Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 65 of 325
Found at i:23450934 original size:16 final size:17
Alignment explanation
Indices: 23450904--23450939 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
23450894 ATATTTAATT
23450904 AATTTTTATAATTTAAA
1 AATTTTTATAATTTAAA
*
23450921 AATTTTT-TATTTTAAA
1 AATTTTTATAATTTAAA
23450937 AAT
1 AAT
23450940 AGTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTTATAATTTAAA
Found at i:23451888 original size:3 final size:3
Alignment explanation
Indices: 23451880--23451916 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
23451870 CCTCCTACAT
* *
23451880 CCA CCA CCA CCA CCA CCA CCA CAA CCA CAA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
23451917 GCCAACCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:23455048 original size:18 final size:18
Alignment explanation
Indices: 23455025--23455059 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
23455015 GGAACCAGAA
23455025 GTTAAAGTATCTAGTACT
1 GTTAAAGTATCTAGTACT
23455043 GTTAAAGTATCTAGTAC
1 GTTAAAGTATCTAGTAC
23455060 AGACGATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (18 bp):
GTTAAAGTATCTAGTACT
Found at i:23467216 original size:9 final size:9
Alignment explanation
Indices: 23467164--23467277 Score: 61
Period size: 9 Copynumber: 12.2 Consensus size: 9
23467154 CTTTCACTTT
23467164 TTTTTTTTA
1 TTTTTTTTA
23467173 CTTTTTTATTA
1 -TTTTTT-TTA
** * *
23467184 ACTTTTGTC
1 TTTTTTTTA
23467193 TTTTTCTTTA
1 TTTTT-TTTA
*
23467203 ATTTTTTTA
1 TTTTTTTTA
23467212 -TTTTTTTA
1 TTTTTTTTA
** *
23467220 AGTTTTATA
1 TTTTTTTTA
23467229 TTTTTTCTTA
1 TTTTTT-TTA
23467239 TTTTATTTT-
1 TTTT-TTTTA
* *
23467248 GTTTATTTA
1 TTTTTTTTA
*
23467257 TTTATTTTA
1 TTTTTTTTA
23467266 TTTTTTGTTA
1 TTTTTT-TTA
23467276 TT
1 TT
23467278 AATTTTAAAA
Statistics
Matches: 77, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
8 11 0.14
9 32 0.42
10 29 0.38
11 5 0.06
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:23467225 original size:17 final size:17
Alignment explanation
Indices: 23467194--23467234 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
23467184 ACTTTTGTCT
* *
23467194 TTTTCTTTAATTTTTTTA
1 TTTT-TTTAAGTTTTATA
23467212 TTTTTTTAAGTTTTATA
1 TTTTTTTAAGTTTTATA
23467229 TTTTTT
1 TTTTTT
23467235 CTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTTTAAGTTTTATA
Found at i:23467348 original size:20 final size:21
Alignment explanation
Indices: 23467317--23467377 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
23467307 AATGTTTTAT
23467317 AATATATATTTTTTAAAATTTT-
1 AATAT-TATTTTTT-AAATTTTG
*
23467339 AA-ATTATTTTTTTAATTTTG
1 AATATTATTTTTTAAATTTTG
23467359 AATATTATTTTTTTAAATT
1 AATATTA-TTTTTTAAATT
23467378 ATTCTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 6 0.18
20 10 0.29
21 6 0.18
22 12 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
AATATTATTTTTTAAATTTTG
Found at i:23467351 original size:21 final size:21
Alignment explanation
Indices: 23467311--23467375 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
23467301 ATTTGAAATG
23467311 TTTTATAATATATATTTTTTAAAA
1 TTTTA-AAT-TAT-TTTTTTAAAA
23467335 TTTTAAATTATTTTTTT--AA
1 TTTTAAATTATTTTTTTAAAA
23467354 TTTTGAATATTATTTTTTTAAA
1 TTTT-AA-ATTATTTTTTTAAA
23467376 TTATTCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 6 0.16
20 2 0.05
21 17 0.46
22 3 0.08
23 4 0.11
24 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTAAATTATTTTTTTAAAA
Found at i:23467405 original size:34 final size:35
Alignment explanation
Indices: 23467335--23467430 Score: 99
Period size: 35 Copynumber: 2.7 Consensus size: 35
23467325 TTTTTTAAAA
* * *
23467335 TTTTAAATTATTTTTTTAATTTT-GAATATTATTT
1 TTTTAAATTATTTTATAAATTTTAAAATATTATTT
23467369 TTTTAAATTATTCTTATAAATTTTAAAATA-TA-TT
1 TTTTAAATTATT-TTATAAATTTTAAAATATTATTT
* *
23467403 TTTGAAATTAATTTTTCTAAATTTTAAA
1 TTTTAAATT-A-TTTTATAAATTTTAAA
23467431 TTTTAAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
34 22 0.42
35 25 0.47
36 6 0.11
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (35 bp):
TTTTAAATTATTTTATAAATTTTAAAATATTATTT
Found at i:23467451 original size:31 final size:33
Alignment explanation
Indices: 23467413--23467491 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
23467403 TTTGAAATTA
23467413 ATTTTTCTAAATTTT-AAATTTT-AAATATATT
1 ATTTTTCTAAATTTTAAAATTTTAAAATATATT
23467444 ATTTTTCTAAATTTTAAAATTTTAAAATATATT
1 ATTTTTCTAAATTTTAAAATTTTAAAATATATT
23467477 ATTTTTCTAAATTTT
1 ATTTTTCTAAATTTT
23467492 TGAAATTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 15 0.33
32 7 0.15
33 24 0.52
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (33 bp):
ATTTTTCTAAATTTTAAAATTTTAAAATATATT
Found at i:23467520 original size:15 final size:13
Alignment explanation
Indices: 23467486--23467512 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23467476 TATTTTTCTA
23467486 AATTTTTGAAATT
1 AATTTTTGAAATT
23467499 AATTTTTGAAATT
1 AATTTTTGAAATT
23467512 A
1 A
23467513 TAATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
AATTTTTGAAATT
Found at i:23467627 original size:19 final size:19
Alignment explanation
Indices: 23467603--23467658 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
23467593 TTAAATATTA
*
23467603 TTAAAAATATATTTAATAT
1 TTAAAAATATATTTAAAAT
23467622 TT-AAAATAATATTTAAAAT
1 TTAAAAAT-ATATTTAAAAT
23467641 TTAAAAATA-ATTTCAAAA
1 TTAAAAATATATTT-AAAA
23467659 ATATATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.27
19 19 0.58
20 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAAAATATATTTAAAAT
Found at i:23467629 original size:30 final size:29
Alignment explanation
Indices: 23467566--23467640 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
23467556 AATTTTTATA
* *
23467566 AAAATTTTATTGAAAA-ATTTTAAATTTT
1 AAAATATTATTAAAAATATTTTAAATTTT
*
23467594 TAAATATTATTAAAAATATATTT-AATATTT
1 AAAATATTATTAAAAATAT-TTTAAAT-TTT
* *
23467624 AAAATAATATTTAAAAT
1 AAAATATTATTAAAAAT
23467641 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 13 0.34
29 5 0.13
30 20 0.53
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAATATTATTAAAAATATTTTAAATTTT
Found at i:23467631 original size:12 final size:12
Alignment explanation
Indices: 23467616--23467640 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23467606 AAAATATATT
23467616 TAATATTTAAAA
1 TAATATTTAAAA
23467628 TAATATTTAAAA
1 TAATATTTAAAA
23467640 T
1 T
23467641 TTAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATATTTAAAA
Found at i:23467691 original size:36 final size:35
Alignment explanation
Indices: 23467624--23467712 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 35
23467614 TTTAATATTT
23467624 AAAATA-ATATTTAAAA-TT-TAAAAATAATTTCA
1 AAAATATATATTTAAAATTTATAAAAATAATTTCA
*
23467656 AAAATATATTTTTAAAATTTATAAGAAATAATTTCA
1 AAAATATATATTTAAAATTTATAA-AAATAATTTCA
23467692 AAAATATATATTTAAAATTTA
1 AAAATATATATTTAAAATTTA
23467713 AAATTTAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 6 0.12
33 9 0.18
34 2 0.04
35 3 0.06
36 31 0.61
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (35 bp):
AAAATATATATTTAAAATTTATAAAAATAATTTCA
Found at i:23467716 original size:43 final size:43
Alignment explanation
Indices: 23467666--23467794 Score: 139
Period size: 43 Copynumber: 3.2 Consensus size: 43
23467656 AAAATATATT
23467666 TTTAAAATTTATAAGAAATAATTTCAAAAATATATATTTAAAA
1 TTTAAAATTTATAAGAAATAATTTCAAAAATATATATTTAAAA
*
23467709 TTTAAAATTTAGAA-AAATTAATTTC--AAATATATA-TT----
1 TTTAAAATTTATAAGAAA-TAATTTCAAAAATATATATTTAAAA
* * * * *
23467745 TTTAAAATTTATAAGACATAATTTTAAAAAAAAATATTCAAAA
1 TTTAAAATTTATAAGAAATAATTTCAAAAATATATATTTAAAA
23467788 TTTAAAA
1 TTTAAAA
23467795 AATAATTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
36 19 0.27
37 2 0.03
38 7 0.10
39 1 0.01
40 2 0.03
41 9 0.13
42 3 0.04
43 27 0.39
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (43 bp):
TTTAAAATTTATAAGAAATAATTTCAAAAATATATATTTAAAA
Found at i:23467750 original size:36 final size:34
Alignment explanation
Indices: 23467633--23467821 Score: 150
Period size: 36 Copynumber: 5.3 Consensus size: 34
23467623 TAAAATAATA
*
23467633 TTTAAAATTT-AAAAATAATTTCAAAAATATATT
1 TTTAAAATTTAAAAAATAATTTCAAATATATATT
23467666 TTTAAAATTTATAAGAAATAATTTCAAAAATATATATTT
1 TTTAAAATTTA-AA-AAATAATTTC--AAATATATA-TT
23467705 AAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATT
1 ----TTTAAAATTTA-AAAAA-TAATTTCAAATATATATT
* * * * * *
23467745 TTTAAAATTTATAAGACATAATTTTAAAAAAAAATA
1 TTTAAAATTTA-AA-AAATAATTTCAAATATATATT
* * *
23467781 TTCAAAATTTAAAAAATAATTT-AAAAATA-ATA
1 TTTAAAATTTAAAAAATAATTTCAAATATATATT
23467813 TTTAAAATT
1 TTTAAAATT
23467822 GAAATTATTT
Statistics
Matches: 131, Mismatches: 13, Indels: 25
0.78 0.08 0.15
Matches are distributed among these distances:
32 11 0.08
33 16 0.12
34 8 0.06
35 4 0.03
36 46 0.35
37 2 0.02
38 8 0.06
39 2 0.02
40 2 0.02
41 9 0.07
42 3 0.02
43 20 0.15
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (34 bp):
TTTAAAATTTAAAAAATAATTTCAAATATATATT
Found at i:23467807 original size:20 final size:21
Alignment explanation
Indices: 23467767--23467808 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23467757 AAGACATAAT
*
23467767 TTTAAAAAAAAATATTCAAAA
1 TTTAAAAAAAAATATTAAAAA
*
23467788 TTTAAAAAATAAT-TTAAAAA
1 TTTAAAAAAAAATATTAAAAA
23467808 T
1 T
23467809 AATATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TTTAAAAAAAAATATTAAAAA
Found at i:23467858 original size:14 final size:14
Alignment explanation
Indices: 23467839--23467867 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23467829 TTTCATTTTG
23467839 TTTAAAAATATATT
1 TTTAAAAATATATT
23467853 TTTAAAAATATATT
1 TTTAAAAATATATT
23467867 T
1 T
23467868 AAAATTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:23467868 original size:12 final size:13
Alignment explanation
Indices: 23467839--23467871 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
23467829 TTTCATTTTG
23467839 TTTAAAAATATATT
1 TTTAAAAATATA-T
23467853 TTTAAAAATATA-
1 TTTAAAAATATAT
23467865 TTTAAAA
1 TTTAAAA
23467872 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:23467915 original size:36 final size:32
Alignment explanation
Indices: 23467871--23467984 Score: 104
Period size: 36 Copynumber: 3.3 Consensus size: 32
23467861 TATATTTAAA
23467871 ATTTAAAATTTAGAAAAATTAATTTCAAATATATAT
1 ATTTAAAATTTA-AAAAA-TAATTT-AAA-ATATAT
* * *
23467907 TTTTAAAATTTATAAGACATAATTTTAAAAAATAAT
1 ATTTAAAATTTA-AA-AAATAA-TTTAAAATAT-AT
*
23467943 ATTCAAAATTTAAAAAATAATTTAAAA-ATAAT
1 ATTTAAAATTTAAAAAATAATTTAAAATAT-AT
23467975 ATTTAAAATT
1 ATTTAAAATT
23467985 GAAATTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
32 14 0.21
33 7 0.10
34 5 0.07
35 5 0.07
36 31 0.46
37 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (32 bp):
ATTTAAAATTTAAAAAATAATTTAAAATATAT
Found at i:23467956 original size:21 final size:20
Alignment explanation
Indices: 23467930--23467971 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
23467920 AAGACATAAT
*
23467930 TTTAAAAAATAATATTCAAAA
1 TTTAAAAAATAAT-TTAAAAA
23467951 TTTAAAAAATAATTTAAAAA
1 TTTAAAAAATAATTTAAAAA
23467971 T
1 T
23467972 AATATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTAAAAAATAATTTAAAAA
Found at i:23468021 original size:14 final size:14
Alignment explanation
Indices: 23468002--23468030 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23467992 TTTCATTTTG
23468002 TTTAAAAATATATT
1 TTTAAAAATATATT
23468016 TTTAAAAATATATT
1 TTTAAAAATATATT
23468030 T
1 T
23468031 AAAATTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:23468031 original size:12 final size:13
Alignment explanation
Indices: 23468002--23468034 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
23467992 TTTCATTTTG
23468002 TTTAAAAATATATT
1 TTTAAAAATATA-T
23468016 TTTAAAAATATA-
1 TTTAAAAATATAT
23468028 TTTAAAA
1 TTTAAAA
23468035 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:23468102 original size:163 final size:163
Alignment explanation
Indices: 23467692--23468113 Score: 801
Period size: 163 Copynumber: 2.6 Consensus size: 163
23467682 AATAATTTCA
23467692 AAAATATATATTTAAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTAT
1 AAAA-ATATATTTAAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTAT
*
23467757 AAGACATAATTTTAAAAAAAAATATTCAAAATTTAAAAAATAATTTAAAAATAATATTTAAAATT
65 AAGACATAATTTTAAAAAATAATATTCAAAATTTAAAAAATAATTTAAAAATAATATTTAAAATT
23467822 GAAATTATTTCATTTTGTTTAAAAATATATTTTT
130 GAAATTATTTCATTTTGTTTAAAAATATATTTTT
23467856 AAAAATATATTTAAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTATA
1 AAAAATATATTTAAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTATA
23467921 AGACATAATTTTAAAAAATAATATTCAAAATTTAAAAAATAATTTAAAAATAATATTTAAAATTG
66 AGACATAATTTTAAAAAATAATATTCAAAATTTAAAAAATAATTTAAAAATAATATTTAAAATTG
23467986 AAATTATTTCATTTTGTTTAAAAATATATTTTT
131 AAATTATTTCATTTTGTTTAAAAATATATTTTT
*
23468019 AAAAATATATTTAAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTGTA
1 AAAAATATATTTAAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTATA
*
23468084 AGACATAATTTTAAAAAATAAT-TTAAAAAT
66 AGACATAATTTTAAAAAATAATATTCAAAAT
23468114 AATATTTAAA
Statistics
Matches: 255, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
162 7 0.03
163 244 0.96
164 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (163 bp):
AAAAATATATTTAAAATTTAAAATTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTATA
AGACATAATTTTAAAAAATAATATTCAAAATTTAAAAAATAATTTAAAAATAATATTTAAAATTG
AAATTATTTCATTTTGTTTAAAAATATATTTTT
Found at i:23468106 original size:13 final size:13
Alignment explanation
Indices: 23468088--23468124 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 13
23468078 TTTGTAAGAC
23468088 ATAATTTTAAAAA
1 ATAATTTTAAAAA
23468101 ATAA-TTT-AAAA
1 ATAATTTTAAAAA
23468112 ATAATATTTAAAA
1 ATAAT-TTTAAAA
23468125 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.38
12 3 0.14
13 7 0.33
14 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATTTTAAAAA
Found at i:23468107 original size:49 final size:48
Alignment explanation
Indices: 23468042--23468166 Score: 121
Period size: 47 Copynumber: 2.6 Consensus size: 48
23468032 AAATTTAAAA
* *
23468042 TTTAGAAAAATTAATTTCAAATATATATTTTTAAAATTTGTAAGACATA-AT
1 TTTA-AAAAA-TAATTTCAAATATA-ATTTTTAAAATTT-TAAAAAATACAT
* *
23468093 TTTAAAAAATAATTT-AAAAATAATATTTAAAATTTTAAAAAATACAT
1 TTTAAAAAATAATTTCAAATATAATTTTTAAAATTTTAAAAAATACAT
* * *
23468140 ATTATAAAA-CATTTCAAATATACATTT
1 TTTAAAAAATAATTTCAAATATA-ATTT
23468167 CAAATTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
46 11 0.18
47 27 0.44
48 9 0.15
49 6 0.10
50 5 0.08
51 4 0.06
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (48 bp):
TTTAAAAAATAATTTCAAATATAATTTTTAAAATTTTAAAAAATACAT
Found at i:23468201 original size:19 final size:18
Alignment explanation
Indices: 23468177--23468215 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
23468167 CAAATTTTTT
*
23468177 TAAAATTAATAACAAAAAA
1 TAAAATAAATAA-AAAAAA
23468196 TAAAATAAATAAAAAAAA
1 TAAAATAAATAAAAAAAA
23468214 TA
1 TA
23468216 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAATAAATAAAAAAAA
Found at i:23468207 original size:9 final size:9
Alignment explanation
Indices: 23468184--23468223 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
23468174 TTTTAAAATT
23468184 AATAACAAAA
1 AATAA-AAAA
*
23468194 AATAAAATA
1 AATAAAAAA
23468203 AATAAAAAA
1 AATAAAAAA
23468212 AATATAAAAA
1 AATA-AAAAA
23468222 AA
1 AA
23468224 ATATAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 15 0.56
10 12 0.44
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (9 bp):
AATAAAAAA
Found at i:23468218 original size:11 final size:11
Alignment explanation
Indices: 23468204--23468231 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
23468194 AATAAAATAA
23468204 ATAAAAAAAAT
1 ATAAAAAAAAT
23468215 ATAAAAAAAAT
1 ATAAAAAAAAT
23468226 ATAAAA
1 ATAAAA
23468232 CTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:23468247 original size:37 final size:37
Alignment explanation
Indices: 23468196--23468283 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
23468186 TAACAAAAAA
* *
23468196 TAAAATAAATAAAAAAAATATAAA-AAAAATATAAAACT
1 TAAAA-AAA-AAAAAAAATATAAAGAAAAAGACAAAACT
* * *
23468234 TAAAAAAAGAAAAAAATTTAAAGAAAAAGACAAAAGT
1 TAAAAAAAAAAAAAAATATAAAGAAAAAGACAAAACT
*
23468271 TAATAAAAAAAAA
1 TAAAAAAAAAAAA
23468284 GTGAGTGGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
36 12 0.29
37 25 0.60
38 5 0.12
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (37 bp):
TAAAAAAAAAAAAAAATATAAAGAAAAAGACAAAACT
Found at i:23468280 original size:20 final size:21
Alignment explanation
Indices: 23468234--23468281 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
23468224 ATATAAAACT
*
23468234 TAAAAAAAGAAAAAAATTTAA
1 TAAAAAAAGAAAAAAAGTTAA
* *
23468255 -AGAAAAAG-ACAAAAGTTAA
1 TAAAAAAAGAAAAAAAGTTAA
23468274 TAAAAAAA
1 TAAAAAAA
23468282 AAGTGAGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (21 bp):
TAAAAAAAGAAAAAAAGTTAA
Found at i:23469797 original size:100 final size:97
Alignment explanation
Indices: 23469701--23469901 Score: 244
Period size: 99 Copynumber: 2.0 Consensus size: 97
23469691 AGTTTTTAAA
* *
23469701 TTTT-TTTTTTAATATCTGAAAATTCGAGTTTTTTAAAAAAAAAATTTTGGTGCTGGCCTGT-AA
1 TTTTATTTTTTAATATCCGAAAATACGAG--TTTTAAAAAAAAAATTTTGGTGCTGGCCTGTCAA
23469764 TGGCTGGCACCAAGTACAAAAAAATCAATTTTTT
64 TGGCTGGCACCAAGTACAAAAAAATCAATTTTTT
* * ** *
23469798 TTTTAAAATTTTTTATTGTCCGAAAATACGAGTTTTAAAATGAAAATTTTGGTGTTGGCCTGTCA
1 TTTT---ATTTTTTAATATCCGAAAATACGAGTTTTAAAAAAAAAATTTTGGTGCTGGCCTGTCA
* *
23469863 ATGGTTGGCACCAAGTACAAAAAAAAATCAAATTTTT
63 ATGGCTGGCACCAAGTAC--AAAAAAATCAATTTTTT
23469900 TT
1 TT
23469902 GGTGCTGGCC
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
97 4 0.05
99 28 0.32
100 18 0.20
101 20 0.23
102 18 0.20
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (97 bp):
TTTTATTTTTTAATATCCGAAAATACGAGTTTTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATG
GCTGGCACCAAGTACAAAAAAATCAATTTTTT
Found at i:23472689 original size:5 final size:5
Alignment explanation
Indices: 23472681--23472777 Score: 50
Period size: 5 Copynumber: 18.0 Consensus size: 5
23472671 GTCTTTTTTT
* * * * *
23472681 TTTCA TTTCT TTTCA TTTTCA TTTCA TTTTA TTTTAA TTTTA ATTCA TTTCAA
1 TTTCA TTTCA TTTCA -TTTCA TTTCA TTTCA -TTTCA TTTCA TTTCA TTTC-A
* * * *
23472734 CTTCA TTTCG TTCTAA TTTCA TTTCCA TTCCCA TTTCCA TTTCA
1 TTTCA TTTCA TT-TCA TTTCA TTT-CA TT-TCA TTT-CA TTTCA
23472778 GATAAAGGGT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
5 40 0.58
6 29 0.42
ACGTcount: A:0.21, C:0.21, G:0.01, T:0.58
Consensus pattern (5 bp):
TTTCA
Found at i:23472693 original size:16 final size:16
Alignment explanation
Indices: 23472672--23472720 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
23472662 GTCTTGTCAG
*
23472672 TCTTTTTTTTTTCATT
1 TCTTTTTATTTTCATT
*
23472688 TCTTTTCATTTTCATT
1 TCTTTTTATTTTCATT
* *
23472704 TCATTTTATTTTAATT
1 TCTTTTTATTTTCATT
23472720 T
1 T
23472721 TAATTCATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.73
Consensus pattern (16 bp):
TCTTTTTATTTTCATT
Found at i:23472700 original size:11 final size:11
Alignment explanation
Indices: 23472675--23472721 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
23472665 TTGTCAGTCT
*
23472675 TTTTTTTTTCA
1 TTTTCTTTTCA
23472686 -TTTCTTTTCA
1 TTTTCTTTTCA
*
23472696 TTTTCATTTCA
1 TTTTCTTTTCA
* *
23472707 TTTTATTTTAA
1 TTTTCTTTTCA
23472718 TTTT
1 TTTT
23472722 AATTCATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCTTTTCA
Found at i:23475365 original size:61 final size:62
Alignment explanation
Indices: 23475298--23475413 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 62
23475288 GAATTTTTAA
*
23475298 TTTTTTTGTACTTGGTGCTGGCCATTGACAGGCCAACACC-TATTTTTTTTTAAATTTAATT
1 TTTTTTTGTACTTGGTGCTGGCCATTGACAGGCCAACACCAAATTTTTTTTTAAATTTAATT
**
23475359 TTTTTTTGTACTTGGTGCTGGTTATTGACAGGCCAACACCAAATTTTTTTTTAAA
1 TTTTTTTGTACTTGGTGCTGGCCATTGACAGGCCAACACCAAATTTTTTTTTAAA
23475414 AACTTGTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 38 0.75
62 13 0.25
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (62 bp):
TTTTTTTGTACTTGGTGCTGGCCATTGACAGGCCAACACCAAATTTTTTTTTAAATTTAATT
Found at i:23475591 original size:84 final size:83
Alignment explanation
Indices: 23475492--23475735 Score: 325
Period size: 84 Copynumber: 2.9 Consensus size: 83
23475482 GCACCAAAAA
* *
23475492 AATTTAATTTTTTTTTTGTACTTGGTGCCGGCCATTAACAGGCCAACACAAAATTTTTTTTAAAA
1 AATTTAATTTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACACAAATTTTTTTTTAAAA
23475557 ACTCGTATTTTCGGAAATC
66 ACTCGTATTTT-GGAAATC
* *
23475576 AATTTGATTTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACAC-TATTTTTTTTTAAAA
1 AATTTAATTTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACACAAATTTTTTTTTAAAA
*
23475640 TACTCGTATTTTGGACATC
66 -ACTCGTATTTTGGAAATC
* * * *
23475659 AA---AATTTTTTTTATTTTCCTTGGTGCCTGCCATTGACAGGCCAGCACCAAATTTTTTTTTTA
1 AATTTAATTTTTTTT-TTGTACTTGGTGCCGGCCATTGACAGGCCAACA-CAAA-TTTTTTTTTA
*
23475721 AAAACTCATATTTTG
63 AAAACTCGTATTTTG
23475736 TATACCAGTA
Statistics
Matches: 143, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
80 9 0.06
81 29 0.20
82 1 0.01
83 33 0.23
84 71 0.50
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (83 bp):
AATTTAATTTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACACAAATTTTTTTTTAAAA
ACTCGTATTTTGGAAATC
Found at i:23475652 original size:143 final size:141
Alignment explanation
Indices: 23475289--23475641 Score: 367
Period size: 143 Copynumber: 2.5 Consensus size: 141
23475279 ACCAGATACG
* * *
23475289 AATTTTTAATTTTTTTGTACTTGGTGCTGGCCATTGACAGGCCAACACCTATTTTTTTTTAAATT
1 AATTTTT-TTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACA-CTATTTTTTTTTAAA-A
* ** * * *
23475354 TAATTTTTTTTTGTACTTGGTGCTGGTTATTGACAGGCCAACACCAAATTTTTTTTTAAAAACTT
63 T-ATTTTTTTTTGTACTTGGTGCCGGCCATTAACAGGCCAACACCAAAATTTTTTTTAAAAACTC
23475419 GTATTTTCGAATATC
127 GTATTTTCGAATATC
* * * * * ******
23475434 AATTTTTTTTTTAAAAAACTCGTA-TTGGTGCCTGCCATTGACAGGCCAGCACCAAAAAAATTT-
1 AATTTTTTTTTT------TTTGTACTTGGTGCCGGCCATTGACAGGCCAACACTATTTTTTTTTA
23475497 -AAT-TTTTTTTTTGTACTTGGTGCCGGCCATTAACAGGCCAACA-CAAAATTTTTTTTAAAAAC
60 AAATATTTTTTTTTGTACTTGGTGCCGGCCATTAACAGGCCAACACCAAAATTTTTTTTAAAAAC
23475559 TCGTATTTTCGGAA-ATC
125 TCGTATTTTC-GAATATC
23475576 AATTTGATTTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACACTATTTTTTTTTAAAAT
1 AATTT--TTTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACACTATTTTTTTTTAAAAT
23475641 A
64 A
23475642 CTCGTATTTT
Statistics
Matches: 164, Mismatches: 31, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
138 4 0.02
139 30 0.18
141 3 0.02
142 35 0.21
143 39 0.24
144 11 0.07
145 8 0.05
146 1 0.01
148 5 0.03
149 24 0.15
150 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (141 bp):
AATTTTTTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACACTATTTTTTTTTAAAATAT
TTTTTTTTGTACTTGGTGCCGGCCATTAACAGGCCAACACCAAAATTTTTTTTAAAAACTCGTAT
TTTCGAATATC
Found at i:23495013 original size:33 final size:33
Alignment explanation
Indices: 23494971--23495034 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
23494961 TTTCTTCTTG
23494971 ACATTCCAGCTCCTGTCCAGCAACAAAACACCC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACCC
*
23495004 ACATTCCAGCTCCTGTCCAGCAACCAAACAC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACAC
23495035 TCCCATTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.42, G:0.09, T:0.16
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACAAAACACCC
Found at i:23497480 original size:81 final size:81
Alignment explanation
Indices: 23497366--23497528 Score: 236
Period size: 81 Copynumber: 2.0 Consensus size: 81
23497356 TCATTACCTG
* * ** *
23497366 TCTTAAATACAATGTTCACACTTGACCGCTGTAGAGTTGTTTATAGTGAAATTCTACAGTTCATT
1 TCTTAAATACAATGCTCACACCTGACCAATGTAGAGTTGTTTATAGTGAAACTCTACAGTTCATT
23497431 TAGATGGTGCTCATCA
66 TAGATGGTGCTCATCA
* * * *
23497447 TCTTAAATATAGTGCTCACACCTGACCAATGTAGAGTTGTTTATAGTGATACTCTATAGTTCATT
1 TCTTAAATACAATGCTCACACCTGACCAATGTAGAGTTGTTTATAGTGAAACTCTACAGTTCATT
*
23497512 TAGATGGTGCTCGTCA
66 TAGATGGTGCTCATCA
23497528 T
1 T
23497529 TCTATCATGC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (81 bp):
TCTTAAATACAATGCTCACACCTGACCAATGTAGAGTTGTTTATAGTGAAACTCTACAGTTCATT
TAGATGGTGCTCATCA
Found at i:23503661 original size:89 final size:89
Alignment explanation
Indices: 23503504--23503684 Score: 317
Period size: 89 Copynumber: 2.0 Consensus size: 89
23503494 CGCTTCAACT
*
23503504 AATAAAAGTGTATTTTAAAAATTCACATGTAAATGTACATAAAAAACAAATTAAAAATATATAAT
1 AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACATAAAAAACAAATTAAAAATATATAAT
*
23503569 TATTTTTATTAATATTATACTTTA
66 TATTTTTATGAATATTATACTTTA
* *
23503593 AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACATAAAAAACAAATTAAAAATATTTATT
1 AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACATAAAAAACAAATTAAAAATATATAAT
*
23503658 TATTTTTATGGATATTATACTTTA
66 TATTTTTATGAATATTATACTTTA
23503682 AAT
1 AAT
23503685 TACACATATG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (89 bp):
AATAAAAGTATATTTTAAAAATTCACATGTAAATGTACATAAAAAACAAATTAAAAATATATAAT
TATTTTTATGAATATTATACTTTA
Found at i:23507305 original size:5 final size:6
Alignment explanation
Indices: 23507288--23507314 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23507278 CCAGGGTTAG
23507288 AGAAAA AGAAAA AGAAAA AGAAAA AGA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGA
23507315 GGAGGAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:23507775 original size:38 final size:36
Alignment explanation
Indices: 23507690--23507775 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
23507680 TTGTAATATT
**
23507690 GTTGCTAGTATATTGTTGCTTATGTTGGTATACATG
1 GTTGCTAGTATATTGTTGCTTACATTGGTATACATG
* *
23507726 GCTGCTAGTATATTGTTGCTTAACATATGTTATACATG
1 GTTGCTAGTATATTGTTGCTT-ACAT-TGGTATACATG
*
23507764 GTTGCTGGTATA
1 GTTGCTAGTATA
23507776 AATGGCTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 20 0.48
37 2 0.05
38 20 0.48
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.44
Consensus pattern (36 bp):
GTTGCTAGTATATTGTTGCTTACATTGGTATACATG
Found at i:23509268 original size:40 final size:40
Alignment explanation
Indices: 23509213--23509310 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 40
23509203 AAAAAATACC
23509213 CACTGCATGCATATTAAAAAATAGGT-AACACACCAACAAT
1 CACTGCATGCATATTAAAAAATA-GTCAACACACCAACAAT
* *
23509253 CACTGCATGTATATTAAAAAATAGTCAACATACCAACAAT
1 CACTGCATGCATATTAAAAAATAGTCAACACACCAACAAT
* *
23509293 CAGTGTATGCATATTAAA
1 CACTGCATGCATATTAAA
23509311 GAACATTCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 2 0.04
40 50 0.96
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.24
Consensus pattern (40 bp):
CACTGCATGCATATTAAAAAATAGTCAACACACCAACAAT
Found at i:23510637 original size:45 final size:44
Alignment explanation
Indices: 23510571--23510675 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 44
23510561 ATGACAAAGA
23510571 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACA-AAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAAA-AG-GAAGG
* * *
23510617 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAAAAGGAAGG
23510661 AAGGAAAGAAAGAAA
1 AA-GAAAGAAAGAAA
23510676 GAAAAGAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
44 6 0.11
45 39 0.74
46 8 0.15
ACGTcount: A:0.65, C:0.09, G:0.27, T:0.00
Consensus pattern (44 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAAAAGGAAGG
Found at i:23511492 original size:37 final size:39
Alignment explanation
Indices: 23511433--23511528 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
23511423 CGGATAGATT
* * * *
23511433 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
23511470 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
23511509 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
23511529 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:23513597 original size:47 final size:46
Alignment explanation
Indices: 23513523--23513671 Score: 141
Period size: 47 Copynumber: 3.2 Consensus size: 46
23513513 GGGAGTTTAG
*
23513523 CGTGCTCTCTGAT-TATTAGCACATCAGTGCTCTCTGTTTAGCACAT
1 CGTGCTCTCTGATAT-TTAGCACGTCAGTGCTCTCTGTTTAGCACAT
23513569 CGGTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGAATATTAG--CA-
1 C-GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG--T-TTAGCACAT
* * *
23513616 C--GCTCTCTGATCA-CTAGCACGTTAGTGCTCTCCGTTTAGCACATT
1 CGTGCTCTCTGAT-ATTTAGCACGTCAGTGCTCTCTGTTTAGCACA-T
*
23513661 TGTGCTCTCTG
1 CGTGCTCTCTG
23513672 TACAGTCCCG
Statistics
Matches: 86, Mismatches: 5, Indels: 23
0.75 0.04 0.20
Matches are distributed among these distances:
41 4 0.05
42 1 0.01
43 2 0.02
44 28 0.33
45 1 0.01
46 1 0.01
47 41 0.48
48 3 0.03
49 1 0.01
50 4 0.05
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (46 bp):
CGTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCACAT
Found at i:23513617 original size:25 final size:24
Alignment explanation
Indices: 23513524--23513616 Score: 127
Period size: 25 Copynumber: 3.8 Consensus size: 24
23513514 GGAGTTTAGC
23513524 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGA-TATTAGCACATCA
*
23513549 GTGCTCTCTG-T-TTAGCACATCG
1 GTGCTCTCTGATATTAGCACATCA
*
23513571 GTGCTCTCTGATATTTAGCACGTCA
1 GTGCTCTCTGATA-TTAGCACATCA
23513596 GTGCTCTCTGAATATTAGCAC
1 GTGCTCTCTG-ATATTAGCAC
23513617 GCTCTCTGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
22 20 0.33
23 2 0.03
25 36 0.59
26 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (24 bp):
GTGCTCTCTGATATTAGCACATCA
Found at i:23513633 original size:19 final size:19
Alignment explanation
Indices: 23513598--23513636 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23513588 GCACGTCAGT
*
23513598 GCTCTCTGAATATTAGCAC
1 GCTCTCTGAATACTAGCAC
23513617 GCTCTCTG-ATCACTAGCAC
1 GCTCTCTGAAT-ACTAGCAC
23513636 G
1 G
23513637 TTAGTGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (19 bp):
GCTCTCTGAATACTAGCAC
Found at i:23513848 original size:6 final size:6
Alignment explanation
Indices: 23513839--23513873 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
23513829 CCCTAAATAG
* *
23513839 AAATCT AAATCT AAATCA AAATCT AAATTT AAATC
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATC
23513874 GAGATCGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:23513854 original size:18 final size:18
Alignment explanation
Indices: 23513839--23513903 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
23513829 CCCTAAATAG
23513839 AAATCTAAATCTAAATCA
1 AAATCTAAATCTAAATCA
* *
23513857 AAATCTAAATTTAAATCG
1 AAATCTAAATCTAAATCA
* *
23513875 AGATCGAAAT-TAAAATCA
1 AAATCTAAATCT-AAATCA
*
23513893 AAATCAAAATC
1 AAATCTAAATC
23513904 AGAATCAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 1 0.03
18 37 0.97
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (18 bp):
AAATCTAAATCTAAATCA
Found at i:23513890 original size:6 final size:6
Alignment explanation
Indices: 23513881--23513928 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
23513871 ATCGAGATCG
* * * * *
23513881 AAATTA AAATCA AAATCA AAATCA GAATCA GAATCA GAATCA GAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
23513929 GTGAGTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (6 bp):
AAATCA
Found at i:23513896 original size:12 final size:12
Alignment explanation
Indices: 23513839--23513928 Score: 63
Period size: 12 Copynumber: 7.5 Consensus size: 12
23513829 CCCTAAATAG
* *
23513839 AAATCTAAATCT
1 AAATCAAAATCA
*
23513851 AAATCAAAATCT
1 AAATCAAAATCA
** *
23513863 AAATTTAAATCG
1 AAATCAAAATCA
* * *
23513875 AGATCGAAATTA
1 AAATCAAAATCA
23513887 AAATCAAAATCA
1 AAATCAAAATCA
*
23513899 AAATCAGAATCA
1 AAATCAAAATCA
* *
23513911 GAATCAGAATCA
1 AAATCAAAATCA
*
23513923 GAATCA
1 AAATCA
23513929 GTGAGTGTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 64 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.23
Consensus pattern (12 bp):
AAATCAAAATCA
Found at i:23513929 original size:6 final size:6
Alignment explanation
Indices: 23513888--23513929 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
23513878 TCGAAATTAA
* *
23513888 AATCAA AATCAA AATCAG AATCAG AATCAG AATCAG AATCAG
1 AATCAG AATCAG AATCAG AATCAG AATCAG AATCAG AATCAG
23513930 TGAGTGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.17
Consensus pattern (6 bp):
AATCAG
Found at i:23513955 original size:12 final size:12
Alignment explanation
Indices: 23513938--23513986 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
23513928 AGTGAGTGTT
*
23513938 TCAAAATTGAAA
1 TCAAAATCGAAA
23513950 TCAAAATCGAAA
1 TCAAAATCGAAA
*
23513962 TCAAAATCAAAA
1 TCAAAATCGAAA
*
23513974 TTAAAATCGAAA
1 TCAAAATCGAAA
23513986 T
1 T
23513987 AACCCTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.22
Consensus pattern (12 bp):
TCAAAATCGAAA
Found at i:23513956 original size:6 final size:6
Alignment explanation
Indices: 23513947--23513986 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
23513937 TTCAAAATTG
* * *
23513947 AAATCA AAATCG AAATCA AAATCA AAATTA AAATCG AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
23513987 AACCCTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.20
Consensus pattern (6 bp):
AAATCA
Found at i:23514477 original size:21 final size:21
Alignment explanation
Indices: 23514451--23514490 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
23514441 AACGTGGCAA
23514451 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
23514472 GTTAACTTGCCACATCAGC
1 GTTAACTTGCCACATCAGC
23514491 GGTCCCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:23514984 original size:23 final size:22
Alignment explanation
Indices: 23514958--23515000 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
23514948 AAAATTATGA
*
23514958 ATAAAATAATAGTAAAATAATAT
1 ATAAAATAAAAGT-AAATAATAT
*
23514981 ATAACATAAAAGTAAATAAT
1 ATAAAATAAAAGTAAATAAT
23515001 TGATGGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (22 bp):
ATAAAATAAAAGTAAATAATAT
Found at i:23522450 original size:3 final size:3
Alignment explanation
Indices: 23522444--23522475 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
23522434 AGAAGAAGAA
*
23522444 GAT GAT GAT GAT GAT GAT AAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
23522476 GGAAGATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:23523708 original size:31 final size:28
Alignment explanation
Indices: 23523631--23523699 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
23523621 TTTTTTAAAA
* * *
23523631 TAAAAAAAAACTTATTAGTTTACTATCT
1 TAAAAAAAAACTTAATAGTCTGCTATCT
23523659 TAAAAAAAAACTTAATAGTCTGCTATCT
1 TAAAAAAAAACTTAATAGTCTGCTATCT
*
23523687 TAAATAAAAACTT
1 TAAAAAAAAACTT
23523700 TCGAATAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAAAAAAAACTTAATAGTCTGCTATCT
Found at i:23526443 original size:27 final size:27
Alignment explanation
Indices: 23526413--23526464 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
23526403 CACAGCTTGT
* *
23526413 GTGAGCAGGCACGTTTTCACAACTCAC
1 GTGAGCAGACACATTTTCACAACTCAC
*
23526440 GTGAGCAGACCCATTTTCACAACTC
1 GTGAGCAGACACATTTTCACAACTC
23526465 GTATGAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (27 bp):
GTGAGCAGACACATTTTCACAACTCAC
Found at i:23528126 original size:110 final size:108
Alignment explanation
Indices: 23527724--23528128 Score: 421
Period size: 111 Copynumber: 3.7 Consensus size: 108
23527714 AATAATTATT
* * * * *
23527724 TATATAA--ATTAAATTAAAATAATTAAACTCGTAAATATAC--GTG--CGTGAATTAAGAAACT
1 TATATAATTATTAAATTAAAATAAATAAACACGTCAATATACATGCGCACGTGATTTAAGAAA-T
*
23527783 AATGAAAATTTTAAAATAATTATTTACTTTAATTGAGTAAAATAAA
65 AAT--AAATTTTAAAATAATTATTTACATTAATTGAGTAAAATAAA
* * *
23527829 TATATAATTATTAAATTAAAACAAATAGACACGAT-AATATA-AGTGTGCACGTGATTTAAGAAA
1 TATATAATTATTAAATTAAAATAAATAAACACG-TCAATATACA-TGCGCACGTGATTTAAGAAA
*
23527892 TTAATAACTTTTAAAAAATAATTATTTACATTAATTGAGTAAAATAAA
64 -TAATAAATTTT--AAAATAATTATTTACATTAATTGAGTAAAATAAA
* * * * * *
23527940 TATATAGTTATTAAATTAAAATAAATAAATACATCAATATACGTGCGCACGTTATTTGAGAAACT
1 TATATAATTATTAAATTAAAATAAATAAACACGTCAATATACATGCGCACGTGATTTAAGAAA-T
* * * *
23528005 AATAATTTTTTAAAATAGTTATTTAAATTAATTAAGTAAAATAAA
65 AATAA-ATTTTAAAATAATTATTTACATTAATTGAGTAAAATAAA
* * ** *
23528050 TATATAATTAATTAAATTAAAATAAAAAAACGCGTCAATGGACATGGGCACGTGATTTAAGAAAT
1 TATATAATT-ATTAAATTAAAATAAATAAACACGTCAATATACATGCGCACGTGATTTAAGAAAT
23528115 AAATAAATTTTAAA
65 -AATAAATTTTAAA
23528129 CATTTAAAAA
Statistics
Matches: 251, Mismatches: 34, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
105 7 0.03
107 26 0.10
108 1 0.00
109 9 0.04
110 48 0.19
111 156 0.62
112 4 0.02
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (108 bp):
TATATAATTATTAAATTAAAATAAATAAACACGTCAATATACATGCGCACGTGATTTAAGAAATA
ATAAATTTTAAAATAATTATTTACATTAATTGAGTAAAATAAA
Found at i:23528863 original size:29 final size:30
Alignment explanation
Indices: 23528807--23528865 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
23528797 TAATTGGATT
23528807 AAATCAAAATTTTATGTATAAAATTACACA
1 AAATCAAAATTTTATGTATAAAATTACACA
*
23528837 AAATCAAAATTTT-TGTATACAATTACACA
1 AAATCAAAATTTTATGTATAAAATTACACA
23528866 TTAAACTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTTTATGTATAAAATTACACA
Found at i:23530419 original size:30 final size:29
Alignment explanation
Indices: 23530383--23530448 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
23530373 AATTAGTAAA
*
23530383 AATAAAATTGTAATTTAA-CCTCTTAAAAAT
1 AATAAAAAT-TAATTTAATCCT-TTAAAAAT
23530413 AATAAAAAATTAATTTAATCCTTTAAAAAT
1 AAT-AAAAATTAATTTAATCCTTTAAAAAT
*
23530443 TATAAA
1 AATAAA
23530449 GATATAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.09
30 21 0.66
31 8 0.25
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (29 bp):
AATAAAAATTAATTTAATCCTTTAAAAAT
Found at i:23530603 original size:7 final size:7
Alignment explanation
Indices: 23530591--23530619 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
23530581 AACTCTAACC
23530591 AGTCCCA
1 AGTCCCA
23530598 AGTCCCA
1 AGTCCCA
23530605 AGTCCCA
1 AGTCCCA
23530612 AGTCCCA
1 AGTCCCA
23530619 A
1 A
23530620 CACATAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.41, G:0.14, T:0.14
Consensus pattern (7 bp):
AGTCCCA
Found at i:23535325 original size:29 final size:34
Alignment explanation
Indices: 23535292--23535354 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 34
23535282 TTTTATTTCA
23535292 ATACTTT-A-ATTTTTAATT-T-AAATAA-AAAT
1 ATACTTTAATATTTTTAATTATAAAATAACAAAT
23535321 ATACTTTAATATTTTTAATTATAAAATAACAAAT
1 ATACTTTAATATTTTTAATTATAAAATAACAAAT
23535355 TTTAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 7 0.24
30 1 0.03
31 10 0.34
32 1 0.03
33 6 0.21
34 4 0.14
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (34 bp):
ATACTTTAATATTTTTAATTATAAAATAACAAAT
Found at i:23536860 original size:3 final size:3
Alignment explanation
Indices: 23536814--23536846 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
23536804 GTTAACCTTC
23536814 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
23536847 TATTTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:23536875 original size:18 final size:18
Alignment explanation
Indices: 23536815--23536876 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
23536805 TTAACCTTCC
23536815 TTCTTCTTCTTCTTCT--T
1 TTCTTCTTCTTCTT-TAAT
*
23536832 CTTCTTCTTCTTCTTTATT
1 -TTCTTCTTCTTCTTTAAT
*
23536851 TTTTTCTTC-TCTTTAGAT
1 TTCTTCTTCTTCTTTA-AT
23536869 TTCTTCTT
1 TTCTTCTT
23536877 GGTATTCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
17 7 0.18
18 30 0.79
19 1 0.03
ACGTcount: A:0.05, C:0.24, G:0.02, T:0.69
Consensus pattern (18 bp):
TTCTTCTTCTTCTTTAAT
Found at i:23543813 original size:22 final size:24
Alignment explanation
Indices: 23543768--23543815 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
23543758 TGGCTCTATG
*
23543768 CTTTATCCTTGTTTTTTCATTAAT
1 CTTTATCCTTGTTTTTTCACTAAT
*
23543792 CTTTGTCCTTG-TTTTTC-CTAAT
1 CTTTATCCTTGTTTTTTCACTAAT
23543814 CT
1 CT
23543816 CTCCTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 6 0.27
24 10 0.45
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.60
Consensus pattern (24 bp):
CTTTATCCTTGTTTTTTCACTAAT
Found at i:23544386 original size:6 final size:6
Alignment explanation
Indices: 23544377--23544407 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
23544367 GTATTTTAGT
23544377 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG A
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG A
23544408 CAACAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (6 bp):
ATTTTG
Found at i:23556024 original size:1 final size:1
Alignment explanation
Indices: 23556020--23556053 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
23556010 AACAAAAACC
* *
23556020 AAAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23556054 CGCAATAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:23559361 original size:30 final size:30
Alignment explanation
Indices: 23559327--23559418 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
23559317 CTTAACAAGT
* *
23559327 AAATGCCTCTAAAATAATAATAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
23559357 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
*
23559387 AAATGCCTTTAAAATAATAAGAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
23559417 AA
1 AA
23559419 TAAAATAAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.26
Consensus pattern (30 bp):
AAATGCCTTTAAAATAATAACAAAATTAAC
Found at i:23560082 original size:22 final size:22
Alignment explanation
Indices: 23560057--23560099 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23560047 TGATGTTGTT
23560057 TTGCTATCATTTTATTATTATG
1 TTGCTATCATTTTATTATTATG
* *
23560079 TTGCTATTATTTTATTGTTAT
1 TTGCTATCATTTTATTATTAT
23560100 CATTTAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (22 bp):
TTGCTATCATTTTATTATTATG
Found at i:23562668 original size:21 final size:22
Alignment explanation
Indices: 23562642--23562700 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
23562632 GTTTTAAGAA
*
23562642 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
23562663 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
23562685 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
23562701 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:23562715 original size:26 final size:24
Alignment explanation
Indices: 23562671--23562720 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
23562661 ATTTGTTTTA
*
23562671 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
23562695 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
23562721 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:23572097 original size:19 final size:21
Alignment explanation
Indices: 23572075--23572127 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
23572065 AGCCAATCAG
23572075 AAGCTC-GAA-AGCTGAACAA
1 AAGCTCAGAAGAGCTGAACAA
*
23572094 AAGCTCATAAGAGCTGAACAA
1 AAGCTCAGAAGAGCTGAACAA
* *
23572115 AAACTCATAAGAG
1 AAGCTCAGAAGAG
23572128 TTTAACAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.20
20 2 0.07
21 22 0.73
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (21 bp):
AAGCTCAGAAGAGCTGAACAA
Found at i:23572134 original size:21 final size:21
Alignment explanation
Indices: 23572084--23572127 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
23572074 GAAGCTCGAA
*
23572084 AGCTGAACAAAAGCTCATAAG
1 AGCTGAACAAAAACTCATAAG
23572105 AGCTGAACAAAAACTCATAAG
1 AGCTGAACAAAAACTCATAAG
23572126 AG
1 AG
23572128 TTTAACAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (21 bp):
AGCTGAACAAAAACTCATAAG
Found at i:23575240 original size:10 final size:10
Alignment explanation
Indices: 23575227--23575334 Score: 55
Period size: 10 Copynumber: 11.1 Consensus size: 10
23575217 ATTTCTTTAC
23575227 ATTTTTTATA
1 ATTTTTTATA
**
23575237 ATTTTCTTACG
1 ATTTT-TTATA
* * *
23575248 ACTTTATAAA
1 ATTTTTTATA
*
23575258 ATTTTATA-A
1 ATTTTTTATA
23575267 ATTTTTCTAT-
1 ATTTTT-TATA
*
23575277 A-TTTCTAT-
1 ATTTTTTATA
*
23575285 ATATTTTATA
1 ATTTTTTATA
* *
23575295 TTTTTTTATG
1 ATTTTTTATA
23575305 A-TTTTTATA
1 ATTTTTTATA
*
23575314 ATTTTTTCTA
1 ATTTTTTATA
*
23575324 ATTTTTAATA
1 ATTTTTTATA
23575334 A
1 A
23575335 AAATTTAATA
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
8 4 0.05
9 22 0.30
10 40 0.55
11 7 0.10
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:23575310 original size:19 final size:19
Alignment explanation
Indices: 23575288--23575330 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
23575278 TTTCTATATA
* *
23575288 TTTTATATTTTTTTATGAT
1 TTTTATAATTTTTTATAAT
*
23575307 TTTTATAATTTTTTCTAAT
1 TTTTATAATTTTTTATAAT
23575326 TTTTA
1 TTTTA
23575331 ATAAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATAATTTTTTATAAT
Found at i:23575343 original size:28 final size:28
Alignment explanation
Indices: 23575312--23575370 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
23575302 ATGATTTTTA
*
23575312 TAATTTTTTCTA-ATTTTTAATAAAAATT
1 TAATTATTTCTATATTTTT-ATAAAAATT
*
23575340 TAA-TATTTCTATATTTTTATTAAAATT
1 TAATTATTTCTATATTTTTATAAAAATT
23575367 TAAT
1 TAAT
23575371 ATAACTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
TAATTATTTCTATATTTTTATAAAAATT
Found at i:23575348 original size:27 final size:27
Alignment explanation
Indices: 23575318--23575372 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
23575308 TTTATAATTT
23575318 TTTCTA-ATTTTTAATAAAAATTTAATA
1 TTTCTATATTTTT-ATAAAAATTTAATA
*
23575345 TTTCTATATTTTTATTAAAATTTAATA
1 TTTCTATATTTTTATAAAAATTTAATA
23575372 T
1 T
23575373 AACTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTCTATATTTTTATAAAAATTTAATA
Found at i:23577036 original size:17 final size:17
Alignment explanation
Indices: 23577011--23577043 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23577001 CCACTGAGTC
*
23577011 TCTATCAATGGACATTA
1 TCTACCAATGGACATTA
23577028 TCTACCAATGGACATT
1 TCTACCAATGGACATT
23577044 CAATGGGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (17 bp):
TCTACCAATGGACATTA
Found at i:23580020 original size:6 final size:6
Alignment explanation
Indices: 23580009--23580047 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
23579999 TGGAGGGATA
23580009 TGTGGC TGTGGC TGTGGC TGTGGC TGTGGC TGTGGC TGT
1 TGTGGC TGTGGC TGTGGC TGTGGC TGTGGC TGTGGC TGT
23580048 TCACAACTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.49, T:0.36
Consensus pattern (6 bp):
TGTGGC
Found at i:23580461 original size:14 final size:14
Alignment explanation
Indices: 23580434--23580478 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
23580424 AAAATAAAAT
23580434 ATTAAAATAATTAGA
1 ATTAAAA-AATTAGA
23580449 ATTAAAAAATTAG-
1 ATTAAAAAATTAGA
*
23580462 ATTAAGAAATTA-A
1 ATTAAAAAATTAGA
23580475 ATTA
1 ATTA
23580479 GGTGCCCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 15 0.54
14 6 0.21
15 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
ATTAAAAAATTAGA
Found at i:23587308 original size:37 final size:37
Alignment explanation
Indices: 23587267--23587339 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
23587257 AAATTTATAC
23587267 TTAAACTATCCTTCCGTTATCCGGTTTAACTTTTTTT
1 TTAAACTATCCTTCCGTTATCCGGTTTAACTTTTTTT
**
23587304 TTAAACTATCCTTCCGTTATCTTGTTTAACTTTTTT
1 TTAAACTATCCTTCCGTTATCCGGTTTAACTTTTTT
23587340 GTAACAGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (37 bp):
TTAAACTATCCTTCCGTTATCCGGTTTAACTTTTTTT
Found at i:23587650 original size:7 final size:7
Alignment explanation
Indices: 23587640--23587686 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
23587630 AAAGAGTTTA
23587640 AAAATAT
1 AAAATAT
23587647 AAAATAT
1 AAAATAT
23587654 AAAATAT
1 AAAATAT
*
23587661 AAAATTCT
1 AAAA-TAT
*
23587669 AAAAAAT
1 AAAATAT
23587676 ATAAATAT
1 A-AAATAT
23587684 AAA
1 AAA
23587687 TTTTAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 22 0.65
8 12 0.35
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATAT
Found at i:23587659 original size:14 final size:14
Alignment explanation
Indices: 23587640--23587686 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
23587630 AAAGAGTTTA
23587640 AAAATATAAAATAT
1 AAAATATAAAATAT
*
23587654 AAAATATAAAATTCT
1 AAAATATAAAA-TAT
*
23587669 AAAAAATATAAATAT
1 AAAATATA-AAATAT
23587684 AAA
1 AAA
23587687 TTTTAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.39
15 14 0.50
16 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATATAAAATAT
Found at i:23587671 original size:22 final size:20
Alignment explanation
Indices: 23587646--23587702 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
23587636 TTTAAAAATA
23587646 TAAAATATAAAATATAAAATTC
1 TAAAA-ATAAAATAT-AAATTC
*
23587668 TAAAAAATATAAATATAAATTT
1 T-AAAAATA-AAATATAAATTC
23587690 TAAAGAATAAAAT
1 TAAA-AATAAAAT
23587703 TATTATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 7 0.23
22 14 0.45
23 10 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAATAAAATATAAATTC
Found at i:23587876 original size:59 final size:61
Alignment explanation
Indices: 23587810--23587926 Score: 166
Period size: 59 Copynumber: 1.9 Consensus size: 61
23587800 TAATGACAAA
* *
23587810 TTTTCAATTTTTACAAAATATTTTGA-TT-TTTTAAAAATTTATATTTATATTTTTTCAAT
1 TTTTCAATTTTTACAAAATATTTTGATTTCTTTTAAAAATTTATAATTATATATTTTCAAT
* * *
23587869 TTTTCAATTTTTATATAATATTTTGATTTTCTTTTTAAAATTTATAATTATATATTTT
1 TTTTCAATTTTTACAAAATATTTTGA-TTTCTTTTAAAAATTTATAATTATATATTTT
23587927 AGAATTTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 24 0.48
61 2 0.04
62 24 0.48
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (61 bp):
TTTTCAATTTTTACAAAATATTTTGATTTCTTTTAAAAATTTATAATTATATATTTTCAAT
Found at i:23588723 original size:12 final size:12
Alignment explanation
Indices: 23588706--23588730 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23588696 AAAATTAATA
23588706 TAAATATTTTTT
1 TAAATATTTTTT
23588718 TAAATATTTTTT
1 TAAATATTTTTT
23588730 T
1 T
23588731 GAGACATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAAATATTTTTT
Found at i:23593098 original size:6 final size:6
Alignment explanation
Indices: 23593090--23593140 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
23593080 TTCGGTTTCA
* * *
23593090 ATTTTA ATTTTG ATTTTG ATTTTG ATTTTG ATTTTT ATTTCG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
23593138 ATT
1 ATT
23593141 ACAATTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.67
Consensus pattern (6 bp):
ATTTTG
Found at i:23593111 original size:18 final size:18
Alignment explanation
Indices: 23593089--23593150 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
23593079 TTTCGGTTTC
*
23593089 AATTTTAATTTTGATTTT
1 AATTTTGATTTTGATTTT
*
23593107 GATTTTGATTTTGATTTT
1 AATTTTGATTTTGATTTT
* * **
23593125 TATTTCGATTTTGATTAC
1 AATTTTGATTTTGATTTT
23593143 AATTTTGA
1 AATTTTGA
23593151 AACACTCACT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.61
Consensus pattern (18 bp):
AATTTTGATTTTGATTTT
Found at i:23593781 original size:15 final size:15
Alignment explanation
Indices: 23593756--23593801 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
23593746 TGAAGAAAAC
23593756 ATGTCTAGTAGTGAT
1 ATGTCTAGTAGTGAT
* *
23593771 GTGTCTGGTAGTGAT
1 ATGTCTAGTAGTGAT
23593786 ATGTCTAGTAGTGAT
1 ATGTCTAGTAGTGAT
23593801 A
1 A
23593802 GTGATGCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.30, T:0.39
Consensus pattern (15 bp):
ATGTCTAGTAGTGAT
Found at i:23595508 original size:40 final size:40
Alignment explanation
Indices: 23595453--23595595 Score: 232
Period size: 40 Copynumber: 3.5 Consensus size: 40
23595443 TAGTAAATGT
* * *
23595453 TTTTTTAATATGCATGCACTGATTGTTGGCGTGTTGACTA
1 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGCCTA
23595493 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGCCTA
1 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGCCTA
*
23595533 TTTTTTAATATGCATGCAGTGATTGTTGATGTGTTGCCTA
1 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGCCTA
*
23595573 TTTTTTTAATATGTATGCAGTGA
1 -TTTTTTAATATGCATGCAGTGA
23595596 CTATTTTTTT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
40 76 0.78
41 21 0.22
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.48
Consensus pattern (40 bp):
TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTTGCCTA
Found at i:23596060 original size:20 final size:20
Alignment explanation
Indices: 23596035--23596074 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23596025 GGGGCACACA
23596035 CCCGTGTAGCCTGGGACATG
1 CCCGTGTAGCCTGGGACATG
*
23596055 CCCGTGTGGCCTGGGACATG
1 CCCGTGTAGCCTGGGACATG
23596075 GCCATGAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.30, G:0.38, T:0.20
Consensus pattern (20 bp):
CCCGTGTAGCCTGGGACATG
Found at i:23599607 original size:38 final size:38
Alignment explanation
Indices: 23599556--23599679 Score: 162
Period size: 38 Copynumber: 3.3 Consensus size: 38
23599546 GTTAGCCATG
23599556 TATACCAGCAACCATGTATAACATATATTAAGCAACAA
1 TATACCAGCAACCATGTATAACATATATTAAGCAACAA
* *
23599594 TATACCAGCAACCATGTATAACATATGTTAAGCAACAG
1 TATACCAGCAACCATGTATAACATATATTAAGCAACAA
* * * *
23599632 TATACCAGTAGCCATGTATACCA-ACA-TAAGCAACAA
1 TATACCAGCAACCATGTATAACATATATTAAGCAACAA
* *
23599668 TTTACTAGCAAC
1 TATACCAGCAAC
23599680 AAAATTACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
36 17 0.23
37 1 0.01
38 56 0.76
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (38 bp):
TATACCAGCAACCATGTATAACATATATTAAGCAACAA
Found at i:23600778 original size:41 final size:41
Alignment explanation
Indices: 23600685--23600885 Score: 219
Period size: 41 Copynumber: 5.0 Consensus size: 41
23600675 ATTTAAAATA
* * *** *
23600685 CAGAGCAATAGCGGCGTTTTACAAAAAACG-CTCTAAAAA-
1 CAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAC
*
23600724 CAGAGCATTAGCGGCGCTTTAGGTAAAACGCCACTAAAAAC
1 CAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAC
* * * *
23600765 CAGAGTAGTAGCGGCGCTTTTGATAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAC
** * *
23600806 CAGAGCATTAGTTGCGCTTTTGGTAAAACGCCGCTAAAATC
1 CAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAC
* *
23600847 CAGGGAATTAGCGGCGCTTTTA-GTAAAACGCCGCTAAAA
1 CAGAGCATTAGCGGCGC-TTTAGGTAAAACGCCGCTAAAA
23600886 GTCATATAAC
Statistics
Matches: 137, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
39 25 0.18
40 8 0.06
41 101 0.74
42 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (41 bp):
CAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAC
Found at i:23600833 original size:82 final size:81
Alignment explanation
Indices: 23600709--23600885 Score: 241
Period size: 82 Copynumber: 2.2 Consensus size: 81
23600699 CGTTTTACAA
* *
23600709 AAAACG-CTCTAAAAACAGAGCATTAGCGGCGCTTTAGGTAAAACGCCACTAAAAACCAGAGTAG
1 AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTAGGTAAAACGCCACTAAAAACCAGAGAAG
23600773 TAGCGGCGCTTTT-GAT
66 TAGCGGCGCTTTTAG-T
** * * * *
23600789 AAAACGCCGCTAAAAACCAGAGCATTAGTTGCGCTTTTGGTAAAACGCCGCTAAAATCCAGGGAA
1 AAAACGCCGCTAAAAA-CAGAGCATTAGCGGCGCTTTAGGTAAAACGCCACTAAAAACCAGAGAA
*
23600854 TTAGCGGCGCTTTTAGT
65 GTAGCGGCGCTTTTAGT
23600871 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
23600886 GTCATATAAC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
80 6 0.07
81 8 0.09
82 70 0.82
83 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (81 bp):
AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTAGGTAAAACGCCACTAAAAACCAGAGAAG
TAGCGGCGCTTTTAGT
Found at i:23601065 original size:14 final size:14
Alignment explanation
Indices: 23601043--23601087 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
23601033 TTAATTATCA
*
23601043 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
23601057 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
23601071 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
23601085 TTA
1 TTA
23601088 AGCAAGTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:23601078 original size:21 final size:21
Alignment explanation
Indices: 23601054--23601138 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 21
23601044 TATAGTTTAA
*
23601054 GGTTTATGGTTTAAGATATAT
1 GGTTTAGGGTTTAAGATATAT
*
23601075 GGTTTAGGGTTTAAGCAAGTTTAT
1 GGTTTAGGGTTTAAG--A-TATAT
*
23601099 GAGTTAACTATGGTTTAAGATATAT
1 G-GTT---TAGGGTTTAAGATATAT
23601124 GGTTTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
23601139 GTTTAGGAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
21 24 0.46
23 1 0.02
24 8 0.15
25 8 0.15
26 1 0.02
28 10 0.19
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.42
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATATAT
Found at i:23601115 original size:49 final size:46
Alignment explanation
Indices: 23601058--23601154 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 46
23601048 GTTTAAGGTT
*
23601058 TATGGTTTAAGATATATGGTTTAGGGTTTAAGCAAGTTTATGAGTTAAC
1 TATGGTTTAAGATATATGGTTTAGGGTTTAAG---GTTTAGGAGTTAAC
23601107 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
23601153 TA
1 TA
23601155 GTATTTGAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
46 15 0.32
49 32 0.68
ACGTcount: A:0.30, C:0.03, G:0.26, T:0.41
Consensus pattern (46 bp):
TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
Found at i:23601621 original size:8 final size:8
Alignment explanation
Indices: 23601608--23601636 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
23601598 TTATGTTTAG
23601608 TATATTAT
1 TATATTAT
23601616 TATATTAT
1 TATATTAT
23601624 TATATTAT
1 TATATTAT
23601632 TATAT
1 TATAT
23601637 AATAAAAATA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:23602969 original size:15 final size:15
Alignment explanation
Indices: 23602949--23603005 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
23602939 CGATGAATTT
23602949 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
23602964 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
23602979 ATTGAATTTATATTG
1 ATTGAATTTATATTG
23602994 ATTGAA-TTATAT
1 ATTGAATTTATAT
23603006 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:23603407 original size:23 final size:23
Alignment explanation
Indices: 23603377--23603463 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
23603367 GCTTTATCGA
* *
23603377 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
23603400 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
23603421 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
23603443 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
23603464 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:23605081 original size:7 final size:7
Alignment explanation
Indices: 23605069--23605096 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
23605059 AAAAAGCTTA
23605069 AATATTT
1 AATATTT
23605076 AATATTT
1 AATATTT
23605083 AATATTT
1 AATATTT
23605090 AATATTT
1 AATATTT
23605097 TAGTCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:23608536 original size:19 final size:19
Alignment explanation
Indices: 23608486--23608564 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 19
23608476 CTTGCTGTAT
* *
23608486 TTTATTTATATCTTTA-TA
1 TTTATTTTTATTTTTATTA
* * *
23608504 TTTAATCTAATTTTTATTA
1 TTTATTTTTATTTTTATTA
* *
23608523 TTTA-TTTTAGTTTTGATTC
1 TTTATTTTTA-TTTTTATTA
* *
23608542 TATATTTTTATTTTTAATA
1 TTTATTTTTATTTTTATTA
23608561 TTTA
1 TTTA
23608565 ATAACTTGAG
Statistics
Matches: 44, Mismatches: 14, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
18 14 0.32
19 25 0.57
20 5 0.11
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATTTTTATTTTTATTA
Found at i:23608885 original size:43 final size:43
Alignment explanation
Indices: 23608821--23608941 Score: 197
Period size: 43 Copynumber: 2.8 Consensus size: 43
23608811 TTTCATGACC
* *
23608821 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCGCGGCT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCGCGGCT
*
23608864 TTTAGCGGCGTTTGTGAGAAAAGCGCAGCTAAAGGTCGCGGCT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCGCGGCT
* *
23608907 TTTAGAGGCGTTTGTGAGAAAAGCGTCGCTAAAGG
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGG
23608942 CTATGACTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.25
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCGCGGCT
Found at i:23608952 original size:43 final size:42
Alignment explanation
Indices: 23608821--23608958 Score: 161
Period size: 43 Copynumber: 3.2 Consensus size: 42
23608811 TTTCATGACC
* * * *
23608821 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCGCGGCT
1 TTTAGCGGCGTTTGTGAGAAAAGCG-CGCTAAAGGTCACGACT
* *
23608864 TTTAGCGGCGTTTGTGAGAAAAGCGCAGCTAAAGGTCGCGGCT
1 TTTAGCGGCGTTTGTGAGAAAAGCGC-GCTAAAGGTCACGACT
* *
23608907 TTTAGAGGCGTTTGTGAGAAAAGCGTCGCTAAAGG-CTATGACT
1 TTTAGCGGCGTTTGTGAGAAAAGCG-CGCTAAAGGTC-ACGACT
23608950 TTTAGCGGC
1 TTTAGCGGC
23608959 ATTTTTTGTA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
42 2 0.02
43 82 0.96
44 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCGCTAAAGGTCACGACT
Found at i:23612988 original size:31 final size:31
Alignment explanation
Indices: 23612919--23612999 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
23612909 TTAATGTATT
* * * *
23612919 AATATATATGTAAAATTTTAATTGTGGTTTA
1 AATATACATTTAAAAATTTAATTGTGATTTA
*
23612950 AATATACATTTAAAAATTTAATTTTGATTTA
1 AATATACATTTAAAAATTTAATTGTGATTTA
*
23612981 ATCATACACATTTTAAAAA
1 A--ATATACA-TTTAAAAA
23613000 ATAAATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 27 0.66
33 6 0.15
34 8 0.20
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (31 bp):
AATATACATTTAAAAATTTAATTGTGATTTA
Found at i:23615184 original size:4 final size:4
Alignment explanation
Indices: 23615177--23615209 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
23615167 ACATACATAC
23615177 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
23615210 AGATACATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:23618297 original size:131 final size:131
Alignment explanation
Indices: 23617974--23618509 Score: 596
Period size: 132 Copynumber: 4.1 Consensus size: 131
23617964 TTTTTTAGAT
** * *
23617974 TTTTTAAGAAACATGAGG-GAAATTCTAAAGGGGATGTTCGATTATTTTGAACTAAC-AGGAAAT
1 TTTTTAA-AAACAT-AGGTGAAATTCTAAA-GGGACCTTCGATTACTTTGAACAAACGA-GAAAT
* * * * * * * ** *
23618037 TGCAAACCAGCATGATAGGGTACGATTCCCCAAATTGCCAAACATCGAACATTACCTTCGTTTTG
62 TGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTA
*
23618102 GA-GA
127 AAGGA
* * * * * *
23618106 GTTTTTAGAAAACATAAGTGAAATTCAAAAGGGACCTTCAACTATTTTGAACAAACGAGAAATTC
1 -TTTTTA-AAAACATAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAACAAACGAGAAATTG
* * *
23618171 CAACCCAGCACGATAGGGCACGATTCCGCGAATTGTCAAATATTGAACATCGCCTTCG-TTTAAA
64 CAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAA
23618235 GGA
129 GGA
*
23618238 TTTTTAAAAGACATAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAGCAAACGAGAAATTGC
1 TTTTTAAAA-ACATAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAACAAACGAGAAATTGC
* * * * *
23618303 AACCCAACAC-ATTATGGCACGATCCCGCGAATTGCCAAGTATCGAATATCGCCTCCGTTTTAAA
65 AACCCAACACGA-TAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAA
23618367 GGA
129 GGA
* * * **
23618370 TTTATAAAAGACATGGGTGAAATTCTAAAGGGATCTTCGATTACTTTGGGCAAACGAGAAATTGC
1 TTTTTAAAA-ACATAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAACAAACGAGAAATTGC
* * *
23618435 AACCCAACACGTTAGGGCACGATTCCTCGAATTGCCAAATATCGAATATCGCCTTCGTTTTAAAG
65 AACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAG
*
23618500 AA
130 GA
*
23618502 TTCTTAAA
1 TTTTTAAA
23618510 TAATTGTGAA
Statistics
Matches: 347, Mismatches: 48, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
130 4 0.01
131 105 0.30
132 214 0.62
133 23 0.07
134 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (131 bp):
TTTTTAAAAACATAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAACAAACGAGAAATTGCA
ACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGG
A
Found at i:23619543 original size:2 final size:2
Alignment explanation
Indices: 23619536--23619566 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23619526 CTTTAACACA
23619536 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
23619567 ATAGACTAAA
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:23619882 original size:30 final size:30
Alignment explanation
Indices: 23619848--23619904 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
23619838 CAAAGTCCAT
23619848 AAGTATAATAGTATATGAGAATATTAAGTC
1 AAGTATAATAGTATATGAGAATATTAAGTC
23619878 AAGTATAATAGTATATGAGAATATTAA
1 AAGTATAATAGTATATGAGAATATTAA
23619905 AATAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (30 bp):
AAGTATAATAGTATATGAGAATATTAAGTC
Found at i:23624411 original size:2 final size:2
Alignment explanation
Indices: 23624404--23624428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23624394 TGATTTAACT
23624404 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
23624429 GATAATATGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23625022 original size:20 final size:20
Alignment explanation
Indices: 23624997--23625036 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23624987 AATATGGGTA
* *
23624997 AATTATATAGATATTCATTT
1 AATTATATAAAAATTCATTT
23625017 AATTATATAAAAATTCATTT
1 AATTATATAAAAATTCATTT
23625037 TAGGCAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
AATTATATAAAAATTCATTT
Found at i:23626412 original size:12 final size:13
Alignment explanation
Indices: 23626395--23626423 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
23626385 GTTAAGATTG
23626395 ATTTAATAT-TTA
1 ATTTAATATATTA
23626407 ATTTAATATATTA
1 ATTTAATATATTA
23626420 ATTT
1 ATTT
23626424 TGATTATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTAATATATTA
Found at i:23636637 original size:42 final size:42
Alignment explanation
Indices: 23636554--23636639 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 42
23636544 GAAGCTAAAT
*
23636554 TAGATCCAAAAAACTAAGCTTGCAAGGAAAATAGTGTTTGTA
1 TAGATCCAAAAAACTAAGCTTGCAAGGAAAATACTGTTTGTA
* *
23636596 TAGATCCAGAAAATTATAG-TTGCAAGGAAAATACTAG-TTGTA
1 TAGATCCAAAAAACTA-AGCTTGCAAGGAAAATACT-GTTTGTA
23636638 TA
1 TA
23636640 AACCCTGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (42 bp):
TAGATCCAAAAAACTAAGCTTGCAAGGAAAATACTGTTTGTA
Found at i:23638997 original size:17 final size:17
Alignment explanation
Indices: 23638977--23639016 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
23638967 AAAATATTTT
23638977 AATATAATTTAATATAA
1 AATATAATTTAATATAA
23638994 AATAT--TTTAATATAA
1 AATATAATTTAATATAA
23639009 AA-ATAATT
1 AATATAATT
23639017 ATATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 12 0.57
16 2 0.10
17 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATAATTTAATATAA
Found at i:23639013 original size:16 final size:15
Alignment explanation
Indices: 23638966--23639010 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
23638956 ATAAAATATT
23638966 TAAAATATTTTAATA
1 TAAAATATTTTAATA
23638981 T---A-A-TTTAATA
1 TAAAATATTTTAATA
23638991 TAAAATATTTTAATA
1 TAAAATATTTTAATA
23639006 TAAAA
1 TAAAA
23639011 ATAATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
10 8 0.32
11 1 0.04
12 1 0.04
13 1 0.04
14 1 0.04
15 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATATTTTAATA
Found at i:23639066 original size:11 final size:10
Alignment explanation
Indices: 23639013--23639079 Score: 59
Period size: 11 Copynumber: 6.6 Consensus size: 10
23639003 ATATAAAAAT
23639013 AATTATATTAA
1 AATTATATT-A
*
23639024 AAATACTATTA
1 AATTA-TATTA
23639035 AATTATA-T-
1 AATTATATTA
23639043 -ATTATTATTA
1 AATTA-TATTA
23639053 AATTATATTA
1 AATTATATTA
*
23639063 AAATATGATTA
1 AATTAT-ATTA
23639074 AATTAT
1 AATTAT
23639080 TTATTTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
7 4 0.09
8 2 0.04
9 2 0.04
10 12 0.26
11 22 0.48
12 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (10 bp):
AATTATATTA
Done.