCATGACATTTCTCCTTAATGAAGACTTATG
12403890 TAACCTTAATGT
65 TAACCTTAATGT
12403902 GTTTATTGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
78 16 0.23
79 55 0.77
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (78 bp):
GTCTCTTTATTAGGATCTGATGTAGCTGAAAAGGCATGACATTTCTCCTTAATGAAGACTTATGT
AACCTTAATGTAA
Found at i:12404244 original size:48 final size:48
Alignment explanation
Indices: 12404175--12404277 Score: 152
Period size: 48 Copynumber: 2.1 Consensus size: 48
12404165 AACGACATAT
* * *
12404175 TTAATAATGCGGATTACTAAACAAATATGCATTTAACAAACAAAACAC
1 TTAATGATGCAGATTACTAAACAAAGATGCATTTAACAAACAAAACAC
* * *
12404223 TTAATGATGCAGATTATTAAACAAAGATGCATTTTACAAACAAAGCAC
1 TTAATGATGCAGATTACTAAACAAAGATGCATTTAACAAACAAAACAC
12404271 TTAATGA
1 TTAATGA
12404278 AGCATAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.27
Consensus pattern (48 bp):
TTAATGATGCAGATTACTAAACAAAGATGCATTTAACAAACAAAACAC
Found at i:12405393 original size:80 final size:81
Alignment explanation
Indices: 12405240--12405406 Score: 327
Period size: 80 Copynumber: 2.1 Consensus size: 81
12405230 TAAAAGGGTG
12405240 AATTAATGGACCTAGATGGTAATTATACCATATTTTTATATGTTGGAAAATATGGATATGTTTAA
1 AATTAATGGACCTAGATGGTAATTATACCATATTTTTATATGTTGGAAAATATGGATATGTTTAA
12405305 GTGAGTTATACCTTAT
66 GTGAGTTATACCTTAT
12405321 AATTAATGGACCTAGATGGTAATTATACCATA-TTTTATATGTTGGAAAATATGGATATGTTTAA
1 AATTAATGGACCTAGATGGTAATTATACCATATTTTTATATGTTGGAAAATATGGATATGTTTAA
12405385 GTGAGTTATACCTTAT
66 GTGAGTTATACCTTAT
12405401 AATTAA
1 AATTAA
12405407 AGGTTAATTT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 54 0.63
81 32 0.37
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (81 bp):
AATTAATGGACCTAGATGGTAATTATACCATATTTTTATATGTTGGAAAATATGGATATGTTTAA
GTGAGTTATACCTTAT
Found at i:12406189 original size:206 final size:205
Alignment explanation
Indices: 12405836--12406244 Score: 746
Period size: 206 Copynumber: 2.0 Consensus size: 205
12405826 TTTTTCATGT
* *
12405836 TACTATGGGTGAAATTAGGCTTACAATGAAATGAAATTATTATCAAATGTGTTTTGAACTTTAAG
1 TACTATGGGTGAAAGTAGGCTTACAATGAAATGAAATTATTATAAAATGTGTTTTGAACTTTAAG
**
12405901 AATAATTGTCTTTTGTACCTTATGTTTTGAAATGAGAATTGCTGGCTGAGCATGAGAACTTGTGT
66 AATAAACGTCTTTTGTACCTTATGTTTTGAAATGAGAATTGCTGGCTGAGCATGAGAACTTGTGT
* * *
12405966 GAATATTTGAATTCTGCATACTTGTTTCGGTAGAACCTTTGGTTGTATCGGTAGAAGTACAGGGT
131 GAATATTTGAATTCTGCATACTTGTTCCGGTAGAACCCTTGGTTGTATCGGTAGAAGTACAAGGT
12406031 AGGAGAGATG
196 AGGAGAGATG
12406041 TACTATGGGTGAAAGTAGGCTTACAATGAAATGAAATGTATTATAAAATGTGTTTTGAACTTTAA
1 TACTATGGGTGAAAGTAGGCTTACAATGAAATGAAAT-TATTATAAAATGTGTTTTGAACTTTAA
12406106 GAATAAACGTCTTTTGTACCTTATGTTTTGAAATGAGAATTGCTGGCTGAGCATGAGAACTTGTG
65 GAATAAACGTCTTTTGTACCTTATGTTTTGAAATGAGAATTGCTGGCTGAGCATGAGAACTTGTG
12406171 TGAATATTTGAATTCTGCATACTTGTTCCGGTAGAACCCTTGGTTGTATCGGTAGAAGTACAAGG
130 TGAATATTTGAATTCTGCATACTTGTTCCGGTAGAACCCTTGGTTGTATCGGTAGAAGTACAAGG
12406236 TAGGAGAGA
195 TAGGAGAGA
12406245 AGTTGTTTAA
Statistics
Matches: 196, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
205 36 0.18
206 160 0.82
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (205 bp):
TACTATGGGTGAAAGTAGGCTTACAATGAAATGAAATTATTATAAAATGTGTTTTGAACTTTAAG
AATAAACGTCTTTTGTACCTTATGTTTTGAAATGAGAATTGCTGGCTGAGCATGAGAACTTGTGT
GAATATTTGAATTCTGCATACTTGTTCCGGTAGAACCCTTGGTTGTATCGGTAGAAGTACAAGGT
AGGAGAGATG
Found at i:12408506 original size:3 final size:3
Alignment explanation
Indices: 12408498--12408600 Score: 87
Period size: 3 Copynumber: 37.0 Consensus size: 3
12408488 TTCCATTTTC
*
12408498 TCT TCT TCT TC- TCC TCT T-T T-T TCT TCT TCT TCT TCT TCT TC- TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * *
12408542 TCT TCT T-T TCT TCT TCT TCT CCA T-T TCT TC- TCT TAT TTT TAT TTT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12408587 TC- TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT
12408601 ATTGCCCAGG
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
2 15 0.18
3 68 0.82
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:12408515 original size:11 final size:11
Alignment explanation
Indices: 12408495--12408575 Score: 89
Period size: 11 Copynumber: 7.6 Consensus size: 11
12408485 TCCTTCCATT
12408495 TTCTCTTCTTC
1 TTCTCTTCTTC
*
12408506 TTCTCCTCTT-
1 TTCTCTTCTTC
*
12408516 TTTTCTTCTTC
1 TTCTCTTCTTC
12408527 -T-TCTTCTTC
1 TTCTCTTCTTC
12408536 TTCTCTTCTTC
1 TTCTCTTCTTC
*
12408547 TTTTCTTCTTC
1 TTCTCTTCTTC
*
12408558 TTCTCCAT-TTC
1 TTCT-CTTCTTC
12408569 TTCTCTT
1 TTCTCTT
12408576 ATTTTTATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
9 8 0.14
10 12 0.20
11 37 0.63
12 2 0.03
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.65
Consensus pattern (11 bp):
TTCTCTTCTTC
Found at i:12411167 original size:11 final size:11
Alignment explanation
Indices: 12411092--12411167 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
12411082 ATTCCAAAAA
*
12411092 TAATATTATTT
1 TAATATTAATT
12411103 TAATAGTTTAATAT
1 TAATA--TTAAT-T
12411117 TAA-ATTAAATT
1 TAATATT-AATT
*
12411128 TAATACTTATTT
1 TAATA-TTAATT
12411140 TAATATT-ATT
1 TAATATTAATT
12411150 T--TATTAATT
1 TAATATTAATT
12411159 TAATATTAA
1 TAATATTAA
12411168 ATTGATTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 3 0.06
11 19 0.36
12 12 0.23
13 7 0.13
14 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:12411175 original size:20 final size:19
Alignment explanation
Indices: 12411138--12411190 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
12411128 TAATACTTAT
* *
12411138 TTTAATATT-ATTTTATTAA
1 TTTAATATTAAATTGATT-A
12411157 TTTAATATTAAATTGATTA
1 TTTAATATTAAATTGATTA
12411176 TCTTAATATTAAATT
1 T-TTAATATTAAATT
12411191 TAATTTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTAATATTAAATTGATTA
Found at i:12411279 original size:18 final size:17
Alignment explanation
Indices: 12411238--12411285 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
12411228 TTTTAATAAG
12411238 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
* **
12411255 ATCTAATATTTTATGTTA
1 ATTTAATATTAAAT-TTA
12411273 ATTTAATATTAAA
1 ATTTAATATTAAA
12411286 GTGATTAAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:12435499 original size:20 final size:20
Alignment explanation
Indices: 12435476--12435517 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12435466 AATCTAGCTG
12435476 CTCCACCACTCTGAACTAGT
1 CTCCACCACTCTGAACTAGT
*
12435496 CTCCACCACTTTGAACTAGT
1 CTCCACCACTCTGAACTAGT
12435516 CT
1 CT
12435518 ACCTCTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.10, T:0.29
Consensus pattern (20 bp):
CTCCACCACTCTGAACTAGT
Found at i:12439386 original size:7 final size:7
Alignment explanation
Indices: 12439374--12439416 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
12439364 CCATTCCTAA
12439374 TCATCCC
1 TCATCCC
*
12439381 TCATCCT
1 TCATCCC
*
12439388 TGATCCC
1 TCATCCC
12439395 TCATCCC
1 TCATCCC
*
12439402 TGATCCC
1 TCATCCC
*
12439409 TTATCCC
1 TCATCCC
12439416 T
1 T
12439417 AATCTTTCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.14, C:0.47, G:0.05, T:0.35
Consensus pattern (7 bp):
TCATCCC
Found at i:12439395 original size:14 final size:14
Alignment explanation
Indices: 12439376--12439416 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
12439366 ATTCCTAATC
*
12439376 ATCCCTCATCCTTG
1 ATCCCTCATCCCTG
12439390 ATCCCTCATCCCTG
1 ATCCCTCATCCCTG
*
12439404 ATCCCTTATCCCT
1 ATCCCTCATCCCT
12439417 AATCTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.15, C:0.46, G:0.05, T:0.34
Consensus pattern (14 bp):
ATCCCTCATCCCTG
Found at i:12439400 original size:21 final size:21
Alignment explanation
Indices: 12439374--12439416 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12439364 CCATTCCTAA
12439374 TCATCCCTCAT-CCTTGATCCC
1 TCATCCCTCATCCCTT-ATCCC
*
12439395 TCATCCCTGATCCCTTATCCC
1 TCATCCCTCATCCCTTATCCC
12439416 T
1 T
12439417 AATCTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.14, C:0.47, G:0.05, T:0.35
Consensus pattern (21 bp):
TCATCCCTCATCCCTTATCCC
Found at i:12447268 original size:36 final size:36
Alignment explanation
Indices: 12447179--12447333 Score: 127
Period size: 36 Copynumber: 4.3 Consensus size: 36
12447169 TTTCTTCAAT
* * * **
12447179 GGAAGAGCTTACATCACGATTAGAGCGTAATGTTAA
1 GGAAGTGCTTACATCTCGGTTAGAGCGTAATACTAA
* * * *
12447215 GTG-ATTG-TATACGTCTCGGTTAAAGCATAATACTAA
1 G-GAAGTGCT-TACATCTCGGTTAGAGCGTAATACTAA
* *
12447251 GGAAGTGCTTACATCTCGGTTAGAGTGTAACT-CTAT
1 GGAAGTGCTTACATCTCGGTTAGAGCGTAA-TACTAA
* * *
12447287 GAAAGTGCTTACGTCTCAGTTAGAGCGTAATACTAA
1 GGAAGTGCTTACATCTCGGTTAGAGCGTAATACTAA
*
12447323 GGAAGAGCTTA
1 GGAAGTGCTTA
12447334 TGTCACAGTT
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
35 3 0.03
36 85 0.93
37 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (36 bp):
GGAAGTGCTTACATCTCGGTTAGAGCGTAATACTAA
Found at i:12447343 original size:36 final size:36
Alignment explanation
Indices: 12447224--12447348 Score: 135
Period size: 36 Copynumber: 3.5 Consensus size: 36
12447214 AGTGATTGTA
* * *
12447224 TACGTCTCGGTTAAAGCATAATACTAAGGAAGTGCT
1 TACGTCTCAGTTAGAGCGTAATACTAAGGAAGTGCT
* * * * *
12447260 TACATCTCGGTTAGAGTGTAACT-CTATGAAAGTGCT
1 TACGTCTCAGTTAGAGCGTAA-TACTAAGGAAGTGCT
*
12447296 TACGTCTCAGTTAGAGCGTAATACTAAGGAAGAGCT
1 TACGTCTCAGTTAGAGCGTAATACTAAGGAAGTGCT
* *
12447332 TATGTCACAGTTAGAGC
1 TACGTCTCAGTTAGAGC
12447349 ATAAGGCTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
35 1 0.01
36 71 0.97
37 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (36 bp):
TACGTCTCAGTTAGAGCGTAATACTAAGGAAGTGCT
Found at i:12448762 original size:29 final size:28
Alignment explanation
Indices: 12448705--12448764 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
12448695 ATATGCATGC
* *
12448705 AATATCATCATGCGATAACACAATGCAG
1 AATAACATCATACGATAACACAATGCAG
*
12448733 AATAACATCATACTGATATCACAACT-CAG
1 AATAACATCATAC-GATAACACAA-TGCAG
12448762 AAT
1 AAT
12448765 CATCACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.41
29 15 0.56
30 1 0.04
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (28 bp):
AATAACATCATACGATAACACAATGCAG
Found at i:12455358 original size:36 final size:36
Alignment explanation
Indices: 12455245--12455416 Score: 105
Period size: 36 Copynumber: 4.8 Consensus size: 36
12455235 CAATGTAAGA
* * * ** *
12455245 GCTTACGTCTAGATTAGAGCGTAATGTTAAGTGATT
1 GCTTACGACTCGATTAGAGCGTAATGCTAAGAAAGT
* * ** * *
12455281 GCATACGTCTCGGCTAGAGCATAATGCTAAGGAAGT
1 GCTTACGACTCGATTAGAGCGTAATGCTAAGAAAGT
* * *
12455317 GCTTAC-ATCTTGGTTAGAGCGTAATGCTATGAAAGT
1 GCTTACGA-CTCGATTAGAGCGTAATGCTAAGAAAGT
* * * *
12455353 TCTTACGACTCGATTAGAGCGT-ATGCCAAGGAAGA
1 GCTTACGACTCGATTAGAGCGTAATGCTAAGAAAGT
* * * * *
12455388 GCTTATGTCTCGGTTAGAGCATAAGGCTA
1 GCTTACGACTCGATTAGAGCGTAATGCTA
12455417 TTTCAGCTCA
Statistics
Matches: 103, Mismatches: 30, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
35 26 0.25
36 76 0.74
37 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (36 bp):
GCTTACGACTCGATTAGAGCGTAATGCTAAGAAAGT
Found at i:12459036 original size:20 final size:20
Alignment explanation
Indices: 12459013--12459065 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
12459003 AGTGATTTTT
12459013 GGAAAATTAATTTTGATCAA
1 GGAAAATTAATTTTGATCAA
12459033 GGAAAATTAATTTTGATCAA
1 GGAAAATTAATTTTGATCAA
*
12459053 GTAAAATTAATTT
1 GGAAAATTAATTT
12459066 AATCCCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (20 bp):
GGAAAATTAATTTTGATCAA
Found at i:12461304 original size:20 final size:22
Alignment explanation
Indices: 12461270--12461311 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12461260 AATATTTAAA
*
12461270 TAAATAATTTGAAT-AATATAT
1 TAAATAATTTAAATAAATATAT
12461291 TAAA-AATTTAAATAAATATAT
1 TAAATAATTTAAATAAATATAT
12461312 CAACATGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATAATTTAAATAAATATAT
Found at i:12476380 original size:5 final size:5
Alignment explanation
Indices: 12476366--12476395 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
12476356 CCTAATAATT
*
12476366 GCCCA ACCCA GCCCA GCCCA GCCCA GCCCA
1 GCCCA GCCCA GCCCA GCCCA GCCCA GCCCA
12476396 ACCACTTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.60, G:0.17, T:0.00
Consensus pattern (5 bp):
GCCCA
Found at i:12483215 original size:30 final size:30
Alignment explanation
Indices: 12483179--12483289 Score: 93
Period size: 30 Copynumber: 3.7 Consensus size: 30
12483169 CTATTTTATT
*
12483179 TAAAAATGATATTTTGACCCTCGAACTTTC
1 TAAAAATGATAATTTGACCCTCGAACTTTC
* *
12483209 TAAAAAT-TTGAATTTGACCC-CTAAACTTTC
1 TAAAAATGAT-AATTTGACCCTC-GAACTTTC
* * *
12483239 TAAAAAT-TTAAATTTAACCCTCGACCTTTC
1 TAAAAATGAT-AATTTGACCCTCGAACTTTC
* **
12483269 CAAAAATTTTAATTTGACCCT
1 TAAAAATGATAATTTGACCCT
12483290 AAAAATTTCC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.03
30 63 0.93
31 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (30 bp):
TAAAAATGATAATTTGACCCTCGAACTTTC
Found at i:12483299 original size:30 final size:30
Alignment explanation
Indices: 12483191--12483336 Score: 127
Period size: 30 Copynumber: 4.9 Consensus size: 30
12483181 AAAATGATAT
** * *
12483191 TTTGACCCTCGAACTTTCTAAAAATTTGAA
1 TTTGACCCTAAAACTTTCCAAAAATTTTAA
* *
12483221 TTTGACCCCT-AAACTTTCTAAAAATTTAAA
1 TTTGA-CCCTAAAACTTTCCAAAAATTTTAA
* ** *
12483251 TTTAACCCTCGACCTTTCCAAAAATTTTAA
1 TTTGACCCTAAAACTTTCCAAAAATTTTAA
* **
12483281 TTTGACCCTAAAAATTTCC-AAAATTTTGT
1 TTTGACCCTAAAACTTTCCAAAAATTTTAA
* *
12483310 TTTTACCTTAAAACTTTCC-AAAATTTT
1 TTTGACCCTAAAACTTTCCAAAAATTTT
12483337 GTTTTTGACC
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
29 36 0.37
30 57 0.59
31 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTGACCCTAAAACTTTCCAAAAATTTTAA
Found at i:12483321 original size:29 final size:29
Alignment explanation
Indices: 12483265--12483347 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
12483255 ACCCTCGACC
** * *
12483265 TTTCCAAAAATTTTAATTTGACCCTAAAAA
1 TTTCC-AAAATTTTGTTTTTACCTTAAAAA
*
12483295 TTTCCAAAATTTTGTTTTTACCTTAAAAC
1 TTTCCAAAATTTTGTTTTTACCTTAAAAA
12483324 TTTCCAAAATTTTGTTTTTGACCT
1 TTTCCAAAATTTTGTTTTT-ACCT
12483348 CGTTTTTCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 38 0.81
30 9 0.19
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTCCAAAATTTTGTTTTTACCTTAAAAA
Found at i:12483835 original size:105 final size:102
Alignment explanation
Indices: 12483706--12483892 Score: 230
Period size: 105 Copynumber: 1.8 Consensus size: 102
12483696 GTAATGTTTC
* * *
12483706 TTTATTTAGGGAACTCGAGAAATTGTGCTCAAACGTACTGGGTACGATTTTTTCTTCGAACCTAA
1 TTTATTTAGGGAACTAGAGAAATTGTGCCCAAACGTACTAGGTACGA--TTTTCTTCGAACCTAA
* *
12483771 GTAATTGAATATCCTATTCAAAAATTGAGATAATATTCT
64 ATAATTGAATATCCCATTCAAAAATTGAGATAATATTCT
* * * ** ** *
12483810 TTTATTTTAGGGAAGTAGAGGAATTGTGCCCTAACGTGTTAGGTGTGATTTTCTTTGAACCTAAA
1 TTTA-TTTAGGGAACTAGAGAAATTGTGCCCAAACGTACTAGGTACGATTTTCTTCGAACCTAAA
12483875 TAATTGAATATCCCATTC
65 TAATTGAATATCCCATTC
12483893 GGAACCTATT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
103 32 0.46
104 4 0.06
105 33 0.48
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (102 bp):
TTTATTTAGGGAACTAGAGAAATTGTGCCCAAACGTACTAGGTACGATTTTCTTCGAACCTAAAT
AATTGAATATCCCATTCAAAAATTGAGATAATATTCT
Found at i:12489773 original size:49 final size:48
Alignment explanation
Indices: 12489682--12489873 Score: 138
Period size: 49 Copynumber: 3.9 Consensus size: 48
12489672 ACAAGTTTGA
* *
12489682 AGGGAAAGATTGAAGCCGCAACGAC-AAGTTTAATACCGTAGAGATATAG
1 AGGGAAAGATTGAAGCCGCAACGACGAACTTT-ATACCTTAGAGATAT-G
* * * * *
12489731 AGGGAAAGGTTGAAGCCGCAATGGCGAACTTTGTACCTTAGAGATGTG
1 AGGGAAAGATTGAAGCCGCAACGACGAACTTTATACCTTAGAGATATG
* * * * * * *
12489779 ATGAGAAAGATTGAAGTCGCAATGA-AAAATCTTGTACCAT-GAAGATATGG
1 A-GGGAAAGATTGAAGCCGCAACGACGAACT-TTATACCTTAG-AGATAT-G
* * * * *
12489829 AGGGGAAGGTTGAAGCCACAACGACGAACCTTATACCTCAGAGAT
1 AGGGAAAGATTGAAGCCGCAACGACGAACTTTATACCTTAGAGAT
12489874 GTGGATTGAT
Statistics
Matches: 109, Mismatches: 27, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
48 6 0.06
49 93 0.85
50 10 0.09
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (48 bp):
AGGGAAAGATTGAAGCCGCAACGACGAACTTTATACCTTAGAGATATG
Found at i:12490013 original size:42 final size:42
Alignment explanation
Indices: 12489918--12490033 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
12489908 TGAAGATGAG
* * *
12489918 GAAAAGTAAATTGAAGCCGTAAAGGCGAATCTCAAGACTTTA
1 GAAAAGCAGATTGAAGCCGTAAAGGCGAATCTCAAGACTGTA
12489960 GAAAAGCAGATTGAAGCCGTAAAGGCGAATCTCAA-AGCTGT-
1 GAAAAGCAGATTGAAGCCGTAAAGGCGAATCTCAAGA-CTGTA
* * *
12490001 -AAAGGACTAGATTGAAGCTGCAAAGGCGAATCT
1 GAAAAG-C-AGATTGAAGCCGTAAAGGCGAATCT
12490034 TACATCCCTA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 59 0.91
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (42 bp):
GAAAAGCAGATTGAAGCCGTAAAGGCGAATCTCAAGACTGTA
Found at i:12490305 original size:78 final size:78
Alignment explanation
Indices: 12490176--12491232 Score: 1201
Period size: 78 Copynumber: 13.5 Consensus size: 78
12490166 AAGCTACCAT
* * * * *
12490176 CCAATCTCATACCCCAATTATGAGGCAAATCGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
12490241 GATTGAAGACACA
66 GATTGAAGACACA
* * * * * *
12490254 CCAATCT-TATACCCTGATCATGAGGCAGATTGAAGCATCTAATCTTTTACCCTAATGAAAAGAC
1 CCAATCTCT-TACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGC
12490318 AGATTGAAGACACA
65 AGATTGAAGACACA
** * *
12490332 CCAATCTGATACCCTGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAAAGGGCA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
12490397 GATTGAAGACACA
66 GATTGAAGACACA
** * * *
12490410 CCAA-CTCTTACCTTGATCATGGGGAAGATTGAAGCATCCAATCTTTTACCCTAATCAAAGGGCA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
12490474 GATTGAAGACACA
66 GATTGAAGACACA
* * *
12490487 CCAATCTCTTACCTCGATCATGAGGCAAATTGAAGCATCCAATATTTTACCCTAATCAGAGGGCA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
12490552 GATTGAAGACACA
66 GATTGAAGACACA
* **
12490565 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAAAGGATA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
*
12490630 GATTGAAGACAAA
66 GATTGAAGACACA
* * * *
12490643 CTAATCTCTTACCCCGATAATGGGGCAGATTGAAGCATCCAATATTTTACCCTAATCAGAGGGCA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
*
12490708 GATTGAAGACATA
66 GATTGAAGACACA
* * * *
12490721 CCAATCTCTTACCCCGATTATGAGGCAAAGTGAAGCATCCAATCTTTTACCCTAATCAGAGGGAA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
12490786 GATTGAAGACACA
66 GATTGAAGACACA
** * * * * * * ** * *
12490799 CTGATCTTTTACCTCAATCATGGGGTAAATTGAAGCATCCAATCTTTTATGCTAATTAGAGGGTA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
*
12490864 GATTAAAGACACA
66 GATTGAAGACACA
* * * *
12490877 CCAATCTCTTACCCCAATCATAAAGCAGATTGAAGCATCCAATCTTTTACCCTAATTAGAGGGCA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
12490942 GATTGAAGACACA
66 GATTGAAGACACA
* *
12490955 CCGATCTCTTACCCCGATCATG-GACAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
1 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
12491019 GATTGAAGACACA
66 GATTGAAGACACA
** * ** * * * * *
12491032 CTGATCTTTTACCTTGATCACGGGGTAGGA-TGAAGTCATCCAATCTCTTACGCC-GATCATG-G
1 CCAATCTCTTACCCCGATCATGAGGCA-GATTGAAG-CATCCAATCTTTTAC-CCTAATCA-GAG
* * *
12491094 GGTAGATTGAAAACCTCA
62 GGCAGATTGAAGA-CACA
* * * * * ** *
12491112 TCCAATCTCTTATCCCGATCATGGGGTAGATTGAAGATACCATCCAACCTCTTACCCCGATAATG
1 -CCAATCTCTTACCCCGATCATGAGGCAGATTGAAG----CATCCAATCTTTTACCCTAATCA-G
* * *
12491177 -GGGTAGATTGAAAACCTCA
60 AGGGCAGATTGAAGA-CACA
* * *
12491196 TCCAATCTTTTACCACGATCATGGGGCAGATTGAAGC
1 -CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGC
12491233 TACCATCTTA
Statistics
Matches: 855, Mismatches: 109, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
77 141 0.16
78 575 0.67
79 32 0.04
80 9 0.01
81 25 0.03
83 2 0.00
84 71 0.08
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (78 bp):
CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
GATTGAAGACACA
Found at i:12491120 original size:42 final size:41
Alignment explanation
Indices: 12491067--12491230 Score: 224
Period size: 42 Copynumber: 3.9 Consensus size: 41
12491057 TAGGATGAAG
12491067 TCATCCAATCTCTTACGCCGATCATGGGGTAGATTGAAAACC
1 TCATCCAATCTCTTAC-CCGATCATGGGGTAGATTGAAAACC
12491109 TCATCCAATCTCTTATCCCGATCATGGGGTAGATTGAAGATA-C
1 TCATCCAATCTCTTA-CCCGATCATGGGGTAGATTGAA-A-ACC
* *
12491152 -CATCCAACCTCTTACCCCGATAATGGGGTAGATTGAAAACC
1 TCATCCAATCTCTTA-CCCGATCATGGGGTAGATTGAAAACC
* *
12491193 TCATCCAATCTTTTACCACGATCATGGGGCAGATTGAA
1 TCATCCAATCTCTTACC-CGATCATGGGGTAGATTGAA
12491231 GCTACCATCT
Statistics
Matches: 109, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
40 1 0.01
41 4 0.04
42 100 0.92
43 3 0.03
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (41 bp):
TCATCCAATCTCTTACCCGATCATGGGGTAGATTGAAAACC
Found at i:12491172 original size:84 final size:84
Alignment explanation
Indices: 12491068--12491239 Score: 274
Period size: 84 Copynumber: 2.0 Consensus size: 84
12491058 AGGATGAAGT
* * *
12491068 CATCCAATCTCTTACGCCGATCATGGGGTAGATTGAAAACCTCATCCAATCTCTTATCC-CGATC
1 CATCCAACCTCTTACCCCGATAATGGGGTAGATTGAAAACCTCATCCAATCTCTTA-CCACGATC
*
12491132 ATGGGGTAGATTGAAGATAC
65 ATGGGGCAGATTGAAGATAC
*
12491152 CATCCAACCTCTTACCCCGATAATGGGGTAGATTGAAAACCTCATCCAATCTTTTACCACGATCA
1 CATCCAACCTCTTACCCCGATAATGGGGTAGATTGAAAACCTCATCCAATCTCTTACCACGATCA
*
12491217 TGGGGCAGATTGAAGCTAC
66 TGGGGCAGATTGAAGATAC
12491236 CATC
1 CATC
12491240 TTACAGAAGT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
83 2 0.02
84 79 0.98
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (84 bp):
CATCCAACCTCTTACCCCGATAATGGGGTAGATTGAAAACCTCATCCAATCTCTTACCACGATCA
TGGGGCAGATTGAAGATAC
Found at i:12492962 original size:30 final size:28
Alignment explanation
Indices: 12492928--12492994 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 28
12492918 CTGTTTTATT
12492928 TAAAAATGATATTTTGACCC-CTGAGCTTTC
1 TAAAAATGA-A-TTTGACCCTC-GAGCTTTC
12492958 TAAAAATTTGAATTTGACCCTCGAGCTTTC
1 TAAAAA--TGAATTTGACCCTCGAGCTTTC
12492988 TAAAAAT
1 TAAAAAT
12492995 TTAAATTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 1 0.03
30 28 0.82
31 2 0.06
32 3 0.09
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (28 bp):
TAAAAATGAATTTGACCCTCGAGCTTTC
Found at i:12492995 original size:30 final size:30
Alignment explanation
Indices: 12492940--12493008 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
12492930 AAAATGATAT
*
12492940 TTTGACCCCTGAGCTTTCTAAAAATTTGAA
1 TTTGACCCCTGAGCTTTCTAAAAATTTAAA
12492970 TTTGA-CCCTCGAGCTTTCTAAAAATTTAAA
1 TTTGACCCCT-GAGCTTTCTAAAAATTTAAA
12493000 TTTGACCCC
1 TTTGACCCC
12493009 AAACTTTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 4 0.11
30 29 0.81
31 3 0.08
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (30 bp):
TTTGACCCCTGAGCTTTCTAAAAATTTAAA
Found at i:12493038 original size:29 final size:29
Alignment explanation
Indices: 12493000--12493066 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
12492990 AAAATTTAAA
12493000 TTTGACCCCAAACTTTTCAAAATTTT-TT
1 TTTGACCCCAAACTTTTCAAAATTTTATT
12493028 TTTGACTCCCAAACTTTTCAAAATTTTATT
1 TTTGAC-CCCAAACTTTTCAAAATTTTATT
*
12493058 TTTAACCCC
1 TTTGACCCC
12493067 GTTTTTCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 6 0.17
29 23 0.64
30 7 0.19
ACGTcount: A:0.28, C:0.24, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTGACCCCAAACTTTTCAAAATTTTATT
Found at i:12494756 original size:26 final size:26
Alignment explanation
Indices: 12494715--12494831 Score: 139
Period size: 26 Copynumber: 4.5 Consensus size: 26
12494705 CCGAACACTG
* *
12494715 TTAAATAAA-CAATTAATAGAA-TCAA
1 TTAATTAAATCAATTAATAAAACT-AA
* *
12494740 TTGATCAAATCAATTAATAAAACTAA
1 TTAATTAAATCAATTAATAAAACTAA
12494766 TTAATTAAATCAATTAATAAAACTAA
1 TTAATTAAATCAATTAATAAAACTAA
* *
12494792 TTAATTAAATCAATTAATAGAATTAA
1 TTAATTAAATCAATTAATAAAACTAA
* *
12494818 TTGATTAAACCAAT
1 TTAATTAAATCAAT
12494832 CACTCTAATC
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
25 6 0.08
26 73 0.91
27 1 0.01
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (26 bp):
TTAATTAAATCAATTAATAAAACTAA
Found at i:12494770 original size:39 final size:38
Alignment explanation
Indices: 12494721--12494827 Score: 112
Period size: 39 Copynumber: 2.8 Consensus size: 38
12494711 ACTGTTAAAT
*
12494721 AAAC-AATTAATAGAATCAATTGATCAAATCAATTAATA
1 AAACTAATTAATAGAATCAATTGAT-AAAACAATTAATA
* *
12494759 AAACTAATTAATTA-AATCAATTAATAAAACTAATTAATT
1 AAACTAATTAA-TAGAATCAATTGATAAAAC-AATTAATA
* *
12494798 AAA-TCAATTAATAGAATTAATTGATTAAAC
1 AAACT-AATTAATAGAATCAATTGATAAAAC
12494828 CAATCACTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
38 11 0.19
39 45 0.78
40 2 0.03
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (38 bp):
AAACTAATTAATAGAATCAATTGATAAAACAATTAATA
Found at i:12494819 original size:13 final size:12
Alignment explanation
Indices: 12494718--12494810 Score: 98
Period size: 13 Copynumber: 7.3 Consensus size: 12
12494708 AACACTGTTA
12494718 AATAAA-CAATT
1 AATAAATCAATT
12494729 AATAGAATCAATT
1 AATA-AATCAATT
*
12494742 GATCAAATCAATT
1 AAT-AAATCAATT
*
12494755 AATAAAACTAATT
1 AATAAATC-AATT
12494768 AATTAAATCAATT
1 AA-TAAATCAATT
*
12494781 AATAAAACTAATT
1 AATAAATC-AATT
12494794 AATTAAATCAATT
1 AA-TAAATCAATT
12494807 AATA
1 AATA
12494811 GAATTAATTG
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.06
12 13 0.19
13 41 0.59
14 11 0.16
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (12 bp):
AATAAATCAATT
Found at i:12495032 original size:15 final size:16
Alignment explanation
Indices: 12495012--12495054 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
12495002 GAAAAGAAAT
12495012 TATTTAATTATTA-AA
1 TATTTAATTATTATAA
12495027 TATTTAAATTATTATAA
1 TATTT-AATTATTATAA
*
12495044 T-TTTAAATATT
1 TATTTAATTATT
12495055 TGAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
16 11 0.44
17 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAATTATTATAA
Found at i:12495035 original size:24 final size:24
Alignment explanation
Indices: 12495008--12495065 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
12494998 AATTGAAAAG
12495008 AAATTATT-TAATTATTAAATATTT
1 AAATTATTATAATT-TTAAATATTT
12495032 AAATTATTATAATTTTAAATATTT
1 AAATTATTATAATTTTAAATATTT
* *
12495056 GAATAATTAT
1 AAATTATTAT
12495066 TTGAATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATTATTATAATTTTAAATATTT
Found at i:12495036 original size:16 final size:16
Alignment explanation
Indices: 12495012--12495104 Score: 59
Period size: 16 Copynumber: 5.8 Consensus size: 16
12495002 GAAAAGAAAT
12495012 TATTT-AATTATTAAA
1 TATTTAAATTATTAAA
12495027 TATTTAAATTATTATAA
1 TATTTAAATTATTA-AA
*
12495044 T-TTTAAA-TATTTGAA
1 TATTTAAATTA-TTAAA
* * *
12495059 TAATT-ATTTGAATAAA
1 TATTTAAATT-ATTAAA
* *
12495075 CGATTTTAAATAATTAAA
1 -TA-TTTAAATTATTAAA
12495093 TATTTAAATTAT
1 TATTTAAATTAT
12495105 AACAGTAATT
Statistics
Matches: 57, Mismatches: 12, Indels: 17
0.66 0.14 0.20
Matches are distributed among these distances:
15 11 0.19
16 31 0.54
17 6 0.11
18 7 0.12
19 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (16 bp):
TATTTAAATTATTAAA
Found at i:12498409 original size:69 final size:69
Alignment explanation
Indices: 12498293--12498666 Score: 455
Period size: 69 Copynumber: 5.4 Consensus size: 69
12498283 ATAATGAAAA
* * * *
12498293 GCAGGGGTGCTTGGAACAGAATCTGCAAAAATAGATGAGCTCGTCCCCTTGAACATGTTATCCGC
1 GCAGGAGTGCTTGGAACAGAATCTGCAAAAACAGATGAGCTCTTCCCCTTGAACATGTTATCTGC
*
12498358 GTAG
66 ATAG
* ** * * * *
12498362 GCAGGAGTGCTTGGAACAGAATCTGCAAATATGGACGAACCCTTCCCCTTGAACAAGTTATCTGC
1 GCAGGAGTGCTTGGAACAGAATCTGCAAAAACAGATGAGCTCTTCCCCTTGAACATGTTATCTGC
12498427 ATAG
66 ATAG
* * * *
12498431 GCAGGAGTGCTTGGAACAGAATCTGCAAACAA-GGACGAGCTCTTCCCCTTAAACATGCTATCTG
1 GCAGGAGTGCTTGGAACAGAATCTGCAAA-AACAGATGAGCTCTTCCCCTTGAACATGTTATCTG
12498495 CATAG
65 CATAG
* *
12498500 GCCGGAGTGCTTGGAACAGAATCTGCAAAAACAGATGAGCCCTTCCCCTTGAACATGTTATCTGC
1 GCAGGAGTGCTTGGAACAGAATCTGCAAAAACAGATGAGCTCTTCCCCTTGAACATGTTATCTGC
*
12498565 ATAA
66 ATAG
* * * ** * *
12498569 GCGGGGGTGCTTGGAACAGATTCCCCAAAAACAGATGAGCTCTT-CCCTTGGAACATGTCACCTG
1 GCAGGAGTGCTTGGAACAGAATCTGCAAAAACAGATGAGCTCTTCCCCTT-GAACATGTTATCTG
*
12498633 CGTAG
65 CATAG
* *
12498638 GCAGGGGTGCTTGGTACAGAATCTGCAAA
1 GCAGGAGTGCTTGGAACAGAATCTGCAAA
12498667 CAATGGACTT
Statistics
Matches: 264, Mismatches: 38, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
68 7 0.03
69 256 0.97
70 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (69 bp):
GCAGGAGTGCTTGGAACAGAATCTGCAAAAACAGATGAGCTCTTCCCCTTGAACATGTTATCTGC
ATAG
Found at i:12498659 original size:207 final size:208
Alignment explanation
Indices: 12498299--12498674 Score: 522
Period size: 207 Copynumber: 1.8 Consensus size: 208
12498289 AAAAGCAGGG
* * * *
12498299 GTGCTTGGAACAGAATCTGCAAAAATAGATGAGCTCGTCCCCTTGAACATGTTATCCGCGTAGGC
1 GTGCTTGGAACAGAATCTGCAAAAACAGATGAGCCCGTCCCCTTGAACATGTTATCCGCATAAGC
** * ** * *
12498364 AGGAGTGCTTGGAACAGAATCTGCAAATATGGACGAACCCTTCCCCTTGAACAAGTTATCTGCAT
66 AGGAGTGCTTGGAACAGAATCCCCAAAAACAGACGAACCCTTCCCCTTGAACAAGTCACCTGCAT
12498429 AGGCAGGAGTGCTTGGAACAGAATCTGCAAACAA-GGACGAGCTCTTCCCCTTAAACATGCTATC
131 AGGCAGGAGTGCTTGGAACAGAATCTGCAAACAATGGACGAGCTCTTCCCCTTAAACATGCTATC
12498493 TGCATAGGCCGGA
196 TGCATAGGCCGGA
* *
12498506 GTGCTTGGAACAGAATCTGCAAAAACAGATGAGCCCTTCCCCTTGAACATGTTATCTGCATAAGC
1 GTGCTTGGAACAGAATCTGCAAAAACAGATGAGCCCGTCCCCTTGAACATGTTATCCGCATAAGC
* * * * * * * *
12498571 GGGGGTGCTTGGAACAGATTCCCCAAAAACAGATGAGCTCTT-CCCTTGGAACATGTCACCTGCG
66 AGGAGTGCTTGGAACAGAATCCCCAAAAACAGACGAACCCTTCCCCTT-GAACAAGTCACCTGCA
* *
12498635 TAGGCAGGGGTGCTTGGTACAGAATCTGCAAACAATGGAC
130 TAGGCAGGAGTGCTTGGAACAGAATCTGCAAACAATGGAC
12498675 TTTTCCCTGG
Statistics
Matches: 144, Mismatches: 23, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
206 5 0.03
207 135 0.94
208 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (208 bp):
GTGCTTGGAACAGAATCTGCAAAAACAGATGAGCCCGTCCCCTTGAACATGTTATCCGCATAAGC
AGGAGTGCTTGGAACAGAATCCCCAAAAACAGACGAACCCTTCCCCTTGAACAAGTCACCTGCAT
AGGCAGGAGTGCTTGGAACAGAATCTGCAAACAATGGACGAGCTCTTCCCCTTAAACATGCTATC
TGCATAGGCCGGA
Found at i:12503458 original size:29 final size:29
Alignment explanation
Indices: 12503417--12503477 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
12503407 CTCATAAGAG
12503417 AAAAAAAATAAAGTGAAAAGAAAAGAGAA
1 AAAAAAAATAAAGTGAAAAGAAAAGAGAA
*
12503446 AAAAAAAATAAAGTGAGAAGAAAAGAGAA
1 AAAAAAAATAAAGTGAAAAGAAAAGAGAA
12503475 AAA
1 AAA
12503478 GGTTAATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (29 bp):
AAAAAAAATAAAGTGAAAAGAAAAGAGAA
Found at i:12514250 original size:21 final size:21
Alignment explanation
Indices: 12514224--12514296 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
12514214 AATCATAGTA
* *
12514224 GTATCGATAGTCTGAATACTT
1 GTATCGGTAGTCCGAATACTT
*
12514245 GTATCGGTAGTCCGAACACTT
1 GTATCGGTAGTCCGAATACTT
* * *
12514266 GTATTGGTAGTCCAAATGCTT
1 GTATCGGTAGTCCGAATACTT
12514287 GTATCGGTAG
1 GTATCGGTAG
12514297 AAGCTGCAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (21 bp):
GTATCGGTAGTCCGAATACTT
Found at i:12518274 original size:28 final size:28
Alignment explanation
Indices: 12518239--12518393 Score: 89
Period size: 28 Copynumber: 5.5 Consensus size: 28
12518229 TTCAGAACTC
* *
12518239 ACCATAAAGACTTTCCTT-TCAAAGATTT
1 ACCATAAAGACATT-CTTAACAAAGATTT
12518267 ACCATAAAGACATTCTTAACAAAGATTT
1 ACCATAAAGACATTCTTAACAAAGATTT
** * * * **
12518295 TTCACAAATACGTTCTTAACGGAGA-TT
1 ACCATAAAGACATTCTTAACAAAGATTT
* * * * * *
12518322 AGCCACAAAGGCGTTTTTAACATAGATTC
1 A-CCATAAAGACATTCTTAACAAAGATTT
* * * * *
12518351 CCCACAAAGGCGTTCTTAACAAAGATCT
1 ACCATAAAGACATTCTTAACAAAGATTT
*
12518379 ACCACAAAGACATTC
1 ACCATAAAGACATTC
12518394 ATAATTGAGA
Statistics
Matches: 99, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
27 5 0.05
28 93 0.94
29 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (28 bp):
ACCATAAAGACATTCTTAACAAAGATTT
Found at i:12521895 original size:16 final size:17
Alignment explanation
Indices: 12521864--12521896 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12521854 TTCTTAACCA
*
12521864 ATATAGCATTTATTTTC
1 ATATAGCATATATTTTC
12521881 ATATA-CATATATTTTC
1 ATATAGCATATATTTTC
12521897 TTCTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (17 bp):
ATATAGCATATATTTTC
Found at i:12523374 original size:24 final size:24
Alignment explanation
Indices: 12523347--12523401 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
12523337 CAGACAATAT
** *
12523347 TTAGCTCATATTAGCCCAAAATGG
1 TTAGCTCATACGAGCCCAAAATGA
**
12523371 TTAGCTTTTACGAGCCCAAAATGA
1 TTAGCTCATACGAGCCCAAAATGA
12523395 TTAGCTC
1 TTAGCTC
12523402 TAATGAGCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAAAATGA
Found at i:12523409 original size:24 final size:24
Alignment explanation
Indices: 12523359--12523412 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12523349 AGCTCATATT
* * *
12523359 AGCCCAAAATGGTTAGCTTTTACG
1 AGCCCAAAATGATTAGCTCTAACG
*
12523383 AGCCCAAAATGATTAGCTCTAATG
1 AGCCCAAAATGATTAGCTCTAACG
12523407 AGCCCA
1 AGCCCA
12523413 GAATCAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (24 bp):
AGCCCAAAATGATTAGCTCTAACG
Found at i:12523450 original size:27 final size:27
Alignment explanation
Indices: 12523405--12523531 Score: 146
Period size: 27 Copynumber: 4.7 Consensus size: 27
12523395 TTAGCTCTAA
* *
12523405 TGAGCCCAGAATCAAAATAAGGCTCTTT
1 TGAG-CCAGAATCAGAATAACGCTCTTT
* * *
12523433 TGAGCTAGAATTAGAATAATGCTCTTT
1 TGAGCCAGAATCAGAATAACGCTCTTT
*
12523460 TGAGCCAGAATCAGAATAACGCTCTTA
1 TGAGCCAGAATCAGAATAACGCTCTTT
* * *
12523487 TGAGCCGGAATCATAATAACGCTATTT
1 TGAGCCAGAATCAGAATAACGCTCTTT
* *
12523514 AGAGCCAAAATCAGAATA
1 TGAGCCAGAATCAGAATA
12523532 CTCCTCAAGC
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
27 79 0.95
28 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (27 bp):
TGAGCCAGAATCAGAATAACGCTCTTT
Found at i:12527689 original size:24 final size:24
Alignment explanation
Indices: 12527588--12527690 Score: 143
Period size: 24 Copynumber: 4.3 Consensus size: 24
12527578 TAGCTTATAT
*
12527588 GAGCCTAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
* *
12527612 GAGCCCAAAACGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
*
12527636 GAGCCTAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
**
12527660 GAGCCCAGAATAATTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
*
12527684 AAGCCCA
1 GAGCCCA
12527691 AAATCAGATA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (24 bp):
GAGCCCAGAATGGTTAGCTCTTAC
Done.