Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 16 of 144
Found at i:3935118 original size:116 final size:114
Alignment explanation
Indices: 3934826--3935129 Score: 342
Period size: 116 Copynumber: 2.6 Consensus size: 114
3934816 AGAACTCATG
* * *** *
3934826 CTTGTATCGGTAGAAGTACAGGGTAAGAGAGAGATTGTTCTCTGACTTGAGTTGTTTCGGTAGTT
1 CTTGTATCGGTAGAAGTACAGGGT-AGAGACAGCTCACTCTCTGACTT-AGTTATTTCGGTAGTT
* * *
3934891 GTATAATAGGTATCGGTAGTTCTTTACATTGAGGTATCGGTAGTTTAAATA
64 GTATAACAGGTATCGATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
* * * *
3934942 CTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTATTCTCTGACTTGAGTTATTTCGGTAGTT
1 CTTGTATCGGTAGAAGTACAGGGTA-GAGACAGCTCACTCTCTGACTT-AGTTATTTCGGTAGTT
*
3935007 GTATAACAGGTATCTATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
64 GTATAACAGGTATCGATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
* ** * *
3935058 CTTGTATCGGTAGAAATTACAGGGTA-AGACTTCTCAGCTCTCTGGAGTT-TTTATTATCGGTAG
1 CTTGTATCGGTAG-AAGTACAGGGTAGAGACAGCTCA-CTCTCT-GACTTAGTTATT-TCGGTAG
*
3935121 TAGTATAAC
62 TTGTATAAC
3935130 TTGTATTGGT
Statistics
Matches: 166, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
115 11 0.07
116 140 0.84
117 15 0.09
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (114 bp):
CTTGTATCGGTAGAAGTACAGGGTAGAGACAGCTCACTCTCTGACTTAGTTATTTCGGTAGTTGT
ATAACAGGTATCGATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
Found at i:3941672 original size:36 final size:36
Alignment explanation
Indices: 3941622--3941716 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 36
3941612 GGTAACAGGC
* * *
3941622 ATGATCTTTAGGTCAATAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
* * *
3941658 ATGACCTTTGGGTCAACAGAGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
3941694 ATGACCTTTGGGGTCAACAGGGA
1 ATGACCTTT-GGGTCAACAGGGA
3941717 ATAAAACGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 39 0.76
37 12 0.24
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
Found at i:3942464 original size:115 final size:116
Alignment explanation
Indices: 3942217--3942592 Score: 612
Period size: 116 Copynumber: 3.2 Consensus size: 116
3942207 AGAACTCATG
** * * * * * *
3942217 CTTGTATCGGTAGAAGCACAGGGTAGGAGAGA-AGTTGTTCTTTGACTGGAGTTGTTTCAGTAGT
1 CTTGTATCGGTAGAAGTTCAGGGTAAGAGAGAGA-TTATTCTCTGACTTGAGTTATTTCGGTAGT
* *
3942281 TGTATAACAGGTATCAGTAGTTCTGTACATTGAGGTATCAGTAGTTTAAATA
65 TGTATAACAGGTATCGGTAGTTTTGTACATTGAGGTATCAGTAGTTTAAATA
3942333 CTTGTATCGGTAGAAGTTCAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
1 CTTGTATCGGTAGAAGTTCAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
3942398 GTATAACAGGTAT-GGTAGTTTTGTACATTGAGGTATCAGTAGTTTAAATA
66 GTATAACAGGTATCGGTAGTTTTGTACATTGAGGTATCAGTAGTTTAAATA
3942448 CTTGTATCGGTAGAAGTTCAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
1 CTTGTATCGGTAGAAGTTCAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
*
3942513 GTATAACAGGTATCGGTAGTTTTGTACATTGAGGTATCAGTAATTTAAATA
66 GTATAACAGGTATCGGTAGTTTTGTACATTGAGGTATCAGTAGTTTAAATA
*
3942564 CTTGTATCGGTAGAAGTTGCAAGGTAAGA
1 CTTGTATCGGTAGAAGTT-CAGGGTAAGA
3942593 CTTCTCAGCT
Statistics
Matches: 245, Mismatches: 12, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
115 113 0.46
116 122 0.50
117 10 0.04
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.36
Consensus pattern (116 bp):
CTTGTATCGGTAGAAGTTCAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
GTATAACAGGTATCGGTAGTTTTGTACATTGAGGTATCAGTAGTTTAAATA
Found at i:3944138 original size:34 final size:35
Alignment explanation
Indices: 3944067--3944139 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
3944057 TTTTTGTCTA
* *
3944067 CTTTTCTTCCAGTTTTGCTCCTAAAAGAAGTATAG
1 CTTTTCTTCCAGTTTTGCTCCTAAAAGAAATACAG
* *
3944102 CTTTTC-TCTAGTTTTGCTCCTAAAATAAATACAG
1 CTTTTCTTCCAGTTTTGCTCCTAAAAGAAATACAG
3944136 CTTT
1 CTTT
3944140 GTATTCCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 28 0.82
35 6 0.18
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (35 bp):
CTTTTCTTCCAGTTTTGCTCCTAAAAGAAATACAG
Found at i:3946726 original size:27 final size:26
Alignment explanation
Indices: 3946696--3946825 Score: 107
Period size: 27 Copynumber: 4.8 Consensus size: 26
3946686 AAAAGAAAAT
*
3946696 TCTTTCAGAGTTTGTCACAAAGGCAGA
1 TCTTTCAGAGTTT-TCATAAAGGCAGA
* * *
3946723 TCTTTCAGAGCTCTCCATAAAGGAAGA
1 TCTTTCAGAG-TTTTCATAAAGGCAGA
* * *
3946750 TCTTTCAAAGTTCTCTATAAAGGCAGT
1 TCTTTCAGAGTTTTC-ATAAAGGCAGA
* * *
3946777 TCTTTCAGAGTTCTCTATAAAGGCGGT
1 TCTTTCAGAGTTTTC-ATAAAGGCAGA
* *
3946804 TCTTTTAGAGTTCGTCATAAAG
1 TCTTTCAGAGTT-TTCATAAAG
3946826 ACAAGCACAA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.02
27 80 0.93
28 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (26 bp):
TCTTTCAGAGTTTTCATAAAGGCAGA
Found at i:3946808 original size:54 final size:54
Alignment explanation
Indices: 3946671--3946825 Score: 150
Period size: 54 Copynumber: 2.9 Consensus size: 54
3946661 AGGTTATTCA
* * * * * * *
3946671 TTCAGAGCTCACCACAAAAGAAAATTCTTTCAGAGTTTGTCACAAAGGCAGATCT
1 TTCAGAGCTCTCCATAAAGGAAGA-TCTTTCAAAGTTCGTCATAAAGGCAGATCT
*
3946726 TTCAGAGCTCTCCATAAAGGAAGATCTTTCAAAGTTC-TCTATAAAGGCAGTTCT
1 TTCAGAGCTCTCCATAAAGGAAGATCTTTCAAAGTTCGTC-ATAAAGGCAGATCT
* * ** * * *
3946780 TTCAGAGTTCTCTATAAAGGCGGTTCTTTTAGAGTTCGTCATAAAG
1 TTCAGAGCTCTCCATAAAGGAAGATCTTTCAAAGTTCGTCATAAAG
3946826 ACAAGCACAA
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
53 2 0.02
54 59 0.71
55 22 0.27
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (54 bp):
TTCAGAGCTCTCCATAAAGGAAGATCTTTCAAAGTTCGTCATAAAGGCAGATCT
Found at i:3951660 original size:30 final size:30
Alignment explanation
Indices: 3951626--3951720 Score: 72
Period size: 30 Copynumber: 3.3 Consensus size: 30
3951616 TTTTTAAAAG
*
3951626 TTATAAAAATTATTGAAAAATCATTAAATA
1 TTATAAAAATTATTGAAAAATAATTAAATA
** * *
3951656 TTAT-AATCTT-TT-AGAAATAATTAAAAA
1 TTATAAAAATTATTGAAAAATAATTAAATA
* * * *
3951683 TTAAAAAAAGTTATAG-AAAATTATTAAATT
1 TTATAAAAA-TTATTGAAAAATAATTAAATA
3951713 TTATAAAA
1 TTATAAAA
3951721 TTAAAAAAAT
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
27 15 0.32
28 4 0.09
29 6 0.13
30 22 0.47
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (30 bp):
TTATAAAAATTATTGAAAAATAATTAAATA
Found at i:3952534 original size:21 final size:20
Alignment explanation
Indices: 3952501--3952540 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3952491 TGTTTAAATA
3952501 AAATTATTAATATTTATTTAC
1 AAATTATTAATATTT-TTTAC
* *
3952522 AAATTTTTCATATTTTTTA
1 AAATTATTAATATTTTTTA
3952541 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTATTAATATTTTTTAC
Found at i:3954119 original size:34 final size:33
Alignment explanation
Indices: 3954051--3954324 Score: 253
Period size: 34 Copynumber: 8.8 Consensus size: 33
3954041 ATTATGCATT
3954051 TAATTTTACAAT-AAATTC-A-ACCC-AT--TA
1 TAATTTTACAATCAAATTCAATACCCTATCATA
* *
3954078 CATTTTTACAATCAAATTCAATACCCTATGCATA
1 TAATTTTACAATCAAATTCAATACCCTAT-CATA
3954112 TAATTTTACAATCAAATTC-A-ACCC-AT--TA
1 TAATTTTACAATCAAATTCAATACCCTATCATA
* * * *
3954140 CATTTTTACAATCAAATTCAATAGCCTATGCATC
1 TAATTTTACAATCAAATTCAATACCCTAT-CATA
*
3954174 TAATTTTACAATCAAA-TCCA-ACCC-AT--TA
1 TAATTTTACAATCAAATTCAATACCCTATCATA
* * * *
3954202 CATTTTTACAATCAAATTCAATATCCTATACATC
1 TAATTTTACAATCAAATTCAATACCCTAT-CATA
* *
3954236 TAATTTTACAATCAAATTCAATACACTAT-ACA
1 TAATTTTACAATCAAATTCAATACCCTATCATA
*
3954268 T--TTTTACAATCAAATTCAATACCCTATGCATC
1 TAATTTTACAATCAAATTCAATACCCTAT-CATA
3954300 TAATTTTACAATCAAATTCAATACC
1 TAATTTTACAATCAAATTCAATACC
3954325 TAGATGGATT
Statistics
Matches: 197, Mismatches: 27, Indels: 39
0.75 0.10 0.15
Matches are distributed among these distances:
27 10 0.05
28 40 0.20
29 5 0.03
30 35 0.18
31 10 0.05
32 11 0.06
33 4 0.02
34 82 0.42
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (33 bp):
TAATTTTACAATCAAATTCAATACCCTATCATA
Found at i:3954156 original size:62 final size:62
Alignment explanation
Indices: 3954006--3954320 Score: 463
Period size: 62 Copynumber: 5.1 Consensus size: 62
3953996 TAACTCTACC
* * * * ** *
3954006 TCAATCCATTACGTTATTATAATCAAATTCAAT-CTATTATGCATTTAATTTTACAAT-AAAT
1 TCAACCCATTACATTTTTACAATCAAATTCAATAC-CCTATGCATCTAATTTTACAATCAAAT
*
3954067 TCAACCCATTACATTTTTACAATCAAATTCAATACCCTATGCATATAATTTTACAATCAAAT
1 TCAACCCATTACATTTTTACAATCAAATTCAATACCCTATGCATCTAATTTTACAATCAAAT
*
3954129 TCAACCCATTACATTTTTACAATCAAATTCAATAGCCTATGCATCTAATTTTACAATCAAAT
1 TCAACCCATTACATTTTTACAATCAAATTCAATACCCTATGCATCTAATTTTACAATCAAAT
* * *
3954191 CCAACCCATTACATTTTTACAATCAAATTCAATATCCTATACATCTAATTTTACAATCAAAT
1 TCAACCCATTACATTTTTACAATCAAATTCAATACCCTATGCATCTAATTTTACAATCAAAT
**
3954253 TCAATACACTATACATTTTTACAATCAAATTCAATACCCTATGCATCTAATTTTACAATCAAAT
1 TCAACCCA-T-TACATTTTTACAATCAAATTCAATACCCTATGCATCTAATTTTACAATCAAAT
3954317 TCAA
1 TCAA
3954321 TACCTAGATG
Statistics
Matches: 233, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
61 48 0.21
62 129 0.55
63 1 0.00
64 55 0.24
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (62 bp):
TCAACCCATTACATTTTTACAATCAAATTCAATACCCTATGCATCTAATTTTACAATCAAAT
Found at i:3957981 original size:21 final size:20
Alignment explanation
Indices: 3957944--3957985 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3957934 CCGGTGTCAT
3957944 ATTCGTTTCCCCCAACAATG
1 ATTCGTTTCCCCCAACAATG
* *
3957964 ATTCGATTTCTCCGAACAATG
1 ATTCG-TTTCCCCCAACAATG
3957985 A
1 A
3957986 ATGAGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
ATTCGTTTCCCCCAACAATG
Found at i:3965621 original size:22 final size:22
Alignment explanation
Indices: 3965593--3965660 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
3965583 ACGTTAGTAC
*
3965593 GCTTCTGTTCAGCACTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
3965615 GCTTCTGTTTAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
3965637 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
3965659 GC
1 GC
3965661 CTACTATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.10, C:0.22, G:0.26, T:0.41
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:3965676 original size:26 final size:23
Alignment explanation
Indices: 3965597--3965692 Score: 83
Period size: 22 Copynumber: 4.2 Consensus size: 23
3965587 TAGTACGCTT
* *
3965597 CTGTTC-AGCACTATGTGTGCTT
1 CTGTTCTAGCACTGTGTGTGCTA
*
3965619 CTGTT-TAGCACTGTGTGTGCTT
1 CTGTTCTAGCACTGTGTGTGCTA
3965641 CTGTTC-AGCACTGTGTGTGCCTA
1 CTGTTCTAGCACTGTGTGTG-CTA
* * *
3965664 CTATTTCCTAGCACT-TATGTGCTT
1 CT-GTT-CTAGCACTGTGTGTGCTA
3965688 CTGTT
1 CTGTT
3965693 AAGTACTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
22 38 0.61
23 6 0.10
24 6 0.10
25 6 0.10
26 6 0.10
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (23 bp):
CTGTTCTAGCACTGTGTGTGCTA
Found at i:3966854 original size:13 final size:12
Alignment explanation
Indices: 3966836--3966869 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3966826 ACATTTTATT
3966836 TATTTTTATATAA
1 TATTTTTATA-AA
3966849 TATTTTTATAAA
1 TATTTTTATAAA
*
3966861 TATATTTAT
1 TATTTTTAT
3966870 GCGTCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTTTATAAA
Found at i:3978697 original size:22 final size:23
Alignment explanation
Indices: 3978671--3978718 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3978661 TCATATTGAT
3978671 TGAATAAATAAATATT-TTAATA
1 TGAATAAATAAATATTCTTAATA
* * *
3978693 TGAATAATTTAATATTCTTTATA
1 TGAATAAATAAATATTCTTAATA
3978716 TGA
1 TGA
3978719 TTGTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (23 bp):
TGAATAAATAAATATTCTTAATA
Found at i:3979805 original size:22 final size:22
Alignment explanation
Indices: 3979792--3979846 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
3979782 TATTTTAATC
3979792 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
3979814 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
3979837 TTAAAATTTA
1 TT-AAATTTA
3979847 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:3979822 original size:6 final size:6
Alignment explanation
Indices: 3979775--3979847 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
3979765 CATTTGAAAA
* * *
3979775 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
3979820 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
3979848 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:3979822 original size:17 final size:17
Alignment explanation
Indices: 3979795--3979862 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
3979785 TTTAATCTTA
*
3979795 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
3979811 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
3979829 AATTTAATTTAAAATTT-
1 AATTTAATTT-AAATTTC
3979846 AATATT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
3979863 AAAAAAGGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.11
17 24 0.53
18 16 0.36
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:3979832 original size:12 final size:12
Alignment explanation
Indices: 3979775--3979847 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
3979765 CATTTGAAAA
3979775 TTAAATTT--AT
1 TTAAATTTAAAT
*
3979785 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
3979798 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
3979808 TTCAATTTAAAT
1 TTAAATTTAAAT
*
3979820 TTAAATTTGAAT
1 TTAAATTTAAAT
3979832 TT-AATTTAAAAT
1 TTAAATTT-AAAT
3979844 TTAA
1 TTAA
3979848 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:3979848 original size:12 final size:11
Alignment explanation
Indices: 3979772--3979848 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
3979762 AACCATTTGA
*
3979772 AAATTAAATTT
1 AAATTTAATTT
*
3979783 -ATTTTAATCTT
1 AAATTTAAT-TT
*
3979794 AAATTTACTTT
1 AAATTTAATTT
*
3979805 AAATTCAATTT
1 AAATTTAATTT
3979816 AAATTTAAATTT
1 AAATTT-AATTT
*
3979828 GAATTTAATTT
1 AAATTTAATTT
3979839 AAAATTTAAT
1 -AAATTTAAT
3979849 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:3981601 original size:161 final size:162
Alignment explanation
Indices: 3981419--3981742 Score: 490
Period size: 161 Copynumber: 2.0 Consensus size: 162
3981409 AATTTTAATT
** **
3981419 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCAGAGGTTGCCACGTGTCATGTATTGGAT
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTGGAT
*
3981484 TATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCC-CAAATCAAC-TTTAT
66 TATTTATACATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA-
* *
3981547 TTTAATTACGAAATTGGCCCAATAATTTTTCAA
130 TTTAATTACAAAATTGGCCCAAAAATTTTTCAA
* * *
3981580 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTTTTTTGAT
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTGGAT
* * * *
3981645 TATTTCTACATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTAT
66 TATTTATACATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTAT
*
3981710 TTAATTACAAAATTGGTCCAAAAATTTTTCAA
131 TTAATTACAAAATTGGCCCAAAAATTTTTCAA
3981742 G
1 G
3981743 ATTTTCAAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
161 104 0.71
162 38 0.26
163 4 0.03
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (162 bp):
GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTGGAT
TATTTATACATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTAT
TTAATTACAAAATTGGCCCAAAAATTTTTCAA
Found at i:3981883 original size:30 final size:30
Alignment explanation
Indices: 3981849--3982215 Score: 472
Period size: 30 Copynumber: 12.3 Consensus size: 30
3981839 AGATATTATC
* * * *
3981849 TTTTGACCCCGAAACTTTTTCAAAATTATA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
* * **
3981879 TTTTGACCCCGAAACTTTTCCAAAATTATG
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
*
3981909 TTTTAACCCCGAAACTTTTCCAAAATTACA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
3981939 TTTTAACCCCAAAACTTTTCCAAAATTACA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
*
3981969 -TTTAACCCTAAAAC-TTTCCAAAATTACA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
* *
3981997 TTTTGACCCCAAAACTTTTCCAAAATTATA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
* * *
3982027 TTTTAACCCTAAAACTTTTCCAAGATTATA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
* * *
3982057 TTTTGACCCTAAAACTTTTCCAAAATTATA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
3982087 TTTTAACCCCAAAACTTTTCCAAAATTACA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
* *
3982117 TTTTAACCCTAAAACTTTTCCAAAACTACA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
*
3982147 TTTTGACCCCAAAACTTTTCCAAAATTACA
1 TTTTAACCCCAAAACTTTTCCAAAATTACA
* * * *
3982177 TCTTGACCCCAAAAC-TTTCAAAAATTGCCA
1 TTTTAACCCCAAAACTTTTCCAAAATT-ACA
3982207 TTTT-ACCCC
1 TTTTAACCCC
3982216 TGAATCTTTT
Statistics
Matches: 307, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
28 14 0.05
29 40 0.13
30 253 0.82
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
TTTTAACCCCAAAACTTTTCCAAAATTACA
Found at i:3982229 original size:29 final size:27
Alignment explanation
Indices: 3982197--3982363 Score: 109
Period size: 29 Copynumber: 5.7 Consensus size: 27
3982187 AAAACTTTCA
3982197 AAAATTGCCATTTTACCCCTGAATCTTTT
1 AAAATT-CCATTTTACCCC-GAATCTTTT
* * ** *
3982226 AAAATTCCATTCTTAACCCTGATTTCACTG
1 AAAATTCCATT-TT-ACCCCGA-ATCTTTT
* *
3982256 AAAATTACCATTTTACCCCGAAGCTTCT
1 AAAATT-CCATTTTACCCCGAATCTTTT
* * ****
3982284 AAAATTCTATTTTTAACCCCGATTACACCG
1 AAAATTCCA-TTTT-ACCCCGAAT-CTTTT
3982314 AAAATTGCCATTTTACCCCGAATCTTTT
1 AAAATT-CCATTTTACCCCGAATCTTTT
3982342 AAAATTCCATTTTTAACCCCGA
1 AAAATTCCA-TTTT-ACCCCGA
3982364 TTACACCAAA
Statistics
Matches: 104, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
27 5 0.05
28 27 0.26
29 38 0.37
30 27 0.26
31 7 0.07
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (27 bp):
AAAATTCCATTTTACCCCGAATCTTTT
Found at i:3982317 original size:58 final size:58
Alignment explanation
Indices: 3982197--3982384 Score: 279
Period size: 58 Copynumber: 3.2 Consensus size: 58
3982187 AAAACTTTCA
* * * * *
3982197 AAAATTGCCATTTTACCCCTGAATCTTTTAAAATTCCATTCTTAACCCTGATTTCACTG
1 AAAATTACCATTTTACCCC-GAATCTTTTAAAATTCCATTTTTAACCCCGATTACACCG
* * *
3982256 AAAATTACCATTTTACCCCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTACACCG
1 AAAATTACCATTTTACCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACCG
*
3982314 AAAATTGCCATTTTACCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTACCATTTTACCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACCG
3982371 AAAATTACCATTTT
1 AAAATTACCATTTT
3982385 GCCCTCGGGT
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
57 13 0.11
58 85 0.73
59 18 0.16
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACCG
Found at i:3982328 original size:30 final size:29
Alignment explanation
Indices: 3982226--3982384 Score: 105
Period size: 29 Copynumber: 5.4 Consensus size: 29
3982216 TGAATCTTTT
* * *
3982226 AAAATTCCATTCTTAACCCTGATTTCACTG
1 AAAATTCCATT-TTAACCCCGATTACACCG
** *
3982256 AAAATTACCATTTT-ACCCCGA--AGCTTCT
1 AAAATT-CCATTTTAACCCCGATTA-CACCG
*
3982284 AAAATTCTATTTTTAACCCCGATTACACCG
1 AAAATTCCA-TTTTAACCCCGATTACACCG
* ****
3982314 AAAATTGCCATTTT-ACCCCGAAT-CTTTT
1 AAAATT-CCATTTTAACCCCGATTACACCG
3982342 AAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTCCA-TTTTAACCCCGATTACACCG
3982371 AAAATTACCATTTT
1 AAAATT-CCATTTT
3982385 GCCCTCGGGT
Statistics
Matches: 98, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
27 5 0.05
28 22 0.22
29 39 0.40
30 24 0.24
31 8 0.08
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCCGATTACACCG
Found at i:3994423 original size:68 final size:68
Alignment explanation
Indices: 3994314--3994962 Score: 1064
Period size: 68 Copynumber: 9.5 Consensus size: 68
3994304 TGCAGGTCAC
* *
3994314 CAACGTCATTCCCTTGAAATTGAAGTAAAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994379 GAG
66 GAG
3994382 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994447 GAG
66 GAG
* * *
3994450 CAATGTCATCCTCTTGAAATTGAAGTAGAGTGGACAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994515 GAG
66 GAG
3994518 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994583 GAG
66 GAG
* * * * *
3994586 CAATGTCATCCTCTTGAAATTGAAGTAGAGTGGACAACACATCTTCATCTCCGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994651 GAG
66 GAG
* * * * *
3994654 CAACGTCATTCTCTTGAAATCGAAGTAGAGTGGACAACACGTCTTCATCTCCGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994719 GAG
66 GAG
* *
3994722 CAAAGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994787 GAG
66 GAG
*
3994790 CAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994855 GAG
66 GAG
* * * * *
3994858 CAATGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
3994923 GAG
66 GAG
* *
3994926 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATA
3994963 GCAAAGTCTT
Statistics
Matches: 549, Mismatches: 31, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
68 543 0.99
69 6 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
GAG
Found at i:3995290 original size:22 final size:22
Alignment explanation
Indices: 3995277--3995331 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
3995267 TATTTTAATC
3995277 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
3995299 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
3995322 TTAAAATTTA
1 TT-AAATTTA
3995332 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:3995307 original size:6 final size:6
Alignment explanation
Indices: 3995260--3995332 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
3995250 CATTTGAAAA
* * *
3995260 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
3995305 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
3995333 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:3995307 original size:17 final size:17
Alignment explanation
Indices: 3995280--3995347 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
3995270 TTTAATCTTA
*
3995280 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
3995296 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
3995314 AATTTAATTTAAAATTT-
1 AATTTAATTT-AAATTTC
3995331 AATATT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
3995348 AAAAAAGGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.11
17 24 0.53
18 16 0.36
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:3995317 original size:12 final size:12
Alignment explanation
Indices: 3995260--3995332 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
3995250 CATTTGAAAA
3995260 TTAAATTT--AT
1 TTAAATTTAAAT
*
3995270 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
3995283 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
3995293 TTCAATTTAAAT
1 TTAAATTTAAAT
*
3995305 TTAAATTTGAAT
1 TTAAATTTAAAT
3995317 TT-AATTTAAAAT
1 TTAAATTT-AAAT
3995329 TTAA
1 TTAA
3995333 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:3995333 original size:12 final size:11
Alignment explanation
Indices: 3995257--3995333 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
3995247 AACCATTTGA
*
3995257 AAATTAAATTT
1 AAATTTAATTT
*
3995268 -ATTTTAATCTT
1 AAATTTAAT-TT
*
3995279 AAATTTACTTT
1 AAATTTAATTT
*
3995290 AAATTCAATTT
1 AAATTTAATTT
3995301 AAATTTAAATTT
1 AAATTT-AATTT
*
3995313 GAATTTAATTT
1 AAATTTAATTT
3995324 AAAATTTAAT
1 -AAATTTAAT
3995334 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:3997290 original size:161 final size:159
Alignment explanation
Indices: 3996950--3997259 Score: 383
Period size: 162 Copynumber: 1.9 Consensus size: 159
3996940 TTTGACTGTG
* *
3996950 CCAGAGGTTGCCACGTGTCATGTATTGGATTATTTATGCATTTAGTCCTTTTCATTTTAATTTGT
1 CCAGAGGCTGCCACGTGTCATGTATTGGATTATTTATACATTTAGTCCTTTTCATTTTAATTTGT
* *
3997015 TTTAATTTAATCCCAAATCAACTTTATTTTAATTACGAAATTGGCCCAATAATTTTTCAAGGTTT
66 TTTAATTTAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAATAATTTTTCAAGATTT
* * *
3997080 ATAAACTAGTCCTTTGACTGTTTGACTGCA
131 ATAAACTAGTCCCTTGACTGCTGGACT-CA
* * * * * *
3997110 CCAGAGGTTGCCACGTGTCATTTTTTTGATTATTTCTACATTTAGTCCTTTTTATTTTTAATTTG
1 CCAGAGGCTGCCACGTGTCATGTATTGGATTATTTATACATTTAGTCCTTTTCA-TTTTAATTTG
* * *
3997175 TTTTAATTTAATCCTTAAATCGACTTT-TATTTAATTACAAAATTGGTCCAA-AATTTTTTCAAG
65 TTTTAATTTAATCC-CAAATCAACTTTAT-TTTAATTACAAAATTGGCCCAATAA-TTTTTCAAG
* *
3997238 ATTT-TCAAATTGGTCCCTTGAC
127 ATTTAT-AAACTAGTCCCTTGAC
3997260 CTCTGGATAC
Statistics
Matches: 131, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
160 48 0.37
161 28 0.21
162 55 0.42
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (159 bp):
CCAGAGGCTGCCACGTGTCATGTATTGGATTATTTATACATTTAGTCCTTTTCATTTTAATTTGT
TTTAATTTAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAATAATTTTTCAAGATTT
ATAAACTAGTCCCTTGACTGCTGGACTCA
Found at i:3997370 original size:30 final size:30
Alignment explanation
Indices: 3997330--3997680 Score: 476
Period size: 30 Copynumber: 11.7 Consensus size: 30
3997320 CCCTAAATTG
*
3997330 TCCAGAAATTATC-TTTTGACCCCGAAACTTT
1 TCCA-AAATTA-CATTTTGACCCCAAAACTTT
* * * *
3997361 TTCAAAATTATATTTTAACCCCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
3997391 TCCAAAATTACATTTTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
3997421 CCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
3997451 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
3997481 TCCAAAACTACATTTTGACCTCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
3997511 TCCAAAATTATATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
3997541 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
3997571 TCCAAAACTACATTTTGACCCTAAAA-TTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
3997600 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
3997630 TCCAAAATTACATTTTGACCCCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
3997659 TCAAAAATTGCCATTTT-ACCCC
1 TCCAAAATT-ACATTTTGACCCC
3997681 CGAATCTTTT
Statistics
Matches: 286, Mismatches: 31, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
29 41 0.14
30 242 0.85
31 3 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:3997710 original size:59 final size:57
Alignment explanation
Indices: 3997343--3997762 Score: 343
Period size: 60 Copynumber: 7.1 Consensus size: 57
3997333 AGAAATTATC
* * * * *
3997343 TTTTGACCCCGAAACTTTTTCAAAATTATATTTTAACCCCGAAACTTTTCCAAAATTACA
1 TTTTAACCCCAAAAC-TTTCCAAAATTACATTTTACCCCCGAAACTTTT-CAAAATT-CA
* *
3997403 TTTTAACCCTAAAACTTTCCCAAAATTACATTTTGA-CCCCAAAACTTTTCCAAAATTACA
1 TTTTAACCCCAAAACTTT-CCAAAATTACATTTT-ACCCCCGAAACTTTT-CAAAATT-CA
* * *
3997463 TTTTAACCCCAAAACTTTTCCAAAACTACATTTTGA-CCTCGAAACTTTTCCAAAATTATA
1 TTTTAACCCCAAAAC-TTTCCAAAATTACATTTT-ACCCCCGAAACTTTT-CAAAATT-CA
* *
3997523 TTTTAACCCCAAAACTTTTCCAAAATTACATTTTGA-CCCCAAAACTTTTCCAAAACTACA
1 TTTTAACCCCAAAAC-TTTCCAAAATTACATTTT-ACCCCCGAAACTTTT-CAAAA-TTCA
* * * * *
3997583 TTTTGACCCTAAAATTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACA
1 TTTTAACCCCAAAACTTTCCAAAATTACATTTTACCCCCGAAACTTTT-CAAAATT-CA
* * * *
3997642 TTTTGACCCCAAAACTTTCAAAAATTGCCATTTTACCCCCGAATCTTTT-AAAATTCTA
1 TTTTAACCCCAAAACTTTCCAAAATT-ACATTTTACCCCCGAAACTTTTCAAAATTC-A
* * *
3997700 TTCTTAACCCC--GA-TTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCT-AAAATTCCA
1 TT-TTAACCCCAAAACTTT--CC-AAAATTA-CATTTTACCCCCGAAACTTTTCAAAATT-CA
3997759 TTTT
1 TTTT
3997763 TTAACCCCGA
Statistics
Matches: 313, Mismatches: 33, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
56 3 0.01
57 2 0.01
58 14 0.04
59 106 0.34
60 183 0.58
61 5 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (57 bp):
TTTTAACCCCAAAACTTTCCAAAATTACATTTTACCCCCGAAACTTTTCAAAATTCA
Found at i:3997741 original size:30 final size:29
Alignment explanation
Indices: 3997662--3997918 Score: 121
Period size: 29 Copynumber: 8.7 Consensus size: 29
3997652 AAAACTTTCA
* ***
3997662 AAAATTGCCATTTTACCCCCGA-ATCTTTT
1 AAAATT-CCATTTTACCCCCGATTTCACCT
* * *
3997691 AAAATTCTATTCTTAACCCCGATTTCACCA
1 AAAATTCCATT-TTACCCCCGATTTCACCT
** **
3997721 AAAATTACCATTTTACCCCCGA-AGCTTCT
1 AAAATT-CCATTTTACCCCCGATTTCACCT
*
3997750 AAAATTCCATTTTTTAACCCCGATTTCA-CT
1 AAAATTCCA--TTTTACCCCCGATTTCACCT
* ** **
3997780 GAAAATTACCATTTTACCCTCGA-AGCTTCT
1 -AAAATT-CCATTTTACCCCCGATTTCACCT
* * * *
3997810 AAAATTCCGTTTTTAACCCCGATTACACCG
1 AAAATTCC-ATTTTACCCCCGATTTCACCT
* ***
3997840 AAAATTGCCATTTTACCCCCGA-ATCTTTT
1 AAAATT-CCATTTTACCCCCGATTTCACCT
* *
3997869 AAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTCCA-TTTTACCCCCGATTTCACCT
*
3997898 AAAATTACCATTTTGCCCCCG
1 AAAATT-CCATTTTACCCCCG
3997919 GGTATCCATA
Statistics
Matches: 166, Mismatches: 47, Indels: 30
0.68 0.19 0.12
Matches are distributed among these distances:
28 12 0.07
29 73 0.44
30 65 0.39
31 13 0.08
32 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTACCCCCGATTTCACCT
Found at i:3997852 original size:59 final size:59
Alignment explanation
Indices: 3997662--3997918 Score: 363
Period size: 59 Copynumber: 4.4 Consensus size: 59
3997652 AAAACTTTCA
* * * * * * *
3997662 AAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCTATTCTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACCG
* *
3997721 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTTAACCCCGATTTCACTG
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCA-TTTTTAACCCCGATTACACCG
* *
3997781 AAAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTACACCG
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACCG
* * *
3997840 AAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACCG
*
3997898 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
3997919 GGTATCCATA
Statistics
Matches: 179, Mismatches: 18, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
58 19 0.11
59 106 0.59
60 54 0.30
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACCG
Found at i:3997882 original size:119 final size:117
Alignment explanation
Indices: 3997662--3997918 Score: 361
Period size: 119 Copynumber: 2.2 Consensus size: 117
3997652 AAAACTTTCA
* * * * *
3997662 AAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCTATTCTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTCTTAACCCCGATTACACCAAAAATT
* *
3997727 ACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTTAACCCCGATTTCACTG
66 ACCATTTTACCCCCGAAGCTTCTAAAATTCCA-TTTTTAACCCCGATTACAC-C
* * * *
3997781 AAAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCGTTTTTAACCCCGATTACACCGAAAATT
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTCTTAACCCCGATTACACCAAAAATT
* * *
3997846 GCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC
66 ACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACC
*
3997898 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
3997919 GGTATCCATA
Statistics
Matches: 122, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
117 19 0.16
118 18 0.15
119 85 0.70
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTCTTAACCCCGATTACACCAAAAATT
ACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACACC
Found at i:3997917 original size:29 final size:28
Alignment explanation
Indices: 3997691--3997918 Score: 97
Period size: 30 Copynumber: 7.7 Consensus size: 28
3997681 CGAATCTTTT
* * *
3997691 AAAATTCTATTCTTAACCCCGATTTCACC
1 AAAATTCCATT-TTACCCCCGATTACACC
* *
3997720 AAAAATTACCATTTTACCCCCGA--AGCTTCT
1 -AAAATT-CCATTTTACCCCCGATTA-C-ACC
* * *
3997750 AAAATTCCATTTTTTAACCCCGATTTCACTG
1 AAAATTCCA--TTTTACCCCCGATTACAC-C
* * *
3997781 AAAATTACCATTTTACCCTCGA--AGCTTCT
1 AAAATT-CCATTTTACCCCCGATTA-C-ACC
* *
3997810 AAAATTCCGTTTTTAACCCCGATTACACC
1 AAAATTCC-ATTTTACCCCCGATTACACC
* ***
3997839 GAAAATTGCCATTTTACCCCCGAAT-CTTTT
1 -AAAATT-CCATTTTACCCCCGATTAC-ACC
*
3997869 AAAATTCCATTTTTAACCCCGATTACACC
1 AAAATTCCA-TTTTACCCCCGATTACACC
*
3997898 AAAATTACCATTTTGCCCCCG
1 AAAATT-CCATTTTACCCCCG
3997919 GGTATCCATA
Statistics
Matches: 146, Mismatches: 32, Indels: 41
0.67 0.15 0.19
Matches are distributed among these distances:
28 8 0.05
29 59 0.40
30 62 0.42
31 14 0.10
32 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCCGATTACACC
Found at i:4007820 original size:25 final size:23
Alignment explanation
Indices: 4007791--4007836 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
4007781 ATTGGATCCA
4007791 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAA-TCT-AAAAAATAATTAG
*
4007816 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
4007837 CCCTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:4009920 original size:8 final size:8
Alignment explanation
Indices: 4009902--4009937 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
4009892 AAATAAAAAT
4009902 AAAATGAAA
1 AAAATG-AA
4009911 AAAATGAA
1 AAAATGAA
4009919 AAAATGAA
1 AAAATGAA
4009927 AAAATGAA
1 AAAATGAA
4009935 AAA
1 AAA
4009938 GAAAATGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAATGAA
Found at i:4009968 original size:6 final size:6
Alignment explanation
Indices: 4009862--4009970 Score: 60
Period size: 6 Copynumber: 17.3 Consensus size: 6
4009852 ATTGCATAAT
* * * * *
4009862 AAAATT AAATTA AAAAT- TAAATA AAACTA AAAATA AAAATA AAATGAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA--ATA
* * * *
4009911 AAAATGAA AAAATGAA AAAATGA AAAA-G AAAATG AACATG AAAATA AAAATA
1 AAAAT--A AAAAT--A AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA
4009963 AAAATA AA
1 AAAATA AA
4009971 TGTATTGATT
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
5 8 0.10
6 51 0.61
7 5 0.06
8 19 0.23
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:4010060 original size:16 final size:17
Alignment explanation
Indices: 4010020--4010064 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
4010010 TCATTTTTTT
4010020 TTAAAAAAATAACATGAA
1 TTAAAAAAATAA-ATGAA
*
4010038 --AATAAAATAAAT-AA
1 TTAAAAAAATAAATGAA
4010052 TTAAAAAAATAAA
1 TTAAAAAAATAAA
4010065 AACACTCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 2 0.09
16 19 0.83
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
TTAAAAAAATAAATGAA
Found at i:4013944 original size:25 final size:23
Alignment explanation
Indices: 4013916--4013961 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
4013906 GTTGGATCCA
4013916 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
4013941 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
4013962 CCCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:4014056 original size:13 final size:13
Alignment explanation
Indices: 4014038--4014065 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4014028 ACAATATAAT
4014038 AATATTAATCCTA
1 AATATTAATCCTA
4014051 AATATTAATCCTA
1 AATATTAATCCTA
4014064 AA
1 AA
4014066 AATAGAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTAATCCTA
Found at i:4031152 original size:25 final size:25
Alignment explanation
Indices: 4031086--4031170 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 25
4031076 ATGCTTGAAT
* *
4031086 TCTGTCTCGTAAGAGCAATATTCTA
1 TCTGGCTCGTAAGAGCGATATTCTA
4031111 TCTGGCTCGTAAGAGCGATATTCTA
1 TCTGGCTCGTAAGAGCGATATTCTA
* * *
4031136 TCTGGCTCGTAAGAGCGTTAATCTT
1 TCTGGCTCGTAAGAGCGATATTCTA
4031161 TCTGGGCTCG
1 TCT-GGCTCG
4031171 ATAGAGCTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 48 0.89
26 6 0.11
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCGATATTCTA
Found at i:4031354 original size:23 final size:23
Alignment explanation
Indices: 4031328--4031373 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4031318 ATTTTCGAAT
**
4031328 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
4031351 TTCGAGTTAAACGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
4031374 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:4032161 original size:51 final size:51
Alignment explanation
Indices: 4032052--4032162 Score: 120
Period size: 52 Copynumber: 2.1 Consensus size: 51
4032042 TGGATTTATG
* *
4032052 TTGTTTACTTGAACTTTTACTTATTTTTTTATTATAATTTTATTGTGTTGTCA
1 TTGTTTACTTGAACTTTTACTTATTTTTTTA-TAT-ATTTTATTGTATAGTCA
* *
4032105 TTGTTTACTTGAATTTTTTCACTTATTTATTTTA-AT-TTTTTTTGTATAGTCA
1 TTGTTTACTTGAA-CTTTT-ACTTATTT-TTTTATATATTTTATTGTATAGTCA
4032157 -TGTTTA
1 TTGTTTA
4032163 AAAACTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
51 6 0.12
52 13 0.25
53 13 0.25
54 6 0.12
55 8 0.16
56 5 0.10
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (51 bp):
TTGTTTACTTGAACTTTTACTTATTTTTTTATATATTTTATTGTATAGTCA
Found at i:4032704 original size:30 final size:30
Alignment explanation
Indices: 4032668--4032738 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
4032658 TGTTTGTTGA
4032668 ACTTGTATCATCTTGATGTAGCCTTCATAG
1 ACTTGTATCATCTTGATGTAGCCTTCATAG
*
4032698 ACTTGTATCATCTTGATGTAGTCTTCATAG
1 ACTTGTATCATCTTGATGTAGCCTTCATAG
* *
4032728 ACATGTTTCAT
1 ACTTGTATCAT
4032739 AAGTAGTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (30 bp):
ACTTGTATCATCTTGATGTAGCCTTCATAG
Found at i:4033277 original size:17 final size:17
Alignment explanation
Indices: 4033255--4033288 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4033245 ATTGTGGGTA
*
4033255 TTATATTTCAAATATTT
1 TTATATGTCAAATATTT
*
4033272 TTATATGTGAAATATTT
1 TTATATGTCAAATATTT
4033289 CAAATAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATATGTCAAATATTT
Found at i:4033971 original size:30 final size:30
Alignment explanation
Indices: 4033937--4033999 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
4033927 ACGTATTTTA
*
4033937 TTGTTAATTTTGTTATTATTTTAGAAGA-AT
1 TTGTTAATTTTGTTACTATTTTAG-AGACAT
4033967 TTGTTAATTTTGTTACTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAGAGACAT
4033997 TTG
1 TTG
4034000 CTTGTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGACAT
Found at i:4034717 original size:29 final size:30
Alignment explanation
Indices: 4034676--4034732 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
4034666 TAGTTTAATA
*
4034676 TGCAATTGTATACATGAACTTT-GATTTTG
1 TGCAATTGTATACATGAAATTTCGATTTTG
*
4034705 TGCAATTTTATACATGAAATTTCGATTT
1 TGCAATTGTATACATGAAATTTCGATTT
4034733 GATGTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (30 bp):
TGCAATTGTATACATGAAATTTCGATTTTG
Found at i:4035293 original size:19 final size:18
Alignment explanation
Indices: 4035253--4035295 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
4035243 ATTACAAAAG
*
4035253 AAAATTAAAATAATTTTT
1 AAAATTAAAATAATTTTA
4035271 AAAATTCAAAAT-ATTTATA
1 AAAATT-AAAATAATTT-TA
4035290 AAAATT
1 AAAATT
4035296 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTAAAATAATTTTA
Found at i:4035334 original size:9 final size:9
Alignment explanation
Indices: 4035253--4035339 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
4035243 ATTACAAAAG
4035253 AAAA-TTAA
1 AAAATTTAA
**
4035261 AATAATTTTT
1 AA-AATTTAA
*
4035271 AAAATTCAA
1 AAAATTTAA
*
4035280 AATATTTATA
1 AAAATTTA-A
*
4035290 AAAATTT-T
1 AAAATTTAA
4035298 AAAATTT-A
1 AAAATTTAA
* **
4035306 TATTTTTAA
1 AAAATTTAA
4035315 AAAATTATAA
1 AAAATT-TAA
4035325 AAAATTTAA
1 AAAATTTAA
4035334 AAAATT
1 AAAATT
4035340 CTAATATATA
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
8 13 0.22
9 25 0.43
10 20 0.34
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTAA
Found at i:4035473 original size:16 final size:16
Alignment explanation
Indices: 4035454--4035484 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4035444 TTTGAAAAAA
4035454 TTTCAAATATATGTGG
1 TTTCAAATATATGTGG
*
4035470 TTTCAAATTTATGTG
1 TTTCAAATATATGTG
4035485 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATGTGG
Found at i:4036455 original size:17 final size:17
Alignment explanation
Indices: 4036425--4036466 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
4036415 CGATCACTGA
4036425 TTTATTCTAGTTTTCTA-T
1 TTTATT-TAGTTTT-TACT
*
4036443 TTTATTTATTTTTTACT
1 TTTATTTAGTTTTTACT
4036460 TTTATTT
1 TTTATTT
4036467 TTATTTTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 14 0.64
18 6 0.27
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTATTTAGTTTTTACT
Found at i:4036531 original size:27 final size:25
Alignment explanation
Indices: 4036496--4036559 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
4036486 TGTTTATTTG
* *
4036496 TTATTTGTTTTATTTTAATTTTTAGAC
1 TTATATGTTTTATTTT-ATTTTGA-AC
4036523 TTATATGTTTTATTTTATTTTGAAC
1 TTATATGTTTTATTTTATTTTGAAC
4036548 TT-TAT-TTTTATT
1 TTATATGTTTTATT
4036560 ATTTTGTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.20
24 3 0.09
25 4 0.11
26 6 0.17
27 15 0.43
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATATGTTTTATTTTATTTTGAAC
Found at i:4039124 original size:2 final size:2
Alignment explanation
Indices: 4039119--4039147 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4039109 CCTGAAAAAA
4039119 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4039148 TTGTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4039184 original size:17 final size:17
Alignment explanation
Indices: 4039162--4039202 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
4039152 TTTAAATGGG
4039162 CATGTGAGTTTAATATA
1 CATGTGAGTTTAATATA
4039179 CATGTGAGTTTAATATA
1 CATGTGAGTTTAATATA
4039196 CATGTGA
1 CATGTGA
4039203 TTAGAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (17 bp):
CATGTGAGTTTAATATA
Found at i:4041160 original size:21 final size:22
Alignment explanation
Indices: 4041134--4041178 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
4041124 ATTAGTCAGC
* *
4041134 AAGAAATGAATAA-AAATGAGG
1 AAGAAATGAAGAAGAAAAGAGG
4041155 AAGAAATGAAGAAGAAAAGAGG
1 AAGAAATGAAGAAGAAAAGAGG
4041177 AA
1 AA
4041179 ATTTCAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (22 bp):
AAGAAATGAAGAAGAAAAGAGG
Found at i:4041163 original size:11 final size:11
Alignment explanation
Indices: 4041134--4041171 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4041124 ATTAGTCAGC
*
4041134 AAGAAATGAAT
1 AAGAAATGAAG
*
4041145 AA-AAATGAGG
1 AAGAAATGAAG
4041155 AAGAAATGAAG
1 AAGAAATGAAG
4041166 AAGAAA
1 AAGAAA
4041172 AGAGGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.11
Consensus pattern (11 bp):
AAGAAATGAAG
Found at i:4053638 original size:16 final size:16
Alignment explanation
Indices: 4053614--4053644 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4053604 GTGTGCTTTT
*
4053614 TGATTGGTTGAAAATA
1 TGATAGGTTGAAAATA
4053630 TGATAGGTTGAAAAT
1 TGATAGGTTGAAAAT
4053645 TCCCCTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.35
Consensus pattern (16 bp):
TGATAGGTTGAAAATA
Found at i:4053936 original size:28 final size:28
Alignment explanation
Indices: 4053883--4053936 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
4053873 ACAGTTTAAT
* **
4053883 AGTTTAGGTATCAATTTTGACTAAAAAA
1 AGTTTAGGTACCAATTTTGAAAAAAAAA
4053911 AGTTTAGGTACCAA-TTTGAAAAAAAA
1 AGTTTAGGTACCAATTTTGAAAAAAAA
4053937 TAATATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (28 bp):
AGTTTAGGTACCAATTTTGAAAAAAAAA
Found at i:4059993 original size:50 final size:50
Alignment explanation
Indices: 4059918--4060016 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
4059908 GTACATGGGC
*
4059918 GTATGCCTTGGGAGAAATAAGTGCAGGGTATACATGGGCAACACACGGGT
1 GTATGCCTTGGGAAAAATAAGTGCAGGGTATACATGGGCAACACACGGGT
*
4059968 GTATGCCTTGGGAAAAATAAGTGCAGGTTATACATGGGCAACACACGGG
1 GTATGCCTTGGGAAAAATAAGTGCAGGGTATACATGGGCAACACACGGG
4060017 CTGGGACACG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.20
Consensus pattern (50 bp):
GTATGCCTTGGGAAAAATAAGTGCAGGGTATACATGGGCAACACACGGGT
Found at i:4063453 original size:23 final size:21
Alignment explanation
Indices: 4063399--4063453 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
4063389 AATATAGTTT
*
4063399 AAATATTCTAATTAAATTTTAT
1 AAATATT-TAATTAAATTTTAC
* *
4063421 AAATAATTAATATAATTTCTTAC
1 AAATATTTAAT-TAAATT-TTAC
4063444 AAATATTTAA
1 AAATATTTAA
4063454 AATTTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 11 0.41
23 12 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATTTAATTAAATTTTAC
Found at i:4072106 original size:23 final size:23
Alignment explanation
Indices: 4072080--4072167 Score: 81
Period size: 23 Copynumber: 3.9 Consensus size: 23
4072070 ACGTTTACGA
*
4072080 CACG-TTTTTCTTCTACCTTTTGG
1 CACGCTTTTCCTT-TACCTTTTGG
* *
4072103 CACGCTTTTCCTTTGCCTTGTGG
1 CACGCTTTTCCTTTACCTTTTGG
* * *
4072126 CACGCTTTTCCTTTGCCTTATGA
1 CACGCTTTTCCTTTACCTTTTGG
* *
4072149 CACG-TTTTCGTCTACCTTT
1 CACGCTTTTCCTTTACCTTT
4072168 GTGTAGATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
22 11 0.20
23 37 0.67
24 7 0.13
ACGTcount: A:0.09, C:0.30, G:0.15, T:0.47
Consensus pattern (23 bp):
CACGCTTTTCCTTTACCTTTTGG
Found at i:4078214 original size:41 final size:41
Alignment explanation
Indices: 4078160--4078366 Score: 122
Period size: 41 Copynumber: 5.0 Consensus size: 41
4078150 GCACCTGAAT
*
4078160 ATCAGGCCTTGAGCTTAGCAGGCTTTGAGCCGATGTATTGA
1 ATCAAGCCTTGAGCTTAGCAGGCTTTGAGCCGATGTATTGA
* *
4078201 ATCAAGCCTTGAGCCTAGCAAGCTTCAT-A-CC-AGTGTATTGA
1 ATCAAGCCTTGAGCTTAGCAGGCTT--TGAGCCGA-TGTATTGA
* *
4078242 ATCAAGCCTTGAG-TCTAGCAGG-TTTAGTGCCGATATATT-A
1 ATCAAGCCTTGAGCT-TAGCAGGCTTT-GAGCCGATGTATTGA
* * * * * ** * *
4078282 ATTCAAGCTTTGTGCCTAGTAGGCTTCGAGTTGGTGTATCGAA
1 A-TCAAGCCTTGAGCTTAGCAGGCTTTGAGCCGATGTATTG-A
* * * * * *
4078325 AT-AGGCCTTGAGCTTGGTAGGCTTTGTGCTGGTGTATTGA
1 ATCAAGCCTTGAGCTTAGCAGGCTTTGAGCCGATGTATTGA
4078365 AT
1 AT
4078367 TAGATAATTA
Statistics
Matches: 126, Mismatches: 27, Indels: 27
0.70 0.15 0.15
Matches are distributed among these distances:
38 1 0.01
40 8 0.06
41 109 0.87
42 5 0.04
43 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (41 bp):
ATCAAGCCTTGAGCTTAGCAGGCTTTGAGCCGATGTATTGA
Found at i:4080273 original size:26 final size:26
Alignment explanation
Indices: 4080243--4080438 Score: 209
Period size: 26 Copynumber: 7.5 Consensus size: 26
4080233 ATGCCATGAT
* *
4080243 TATAAGTTTACGCTCGTCAACAT-GA
1 TATACGTTTACGCTCGTCAGCATGGA
*
4080268 TTATAAGTTTACGCTCGTCAGCAT-GA
1 -TATACGTTTACGCTCGTCAGCATGGA
* *
4080294 TTATGCGTTTACGCTCGCCAGCAT-GA
1 -TATACGTTTACGCTCGTCAGCATGGA
* * *
4080320 TTATGCGTCTACGCTCGCCAGCATGGA
1 -TATACGTTTACGCTCGTCAGCATGGA
* *
4080347 TATACGTTTACACTCGTCAGTATGGA
1 TATACGTTTACGCTCGTCAGCATGGA
* *
4080373 TATACGTTTACACTCGTCAGCATAGA
1 TATACGTTTACGCTCGTCAGCATGGA
* * *
4080399 TATACATTTATGCTCGCCAGCATGGA
1 TATACGTTTACGCTCGTCAGCATGGA
4080425 TATACGTTTACGCT
1 TATACGTTTACGCT
4080439 ACTAGAGCTC
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
26 148 0.99
27 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (26 bp):
TATACGTTTACGCTCGTCAGCATGGA
Found at i:4080366 original size:78 final size:78
Alignment explanation
Indices: 4080237--4080435 Score: 233
Period size: 78 Copynumber: 2.6 Consensus size: 78
4080227 CTAAACATGC
* * * * * *
4080237 CATGATTATAAGTTTACGCTCGTCAACAT-GATTATAAGTTTACGCTCGTCAGCAT-GATTATGC
1 CATGATTATACGTTTACGCTCGCCAGCATGGA-TATACGTTTACACTCGTCAGCATGGA-TATAC
*
4080300 GTTTACGCTCGCCAG
64 GTTTACACTCGCCAG
* * *
4080315 CATGATTATGCGTCTACGCTCGCCAGCATGGATATACGTTTACACTCGTCAGTATGGATATACGT
1 CATGATTATACGTTTACGCTCGCCAGCATGGATATACGTTTACACTCGTCAGCATGGATATACGT
*
4080380 TTACACTCGTCAG
66 TTACACTCGCCAG
* *
4080393 CATAGA-TATACATTTATGCTCGCCAGCATGGATATACGTTTAC
1 CAT-GATTATACGTTTACGCTCGCCAGCATGGATATACGTTTAC
4080436 GCTACTAGAG
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 97 0.94
79 6 0.06
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (78 bp):
CATGATTATACGTTTACGCTCGCCAGCATGGATATACGTTTACACTCGTCAGCATGGATATACGT
TTACACTCGCCAG
Found at i:4085122 original size:39 final size:41
Alignment explanation
Indices: 4085033--4085131 Score: 159
Period size: 39 Copynumber: 2.5 Consensus size: 41
4085023 TGGGACAAGT
*
4085033 CTCTTCCAAAAGGTGTCCATCTAATATGAAAAGGGTTGTGA
1 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
*
4085074 CT-TTCCAAAAGGTGTCTATCCAATATG-AAAGGGTTGTGA
1 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
4085113 CTCTT-CAAAAGGTGTCCAT
1 CTCTTCCAAAAGGTGTCCAT
4085132 TAAGTGCATA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
39 27 0.50
40 25 0.46
41 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (41 bp):
CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
Found at i:4089924 original size:52 final size:52
Alignment explanation
Indices: 4089831--4090010 Score: 254
Period size: 52 Copynumber: 3.5 Consensus size: 52
4089821 ATTTCATTTC
*
4089831 ATTCATATACTCATGATGAAACATAACCACTT-GACCTCATAATCCGTAAAGG
1 ATTCATATACTCATGATGACACATAACCA-TTGGACCTCATAATCCGTAAAGG
* * ** * *
4089883 ATTCATATACTCAAGATGACACACAGTCATTGGACCCCATAATCTGTAAAGG
1 ATTCATATACTCATGATGACACATAACCATTGGACCTCATAATCCGTAAAGG
* *
4089935 ATTCATATACTCATGATGACACATAACCATCGGACCTCATAATCCGTAAGGG
1 ATTCATATACTCATGATGACACATAACCATTGGACCTCATAATCCGTAAAGG
*
4089987 ATTCATATACTCACGATGACACAT
1 ATTCATATACTCATGATGACACAT
4090011 GTCCTTTGTG
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 2 0.02
52 109 0.98
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (52 bp):
ATTCATATACTCATGATGACACATAACCATTGGACCTCATAATCCGTAAAGG
Found at i:4104739 original size:26 final size:26
Alignment explanation
Indices: 4104710--4104803 Score: 81
Period size: 26 Copynumber: 3.7 Consensus size: 26
4104700 AAAATTATTA
4104710 TTAAATATAATTTAATAATAAATAAT
1 TTAAATATAATTTAATAATAAATAAT
* * *
4104736 TT-AATCATATTTTAAT-ATAATTATT
1 TTAAAT-ATAATTTAATAATAAATAAT
*
4104761 ATTAAATATAATTTAGTAA-AAATAA-
1 -TTAAATATAATTTAATAATAAATAAT
*
4104786 -AAATATATAATTTAATAA
1 TTAA-ATATAATTTAATAA
4104804 CATTCTTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
23 2 0.04
24 13 0.24
25 10 0.19
26 25 0.46
27 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
TTAAATATAATTTAATAATAAATAAT
Found at i:4105576 original size:14 final size:13
Alignment explanation
Indices: 4105555--4105588 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
4105545 AGTGTCCTAT
4105555 AAAAATATTCAAA
1 AAAAATATTCAAA
4105568 AATAAATATTCAAA
1 AA-AAATATTCAAA
4105582 AAAAATA
1 AAAAATA
4105589 AAATACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATATTCAAA
Found at i:4107481 original size:14 final size:15
Alignment explanation
Indices: 4107448--4107488 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
4107438 TAAAGGGGCC
4107448 ATTAAATAAATTTGA
1 ATTAAATAAATTTGA
*
4107463 ATTAAATCAATTT-A
1 ATTAAATAAATTTGA
4107477 ATTAAATAAATT
1 ATTAAATAAATT
4107489 AAACCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTAAATAAATTTGA
Found at i:4108821 original size:5 final size:5
Alignment explanation
Indices: 4108811--4108888 Score: 52
Period size: 5 Copynumber: 15.6 Consensus size: 5
4108801 AAACATAACT
* * * * **
4108811 TATCA TATCA TAACG TATCGA -ATCA TATCA TATCA CATCA TATCG GGTCA
1 TATCA TATCA TATCA TATC-A TATCA TATCA TATCA TATCA TATCA TATCA
* *
4108861 TATCA TGTCA TAT-A GGATCA TATCA TAT
1 TATCA TATCA TATCA -TATCA TATCA TAT
4108889 AATGCCTTAC
Statistics
Matches: 53, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
4 2 0.04
5 50 0.94
6 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (5 bp):
TATCA
Found at i:4108886 original size:20 final size:20
Alignment explanation
Indices: 4108837--4108888 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
4108827 ATCGAATCAT
* *
4108837 ATCATATCACATCATATCGG
1 ATCATATCATATCATATAGG
* *
4108857 GTCATATCATGTCATATAGG
1 ATCATATCATATCATATAGG
4108877 ATCATATCATAT
1 ATCATATCATAT
4108889 AATGCCTTAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (20 bp):
ATCATATCATATCATATAGG
Found at i:4124339 original size:72 final size:72
Alignment explanation
Indices: 4124253--4124645 Score: 536
Period size: 72 Copynumber: 5.6 Consensus size: 72
4124243 AATGCTAAAC
* *
4124253 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATG
4124318 TGTAATT
66 TGTAATT
** *
4124325 TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTT-T-GGT-TCT-TG
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATG
4124386 -G-ATATT
66 TGTA-ATT
* * *
4124392 GA-ATTTAT-GATA-TTGAATTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTA
1 TAGTTTTATCAATAGTTG--TTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTA
*
4124454 TGTGTAATC
64 TGTGTAATT
* *
4124463 TAATTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATG
*
4124528 TGCAATT
66 TGTAATT
* *
4124535 TAGTTTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATG
*
4124600 TGTATTT
66 TGTAATT
* *
4124607 TAGTTTTATCAATAGTTGTTTATATTTGATT-TTGGATAT
1 TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATAT
4124646 AAAATTTGTT
Statistics
Matches: 282, Mismatches: 27, Indels: 25
0.84 0.08 0.07
Matches are distributed among these distances:
64 3 0.01
65 3 0.01
66 40 0.14
67 6 0.02
68 3 0.01
69 4 0.01
70 3 0.01
71 13 0.05
72 201 0.71
73 3 0.01
74 3 0.01
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.55
Consensus pattern (72 bp):
TAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATG
TGTAATT
Found at i:4124379 original size:26 final size:26
Alignment explanation
Indices: 4124343--4124400 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
4124333 TCAATAGTTG
4124343 TTTATGTTTGGTTCTTGGATATTGAA
1 TTTATGTTTGGTTCTTGGATATTGAA
4124369 TTTATGTTTGGTTCTTGGATATTGAA
1 TTTATGTTTGGTTCTTGGATATTGAA
4124395 TTTATG
1 TTTATG
4124401 ATATTGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.55
Consensus pattern (26 bp):
TTTATGTTTGGTTCTTGGATATTGAA
Found at i:4124404 original size:40 final size:40
Alignment explanation
Indices: 4124360--4124440 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
4124350 TTGGTTCTTG
4124360 GATATTGAATTTATGTTTGGTTCTTGGATATTGAATTTAT
1 GATATTGAATTTATGTTTGGTTCTTGGATATTGAATTTAT
4124400 GATATTGAATTTATGTTTGGTTCTTGGATATTGAATTTAT
1 GATATTGAATTTATGTTTGGTTCTTGGATATTGAATTTAT
4124440 G
1 G
4124441 TTCTACTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.25, C:0.02, G:0.21, T:0.52
Consensus pattern (40 bp):
GATATTGAATTTATGTTTGGTTCTTGGATATTGAATTTAT
Found at i:4124405 original size:14 final size:14
Alignment explanation
Indices: 4124386--4124414 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4124376 TTGGTTCTTG
4124386 GATATTGAATTTAT
1 GATATTGAATTTAT
4124400 GATATTGAATTTAT
1 GATATTGAATTTAT
4124414 G
1 G
4124415 TTTGGTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
GATATTGAATTTAT
Found at i:4124490 original size:138 final size:144
Alignment explanation
Indices: 4124257--4124645 Score: 546
Period size: 138 Copynumber: 2.8 Consensus size: 144
4124247 CTAAACTAGT
* *
4124257 TTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGTA
1 TTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGTA
*
4124322 ATTTAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTT-T-GGT-TCT
66 ATTTAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACGTATCT
4124384 -TG-G-ATATTGA-A
131 ATGTGCA-ATTGAGA
* *
4124395 TTTAT-GAT-ATTGAATTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACTTATTTATGTG
1 TTTATCAATAATTG--TTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTG
* * * *
4124458 TAATCTAATTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTGAATTTATGTTCTACTTAT
64 TAATTTAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACGTAT
* * *
4124523 TTATGTGCAATTTAGT
129 CTATGTGCAATTGAGA
4124539 TTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGTA
1 TTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGTA
* * *
4124604 TTTTAGTTTTATCAATAGTTGTTTATATTTGATT-TTGGATAT
66 ATTTAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATAT
4124646 AAAATTTGTT
Statistics
Matches: 220, Mismatches: 20, Indels: 17
0.86 0.08 0.07
Matches are distributed among these distances:
136 3 0.01
137 2 0.01
138 106 0.48
139 1 0.00
140 1 0.00
141 2 0.01
142 2 0.01
143 12 0.05
144 85 0.39
145 2 0.01
146 4 0.02
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.56
Consensus pattern (144 bp):
TTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGTA
ATTTAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGGATATTGAATTTATGTTCTACGTATCT
ATGTGCAATTGAGA
Found at i:4126024 original size:3 final size:3
Alignment explanation
Indices: 4126016--4126044 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4126006 ATGGAGAAAG
4126016 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
4126045 GTGGTGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:4127081 original size:18 final size:18
Alignment explanation
Indices: 4127033--4127117 Score: 55
Period size: 18 Copynumber: 4.8 Consensus size: 18
4127023 CTTCCCACGG
** *
4127033 AGTTGTGAGCTCTCTTGA
1 AGTTGTGAGCTCAATTAA
* *
4127051 AGTTGCGAACTCAATTAA
1 AGTTGTGAGCTCAATTAA
**
4127069 AGTTGTGAGCTCACCTAA
1 AGTTGTGAGCTCAATTAA
***
4127087 AGAAATGAGCTC-ATTAA
1 AGTTGTGAGCTCAATTAA
* *
4127104 AGCTGCGAGCTCAA
1 AGTTGTGAGCTCAA
4127118 CTTAGTTACG
Statistics
Matches: 48, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
17 11 0.23
18 37 0.77
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (18 bp):
AGTTGTGAGCTCAATTAA
Found at i:4132448 original size:41 final size:41
Alignment explanation
Indices: 4132386--4132553 Score: 157
Period size: 41 Copynumber: 4.1 Consensus size: 41
4132376 GCACCTAAAT
* * *
4132386 ATCAGGCCTTGAGCTTAGCAGGCTTTGAGTCGATGTATTGA
1 ATCAAGCCTTGAGCCTAGCAGGCTTTGAGTCGGTGTATTGA
*
4132427 ATCAAGCCTTGAGCCTAGCAGG-TTT-AGTGCCGGTATATT-A
1 ATCAAGCCTTGAGCCTAGCAGGCTTTGAGT--CGGTGTATTGA
* * * * *
4132467 ATTCAAGCTTTGTGCCTAGCAGGCTTCGAGTTGGTGTATCGAA
1 A-TCAAGCCTTGAGCCTAGCAGGCTTTGAGTCGGTGTATTG-A
* *
4132510 AT-AGGCCTTGAGCCTAGCAGGCTTTGTG-CTGGTGTATTGA
1 ATCAAGCCTTGAGCCTAGCAGGCTTTGAGTC-GGTGTATTGA
4132550 ATCA
1 ATCA
4132554 GATAATTATA
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
39 3 0.03
40 8 0.08
41 82 0.81
42 3 0.03
43 5 0.05
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (41 bp):
ATCAAGCCTTGAGCCTAGCAGGCTTTGAGTCGGTGTATTGA
Found at i:4134699 original size:26 final size:26
Alignment explanation
Indices: 4134432--4134707 Score: 258
Period size: 26 Copynumber: 10.6 Consensus size: 26
4134422 CGTTCGCCAC
* * *
4134432 CATGATTATAAGTTTATGCTCGTCAA
1 CATGATTATACGTTTACGCTCGTCAG
*
4134458 CATGATTATAAGTTTACGCTCGTCAG
1 CATGATTATACGTTTACGCTCGTCAG
* *
4134484 CATGATTATGCGTTTACGCTCGCCAG
1 CATGATTATACGTTTACGCTCGTCAG
* *
4134510 CATGATTATACATTTACGCTCGCCAG
1 CATGATTATACGTTTACGCTCGTCAG
*
4134536 CATGATTATACATTTACGCTCGTCAG
1 CATGATTATACGTTTACGCTCGTCAG
* * * ** *
4134562 CATGATTATGCGTCTATGCTCACCAA
1 CATGATTATACGTTTACGCTCGTCAG
* *
4134588 CATGATTATGCGTCTACGCTCG-CTAG
1 CATGATTATACGTTTACGCTCGTC-AG
4134614 CATGGA-TATACGTTTA-GACTCGTCAG
1 CAT-GATTATACGTTTACG-CTCGTCAG
* *
4134640 TATGGA-TATACGTTTACACTCGTCAG
1 CAT-GATTATACGTTTACGCTCGTCAG
* *
4134666 TATGGA-TATACGTTTACACTCGTCAG
1 CAT-GATTATACGTTTACGCTCGTCAG
*
4134692 CATAGA-TATACATTTA
1 CAT-GATTATACGTTTA
4134708 TGTTCGCCAA
Statistics
Matches: 220, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
25 2 0.01
26 215 0.98
27 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (26 bp):
CATGATTATACGTTTACGCTCGTCAG
Found at i:4134723 original size:52 final size:52
Alignment explanation
Indices: 4134614--4134734 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
4134604 CGCTCGCTAG
* * * * * *
4134614 CATGGATATACGTTTAGACTCGTCAGTATGGATATACGTTTACACTCGTCAG
1 CATGGATATACGTTTACACTCGTCAGCATAGATATACATTTACACTCGCCAA
* ***
4134666 TATGGATATACGTTTACACTCGTCAGCATAGATATACATTTATGTTCGCCAA
1 CATGGATATACGTTTACACTCGTCAGCATAGATATACATTTACACTCGCCAA
*
4134718 CATGGATATACATTTAC
1 CATGGATATACGTTTAC
4134735 GCTACTAGAG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (52 bp):
CATGGATATACGTTTACACTCGTCAGCATAGATATACATTTACACTCGCCAA
Found at i:4135915 original size:2 final size:2
Alignment explanation
Indices: 4135908--4135938 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4135898 CAACCCATGG
*
4135908 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4135939 TAACATCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:4139389 original size:40 final size:38
Alignment explanation
Indices: 4139333--4139429 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 38
4139323 GGACAAGTCT
4139333 CTTCCAAAAGGTGTCCATCAAATATGAAAAGGGTTGTGA
1 CTTCCAAAAGGTGTCCATCAAATATG-AAAGGGTTGTGA
*
4139372 CGTTCCAAAAGGTGTCCATCCAATATGAAAGGGTTGTGA
1 C-TTCCAAAAGGTGTCCATCAAATATGAAAGGGTTGTGA
*
4139411 CTCTTCAAAAGGTGTCCAT
1 CT-TCCAAAAGGTGTCCAT
4139430 TTAGTGCATA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
38 1 0.02
39 29 0.54
40 24 0.44
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (38 bp):
CTTCCAAAAGGTGTCCATCAAATATGAAAGGGTTGTGA
Found at i:4143877 original size:39 final size:41
Alignment explanation
Indices: 4143783--4143881 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 41
4143773 TGGGACAAGT
* *
4143783 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGG
1 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTATGA
4143824 CT-TTCCAAAAGGTGTCCATCCAATATG-AAAGGGTTATGA
1 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTATGA
*
4143863 CTCTT-CAAATGGTGTCCAT
1 CTCTTCCAAAAGGTGTCCAT
4143882 TGAGTGCATA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
39 25 0.46
40 27 0.50
41 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGGGTTATGA
Found at i:4145909 original size:3 final size:3
Alignment explanation
Indices: 4145897--4145931 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4145887 AAGGAAAAAA
*
4145897 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
4145932 AAAAATGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4146978 original size:32 final size:27
Alignment explanation
Indices: 4146909--4146998 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 27
4146899 CAGTCCGTAT
4146909 TATTTTTTAATTTTTTTTAAAATATTTA
1 TATTTTTT-ATTTTTTTTAAAATATTTA
4146937 TATTATTTTATTTTAATATTTAATAATATTATA
1 TATT-TTTTATTTT--T-TTTAA-AATATT-TA
* * *
4146970 TATTTTTTA-TTTATTGAAAATTTTTA
1 TATTTTTTATTTTTTTTAAAATATTTA
4146996 TAT
1 TAT
4146999 AGTTATTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
26 5 0.09
27 5 0.09
28 13 0.25
29 4 0.08
30 1 0.02
31 8 0.15
32 11 0.21
33 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (27 bp):
TATTTTTTATTTTTTTTAAAATATTTA
Found at i:4148238 original size:21 final size:21
Alignment explanation
Indices: 4148214--4148264 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
4148204 TTTAAATTAA
4148214 TTTGTTAGTAAGCAATTTTAT
1 TTTGTTAGTAAGCAATTTTAT
*
4148235 TTTGTTAG-AAGTAATTTTAT
1 TTTGTTAGTAAGCAATTTTAT
4148255 TTTGTTAGTA
1 TTTGTTAGTA
4148265 GTAGTAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTGTTAGTAAGCAATTTTAT
Found at i:4148343 original size:17 final size:17
Alignment explanation
Indices: 4148323--4148355 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4148313 AAAGAGATAT
4148323 TTATTTACCAAAATGGG
1 TTATTTACCAAAATGGG
4148340 TTATTTACCAAAATGG
1 TTATTTACCAAAATGG
4148356 TACAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (17 bp):
TTATTTACCAAAATGGG
Found at i:4148520 original size:29 final size:30
Alignment explanation
Indices: 4148473--4148540 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
4148463 TAAATAACTC
*
4148473 ATTTTGATATATAAATATT-TTTTTGTACT
1 ATTTTGGTATATAAATATTATTTTTGTACT
* * *
4148502 ATTTTGGTATTTAATTATTATTTTTGTATT
1 ATTTTGGTATATAAATATTATTTTTGTACT
*
4148532 ATATTGGTA
1 ATTTTGGTA
4148541 AAAAATCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.60
Consensus pattern (30 bp):
ATTTTGGTATATAAATATTATTTTTGTACT
Found at i:4153109 original size:24 final size:24
Alignment explanation
Indices: 4153077--4153123 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4153067 ACCATACACG
4153077 GAGTTGGATCTTCATTTTCTACTA
1 GAGTTGGATCTTCATTTTCTACTA
*
4153101 GAGTTGGATCTTCATTTTGTACT
1 GAGTTGGATCTTCATTTTCTACT
4153124 GGTTCCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (24 bp):
GAGTTGGATCTTCATTTTCTACTA
Found at i:4153713 original size:12 final size:13
Alignment explanation
Indices: 4153666--4153732 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 13
4153656 AAAAAAATTA
*
4153666 TCTTTCTTTCCTTAT
1 TCTTTCTTT-CTT-C
* *
4153681 TCTTTTTTTCCTC
1 TCTTTCTTTCTTC
4153694 TCCTTTCTTTCTT-
1 T-CTTTCTTTCTTC
4153707 TCTTTCTTTCTTC
1 TCTTTCTTTCTTC
4153720 TCTCTTCTCTTCT
1 TCT-TTCT-TTCT
4153733 CTCCCGTTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
12 11 0.26
13 5 0.12
14 15 0.35
15 12 0.28
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (13 bp):
TCTTTCTTTCTTC
Found at i:4155082 original size:22 final size:22
Alignment explanation
Indices: 4155037--4155084 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
4155027 TATGGGTTTT
* * *
4155037 TTTTCTTAATTTATTACTTGAA
1 TTTTCATAATTTATCACTTAAA
*
4155059 TTTTCATAATTTATCCCTTAAA
1 TTTTCATAATTTATCACTTAAA
4155081 TTTT
1 TTTT
4155085 GAAGTTGTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTCATAATTTATCACTTAAA
Found at i:4156099 original size:27 final size:28
Alignment explanation
Indices: 4156048--4156103 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
4156038 GAATTTTAGG
*
4156048 GTTTTTTACCTAAATAATACAAAAAAAA
1 GTTTTTAACCTAAATAATACAAAAAAAA
4156076 GTTTTTAACCTAAATAATACAAAAAAAA
1 GTTTTTAACCTAAATAATACAAAAAAAA
4156104 ATTATACACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (28 bp):
GTTTTTAACCTAAATAATACAAAAAAAA
Found at i:4156119 original size:28 final size:27
Alignment explanation
Indices: 4156055--4156154 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 27
4156045 AGGGTTTTTT
* *
4156055 ACCTAAATAATACAAAAAAAAGTTTTTA
1 ACCTAAATAATACAAAAAAAA-ATTATA
4156083 ACCTAAATAATACAAAAAAAAATTATA
1 ACCTAAATAATACAAAAAAAAATTATA
*
4156110 CACCAGAATATAAAATA-AAAAATAAAATTAATA
1 -ACC-TAA-AT--AATACAAAAA-AAAATT-ATA
*
4156143 ACTTAAATAATA
1 ACCTAAATAATA
4156155 TAAATATATA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
27 4 0.07
28 28 0.47
29 2 0.03
30 4 0.07
31 7 0.12
32 12 0.20
33 3 0.05
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (27 bp):
ACCTAAATAATACAAAAAAAAATTATA
Found at i:4156433 original size:15 final size:14
Alignment explanation
Indices: 4156407--4156436 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4156397 GTATTTTTAT
4156407 ATTAAAAAAATTAA
1 ATTAAAAAAATTAA
4156421 ATTAAATAAAATTAA
1 ATTAAA-AAAATTAA
4156436 A
1 A
4156437 ATTTGACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTAAAAAAATTAA
Found at i:4159490 original size:26 final size:26
Alignment explanation
Indices: 4159441--4159490 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4159431 TCTGTTTAAA
**
4159441 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
4159467 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
4159491 ACAGATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:4159584 original size:6 final size:6
Alignment explanation
Indices: 4159573--4159602 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4159563 CATAAATAAG
*
4159573 AACATA AACATA AATATA AACATA AACATA
1 AACATA AACATA AACATA AACATA AACATA
4159603 TTTAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (6 bp):
AACATA
Found at i:4159584 original size:18 final size:18
Alignment explanation
Indices: 4159561--4159602 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
4159551 TGCATGCATG
4159561 AACATAAATA-AGAACATA
1 AACATAAATATA-AACATA
4159579 AACATAAATATAAACATA
1 AACATAAATATAAACATA
4159597 AACATA
1 AACATA
4159603 TTTAATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.19
Consensus pattern (18 bp):
AACATAAATATAAACATA
Found at i:4160047 original size:6 final size:6
Alignment explanation
Indices: 4160036--4160065 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4160026 AGTGCTACGA
4160036 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG
4160066 TGACTGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
CTCAGG
Found at i:4162048 original size:16 final size:17
Alignment explanation
Indices: 4162027--4162064 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
4162017 TCATTTTAAA
4162027 AAATATTT-AATATATC
1 AAATATTTAAATATATC
4162043 AAATATTTAAATATATC
1 AAATATTTAAATATATC
4162060 AAATA
1 AAATA
4162065 AATTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTTAAATATATC
Found at i:4162843 original size:17 final size:17
Alignment explanation
Indices: 4162821--4162854 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4162811 CTTACAATAA
4162821 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
4162838 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
4162855 GAATTTTTTT
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:4162929 original size:11 final size:11
Alignment explanation
Indices: 4162913--4162937 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4162903 AAAACATACA
4162913 TTTTTTCTTCT
1 TTTTTTCTTCT
4162924 TTTTTTCTTCT
1 TTTTTTCTTCT
4162935 TTT
1 TTT
4162938 CTCTCCTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:4184039 original size:4 final size:4
Alignment explanation
Indices: 4184030--4184077 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
4184020 ATGTTACTTT
4184030 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4184078 CGGACGGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:4193425 original size:21 final size:21
Alignment explanation
Indices: 4193400--4193445 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4193390 ACTTAGACCA
4193400 AAACCC-TAAATCTTAAACCCC
1 AAACCCTTAAA-CTTAAACCCC
* *
4193421 AAACCCTTAAACTTGAACCCT
1 AAACCCTTAAACTTAAACCCC
4193442 AAAC
1 AAAC
4193446 TCGTACCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACCCTTAAACTTAAACCCC
Found at i:4195504 original size:43 final size:43
Alignment explanation
Indices: 4195455--4195537 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
4195445 AAAATGCTCA
*
4195455 CAATCAATCACATACTTTCAATAATAGGAATCAGTGTTCCTCT
1 CAATCAATCACATACTTTCAATAATAGGAAACAGTGTTCCTCT
*
4195498 CAATCAATCACATACTTTCAATAATAGTAAACAGTGTTCC
1 CAATCAATCACATACTTTCAATAATAGGAAACAGTGTTCC
4195538 AACTTTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.31
Consensus pattern (43 bp):
CAATCAATCACATACTTTCAATAATAGGAAACAGTGTTCCTCT
Found at i:4198773 original size:16 final size:16
Alignment explanation
Indices: 4198754--4198784 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4198744 ATAAAGTGTC
4198754 GATAAAATAAAGAAAA
1 GATAAAATAAAGAAAA
4198770 GATAAAATAAAGAAA
1 GATAAAATAAAGAAA
4198785 TGATGACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
GATAAAATAAAGAAAA
Found at i:4200885 original size:6 final size:6
Alignment explanation
Indices: 4200874--4200898 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4200864 GCTTGTCCCC
4200874 TTCTCT TTCTCT TTCTCT TTCTCT T
1 TTCTCT TTCTCT TTCTCT TTCTCT T
4200899 CCTCAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTCTCT
Found at i:4206608 original size:30 final size:33
Alignment explanation
Indices: 4206569--4206636 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
4206559 GTGCATAATA
4206569 TATTCTTATA-TGTGTA-A-TGTCATATCAATT
1 TATTCTTATATTGTGTAGATTGTCATATCAATT
* * *
4206599 TATTTTTATATTTTTTTAGATTGTCATATCAATT
1 TATTCTTATA-TTGTGTAGATTGTCATATCAATT
4206633 TATT
1 TATT
4206637 ATTTTCACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 9 0.29
32 4 0.13
33 1 0.03
34 17 0.55
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (33 bp):
TATTCTTATATTGTGTAGATTGTCATATCAATT
Found at i:4215320 original size:21 final size:21
Alignment explanation
Indices: 4215296--4215336 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4215286 TGATCTTATG
4215296 TTCTACTCATTTATTTTTTTA
1 TTCTACTCATTTATTTTTTTA
** *
4215317 TTCTTTTCCTTTATTTTTTT
1 TTCTACTCATTTATTTTTTT
4215337 CTTTTCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCTACTCATTTATTTTTTTA
Found at i:4215364 original size:23 final size:22
Alignment explanation
Indices: 4215311--4215365 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4215301 CTCATTTATT
* *
4215311 TTTTTATTCTTTTCCTTTATTTT
1 TTTTT-TTCTTTTCCTTTATCTC
*
4215334 TTTCTTTTCTTTTCACTTTCTCTC
1 TTT-TTTTCTTTTC-CTTTATCTC
4215358 TTTTTTTC
1 TTTTTTTC
4215366 CTCTCTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTTCTTTTCCTTTATCTC
Found at i:4218422 original size:3 final size:3
Alignment explanation
Indices: 4218414--4218481 Score: 91
Period size: 3 Copynumber: 22.7 Consensus size: 3
4218404 AGGGGAAGGG
* *
4218414 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGT GGA GGG GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
* **
4218462 GGG GGA GGA GCT GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GG
4218482 GGGAAGTATG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.26, C:0.01, G:0.69, T:0.03
Consensus pattern (3 bp):
GGA
Found at i:4233362 original size:263 final size:263
Alignment explanation
Indices: 4232887--4233935 Score: 1387
Period size: 263 Copynumber: 4.0 Consensus size: 263
4232877 AGTGCAAACG
* * * * * *
4232887 ATAAGATA-TGCAAATTAATACACAAATGACATGTCCACTGAATTATCTCAAAAAAGGAGAAAAA
1 ATAAGACATTGCAAATTAATACACAAATGTCATGTCCACTGAATAATCCCAAAAGAGGAGAAAGA
* * * * *
4232951 CAAACTTATTATAACTATAACACTCGAAGAATTCAAAAACAAACTAAAGATGCATCACATAGATC
66 CAAACTGACTATAACCATAACACTCGAAGAATTCAAAAACAAACTAAAGATGCATCACCTTGATC
* * * * * * * *
4233016 AAACCACTAAAATTGCATCATAACCGTGTCATTATCAAACAAACTTAATGATGAACTCCAATTAT
131 AAACCACTGAAATTGCATCACAACCTTGTCATTATCAGACCAACCTGATGATGAACTCCAATTAA
* * *
4233081 CCAATAAATCACTGCCAAGACCCTAAAAGACCCACCAAATCAATGATGTACAAAAGACCAATTCT
196 CCAATAAATCACTGCCAAGACCCCAAAAGACCCACCATATCAATGATGCACAAAAGACCAATTCT
4233146 CAT
261 CAT
*
4233149 ATAAGACCTTGCAAATTAATACACAAATGTCATGTCC-CTTGAATAATCCCAAAAGAGGAGAAAG
1 ATAAGACATTGCAAATTAATACACAAATGTCATGTCCAC-TGAATAATCCCAAAAGAGGAGAAAG
* * *
4233213 ACAAACTGACTATAGCTATAACACTCGAAGAATTCAAAAATAAACTAAAGATGCATCACCTTGAT
65 ACAAACTGACTATAACCATAACACTCGAAGAATTCAAAAACAAACTAAAGATGCATCACCTTGAT
4233278 CAAACCACTGAAATTGCATCACAACCTTGTCATTATCAGACCAACCTGATGATGAACTCCAATTA
130 CAAACCACTGAAATTGCATCACAACCTTGTCATTATCAGACCAACCTGATGATGAACTCCAATTA
* *
4233343 ACCAATAAACCATTGCCAAGACCCCAAAAGACCCACCATATCAATGATGCACAAAAGACCAAGTT
195 ACCAATAAATCACTGCCAAGACCCCAAAAGACCCACCATATCAATGATGCACAAAAGACCAA-TT
*
4233408 -TCAA
259 CTCAT
* * *
4233412 ATAAGACATTGCAAAGTAATACACAAATATCATGTCCACTGAATAATCCCAGAAGAGGAGAAAGA
1 ATAAGACATTGCAAATTAATACACAAATGTCATGTCCACTGAATAATCCCAAAAGAGGAGAAAGA
* * * *
4233477 CATACTGACTATAGCCATCACACTCGAAAAATTCAAAAACAAACTAAAGATGCATCATCC-TGAT
66 CAAACTGACTATAACCATAACACTCGAAGAATTCAAAAACAAACTAAAGATGCATCA-CCTTGAT
* * * *
4233541 ---ACCATTGAAATTGCATCACAACCCTGTCATTATCAGACCAACCTGATGATGAAGTCTAATTA
130 CAAACCACTGAAATTGCATCACAACCTTGTCATTATCAGACCAACCTGATGATGAACTCCAATTA
* * * * *
4233603 ACCAAGAAATCACTAG-CAGGACCCTAAAAAACCCACCATATCAATGATGCACAAAAGACCAAAT
195 ACCAATAAATCACT-GCCAAGACCCCAAAAGACCCACCATATCAATGATGCACAAAAGACCAATT
4233667 CTCAT
259 CTCAT
* *
4233672 ATAAGACATTGCAAATTAATACACAAATGTCATGTCCATTGAATAATCTCAAAAGAGGAGAAAGA
1 ATAAGACATTGCAAATTAATACACAAATGTCATGTCCACTGAATAATCCCAAAAGAGGAGAAAGA
* * * *
4233737 CAAACTAACTATAACCATAACACTCGGAGAATCCAAAAACAAACTAAAGATGCATCACCTTTATC
66 CAAACTGACTATAACCATAACACTCGAAGAATTCAAAAACAAACTAAAGATGCATCACCTTGATC
* * * * * *
4233802 AAACCACAGAAATTACATCATAACTCTT-TCATTATCATATCAACCTGATGATGAACTCTAATTA
131 AAACCACTGAAATTGCATCACAAC-CTTGTCATTATCAGACCAACCTGATGATGAACTCCAATTA
* * * * * * ** *
4233866 ACTAAAAAAATCACTGCTAAGACCCCAAAAGACCCATCACATCAGTGATGTGCAAAAGACCAAGT
195 AC-CAATAAATCACTGCCAAGACCCCAAAAGACCCACCATATCAATGATGCACAAAAGACCAATT
4233931 CTCAT
259 CTCAT
4233936 GTAATTTAAC
Statistics
Matches: 692, Mismatches: 81, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
259 3 0.00
260 228 0.33
261 1 0.00
262 7 0.01
263 393 0.57
264 60 0.09
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.22
Consensus pattern (263 bp):
ATAAGACATTGCAAATTAATACACAAATGTCATGTCCACTGAATAATCCCAAAAGAGGAGAAAGA
CAAACTGACTATAACCATAACACTCGAAGAATTCAAAAACAAACTAAAGATGCATCACCTTGATC
AAACCACTGAAATTGCATCACAACCTTGTCATTATCAGACCAACCTGATGATGAACTCCAATTAA
CCAATAAATCACTGCCAAGACCCCAAAAGACCCACCATATCAATGATGCACAAAAGACCAATTCT
CAT
Found at i:4234304 original size:6 final size:6
Alignment explanation
Indices: 4234283--4234320 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
4234273 TAACTTTATA
*
4234283 TATTTT TATTAGT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT T
4234321 TTTATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:4234320 original size:13 final size:13
Alignment explanation
Indices: 4234283--4234321 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4234273 TAACTTTATA
**
4234283 TATTTTTATTAGT
1 TATTTTTATTTTT
4234296 TATTTTTA-TTTT
1 TATTTTTATTTTT
4234308 TATTTTTATTTTT
1 TATTTTTATTTTT
4234321 T
1 T
4234322 TTATATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:4238418 original size:19 final size:19
Alignment explanation
Indices: 4238391--4238453 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
4238381 TTTTTTTAAA
*
4238391 AAAAGTTAAAATTATTTTT
1 AAAATTTAAAATTATTTTT
*
4238410 AAAATTTAAAA-TATTTATA
1 AAAATTTAAAATTATTT-TT
*
4238429 AAAATTTCAAAATTTATATTT
1 AAAATTT-AAAA-TTATTTTT
4238450 AAAA
1 AAAA
4238454 AAATATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 5 0.14
19 18 0.50
20 4 0.11
21 5 0.14
22 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATTTAAAATTATTTTT
Found at i:4238482 original size:27 final size:25
Alignment explanation
Indices: 4238410--4238482 Score: 58
Period size: 27 Copynumber: 2.8 Consensus size: 25
4238400 AATTATTTTT
**
4238410 AAAATTTAAAATATTTATAAAAATTTC
1 AAAATTTAAAAT-TTTA-AAAAATTAA
* *
4238437 AAAATTT-ATATTTAAAAAAATATATAA
1 AAAATTTAAAATTT-TAAAAA-AT-TAA
4238464 AAAATTTAAAATTTTAAAA
1 AAAATTTAAAATTTTAAAA
4238483 TTTTCTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
25 6 0.17
26 6 0.17
27 19 0.53
28 5 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAATTTAAAATTTTAAAAAATTAA
Done.