Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 31 of 91
Found at i:10812793 original size:18 final size:19
Alignment explanation
Indices: 10812768--10812810 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
10812758 GGGTGAGAAA
10812768 AATATTTTA-AAATAAAAT
1 AATATTTTACAAATAAAAT
*
10812786 ATTATTTTACAAATAAAAT
1 AATATTTTACAAATAAAAT
10812805 AATATT
1 AATATT
10812811 AAAATATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATTTTACAAATAAAAT
Found at i:10813935 original size:16 final size:17
Alignment explanation
Indices: 10813885--10813943 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
10813875 GCTAAAAAAA
10813885 AAAAAGAAA--AAGAA-
1 AAAAAGAAATGAAGAAG
*
10813899 AGAAAAGAAGTGAAGAAG
1 A-AAAAGAAATGAAGAAG
*
10813917 AAAAAGAAATGAA-ATG
1 AAAAAGAAATGAAGAAG
*
10813933 AAAAAAAAATG
1 AAAAAGAAATG
10813944 GGCATAGCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 1 0.03
15 7 0.19
16 12 0.32
17 16 0.43
18 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (17 bp):
AAAAAGAAATGAAGAAG
Found at i:10813964 original size:23 final size:23
Alignment explanation
Indices: 10813934--10813991 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 23
10813924 AATGAAATGA
10813934 AAAAAAAATGGGCATAGCCCAAT
1 AAAAAAAATGGGCATAGCCCAAT
*
10813957 AAAAAAAA-GGGCATGGCCCAAT
1 AAAAAAAATGGGCATAGCCCAAT
*
10813979 AAGAATAAATGGG
1 AA-AAAAAATGGG
10813992 AGGAGCCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 15 0.48
23 13 0.42
24 3 0.10
ACGTcount: A:0.52, C:0.14, G:0.22, T:0.12
Consensus pattern (23 bp):
AAAAAAAATGGGCATAGCCCAAT
Found at i:10814814 original size:60 final size:60
Alignment explanation
Indices: 10814721--10814900 Score: 263
Period size: 60 Copynumber: 3.0 Consensus size: 60
10814711 TTTAATTTAA
* *
10814721 AAAGGGGGACCTGAAGCCTCAATTTATATATGGTGGCATGGGTAGTTCCTACGAGTAGGT
1 AAAGGGGGACCTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTCCCACGAGTAGGT
* * * * * *
10814781 AAAGGGGGACATGAAGCCTCGATTTATATATGGTGACGTGGGTAGTCCCCATGAATAGGT
1 AAAGGGGGACCTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTCCCACGAGTAGGT
*
10814841 AAAAGGGGACCTGAAGTCC-CGATTTATATATGGTGGCATGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAG-CCTCGATTTATATATGGTGGCATGGGTAGTTCCCACGAGTAGGT
10814901 GACAATGTCT
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 102 0.98
61 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.26
Consensus pattern (60 bp):
AAAGGGGGACCTGAAGCCTCGATTTATATATGGTGGCATGGGTAGTTCCCACGAGTAGGT
Found at i:10824304 original size:43 final size:43
Alignment explanation
Indices: 10824250--10824361 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
10824240 TATTGACTCC
* * *
10824250 GCTATGTGCGAGTAGGGAGTGCGCATAAGTCGAG-GATGA-CTA
1 GCTATGTGCGAGTAGGGAGTGCGCATAA-CCCAGTGATGACCCA
*
10824292 GGTTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCA
1 -GCTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCA
*
10824336 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
10824362 GAGCTGGTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 3 0.05
43 56 0.92
44 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCA
Found at i:10824372 original size:43 final size:43
Alignment explanation
Indices: 10824253--10824374 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 43
10824243 TGACTCCGCT
* **
10824253 ATGTGCGAGTAGGGAGTGCGCATAAG-TCGAG-GATGACTAGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCT-G-GTGATGACCAGGCC
* **
10824296 ATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCA-GCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA-CCAGGCC
*
10824339 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA
10824375 TGATGATGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
42 1 0.02
43 63 0.95
44 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCAGGCC
Found at i:10826737 original size:10 final size:10
Alignment explanation
Indices: 10826722--10826760 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
10826712 TAAAACACTT
10826722 TACATATATG
1 TACATATATG
10826732 TACATATATG
1 TACATATATG
10826742 TACATATATG
1 TACATATATG
*
10826752 TATATATAT
1 TACATATAT
10826761 AGTTTACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (10 bp):
TACATATATG
Found at i:10832651 original size:27 final size:26
Alignment explanation
Indices: 10832606--10832657 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
10832596 TTCGAGCATA
**
10832606 AAGGGCAAAATAGTCATTTTGTCACCT
1 AAGGGCAAAATAGGAATTTTG-CACCT
*
10832633 AAGGGCAAAATTGGAATTTTGCACC
1 AAGGGCAAAATAGGAATTTTGCACC
10832658 ACCCAACACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (26 bp):
AAGGGCAAAATAGGAATTTTGCACCT
Found at i:10836078 original size:68 final size:68
Alignment explanation
Indices: 10835973--10836229 Score: 223
Period size: 68 Copynumber: 3.8 Consensus size: 68
10835963 CATGTTTGGT
* * * * *
10835973 ATGATGAATGCCATAAGATTATGTATATGATGCAAATTTCATATACCGTATGA-GATGATTAAGT
1 ATGATAAATACCATAAGATTATGTATATGATGTAAATTTCATATACCATATGATG-TGAATAAGT
10836037 ATGC
65 ATGC
** * * *
10836041 ATGATGTATACTATAAGATTATATATATGATGTAAATTTCATAAACCATATGATGTGAATAAGTA
1 ATGATAAATACCATAAGATTATGTATATGATGTAAATTTCATATACCATATGATGTGAATAAGTA
10836106 TGC
66 TGC
* * * * * * * * * *
10836109 ATGATAAATACCATGAGATAATGTATATGATGTATATTCCATATACTACATGA-GAGGGATGAGA
1 ATGATAAATACCATAAGATTATGTATATGATGTAAATTTCATATACCATATGATG-TGAATAAGT
*
10836173 AAGC
65 ATGC
* * * * * *
10836177 ATGATGAATGCCATGAGATTAAGTATATGATGT-ATTTTCCATATACCTTATGA
1 ATGATAAATACCATAAGATTATGTATATGATGTAAATTT-CATATACCATATGA
10836230 GATGCGTAAG
Statistics
Matches: 152, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
67 3 0.02
68 148 0.97
69 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (68 bp):
ATGATAAATACCATAAGATTATGTATATGATGTAAATTTCATATACCATATGATGTGAATAAGTA
TGC
Found at i:10836717 original size:21 final size:21
Alignment explanation
Indices: 10836691--10836782 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 21
10836681 TTATATGTGA
10836691 AATGTATCGATACATTTTACT
1 AATGTATCGATACATTTTACT
* *
10836712 AATGTATCGATA-AATGTA-T
1 AATGTATCGATACATTTTACT
** * *
10836731 GAAACTATCAATACA--TT-CA
1 -AATGTATCGATACATTTTACT
*
10836750 AATGTATCGATGCATTTTACT
1 AATGTATCGATACATTTTACT
10836771 AATGTATCGATA
1 AATGTATCGATA
10836783 AATGTATGAA
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
18 10 0.19
19 2 0.04
20 15 0.29
21 25 0.48
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTTACT
Found at i:10836757 original size:59 final size:60
Alignment explanation
Indices: 10836690--10836822 Score: 225
Period size: 59 Copynumber: 2.2 Consensus size: 60
10836680 TTTATATGTG
10836690 AAATGTATCGATACATTTTACTAATGTATCGATAAATGTATGAAA-CTATCAATACATTC-
1 AAATGTATCGATACATTTTACTAATGTATCGATAAATGTATGAAAGC-ATCAATACATTCA
*
10836749 AAATGTATCGATGCATTTTACTAATGTATCGATAAATGTATGAAAGCATCAATACATTCA
1 AAATGTATCGATACATTTTACTAATGTATCGATAAATGTATGAAAGCATCAATACATTCA
10836809 AGAATGTATCGATA
1 A-AATGTATCGATA
10836823 AATGTATGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
59 56 0.81
60 2 0.03
61 11 0.16
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (60 bp):
AAATGTATCGATACATTTTACTAATGTATCGATAAATGTATGAAAGCATCAATACATTCA
Found at i:10836826 original size:40 final size:40
Alignment explanation
Indices: 10836771--10836862 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
10836761 GCATTTTACT
10836771 AATGTATCGATAAATGTATGAAAGC-ATCAATACATTCAAG
1 AATGTATCGATAAATGTATGAAA-CTATCAATACATTCAAG
10836811 AATGTATCGATAAATGTATGAAACTATCAATACATTCAAG
1 AATGTATCGATAAATGTATGAAACTATCAATACATTCAAG
10836851 AATGTATCGATA
1 AATGTATCGATA
10836863 GCTTTTGTGC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 1 0.02
40 50 0.98
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (40 bp):
AATGTATCGATAAATGTATGAAACTATCAATACATTCAAG
Found at i:10844486 original size:40 final size:37
Alignment explanation
Indices: 10844424--10844525 Score: 123
Period size: 37 Copynumber: 2.7 Consensus size: 37
10844414 ATCCAGCTCA
* *
10844424 TGTGCATCCCCCTACATCGTGCACATAACCCGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAA---GAGCCATCG
* * * *
10844464 TGTGCATCCCCCCACATTGTGCACATTAGTGCCATTG
1 TGTGCATCCCCCCACATCGTGCACATAAGAGCCATCG
10844501 TGTGCATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
10844526 CGGGCACTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 30 0.55
40 25 0.45
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.25
Consensus pattern (37 bp):
TGTGCATCCCCCCACATCGTGCACATAAGAGCCATCG
Found at i:10847550 original size:42 final size:42
Alignment explanation
Indices: 10847468--10847593 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
10847458 TCTCCTATCG
* * * *
10847468 TCATCAGCTCATGTGCACTCCCCACTAGCACATGGTTGGGTCA
1 TCATCAGCTTATGTGCACT-CCCACTCGCACATAGCTGGGTCA
10847511 TCATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCA
1 TCATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCA
* * * * *
10847553 TCATCGGCTTATGTACACTCCTACTCACACATAGCCGGGTC
1 TCATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTC
10847594 CACATCAACA
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 56 0.76
43 18 0.24
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (42 bp):
TCATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCA
Found at i:10853324 original size:54 final size:54
Alignment explanation
Indices: 10853232--10853446 Score: 340
Period size: 54 Copynumber: 4.0 Consensus size: 54
10853222 TTTCCAGCAA
* * *
10853232 ACATCTCATCTCACCCAACTCATGTGCATCCCATCACATCATGCACATAGCCAG
1 ACATCCCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCAG
** * * *
10853286 ATGTACCATCTCACCCAACGCATGTGCATCCCACCACATCTTGCACATAGCCAG
1 ACATCCCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCAG
*
10853340 ACATCCCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGG
1 ACATCCCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCAG
*
10853394 ACATCCCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCA
1 ACATCCCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCA
10853447 AACAATATCA
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 146 1.00
ACGTcount: A:0.27, C:0.41, G:0.12, T:0.20
Consensus pattern (54 bp):
ACATCCCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCAG
Found at i:10853423 original size:25 final size:25
Alignment explanation
Indices: 10853341--10853426 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 25
10853331 CATAGCCAGA
*
10853341 CATCCCATCTCACCCAACTCATGTG
1 CATCCCATCTCACCCAGCTCATGTG
* * * ** * *
10853366 CATCCCACCACATCGTGCACATAGCCGG
1 CATCCCATCTCACCCAGCTCAT-G--TG
10853394 ACATCCCATCTCACCCAGCTCATGTG
1 -CATCCCATCTCACCCAGCTCATGTG
10853420 CATCCCA
1 CATCCCA
10853427 CCACATCGTG
Statistics
Matches: 42, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
25 22 0.52
26 2 0.05
28 2 0.05
29 16 0.38
ACGTcount: A:0.24, C:0.44, G:0.12, T:0.20
Consensus pattern (25 bp):
CATCCCATCTCACCCAGCTCATGTG
Found at i:10860644 original size:45 final size:45
Alignment explanation
Indices: 10860589--10860755 Score: 246
Period size: 45 Copynumber: 3.7 Consensus size: 45
10860579 TTTCCACTTG
*
10860589 GGTTATTTCTCCATTTCTT-TTTCTTCCTCATTCTCTTTTGTGGTA
1 GGTTCTTTCTCCATTT-TTCTTTCTTCCTCATTCTCTTTTGTGGTA
* *
10860634 GGTTCTTTCTCCATTTCTCTTTCTTCCTCATTCTCTTTTGTGATA
1 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTTTGTGGTA
* * *
10860679 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTCTATGGTT
1 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTTTGTGGTA
* *
10860724 GGTTCTTTTTCCATTTTTCTTTCTTTCTCATT
1 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATT
10860756 TTTTTCTATG
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 1 0.01
45 110 0.99
ACGTcount: A:0.08, C:0.25, G:0.09, T:0.59
Consensus pattern (45 bp):
GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTTTGTGGTA
Found at i:10860763 original size:45 final size:45
Alignment explanation
Indices: 10860589--10860784 Score: 238
Period size: 45 Copynumber: 4.4 Consensus size: 45
10860579 TTTCCACTTG
* *
10860589 GGTTATTTCTCCATTTCTT-TTTCTTCCTCATTCTCTTTTGTGGTA
1 GGTTCTTTCTCCATTT-TTCTTTCTTCCTCATTCTCTTTTATGGTA
* * *
10860634 GGTTCTTTCTCCATTTCTCTTTCTTCCTCATTCTCTTTTGTGATA
1 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTTTATGGTA
* *
10860679 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTCTATGGTT
1 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTTTATGGTA
* * * *
10860724 GGTTCTTTTTCCATTTTTCTTTCTTTCTCATT-TTTTTCTATGGTT
1 GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTT-TATGGTA
10860769 GGTCTCTTT-TCC-TTTT
1 GGT-TCTTTCTCCATTTT
10860785 CATGTTCTTC
Statistics
Matches: 136, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
44 8 0.06
45 123 0.90
46 5 0.04
ACGTcount: A:0.07, C:0.23, G:0.10, T:0.60
Consensus pattern (45 bp):
GGTTCTTTCTCCATTTTTCTTTCTTCCTCATTCTCTTTTATGGTA
Found at i:10864687 original size:5 final size:5
Alignment explanation
Indices: 10864679--10864730 Score: 63
Period size: 5 Copynumber: 10.6 Consensus size: 5
10864669 TATATTCTTT
* *
10864679 TTTTC TTTT- TTCTTC TTTTC TTTTN TTTTC TTTT- TCTTC TTTTC TTTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
10864728 TTT
1 TTT
10864731 GTTCTCTCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 5 0.12
5 33 0.82
6 2 0.05
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:10864697 original size:15 final size:15
Alignment explanation
Indices: 10864673--10864724 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
10864663 CATTATTATA
*
10864673 TTCTTTTTTTCTTTT
1 TTCTTCTTTTCTTTT
10864688 TTCTTCTTTTCTTTT
1 TTCTTCTTTTCTTTT
10864703 NTT-TTCTTTTTCTTCTT
1 -TTCTTC-TTTTCTT-TT
10864720 TTCTT
1 TTCTT
10864725 TTCTTTGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 17 0.53
16 11 0.34
17 4 0.12
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTTCTTTTCTTTT
Found at i:10864717 original size:24 final size:24
Alignment explanation
Indices: 10864676--10864726 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
10864666 TATTATATTC
10864676 TTTTTTTCTTTTTTCTTCTTTTCT
1 TTTTTTTCTTTTTTCTTCTTTTCT
10864700 TTTNTTTTC-TTTTTCTTCTTTTCT
1 TTT-TTTTCTTTTTTCTTCTTTTCT
10864724 TTT
1 TTT
10864727 CTTTGTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTTTCTTTTTTCTTCTTTTCT
Found at i:10864718 original size:19 final size:19
Alignment explanation
Indices: 10864686--10864735 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
10864676 TTTTTTTCTT
* *
10864686 TTTTCTTCTT-TTCTTTTN
1 TTTTCTTTTTCTTCTTTTC
10864704 TTTTCTTTTTCTTCTTTTC
1 TTTTCTTTTTCTTCTTTTC
10864723 TTTTCTTTGTTCT
1 TTTTCTTT-TTCT
10864736 CTCTCCCGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 9 0.32
19 15 0.54
20 4 0.14
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTTCTTCTTTTC
Found at i:10864937 original size:34 final size:34
Alignment explanation
Indices: 10864869--10864988 Score: 120
Period size: 34 Copynumber: 3.5 Consensus size: 34
10864859 CCAAAATTTT
**
10864869 TCAACAGCCAAAGCTGCTC-ATATCAACCTC-AAAA
1 TCAACAGCC-AAGCTGCTCTAT-TCTTCCTCAAAAA
*
10864903 TCAACAGCCAAGCTGTTCTATTCTTCCTCAAAAA
1 TCAACAGCCAAGCTGCTCTATTCTTCCTCAAAAA
* * *
10864937 TCATCAGCTAAGCTACTCTATT-TGTCCTCCAAAAA
1 TCAACAGCCAAGCTGCTCTATTCT-TCCT-CAAAAA
*
10864972 TCAGCAGCCAAGCTGCT
1 TCAACAGCCAAGCTGCT
10864989 TCTTCCTCCC
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
33 15 0.21
34 37 0.51
35 20 0.28
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.25
Consensus pattern (34 bp):
TCAACAGCCAAGCTGCTCTATTCTTCCTCAAAAA
Found at i:10867679 original size:57 final size:57
Alignment explanation
Indices: 10867576--10867685 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
10867566 ACGGTTAGGT
*
10867576 TCCACTCATAGGGGATGACCCTCGCTACAAGCAACCATTTCCTCCTTCAGCGGGGGC
1 TCCACTCATAGGGGATAACCCTCGCTACAAGCAACCATTTCCTCCTTCAGCGGGGGC
* * * *
10867633 TCCACT-AGTAGGGGATAACCCTCGCTACAAGTAGCCTTTTCTTCCTTCAGCGG
1 TCCACTCA-TAGGGGATAACCCTCGCTACAAGCAACCATTTCCTCCTTCAGCGG
10867686 TGGCAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 1 0.02
57 46 0.98
ACGTcount: A:0.21, C:0.33, G:0.22, T:0.25
Consensus pattern (57 bp):
TCCACTCATAGGGGATAACCCTCGCTACAAGCAACCATTTCCTCCTTCAGCGGGGGC
Found at i:10873432 original size:23 final size:23
Alignment explanation
Indices: 10873402--10873460 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
10873392 TGAGTTGGTG
* * *
10873402 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGATGTGC
10873425 ATGATGATGATGGGATGATGTGC
1 ATGATGATGATGGGATGATGTGC
*
10873448 ATGATAATGATGG
1 ATGATGATGATGG
10873461 ATATACGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (23 bp):
ATGATGATGATGGGATGATGTGC
Found at i:10873799 original size:21 final size:21
Alignment explanation
Indices: 10873766--10873807 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10873756 TTCATCAACT
*
10873766 GAATTTCGCTGCAGCAAGAAA
1 GAATCTCGCTGCAGCAAGAAA
* *
10873787 GAATCTCGTTGCAGCGAGAAA
1 GAATCTCGCTGCAGCAAGAAA
10873808 CCTTTTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (21 bp):
GAATCTCGCTGCAGCAAGAAA
Found at i:10911931 original size:19 final size:19
Alignment explanation
Indices: 10911872--10911932 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
10911862 GATTGTGCAC
* *
10911872 GATGTGGGGGGATGCACGT
1 GATGTGGGGGGATGTACAT
* ** *
10911891 GATGGTGCCGGCTATGTGCAT
1 GAT-GTG-GGGGGATGTACAT
10911912 GATGTGGGGGGATGTACAT
1 GATGTGGGGGGATGTACAT
10911931 GA
1 GA
10911933 ACTGGGAGTG
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 14 0.47
20 6 0.20
21 10 0.33
ACGTcount: A:0.18, C:0.11, G:0.46, T:0.25
Consensus pattern (19 bp):
GATGTGGGGGGATGTACAT
Found at i:10919971 original size:43 final size:43
Alignment explanation
Indices: 10919901--10920019 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
10919891 GTAATTATGT
* *
10919901 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
10919944 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
10919987 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
10920020 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:10920029 original size:43 final size:43
Alignment explanation
Indices: 10919911--10920032 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
10919901 TGACTCGGCT
* **
10919911 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
10919954 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
10919997 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
10920033 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:10920043 original size:20 final size:20
Alignment explanation
Indices: 10920018--10920080 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
10920008 GGGAGTGCGC
10920018 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
10920038 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
10920058 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
10920077 ATGA
1 ATGA
10920081 TGGGTATACA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:10920105 original size:12 final size:12
Alignment explanation
Indices: 10920088--10920114 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10920078 TGATGGGTAT
10920088 ACACACAAACAC
1 ACACACAAACAC
10920100 ACACACAAACAC
1 ACACACAAACAC
10920112 ACA
1 ACA
10920115 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (12 bp):
ACACACAAACAC
Found at i:10920204 original size:20 final size:20
Alignment explanation
Indices: 10920147--10920209 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
10920137 TATATACCCA
*
10920147 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
10920166 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
10920186 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
10920206 TCAT
1 TCAT
10920210 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:10920256 original size:43 final size:43
Alignment explanation
Indices: 10920208--10920326 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
10920198 TCACCAGCTC
** * *
10920208 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
10920251 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
10920294 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
10920327 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:10924815 original size:19 final size:19
Alignment explanation
Indices: 10924791--10924965 Score: 61
Period size: 19 Copynumber: 9.1 Consensus size: 19
10924781 TGCCCGTGTG
10924791 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
10924810 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
* *
10924829 CACGAT-TTGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* * ** *
10924847 CATGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
10924868 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
* ** * *
10924887 CATGATG-GCAGTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
10924906 CACGATGT-GGGGGATGCA
1 CACGATGTGGGGGGATGTA
* * ** *
10924924 CATGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
10924945 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
10924964 CA
1 CA
10924966 TGAGCCGGGA
Statistics
Matches: 100, Mismatches: 46, Indels: 20
0.60 0.28 0.12
Matches are distributed among these distances:
18 21 0.21
19 52 0.52
20 7 0.07
21 20 0.20
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.24
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:10924854 original size:37 final size:38
Alignment explanation
Indices: 10924787--10924968 Score: 192
Period size: 38 Copynumber: 4.7 Consensus size: 38
10924777 ATAGTGCCCG
* *
10924787 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGCACATGATGGCACTGAT
* * *
10924825 TGTGCACGAT-TTGGGGGATGCACATGATGGTGC-CGGCT
1 TGTGCACGATGTGGGGGGATGCACATGAT-G-GCACTGAT
* *
10924863 ATGTGCACGATGTGGGGGGATGTACATGATGGCAGTGAT
1 -TGTGCACGATGTGGGGGGATGCACATGATGGCACTGAT
* *
10924902 TGTGCACGATGT-GGGGGATGCACATGATGGTGC-CGGCT
1 TGTGCACGATGTGGGGGGATGCACATGAT-G-GCACTGAT
*
10924940 ATGTGCACGATGTGGGGGGATGTACATGA
1 -TGTGCACGATGTGGGGGGATGCACATGA
10924969 GCCGGGAGTG
Statistics
Matches: 120, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
37 30 0.25
38 31 0.26
39 29 0.24
40 30 0.25
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACATGATGGCACTGAT
Found at i:10924966 original size:77 final size:77
Alignment explanation
Indices: 10924787--10924968 Score: 337
Period size: 77 Copynumber: 2.4 Consensus size: 77
10924777 ATAGTGCCCG
* *
10924787 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGATTGTGCACGATTTGGGGGATGCACATGA
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGATTGTGCACGATGTGGGGGATGCACATGA
10924852 TGGTGCCGGCTA
66 TGGTGCCGGCTA
*
10924864 TGTGCACGATGTGGGGGGATGTACATGATGGCAGTGATTGTGCACGATGTGGGGGATGCACATGA
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGATTGTGCACGATGTGGGGGATGCACATGA
10924929 TGGTGCCGGCTA
66 TGGTGCCGGCTA
10924941 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
10924969 GCCGGGAGTG
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 102 1.00
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.25
Consensus pattern (77 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACTGATTGTGCACGATGTGGGGGATGCACATGA
TGGTGCCGGCTA
Found at i:10928276 original size:19 final size:19
Alignment explanation
Indices: 10928252--10928289 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
10928242 ACGTCTAAAC
*
10928252 CTTAAATCTTACTCCAATA
1 CTTAAATCATACTCCAATA
10928271 CTTAAATCATACTCCAATA
1 CTTAAATCATACTCCAATA
10928290 AGTCGAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (19 bp):
CTTAAATCATACTCCAATA
Found at i:10931121 original size:22 final size:22
Alignment explanation
Indices: 10931093--10931135 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
10931083 TTTAAAACAA
*
10931093 CTTTAAAACCAAATGTTCTGAC
1 CTTTAAAACCAAATGCTCTGAC
10931115 CTTTAAAACCAAATGCTCTGA
1 CTTTAAAACCAAATGCTCTGA
10931136 TACCACTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.30
Consensus pattern (22 bp):
CTTTAAAACCAAATGCTCTGAC
Found at i:10941283 original size:42 final size:42
Alignment explanation
Indices: 10941158--10941283 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
10941148 TCTCCCATCG
* * *
10941158 TCATCAGCTCATGTGCACTCCCCACTAGCACATGGCTGGGTCA
1 TCATCAGCTTATGTGCACT-CCCACTCGCACATAGCTGGGTCA
** * *
10941201 TCATTGGCTTATGTGCACTCCGACTCGCACATAGCCGGGTCA
1 TCATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCA
* ** *
10941243 TCATCAGCTTATGTACACTCTTACTCGCACATAGTTGGGTC
1 TCATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTC
10941284 CACATCAACA
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 53 0.77
43 16 0.23
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (42 bp):
TCATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCA
Found at i:10948927 original size:21 final size:18
Alignment explanation
Indices: 10948897--10948939 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 18
10948887 TTAAATGTTA
10948897 AATTCTCAAAAGCATCATG
1 AATTCTCAAAAGCAT-ATG
10948916 CAATTCATCAAAAGCATATG
1 -AATTC-TCAAAAGCATATG
10948936 AATT
1 AATT
10948940 AAGTTCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 8 0.36
21 10 0.45
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (18 bp):
AATTCTCAAAAGCATATG
Found at i:10952996 original size:14 final size:14
Alignment explanation
Indices: 10952977--10953006 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10952967 AAGAAATGAA
10952977 AAGAAAATAAAAAG
1 AAGAAAATAAAAAG
*
10952991 AAGAAAGTAAAAAG
1 AAGAAAATAAAAAG
10953005 AA
1 AA
10953007 ATGTAAGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAGAAAATAAAAAG
Found at i:10953526 original size:24 final size:25
Alignment explanation
Indices: 10953486--10953532 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
10953476 TTTGTGCAGG
10953486 AAAATTGGACAGCTTTG-TGCTGCC
1 AAAATTGGACAGCTTTGTTGCTGCC
*
10953510 AAAATTGAGA-AGTTTTGTTGCTG
1 AAAATTG-GACAGCTTTGTTGCTG
10953533 AAAATTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (25 bp):
AAAATTGGACAGCTTTGTTGCTGCC
Found at i:10953727 original size:16 final size:17
Alignment explanation
Indices: 10953702--10953745 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
10953692 AAGAAACGTG
10953702 GAAAAGAGAAAAAG-AAA
1 GAAAA-AGAAAAAGAAAA
10953719 GAAAAAG-AAAAGAAAA
1 GAAAAAGAAAAAGAAAA
*
10953735 GAAATAGAAAA
1 GAAAAAGAAAA
10953746 TAAATGGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAA
Found at i:10953750 original size:11 final size:11
Alignment explanation
Indices: 10953670--10953750 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 11
10953660 GACGGGCTGG
10953670 AAAGAAATA-A
1 AAAGAAATAGA
10953680 AAAGAAA-AGA
1 AAAGAAATAGA
*
10953690 AGAAGAAACGTGGA
1 A-AAGAAA--TAGA
*
10953704 AAAG--AGA-A
1 AAAGAAATAGA
*
10953712 AAAGAAAGA-A
1 AAAGAAATAGA
10953722 AAAGAAA-AGA
1 AAAGAAATAGA
10953732 AAAGAAATAGA
1 AAAGAAATAGA
*
10953743 AAATAAAT
1 AAAGAAAT
10953751 GGGCATGACC
Statistics
Matches: 58, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
8 5 0.09
9 2 0.03
10 28 0.48
11 17 0.29
13 3 0.05
14 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (11 bp):
AAAGAAATAGA
Found at i:10953767 original size:25 final size:25
Alignment explanation
Indices: 10953737--10953824 Score: 149
Period size: 25 Copynumber: 3.5 Consensus size: 25
10953727 AAAGAAAAGA
10953737 AATAGAAAATAAATGGGCATGACCC
1 AATAGAAAATAAATGGGCATGACCC
10953762 AATAGAAAATAAATGGGCATGACCC
1 AATAGAAAATAAATGGGCATGACCC
* *
10953787 AATAGAAAATAAGTGGGCATGGCCC
1 AATAGAAAATAAATGGGCATGACCC
*
10953812 AATAGGAAATAAA
1 AATAGAAAATAAA
10953825 AATAAATGGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.16
Consensus pattern (25 bp):
AATAGAAAATAAATGGGCATGACCC
Found at i:10953835 original size:31 final size:33
Alignment explanation
Indices: 10953787--10953852 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 33
10953777 GGCATGACCC
* *
10953787 AATAGAAAATAAGTGGGCATGGCCC-AATAGGA
1 AATAGAAAATAAATGGGCATAGCCCAAATAGGA
*
10953819 AATA-AAAATAAATGGGCTTAGCCCAAATAGGA
1 AATAGAAAATAAATGGGCATAGCCCAAATAGGA
10953851 AA
1 AA
10953853 AATGGAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (33 bp):
AATAGAAAATAAATGGGCATAGCCCAAATAGGA
Found at i:10957226 original size:35 final size:35
Alignment explanation
Indices: 10957184--10957418 Score: 251
Period size: 35 Copynumber: 6.7 Consensus size: 35
10957174 GAAGCTTAAT
***
10957184 TAACTTAATTATTTAATTTAATCAATTAGGCCCAA
1 TAACTTAATTAAACAATTTAATCAATTAGGCCCAA
* *
10957219 TAACTTAATTAAACAATTTAATTAATTAAGCCCAA
1 TAACTTAATTAAACAATTTAATCAATTAGGCCCAA
* * * *
10957254 CAATTTAATTAGACAATTTTAATCAACTAGGCCCAA
1 TAACTTAATTAAACAA-TTTAATCAATTAGGCCCAA
*
10957290 TGACTTAATTAAACAAATTTAATCAATTAGGCCCAA
1 TAACTTAATTAAAC-AATTTAATCAATTAGGCCCAA
**** *
10957326 TAACTTAATTGTTTAATTTAATTAATTAGGCCCAA
1 TAACTTAATTAAACAATTTAATCAATTAGGCCCAA
* * * *
10957361 TGATTTAATTAAACAATTTAGTTAATTAGGCCC--
1 TAACTTAATTAAACAATTTAATCAATTAGGCCCAA
10957394 -AACTTAATTAAACAATTTTAATCAA
1 TAACTTAATTAAACAA-TTTAATCAA
10957419 GTGCTTGAGA
Statistics
Matches: 164, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
32 13 0.08
33 7 0.04
35 89 0.54
36 53 0.32
37 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (35 bp):
TAACTTAATTAAACAATTTAATCAATTAGGCCCAA
Found at i:10957285 original size:71 final size:70
Alignment explanation
Indices: 10957200--10957418 Score: 275
Period size: 71 Copynumber: 3.1 Consensus size: 70
10957190 AATTATTTAA
* *
10957200 TTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAATTA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCCAACAA-TTAATTA
10957265 GACAAT
65 GACAAT
* * *
10957271 TTTAATCAACTAGGCCCAATGACTTAATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATT
1 TTTAATCAATTAGGCCCAATGACTTAATTAAAC-AATTTAATTAATTAGGCCCAACAA-TTAATT
**
10957336 -GTTTAA-
64 AG-ACAAT
* * * *
10957342 TTTAATTAATTAGGCCCAATGATTTAATTAAACAATTTAGTTAATTAGGCCCAAC--TTAATTAA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCCAACAATTAATTAG
10957405 ACAAT
66 ACAAT
10957410 TTTAATCAA
1 TTTAATCAA
10957419 GTGCTTGAGA
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
67 8 0.06
68 8 0.06
70 19 0.15
71 62 0.49
72 29 0.23
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (70 bp):
TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCCAACAATTAATTAG
ACAAT
Found at i:10957317 original size:107 final size:103
Alignment explanation
Indices: 10957198--10957418 Score: 298
Period size: 107 Copynumber: 2.1 Consensus size: 103
10957188 TTAATTATTT
10957198 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
*
10957263 TAGACAATTTTAATCAACTAGGCCCAATGACTTAATTAAACA
66 TAAACAA-TTTAATCAACTAGGCCC-A--ACTTAATTAAACA
**** * **
10957305 AATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATGATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
* * *
10957370 TAAACAATTTAGTTAATTAGGCCCAACTTAATTAAACA
66 TAAACAATTTAATCAACTAGGCCCAACTTAATTAAACA
*
10957408 ATTTTAATCAA
1 AATTTAATCAA
10957419 GTGCTTGAGA
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
103 23 0.23
105 1 0.01
106 14 0.14
107 64 0.63
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (103 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
TAAACAATTTAATCAACTAGGCCCAACTTAATTAAACA
Found at i:10959701 original size:2 final size:2
Alignment explanation
Indices: 10959694--10959729 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10959684 CATTATGTTG
10959694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10959730 GTTGTGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10961171 original size:14 final size:15
Alignment explanation
Indices: 10961146--10961175 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
10961136 TTACAATATG
10961146 GGTTTGAGAAATGAT
1 GGTTTGAGAAATGAT
10961161 GGTTT-AGAAATGAT
1 GGTTTGAGAAATGAT
10961175 G
1 G
10961176 ATCAGGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (15 bp):
GGTTTGAGAAATGAT
Found at i:10963310 original size:17 final size:16
Alignment explanation
Indices: 10963288--10963321 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
10963278 TAGCGAGAAA
*
10963288 TATTCTGTTTGGCTTGC
1 TATTCTATTTGG-TTGC
10963305 TATTCTATTTGGTTGC
1 TATTCTATTTGGTTGC
10963321 T
1 T
10963322 GACCCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.15, G:0.21, T:0.56
Consensus pattern (16 bp):
TATTCTATTTGGTTGC
Found at i:10968841 original size:28 final size:28
Alignment explanation
Indices: 10968782--10968841 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
10968772 TGGGTGGTGT
* * *
10968782 AAAATGACAATTTTGCCCCTAAGGTGGC
1 AAAATGACAATTTTGCCCCTAAGCTCGA
* * *
10968810 AAAATGACTATTTTGCCCTTATGCTCGA
1 AAAATGACAATTTTGCCCCTAAGCTCGA
10968838 AAAA
1 AAAA
10968842 ATGCTGAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
AAAATGACAATTTTGCCCCTAAGCTCGA
Found at i:10973113 original size:22 final size:22
Alignment explanation
Indices: 10973085--10973145 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
10973075 TTTAAAACAA
*
10973085 CTTTAAACCCAAAAGCTCTAAT
1 CTTTAAAACCAAAAGCTCTAAT
*
10973107 CTTTAAAACCAAAGGCTCTAAT
1 CTTTAAAACCAAAAGCTCTAAT
*
10973129 TTTTAAAACCAAAAGCT
1 CTTTAAAACCAAAAGCT
10973146 TTTATACCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.28
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTAAT
Found at i:10980622 original size:18 final size:19
Alignment explanation
Indices: 10980589--10980625 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
10980579 AAGTGGCATA
*
10980589 TTGTGAGAAATTATGGTTG
1 TTGTGAGAAATGATGGTTG
10980608 TTGTG-GAAATGATGGTTG
1 TTGTGAGAAATGATGGTTG
10980626 AACTTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (19 bp):
TTGTGAGAAATGATGGTTG
Found at i:10981301 original size:35 final size:35
Alignment explanation
Indices: 10981258--10981367 Score: 175
Period size: 35 Copynumber: 3.1 Consensus size: 35
10981248 AGTGTGGAAA
*
10981258 ATGATGTTGAAGTGTGCGAGTAGGGAATGCACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACATG
10981293 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACATG
* * * *
10981328 ATGATATAGAAATGTGCGTGTAGGGAGTGCACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACATG
10981363 ATGAT
1 ATGAT
10981368 AAATAGTGTG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.29, C:0.08, G:0.36, T:0.26
Consensus pattern (35 bp):
ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACATG
Found at i:10981394 original size:36 final size:36
Alignment explanation
Indices: 10981266--10981402 Score: 158
Period size: 35 Copynumber: 3.9 Consensus size: 36
10981256 AAATGATGTT
* * *
10981266 GAAGTGTGCGA-GTAGGGAATGCACATGATGATGTT
1 GAAGTGTGCGATGTAGGGAGTGCACATGATGATATA
10981301 GAAGTGTGCGA-GTAGGGAGTGCACATGATGATATA
1 GAAGTGTGCGATGTAGGGAGTGCACATGATGATATA
*
10981336 GAAATGTGCG-TGTAGGGAGTGCACATGATGATAAATA
1 GAAGTGTGCGATGTAGGGAGTGCACATGATGAT--ATA
* * *
10981373 G-TGTGTGCGATGT-GGGGGTGCACACGATGA
1 GAAGTGTGCGATGTAGGGAGTGCACATGATGA
10981403 CTCCAGCTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
35 62 0.69
36 21 0.23
37 7 0.08
ACGTcount: A:0.28, C:0.09, G:0.38, T:0.24
Consensus pattern (36 bp):
GAAGTGTGCGATGTAGGGAGTGCACATGATGATATA
Found at i:10986610 original size:21 final size:20
Alignment explanation
Indices: 10986585--10986644 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
10986575 AGATGTCTAA
*
10986585 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
10986606 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
10986626 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
10986644 A
1 A
10986645 TTCTATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:10989964 original size:13 final size:13
Alignment explanation
Indices: 10989946--10989970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10989936 GGAAAATGGG
10989946 ATTTTATAAAATA
1 ATTTTATAAAATA
10989959 ATTTTATAAAAT
1 ATTTTATAAAAT
10989971 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:10992734 original size:21 final size:22
Alignment explanation
Indices: 10992692--10992734 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
10992682 GATAATGATA
10992692 AGAGATGTAAATACTAAGTTTTG
1 AGAGATGTAAATAC-AAGTTTTG
10992715 AGAG-TGTAAATA-AAGCTTTT
1 AGAGATGTAAATACAAG-TTTT
10992735 AAGAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 4 0.21
22 8 0.42
23 4 0.21
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (22 bp):
AGAGATGTAAATACAAGTTTTG
Found at i:11006681 original size:19 final size:19
Alignment explanation
Indices: 11006657--11006754 Score: 56
Period size: 19 Copynumber: 5.1 Consensus size: 19
11006647 TGCCCGTGTG
11006657 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
11006676 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
11006695 CACGATGT-GGGGGATGCA
1 CACGATGTGGGGGGATGTA
* * ** *
11006713 CATGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
11006734 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
11006753 CA
1 CA
11006755 TGAGCCGGGA
Statistics
Matches: 52, Mismatches: 22, Indels: 10
0.62 0.26 0.12
Matches are distributed among these distances:
18 10 0.19
19 29 0.56
20 3 0.06
21 10 0.19
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:11014982 original size:38 final size:38
Alignment explanation
Indices: 11014931--11015027 Score: 176
Period size: 38 Copynumber: 2.6 Consensus size: 38
11014921 ATAGTGCCCG
* *
11014931 TGTGCACGATGTGGGGGGATGTACACTATAGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACACGATAGCACTAAT
11014969 TGTGCACGATGTGGGGGGATGTACACGATAGCACTAAT
1 TGTGCACGATGTGGGGGGATGTACACGATAGCACTAAT
11015007 TGTGCACGATGTGGGGGGATG
1 TGTGCACGATGTGGGGGGATG
11015028 CAGATGATGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACACGATAGCACTAAT
Found at i:11015576 original size:21 final size:21
Alignment explanation
Indices: 11015537--11015576 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11015527 AACAATTTCT
**
11015537 CTGCAGCGAAATTCATTCTCA
1 CTGCAGCGAAAAACATTCTCA
*
11015558 CTGCAGCGAAAAACGTTCT
1 CTGCAGCGAAAAACATTCT
11015577 ATTTTGTCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
CTGCAGCGAAAAACATTCTCA
Found at i:11020348 original size:22 final size:22
Alignment explanation
Indices: 11020308--11020372 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
11020298 TTTAAATTAA
* * **
11020308 CTTTAAGACCAAAAACTCTGTT
1 CTTTAAAACCAAAAGCTCTAAT
*
11020330 CTTTAAAACCGAAAGCTCTAAT
1 CTTTAAAACCAAAAGCTCTAAT
11020352 CTTTAAAACCAAAAGCTCTAA
1 CTTTAAAACCAAAAGCTCTAA
11020373 CACCAATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.28
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTAAT
Found at i:11031294 original size:54 final size:54
Alignment explanation
Indices: 11031225--11031384 Score: 266
Period size: 54 Copynumber: 3.0 Consensus size: 54
11031215 ATGGTGATAT
* *
11031225 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACGTGAGCTAGGTGAGATGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
*
11031279 TGTCTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
* * *
11031333 GGTCCGACTATGTGCACAATGTGGTGGGATGCACATGAGCTGGGTGAGATGG
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGG
11031385 AATGATTGCT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.19, C:0.14, G:0.42, T:0.24
Consensus pattern (54 bp):
TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
Found at i:11034139 original size:43 final size:43
Alignment explanation
Indices: 11034069--11034226 Score: 183
Period size: 43 Copynumber: 3.7 Consensus size: 43
11034059 GTAATTATGT
* * *
11034069 TGACTCGGCTATGTACGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
* *
11034112 TGACCCGGTTATGTGCGAGTAGGGAGTGCACATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* * **
11034155 TGACCCGGTTATGTGCGAGTAGAGAGTAAGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* ** *
11034198 AGACCTAGCCATGTGCGAGTAGGGAGTGC
1 TGACCCGGCTATGTGCGAGTAGGGAGTGC
11034227 ACATGAGCTA
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
42 1 0.01
43 96 0.99
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:11039650 original size:21 final size:19
Alignment explanation
Indices: 11039614--11039654 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
11039604 ACATGTTGAG
11039614 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
11039633 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
11039654 T
1 T
11039655 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:11041066 original size:21 final size:21
Alignment explanation
Indices: 11041042--11041090 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
11041032 TCTTGTTGCG
11041042 GCGAGAATGAATCTCGCTGCA
1 GCGAGAATGAATCTCGCTGCA
*
11041063 GCGAGAATGAATCTTGCTGCA
1 GCGAGAATGAATCTCGCTGCA
*
11041084 GCAAGAA
1 GCGAGAA
11041091 GCTACAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (21 bp):
GCGAGAATGAATCTCGCTGCA
Found at i:11041127 original size:21 final size:21
Alignment explanation
Indices: 11041101--11041143 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
11041091 GCTACAGTAA
**
11041101 CATTCTCGCTACAGTGAGATT
1 CATTCTCGCTACAACGAGATT
11041122 CATTCTCGCTACAACGAGATT
1 CATTCTCGCTACAACGAGATT
11041143 C
1 C
11041144 TCGGCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (21 bp):
CATTCTCGCTACAACGAGATT
Found at i:11041447 original size:42 final size:42
Alignment explanation
Indices: 11041395--11041520 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
11041385 CATCTCATAT
*
11041395 GCAACGGCTTATGCGCACTCCCACTCGCACATAGTCGGGTTA
1 GCAACGGCTTATGCGCACTCCCACTCGCACATAGTCGGGTCA
* *
11041437 GCAATGGCTTATGCGCACTCCCACTAGCACATAG-CTGGGTCA
1 GCAACGGCTTATGCGCACTCCCACTCGCACATAGTC-GGGTCA
* *
11041479 GCAACGGCTTATGTGGACTCCCACTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGCGCACTCCCACTCGCACATAGTCGGGTCA
11041521 ATATCATTAC
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 73 0.97
43 1 0.01
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.21
Consensus pattern (42 bp):
GCAACGGCTTATGCGCACTCCCACTCGCACATAGTCGGGTCA
Found at i:11042219 original size:167 final size:165
Alignment explanation
Indices: 11041941--11042273 Score: 639
Period size: 167 Copynumber: 2.0 Consensus size: 165
11041931 GAGTCAATAC
11041941 ACAATCTCAACAATAAAACTCACAAACCAATCACTAGACATTATTAACACTTAAAACCTAATGCT
1 ACAATCTCAACAATAAAACTCACAAACCAATCACTAGACATTATTAACACTTAAAACCTAATGCT
11042006 AATTTACTATTCACCTTGATAGCTTTGTAACTTTGAACTTCTTTCCAACAATTCCCAAGCTATTA
66 AATTTACTATTCACCTTGATAGCTTTGTAACTTTGAACTTCTTTCCAACAATTCCCAAGCTATTA
*
11042071 TAAGGGCTTTCTCTCTCTCTCTCTCTCTCTCTACTA
131 TAAGGGCGTTCTCTCTCTCTCTCTCTCTCTCT-CTA
11042107 ACNAATCTCAACAATAAAACTCACAAACCAATCACTAGACATTATTAACACTTAAAACCTAATGC
1 AC-AATCTCAACAATAAAACTCACAAACCAATCACTAGACATTATTAACACTTAAAACCTAATGC
11042172 TAATTTACTATTCACCTTGATAGCTTTGTAACTTTGAACTTCTTTCCAACAATTCCCAAGCTATT
65 TAATTTACTATTCACCTTGATAGCTTTGTAACTTTGAACTTCTTTCCAACAATTCCCAAGCTATT
11042237 ATAAGGGCGTTCTCTCTCTCTCTCTCTCTCTCTCTA
130 ATAAGGGCGTTCTCTCTCTCTCTCTCTCTCTCTCTA
11042273 A
1 A
11042274 ACACCTAGTT
Statistics
Matches: 165, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
166 6 0.04
167 159 0.96
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.34
Consensus pattern (165 bp):
ACAATCTCAACAATAAAACTCACAAACCAATCACTAGACATTATTAACACTTAAAACCTAATGCT
AATTTACTATTCACCTTGATAGCTTTGTAACTTTGAACTTCTTTCCAACAATTCCCAAGCTATTA
TAAGGGCGTTCTCTCTCTCTCTCTCTCTCTCTCTA
Found at i:11042254 original size:2 final size:2
Alignment explanation
Indices: 11042247--11042271 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11042237 ATAAGGGCGT
11042247 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 T
11042272 AAACACCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11051815 original size:56 final size:56
Alignment explanation
Indices: 11051728--11051841 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
11051718 GGAGTGCTAC
* * * *
11051728 TGCCTTACCTTCAATTTTCCACTTTATAAGTTGCAAGTGGGTTTTTAATGCCCGTT
1 TGCCTTACCTTCAAGTTTCCACTTTACAAGTTACAAGTGGGTTTTTAATGCCCATT
* * *
11051784 TGCCTTACTTTTAAGTTTCCACTTTACAAGTTACAAGTGGGTTTTTAGTGCCCATT
1 TGCCTTACCTTCAAGTTTCCACTTTACAAGTTACAAGTGGGTTTTTAATGCCCATT
11051840 TG
1 TG
11051842 GCCTAGCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (56 bp):
TGCCTTACCTTCAAGTTTCCACTTTACAAGTTACAAGTGGGTTTTTAATGCCCATT
Found at i:11059996 original size:2 final size:2
Alignment explanation
Indices: 11059984--11060089 Score: 137
Period size: 2 Copynumber: 54.0 Consensus size: 2
11059974 ATACCTTGAA
11059984 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* **
11060027 AT -T AT AT AT -T GT -T NG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
11060066 AT AT AT AT AT AT AC AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
11060090 GTTTGCATAG
Statistics
Matches: 93, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
1 3 0.03
2 88 0.95
3 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11060683 original size:19 final size:20
Alignment explanation
Indices: 11060656--11060696 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
11060646 TTATCTAAAC
*
11060656 AATTAAAATTAA-AAAGAAA
1 AATTAAAATTAATAAACAAA
*
11060675 AATTTAAATTAATAAACAAA
1 AATTAAAATTAATAAACAAA
11060695 AA
1 AA
11060697 CTAATATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AATTAAAATTAATAAACAAA
Found at i:11062341 original size:35 final size:35
Alignment explanation
Indices: 11062222--11062454 Score: 121
Period size: 35 Copynumber: 6.5 Consensus size: 35
11062212 CATAGTCTAG
* * *
11062222 GAGTGGGGCATAAAATACCACTACTCTTTTTTGCCAT
1 GAGTGGGGCA-AAAATACCACCA-TCTATATTGCCAT
* * * * *
11062259 AAGTGGGGCTAATAATGCCACCATTTCT-TTGCCCAT
1 GAGTGGGGC-AAAAATACCACCATCTATATTG-CCAT
* * * *
11062295 AAGTGGAGCAAAAATACCACTATCTATATTGCCTT
1 GAGTGGGGCAAAAATACCACCATCTATATTGCCAT
* * * *
11062330 GAGTGGGGCAAAAATATCACCATTTTATAATAGCCTTT
1 GAGTGGGGCAAAAATACCACCA-TCTAT-ATTGCC-AT
* *
11062368 GAGTAGGGCAAAAATACCACCATC-ATATAGCCAT
1 GAGTGGGGCAAAAATACCACCATCTATATTGCCAT
* * *** ** * * *
11062402 AACTGGGGTGGATGTACCACTA-CTATATTACCTT
1 GAGTGGGGCAAAAATACCACCATCTATATTGCCAT
*
11062436 GAGTAGGGCAAAAATACCA
1 GAGTGGGGCAAAAATACCA
11062455 TCACCCAAGC
Statistics
Matches: 146, Mismatches: 43, Indels: 17
0.71 0.21 0.08
Matches are distributed among these distances:
33 1 0.01
34 32 0.22
35 43 0.29
36 24 0.16
37 23 0.16
38 23 0.16
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (35 bp):
GAGTGGGGCAAAAATACCACCATCTATATTGCCAT
Found at i:11063188 original size:35 final size:35
Alignment explanation
Indices: 11063113--11063190 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
11063103 ATCAAGCAAG
* * *
11063113 AACCCACATTATGGTTTTTAACAAGATCAACCACA
1 AACCCTCATAATGATTTTTAACAAGATCAACCACA
* * *
11063148 AACCCTCATAATGATTTTTAACAGGCTCAACTACA
1 AACCCTCATAATGATTTTTAACAAGATCAACCACA
11063183 AACCCTCA
1 AACCCTCA
11063191 CTAACTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (35 bp):
AACCCTCATAATGATTTTTAACAAGATCAACCACA
Found at i:11068000 original size:24 final size:23
Alignment explanation
Indices: 11067954--11068000 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
11067944 GTGAAATGGG
* *
11067954 TCTTGTTACATCAAAAGCCATTT
1 TCTTGTTACATCAAAAACAATTT
*
11067977 TCTTGTTGACATGAAAAACAATTT
1 TCTTGTT-ACATCAAAAACAATTT
11068001 GGGAGCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (23 bp):
TCTTGTTACATCAAAAACAATTT
Found at i:11068223 original size:38 final size:38
Alignment explanation
Indices: 11068123--11068233 Score: 105
Period size: 38 Copynumber: 2.9 Consensus size: 38
11068113 ACTCAGCTCA
* **** *
11068123 TGTGCATCCCCCCACATCGTGCACATCGCTGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACA-AGAAATA-TTATCG
* *
11068163 TGTGCATCCCCCCACATTGTGCATAAGAAATATTATCG
1 TGTGCATCCCCCCACATCGTGCACAAGAAATATTATCG
* * *
11068201 TGTGCATCCCCGCATATCGTGCACAAGCAATAT
1 TGTGCATCCCCCCACATCGTGCACAAGAAATAT
11068234 CATCACCCAC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
38 33 0.57
39 2 0.03
40 23 0.40
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAAGAAATATTATCG
Found at i:11070326 original size:22 final size:22
Alignment explanation
Indices: 11070301--11070352 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
11070291 CTAAGCCAAG
* *
11070301 TTTGTGCTAGCAAACTCTCAAC
1 TTTGAGCTAGAAAACTCTCAAC
11070323 TTTGAGCTAGAAAACTCTCAAC
1 TTTGAGCTAGAAAACTCTCAAC
11070345 TTTGAGCT
1 TTTGAGCT
11070353 CCCTTGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (22 bp):
TTTGAGCTAGAAAACTCTCAAC
Found at i:11071920 original size:13 final size:14
Alignment explanation
Indices: 11071885--11071922 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
11071875 TTTTAGTTTA
*
11071885 AATTTTGGTTAATT
1 AATTTTAGTTAATT
11071899 AATTTTAGTTAATT
1 AATTTTAGTTAATT
11071913 AA-TTTAGTTA
1 AATTTTAGTTA
11071923 TTTGATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (14 bp):
AATTTTAGTTAATT
Found at i:11087536 original size:28 final size:29
Alignment explanation
Indices: 11087495--11087554 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
11087485 GTCTATGGGC
*
11087495 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
11087523 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
11087553 AA
1 AA
11087555 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:11092467 original size:21 final size:19
Alignment explanation
Indices: 11092441--11092481 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
11092431 AATTTAAAAC
11092441 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
11092462 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
11092481 A
1 A
11092482 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:11098458 original size:27 final size:28
Alignment explanation
Indices: 11098428--11098484 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
11098418 TTCTAAGGAT
11098428 AAGGGCAAAATAG-ACATTTTAC-CACCC
1 AAGGGCAAAATAGTA-ATTTTACACACCC
*
11098455 AAGGGCAAAATTGTAATTTTACACACCC
1 AAGGGCAAAATAGTAATTTTACACACCC
11098483 AA
1 AA
11098485 CACTTGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (28 bp):
AAGGGCAAAATAGTAATTTTACACACCC
Found at i:11101138 original size:13 final size:13
Alignment explanation
Indices: 11101120--11101144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11101110 ATTTTCAAAA
11101120 ATTTTATAAAATT
1 ATTTTATAAAATT
11101133 ATTTTATAAAAT
1 ATTTTATAAAAT
11101145 CCCATTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:11102362 original size:29 final size:29
Alignment explanation
Indices: 11102301--11102364 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
11102291 GTAAATTTTT
** *
11102301 AAAAATTACACTTTTACCCCTGTAAAGTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
*
11102330 AAAAATTACATTTTTACCCC-AAAAACTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
11102358 AAAAATT
1 AAAAATT
11102365 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCTAAAAACTG
Found at i:11105054 original size:38 final size:40
Alignment explanation
Indices: 11105011--11105114 Score: 142
Period size: 38 Copynumber: 2.6 Consensus size: 40
11105001 GATAGTGCCC
* *
11105011 GTGTGCACGATGTGAGGGGATGTACACGAT-G-GCACTAAT
1 GTGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGAAT
* *
11105050 -TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGACT
1 GTGTGCACGATGTGGGGGGATGTACACGATGGTGCCGAAT
11105089 GTGTGCACGATGTGGGGGGATGTACA
1 GTGTGCACGATGTGGGGGGATGTACA
11105115 TGAGCCGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
38 27 0.47
39 4 0.07
40 26 0.46
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.22
Consensus pattern (40 bp):
GTGTGCACGATGTGGGGGGATGTACACGATGGTGCCGAAT
Found at i:11108165 original size:42 final size:42
Alignment explanation
Indices: 11108130--11108266 Score: 202
Period size: 42 Copynumber: 3.3 Consensus size: 42
11108120 CCACTTGCAT
* *
11108130 ATAGCCGAGTCATCATCGGCTTATGCACACTCCCACTCACAC
1 ATAGCCGGGTCATCATCGACTTATGCACACTCCCACTCACAC
*
11108172 ATAGCCGGGTCATCATCGACTTATGCACACTCCTACTCACAC
1 ATAGCCGGGTCATCATCGACTTATGCACACTCCCACTCACAC
* * * * *
11108214 ATAGTCGGGTCATCATCGACGTATGCGCACTCCTACTCGCAC
1 ATAGCCGGGTCATCATCGACTTATGCACACTCCCACTCACAC
11108256 ATAGCCGGGTC
1 ATAGCCGGGTC
11108267 CACATCAACA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (42 bp):
ATAGCCGGGTCATCATCGACTTATGCACACTCCCACTCACAC
Found at i:11117708 original size:35 final size:35
Alignment explanation
Indices: 11117669--11117741 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
11117659 CTTACTTAGC
*
11117669 TCATGTGCACTCCTTACACGCACAAGGCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
* ***
11117704 TCATGTGCACTCCCTACATGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACAAGGCAATATCA
11117739 TCA
1 TCA
11117742 CACGCACTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCACAAGGCAATATCA
Found at i:11121660 original size:20 final size:20
Alignment explanation
Indices: 11121635--11121680 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
11121625 TTTTGACCCC
11121635 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
11121655 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
11121675 ATTTGA
1 ATTTGA
11121681 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:11126431 original size:34 final size:34
Alignment explanation
Indices: 11126393--11126504 Score: 91
Period size: 34 Copynumber: 3.1 Consensus size: 34
11126383 CACTATTAGG
11126393 TGATAGTGGTGTGCTGTGTGAGTGCACACACTAA
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTAA
* * * *
11126427 TGATATATGCCATGTGCAGTGTGGGAGTGCACATGAC-AA
1 TGATA-GTG--GTGTGC--TGTGTGAGTGCACA-CACTAA
* * * *
11126466 TGATAGTGGTGTGTTGTGTGAGTACATACACTGA
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTAA
11126500 TGATA
1 TGATA
11126505 TATGCCATGT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
33 2 0.03
34 22 0.37
35 2 0.03
36 4 0.07
37 5 0.08
38 2 0.03
39 20 0.34
40 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.30
Consensus pattern (34 bp):
TGATAGTGGTGTGCTGTGTGAGTGCACACACTAA
Found at i:11126512 original size:73 final size:73
Alignment explanation
Indices: 11126393--11126535 Score: 225
Period size: 73 Copynumber: 2.0 Consensus size: 73
11126383 CACTATTAGG
* *
11126393 TGATAGTGGTGTGCTGTGTGAGTGCACACACTAATGATATATGCCATGTGC-AGTGTGGGAGTGC
1 TGATAGTGGTGTGCTGTGTGAGTACACACACTAATGATATATGCCATGTGCGA-TGTGAGAGTGC
11126457 ACATGACAA
65 ACATGACAA
* * *
11126466 TGATAGTGGTGTGTTGTGTGAGTACATACACTGATGATATATGCCATGTGCGATGTGAGAGTGCA
1 TGATAGTGGTGTGCTGTGTGAGTACACACACTAATGATATATGCCATGTGCGATGTGAGAGTGCA
11126531 CATGA
66 CATGA
11126536 TGATATTCCT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 63 0.98
74 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.29
Consensus pattern (73 bp):
TGATAGTGGTGTGCTGTGTGAGTACACACACTAATGATATATGCCATGTGCGATGTGAGAGTGCA
CATGACAA
Found at i:11126538 original size:36 final size:35
Alignment explanation
Indices: 11126497--11126606 Score: 107
Period size: 36 Copynumber: 3.1 Consensus size: 35
11126487 GTACATACAC
* *
11126497 TGATGATATATGCCATGTGCGATGTGAGAGTGCACA
1 TGATGATAT-TGCCATGTGCGGTGTGGGAGTGCACA
* *
11126533 TGATGATATT-CCTTTGTGTGGTGTGGGAGTGCACA
1 TGATGATATTGCC-ATGTGCGGTGTGGGAGTGCACA
* * *
11126568 GGATGAT-TCTAGCTATGTACGGTGTGGGAGTGCACA
1 TGATGATAT-T-GCCATGTGCGGTGTGGGAGTGCACA
11126604 TGA
1 TGA
11126607 GATGGTGAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
34 3 0.05
35 26 0.43
36 30 0.50
37 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.31
Consensus pattern (35 bp):
TGATGATATTGCCATGTGCGGTGTGGGAGTGCACA
Found at i:11131476 original size:43 final size:43
Alignment explanation
Indices: 11131322--11131692 Score: 353
Period size: 43 Copynumber: 9.0 Consensus size: 43
11131312 CGTGATAATT
* * *
11131322 ATGACCTAGCTATGTGCGGTGTA-GGAGTGCACATGAGTTG-TG
1 ATGACCCAGCTATGTGC-GAGTAGGGAGTGCACATGAGCTGATG
* * *
11131364 CTGACCCAGCCATGTGTG-G-A-GGAGTGCACATGAGCTG-TG
1 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* * * * *
11131403 CTGACCCAGCCATGTGTG-G-A-GGAGTACACATGAGCTAATG
1 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* * *
11131443 ATGACCCATCTATGTACGAGTAGGGAGTGCACATGAGTTGATG
1 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* ** *
11131486 ATGACCCAGCCATGTATG-G-A-GGAGTACACATGAGCTGATG
1 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
11131526 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* * * *
11131569 ATGACCCAGCCATGTGTG-G-A-GGAGTTCCCATGAG-TAGATG
1 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCT-GATG
* *
11131609 ATGACCTAGTTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* * *
11131652 ATGACCCAACTATGTGCG-GTGTGGGAGTGCACATAAGCTGA
1 ATGACCCAGCTATGTGCGAGT-AGGGAGTGCACATGAGCTGA
11131693 GAGAGAGTTT
Statistics
Matches: 277, Mismatches: 39, Indels: 25
0.81 0.11 0.07
Matches are distributed among these distances:
39 55 0.20
40 79 0.29
41 6 0.02
42 20 0.07
43 116 0.42
44 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (43 bp):
ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
Found at i:11131657 original size:166 final size:161
Alignment explanation
Indices: 11131344--11131659 Score: 456
Period size: 166 Copynumber: 1.9 Consensus size: 161
11131334 TGTGCGGTGT
* * * * *
11131344 AGGAGTGCACATGAGTTGTGCTGACCCAGCCATGTGTGGAGGAGTGCACATGAGCTGTGCTGACC
1 AGGAGTACACATGAGCTGTGATGACCCAGCCATGTGCGGAGGAGTGCACATGAGCTGTGATGACC
11131409 CAGCCATGTGTGGAGGAGTACACATGAGCTAATGATGACCCATCTATGTACGAGTAGGGAGTGCA
66 CAGCCATGTGTGGAGGAGTACACATGAGCTAATGATGACCCATCTATGTACGAGTAGGGAGTGCA
*
11131474 CATGAGTTGATGATGACCCAGCCATGTATGG
131 CATGAGCTGATGATGACCCAGCCATGTATGG
*
11131505 AGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATGA
1 AGGAGTACACATGAGCTG-TGATGACCCAGCCATGTGCG-G-A-GGAGTGCACATGAGCTG-TGA
* * * *
11131570 TGACCCAGCCATGTGTGGAGGAGTTCCCATGAG-TAGATGATGACCTAGT-TATGTGCGAGTAGG
61 TGACCCAGCCATGTGTGGAGGAGTACACATGAGCTA-ATGATGACCCA-TCTATGTACGAGTAGG
11131633 GAGTGCACATGAGCTGATGATGACCCA
124 GAGTGCACATGAGCTGATGATGACCCA
11131660 ACTATGTGCG
Statistics
Matches: 137, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
161 16 0.12
162 17 0.12
163 1 0.01
164 1 0.01
165 19 0.14
166 82 0.60
167 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (161 bp):
AGGAGTACACATGAGCTGTGATGACCCAGCCATGTGCGGAGGAGTGCACATGAGCTGTGATGACC
CAGCCATGTGTGGAGGAGTACACATGAGCTAATGATGACCCATCTATGTACGAGTAGGGAGTGCA
CATGAGCTGATGATGACCCAGCCATGTATGG
Found at i:11131667 original size:83 final size:84
Alignment explanation
Indices: 11131384--11131659 Score: 436
Period size: 83 Copynumber: 3.3 Consensus size: 84
11131374 CATGTGTGGA
*
11131384 GGAGTGCACATGAGCTG-TGCTGACCCAGCCATGTGTGGAGGAGTACACATGAGCTA-ATGATGA
1 GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTAGATGATGA
*
11131447 CCCA-TCTATGTACGAGTAG
66 CCCAGT-TATGTGCGAGTAG
* *
11131466 GGAGTGCACATGAGTTGATGATGACCCAGCCATGTATGGAGGAGTACACATGAGCT-GATGATGA
1 GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTAGATGATGA
*
11131530 CCCAGCTATGTGCGAGTAG
66 CCCAGTTATGTGCGAGTAG
* *
11131549 GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGGAGTTCCCATGAG-TAGATGATGA
1 GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTAGATGATGA
*
11131613 CCTAGTTATGTGCGAGTAG
66 CCCAGTTATGTGCGAGTAG
11131632 GGAGTGCACATGAGCTGATGATGACCCA
1 GGAGTGCACATGAGCTGATGATGACCCA
11131660 ACTATGTGCG
Statistics
Matches: 179, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
82 17 0.09
83 162 0.91
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (84 bp):
GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTAGATGATGA
CCCAGTTATGTGCGAGTAG
Found at i:11134500 original size:2 final size:2
Alignment explanation
Indices: 11134493--11134533 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11134483 TATAACATAC
11134493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11134534 CAGGTACACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11136145 original size:2 final size:2
Alignment explanation
Indices: 11136138--11136168 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11136128 AGACACTAAA
11136138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11136169 ATAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11137617 original size:21 final size:21
Alignment explanation
Indices: 11137576--11137628 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
11137566 ATTTACTACA
*
11137576 AATATATAATAAAAATAAAAAT
1 AATA-ATAATAAAAAGAAAAAT
* *
11137598 AGTAATAATAAAAAGGAAAAT
1 AATAATAATAAAAAGAAAAAT
*
11137619 AATAGTAATA
1 AATAATAATA
11137629 TTCCACGACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (21 bp):
AATAATAATAAAAAGAAAAAT
Found at i:11142591 original size:21 final size:21
Alignment explanation
Indices: 11142546--11142591 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
11142536 TACCCTTTTC
*
11142546 TATAGCATATAAAAACATATC
1 TATAGCATATAAAAACATATA
* * *
11142567 TATAGCATATATATATATATA
1 TATAGCATATAAAAACATATA
11142588 TATA
1 TATA
11142592 TACATACAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (21 bp):
TATAGCATATAAAAACATATA
Found at i:11143705 original size:32 final size:32
Alignment explanation
Indices: 11143669--11143772 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
11143659 TTTACCGGGA
*
11143669 TCAACTAAAATCCAAAGTGGTTTTTCAAAAGC
1 TCAACTAAAATCCAAAGTGGTTTTTCAAAGGC
* * * ***
11143701 TCAACCACAACCTTTCACAA-TGGTTTTTCGCGGGC
1 TCAACTA-AA--ATCCA-AAGTGGTTTTTCAAAGGC
11143736 TCAACTAAAA-CCGAAAGTGGTTTTTCAAAGGC
1 TCAACTAAAATCC-AAAGTGGTTTTTCAAAGGC
11143768 TCAAC
1 TCAAC
11143773 CACAACCTAC
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
31 3 0.06
32 24 0.45
33 2 0.04
34 2 0.04
35 20 0.38
36 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (32 bp):
TCAACTAAAATCCAAAGTGGTTTTTCAAAGGC
Found at i:11143740 original size:67 final size:66
Alignment explanation
Indices: 11143630--11143814 Score: 248
Period size: 67 Copynumber: 2.8 Consensus size: 66
11143620 TGCTTTTTCC
* *
11143630 AAGCTCAACCAAAACCTTTCACAATAGTTTTTACCGGGATCAACTAAAATCC-AAAGTGGTTTTT
1 AAGCTCAACCACAACCTTTCACAATGGTTTTT-CCGGGATCAACTAAAA-CCGAAAGTGGTTTTT
11143694 CAA
64 CAA
*
11143697 AAGCTCAACCACAACCTTTCACAATGGTTTTTCGCGGGCTCAACTAAAACCGAAAGTGGTTTTTC
1 AAGCTCAACCACAACCTTTCACAATGGTTTTTC-CGGGATCAACTAAAACCGAAAGTGGTTTTTC
11143762 AA
65 AA
* * * *
11143764 AGGCTCAACCACAACC-TACAATAATGGTTTTTCACGGGATCAACCAAAACC
1 AAGCTCAACCACAACCTTTC-ACAATGGTTTTTC-CGGGATCAACTAAAACC
11143815 TAACAACTAA
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
66 5 0.05
67 101 0.95
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (66 bp):
AAGCTCAACCACAACCTTTCACAATGGTTTTTCCGGGATCAACTAAAACCGAAAGTGGTTTTTCA
A
Found at i:11147948 original size:21 final size:20
Alignment explanation
Indices: 11147923--11147982 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
11147913 AGATGTCTAA
*
11147923 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
11147944 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
11147964 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
11147982 A
1 A
11147983 TTCTATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:11153300 original size:33 final size:34
Alignment explanation
Indices: 11153257--11153341 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 34
11153247 AATGCAATAT
*
11153257 CATCGTCATGTGTGCA-CTACTCACACACT-TCAA
1 CATCATCATGTGTGCACCTACTCACACACTCT-AA
* *
11153290 CATCATCATGTGTACACTCCCTACTCGCACACTCTAA
1 CATCATCATGTGTGCA---CCTACTCACACACTCTAA
11153327 CATCATCATGTGTGC
1 CATCATCATGTGTGC
11153342 CATGTGTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
33 14 0.33
37 28 0.65
38 1 0.02
ACGTcount: A:0.26, C:0.34, G:0.12, T:0.28
Consensus pattern (34 bp):
CATCATCATGTGTGCACCTACTCACACACTCTAA
Found at i:11153314 original size:37 final size:37
Alignment explanation
Indices: 11153273--11153417 Score: 157
Period size: 37 Copynumber: 3.7 Consensus size: 37
11153263 CATGTGTGCA
11153273 CTACTCACACACTTCAACATCATCATGTGTACACTCC
1 CTACTCACACACTTCAACATCATCATGTGTACACTCC
*
11153310 CTACTCGCACAC-TCTAACATCATCATGTGTGCCATGTGTGCACTCC
1 CTACTCACACACTTC-AACATCATCATGTGT---A------CACTCC
* *
11153356 CTACTCACACACTTCAACATAATCATGTGTGCACTCC
1 CTACTCACACACTTCAACATCATCATGTGTACACTCC
*
11153393 CTACTCGCACACTTCAACATCATCA
1 CTACTCACACACTTCAACATCATCA
11153418 CACAACATTA
Statistics
Matches: 91, Mismatches: 6, Indels: 22
0.76 0.05 0.18
Matches are distributed among these distances:
36 2 0.02
37 55 0.60
40 1 0.01
46 31 0.34
47 2 0.02
ACGTcount: A:0.28, C:0.37, G:0.09, T:0.27
Consensus pattern (37 bp):
CTACTCACACACTTCAACATCATCATGTGTACACTCC
Found at i:11153367 original size:46 final size:46
Alignment explanation
Indices: 11153296--11153387 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
11153286 TCAACATCAT
* *
11153296 CATGTGTACACTCCCTACTCGCACAC-TCTAACATCATCATGTGTGC
1 CATGTGTACACTCCCTACTCACACACTTC-AACATAATCATGTGTGC
*
11153342 CATGTGTGCACTCCCTACTCACACACTTCAACATAATCATGTGTGC
1 CATGTGTACACTCCCTACTCACACACTTCAACATAATCATGTGTGC
11153388 ACTCCCTACT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
46 40 0.95
47 2 0.05
ACGTcount: A:0.25, C:0.34, G:0.13, T:0.28
Consensus pattern (46 bp):
CATGTGTACACTCCCTACTCACACACTTCAACATAATCATGTGTGC
Found at i:11158065 original size:35 final size:34
Alignment explanation
Indices: 11158022--11158091 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
11158012 TTTCATCATG
* *
11158022 CTTTACAATGGCTTTTACCAAGCTCAACCAAAAC
1 CTTTACAATAGCTTTTACCAAGATCAACCAAAAC
* *
11158056 CTTTCACAATAGTTTTTACCAAGATCAACTAAAAC
1 CTTT-ACAATAGCTTTTACCAAGATCAACCAAAAC
11158091 C
1 C
11158092 CAAAGTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 4 0.13
35 27 0.87
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (34 bp):
CTTTACAATAGCTTTTACCAAGATCAACCAAAAC
Found at i:11158116 original size:32 final size:32
Alignment explanation
Indices: 11158080--11158185 Score: 106
Period size: 32 Copynumber: 3.2 Consensus size: 32
11158070 TTTACCAAGA
* *
11158080 TCAACTAAAACCCAAAGTGGTTTTTCAATGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * **
11158112 TCAACCATAATCTTTCACAA-TGGTTTTTCACGGGC
1 TCAACCA-AAAC--CCA-AAGTGGTTTTTCAAAGGC
*
11158147 TCAACCAAAACCCAAAGTGGTTTTTCAAAAGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
11158179 TCAACCA
1 TCAACCA
11158186 CAACTTACAA
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
31 2 0.03
32 27 0.46
33 3 0.05
34 3 0.05
35 22 0.37
36 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.27
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:11158136 original size:35 final size:33
Alignment explanation
Indices: 11158097--11158208 Score: 95
Period size: 35 Copynumber: 3.3 Consensus size: 33
11158087 AAACCCAAAG
* *
11158097 TGGTTTTTCAATGGCTCAACCATAATCTTTCACAA
1 TGGTTTTTCAAAGGCTCAACCA-AA-CTTACACAA
** *
11158132 TGGTTTTTCACGGGCTCAACCAAA---ACCCAAA
1 TGGTTTTTCAAAGGCTCAACCAAACTTACAC-AA
*
11158163 GTGGTTTTTCAAAAGCTCAACCACAACTTACAACAA
1 -TGGTTTTTCAAAGGCTCAACCA-AACTTAC-ACAA
11158199 TGGTTTTTCA
1 TGGTTTTTCA
11158209 CGAGATCAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
30 2 0.03
31 2 0.03
32 19 0.31
33 2 0.03
34 2 0.03
35 30 0.48
36 4 0.06
37 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (33 bp):
TGGTTTTTCAAAGGCTCAACCAAACTTACACAA
Found at i:11158151 original size:67 final size:66
Alignment explanation
Indices: 11158041--11158228 Score: 243
Period size: 67 Copynumber: 2.8 Consensus size: 66
11158031 GGCTTTTACC
* * *
11158041 AAGCTCAACCAAAACCTTTCACAATAGTTTTT-ACCAAGATCAACTAAAACCCAAAGTGGTTTTT
1 AAGCTCAACCAAAA-CTTTCACAATGGTTTTTCA-CGAGATCAACCAAAACCCAAAGTGGTTTTT
11158105 CAA
64 CAA
** * * *
11158108 TGGCTCAACCATAATCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTC
1 AAGCTCAACCA-AAACTTTCACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTC
11158173 AA
65 AA
* *
11158175 AAGCTCAACCACAACTTACAACAATGGTTTTTCACGAGATCAACCAAAACCCAA
1 AAGCTCAACCAAAACTTTC-ACAATGGTTTTTCACGAGATCAACCAAAACCCAA
11158229 CAACTAACTT
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
66 5 0.05
67 95 0.92
68 3 0.03
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (66 bp):
AAGCTCAACCAAAACTTTCACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTCA
A
Found at i:11158218 original size:35 final size:33
Alignment explanation
Indices: 11158128--11158231 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 33
11158118 ATAATCTTTC
* *
11158128 ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
1 ACAATGGTTTTTCACGAGCTCAACCAAAACACA
* ** *
11158161 A-AGTGGTTTTTCAAAAGCTCAACCACAACTTACA
1 ACAATGGTTTTTCACGAGCTCAACCAAAAC--ACA
* *
11158195 ACAATGGTTTTTCACGAGATCAACCAAAACCCA
1 ACAATGGTTTTTCACGAGCTCAACCAAAACACA
11158228 ACAA
1 ACAA
11158232 CTAACTTTTC
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
32 23 0.41
33 7 0.12
34 3 0.05
35 23 0.41
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.22
Consensus pattern (33 bp):
ACAATGGTTTTTCACGAGCTCAACCAAAACACA
Found at i:11163167 original size:2 final size:2
Alignment explanation
Indices: 11163160--11163190 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11163150 ACTTTCTATA
11163160 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
11163191 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11163318 original size:42 final size:43
Alignment explanation
Indices: 11163229--11163320 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
11163219 TACAATCCCA
11163229 TCATCATAAGCTAATGTGCACTCCCTACTCGCACATAGCTGGG
1 TCATCATAAGCTAATGTGCACTCCCTACTCGCACATAGCTGGG
* *
11163272 TCATCATCAA-CTGATGTGCACTCCC-ACAT-GCACATAGTTGGG
1 TCATCAT-AAGCTAATGTGCACTCCCTAC-TCGCACATAGCTGGG
11163314 TCATCAT
1 TCATCAT
11163321 TATCACATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
42 21 0.47
43 22 0.49
44 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (43 bp):
TCATCATAAGCTAATGTGCACTCCCTACTCGCACATAGCTGGG
Found at i:11173186 original size:68 final size:68
Alignment explanation
Indices: 11173097--11173431 Score: 402
Period size: 68 Copynumber: 4.9 Consensus size: 68
11173087 CACATACATG
* * *
11173097 CTTACTCATCTCATGAGGTATATGGAATTTACATCATATACATAATCTCATGGCATTTATCATGC
1 CTTAATCATCTCATGTGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
* *
11173162 TTG
66 ATA
* * *
11173165 CTCAATCATCTCATGTAGTATATGGAATATACATCATATACATAATCTCATGGCATTAATCATGC
1 CTTAATCATCTCATGTGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
11173230 ATA
66 ATA
* * * *
11173233 CTTAATCACCTCATGTGGTATGTGGAATATACATCATATACAAAATCTCATGGCATTAATCATGC
1 CTTAATCATCTCATGTGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
11173298 ATA
66 ATA
* * * * * * * * *
11173301 CTTTATCACCTCATATGGTATATGGAATTTACATCATATACACAATCTTATAGTA-TACATTATT
1 CTTAATCATCTCATGTGGTATATGGAATTTACATCATATACATAATCTCATGGCATTA-ATCATG
11173365 CATA
65 CATA
* * * * * * *
11173369 CTTGATCATTTCATATGGTATATGGAATTTGCATTATATACATAATCTTATGGCATTCATCAT
1 CTTAATCATCTCATGTGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCAT
11173432 ACCAAACATG
Statistics
Matches: 232, Mismatches: 33, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
67 2 0.01
68 229 0.99
69 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.37
Consensus pattern (68 bp):
CTTAATCATCTCATGTGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
ATA
Found at i:11174459 original size:16 final size:16
Alignment explanation
Indices: 11174434--11174472 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
11174424 GATTTAATAA
11174434 AAAAAT-CAAAAAAAT
1 AAAAATCCAAAAAAAT
*
11174449 AAAAATCCAAAAGAAT
1 AAAAATCCAAAAAAAT
*
11174465 CAAAATCC
1 AAAAATCC
11174473 CAGTTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.69, C:0.15, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAATCCAAAAAAAT
Found at i:11176288 original size:35 final size:35
Alignment explanation
Indices: 11176237--11176340 Score: 120
Period size: 35 Copynumber: 3.0 Consensus size: 35
11176227 AAGTGTGGAT
11176237 AGTGATATTGAAGTGTGCGAGTAGGGAGTGCACAC
1 AGTGATATTGAAGTGTGCGAGTAGGGAGTGCACAC
* *
11176272 AGTGATGTTGATGTGTGCGAGTAGGGAGTGCACA-
1 AGTGATATTGAAGTGTGCGAGTAGGGAGTGCACAC
* *** * *
11176306 TGATGATATTGCCTTGTGTGTGTAGGGAGTGCACA
1 AG-TGATATTGAAGTGTGCGAGTAGGGAGTGCACA
11176341 TTGGCTGAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 1 0.02
35 58 0.98
ACGTcount: A:0.24, C:0.11, G:0.38, T:0.28
Consensus pattern (35 bp):
AGTGATATTGAAGTGTGCGAGTAGGGAGTGCACAC
Found at i:11180874 original size:20 final size:20
Alignment explanation
Indices: 11180846--11180888 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11180836 GGAAAGAAGA
* * *
11180846 AGAAGAAGCTGCTGGAAGTT
1 AGAAAAAGCTACTAGAAGTT
11180866 AGAAAAAGCTACTAGAAGTT
1 AGAAAAAGCTACTAGAAGTT
11180886 AGA
1 AGA
11180889 TATTTATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (20 bp):
AGAAAAAGCTACTAGAAGTT
Found at i:11185851 original size:62 final size:61
Alignment explanation
Indices: 11185756--11185951 Score: 266
Period size: 62 Copynumber: 3.2 Consensus size: 61
11185746 GAACTACGGT
* * * *
11185756 GAGAACAGTGACTCCCAAGATAGAAAGTCTCTCGCTGTGACGAAAATCAATTTGGCTGCGGT
1 GAGAACAGTGACT-CCAAGACAGAAAGTTTCTCGCTGTGGCGAAAATCAATTTGGCTGCGGC
* * ** *
11185818 GAGAACAGTGACTCGCAAGACAAAAAGTTTCTCGGTACGGCGAAAATCAATTTGGCTACGGC
1 GAGAACAGTGACTC-CAAGACAGAAAGTTTCTCGCTGTGGCGAAAATCAATTTGGCTGCGGC
* *
11185880 GAGAACAGTGACTCCGAAGACAGAAAGTTTCTCACTGTGGTGAAAATCAATTTGGCTGCGGC
1 GAGAACAGTGACTCC-AAGACAGAAAGTTTCTCGCTGTGGCGAAAATCAATTTGGCTGCGGC
11185942 GAGAACAGTG
1 GAGAACAGTG
11185952 CAAATGGGGT
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
61 2 0.02
62 114 0.98
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (61 bp):
GAGAACAGTGACTCCAAGACAGAAAGTTTCTCGCTGTGGCGAAAATCAATTTGGCTGCGGC
Found at i:11189133 original size:43 final size:43
Alignment explanation
Indices: 11189008--11189133 Score: 157
Period size: 42 Copynumber: 3.0 Consensus size: 43
11188998 AGTGATAATT
* *
11189008 ATGACCTAGCCATGTGCAGTGTAGGAGTGCACATGAGCTG-TG
1 ATGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGATG
* * * *
11189050 TTGACCCAACCATGTGCGGTGTAAGAGTGTACATGAGCTGATG
1 ATGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGATG
* *
11189093 ATGACCCAGCTATGTGCGGTGT-GGTAGTGCACATAAGCTGA
1 ATGACCCAGCCATGTGCGGTGTAGG-AGTGCACATGAGCTGA
11189134 GACAGAGTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 35 0.50
43 35 0.50
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (43 bp):
ATGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGATG
Found at i:11193109 original size:13 final size:13
Alignment explanation
Indices: 11193091--11193115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11193081 GGAGAAATTG
11193091 TGATTTTATAAAA
1 TGATTTTATAAAA
11193104 TGATTTTATAAA
1 TGATTTTATAAA
11193116 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Done.