Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 64 of 356
Found at i:20309475 original size:30 final size:29
Alignment explanation
Indices: 20309426--20309491 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
20309416 GTTTAATGTA
* * *
20309426 TAATTGTATATATAAATTTTAATTTTATG
1 TAATTTTATATATAAATTTTAATTTGATC
20309455 TAATTTTATATATGAAATTTTAATTTGATC
1 TAATTTTATATAT-AAATTTTAATTTGATC
20309485 TAATTTT
1 TAATTTT
20309492 TTTGTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (29 bp):
TAATTTTATATATAAATTTTAATTTGATC
Found at i:20325119 original size:69 final size:69
Alignment explanation
Indices: 20325008--20325146 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
20324998 GATAGGAAAA
* *
20325008 ACAGGTTCCAAAACAGGAGTAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
20325073 GCTG
66 GCTG
20325077 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
20325142 GCTG
66 GCTG
20325146 A
1 A
20325147 TAGAGTCTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
GCTG
Found at i:20331282 original size:27 final size:27
Alignment explanation
Indices: 20331262--20331314 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
20331252 AAATTTATAT
20331262 TTCT-TTATATAAATTATAAATCTATTG
1 TTCTCTTA-ATAAATTATAAATCTATTG
*
20331289 TTCTCTTAATAAATTATAAATGTATT
1 TTCTCTTAATAAATTATAAATCTATT
20331315 ATGTTGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (27 bp):
TTCTCTTAATAAATTATAAATCTATTG
Found at i:20331891 original size:6 final size:6
Alignment explanation
Indices: 20331868--20331933 Score: 107
Period size: 6 Copynumber: 11.0 Consensus size: 6
20331858 ATGCTGATCT
20331868 ATACTA TATACT- ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA
1 ATACTA -ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA
*
20331916 ATACTA ATACTG ATACTA
1 ATACTA ATACTA ATACTA
20331934 TACAGAGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.09
6 46 0.82
7 5 0.09
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.35
Consensus pattern (6 bp):
ATACTA
Found at i:20335443 original size:10 final size:11
Alignment explanation
Indices: 20335409--20335449 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
20335399 AAATAGAAGA
20335409 TATTATTTTAT
1 TATTATTTTAT
* *
20335420 T-CTGTTTTAT
1 TATTATTTTAT
20335430 TATT-TTTTAT
1 TATTATTTTAT
20335440 TATTATTTTA
1 TATTATTTTA
20335450 GGATTAAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:20342262 original size:15 final size:15
Alignment explanation
Indices: 20342242--20342270 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20342232 AAAACTACCC
20342242 ATCCATCAACCCAAT
1 ATCCATCAACCCAAT
20342257 ATCCATCAACCCAA
1 ATCCATCAACCCAA
20342271 ACCAATTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (15 bp):
ATCCATCAACCCAAT
Found at i:20345669 original size:5 final size:5
Alignment explanation
Indices: 20345661--20345707 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
20345651 ATAGAATATA
* *
20345661 TTATT TTATT TTGTT TTA-- TTATT TTATT AT-TT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
20345708 ATTTTAGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.09
4 3 0.09
5 29 0.83
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:20345670 original size:8 final size:8
Alignment explanation
Indices: 20345659--20345713 Score: 56
Period size: 8 Copynumber: 6.2 Consensus size: 8
20345649 AAATAGAATA
20345659 TATTATTT
1 TATTATTT
*
20345667 TATTTTGTTT
1 TA--TTATTT
20345677 TATTATTT
1 TATTATTT
20345685 TATTATTTT
1 TATTA-TTT
20345694 TATTTTATTT
1 TA--TTATTT
20345704 TATTATTT
1 TATTATTT
20345712 TA
1 TA
20345714 GGATTAAGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 20 0.50
9 5 0.12
10 12 0.30
11 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:20345699 original size:22 final size:22
Alignment explanation
Indices: 20345659--20345710 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
20345649 AAATAGAATA
* *
20345659 TATTATTTTATTTTGTTTTATTAT
1 TATTATTAT-TTTTATTTTATT-T
20345683 T-TTATTATTTTTATTTTATTT
1 TATTATTATTTTTATTTTATTT
20345704 TATTATT
1 TATTATT
20345711 TTAGGATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 6 0.24
24 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TATTATTATTTTTATTTTATTT
Found at i:20345699 original size:27 final size:26
Alignment explanation
Indices: 20345659--20345713 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
20345649 AAATAGAATA
*
20345659 TATTATTTTATTTTGTTTTATTATTT
1 TATTATTTTATTTTATTTTATTATTT
20345685 TATTATTTTTATTTTATTTTATTATTT
1 TATTA-TTTTATTTTATTTTATTATTT
20345712 TA
1 TA
20345714 GGATTAAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (26 bp):
TATTATTTTATTTTATTTTATTATTT
Found at i:20346807 original size:19 final size:19
Alignment explanation
Indices: 20346783--20346819 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20346773 AAAATAGAGT
20346783 GAAAGCAACTCAAAAGCAC
1 GAAAGCAACTCAAAAGCAC
20346802 GAAAGCAACTCAAAAGCA
1 GAAAGCAACTCAAAAGCA
20346820 AAGGAGTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.24, G:0.16, T:0.05
Consensus pattern (19 bp):
GAAAGCAACTCAAAAGCAC
Found at i:20347350 original size:21 final size:20
Alignment explanation
Indices: 20347320--20347363 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
20347310 TAAAACTATC
20347320 ATTTTTAAT-ATTATAATATT
1 ATTTTTAATAATTATAAT-TT
20347340 ATTTTTAAATAAATTATAATTT
1 ATTTTT-AAT-AATTATAATTT
20347362 AT
1 AT
20347364 AACGCTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 3 0.14
22 4 0.19
23 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTAATAATTATAATTT
Found at i:20366903 original size:23 final size:22
Alignment explanation
Indices: 20366852--20366903 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
20366842 CCTCGTCTTT
*
20366852 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
20366874 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
20366897 TTCTTTT
1 TTCTTTT
20366904 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:20366918 original size:18 final size:18
Alignment explanation
Indices: 20366897--20366935 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20366887 TTTCTTCAAC
* *
20366897 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
20366915 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
20366933 TTC
1 TTC
20366936 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:20376032 original size:18 final size:18
Alignment explanation
Indices: 20376009--20376048 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
20375999 CAATTCTTGA
20376009 TATAACATCATTTTATTT
1 TATAACATCATTTTATTT
20376027 TATAACATCATTTTATTT
1 TATAACATCATTTTATTT
20376045 TATA
1 TATA
20376049 TGTTGCATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAACATCATTTTATTT
Found at i:20376080 original size:49 final size:47
Alignment explanation
Indices: 20376027--20376119 Score: 159
Period size: 49 Copynumber: 1.9 Consensus size: 47
20376017 CATTTTATTT
*
20376027 TATAACATCATTTTATTTTATATGTTGCATACTTTAACACAATTATTGA
1 TATAACATCATTTTATTTTATATGTTGCATAC-ATAA-ACAATTATTGA
20376076 TATAACATCATTTTATTTTATATGTTGCATACATAAACAATTAT
1 TATAACATCATTTTATTTTATATGTTGCATACATAAACAATTAT
20376120 ATTTATCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
47 8 0.19
48 3 0.07
49 32 0.74
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (47 bp):
TATAACATCATTTTATTTTATATGTTGCATACATAAACAATTATTGA
Found at i:20376245 original size:30 final size:30
Alignment explanation
Indices: 20376166--20376233 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
20376156 CTTTAAATAT
*
20376166 GTAT-GATTAAATCAAAATTAAAACTTTAA
1 GTATAGATTAAATCAAAATTAAAACTTCAA
20376195 GTATAGATTAAATCAAAATTAAAACTTCAA
1 GTATAGATTAAATCAAAATTAAAACTTCAA
20376225 GTATAGATT
1 GTATAGATT
20376234 TGAACACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (30 bp):
GTATAGATTAAATCAAAATTAAAACTTCAA
Found at i:20380323 original size:19 final size:20
Alignment explanation
Indices: 20380291--20380334 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
20380281 AAATAAATCA
* *
20380291 ATTTTTTAATAAATTGA-TT
1 ATTTTATAAAAAATTGATTT
*
20380310 ATTTTATAAAAAATTTATTT
1 ATTTTATAAAAAATTGATTT
20380330 ATTTT
1 ATTTT
20380335 TATTGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTTATAAAAAATTGATTT
Found at i:20382527 original size:29 final size:28
Alignment explanation
Indices: 20382490--20382562 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 28
20382480 GTAATTTATA
*
20382490 TATTTTATATAAAAAATAGATAAATTAGT
1 TATTTTATATAAAAAATAG-CAAATTAGT
*
20382519 TATTGTATATTAAATCAAATAGCAAATTAGT
1 TATTTTATA-TAAA--AAATAGCAAATTAGT
20382550 TATTTTAT-TAAAA
1 TATTTTATATAAAA
20382563 GTATCATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.03
29 12 0.32
30 4 0.11
31 15 0.39
32 6 0.16
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (28 bp):
TATTTTATATAAAAAATAGCAAATTAGT
Found at i:20383791 original size:41 final size:41
Alignment explanation
Indices: 20383746--20383824 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
20383736 CTTAATTGGC
20383746 CGCAAAAAATAGGGATATAAAGCCCCTTTAAATAGGCTGGT
1 CGCAAAAAATAGGGATATAAAGCCCCTTTAAATAGGCTGGT
20383787 CGCAAAAAATAGGGATATAAAGCCCCTTTAAATAGGCT
1 CGCAAAAAATAGGGATATAAAGCCCCTTTAAATAGGCT
20383825 AAGGTTAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (41 bp):
CGCAAAAAATAGGGATATAAAGCCCCTTTAAATAGGCTGGT
Found at i:20384798 original size:15 final size:15
Alignment explanation
Indices: 20384765--20384797 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20384755 TATAACGAAT
*
20384765 AAAATAAAATTGAAG
1 AAAATAAAATTCAAG
20384780 AAAATAAAATTC-AG
1 AAAATAAAATTCAAG
20384794 AAAA
1 AAAA
20384798 AGAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (15 bp):
AAAATAAAATTCAAG
Found at i:20387324 original size:22 final size:20
Alignment explanation
Indices: 20387293--20387349 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
20387283 AATAATAAGG
*
20387293 GCAAGAATAAAAATAAACAA
1 GCAAAAATAAAAATAAACAA
* *
20387313 GCCAATAAATAATAATAAATAA
1 G-CAA-AAATAAAAATAAACAA
20387335 GCAAAAACTAAAAAT
1 GCAAAAA-TAAAAAT
20387350 TTGAAACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 4 0.13
21 12 0.40
22 14 0.47
ACGTcount: A:0.67, C:0.11, G:0.07, T:0.16
Consensus pattern (20 bp):
GCAAAAATAAAAATAAACAA
Found at i:20387954 original size:14 final size:14
Alignment explanation
Indices: 20387937--20387965 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20387927 AAAATTAAAG
20387937 ATAAAAAAAGACTT
1 ATAAAAAAAGACTT
20387951 ATAAAAAAAGACTT
1 ATAAAAAAAGACTT
20387965 A
1 A
20387966 ATTGCAAAAA
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:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
ATAAAAAAAGACTT
Found at i:20394559 original size:14 final size:13
Alignment explanation
Indices: 20394523--20394560 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
20394513 AAATTTAAAT
20394523 CTAAATAATTATC
1 CTAAATAATTATC
*
20394536 CTTAATAATTATC
1 CTAAATAATTATC
20394549 CTAATATAATTA
1 CTAA-ATAATTA
20394561 AACATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (13 bp):
CTAAATAATTATC
Found at i:20397240 original size:43 final size:43
Alignment explanation
Indices: 20397165--20397281 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
20397155 ATCAGAACAA
* * *
20397165 TATACTGGCACACATAGTGCATCATCGAATATACCAAAGTAAT
1 TATACTGACACACATAGTGCATCATTGGATATACCAAAGTAAT
* * *
20397208 TATGCTGACACATATAGTGCATCATTGGATATACCGAAGTAAT
1 TATACTGACACACATAGTGCATCATTGGATATACCAAAGTAAT
* **
20397251 TATATTGGTACACATAGTGCATCATTGGATA
1 TATACTGACACACATAGTGCATCATTGGATA
20397282 AATCGAAGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (43 bp):
TATACTGACACACATAGTGCATCATTGGATATACCAAAGTAAT
Found at i:20397289 original size:43 final size:43
Alignment explanation
Indices: 20397095--20397289 Score: 151
Period size: 43 Copynumber: 4.6 Consensus size: 43
20397085 ATACACTCAC
* * * * * *
20397095 AGTGCATCATTGGACAAGCCGAAATAATTATACTGATACGCGT
1 AGTGCATCATTGGATAAACCGAAGTAATTATACTGACACACAT
* * ** * * *
20397138 AGTACATTATCAGATAAATCAGAA-CAA-TATACTGGCACACAT
1 AGTGCATCATTGGATAAA-CCGAAGTAATTATACTGACACACAT
* * * * * *
20397180 AGTGCATCATCGAATATACCAAAGTAATTATGCTGACACATAT
1 AGTGCATCATTGGATAAACCGAAGTAATTATACTGACACACAT
* * **
20397223 AGTGCATCATTGGATATACCGAAGTAATTATATTGGTACACAT
1 AGTGCATCATTGGATAAACCGAAGTAATTATACTGACACACAT
*
20397266 AGTGCATCATTGGATAAATCGAAG
1 AGTGCATCATTGGATAAACCGAAG
20397290 AATAGCCTGT
Statistics
Matches: 116, Mismatches: 33, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
41 3 0.03
42 26 0.22
43 83 0.72
44 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (43 bp):
AGTGCATCATTGGATAAACCGAAGTAATTATACTGACACACAT
Found at i:20401581 original size:16 final size:16
Alignment explanation
Indices: 20401560--20401615 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
20401550 AATTGAAAGC
20401560 AAATTAGAATTTTTTG
1 AAATTAGAATTTTTTG
* *
20401576 AAATTAAAATTTTTTT
1 AAATTAGAATTTTTTG
* * *
20401592 AATTTTAGAAATTTTAG
1 AA-ATTAGAATTTTTTG
20401609 AAATTAG
1 AAATTAG
20401616 TAACAAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
AAATTAGAATTTTTTG
Found at i:20401671 original size:16 final size:16
Alignment explanation
Indices: 20401640--20401673 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
20401630 ATCAATTTAG
20401640 AATTTAAAAATCATAA
1 AATTTAAAAATCATAA
20401656 AATTATAAAAAT-ATAA
1 AATT-TAAAAATCATAA
20401672 AA
1 AA
20401674 AAATTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTTAAAAATCATAA
Found at i:20406540 original size:22 final size:22
Alignment explanation
Indices: 20406514--20406580 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
20406504 ATATCTAAAT
*
20406514 AATAACAATAAAATAATAGCAA
1 AATAATAATAAAATAATAGCAA
* * * * *
20406536 TATAATAGTGAAATGATATCAA
1 AATAATAATAAAATAATAGCAA
*
20406558 AATAATAATAAAATAATAACAA
1 AATAATAATAAAATAATAGCAA
20406580 A
1 A
20406581 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (22 bp):
AATAATAATAAAATAATAGCAA
Found at i:20407750 original size:15 final size:15
Alignment explanation
Indices: 20407730--20407759 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20407720 CTAAAAACTA
*
20407730 AAATTTTATACTATT
1 AAATTTTATAATATT
20407745 AAATTTTATAATATT
1 AAATTTTATAATATT
20407760 CAAAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTTTATAATATT
Found at i:20414982 original size:21 final size:22
Alignment explanation
Indices: 20414947--20415006 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 22
20414937 ATATGGATTG
20414947 AAAAATAAT--TA-TTACACAT
1 AAAAATAATGATATTTACACAT
*
20414966 AAAAA-AATTATATTT--AC-T
1 AAAAATAATGATATTTACACAT
20414984 AAAAATAATGATATTTACA-AT
1 AAAAATAATGATATTTACACAT
20415005 AA
1 AA
20415007 TTATTTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 9 0.27
19 16 0.48
20 2 0.06
21 6 0.18
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAATAATGATATTTACACAT
Found at i:20415258 original size:75 final size:75
Alignment explanation
Indices: 20415135--20415287 Score: 297
Period size: 75 Copynumber: 2.0 Consensus size: 75
20415125 TGAAACAAAA
20415135 AACACATATTAATGCTTATAATAAGAGGAATTGAATCTAAGACTCAATGATGAAATCACAATTAT
1 AACACATATTAATGCTTATAATAAGAGGAATTGAATCTAAGACTCAATGATGAAATCACAATTAT
20415200 CTATCCATCT
66 CTATCCATCT
20415210 AACACATATTAATGCTTATAATAAGAGGAATTGAATCTAAGACTCAATGATGAAATCACAATTAT
1 AACACATATTAATGCTTATAATAAGAGGAATTGAATCTAAGACTCAATGATGAAATCACAATTAT
*
20415275 CTATCCATTT
66 CTATCCATCT
20415285 AAC
1 AAC
20415288 CAAAAGAGTT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (75 bp):
AACACATATTAATGCTTATAATAAGAGGAATTGAATCTAAGACTCAATGATGAAATCACAATTAT
CTATCCATCT
Found at i:20415865 original size:84 final size:83
Alignment explanation
Indices: 20415724--20415890 Score: 325
Period size: 84 Copynumber: 2.0 Consensus size: 83
20415714 ACTAAAATAA
20415724 AATTTAATTTAAGATCTAAGTTCTATCTTTTCCTTAGTTTCTTGACAACCAAACATAGAACAAAA
1 AATTTAATTTAAGATCTAAGTTCTATCTTTTCCTTAGTTTCTTGACAACCAAACATAGAAC-AAA
20415789 AAAAAATGAAGAAAGAAAT
65 AAAAAATGAAGAAAGAAAT
20415808 AATTTAATTTAAGATCTAAGTTCTATCTTTTCCTTAGTTTCTTGACAACCAAACATAGAACAAAA
1 AATTTAATTTAAGATCTAAGTTCTATCTTTTCCTTAGTTTCTTGACAACCAAACATAGAACAAAA
20415873 AAAAATGAAGAAAGAAAT
66 AAAAATGAAGAAAGAAAT
20415891 CTCAATATTA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 22 0.27
84 61 0.73
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (83 bp):
AATTTAATTTAAGATCTAAGTTCTATCTTTTCCTTAGTTTCTTGACAACCAAACATAGAACAAAA
AAAAATGAAGAAAGAAAT
Found at i:20416619 original size:28 final size:28
Alignment explanation
Indices: 20416579--20416634 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
20416569 CTCAATCAAA
20416579 ATTTGGGATTTAATTAATTTATTATTAT
1 ATTTGGGATTTAATTAATTTATTATTAT
20416607 ATTTGGGATTTAATTAATTTATTATTAT
1 ATTTGGGATTTAATTAATTTATTATTAT
20416635 TTTCCTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (28 bp):
ATTTGGGATTTAATTAATTTATTATTAT
Found at i:20417128 original size:3 final size:3
Alignment explanation
Indices: 20417114--20417153 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
20417104 AGGAATCATA
*
20417114 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20417154 TGAGACATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20427286 original size:3 final size:3
Alignment explanation
Indices: 20427265--20427306 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
20427255 AAGCGTAAAC
* * *
20427265 TAA TAA AAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20427307 CATTGGAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:20427366 original size:24 final size:25
Alignment explanation
Indices: 20427339--20427385 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
20427329 ACATAAGATT
*
20427339 AATAAAATATTAGA-ATGAAAATGA
1 AATAAAATATTAAATATGAAAATGA
20427363 AATAAAATATTAAATATGAAAAT
1 AATAAAATATTAAATATGAAAAT
20427386 ATATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (25 bp):
AATAAAATATTAAATATGAAAATGA
Found at i:20427427 original size:21 final size:22
Alignment explanation
Indices: 20427403--20427462 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
20427393 TGTATACACG
20427403 TACATAA-AA-AATATATACTAA
1 TACATAATAATAATA-ATACTAA
*
20427424 TACATAATAATAATAATAGTAA
1 TACATAATAATAATAATACTAA
*
20427446 TAC-TAATAATACTAATA
1 TACATAATAATAATAATA
20427463 ATATAAAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 20 0.57
22 11 0.31
23 4 0.11
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (22 bp):
TACATAATAATAATAATACTAA
Found at i:20427435 original size:3 final size:3
Alignment explanation
Indices: 20427421--20427465 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
20427411 AAATATATAC
* * *
20427421 TAA TACA TAA TAA TAA TAA TAG TAA TAC TAA TAA TAC TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20427466 TAAAGACAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20428624 original size:35 final size:35
Alignment explanation
Indices: 20428579--20428647 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
20428569 GGGTGTGTGA
20428579 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
20428614 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
20428648 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:20429283 original size:100 final size:99
Alignment explanation
Indices: 20429110--20429610 Score: 582
Period size: 99 Copynumber: 5.0 Consensus size: 99
20429100 TGCTTAGGGG
** * *
20429110 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTTGGGGGACAAGATTCGCCA
1 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCAGGGAACAAGATTCGCCG
* * * * *
20429175 TTGTAGCTTCAATTTGATCCACTGCA-TCACCAG-
66 TCGTAGCTTTAATCTGCTCCACTGCACT-GCCAGA
* * * * * * *
20429208 GAAAGTAAGATTCACCGTTGCGGTTTCAATCT-TTTAAATTGCAATATCAGGGAAGCAAGATTCA
1 G-AAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTT-AATTGCAATGTCAGGGAA-CAAGATTCG
*
20429272 CCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGA
63 CCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGA
* * *
20429309 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCTGGGAACAAGAGTCGCCA
1 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCAGGGAACAAGATTCGCCG
* * *
20429374 TTGTAGCTTCAATCTGATCCACTGCA-TCGCCAG-
66 TCGTAGCTTTAATCTGCTCCACTGCACT-GCCAGA
* * * * *
20429407 GAAAGTAAGATTTGCCGTTGCGGCTTCAATCT-TTTAAATTGCAATATCAGGGAAGCAAGATTCG
1 G-AAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTT-AATTGCAATGTCAGGGAA-CAAGATTCG
*
20429471 CCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGA
63 CCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGA
* *
20429508 GAAGTGAGATTCACCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCG
1 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCAGGGAACAAGATTCGCCG
* * *
20429573 TCGTAGCTTTAATTTGCTCCACTACACTGCCAGG
66 TCGTAGCTTTAATCTGCTCCACTGCACTGCCAGA
20429607 GAAG
1 GAAG
20429611 GTAACTTCAT
Statistics
Matches: 336, Mismatches: 54, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
98 9 0.03
99 163 0.49
100 154 0.46
101 10 0.03
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (99 bp):
GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCAGGGAACAAGATTCGCCG
TCGTAGCTTTAATCTGCTCCACTGCACTGCCAGA
Found at i:20429450 original size:199 final size:199
Alignment explanation
Indices: 20429110--20429595 Score: 830
Period size: 199 Copynumber: 2.4 Consensus size: 199
20429100 TGCTTAGGGG
*
20429110 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGT-TGGGGGACAAGATTCGCC
1 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCT-GGGAACAAGATTCGCC
*
20429174 ATTGTAGCTTCAATTTGATCCACTGCATCACCAGGAAAGTAAGATTCACCGTTGCGGTTTCAATC
65 ATTGTAGCTTCAATTTGATCCACTGCATCACCAGGAAAGTAAGATTCACCGTTGCGGCTTCAATC
20429239 TTTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGTACTG
130 TTTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGTACTG
20429304 CCAGA
195 CCAGA
*
20429309 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCTGGGAACAAGAGTCGCCA
1 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCTGGGAACAAGATTCGCCA
* * **
20429374 TTGTAGCTTCAATCTGATCCACTGCATCGCCAGGAAAGTAAGATTTGCCGTTGCGGCTTCAATCT
66 TTGTAGCTTCAATTTGATCCACTGCATCACCAGGAAAGTAAGATTCACCGTTGCGGCTTCAATCT
*
20429439 TTTAAATTGCAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGTACTGC
131 TTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGTACTGC
20429504 CAGA
196 CAGA
* * *
20429508 GAAGTGAGATTCACCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCG
1 GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCTGGGAACAAGATTCGCCA
* * *
20429573 TCGTAGCTTTAATTTGCTCCACT
66 TTGTAGCTTCAATTTGATCCACT
20429596 ACACTGCCAG
Statistics
Matches: 270, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
199 269 1.00
200 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (199 bp):
GAAGTGAGATTCGCCGTTGTGGCTTCGATCTCTTTAATTGCAATGTCTGGGAACAAGATTCGCCA
TTGTAGCTTCAATTTGATCCACTGCATCACCAGGAAAGTAAGATTCACCGTTGCGGCTTCAATCT
TTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGTACTGC
CAGA
Found at i:20429467 original size:50 final size:50
Alignment explanation
Indices: 20429116--20429573 Score: 205
Period size: 50 Copynumber: 9.2 Consensus size: 50
20429106 GGGGGAAGTG
* ** *
20429116 AGATTCGCCGTTGTGGCTTCGATCTCTTT-AATTGCAATGTTGGGGGA-CA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCAGGGAAGCA
* * * ** * ** * *
20429165 AGATTCGCCATTGTAGCTTCAAT-TTGATCCACTGC-ATCACCAGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTT-TTAAATTGCAAT-GTCAGGGAAGCA
* * * *
20429215 AGATTCACCGTTGCGGTTTCAATCTTTTAAATTGCAATATCAGGGAAGCA
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCA
* * * * ** ** * * * * * **
20429265 AGATTCACCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGAGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCA
* *
20429315 AGATTCGCCGTTGTGGCTTCGATCTCTTT-AATTGCAATGTCTGGGAA-CA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCAGGGAAGCA
* * * ** ** * * * *
20429364 AGAGTCGCCATTGTAGCTTCAATCTGATCCACTGC-ATCGCCAGGAAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAAT-GTCAGGGAAGCA
* * *
20429414 AGATTTGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCAGGGAAGCA
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCA
* * * ** ** * * * * * **
20429464 AGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGAGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCA
* * *
20429514 AGATTCACCGTTGTGGCTTCGATCTCTTT-AATTGCAATGTCGGGGAA-CA
1 AGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCAGGGAAGCA
20429563 AGATTCGCCGT
1 AGATTCGCCGT
20429574 CGTAGCTTTA
Statistics
Matches: 279, Mismatches: 118, Indels: 24
0.66 0.28 0.06
Matches are distributed among these distances:
47 1 0.00
48 7 0.03
49 68 0.24
50 195 0.70
51 8 0.03
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (50 bp):
AGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCA
Found at i:20429686 original size:41 final size:42
Alignment explanation
Indices: 20429631--20429731 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 42
20429621 TGATCTGTTT
* * * *
20429631 TCTTCGATCTACTTCACCAGTATGGGAAGACAATATCTGC-A
1 TCTTCGATCTACTTCACCAATATAGGAAGACAAGATCAGCTA
*
20429672 TCTTCGATCCACTTCTTACCAATATAGGAAGACAAGATCAGCTA
1 TCTTCGATCTACTTC--ACCAATATAGGAAGACAAGATCAGCTA
20429716 TCTTCGATCTACTTCA
1 TCTTCGATCTACTTCA
20429732 TTCCCCGGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
41 14 0.27
42 1 0.02
43 21 0.41
44 15 0.29
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (42 bp):
TCTTCGATCTACTTCACCAATATAGGAAGACAAGATCAGCTA
Found at i:20429846 original size:44 final size:44
Alignment explanation
Indices: 20429738--20430249 Score: 257
Period size: 44 Copynumber: 11.8 Consensus size: 44
20429728 TTCATTCCCC
* * * * * **
20429738 GGGAGAT-AGAACTACCAGCTTCAATGTACTCCACT-GTAATCA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
* * * * * * * *
20429780 GGGAGGTAAAATCCGCCGTCTTCGACCTGCTCCACTATTGCTTA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
** * * * *
20429824 GGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
* * * * * **
20429868 GGGAGAT-AGAACTACCAGCTTCAATGTACTCCACT-GTAATCA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
* * * * * * * *
20429910 GGGAGGTAAAATCCGCCGTCTTCGACCTGCTCCACTATTGCTTA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
** * * * *
20429954 GGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
* * * * * **
20429998 GGGAGAT-AGAACTACCAGCTTCAATGTACTCCACT-GTAATCA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
* * * * * * *
20430040 GGGAGGTAAAATCCGCCGTCTTCAACCTGCTCCACTATTGCTTA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
** * * * *
20430084 GGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
* * * * * **
20430128 GGGAGAT-AGAACTACCAGCTTCAATGTACTCCACT-GTAATCA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
* * * * * * *
20430170 GGGAGGTAAAATCCGCCGTCTTCAACCTGCTCCACTATTGCTTA
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
** *
20430214 GGGAGATAAGATCTGTAATCTTCAATCTATTCCACT
1 GGGAGATAAGATCTGCCATCTTCAATCTACTCCACT
20430250 GCCAAATACA
Statistics
Matches: 322, Mismatches: 140, Indels: 14
0.68 0.29 0.03
Matches are distributed among these distances:
42 33 0.10
43 134 0.42
44 155 0.48
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (44 bp):
GGGAGATAAGATCTGCCATCTTCAATCTACTCCACTATTGCTCA
Found at i:20429901 original size:130 final size:130
Alignment explanation
Indices: 20429738--20430326 Score: 1007
Period size: 130 Copynumber: 4.5 Consensus size: 130
20429728 TTCATTCCCC
20429738 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
20429803 GACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
66 GACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
20429868 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
20429933 GACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
66 GACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
20429998 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
*
20430063 AACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
66 GACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
20430128 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
* * *****
20430193 AACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAAATA
66 GACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTG--TTGCC
20430258 CA
129 CA
** * * * * * * *
20430260 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCTGGGAGGTAAACTCTGCCATCTTC
1 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
20430325 GA
66 GA
20430327 TCTTCAATCT
Statistics
Matches: 440, Mismatches: 17, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
130 381 0.87
132 59 0.13
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (130 bp):
GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
GACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTATTCCACTGTTGCCCA
Found at i:20430338 original size:95 final size:95
Alignment explanation
Indices: 20430231--20430521 Score: 521
Period size: 95 Copynumber: 3.0 Consensus size: 95
20430221 AAGATCTGTA
20430231 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
20430296 TAGTCTGGGAGGTAAACTCTGCCATCTTCG
66 TAGTCTGGGAGGTAAACTCTGCCATCTTCG
*
20430326 ATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
20430391 TAGTCTGGGAGGTAAACTCTGCCATCTTCG
66 TAGTCTGGGAGGTAAACTCTGCCATCTTCG
20430421 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
20430486 TAGTCACAT-GGAGGTAAAATCTGCCATCTTTG
66 TAGT--C-TGGGAGGTAAACTCTGCCATCTTCG
20430518 ATCT
1 ATCT
20430522 GCTTCGCTGC
Statistics
Matches: 189, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
95 162 0.86
97 26 0.14
98 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCTGGGAGGTAAACTCTGCCATCTTCG
Found at i:20430709 original size:97 final size:97
Alignment explanation
Indices: 20430550--20430915 Score: 648
Period size: 97 Copynumber: 3.8 Consensus size: 97
20430540 GGAAGGCAAG
* *
20430550 ATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATGGGCTTCAATGTAC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTAC
20430615 TCCACTGTAGTCACATGGAGGTAAAATCTGCC
66 TCCACTGTAGTCACATGGAGGTAAAATCTGCC
*
20430647 ATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTAC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTAC
20430712 TCCACTGTAGTCACATGGAGGTAAAATCTGCC
66 TCCACTGTAGTCACATGGAGGTAAAATCTGCC
*
20430744 ATCTTCGATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATC-GCTTCAATGTAC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTAC
*
20430808 TCCACTGTAGT--CAGGGAGGTAAAATCTGCC
66 TCCACTGTAGTCACATGGAGGTAAAATCTGCC
* *
20430838 ATCTTCGATCTTCAATCTATTCCACTGCCAAATACAGGAAGATAGAGTTATCGGCTTCAATGTAC
1 ATCTTCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTAC
20430903 TCCACTGTAGTCA
66 TCCACTGTAGTCA
20430916 GGAGTTATCG
Statistics
Matches: 259, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
94 69 0.27
95 23 0.09
96 23 0.09
97 144 0.56
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (97 bp):
ATCTTCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTAC
TCCACTGTAGTCACATGGAGGTAAAATCTGCC
Found at i:20430731 original size:233 final size:231
Alignment explanation
Indices: 20430326--20430754 Score: 770
Period size: 233 Copynumber: 1.8 Consensus size: 231
20430316 GCCATCTTCG
20430326 ATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* * *
20430391 TAGTCTGGGAGGTAAACTCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAAATACAGGGAGA
66 TAGTCTGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGGAGA
*
20430456 TAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTTGATC
131 TAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTCGATC
20430521 TGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCA
196 TGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCA
* *
20430557 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATGGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
20430622 TAGTCACAT-GGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGG
66 TAGT--C-TGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGG
20430686 AGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTCG
128 AGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTCG
20430751 ATCT
193 ATCT
20430755 TCAATCTATT
Statistics
Matches: 189, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
231 67 0.35
233 121 0.64
234 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (231 bp):
ATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCTGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGGAGA
TAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTCGATC
TGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCA
Found at i:20430884 original size:191 final size:193
Alignment explanation
Indices: 20430557--20430915 Score: 650
Period size: 191 Copynumber: 1.9 Consensus size: 193
20430547 AAGATCTGCA
*
20430557 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATGGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATGCGCTTCAATGTACTCCACTG
* *
20430622 TAGTCACATGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGGA
66 TAGT-ACAGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGAA
20430687 GATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTCG
130 GATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTCG
20430751 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-CGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATGCGCTTCAATGTACTCCACTG
* *
20430815 TAGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAAATACAGGAAG
66 TAGTACAGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGAAG
20430879 ATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCA
131 ATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCA
20430916 GGAGTTATCG
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
191 93 0.58
193 23 0.14
194 44 0.28
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (193 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATGCGCTTCAATGTACTCCACTG
TAGTACAGGGAGGTAAAATCTGCCATCTTCAATCTTCAATCTATTCCACTACCAAATACAGGAAG
ATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTCG
Found at i:20430928 original size:35 final size:35
Alignment explanation
Indices: 20430882--20430952 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
20430872 CAGGAAGATA
20430882 GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
1 GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
20430917 GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
1 GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
20430952 G
1 G
20430953 GAGGTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (35 bp):
GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
Found at i:20431029 original size:130 final size:129
Alignment explanation
Indices: 20430788--20431045 Score: 480
Period size: 130 Copynumber: 2.0 Consensus size: 129
20430778 CAGGGAGATA
*
20430788 GAGTTATCGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTTCAA
1 GAGTTATCGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTACCATCTTCGATCTTCAA
*
20430853 TCTATTCCACTGCCAAATACAGGAAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
66 TCTATTCCACTACCAAATACAGGAAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
20430917 GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTACCATCTTCGATCTTCA
1 GAGTTATC-GCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTACCATCTTCGATCTTCA
*
20430982 ATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCA
65 ATCTATTCCACTACCAAATACAGGAAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCA
20431046 CATGGAGGTA
Statistics
Matches: 125, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
129 8 0.06
130 117 0.94
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (129 bp):
GAGTTATCGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTACCATCTTCGATCTTCAA
TCTATTCCACTACCAAATACAGGAAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
Found at i:20431211 original size:82 final size:84
Alignment explanation
Indices: 20431066--20431238 Score: 235
Period size: 82 Copynumber: 2.0 Consensus size: 84
20431056 AAATCTTCCA
*
20431066 TCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCTATATTCAACCTACCCTGCTA
1 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCTATATTCAACCTACCCTGCTA
20431131 CAAAC-GAGGCAAGGTTTG
66 CAAACAGAGGCAAGGTTTG
* * * * *
20431149 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATTTGCTATCTTCAA-CTAGCTCTGCT
1 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCTATATTCAACCTA-CCCTGCT
20431212 ACAAACGAGAGAGGCAAGGTTTG
65 ACAAAC---AGAGGCAAGGTTTG
20431235 TCTT
1 TCTT
20431239 TGATTTTTAC
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
81 3 0.04
82 40 0.51
83 19 0.24
86 17 0.22
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (84 bp):
TCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCTATATTCAACCTACCCTGCTA
CAAACAGAGGCAAGGTTTG
Found at i:20432902 original size:23 final size:21
Alignment explanation
Indices: 20432855--20432904 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
20432845 TGCTATAGAT
*
20432855 AAATCAAAGAAAACAGAAATG
1 AAATCAAAGAAAACAGAAATC
20432876 AAATCGAAAGAAAA-ATGAGAATC
1 AAATC-AAAGAAAACA-GA-AATC
20432899 AAATCA
1 AAATCA
20432905 CCTTGTGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.24
22 11 0.44
23 8 0.32
ACGTcount: A:0.64, C:0.10, G:0.14, T:0.12
Consensus pattern (21 bp):
AAATCAAAGAAAACAGAAATC
Found at i:20433190 original size:35 final size:35
Alignment explanation
Indices: 20433145--20433213 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
20433135 GGGTGTGTGA
20433145 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
20433180 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
20433214 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:20436021 original size:16 final size:17
Alignment explanation
Indices: 20435987--20436021 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20435977 TTAGGTTTTT
*
20435987 TTAAAAAAAATTTATAA
1 TTAAAAAAAATATATAA
20436004 TTAAAAAAAATATA-AA
1 TTAAAAAAAATATATAA
20436020 TT
1 TT
20436022 TTAGAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAAAAATATATAA
Found at i:20436037 original size:18 final size:19
Alignment explanation
Indices: 20436014--20436054 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20436004 TTAAAAAAAA
20436014 TATAAAT-TTTAGAACTTT
1 TATAAATATTTAGAACTTT
* *
20436032 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAACTTT
20436051 TATA
1 TATA
20436055 GAGTTACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAACTTT
Found at i:20448222 original size:26 final size:26
Alignment explanation
Indices: 20448186--20448236 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
20448176 ACAGAGGCTT
20448186 AGTTGTGACCACAC-GTTCATAAACTC
1 AGTTGTGACCACACAG-TCATAAACTC
20448212 AGTTGTGACCACACAGTCATAAACT
1 AGTTGTGACCACACAGTCATAAACT
20448237 TTGTTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (26 bp):
AGTTGTGACCACACAGTCATAAACTC
Found at i:20452782 original size:11 final size:11
Alignment explanation
Indices: 20452768--20452817 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
20452758 TAAATATTAA
20452768 TTTATTAATAT
1 TTTATTAATAT
*
20452779 TTTAATAATAT
1 TTTATTAATAT
*
20452790 TTT-TTATTAT
1 TTTATTAATAT
*
20452800 TTTATTATTA-
1 TTTATTAATAT
20452810 TTTATTAA
1 TTTATTAA
20452818 GTATAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 15 0.44
11 19 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:20452800 original size:21 final size:21
Alignment explanation
Indices: 20452767--20452817 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
20452757 ATAAATATTA
20452767 ATTTATTAATATTTTAATAAT
1 ATTTATTAATATTTTAATAAT
* * * *
20452788 ATTTTTTATTATTTTATTATT
1 ATTTATTAATATTTTAATAAT
20452809 ATTTATTAA
1 ATTTATTAA
20452818 GTATAAAAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTATTAATATTTTAATAAT
Found at i:20454100 original size:51 final size:51
Alignment explanation
Indices: 20454024--20454138 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
20454014 AGTTATCTGA
*
20454024 ATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAATTCCGG
1 ATGAAATATGAAGCTCTTATTGAAGCTAGAGCAACAAAGTAATAATTCCGG
* **
20454075 ATGAAATATGAAGCTCTTATTGAAGCTAGAGCAACAAGGTAATAATTTTGG
1 ATGAAATATGAAGCTCTTATTGAAGCTAGAGCAACAAAGTAATAATTCCGG
20454126 AT-AAAGTATGAAG
1 ATGAAA-TATGAAG
20454139 TAAGCTTGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 3 0.05
51 56 0.95
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (51 bp):
ATGAAATATGAAGCTCTTATTGAAGCTAGAGCAACAAAGTAATAATTCCGG
Found at i:20460286 original size:17 final size:17
Alignment explanation
Indices: 20460250--20460288 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20460240 TGATTTTGCG
*
20460250 TCTGTATTTGTAATGCA
1 TCTGTATTTGTAATGAA
20460267 TCTGTATTTGTAACT-AA
1 TCTGTATTTGTAA-TGAA
20460284 TCTGT
1 TCTGT
20460289 CTGTCATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (17 bp):
TCTGTATTTGTAATGAA
Found at i:20461615 original size:56 final size:56
Alignment explanation
Indices: 20461521--20461666 Score: 213
Period size: 56 Copynumber: 2.6 Consensus size: 56
20461511 GTAGTCACAC
*
20461521 AGGAATCAAATTGCTAAAAGATAATATCCC-TCAGTAATATAATATAATATCCCATT
1 AGGAATCAAATTGCTAAAAGATAATATCCCAT-AATAATATAATATAATATCCCATT
* ** *
20461577 AGGAATCAAATTGCTAAGAGATAATATCCCATAATAATATCCTATAATATCTCATT
1 AGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATAATATAATATCCCATT
* *
20461633 AGGAATTAAATTGCAAAAAGATAATATCCCATAA
1 AGGAATCAAATTGCTAAAAGATAATATCCCATAA
20461667 CCTCAAGTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
56 80 0.99
57 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (56 bp):
AGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATAATATAATATCCCATT
Found at i:20465913 original size:52 final size:48
Alignment explanation
Indices: 20465851--20466025 Score: 187
Period size: 47 Copynumber: 3.6 Consensus size: 48
20465841 GAAATGTGAT
* *
20465851 TTCCGTATAAGACCATAGT-TGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATA-TCTGGGATATGGCATC-GAG---TGTGATATGTGC
*
20465903 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATATCTGGGATATGGCATCGAGTGTGATATGTGC
* *
20465950 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATATCTGGGATATGGCATCGAGTGTGATATGTGC
* * ** *
20465996 ATCCGTGTAAGACCATGGCTGGGCTATGGC
1 TTCCGTATAAGACCATATCTGGGATATGGC
20466026 CTCGGTATGT
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
46 23 0.21
47 54 0.50
50 1 0.01
51 2 0.02
52 28 0.26
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (48 bp):
TTCCGTATAAGACCATATCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:20466429 original size:24 final size:22
Alignment explanation
Indices: 20466386--20466429 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
20466376 ATAAATTGTG
* *
20466386 AAAATTGAGTTAAGGGCTGAAT
1 AAAATTGAGTTAAAGCCTGAAT
20466408 AAAATATGAGATTAAAGCCTGA
1 AAAAT-TGAG-TTAAAGCCTGA
20466430 TGAGTCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 4 0.22
24 9 0.50
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (22 bp):
AAAATTGAGTTAAAGCCTGAAT
Found at i:20471984 original size:17 final size:17
Alignment explanation
Indices: 20471948--20471987 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20471938 ATTATATAAG
* *
20471948 TATATTATTAAATTATA
1 TATATTATTAAATGAAA
*
20471965 TATATTATTAAGTGAAA
1 TATATTATTAAATGAAA
20471982 TATATT
1 TATATT
20471988 TATATAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TATATTATTAAATGAAA
Found at i:20473127 original size:15 final size:16
Alignment explanation
Indices: 20473092--20473129 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20473082 AGTCCCATTA
*
20473092 TATTTAAAAATTTATT
1 TATTTTAAAATTTATT
*
20473108 TATTTTAAACTTTA-T
1 TATTTTAAAATTTATT
20473123 TATTTTA
1 TATTTTA
20473130 TATTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTAAAATTTATT
Found at i:20473798 original size:22 final size:23
Alignment explanation
Indices: 20473773--20473817 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
20473763 CACTACTTTT
20473773 CTTAT-ATACTAAGTTAT-TATAC
1 CTTATAATA-TAAGTTATATATAC
*
20473795 CTTATAATATAATTTATATATAC
1 CTTATAATATAAGTTATATATAC
20473818 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (23 bp):
CTTATAATATAAGTTATATATAC
Found at i:20496184 original size:3 final size:3
Alignment explanation
Indices: 20496176--20496214 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20496166 TATTCCAATG
20496176 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20496215 GTTTATGCGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20499327 original size:17 final size:18
Alignment explanation
Indices: 20499307--20499503 Score: 65
Period size: 17 Copynumber: 11.1 Consensus size: 18
20499297 CTCGTATTTC
20499307 AAAAATTTC-CGTGCTTT
1 AAAAATTTCTCGTGCTTT
* * *
20499324 AAAAAAAATCCTCGTGTTTT
1 --AAAAATTTCTCGTGCTTT
*
20499344 AAAAATTTC-CGTGTTTT
1 AAAAATTTCTCGTGCTTT
* * * *
20499361 AAAATTTTCGCGTTC-TC
1 AAAAATTTCTCGTGCTTT
20499378 AAAAATTTCTCGTG-TTT
1 AAAAATTTCTCGTGCTTT
* *
20499395 CAAAAAAATTGTCGTG-TTT
1 --AAAAATTTCTCGTGCTTT
** *
20499414 CGCAAATTT-TCGTGTTTT
1 -AAAAATTTCTCGTGCTTT
* *
20499432 TAAAA-TTCTCGT-ATTT
1 AAAAATTTCTCGTGCTTT
* *
20499448 CAAAAGTTTC-CGTGTTTT
1 -AAAAATTTCTCGTGCTTT
20499466 AAAAAAATTTCTCGTG-TTT
1 --AAAAATTTCTCGTGCTTT
* *
20499485 CACAAATTTC-CGTGTTTT
1 -AAAAATTTCTCGTGCTTT
20499503 A
1 A
20499504 TTTTGTGTTC
Statistics
Matches: 136, Mismatches: 29, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
16 5 0.04
17 52 0.38
18 35 0.26
19 33 0.24
20 11 0.08
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (18 bp):
AAAAATTTCTCGTGCTTT
Found at i:20499384 original size:18 final size:18
Alignment explanation
Indices: 20499303--20499494 Score: 65
Period size: 19 Copynumber: 10.7 Consensus size: 18
20499293 AATTCTCGTA
*
20499303 TTTCAAAAATTTC-CGTG
1 TTTCAAAAATTTCTCGCG
* * * *
20499320 CTTTAAAAAAAATCCTCGTG
1 -TTT-CAAAAATTTCTCGCG
* *
20499340 TTTTAAAAATTTC-CGTG
1 TTTCAAAAATTTCTCGCG
*
20499357 TTT-TAAAATTT-TCGCG
1 TTTCAAAAATTTCTCGCG
*
20499373 TTCTCAAAAATTTCTCGTG
1 TT-TCAAAAATTTCTCGCG
* * *
20499392 TTTCAAAAAAATTGTCGTG
1 TTTC-AAAAATTTCTCGCG
** *
20499411 TTTCGCAAATTT-TCGTG
1 TTTCAAAAATTTCTCGCG
** **
20499428 TTTTTAAAA-TTCTCGTA
1 TTTCAAAAATTTCTCGCG
* *
20499445 TTTCAAAAGTTTC-CGTG
1 TTTCAAAAATTTCTCGCG
* *
20499462 TTTTAAAAAAATTTCTCGTG
1 -TTT-CAAAAATTTCTCGCG
*
20499482 TTTCACAAATTTC
1 TTTCAAAAATTTC
20499495 CGTGTTTTAT
Statistics
Matches: 135, Mismatches: 27, Indels: 24
0.73 0.15 0.13
Matches are distributed among these distances:
16 14 0.10
17 32 0.24
18 38 0.28
19 43 0.32
20 8 0.06
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTCAAAAATTTCTCGCG
Found at i:20499402 original size:71 final size:70
Alignment explanation
Indices: 20499288--20499577 Score: 265
Period size: 71 Copynumber: 4.2 Consensus size: 70
20499278 TTTCATGTTC
* * * * * *
20499288 TTTT-AAATTCTCGTATT-TCAAAAATTTCCGTGCTTTAAAAAAAATCCTCGTGTTTTAAAAATT
1 TTTTAAAATTTTCGTGTTCTCAAAAATTTCCGTG-TTTCAAAAAAATTCTCGTGTTTCACAAATT
20499351 TCCGTG
65 TCCGTG
* * *
20499357 TTTTAAAATTTTCGCGTTCTCAAAAATTTCTCGTGTTTCAAAAAAATTGTCGTGTTTCGCAAATT
1 TTTTAAAATTTTCGTGTTCTCAAAAATTTC-CGTGTTTCAAAAAAATTCTCGTGTTTCACAAATT
*
20499422 TTCGTG
65 TCCGTG
* * * *
20499428 TTTTTAAAATTCTCGTATT-TCAAAAGTTTCCGTGTTTTAAAAAAATTTCTCGTGTTTCACAAAT
1 -TTTTAAAATTTTCGTGTTCTCAAAAATTTCCGTGTTTCAAAAAAA-TTCTCGTGTTTCACAAAT
20499492 TTCCGTG
64 TTCCGTG
* * * * *
20499499 TTTT---ATTTT-GTGTTCTCAAAAAATTCTCGTGTTTC--GAAAATTGTCATGTTTCGCAAATT
1 TTTTAAAATTTTCGTGTTCTCAAAAATTTC-CGTGTTTCAAAAAAATTCTCGTGTTTCACAAATT
* *
20499558 TTCGTA
65 TCCGTG
*
20499564 TTGTAAAAATTTTC
1 TT-TTAAAATTTTC
20499578 AGGTTTTTTA
Statistics
Matches: 179, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
65 22 0.12
66 9 0.05
67 13 0.07
68 7 0.04
69 9 0.05
70 28 0.16
71 72 0.40
72 19 0.11
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (70 bp):
TTTTAAAATTTTCGTGTTCTCAAAAATTTCCGTGTTTCAAAAAAATTCTCGTGTTTCACAAATTT
CCGTG
Found at i:20499529 original size:119 final size:120
Alignment explanation
Indices: 20499389--20499622 Score: 280
Period size: 119 Copynumber: 2.0 Consensus size: 120
20499379 AAAATTTCTC
* * * * ** *
20499389 GTGTTTCAAAAAAATTGTCGTGTTTCGCAAATTTTCGTGTTTTTAAAATTCTCGTATT-TCAAAA
1 GTGTTTCAAAAAAATTCTCGTGTTTCGAAAATTGTCATGTTTCGAAAATTCTCGTATTGTAAAAA
*
20499453 GTTTC-CGTGTTTTAAAAAAATTTCTCGTGTTTC-ACAAATT-TCCGTGTTTTATTTT
66 GTTTCACGTGTTTTAAAAAAAATT-TCGTGTTTCTA-AAATTCT-CGTGTTTTATTTT
* *
20499508 GTGTTCTC-AAAAAATTCTCGTGTTTCGAAAATTGTCATGTTTCGCAAATTTTCGTATTGTAAAA
1 GTGTT-TCAAAAAAATTCTCGTGTTTCGAAAATTGTCATGTTTCGAAAATTCTCGTATTGTAAAA
* * *
20499572 ATTTTCAGGTTTTTTAAAAAAAATTTCGTGTTTCTAAAATTCTCGTGTTTT
65 AGTTTCACGTGTTTTAAAAAAAATTTCGTGTTTCTAAAATTCTCGTGTTTT
20499623 CAAAAAAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
119 47 0.48
120 33 0.34
121 17 0.18
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (120 bp):
GTGTTTCAAAAAAATTCTCGTGTTTCGAAAATTGTCATGTTTCGAAAATTCTCGTATTGTAAAAA
GTTTCACGTGTTTTAAAAAAAATTTCGTGTTTCTAAAATTCTCGTGTTTTATTTT
Found at i:20499540 original size:17 final size:17
Alignment explanation
Indices: 20499518--20499562 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
20499508 GTGTTCTCAA
20499518 AAAATTCTCGTGTTTCG
1 AAAATTCTCGTGTTTCG
* *
20499535 AAAATTGTCATGTTTCG
1 AAAATTCTCGTGTTTCG
* *
20499552 CAAATTTTCGT
1 AAAATTCTCGT
20499563 ATTGTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (17 bp):
AAAATTCTCGTGTTTCG
Found at i:20499627 original size:17 final size:17
Alignment explanation
Indices: 20499590--20499681 Score: 75
Period size: 18 Copynumber: 5.2 Consensus size: 17
20499580 GTTTTTTAAA
20499590 AAAAATTTCGTG-TTTC
1 AAAAATTTCGTGTTTTC
*
20499606 TAAAATTCTCGTGTTTTC
1 AAAAATT-TCGTGTTTTC
*
20499624 AAAAAAAATTTCGCGTTTTC
1 ---AAAAATTTCGTGTTTTC
20499644 AAAAAATATT-GTG-TTTC
1 -AAAAAT-TTCGTGTTTTC
20499661 -AAAATTCTCGTGTTTTC
1 AAAAATT-TCGTGTTTTC
20499678 AAAA
1 AAAA
20499682 CAAGAGATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.02
15 6 0.10
16 9 0.15
17 13 0.21
18 16 0.26
19 2 0.03
20 9 0.15
21 6 0.10
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:20499641 original size:20 final size:21
Alignment explanation
Indices: 20499607--20499649 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
20499597 TCGTGTTTCT
*
20499607 AAAATTCTCGTGTTTTCAAAA
1 AAAATTCTCGCGTTTTCAAAA
20499628 AAAATT-TCGCGTTTTCAAAA
1 AAAATTCTCGCGTTTTCAAAA
20499648 AA
1 AA
20499650 TATTGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (21 bp):
AAAATTCTCGCGTTTTCAAAA
Found at i:20499661 original size:37 final size:37
Alignment explanation
Indices: 20499582--20499664 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
20499572 ATTTTCAGGT
* * * * *
20499582 TTTTTAAAAAAAATTTCGTGTTTCTAAAATTCTCGTG
1 TTTTCAAAAAAAATTTCGCGTTTCAAAAAATATCGTG
*
20499619 TTTTCAAAAAAAATTTCGCGTTTTCAAAAAATATTGTG
1 TTTTCAAAAAAAATTTCGCG-TTTCAAAAAATATCGTG
20499657 -TTTCAAAA
1 TTTTCAAAA
20499665 TTCTCGTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 26 0.67
38 13 0.33
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (37 bp):
TTTTCAAAAAAAATTTCGCGTTTCAAAAAATATCGTG
Found at i:20501282 original size:30 final size:31
Alignment explanation
Indices: 20501214--20501272 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
20501204 CACCCTTAAA
**
20501214 ATATTTACACTATTAGTCCTTCAACTTTTTC
1 ATATTTACACTATTAACCCTTCAACTTTTTC
20501245 ATATTTACACT-TTAACCCTTCAACTTTT
1 ATATTTACACTATTAACCCTTCAACTTTT
20501273 GAGTATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.47
Consensus pattern (31 bp):
ATATTTACACTATTAACCCTTCAACTTTTTC
Found at i:20502023 original size:25 final size:25
Alignment explanation
Indices: 20501995--20502044 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20501985 ATAACTTTGG
20501995 TTGAAATGATAAAATTGATTTTACT
1 TTGAAATGATAAAATTGATTTTACT
20502020 TTGAAATGATAAAATTGATTTTACT
1 TTGAAATGATAAAATTGATTTTACT
20502045 AAAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (25 bp):
TTGAAATGATAAAATTGATTTTACT
Found at i:20502055 original size:24 final size:25
Alignment explanation
Indices: 20501998--20502055 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
20501988 ACTTTGGTTG
**
20501998 AAATGATAAAATTGATTTTACTTTG
1 AAATGATAAAATTGATTTTACTTAA
20502023 AAATGATAAAATTGATTTTAC-TAA
1 AAATGATAAAATTGATTTTACTTAA
*
20502047 AAATAATAA
1 AAATGATAA
20502056 TATTTTGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (25 bp):
AAATGATAAAATTGATTTTACTTAA
Found at i:20502404 original size:6 final size:6
Alignment explanation
Indices: 20502380--20502423 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
20502370 TGCCTTCTTC
* * *
20502380 TCCCCTT TCCCCT TTCCCT TCCCCT TCCCTT TTCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
20502424 GGATTGCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TCCCCT
Found at i:20502407 original size:18 final size:18
Alignment explanation
Indices: 20502380--20502423 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
20502370 TGCCTTCTTC
20502380 TCCCCTTTCCCCTTTCCCT
1 TCCCC-TTCCCCTTTCCCT
*
20502399 TCCCCTTCCCTTTTCCCT
1 TCCCCTTCCCCTTTCCCT
20502417 TCCCCTT
1 TCCCCTT
20502424 GGATTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCCCTTCCCCTTTCCCT
Found at i:20502517 original size:25 final size:25
Alignment explanation
Indices: 20502483--20502532 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
20502473 CAGGTAAGGC
20502483 TCCTTCTTCTTCTTCCGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* * *
20502508 TCCTTTTTCTTTTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
20502533 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:20506162 original size:22 final size:20
Alignment explanation
Indices: 20506119--20506157 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20506109 TAATTTAAAA
20506119 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
20506139 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
20506158 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:20506286 original size:20 final size:20
Alignment explanation
Indices: 20506257--20506295 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20506247 ATATTTTCCA
*
20506257 GTAAATCATTTTACAGAAAG
1 GTAAAACATTTTACAGAAAG
*
20506277 GTAAAACATTTTCCAGAAA
1 GTAAAACATTTTACAGAAA
20506296 TCATTTTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (20 bp):
GTAAAACATTTTACAGAAAG
Found at i:20506301 original size:34 final size:35
Alignment explanation
Indices: 20506244--20506309 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
20506234 CAAACACCAA
*
20506244 AAAATATTTTCCAGTAAATCATTTTACAGAAAGGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAGGT
*
20506279 AAAACATTTTCCAG-AAATCATTTTACGGAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAA
20506310 ACATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAGGT
Found at i:20506302 original size:14 final size:14
Alignment explanation
Indices: 20506279--20506318 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20506269 ACAGAAAGGT
*
20506279 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
20506293 AAATCATTTTACGG
1 AAAACATTTTACAG
20506307 AAAACATTTTAC
1 AAAACATTTTAC
20506319 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:20508202 original size:23 final size:22
Alignment explanation
Indices: 20508176--20508229 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
20508166 TGTATACGCG
20508176 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
20508199 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
20508221 TAC-TAATAA
1 TACATAATAA
20508230 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:20508210 original size:3 final size:3
Alignment explanation
Indices: 20508179--20508247 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
20508169 ATACGCGTAC
* * * *
20508179 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
20508226 ATA ATA CTA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
20508248 CAAGGATATT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20508730 original size:11 final size:12
Alignment explanation
Indices: 20508710--20508747 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
20508700 AAAGAAAAAA
20508710 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
20508723 GAAGAGAGAAGG
1 GAAGAGAGAAGG
20508735 G-AGAGAGAAGG
1 GAAGAGAGAAGG
20508746 GA
1 GA
20508748 GGGGGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 4 0.17
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:20509179 original size:54 final size:54
Alignment explanation
Indices: 20509108--20509224 Score: 225
Period size: 54 Copynumber: 2.2 Consensus size: 54
20509098 AAAATAAAAA
*
20509108 AAAATCCCCCTTAAATACAACCGATTCTTCCCTTTGAAATCTCCAAAAAACATC
1 AAAATCCCCCTCAAATACAACCGATTCTTCCCTTTGAAATCTCCAAAAAACATC
20509162 AAAATCCCCCTCAAATACAACCGATTCTTCCCTTTGAAATCTCCAAAAAACATC
1 AAAATCCCCCTCAAATACAACCGATTCTTCCCTTTGAAATCTCCAAAAAACATC
20509216 AAAATCCCC
1 AAAATCCCC
20509225 TCCCAGTTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.39, C:0.33, G:0.03, T:0.24
Consensus pattern (54 bp):
AAAATCCCCCTCAAATACAACCGATTCTTCCCTTTGAAATCTCCAAAAAACATC
Found at i:20514581 original size:17 final size:17
Alignment explanation
Indices: 20514559--20514592 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20514549 ATCCACTAAT
*
20514559 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
20514576 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
20514593 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:20519220 original size:17 final size:17
Alignment explanation
Indices: 20519198--20519231 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20519188 ATCCACTAAT
*
20519198 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
20519215 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
20519232 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:20519317 original size:21 final size:19
Alignment explanation
Indices: 20519292--20519331 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
20519282 TTCACTCTTT
*
20519292 TTTCTTGATTGTTATTTTTTC
1 TTTCTTAATT-TT-TTTTTTC
20519313 TTTCTTAATTTTTTTTTTC
1 TTTCTTAATTTTTTTTTTC
20519332 AATTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTCTTAATTTTTTTTTTC
Found at i:20524317 original size:35 final size:35
Alignment explanation
Indices: 20524267--20524337 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
20524257 TTTTAGGGGG
*
20524267 GTCGAGGCCCTTGCCTATTCCTTGGCTCCGCCACT
1 GTCGAGGCCCCTGCCTATTCCTTGGCTCCGCCACT
20524302 GTCGAGGCCCCTGCCTATTCCTTGGCTCCGCCACT
1 GTCGAGGCCCCTGCCTATTCCTTGGCTCCGCCACT
20524337 G
1 G
20524338 ATCTTAATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.08, C:0.41, G:0.24, T:0.27
Consensus pattern (35 bp):
GTCGAGGCCCCTGCCTATTCCTTGGCTCCGCCACT
Found at i:20533224 original size:36 final size:36
Alignment explanation
Indices: 20533177--20533251 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
20533167 ATTTATTTAC
20533177 TAAGATAAATTAATTTACATTTTAATTTAATAGAAA
1 TAAGATAAATTAATTTACATTTTAATTTAATAGAAA
20533213 TAAGATAAATTAATTTACATTTTAATTTAATAGAAA
1 TAAGATAAATTAATTTACATTTTAATTTAATAGAAA
20533249 TAA
1 TAA
20533252 CACATTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (36 bp):
TAAGATAAATTAATTTACATTTTAATTTAATAGAAA
Found at i:20537201 original size:21 final size:22
Alignment explanation
Indices: 20537172--20537218 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
20537162 CAGAAGGAGT
*
20537172 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
20537194 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
20537215 GAGT
1 GAGT
20537219 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:20543480 original size:25 final size:28
Alignment explanation
Indices: 20543452--20543516 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
20543442 TATATTCCCT
*
20543452 CAAAACATA-TT-ATA-TATAAATATAC
1 CAAAACATATTTAATAGCATAAATATAC
20543477 CAAAACATTATTTGAATAGCATAAATATAC
1 CAAAACA-TATTT-AATAGCATAAATATAC
20543507 CAAAAGCATA
1 CAAAA-CATA
20543517 ATTCAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 7 0.21
26 2 0.06
27 2 0.06
29 3 0.09
30 17 0.52
31 2 0.06
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.28
Consensus pattern (28 bp):
CAAAACATATTTAATAGCATAAATATAC
Found at i:20544550 original size:25 final size:26
Alignment explanation
Indices: 20544498--20544550 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
20544488 TTGAGTTAAT
20544498 AAATTCCTTTTATGTTTTCTTTTCAG
1 AAATTCCTTTTATGTTTTCTTTTCAG
*
20544524 AAATTCCTTTTGA-G-TTTCTTTTTAG
1 AAATTCCTTTT-ATGTTTTCTTTTCAG
20544549 AA
1 AA
20544551 GAGTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 12 0.48
26 12 0.48
27 1 0.04
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (26 bp):
AAATTCCTTTTATGTTTTCTTTTCAG
Found at i:20547746 original size:34 final size:35
Alignment explanation
Indices: 20547682--20547747 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
20547672 TTAACAGTTG
** *
20547682 AATTTGCATCTTTGATGAGCTCTTATCTTTGATTA
1 AATTTGCATCTTTGATGAGCTCGCACCTTTGATTA
*
20547717 AATTTGCGTC-TTGATGAGCTCGCACCTTTGA
1 AATTTGCATCTTTGATGAGCTCGCACCTTTGA
20547748 ATTAGCTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 18 0.67
35 9 0.33
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (35 bp):
AATTTGCATCTTTGATGAGCTCGCACCTTTGATTA
Found at i:20571318 original size:16 final size:16
Alignment explanation
Indices: 20571282--20571327 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
20571272 TTAATTCGCC
* *
20571282 GTAATGGAATAGAGGT
1 GTAATGGAATAAAGCT
*
20571298 CTAATGGAATAAAGCT
1 GTAATGGAATAAAGCT
*
20571314 GTAATAGAATAAAG
1 GTAATGGAATAAAG
20571328 GCGTAATAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.26, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAAAGCT
Found at i:20571333 original size:16 final size:16
Alignment explanation
Indices: 20571281--20571336 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
20571271 TTTAATTCGC
* *
20571281 CGTAATGGAATAGAGG
1 CGTAATAGAATAAAGG
*
20571297 TC-TAATGGAATAAA-G
1 -CGTAATAGAATAAAGG
20571312 CTGTAATAGAATAAAGG
1 C-GTAATAGAATAAAGG
20571329 CGTAATAG
1 CGTAATAG
20571337 TAATTCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 1 0.03
16 29 0.85
17 3 0.09
ACGTcount: A:0.43, C:0.07, G:0.27, T:0.23
Consensus pattern (16 bp):
CGTAATAGAATAAAGG
Found at i:20571617 original size:19 final size:18
Alignment explanation
Indices: 20571568--20571603 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20571558 TTATTATTAA
20571568 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
20571586 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
20571604 CTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:20571737 original size:19 final size:18
Alignment explanation
Indices: 20571688--20571723 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20571678 TTATTATTAA
20571688 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
20571706 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
20571724 CTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:20571921 original size:13 final size:12
Alignment explanation
Indices: 20571897--20571937 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
20571887 TATAATACTA
20571897 TAAAATATAATT
1 TAAAATATAATT
20571909 TAAAATAATAATT
1 TAAAAT-ATAATT
*
20571922 ATTAAATATAATT
1 -TAAAATATAATT
20571935 TAA
1 TAA
20571938 TAAAATTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:20571929 original size:119 final size:120
Alignment explanation
Indices: 20571548--20571942 Score: 729
Period size: 120 Copynumber: 3.3 Consensus size: 120
20571538 TTAATCATAT
*
20571548 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAATCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAATCTTAATATT
*
20571613 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATCTATAATACTATAAAATATAA
20571668 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAATCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAATCTTAATATT
20571733 AAATATTCTTATATGAATTTACTAAAATCATAATCTATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATCTATAATACTATAAAATATAA
* *
20571788 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTACTA-T
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAATCTTAATATT
*
20571852 AATTATTCTTATATGAATTTACTAAAATCATAATCTATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATCTATAATACTATAAAATATAA
*
20571907 TTTAAAATAATAATTATTAAATATAATTTAATAAAA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAA
20571943 TTCTTAATAT
Statistics
Matches: 269, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
119 90 0.33
120 179 0.67
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAATCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATCTATAATACTATAAAATATAA
Found at i:20571930 original size:26 final size:23
Alignment explanation
Indices: 20571899--20571956 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 23
20571889 TAATACTATA
20571899 AAATATAATTTAAAATAATAATTATT
1 AAATATAATTT--AATAA-AATTATT
*
20571925 AAATATAATTTAATAAAATTCTT
1 AAATATAATTTAATAAAATTATT
20571948 -AATATAATT
1 AAATATAATT
20571957 ATTCTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 9 0.29
23 6 0.19
24 5 0.16
26 11 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATATAATTTAATAAAATTATT
Found at i:20571944 original size:101 final size:100
Alignment explanation
Indices: 20571826--20572007 Score: 319
Period size: 101 Copynumber: 1.8 Consensus size: 100
20571816 TAATAAAAAT
* *
20571826 ATATAATTTAATAAAATTCTTACTATAATTATTCTTATATGAATTTACTAAAATCATAATCTATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
*
20571891 ATACTATAAAATATAATTTAAAATAATAATTATTAA
66 ATAATATAAAA-ATAATTTAAAATAATAATTATTAA
*
20571927 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTAGTAAAATCATAATATATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
20571992 ATAATATAAAAATAAT
66 ATAATATAAAAATAAT
20572008 ATATAATCTA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 5 0.06
101 72 0.94
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (100 bp):
ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
ATAATATAAAAATAATTTAAAATAATAATTATTAA
Found at i:20572138 original size:19 final size:19
Alignment explanation
Indices: 20572077--20572145 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
20572067 TAGTGAAACA
*
20572077 AATAATTTAATTATTTTAC
1 AATAATTTAATTATTCTAC
*
20572096 AATAA--AAATTA-T-TAGC
1 AATAATTTAATTATTCTA-C
*
20572112 AGTAATTTAATTATTCTAC
1 AATAATTTAATTATTCTAC
20572131 AATAATTTAA-TATTC
1 AATAATTTAATTATTC
20572146 ATATATTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 2 0.05
16 6 0.15
17 5 0.12
18 10 0.24
19 16 0.39
20 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (19 bp):
AATAATTTAATTATTCTAC
Found at i:20572199 original size:12 final size:12
Alignment explanation
Indices: 20572182--20572208 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20572172 TTCTATGTCA
20572182 TAACCCATATGT
1 TAACCCATATGT
20572194 TAACCCATATGT
1 TAACCCATATGT
20572206 TAA
1 TAA
20572209 GAGATTTAGA
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:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (12 bp):
TAACCCATATGT
Found at i:20572422 original size:12 final size:12
Alignment explanation
Indices: 20572405--20572431 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20572395 TGTCCAACAC
20572405 TAGTAGGCCCAA
1 TAGTAGGCCCAA
20572417 TAGTAGGCCCAA
1 TAGTAGGCCCAA
20572429 TAG
1 TAG
20572432 CCAATTTTCA
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:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (12 bp):
TAGTAGGCCCAA
Found at i:20578040 original size:8 final size:8
Alignment explanation
Indices: 20578029--20578057 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
20578019 CCAAAAAAAT
20578029 AAAAAGAG
1 AAAAAGAG
20578037 AAAAAGAG
1 AAAAAGAG
20578045 AAAAAGAG
1 AAAAAGAG
20578053 AAAAA
1 AAAAA
20578058 TGGAGAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:20580678 original size:132 final size:132
Alignment explanation
Indices: 20579412--20580665 Score: 1472
Period size: 132 Copynumber: 9.5 Consensus size: 132
20579402 TAGACAGCGA
* * *
20579412 AGCAGATCAAAGATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
20579477 TCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCT-TCT-TGCATCGA
66 TCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCA--G-
* * *
20579539 CAATGA
127 TAGTGG
*
20579545 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
20579610 TCTATCTCCCTGGGCAACAGTGAAATAGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGT
66 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
20579675 GG
131 GG
* * *
20579677 AGCAGATCAAAGATGGCAGATTTTACCTCCCTAAGGTTACAGTGCAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
20579742 TCTATCTCCTTGGGC-GACAATGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAG
66 TCTATCTCCCTGGGCAG-CAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
20579806 TGG
130 TGG
* * * * *
20579809 AGCAGATCGAAGATGGCGGATTTTACCTCTCTGAAGTTGCAGTGGAGTATATT------AGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* ** **
20579868 TCTA-CTTCCCCTGTTG--GC-GT-GAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTG
66 TCTATC-T-CCCTG-GGCAGCAGTGGAA-TAGATTGAAGATTTCAGATCTTGTC-TCCC-TA---
*
20579928 GTGGCGAAGTAGATCGAAG
122 --AGC--AGTAG-T-G--G
* * *
20579947 AAAGTAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
1 --AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
* * *
20580012 ATTCTATCTCCCTGGGCAACAGTGGAGTAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTA
64 ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
20580077 GTGG
129 GTGG
* * *
20580081 AGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *** *
20580146 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAGGAAAACAGATCTTGTCTCCCCAAGCAGTAGT
66 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
20580211 GG
131 GG
* * **
20580213 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAACGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
20580278 TCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAATATTTCAGATCTTGTCTCCCTAAGCAGTAG
66 TCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
20580342 TGG
130 TGG
* * * *
20580345 AGCATATCAAAGATGGTGAATTTTACCTCCCTGTGGTTAC-----AGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
20580405 TCTA-CTTCCCTGGGCAGCAGTGAAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
66 TCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
20580469 TGG
130 TGG
* * ** * * *
20580472 AGCAGATCAAAGATGGTGAATTTTACCTCATTGTGGTTATAGTGGAGTATATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
20580537 TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCTCTAAGCAGTAGT
66 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
20580602 GG
131 GG
* *** *
20580604 AGTAGATCAAAGATAATGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT
20580666 TACCCTATCT
Statistics
Matches: 979, Mismatches: 101, Indels: 83
0.84 0.09 0.07
Matches are distributed among these distances:
124 3 0.00
125 21 0.02
126 16 0.02
127 127 0.13
128 1 0.00
131 1 0.00
132 581 0.59
133 109 0.11
134 9 0.01
135 4 0.00
136 2 0.00
137 1 0.00
138 6 0.01
140 49 0.05
144 1 0.00
145 6 0.01
146 16 0.02
147 24 0.02
148 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
GG
Found at i:20582474 original size:62 final size:62
Alignment explanation
Indices: 20582405--20582528 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
20582395 TTTGATTCCA
20582405 TAGTTTTTATAAACAAGTATATATATATACATGTACATACACTTTTATTTTATAGTACATAC
1 TAGTTTTTATAAACAAGTATATATATATACATGTACATACACTTTTATTTTATAGTACATAC
20582467 TAGTTTTTATAAACAAGTATATATATATACATGTACATACACTTTTATTTTATAGTACATAC
1 TAGTTTTTATAAACAAGTATATATATATACATGTACATACACTTTTATTTTATAGTACATAC
20582529 GAATTTTCCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (62 bp):
TAGTTTTTATAAACAAGTATATATATATACATGTACATACACTTTTATTTTATAGTACATAC
Found at i:20588712 original size:21 final size:21
Alignment explanation
Indices: 20588686--20588726 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20588676 ATCTGCTCAA
* *
20588686 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
20588707 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
20588727 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:20593315 original size:21 final size:22
Alignment explanation
Indices: 20593266--20593315 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
20593256 GGGGTTTTGT
*
20593266 AGGAAATTACTTTGAATTTTTAT
1 AGGAAATTA-TTTGAATTTTTAG
*
20593289 AAGAAATT-TTTGAATTTTTAG
1 AGGAAATTATTTGAATTTTTAG
20593310 AGGAAA
1 AGGAAA
20593316 ATTTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.71
23 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (22 bp):
AGGAAATTATTTGAATTTTTAG
Found at i:20593348 original size:17 final size:17
Alignment explanation
Indices: 20593315--20593347 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20593305 TTTAGAGGAA
20593315 AATTTATTTTATCTTTT
1 AATTTATTTTATCTTTT
*
20593332 AATTTCTTTTA-CTTTT
1 AATTTATTTTATCTTTT
20593348 TCTTTTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (17 bp):
AATTTATTTTATCTTTT
Found at i:20596105 original size:35 final size:32
Alignment explanation
Indices: 20596048--20596190 Score: 110
Period size: 34 Copynumber: 4.2 Consensus size: 32
20596038 ATACGAAATT
* *
20596048 TTTTTTAAAACTCGATAA-TTTTGAAACACAATA
1 TTTTTTGAAACACGA-AACTTTTGAAACACAA-A
* *
20596081 TTTTTTGAAGACAAGGAAATTTTTGAAACACAGGAA
1 TTTTTTGAA-AC-ACGAAACTTTTGAAACACA--AA
20596117 TTTTTTGAAACACGAAACTTTTGAAACACAAAAA
1 TTTTTTGAAACACGAAACTTTTGAAACAC--AAA
* **
20596151 ATTTTTGAAAACAC-AAAAATTTGAAACACGAGAA
1 TTTTTTG-AAACACGAAACTTTTGAAACAC-A-AA
20596185 TTTTTT
1 TTTTTT
20596191 TAAAAGGACG
Statistics
Matches: 91, Mismatches: 10, Indels: 17
0.77 0.08 0.14
Matches are distributed among these distances:
33 9 0.10
34 48 0.53
35 22 0.24
36 11 0.12
37 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (32 bp):
TTTTTTGAAACACGAAACTTTTGAAACACAAA
Found at i:20596168 original size:18 final size:17
Alignment explanation
Indices: 20596066--20596189 Score: 94
Period size: 18 Copynumber: 7.2 Consensus size: 17
20596056 AACTCGATAA
* *
20596066 TTTTGAAACACAATATT
1 TTTTGAAACACAAAAAT
*
20596083 TTTTGAAGACA-AGGAAAT
1 TTTTGAA-ACACA-AAAAT
* *
20596101 TTTTGAAACACAGGAATT
1 TTTTGAAACACA-AAAAT
* *
20596119 TTTTGAAACAC-GAAAC
1 TTTTGAAACACAAAAAT
20596135 TTTTGAAACACAAAAAAT
1 TTTTGAAACAC-AAAAAT
20596153 TTTTGAAAACACAAAAA-
1 TTTTG-AAACACAAAAAT
* *
20596170 -TTTGAAACACGAGAAT
1 TTTTGAAACACAAAAAT
20596186 TTTT
1 TTTT
20596190 TTAAAAGGAC
Statistics
Matches: 89, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.10
16 18 0.20
17 14 0.16
18 42 0.47
19 6 0.07
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTGAAACACAAAAAT
Found at i:20596671 original size:14 final size:13
Alignment explanation
Indices: 20596652--20596697 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
20596642 ACGAGCTTGG
20596652 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
*
20596665 CTTTTTTTCTTTTT
1 -TTTTTTCCTTTTT
20596679 TTTTCTTCCTCTTTT
1 TTTT-TTCCT-TTTT
20596694 TTTT
1 TTTT
20596698 CTGGACTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.14
14 16 0.57
15 8 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCCTTTTT
Done.