Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 84 of 187
Found at i:25013104 original size:15 final size:16
Alignment explanation
Indices: 25013084--25013121 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
25013074 TTAATTTTGT
*
25013084 ATTTTAATTTC-ATCA
1 ATTTTAATTTCTATAA
25013099 ATTTTAATTTCTATAA
1 ATTTTAATTTCTATAA
25013115 ATTTTAA
1 ATTTTAA
25013122 AATTAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAATTTCTATAA
Found at i:25027579 original size:8 final size:7
Alignment explanation
Indices: 25027553--25027583 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
25027543 TGACTCGGGG
25027553 CCCAAAA
1 CCCAAAA
25027560 CCCAAAA
1 CCCAAAA
25027567 CCCAAACA
1 CCCAAA-A
25027575 CCCAAAA
1 CCCAAAA
25027582 CC
1 CC
25027584 TAAACTGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (7 bp):
CCCAAAA
Found at i:25027579 original size:15 final size:15
Alignment explanation
Indices: 25027553--25027588 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
25027543 TGACTCGGGG
25027553 CCCAAA-ACCCAAAA
1 CCCAAACACCCAAAA
25027567 CCCAAACACCCAAAA
1 CCCAAACACCCAAAA
*
25027582 CCTAAAC
1 CCCAAAC
25027589 TGCTACTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.53, C:0.44, G:0.00, T:0.03
Consensus pattern (15 bp):
CCCAAACACCCAAAA
Found at i:25028940 original size:2 final size:2
Alignment explanation
Indices: 25028933--25028983 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
25028923 ATAATTTACT
*
25028933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25028975 CT- TA TA TA T
1 -TA TA TA TA T
25028984 TTTTATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25029072 original size:44 final size:40
Alignment explanation
Indices: 25028929--25029072 Score: 118
Period size: 44 Copynumber: 3.5 Consensus size: 40
25028919 TTTCATAATT
* *
25028929 TACTTATATATATATATATATATATATATATATATATATATACA
1 TACTTATATATATAT-T-TTTAT-TTTATA-ATATATATATACA
* *
25028973 TACTTATATAT-T-TTTATATTTTATAA-CT-TATATACA
1 TACTTATATATATATTTTTATTTTATAATATATATATACA
*
25029009 TA-TCTATATACATATTTTTTAATTTTCATAAATATATATATACA
1 TACT-TATATATATA-TTTTT-ATTTT-AT-AATATATATATACA
25029053 TACTTATATATATAATTTTT
1 TACTTATATATAT-ATTTTT
25029073 TATATTTTAT
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
35 1 0.01
36 16 0.19
37 2 0.02
38 1 0.01
39 9 0.11
40 10 0.12
41 3 0.04
42 3 0.04
43 2 0.02
44 34 0.41
45 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (40 bp):
TACTTATATATATATTTTTATTTTATAATATATATATACA
Found at i:25029097 original size:80 final size:80
Alignment explanation
Indices: 25028960--25029114 Score: 172
Period size: 80 Copynumber: 1.9 Consensus size: 80
25028950 ATATATATAT
* * *
25028960 ATATATATATACATACTTATATATTTTTATATTTTATAACTTATATACATATCTATATACATAT-
1 ATATATATATACATACTTATATATTATAATATTTTATAACTTATATACATA--TATATATATATC
25029024 TTTTTA-ATTTTCATAA
64 TTTTTACATTTTCATAA
* ** *** *
25029040 ATATATATATACATACTTATATA-TATAATTTTTTATATTTTATAATTTTTTTATATATATATCT
1 ATATATATATACATACTTATATATTATAATATTTTATAACTTAT-ATACATATATATATATATCT
25029104 TTTTACATTTT
65 TTTTACATTTT
25029115 TATATTTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
78 10 0.16
79 21 0.34
80 31 0.50
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (80 bp):
ATATATATATACATACTTATATATTATAATATTTTATAACTTATATACATATATATATATATCTT
TTTACATTTTCATAA
Found at i:25029099 original size:34 final size:34
Alignment explanation
Indices: 25029056--25029122 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
25029046 ATATACATAC
*
25029056 TTATATATATAAT-TTTTTATA-TTTTATAATTTTT
1 TTATATATAT-ATCTTTTTACATTTTTAT-ATTTTT
25029090 TTATATATATATCTTTTTACATTTTTATATTTT
1 TTATATATATATCTTTTTACATTTTTATATTTT
25029123 ATTCATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 22 0.73
35 6 0.20
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (34 bp):
TTATATATATATCTTTTTACATTTTTATATTTTT
Found at i:25029100 original size:17 final size:16
Alignment explanation
Indices: 25029056--25029100 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
25029046 ATATACATAC
25029056 TTATATATATAATTTT
1 TTATATATATAATTTT
*
25029072 TTATATTTTATAATTTTT
1 TTATA-TATATAA-TTTT
25029090 TTATATATATA
1 TTATATATATA
25029101 TCTTTTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.20
17 11 0.44
18 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATATATAATTTT
Found at i:25029106 original size:17 final size:16
Alignment explanation
Indices: 25029056--25029108 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
25029046 ATATACATAC
*
25029056 TTATATATATAATTTT
1 TTATATATATATTTTT
*
25029072 TTATATTTTATAATTTTT
1 TTATA-TATAT-ATTTTT
*
25029090 TTATATATATATCTTT
1 TTATATATATATTTTT
25029106 TTA
1 TTA
25029109 CATTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 10 0.32
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATATATATATTTTT
Found at i:25029131 original size:24 final size:24
Alignment explanation
Indices: 25029087--25029132 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
25029077 TTTTATAATT
*
25029087 TTTTTATATATATATCTTTTTACA
1 TTTTTATATATATATCATTTTACA
*
25029111 TTTTTATAT-TTTATTCATTTTA
1 TTTTTATATATATA-TCATTTTA
25029133 TTTATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTATATATATATCATTTTACA
Found at i:25040678 original size:3 final size:3
Alignment explanation
Indices: 25040670--25040705 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
25040660 ACCACTTAAG
25040670 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
25040706 CCTCTTTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:25048239 original size:15 final size:15
Alignment explanation
Indices: 25048167--25048274 Score: 71
Period size: 15 Copynumber: 7.1 Consensus size: 15
25048157 CATAATATAG
25048167 CATAGTTCGCAAT-T
1 CATAGTTCGCAATAT
*
25048181 CATAGTTCTCAATAT
1 CATAGTTCGCAATAT
* *
25048196 CACT-GTTCTCAATTTAG
1 CA-TAGTTCGCAA--TAT
* *
25048213 CAGAGCTCGCAATAT
1 CATAGTTCGCAATAT
25048228 CATAGTTCGCAAT-T
1 CATAGTTCGCAATAT
* * *
25048242 GATAGTTTGCTAATAA
1 CATAGTTCGC-AATAT
25048258 CATAGGTTCGC-ATAT
1 CATA-GTTCGCAATAT
25048273 CA
1 CA
25048275 GCATAAGTCA
Statistics
Matches: 72, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
14 21 0.29
15 32 0.44
16 4 0.06
17 15 0.21
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (15 bp):
CATAGTTCGCAATAT
Found at i:25048294 original size:34 final size:34
Alignment explanation
Indices: 25048254--25048373 Score: 107
Period size: 34 Copynumber: 3.5 Consensus size: 34
25048244 TAGTTTGCTA
* * *
25048254 ATAACATAGGTTCGCATATCAGCATAAGTCATAC
1 ATAACATAGGTTCGCATAACAGAATAAGTCACAC
** *
25048288 ATAACATAGAATCGCATAACAGAATAATTCACAC
1 ATAACATAGGTTCGCATAACAGAATAAGTCACAC
* * * * **
25048322 ATAACATAGGTTAGGATCACAGTAT-AGTTTGCAC
1 ATAACATAGGTTCGCATAACAGAATAAG-TCACAC
*
25048356 ATAATATAGGTTCGCATA
1 ATAACATAGGTTCGCATA
25048374 TAACATTGGT
Statistics
Matches: 66, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
33 1 0.02
34 65 0.98
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (34 bp):
ATAACATAGGTTCGCATAACAGAATAAGTCACAC
Found at i:25048384 original size:17 final size:17
Alignment explanation
Indices: 25048364--25048406 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
25048354 ACATAATATA
*
25048364 GGTTCGCATATAACATT
1 GGTTCGCATATAACATG
*
25048381 GGTTTGCATATAACATG
1 GGTTCGCATATAACATG
25048398 GGTTCGCAT
1 GGTTCGCAT
25048407 CATAGTATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (17 bp):
GGTTCGCATATAACATG
Found at i:25048459 original size:68 final size:68
Alignment explanation
Indices: 25048314--25048466 Score: 153
Period size: 68 Copynumber: 2.2 Consensus size: 68
25048304 TAACAGAATA
* * **
25048314 ATTCACACATAACATAGGTTAGGATCACAGTATAGTTTGCACATAATATAGGTTCGCATATAACA
1 ATTCACATATAACATAGGTTAGCATCACAGTATAGTTCACACATAATATAGGTTCGCATATAACA
*
25048379 TTG
66 TAG
* ** * * * * * ** *
25048382 GTTTGCATATAACATGGGTTCGCATCATAGTATAGTTCACACGTAGTATAGGTTTTCATATCACA
1 ATTCACATATAACATAGGTTAGCATCACAGTATAGTTCACACATAATATAGGTTCGCATATAACA
25048447 TAG
66 TAG
*
25048450 ATTCACATATAGCATAG
1 ATTCACATATAACATAG
25048467 TAAGGCTCGC
Statistics
Matches: 64, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (68 bp):
ATTCACATATAACATAGGTTAGCATCACAGTATAGTTCACACATAATATAGGTTCGCATATAACA
TAG
Found at i:25053836 original size:43 final size:42
Alignment explanation
Indices: 25053760--25053885 Score: 137
Period size: 43 Copynumber: 3.0 Consensus size: 42
25053750 GAAACACATA
* * *
25053760 TATCACATAT-AATGCCATATCCCAGATATGGTCTTACATGT
1 TATCACATATCGATGCCATGTCCCAGACATGGTCTTACATGT
* *
25053801 TATCACATATCGATGCCACTGTCCCAGACAGGGTCTTACACGT
1 TATCACATATCGATGCCA-TGTCCCAGACATGGTCTTACATGT
* * * * *
25053844 AATCTCATATCGATGTCAATGTCTCAGACATAGTCTTACATG
1 TATCACATATCGATG-CCATGTCCCAGACATGGTCTTACATG
25053886 AAATCACACC
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 10 0.14
42 6 0.09
43 52 0.74
44 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (42 bp):
TATCACATATCGATGCCATGTCCCAGACATGGTCTTACATGT
Found at i:25069653 original size:24 final size:23
Alignment explanation
Indices: 25069609--25069671 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
25069599 TATTTTTTTG
* *
25069609 TTATTTTTCTCTTTCTCATATAT
1 TTATTTTTTTATTTCTCATATAT
* *
25069632 TTATTTTTTTATTTGCTTATATTT
1 TTATTTTTTTATTT-CTCATATAT
25069656 TTAATATTTTTTATTT
1 TT-AT-TTTTTTATTT
25069672 ATTTTACCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 12 0.36
24 9 0.27
25 2 0.06
26 10 0.30
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (23 bp):
TTATTTTTTTATTTCTCATATAT
Found at i:25069909 original size:19 final size:21
Alignment explanation
Indices: 25069881--25069929 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
25069871 GGTTTTTTAT
*
25069881 TAAAATAATAC-AAAAGAA-A
1 TAAAAAAATACTAAAAGAATA
*
25069900 TAAAAAAATACTAAAATAATA
1 TAAAAAAATACTAAAAGAATA
25069921 TACAAAAAA
1 TA-AAAAAA
25069930 ATAATTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 6 0.24
21 3 0.12
22 6 0.24
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAAAAAATACTAAAAGAATA
Found at i:25069955 original size:28 final size:28
Alignment explanation
Indices: 25069882--25069958 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
25069872 GTTTTTTATT
*
25069882 AAAATAATACAAAAGAAATAAAAAAATACT
1 AAAATAATACAAAA-AAA-AAAAAAATACC
* * * **
25069912 AAAATAATATACAAAAAAATAATTTACC
1 AAAATAATACAAAAAAAAAAAAAATACC
25069940 AAAATAATACAAAAAAAAA
1 AAAATAATACAAAAAAAAA
25069959 GACGGCTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 24 0.62
29 3 0.08
30 12 0.31
ACGTcount: A:0.73, C:0.08, G:0.01, T:0.18
Consensus pattern (28 bp):
AAAATAATACAAAAAAAAAAAAAATACC
Found at i:25070013 original size:27 final size:27
Alignment explanation
Indices: 25069983--25070045 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
25069973 GGTAATGGAA
* *
25069983 TGGCGGCACCGGTGGTGCCTTTCTCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
25070010 TGGCGGCACCGGTGGTGCCATTCCCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
25070037 TGGCGGCAC
1 TGGCGGCAC
25070046 AGGACTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.10, C:0.32, G:0.35, T:0.24
Consensus pattern (27 bp):
TGGCGGCACCGGTGGTGCCATTCCCAT
Found at i:25071878 original size:27 final size:27
Alignment explanation
Indices: 25071847--25071912 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
25071837 ACATTTTAGT
* *
25071847 CCTGTGCCGCCAATGGGAATGGCACCA
1 CCTGTGCCGCCAATGAGAAAGGCACCA
25071874 CCTGTGCCGCCAATGAGAAAGGCACCA
1 CCTGTGCCGCCAATGAGAAAGGCACCA
*
25071901 CCGGTGCCGCCA
1 CCTGTGCCGCCA
25071913 TTCCATTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.36, G:0.29, T:0.12
Consensus pattern (27 bp):
CCTGTGCCGCCAATGAGAAAGGCACCA
Found at i:25072007 original size:19 final size:21
Alignment explanation
Indices: 25071966--25072014 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
25071956 TGTAAATAAT
25071966 TTTTTTGTATATTATTTTGGTA
1 TTTTTT-TATATTATTTTGGTA
*
25071988 TTTTTTTAT-TTCTTTT-GTA
1 TTTTTTTATATTATTTTGGTA
*
25072007 TTATTTTA
1 TTTTTTTA
25072015 GTAAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 6 0.24
21 3 0.12
22 6 0.24
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.73
Consensus pattern (21 bp):
TTTTTTTATATTATTTTGGTA
Found at i:25072414 original size:15 final size:14
Alignment explanation
Indices: 25072392--25072427 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
25072382 TTTCATGAAC
25072392 TTTT-TTTAATATTT
1 TTTTATTTAATA-TT
25072406 TTTTATTTAATATT
1 TTTTATTTAATATT
25072420 TTTTATTT
1 TTTTATTT
25072428 TTATAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTAATATT
Found at i:25072430 original size:16 final size:16
Alignment explanation
Indices: 25072394--25072439 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
25072384 TCATGAACTT
25072394 TTTTTAATATTTTTT-
1 TTTTTAATATTTTTTA
*
25072409 TATTTAATATTTTTTA
1 TTTTTAATATTTTTTA
*
25072425 TTTTT-ATAATTTTTA
1 TTTTTAATATTTTTTA
25072440 AATTATCTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAATATTTTTTA
Found at i:25089883 original size:13 final size:12
Alignment explanation
Indices: 25089865--25089908 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
25089855 ATTTGCGTTC
25089865 TTTTTTTGTCTT
1 TTTTTTTGTCTT
25089877 TTCTTTTTGTCTT
1 TT-TTTTTGTCTT
25089890 TTTTTTCT-T-TT
1 TTTTTT-TGTCTT
25089901 TTTTTTTG
1 TTTTTTTG
25089909 CGCTTTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 8 0.28
12 7 0.24
13 13 0.45
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (12 bp):
TTTTTTTGTCTT
Found at i:25089889 original size:23 final size:22
Alignment explanation
Indices: 25089863--25089906 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25089853 GCATTTGCGT
25089863 TCTTTTTTTGTCTTTTCTTTTTG
1 TCTTTTTTT-TCTTTTCTTTTTG
*
25089886 TCTTTTTTTTCTTTTTTTTTT
1 TCTTTTTTTTCTTTTCTTTTT
25089907 TGCGCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (22 bp):
TCTTTTTTTTCTTTTCTTTTTG
Found at i:25089907 original size:23 final size:23
Alignment explanation
Indices: 25089863--25089925 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
25089853 GCATTTGCGT
*
25089863 TCTTTTTTTGTC-TTTTCTTTTTG
1 TCTTTTTTT-TCTTTTTTTTTTTG
25089886 TCTTTTTTTTCTTTTTTTTTTTG
1 TCTTTTTTTTCTTTTTTTTTTTG
** *
25089909 -CGCTTTTTACTTTTTTT
1 TCTTTTTTTTCTTTTTTT
25089926 GCGCTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (23 bp):
TCTTTTTTTTCTTTTTTTTTTTG
Found at i:25089940 original size:18 final size:17
Alignment explanation
Indices: 25089897--25089943 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
25089887 CTTTTTTTTC
25089897 TTTTTTTTTTTGCGCTT
1 TTTTTTTTTTTGCGCTT
*
25089914 TTTACTTTTTTTGCGCTT
1 TTT-TTTTTTTTGCGCTT
25089932 TTTTGTTTTTTT
1 TTTT-TTTTTTT
25089944 TTTAAGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.02, C:0.11, G:0.11, T:0.77
Consensus pattern (17 bp):
TTTTTTTTTTTGCGCTT
Found at i:25090580 original size:31 final size:32
Alignment explanation
Indices: 25090512--25090585 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
25090502 NNNNNNNNNN
*
25090512 AACTCTTTCAAGAGTAATTGAATCCTAATAAA
1 AACTCTTTAAAGAGTAATTGAATCCTAATAAA
25090544 AACTCTTTAAAGAGTAATTGAATCCTAAT-AA
1 AACTCTTTAAAGAGTAATTGAATCCTAATAAA
25090575 AACTCTTTAAA
1 AACTCTTTAAA
25090586 ATTATCTAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 13 0.32
32 28 0.68
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (32 bp):
AACTCTTTAAAGAGTAATTGAATCCTAATAAA
Found at i:25091369 original size:8 final size:8
Alignment explanation
Indices: 25091356--25091385 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
25091346 GCATTCTCAT
25091356 TTTTCCCA
1 TTTTCCCA
25091364 TTTTCCCA
1 TTTTCCCA
25091372 TTTTCCCCA
1 TTTT-CCCA
25091381 TTTTC
1 TTTTC
25091386 ATTAGTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTCCCA
Found at i:25091375 original size:17 final size:17
Alignment explanation
Indices: 25091353--25091385 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25091343 TTTGCATTCT
*
25091353 CATTTTTCCCATTTTCC
1 CATTTTCCCCATTTTCC
25091370 CATTTTCCCCATTTTC
1 CATTTTCCCCATTTTC
25091386 ATTAGTTACA
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:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (17 bp):
CATTTTCCCCATTTTCC
Found at i:25091385 original size:9 final size:9
Alignment explanation
Indices: 25091353--25091385 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
25091343 TTTGCATTCT
*
25091353 CATTTTTCC
1 CATTTTCCC
25091362 CATTTT-CC
1 CATTTTCCC
25091370 CATTTTCCC
1 CATTTTCCC
25091379 CATTTTC
1 CATTTTC
25091386 ATTAGTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (9 bp):
CATTTTCCC
Found at i:25093062 original size:27 final size:29
Alignment explanation
Indices: 25093020--25093077 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 29
25093010 CCTAAACCAT
25093020 AACCCTAAAATCCCTTATTTT-ATCCCTA
1 AACCCTAAAATCCCTTATTTTCATCCCTA
*
25093048 AACCCT-AAATCCCTTATTTTCCTCCCTA
1 AACCCTAAAATCCCTTATTTTCATCCCTA
25093076 AA
1 AA
25093078 AATTTGAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (29 bp):
AACCCTAAAATCCCTTATTTTCATCCCTA
Found at i:25093970 original size:2 final size:2
Alignment explanation
Indices: 25093963--25094002 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
25093953 AAACTTATGC
25093963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25094003 GTCTAAACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25099690 original size:11 final size:11
Alignment explanation
Indices: 25099654--25099734 Score: 103
Period size: 11 Copynumber: 7.4 Consensus size: 11
25099644 TAAATCCTTT
*
25099654 CTCTC-AATTT
1 CTCTCAAATTC
25099664 CTCTCCAATATT-
1 CTCT-CAA-ATTC
25099676 CTCTCAAATTC
1 CTCTCAAATTC
25099687 CTCTCAAATTC
1 CTCTCAAATTC
25099698 CTCTCAAATTC
1 CTCTCAAATTC
* *
25099709 CTTTCAATTTC
1 CTCTCAAATTC
25099720 CTCTCAAATTC
1 CTCTCAAATTC
25099731 CTCT
1 CTCT
25099735 TAAAAAAGCT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
10 7 0.11
11 48 0.76
12 5 0.08
13 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:25099959 original size:21 final size:20
Alignment explanation
Indices: 25099934--25099999 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
25099924 GATTTTTTGA
25099934 TTTATTCAATTTTAAATAATT
1 TTTATT-AATTTTAAATAATT
*
25099955 TTTATT--TTATTAGA-AATT
1 TTTATTAATT-TTAAATAATT
25099973 TCTTA-TAATTTTTAAATAATT
1 T-TTATTAA-TTTTAAATAATT
25099994 TTTATT
1 TTTATT
25100000 TTATTATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 7 0.19
21 14 0.39
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATTAATTTTAAATAATT
Found at i:25100947 original size:7 final size:7
Alignment explanation
Indices: 25100935--25100974 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
25100925 TAGTCGATTG
25100935 GTATTTA
1 GTATTTA
25100942 GTATTTA
1 GTATTTA
*
25100949 GTGA-TTG
1 GT-ATTTA
25100956 GTATTTA
1 GTATTTA
25100963 GTATTTA
1 GTATTTA
25100970 GTATT
1 GTATT
25100975 ATGTATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 1 0.03
7 27 0.93
8 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (7 bp):
GTATTTA
Found at i:25100954 original size:21 final size:22
Alignment explanation
Indices: 25100925--25100971 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
25100915 CATCATGAGA
25100925 TAGTCGATTGGTATTTAGTATT
1 TAGTCGATTGGTATTTAGTATT
25100947 TAGT-GATTGGTATTTAGTATT
1 TAGTCGATTGGTATTTAGTATT
25100968 TAGT
1 TAGT
25100972 ATTATGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.51
Consensus pattern (22 bp):
TAGTCGATTGGTATTTAGTATT
Found at i:25100980 original size:7 final size:7
Alignment explanation
Indices: 25100970--25101001 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
25100960 TTAGTATTTA
25100970 GTATTAT
1 GTATTAT
25100977 GTATTAT
1 GTATTAT
25100984 GTATTAT
1 GTATTAT
25100991 GTATTAT
1 GTATTAT
25100998 GTAT
1 GTAT
25101002 ATAACTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:25100980 original size:14 final size:15
Alignment explanation
Indices: 25100963--25101001 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
25100953 TTGGTATTTA
25100963 GTATTTA-GTATTAT
1 GTATTTATGTATTAT
25100977 GTA-TTATGTATTAT
1 GTATTTATGTATTAT
25100991 GTA-TTATGTAT
1 GTATTTATGTAT
25101002 ATAACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 3 0.12
14 21 0.88
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (15 bp):
GTATTTATGTATTAT
Found at i:25100980 original size:21 final size:21
Alignment explanation
Indices: 25100935--25101001 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
25100925 TAGTCGATTG
*
25100935 GTATTTAGTATTTAGTGATT-G
1 GTATTTAGTATTTAGT-ATTAT
25100956 GTATTTAGTATTTAGTATTAT
1 GTATTTAGTATTTAGTATTAT
25100977 GTA-TTATGTA-TTATGTATTAT
1 GTATTTA-GTATTTA-GTATTAT
25100998 GTAT
1 GTAT
25101002 ATAACTAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
20 9 0.22
21 32 0.78
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (21 bp):
GTATTTAGTATTTAGTATTAT
Found at i:25101919 original size:21 final size:21
Alignment explanation
Indices: 25101895--25101935 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25101885 ATCCCCTACC
* *
25101895 GGAGGAACCAGAATCCCCGCT
1 GGAGGAACCACAACCCCCGCT
*
25101916 GGAGTAACCACAACCCCCGC
1 GGAGGAACCACAACCCCCGC
25101936 CGAAAGCTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.39, G:0.24, T:0.07
Consensus pattern (21 bp):
GGAGGAACCACAACCCCCGCT
Found at i:25104332 original size:126 final size:126
Alignment explanation
Indices: 25104107--25104398 Score: 467
Period size: 126 Copynumber: 2.3 Consensus size: 126
25104097 TCAGGCCAAA
*
25104107 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * * *
25104172 ATCCAGCTTAAAGCATTTTTGACACTATTTGCTCAGAAATGCCTACTCGAAATTATTTTTT
66 ATACAGCTTAAAGCATTTTTGACACTATTGGCTCAGAAACGCCTACTCAAAATTATTTTTT
* * *
25104233 CAGGAGCTACTATAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACGAAGC
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
** * * *
25104298 ATATTGCTTAAAGCGTTTTTGACACTATTGGCTCAGAAACGTCTTCTCAAAATTATTTTTT
66 ATACAGCTTAAAGCATTTTTGACACTATTGGCTCAGAAACGCCTACTCAAAATTATTTTTT
25104359 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
1 CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
25104399 TTTTAAATTA
Statistics
Matches: 151, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 151 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATACAGCTTAAAGCATTTTTGACACTATTGGCTCAGAAACGCCTACTCAAAATTATTTTTT
Found at i:25104536 original size:96 final size:94
Alignment explanation
Indices: 25104429--25104602 Score: 233
Period size: 96 Copynumber: 1.8 Consensus size: 94
25104419 CTAATCTGAT
* * * *
25104429 TTTTTAAAAATTTTTAATTAATTTAGTCAAGT-AACCCTAAACCCTAATTTAATTGATTTTTTTC
1 TTTTGAAAAATTTATAATTAATTTAATCAA-TAAACCCTAAACCCTAATTT-ATTGAATTTTTTC
25104493 TTTAAAAACCATAAACATGAAACCTAATCCAA
64 TTT-AAAACCATAAACATGAAACCTAATCCAA
* * * *
25104525 TTTTGAAAAATTTATAATTAATTTAATTAATAAACCCTAATCCCTTATTTATTTAATTTTTTCTT
1 TTTTGAAAAATTTATAATTAATTTAATCAATAAACCCTAAACCCTAATTTATTGAATTTTTTCTT
*
25104590 TAAAACCCTAAAC
66 TAAAACCATAAAC
25104603 CTAAAAACTA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 11 0.16
95 15 0.22
96 42 0.62
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.43
Consensus pattern (94 bp):
TTTTGAAAAATTTATAATTAATTTAATCAATAAACCCTAAACCCTAATTTATTGAATTTTTTCTT
TAAAACCATAAACATGAAACCTAATCCAA
Found at i:25104637 original size:21 final size:21
Alignment explanation
Indices: 25104590--25104657 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
25104580 ATTTTTTCTT
* **
25104590 TAAAACCCTAAACCTAAAAACTA
1 TAAAACCCTAACCCT--AAACCC
25104613 TAAAACCCTAACCCTAAACCC
1 TAAAACCCTAACCCTAAACCC
*** *
25104634 TAAAACAAAAACCCAAAACCC
1 TAAAACCCTAACCCTAAACCC
25104655 TAA
1 TAA
25104658 CCAGCAGGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 24 0.63
23 14 0.37
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.13
Consensus pattern (21 bp):
TAAAACCCTAACCCTAAACCC
Found at i:25105597 original size:23 final size:25
Alignment explanation
Indices: 25105571--25105633 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 25
25105561 TATTTATTTA
25105571 TTTT-AAAAG-AAAACTTAACCTAT
1 TTTTAAAAAGCAAAACTTAACCTAT
25105594 TTTTAGAAAAGCACAAAACTTAACCTA-
1 TTTTA-AAAAG--CAAAACTTAACCTAT
25105621 TTTTAGAAAAGCA
1 TTTTA-AAAAGCA
25105634 CCCGAGCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.11
25 7 0.20
27 11 0.31
28 13 0.37
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (25 bp):
TTTTAAAAAGCAAAACTTAACCTAT
Found at i:25105632 original size:27 final size:28
Alignment explanation
Indices: 25105580--25105634 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
25105570 ATTTTAAAAG
25105580 AAAACTTAACCTATTTTTAGAAAAGCAC
1 AAAACTTAACCTATTTTTAGAAAAGCAC
25105608 AAAACTTAACCTA-TTTTAGAAAAGCAC
1 AAAACTTAACCTATTTTTAGAAAAGCAC
25105635 CCGAGCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.27
Consensus pattern (28 bp):
AAAACTTAACCTATTTTTAGAAAAGCAC
Found at i:25109588 original size:47 final size:47
Alignment explanation
Indices: 25109534--25109760 Score: 251
Period size: 47 Copynumber: 4.8 Consensus size: 47
25109524 ATAAAAGTTG
* * * * *
25109534 CTAAAATACATTGTGGATATACCACTAGTTGAGAAGGTGACTGTAGA
1 CTAAAATACGTTGTGGATAAACCACTGGTCGAGAAGGTGACTGTCGA
* **
25109581 CTAAAATACGTTATGGATAAACCACTGGTCGACCAGGTGACTGTCGA
1 CTAAAATACGTTGTGGATAAACCACTGGTCGAGAAGGTGACTGTCGA
* * * *
25109628 TTAAAATAAGTTGTGGATAAACCATTGGTCGAGTAGGTGACTG-CTGA
1 CTAAAATACGTTGTGGATAAACCACTGGTCGAGAAGGTGACTGTC-GA
* * **
25109675 CTAAAATACGTAGTGGATAAACCACTGGTAGA-ACATATGACTGTCGA
1 CTAAAATACGTTGTGGATAAACCACTGGTCGAGA-AGGTGACTGTCGA
* * *
25109722 CTAAGATACGTTGTGGATAAACCACTGGTCAAGCAGGTG
1 CTAAAATACGTTGTGGATAAACCACTGGTCGAGAAGGTG
25109761 TGTCACATCC
Statistics
Matches: 147, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
46 1 0.01
47 145 0.99
48 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (47 bp):
CTAAAATACGTTGTGGATAAACCACTGGTCGAGAAGGTGACTGTCGA
Found at i:25109696 original size:94 final size:94
Alignment explanation
Indices: 25109534--25109760 Score: 280
Period size: 94 Copynumber: 2.4 Consensus size: 94
25109524 ATAAAAGTTG
* * *
25109534 CTAAAATACA-TTGTGGATATACCACTAGTTGAGAAGGTGACTGTAGACTAAAATACGTTATGGA
1 CTAAAATA-AGTTGTGGATAAACCACTGGTCGAGAAGGTGACTGTAGACTAAAATACGTTATGGA
* * *
25109598 TAAACCACTGGTCGACCAGGTGACTGTCGA
65 TAAACCACTGGTAGAACAGATGACTGTCGA
* * *
25109628 TTAAAATAAGTTGTGGATAAACCATTGGTCGAGTAGGTGACTGCT-GACTAAAATACG-TAGTGG
1 CTAAAATAAGTTGTGGATAAACCACTGGTCGAGAAGGTGACTG-TAGACTAAAATACGTTA-TGG
*
25109691 ATAAACCACTGGTAGAACATATGACTGTCGA
64 ATAAACCACTGGTAGAACAGATGACTGTCGA
* * * *
25109722 CTAAGATACGTTGTGGATAAACCACTGGTCAAGCAGGTG
1 CTAAAATAAGTTGTGGATAAACCACTGGTCGAGAAGGTG
25109761 TGTCACATCC
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
93 3 0.03
94 110 0.96
95 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (94 bp):
CTAAAATAAGTTGTGGATAAACCACTGGTCGAGAAGGTGACTGTAGACTAAAATACGTTATGGAT
AAACCACTGGTAGAACAGATGACTGTCGA
Found at i:25111763 original size:14 final size:14
Alignment explanation
Indices: 25111744--25111773 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25111734 TTTAATTCAT
25111744 ATTTTAAAAATATG
1 ATTTTAAAAATATG
25111758 ATTTTAAAAATATG
1 ATTTTAAAAATATG
25111772 AT
1 AT
25111774 AATTGAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTTTAAAAATATG
Found at i:25121886 original size:9 final size:9
Alignment explanation
Indices: 25121874--25121943 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
25121864 CCCCATTTAG
25121874 TTTATTTTT
1 TTTATTTTT
25121883 TTTATTTTT
1 TTTATTTTT
*
25121892 TATATTTTT
1 TTTATTTTT
25121901 ATATTATATATTT
1 -T-TTAT-T-TTT
*
25121914 ATTA-TTTT
1 TTTATTTTT
*
25121922 TCTATTTTT
1 TTTATTTTT
*
25121931 TCTATTTATT
1 TTTATTT-TT
25121941 TTT
1 TTT
25121944 TACTTTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 5 0.10
9 29 0.59
10 5 0.10
11 6 0.12
12 1 0.02
13 3 0.06
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTT
Found at i:25121938 original size:24 final size:23
Alignment explanation
Indices: 25121874--25121944 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
25121864 CCCCATTTAG
* *
25121874 TTTATTTTTTTTATTTTTTATATT
1 TTTATTTTTTATATTTATTAT-TT
* *
25121898 TTTATATTATATATTTATTATTT
1 TTTATTTTTTATATTTATTATTT
*
25121921 TTCTATTTTTTCTATTTATT-TTT
1 TT-TATTTTTTATATTTATTATTT
25121944 T
1 T
25121945 ACTTTATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 8 0.21
24 31 0.79
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTTTTTATATTTATTATTT
Found at i:25121960 original size:5 final size:4
Alignment explanation
Indices: 25121868--25121961 Score: 54
Period size: 4 Copynumber: 22.8 Consensus size: 4
25121858 CTTTTTCCCC
* *
25121868 ATTT AGTTT ATTTT TTTT ATTT -TTT ATATT -TTT ATATT ATAT ATTT
1 ATTT A-TTT A-TTT ATTT ATTT ATTT AT-TT ATTT AT-TT ATTT ATTT
*
25121914 A-TT ATTT -TTCT ATTT TTTCT ATTT ATTT -TTT ACTTT ATTT ATGTT
1 ATTT ATTT ATT-T ATTT ATT-T ATTT ATTT ATTT A-TTT ATTT AT-TT
25121959 ATT
1 ATT
25121962 CTTCTGCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 24
0.70 0.07 0.24
Matches are distributed among these distances:
3 13 0.18
4 32 0.45
5 26 0.37
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:25121960 original size:21 final size:21
Alignment explanation
Indices: 25121915--25121966 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
25121905 TATATATTTA
*
25121915 TTATTTTTCTATTTTTTCTAT
1 TTATTTTTCTATTTATTCTAT
25121936 TTATTTTT-TACTTTATT-TAT
1 TTATTTTTCTA-TTTATTCTAT
*
25121956 GTTATTCTTCT
1 -TTATTTTTCT
25121967 GCTTCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATTTTTCTATTTATTCTAT
Found at i:25122197 original size:6 final size:6
Alignment explanation
Indices: 25122172--25122224 Score: 52
Period size: 6 Copynumber: 8.0 Consensus size: 6
25122162 TGTTTACTCA
*
25122172 TTATTT TTAGTTT GTATTT TTATTT TTATTAGT ATTATTT TTATTT ATTATTT
1 TTATTT TTA-TTT TTATTT TTATTT TTATT--T -TTATTT TTATTT -TTATTT
25122225 ACGTATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 22 0.55
7 12 0.30
8 1 0.03
9 5 0.12
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (6 bp):
TTATTT
Found at i:25122211 original size:15 final size:13
Alignment explanation
Indices: 25122172--25122224 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
25122162 TGTTTACTCA
25122172 TTATTT-TTAGTTT
1 TTATTTATTA-TTT
*
25122185 GTATTT-TTATTT
1 TTATTTATTATTT
25122197 TTATTAGTATTATTT
1 TTATT--TATTATTT
25122212 TTATTTATTATTT
1 TTATTTATTATTT
25122225 ACGTATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 7 0.20
13 16 0.46
14 1 0.03
15 11 0.31
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (13 bp):
TTATTTATTATTT
Found at i:25122218 original size:19 final size:20
Alignment explanation
Indices: 25122172--25122221 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
25122162 TGTTTACTCA
*
25122172 TTATTT-TTAGTTTGTATTT
1 TTATTTATTAGTATGTATTT
25122191 TTATTTTTATTAGTAT-TATTT
1 TTA--TTTATTAGTATGTATTT
25122212 TTATTTATTA
1 TTATTTATTA
25122222 TTTACGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
21 11 0.41
22 6 0.22
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (20 bp):
TTATTTATTAGTATGTATTT
Found at i:25122253 original size:16 final size:16
Alignment explanation
Indices: 25122216--25122261 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
25122206 TTATTTTTAT
25122216 TTATTATTTACGTATT-
1 TTATTA-TTACGTATTA
25122232 TTATTATTAC-TATTA
1 TTATTATTACGTATTA
25122247 TTGATTATT-CGTATT
1 TT-ATTATTACGTATT
25122262 TCTTTTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.15
15 7 0.26
16 16 0.59
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.61
Consensus pattern (16 bp):
TTATTATTACGTATTA
Found at i:25123697 original size:13 final size:12
Alignment explanation
Indices: 25123681--25123724 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
25123671 TTTCTTTTTC
25123681 TTTTTATTTATG
1 TTTTTATTTATG
*
25123693 TTTTTATTTCTG
1 TTTTTATTTATG
* *
25123705 TTTTTAGTTGT-
1 TTTTTATTTATG
25123716 TTTTTATTT
1 TTTTTATTT
25123725 TTAGACTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTTTATTTATG
Found at i:25127470 original size:27 final size:27
Alignment explanation
Indices: 25127440--25127495 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
25127430 AAACTAATAT
*
25127440 AATTGCACATATACTGCACAAGTTTTG
1 AATTGCACATATACTACACAAGTTTTG
25127467 AATTGCACATATACTACACAAGTTTTG
1 AATTGCACATATACTACACAAGTTTTG
25127494 AA
1 AA
25127496 CTTCAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (27 bp):
AATTGCACATATACTACACAAGTTTTG
Found at i:25131099 original size:2 final size:2
Alignment explanation
Indices: 25131092--25131120 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25131082 TGGTTTTCCC
25131092 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 A
25131121 AACTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25131355 original size:68 final size:68
Alignment explanation
Indices: 25131267--25131402 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 68
25131257 TGTTTTCACG
* * *
25131267 TCAATCACATTTCTCTTTATGAGATAATCCAAATTTATAAGGAAGCGAC-AGTTATCGATATCGA
1 TCAAGCACATTTCTCTTTATGAGATAATCCAAATTCATAAGGAAACGACGA-TTATCGATATCGA
25131331 CCCA
65 CCCA
* * *
25131335 TCAAGCACATTTCTCTTTATGAGGTAATCCAAATTCATAAGGAAACGACGATTATCGATGTTGAC
1 TCAAGCACATTTCTCTTTATGAGATAATCCAAATTCATAAGGAAACGACGATTATCGATATCGAC
25131400 CCA
66 CCA
25131403 AACAAATAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 60 0.98
69 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (68 bp):
TCAAGCACATTTCTCTTTATGAGATAATCCAAATTCATAAGGAAACGACGATTATCGATATCGAC
CCA
Found at i:25133816 original size:40 final size:40
Alignment explanation
Indices: 25133735--25133818 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
25133725 ACCTGGATGT
* * *
25133735 CCCTGTAAACAGTTCGGTGTCCCTATTTGCACAACTGTGC
1 CCCTGTAAACACTTCGGTGTCCCTAATTGCACAACTATGC
* **
25133775 CCCTGTAAACACTTCGGTGTCTCTAATTGCACATTTATGC
1 CCCTGTAAACACTTCGGTGTCCCTAATTGCACAACTATGC
25133815 CCCT
1 CCCT
25133819 AAATGCACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.32
Consensus pattern (40 bp):
CCCTGTAAACACTTCGGTGTCCCTAATTGCACAACTATGC
Found at i:25133885 original size:20 final size:20
Alignment explanation
Indices: 25133812--25133886 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
25133802 TGCACATTTA
*
25133812 TGCCCCTAAATGCACTCTAG
1 TGCCCCTGAATGCACTCTAG
* *
25133832 TGCCCCTCACA-GCACAT-TCG
1 TGCCCCTGA-ATGCAC-TCTAG
*
25133852 TGCCCTTGAATGCACTCTAG
1 TGCCCCTGAATGCACTCTAG
*
25133872 TGCCCCTGATTGCAC
1 TGCCCCTGAATGCAC
25133887 ACTCGTGTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.25
Consensus pattern (20 bp):
TGCCCCTGAATGCACTCTAG
Found at i:25133887 original size:40 final size:40
Alignment explanation
Indices: 25133800--25133893 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
25133790 GGTGTCTCTA
**
25133800 ATTGCACATTTATGCCCCTAAATGCACTCTAGTGCCCCTC
1 ATTGCACATTCGTGCCCCTAAATGCACTCTAGTGCCCCTC
** * * *
25133840 ACAGCACATTCGTGCCCTTGAATGCACTCTAGTGCCCCTG
1 ATTGCACATTCGTGCCCCTAAATGCACTCTAGTGCCCCTC
*
25133880 ATTGCACACTCGTG
1 ATTGCACATTCGTG
25133894 TTCCTAATTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (40 bp):
ATTGCACATTCGTGCCCCTAAATGCACTCTAGTGCCCCTC
Found at i:25147751 original size:10 final size:10
Alignment explanation
Indices: 25147736--25147766 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25147726 TTTTTTTCAA
*
25147736 AAATAATAAT
1 AAATAAAAAT
25147746 AAATAAAAAT
1 AAATAAAAAT
25147756 AAATAAAAAT
1 AAATAAAAAT
25147766 A
1 A
25147767 TTAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:25147755 original size:16 final size:15
Alignment explanation
Indices: 25147734--25147788 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 15
25147724 TTTTTTTTTC
25147734 AAAAATAATAATAAAT
1 AAAAATAATAA-AAAT
25147750 AAAAATAAATAAAAAT
1 AAAAAT-AATAAAAAT
*
25147766 ATTAAAATATTAAAAAAT
1 A--AAAATAAT-AAAAAT
25147784 AAAAA
1 AAAAA
25147789 ATATTAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 15 0.44
17 7 0.21
18 12 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAATAAAAAT
Found at i:25147789 original size:17 final size:17
Alignment explanation
Indices: 25147734--25147797 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 17
25147724 TTTTTTTTTC
* *
25147734 AAAAATAATAATAAAT-
1 AAAAATATTAAAAAATA
*
25147750 AAAAATA-AATAAAAATA
1 AAAAATATTA-AAAAATA
*
25147767 TTAAAATATTAAAAAATA
1 -AAAAATATTAAAAAATA
25147785 AAAAATATTAAAA
1 AAAAATATTAAAA
25147798 TTTTACCTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 1 0.03
16 12 0.31
17 12 0.31
18 13 0.33
19 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATATTAAAAAATA
Found at i:25148042 original size:26 final size:26
Alignment explanation
Indices: 25148005--25148069 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
25147995 TTGTTTAGTA
*
25148005 AAAATATTTTTTTATTTTTTTAATTTT
1 AAAATAATTTTTTA-TTTTTTAATTTT
* *
25148032 AAAATACTTTTTTATTTTTTATTTTT
1 AAAATAATTTTTTATTTTTTAATTTT
25148058 AAAATAATTTTT
1 AAAATAATTTTT
25148070 GGTTTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 22 0.63
27 13 0.37
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
AAAATAATTTTTTATTTTTTAATTTT
Found at i:25148069 original size:25 final size:26
Alignment explanation
Indices: 25148013--25148080 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
25148003 TAAAAATATT
* *
25148013 TTTTTATTTTTTTAATTTTAAAATACT
1 TTTTTA-TTTTTTATTTTTAAAATACA
25148040 TTTTTATTTTTTATTTTTAAAATA-A
1 TTTTTATTTTTTATTTTTAAAATACA
**
25148065 TTTTTGGTTTTTATTT
1 TTTTTATTTTTTATTT
25148081 AAAAAAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 14 0.38
26 17 0.46
27 6 0.16
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (26 bp):
TTTTTATTTTTTATTTTTAAAATACA
Found at i:25148075 original size:26 final size:26
Alignment explanation
Indices: 25148005--25148080 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
25147995 TTGTTTAGTA
* * *
25148005 AAAATATTTTTTTATTTTTTTAATTTT
1 AAAATAATTTTTGA-TTTTTTATTTTT
* *
25148032 AAAATACTTTTTTATTTTTTATTTTT
1 AAAATAATTTTTGATTTTTTATTTTT
*
25148058 AAAATAATTTTTG-GTTTTTATTT
1 AAAATAATTTTTGATTTTTTATTT
25148081 AAAAAAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 9 0.20
26 22 0.50
27 13 0.30
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (26 bp):
AAAATAATTTTTGATTTTTTATTTTT
Found at i:25148602 original size:20 final size:20
Alignment explanation
Indices: 25148574--25148612 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25148564 CTAAAAATTA
25148574 TTTAGATATATA-TAATATTG
1 TTTAGATATA-ACTAATATTG
*
25148594 TTTATATATAACTAATATT
1 TTTAGATATAACTAATATT
25148613 ATTTTGCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTAGATATAACTAATATTG
Found at i:25148948 original size:23 final size:23
Alignment explanation
Indices: 25148901--25148948 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25148891 TTGGTTTTAA
* *
25148901 AAAAATATTTTATATATGTATAT
1 AAAAATATTTTAAATATGTAAAT
25148924 AAAAATATTTATAAATAT-TAAAT
1 AAAAATATTT-TAAATATGTAAAT
25148947 AA
1 AA
25148949 TGAGATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAAATATTTTAAATATGTAAAT
Found at i:25149659 original size:17 final size:17
Alignment explanation
Indices: 25149618--25149659 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
25149608 CTTCTAGCCC
25149618 GACGCCGCCACCATTCT
1 GACGCCGCCACCATTCT
* * *
25149635 GTCACCGCCACCGTTCT
1 GACGCCGCCACCATTCT
25149652 GACGCCGC
1 GACGCCGC
25149660 GCCGCACATC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.14, C:0.48, G:0.21, T:0.17
Consensus pattern (17 bp):
GACGCCGCCACCATTCT
Found at i:25150137 original size:30 final size:29
Alignment explanation
Indices: 25150095--25150151 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
25150085 TTTTTGGTTT
25150095 TTTTTTGGAG-AAAATAGTGGTTGAAATGG
1 TTTTTTGGAGAAAAATAG-GGTTGAAATGG
*
25150124 TTTTTTGGAAGAAAAATAGGGTTTAAAT
1 TTTTTTGG-AGAAAAATAGGGTTGAAAT
25150152 ACCCTGAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 10 0.40
31 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (29 bp):
TTTTTTGGAGAAAAATAGGGTTGAAATGG
Found at i:25150579 original size:3 final size:3
Alignment explanation
Indices: 25150571--25150653 Score: 121
Period size: 3 Copynumber: 27.7 Consensus size: 3
25150561 GTTTTATAAG
* *
25150571 ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
25150619 ATT ATT AAT ATC AAT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
25150654 ATTTCCATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:25150795 original size:16 final size:16
Alignment explanation
Indices: 25150729--25150797 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 16
25150719 AAGTGCTTAT
*
25150729 ATATATATATATTT-C
1 ATATATATTTATTTAC
25150744 ATATA-ATTTATTTA-
1 ATATATATTTATTTAC
**
25150758 ATATATATATTACTTTTT
1 ATATATAT-TTA-TTTAC
25150776 ATATATATTTATTTAC
1 ATATATATTTATTTAC
25150792 ATATAT
1 ATATAT
25150798 CTATGTACTC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
14 12 0.27
15 7 0.16
16 12 0.27
17 6 0.13
18 8 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATATATTTATTTAC
Found at i:25151300 original size:109 final size:108
Alignment explanation
Indices: 25151109--25151512 Score: 571
Period size: 110 Copynumber: 3.7 Consensus size: 108
25151099 TTTCTAATTG
*
25151109 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGA-TTTTCT
25151174 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
65 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
* * *
25151218 AGGCAACGTTTTACGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTGTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT-TTCT
* * *
25151283 TGTTCAACCAAATGGCTTAATATCCTTTTCAAAAATCTTAAAATA
65 CGTTTAACCAAATGGCTTAATATCCTTTT-AAAAATTTTAAAATA
*
25151328 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCTCTAAGGTGCTGGGTGTCGATTTTCCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTT-CT
* * *
25151393 CGTTTAACCAAATAG-TTAAATATCCTTTCAAAAAATTTCAAAATA
65 CGTTTAACCAAATGGCTT-AATATCCTTT-TAAAAATTTTAAAATA
* * * * * *
25151438 AGGTAATGTTTTGCGTTTGGAAATTCGAG-GAACGTACCCTAAGGTGCTGGGTTTCGA-TTTCTT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCTC
*
25151501 GATTAACCAAAT
66 GTTTAACCAAAT
25151513 TGCCAAATAT
Statistics
Matches: 265, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
107 13 0.05
108 5 0.02
109 112 0.42
110 135 0.51
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (108 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCTC
GTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
Found at i:25151488 original size:219 final size:217
Alignment explanation
Indices: 25151109--25151512 Score: 616
Period size: 219 Copynumber: 1.9 Consensus size: 217
25151099 TTTCTAATTG
* *
25151109 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCCT
* * *
25151174 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGGCAACGTTTTACGTTTGAA
66 CGTTTAACCAAATAGCTTAATATCCTTTAAAAAATTTCAAAATAAGGCAACGTTTTACGTTTGAA
*
25151239 AATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTGTTCTTG-TTCAACCAAATGGCTTAA
131 AATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGA-T-TTCTTGATT-AACCAAATGGCTTAA
25151303 TATCCTTTTCAAAAATCTTAAAATA
193 TATCCTTTTCAAAAATCTTAAAATA
*
25151328 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCTCTAAGGTGCTGGGTGTCGATTTTCCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCCT
* * *
25151393 CGTTTAACCAAATAG-TTAAATATCCTTTCAAAAAATTTCAAAATAAGGTAATGTTTTGCGTTTG
66 CGTTTAACCAAATAGCTT-AATATCCTTT-AAAAAATTTCAAAATAAGGCAACGTTTTACGTTTG
* * * *
25151457 GAAATTCGAG-GAACGTACCCTAAGGTGCTGGGTTTCGATTTCTTGATTAACCAAAT
129 AAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTCTTGATTAACCAAAT
25151513 TGCCAAATAT
Statistics
Matches: 168, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
217 14 0.08
218 5 0.03
219 110 0.65
220 39 0.23
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (217 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTCCT
CGTTTAACCAAATAGCTTAATATCCTTTAAAAAATTTCAAAATAAGGCAACGTTTTACGTTTGAA
AATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTCTTGATTAACCAAATGGCTTAATAT
CCTTTTCAAAAATCTTAAAATA
Found at i:25154978 original size:9 final size:9
Alignment explanation
Indices: 25154964--25155003 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
25154954 ATGAGTTCAA
25154964 AAAAAAATC
1 AAAAAAATC
25154973 AAAAAAATC
1 AAAAAAATC
*
25154982 AAAAAAAATA
1 -AAAAAAATC
25154992 AAAAAAATC
1 AAAAAAATC
25155001 AAA
1 AAA
25155004 GTCAAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:25154987 original size:19 final size:19
Alignment explanation
Indices: 25154963--25155003 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
25154953 CATGAGTTCA
*
25154963 AAAAAAAATCAAAAAAATC
1 AAAAAAAATAAAAAAAATC
25154982 AAAAAAAATAAAAAAAATC
1 AAAAAAAATAAAAAAAATC
25155001 AAA
1 AAA
25155004 GTCAAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAAAAATAAAAAAAATC
Found at i:25157171 original size:88 final size:88
Alignment explanation
Indices: 25157071--25157745 Score: 1041
Period size: 88 Copynumber: 7.7 Consensus size: 88
25157061 AGTTAAAGAT
*
25157071 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGTATTGACAG
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
25157136 CGAAGCAGGTCGAAGACACAAAC
66 CGAAGCAGGTCGAAGACACAAAC
25157159 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
25157224 CGAAGCAGGTCGAAGACACAAAC
66 CGAAGCAGGTCGAAGACACAAAC
** * *
25157247 CTCACCTCTCTCCGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAG
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
25157312 CGAAGCAGGTCGAAGACACAAAC
66 CGAAGCAGGTCGAAGACACAAAC
*
25157335 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAG
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
*
25157400 TGAAGCAGGTCGAAGACACAAAC
66 CGAAGCAGGTCGAAGACACAAAC
*
25157423 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAATAGATCTTGCCTTCCTGCATTGACAG
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
* *
25157488 CGAAGTAGGTCGAAGACATAAAC
66 CGAAGCAGGTCGAAGACACAAAC
* **
25157511 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTGACAG
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
*
25157576 CGAAGCAGGTCAAAGACACAAAC
66 CGAAGCAGGTCGAAGACACAAAC
* * * * ** * * *
25157599 CTTGCCTCTCTCGGTTATGGTGGAGCTGATTGAATATAGCAGATCTTGCCTTCCTGCGTTAACAA
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
* * *
25157664 CGAAGCAGATTGAAAACA-AAAC
66 CGAAGCAGGTCGAAGACACAAAC
* * **
25157686 CTTGTCTC-CATCGGTTGT-AGTGGAGCTGATTGAAGATAGCAGATCTTGCCTTCCTGCATT
1 CTTGCCTCTC-TCGGTTGTGA-TGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATT
25157746 AACAACAGAG
Statistics
Matches: 548, Mismatches: 37, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
86 1 0.00
87 56 0.10
88 491 0.90
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (88 bp):
CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAG
CGAAGCAGGTCGAAGACACAAAC
Found at i:25157923 original size:46 final size:44
Alignment explanation
Indices: 25157856--25157971 Score: 126
Period size: 46 Copynumber: 2.6 Consensus size: 44
25157846 TCGCACTAGG
* *
25157856 TCTTATTTCCCTGAGATTACAGTGGAACAAACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAAACCGAAGATA-GT-A-A
* * * **
25157902 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAAACCGAAGATAGTAA
*
25157946 TCCTATCTCCCTGAGATTACAGTGGA
1 TCTTATCTCCCTGAGATTACAGTGGA
25157972 GCGGATTAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 25 0.42
45 1 0.02
46 33 0.55
47 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAAACCGAAGATAGTAA
Found at i:25158014 original size:175 final size:175
Alignment explanation
Indices: 25157790--25158227 Score: 725
Period size: 175 Copynumber: 2.5 Consensus size: 175
25157780 CCATCGGTTG
* * *
25157790 CAGTGAAGCTGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACTAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACTAG
25157855 GTCTTATTTCCCTGAGATTACAGTGGAACAAACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAAACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
25157920 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
** * *
25157965 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACTAG
* *
25158030 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGATATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAAACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
*
25158095 ACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
* * * *
25158140 CAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGAAGATCGTA-TCA
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACT-A
*
25158204 GGTCTTATCTCCCTGAGATTACAG
65 GGTCTTATTTCCCTGAGATTACAG
25158228 CGGAGCAGAT
Statistics
Matches: 244, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
175 244 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (175 bp):
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACTAG
GTCTTATTTCCCTGAGATTACAGTGGAACAAACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
Found at i:25158229 original size:129 final size:129
Alignment explanation
Indices: 25158072--25158518 Score: 705
Period size: 129 Copynumber: 3.5 Consensus size: 129
25158062 CCGAAGAATT
* * *
25158072 TCAGATCTTATCTCCCTGATATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
25158137 TTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
25158201 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
25158266 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
*
25158330 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * * * *
25158395 TTACAGTAGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* * * * * * * * * *
25158459 TCAGGTTTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
25158519 CGACGTTGCG
Statistics
Matches: 296, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 296 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (129 bp):
TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
Found at i:25158430 original size:44 final size:43
Alignment explanation
Indices: 25157900--25158436 Score: 306
Period size: 44 Copynumber: 12.4 Consensus size: 43
25157890 AAGAATTTCA
* *
25157900 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGA-TAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ACAAG
* * * * *
25157943 TAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACCAAT
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAA-CAAG
* * * * * *
25157988 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG-CACCAG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAACAAG
* * **
25158030 G-TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGA-ATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ACA----AG
* * ***
25158075 GATCTTATCTCCCTGATATTACAGCGGAGCAGATTGAAGTTAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAACAAG
* * ** * *
25158118 TAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAA-CAAG
* * * * * * *
25158163 GATCTTATCTCTCT-AAAGTTACAGTAGAGAAGATCGTATC-AG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAACAAG
* * *
25158205 G-TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAACAAG
* * * * *
25158247 TAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAA-CAAG
* * * * * *
25158292 GATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCGTATC-AG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAACAAG
* * *
25158334 G-TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAACAAG
* * * * * *
25158376 TAATCCTATCTCCTTGAGATTACAGTAGAGCGGATTAAAACAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAAC-AAG
*
25158421 GATCTTATCTCTCTGA
1 GATCTTATCTCCCTGA
25158437 AGTTATAGTA
Statistics
Matches: 363, Mismatches: 103, Indels: 54
0.70 0.20 0.10
Matches are distributed among these distances:
41 82 0.23
42 18 0.05
43 7 0.02
44 217 0.60
45 8 0.02
46 31 0.09
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAACAAG
Found at i:25159556 original size:30 final size:30
Alignment explanation
Indices: 25159526--25159582 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
25159516 ATTTTTTGGT
25159526 TTTTTTGG-AG-AAAATAGTGGTTGAAATGG
1 TTTTTTGGAAGAAAAATAG-GGTTGAAATGG
*
25159555 TTTTTTGGAAGAAAAATAGGGTTTAAAT
1 TTTTTTGGAAGAAAAATAGGGTTGAAAT
25159583 ACCCTGAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 10 0.40
31 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (30 bp):
TTTTTTGGAAGAAAAATAGGGTTGAAATGG
Found at i:25159992 original size:3 final size:3
Alignment explanation
Indices: 25159986--25160097 Score: 174
Period size: 3 Copynumber: 37.7 Consensus size: 3
25159976 TAATGTTACC
25159986 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
25160034 ATT ATT ATC ATCT -TT ATT ATT ATT ATT ATT AAT ATC A-T ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25160078 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
25160098 ATTCTATAAT
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.02
3 98 0.98
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:25160239 original size:16 final size:16
Alignment explanation
Indices: 25160173--25160241 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 16
25160163 GCTTATATAT
*
25160173 ATATATATATATTT-C
1 ATATATATTTATTTAC
25160188 ATATA-ATTTATTTA-
1 ATATATATTTATTTAC
**
25160202 ATATATATATTACTTTTT
1 ATATATAT-TTA-TTTAC
25160220 ATATATATTTATTTAC
1 ATATATATTTATTTAC
25160236 ATATAT
1 ATATAT
25160242 CTATGTACTC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
14 12 0.27
15 7 0.16
16 12 0.27
17 6 0.13
18 8 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATATATTTATTTAC
Found at i:25160807 original size:110 final size:109
Alignment explanation
Indices: 25160555--25160958 Score: 600
Period size: 110 Copynumber: 3.7 Consensus size: 109
25160545 TTTCTAATTG
*
25160555 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
25160620 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
66 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
* * *
25160664 AGGCAACGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTGTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * *
25160729 TGTTCAACCAAATGGCTTAATATCCTTTTTAAAAATCTTAAAATA
66 CGTTTAACCAAATGGCTTAATATCC-TTTTAAAAATTTTAAAATA
*
25160774 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCTCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
25160839 CGTTTAACCAAATAG-TTAAATATCCTTTCAAAAATTTTCAAAATA
66 CGTTTAACCAAATGGCTT-AATATCCTTTTAAAAATTTT-AAAATA
* * * * * *
25160884 AGGTAATATTTTGCGTTTGGAAATTCGAG-GAACGTACCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
25160946 TGTTTAACCAAAT
66 CGTTTAACCAAAT
25160959 TGTCAAATAT
Statistics
Matches: 268, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
107 17 0.06
109 120 0.45
110 131 0.49
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
Found at i:25160934 original size:219 final size:217
Alignment explanation
Indices: 25160555--25160958 Score: 641
Period size: 219 Copynumber: 1.9 Consensus size: 217
25160545 TTTCTAATTG
*
25160555 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * *
25160620 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGGCAACGTTTTGCGTTTGAA
66 CGTTTAACCAAATAGCTTAATATCCTTTCAAAAATTTTAAAATAAGGCAACATTTTGCGTTTGAA
*
25160685 AATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTGTTCTTGTTCAACCAAATGGCTTAAT
131 AATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGA-T-TTCTTGTTCAACCAAATGGCTTAAT
25160750 ATCCTTTTTAAAAATCTTAAAATA
194 ATCCTTTTTAAAAATCTTAAAATA
*
25160774 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCTCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
25160839 CGTTTAACCAAATAG-TTAAATATCCTTTCAAAAATTTTCAAAATAAGGTAATATTTTGCGTTTG
66 CGTTTAACCAAATAGCTT-AATATCCTTTCAAAAATTTT-AAAATAAGGCAACATTTTGCGTTTG
* * * * *
25160903 GAAATTCGAG-GAACGTACCCTAAGGTGCTGGGTTTCGATTTCTTGTTTAACCAAAT
129 AAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTCTTGTTCAACCAAAT
25160959 TGTCAAATAT
Statistics
Matches: 170, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
217 16 0.09
218 3 0.02
219 120 0.71
220 31 0.18
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (217 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTTAACCAAATAGCTTAATATCCTTTCAAAAATTTTAAAATAAGGCAACATTTTGCGTTTGAA
AATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTCTTGTTCAACCAAATGGCTTAATAT
CCTTTTTAAAAATCTTAAAATA
Found at i:25165618 original size:17 final size:18
Alignment explanation
Indices: 25165586--25165620 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
25165576 TTTGGACTTG
*
25165586 TTTATTTATTTTTTTGGT
1 TTTATTTATTTATTTGGT
25165604 TTTATTTA-TTATTTGGT
1 TTTATTTATTTATTTGGT
25165621 CTTGGGCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTATTTATTTATTTGGT
Found at i:25166116 original size:51 final size:51
Alignment explanation
Indices: 25166040--25166163 Score: 221
Period size: 51 Copynumber: 2.4 Consensus size: 51
25166030 GTTTGATATG
25166040 ATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGCAATTTATAGTTTCA
1 ATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGCAATTTATAGTTTCA
25166091 ATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGCAATTTATAGTTTCA
1 ATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGCAATTTATAGTTTCA
* * *
25166142 ATCTGTTCCACTACAACTTCAG
1 ATCTGCTCTACTGCAACTTCAG
25166164 GGAAATAAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (51 bp):
ATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGCAATTTATAGTTTCA
Found at i:25166260 original size:44 final size:45
Alignment explanation
Indices: 25165910--25166261 Score: 247
Period size: 44 Copynumber: 7.7 Consensus size: 45
25165900 TCATTGTTTT
* * *
25165910 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAG-TAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTAACTTC
* * * *
25165954 AATCTGCTCCACTGCAATTTTAGGGAGATAAGATT-GGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTAACTTC
* * * * *
25165998 AACCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGAT-A--T-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTAACTTC
* * * * *
25166039 GATCTGCTCTACTGCAACTTCAGAGAGATAATA-TCTGCAATTTATAGTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GC----TA-A-CTTC
* * * *
25166090 AATCTGCTCTACTGCAACTTCAGAGAGATAATA-TCTGCAATTTATAGTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GC----TA-A-CTTC
* * * *
25166141 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTAACTTC
* *
25166186 AGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTT-G-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTAACTTC
*
25166230 AACCTGCTCCACTGCAACTTCAGGGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
25166262 GTTTGATATG
Statistics
Matches: 255, Mismatches: 38, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
40 1 0.00
41 27 0.11
42 1 0.00
43 1 0.00
44 103 0.40
45 35 0.14
46 2 0.01
47 3 0.01
50 1 0.00
51 79 0.31
52 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTAACTTC
Found at i:25166281 original size:188 final size:185
Alignment explanation
Indices: 25165951--25166299 Score: 400
Period size: 188 Copynumber: 1.9 Consensus size: 185
25165941 GATTAGTAGC
* * * * *
25165951 TTCAATCTGCTCCACTGCAATTTTAGGGAGATAAGATTGGTATCTTCAACCTGCTCCACTGCAAC
1 TTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATTGCTATCTTCAACCTGCTCCACTGCAAC
* * * * * *
25166016 TTCAAGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGCAATT
66 TTCAAGGAGATAAGCTTTAATATAACCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-AA-T
** * *
25166081 TATAGTTTCAATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGCAATTTATAGT
129 TATAGTTTCAATCCACCCTAATGCAACTTCAGAGAGATAATATCTGCAATTTATAGT
* **
25166138 TTCAATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAA
1 TTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATT-GCTATCTTCAACCTGCTCCACTGCAA
* * *
25166203 CTTCAAGGAGATAAGACTTGTAACT-TCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG
65 CTTCAAGGAGATAAG-CTT-TAA-TAT-AACCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG
25166267 -A-TAT-GATCTTCAATCCACCCTAATGCAACTTCA
126 AATTATAG-T-TTCAATCCACCCTAATGCAACTTCA
25166300 AGGGTATAGG
Statistics
Matches: 134, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
186 1 0.01
187 37 0.28
188 59 0.44
189 3 0.02
190 3 0.02
191 31 0.23
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (185 bp):
TTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATTGCTATCTTCAACCTGCTCCACTGCAAC
TTCAAGGAGATAAGCTTTAATATAACCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGAATTA
TAGTTTCAATCCACCCTAATGCAACTTCAGAGAGATAATATCTGCAATTTATAGT
Found at i:25167158 original size:6 final size:6
Alignment explanation
Indices: 25167147--25167194 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
25167137 TGGCCTCTCA
* *
25167147 TTCTTT TTCTTT TTC-TT TT-TTT TTATTT TTCTTT TCCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
25167193 TT
1 TT
25167195 TTTAAAGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 8 0.22
6 29 0.78
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTCTTT
Found at i:25167175 original size:16 final size:16
Alignment explanation
Indices: 25167150--25167181 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25167140 CCTCTCATTC
*
25167150 TTTTTCTTTTTCTTTT
1 TTTTTATTTTTCTTTT
25167166 TTTTTATTTTTCTTTT
1 TTTTTATTTTTCTTTT
25167182 CCTTTTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTATTTTTCTTTT
Found at i:25170868 original size:43 final size:43
Alignment explanation
Indices: 25170821--25171331 Score: 564
Period size: 43 Copynumber: 11.8 Consensus size: 43
25170811 AAGCGCCGCA
* * * *
25170821 ATAGACTATGGTCTTTAGCGGCGCTAACACAAAAAATGCCGCT
1 ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAACGCCACT
* * *
25170864 ATAGACCATAGTCTTTCGCGGCGC-TATACAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAACGCCACT
* * * ** *
25170906 ATAGATCATGGTCTTTTAGCGGTGTTTGTACATAAAACGCCACT
1 ATAGACCATGGTC-TTTAGCGGCGCTTACACAAAAAACGCCACT
* **
25170950 ATAGACCATGGTCTTTAGCGGTGCTTGGACAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAACGCCACT
* * * * ** *
25170993 ATAGATCGTGTTCTTTAGCGGCGATTGGACAAAAAAGGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAACGCCACT
25171036 ATAGACCATGGTCTTTAGCGGCGCTTGGACA-AAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTT--ACACAAAAAACGCCACT
* * * *
25171080 ATAGGCCATTGTCTTTAGCGGCGTTTAGACAAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTACAC-AAAAAACGCCACT
*
25171124 ATA-AGCCATGGTATTTAGCGGCGCTTAGC-CAAAAAACGCCACT
1 ATAGA-CCATGGTCTTTAGCGGCGCTTA-CACAAAAAACGCCACT
* *
25171167 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAATGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAACGCCACT
*
25171210 ATAGACCATGGTCTTTAGCGGCACTTAGC-CAAAAAACGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTA-CACAAAAAACGCCACT
* * * *
25171253 CTAGACCATGGTCTTTAGCGGCGCTTATACGAAAAATGCCACT
1 ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAACGCCACT
* * * * *
25171296 ATAGGCCGTGTTCTTTAGTGGCGCTTACCCAAAAAA
1 ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAA
25171332 TGCCGCTAAT
Statistics
Matches: 397, Mismatches: 59, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
42 27 0.07
43 269 0.68
44 100 0.25
45 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (43 bp):
ATAGACCATGGTCTTTAGCGGCGCTTACACAAAAAACGCCACT
Found at i:25171143 original size:174 final size:172
Alignment explanation
Indices: 25170821--25171298 Score: 604
Period size: 174 Copynumber: 2.8 Consensus size: 172
25170811 AAGCGCCGCA
* * * * * * *
25170821 ATAGACTATGGTCTTTAGCGGCGCTAACACAAAAAATGCCGCTATAGACCATAGTCTTTCGCGGC
1 ATAGACCATGGTCTTTAGCGGCGATTAGACAAAAAATGCCACTATAGACCATGGTCTTTAGCGGC
* * *
25170886 GCTAT-ACAAAAAACGCCACTATAGATCATGGTCTTTTAGCGGTGTTT-GTACATAAAACGCCAC
66 GCT-TGACAAAAAACGCCACTATAGACCATGGTC-TTTAGCGGCGTTTAG-ACAAAAAACGCCAC
* * *
25170949 TAT-AGACCATGGTCTTTAGCGGTGCTTGGACAAAAAACGCCACT
128 TATAAGACCATGGTATTTAGCGGCGCTTAGACAAAAAACGCCACT
* * * * *
25170993 ATAGATCGTGTTCTTTAGCGGCGATTGGACAAAAAAGGCCACTATAGACCATGGTCTTTAGCGGC
1 ATAGACCATGGTCTTTAGCGGCGATTAGACAAAAAATGCCACTATAGACCATGGTCTTTAGCGGC
* *
25171058 GCTTGGACAAAAAAACGCCACTATAGGCCATTGTCTTTAGCGGCGTTTAGACAAAAAAACGCCAC
66 GCTT-GAC-AAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGTTTAGAC-AAAAAACGCCAC
*
25171123 TATAAG-CCATGGTATTTAGCGGCGCTTAGCCAAAAAACGCCACT
128 TATAAGACCATGGTATTTAGCGGCGCTTAGACAAAAAACGCCACT
*
25171167 ATAGACCATGGTCTTTAGCGGCGCTTAGACAAAAAATGCCACTATAGACCATGGTCTTTAGCGGC
1 ATAGACCATGGTCTTTAGCGGCGATTAGACAAAAAATGCCACTATAGACCATGGTCTTTAGCGGC
* * * * * * *
25171232 ACTTAGCCAAAAAACGCCACTCTAGACCATGGTCTTTAGCGGCGCTTATACGAAAAATGCCACTA
66 GCTT-GACAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGTTTAGACAAAAAACGCCACTA
25171297 TA
130 TA
25171299 GGCCGTGTTC
Statistics
Matches: 263, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
171 1 0.00
172 70 0.27
173 54 0.21
174 136 0.52
175 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (172 bp):
ATAGACCATGGTCTTTAGCGGCGATTAGACAAAAAATGCCACTATAGACCATGGTCTTTAGCGGC
GCTTGACAAAAAACGCCACTATAGACCATGGTCTTTAGCGGCGTTTAGACAAAAAACGCCACTAT
AAGACCATGGTATTTAGCGGCGCTTAGACAAAAAACGCCACT
Found at i:25171752 original size:87 final size:87
Alignment explanation
Indices: 25171646--25171839 Score: 230
Period size: 87 Copynumber: 2.2 Consensus size: 87
25171636 ATGCTGTTCT
* * * * * *
25171646 GCTTCCCTCGTTGCAGCCTCTAATTCCCTCGCTGCTGCATCTGCTTTAAGCTGCT-GTTGGAGTT
1 GCTTCTCTCGATGCTGCCTCTAATTCCCTCGCTGCCGCATCTACTTTAAGCTG-TAGCTGGAGTT
25171710 CTTCATA-CTTTCGTTGAACCTCA
65 CTTCATATCTTT-GTTGAACCTCA
* ** * * *
25171733 GCTTCTCTCGCTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTACTTTAAGTTGTAGCTGGAGTTC
1 GCTTCTCTCGATGCTGCCTCTAATTCCCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTC
*
25171798 TTCATATCTTTTTTGAACCTCA
66 TTCATATCTTTGTTGAACCTCA
*
25171820 GCTTCTCTCGATGTTGCCTC
1 GCTTCTCTCGATGCTGCCTC
25171840 CACTTTAAGT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 1 0.01
87 86 0.95
88 4 0.04
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.39
Consensus pattern (87 bp):
GCTTCTCTCGATGCTGCCTCTAATTCCCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTC
TTCATATCTTTGTTGAACCTCA
Found at i:25177214 original size:25 final size:25
Alignment explanation
Indices: 25177186--25177290 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
25177176 GTTACATAAT
*
25177186 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
25177211 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
* * *
25177237 TCATGTATTAAGTAAGCTATGTAAA
1 TTATGTATTAAGTAAGTTATGTAAG
* * *
25177262 TTGTGTATTATGTAACTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
25177287 TTAT
1 TTAT
25177291 CAAAGTAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
23 1 0.02
24 2 0.03
25 40 0.62
26 18 0.28
27 2 0.03
28 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:25177236 original size:9 final size:9
Alignment explanation
Indices: 25177197--25177683 Score: 250
Period size: 9 Copynumber: 56.3 Consensus size: 9
25177187 TATGTATTAA
*
25177197 GTAAATTAT
1 GTAAGTTAT
25177206 GTAAGTTAT
1 GTAAGTTAT
*
25177215 GTACGTGTA-
1 GTAAGT-TAT
25177224 -TAAGTTAT
1 GTAAGTTAT
*
25177232 GTAAGTCAT
1 GTAAGTTAT
*
25177241 GT-A-TTAA
1 GTAAGTTAT
*
25177248 GTAAGCTAT
1 GTAAGTTAT
* *
25177257 GTAAATTGT
1 GTAAGTTAT
25177266 GT-A-TTAT
1 GTAAGTTAT
*
25177273 GTAACTTAT
1 GTAAGTTAT
25177282 GTAAGTTAT
1 GTAAGTTAT
** *
25177291 CAAAGTAAT
1 GTAAGTTAT
*
25177300 GTATGTTAT
1 GTAAGTTAT
25177309 GTAAG-T-T
1 GTAAGTTAT
25177316 GTAAGTTAT
1 GTAAGTTAT
25177325 GT-A-TTAT
1 GTAAGTTAT
*
25177332 GTAACTTAT
1 GTAAGTTAT
25177341 GTAAGTTA-
1 GTAAGTTAT
** *
25177349 CCAAATTAAT
1 GTAAGTT-AT
**
25177359 GTCTGTTAT
1 GTAAGTTAT
25177368 GTAAG-T-T
1 GTAAGTTAT
25177375 GTAAGTTAT
1 GTAAGTTAT
25177384 GT-A-TTAT
1 GTAAGTTAT
*
25177391 GTAACTTAT
1 GTAAGTTAT
25177400 GTAAGTTA-
1 GTAAGTTAT
** *
25177408 CCAAATTAAT
1 GTAAGTT-AT
*
25177418 GTATGTTAT
1 GTAAGTTAT
25177427 GTAAG-T-T
1 GTAAGTTAT
25177434 GTAAGTTAT
1 GTAAGTTAT
*
25177443 -TATATATTAT
1 GTA-A-GTTAT
25177453 GTAAGTTAT
1 GTAAGTTAT
25177462 GTAAGTTAT
1 GTAAGTTAT
25177471 GTAAGTTAT
1 GTAAGTTAT
25177480 GT-A-TTAT
1 GTAAGTTAT
*
25177487 GTAGGTTAT
1 GTAAGTTAT
*
25177496 GTAAGTTGT
1 GTAAGTTAT
*
25177505 GTAAGATAT
1 GTAAGTTAT
*
25177514 TTAAGTTAT
1 GTAAGTTAT
*
25177523 GTAAGTTTT
1 GTAAGTTAT
25177532 GT-A-TTAT
1 GTAAGTTAT
25177539 GTAAGTTAT
1 GTAAGTTAT
* *
25177548 GTATGCTAT
1 GTAAGTTAT
25177557 GT-A-TTAT
1 GTAAGTTAT
25177564 GTAAGTTTAT
1 GTAAG-TTAT
* *
25177574 ATAAAAATTTTAT
1 GT---AA-GTTAT
*
25177587 ATAAGTTAT
1 GTAAGTTAT
25177596 GT-A-TTAT
1 GTAAGTTAT
*
25177603 GTAAGGTAACAT
1 GTAA-GT--TAT
*
25177615 ATAAGTTTAT
1 GTAAG-TTAT
25177625 GTAAGTTAT
1 GTAAGTTAT
25177634 G--A---AT
1 GTAAGTTAT
25177638 GTAAGTTAT
1 GTAAGTTAT
25177647 GT-A-TTAT
1 GTAAGTTAT
25177654 GTAAGTTAT
1 GTAAGTTAT
* *
25177663 TTAAATTAT
1 GTAAGTTAT
* *
25177672 TTAAGTTGT
1 GTAAGTTAT
25177681 GTA
1 GTA
25177684 TTAAGTAAGT
Statistics
Matches: 360, Mismatches: 70, Indels: 96
0.68 0.13 0.18
Matches are distributed among these distances:
4 3 0.01
6 1 0.00
7 70 0.19
8 36 0.10
9 207 0.57
10 26 0.07
11 3 0.01
12 6 0.02
13 8 0.02
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:25177290 original size:59 final size:57
Alignment explanation
Indices: 25177224--25177507 Score: 289
Period size: 59 Copynumber: 4.8 Consensus size: 57
25177214 TGTACGTGTA
** * * * *
25177224 TAAGTTATGTAAGTCATGTATTAAGTAAGCTATGTAAATTGTGTATTATGTAACTTATG
1 TAAGTTATCAAAGTAATGTATTATGTAAG-T-TGTAAGTTATGTATTATGTAACTTATG
25177283 TAAGTTATCAAAGTAATGTATGTTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
1 TAAGTTATCAAAGTAATGTA--TTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
* * *
25177342 TAAGTTACCAAATTAATGTCTGTTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
1 TAAGTTATCAAAGTAATG--TATTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
* * * *
25177401 TAAGTTACCAAATTAATGTATGTTATGTAAGTTGTAAGTTATTATATATTATGTAAGTTATG
1 TAAGTTATCAAAGTAATGTA--TTATGTAAGTTGTAAG---TTATGTATTATGTAACTTATG
** * * *
25177463 TAAGTTATGTAAGTTATGTATTATGTAGGTTATGTAAGTTGTGTA
1 TAAGTTATCAAAGTAATGTATTATGTAAG-T-TGTAAGTTATGTA
25177508 AGATATTTAA
Statistics
Matches: 194, Mismatches: 20, Indels: 22
0.82 0.08 0.09
Matches are distributed among these distances:
57 1 0.01
59 134 0.69
60 9 0.05
61 10 0.05
62 40 0.21
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (57 bp):
TAAGTTATCAAAGTAATGTATTATGTAAGTTGTAAGTTATGTATTATGTAACTTATG
Found at i:25177384 original size:16 final size:17
Alignment explanation
Indices: 25177203--25177569 Score: 150
Period size: 16 Copynumber: 21.1 Consensus size: 17
25177193 TTAAGTAAAT
*
25177203 TATGTAAGTTATGTACG
1 TATGTAAGTTATGTAAG
* *
25177220 TGTATAAGTTATGTAAG
1 TATGTAAGTTATGTAAG
*
25177237 TCATGT-A-TTAAGTAAG
1 T-ATGTAAGTTATGTAAG
*
25177253 CTATGTAAATTGTGTATTATGTAACT
1 -TATGT-AA----G--TTATGTAA-G
**
25177279 TATGTAAGTTATCAAAG
1 TATGTAAGTTATGTAAG
*
25177296 TAATGTATGTTATGTAAG
1 T-ATGTAAGTTATGTAAG
*
25177314 T-TGTAAGTTATGT-AT
1 TATGTAAGTTATGTAAG
*
25177329 TATGTAACTTATGTAAG
1 TATGTAAGTTATGTAAG
** * **
25177346 T-TACCAAATTAATGTCTG
1 TAT-GTAAGTT-ATGTAAG
25177364 TTATGTAAG-T-TGTAAG
1 -TATGTAAGTTATGTAAG
*
25177380 TTATGT-A-TTATGTAACT
1 -TATGTAAGTTATGTAA-G
*** *
25177397 TATGTAAGTTACCAAAT
1 TATGTAAGTTATGTAAG
*
25177414 TAATGTATGTTATGTAAG
1 T-ATGTAAGTTATGTAAG
* *
25177432 T-TGTAAGTTATTATATAT
1 TATGTAAGTTA-TGTA-AG
25177450 TATGTAAGTTATGTAAG
1 TATGTAAGTTATGTAAG
*
25177467 TTATGTAAGTTATGT-AT
1 -TATGTAAGTTATGTAAG
*
25177484 TATGTAGGTTATGTAAG
1 TATGTAAGTTATGTAAG
* * *
25177501 TTGTGTAAGATATTTAAG
1 -TATGTAAGTTATGTAAG
* *
25177519 TTATGTAAGTTTTGT-AT
1 -TATGTAAGTTATGTAAG
*
25177536 TATGTAAGTTATGTATG
1 TATGTAAGTTATGTAAG
25177553 CTATGT-A-TTATGTAAG
1 -TATGTAAGTTATGTAAG
25177569 T
1 T
25177570 TTATATAAAA
Statistics
Matches: 259, Mismatches: 58, Indels: 68
0.67 0.15 0.18
Matches are distributed among these distances:
15 5 0.02
16 97 0.37
17 35 0.14
18 94 0.36
19 12 0.05
20 2 0.01
24 2 0.01
25 12 0.05
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (17 bp):
TATGTAAGTTATGTAAG
Found at i:25177437 original size:34 final size:32
Alignment explanation
Indices: 25177367--25177504 Score: 109
Period size: 34 Copynumber: 4.1 Consensus size: 32
25177357 ATGTCTGTTA
* * *
25177367 TGTAAGTTGTAAGTTATGT-A-TTATGTAACTT
1 TGTAAGTTATAAATTATGTAAGTTATGTAA-GT
* *
25177398 ATGTAAGTTACCAAATTAATGTATGTTATGTAAGT
1 -TGTAAGTTA-TAAATT-ATGTAAGTTATGTAAGT
25177433 TGTAAGTTATTATATATTATGTAAGTTATGTAAGTT
1 TGTAAGTTA-TA-A-ATTATGTAAGTTATGTAAG-T
** *
25177469 ATGTAAGTTATGTATTATGTAGGTTATGTAAGT
1 -TGTAAGTTATAAATTATGTAAGTTATGTAAGT
25177502 TGT
1 TGT
25177505 GTAAGATATT
Statistics
Matches: 87, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
32 11 0.13
33 5 0.06
34 32 0.37
35 17 0.20
36 13 0.15
37 9 0.10
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (32 bp):
TGTAAGTTATAAATTATGTAAGTTATGTAAGT
Found at i:25177508 original size:43 final size:42
Alignment explanation
Indices: 25177442--25177566 Score: 139
Period size: 43 Copynumber: 3.0 Consensus size: 42
25177432 TTGTAAGTTA
* *
25177442 TTATATATTATGTAAGTTATGTAAGTTATGTAAGTTATGTA-
1 TTATGTATTATGTAAGTTATGTAAGATATGTAAGTTATGTAG
* *
25177483 TTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAG
1 TTATGTA--TTATGTAAGTTATGTAAGATATGTAAGTTATGT-AG
* * *
25177528 TTTTGTATTATGTAAGTTATGTATGCTATGT-A-TTATGTA
1 TTATGTATTATGTAAGTTATGTAAGATATGTAAGTTATGTA
25177567 AGTTTATATA
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
40 1 0.01
41 12 0.17
42 1 0.01
43 50 0.70
44 1 0.01
45 6 0.08
ACGTcount: A:0.30, C:0.01, G:0.20, T:0.49
Consensus pattern (42 bp):
TTATGTATTATGTAAGTTATGTAAGATATGTAAGTTATGTAG
Found at i:25177568 original size:25 final size:25
Alignment explanation
Indices: 25177201--25177671 Score: 108
Period size: 25 Copynumber: 18.9 Consensus size: 25
25177191 TATTAAGTAA
* *
25177201 ATTATGTAAGTTATGTACGTGTAT-A
1 ATTATGTAAGTTATGTAAGT-TATGT
* *
25177226 AGTTATGTAAGTCATGT-A-TTAAGT
1 A-TTATGTAAGTTATGTAAGTTATGT
* * *
25177250 AAGCTATGTAAATTGTGT-A-TTATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
** *
25177275 AACTTATGTAAGTTATCAAAGTAATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
25177302 ATGTTATGTAAG-T-TGTAAGTTATGT
1 A--TTATGTAAGTTATGTAAGTTATGT
* ***
25177327 ATTATGTAACTTATGTAAGTTACCAA
1 ATTATGTAAGTTATGTAAGTTA-TGT
**
25177353 ATTAATGTCTGTTATGTAAG-T-TGT
1 ATT-ATGTAAGTTATGTAAGTTATGT
*
25177377 AAGTTATGT-A-TTATGTAACTTATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
** * *
25177402 AAGTTA-CCAAATTAATGTATGTTATGT
1 -A-TTATGTAAGTT-ATGTAAGTTATGT
*
25177429 AAGT-TGTAAGTTAT-T-A--TA--T
1 -ATTATGTAAGTTATGTAAGTTATGT
25177448 ATTATGTAAGTTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTATGT
*
25177473 AAGTTATGT-A-TTATGTAGGTTATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
* * *
25177498 AAGTTGTGTAAGATATTTAAGTTATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
*
25177525 AAGTTTTGT-A-TTATGTAAGTTATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
*
25177550 ATGCTATGT-A-TTATGTAAGTT-TAT
1 AT--TATGTAAGTTATGTAAGTTATGT
** * *
25177574 A-TA-AAAATTTTATATAAGTTATGT
1 ATTATGTAA-GTTATGTAAGTTATGT
* *
25177598 ATTATGTAAG----GTAACATATAAGT
1 ATTATGTAAGTTATGTAA-GT-TATGT
25177621 -TTATGTAAGTTATGAATGTAAGTTATGT
1 ATTATGTAAG-T-T--ATGTAAGTTATGT
* *
25177649 ATTATGTAAGTTATTTAAATTAT
1 ATTATGTAAGTTATGTAAGTTAT
25177672 TTAAGTTGTG
Statistics
Matches: 332, Mismatches: 66, Indels: 96
0.67 0.13 0.19
Matches are distributed among these distances:
18 2 0.01
19 11 0.03
20 1 0.00
21 9 0.03
22 10 0.03
23 35 0.11
24 11 0.03
25 131 0.39
26 36 0.11
27 67 0.20
28 5 0.02
29 10 0.03
30 4 0.01
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATGTAAGTTATGT
Found at i:25177633 original size:38 final size:39
Alignment explanation
Indices: 25177540--25177634 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 39
25177530 TTGTATTATG
* * * * *
25177540 TAAG-TTATGTATGCTATGTATTATGTAAGTTTATATAA
1 TAAGTTTATGTAAGTTATGTATTATGTAAGGTAACATAA
* * *
25177578 AAATTTTATATAAGTTATGTATTATGTAAGGTAACAT-A
1 TAAGTTTATGTAAGTTATGTATTATGTAAGGTAACATAA
25177616 TAAGTTTATGTAAGTTATG
1 TAAGTTTATGTAAGTTATG
25177635 AATGTAAGTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 19 0.42
39 26 0.58
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (39 bp):
TAAGTTTATGTAAGTTATGTATTATGTAAGGTAACATAA
Found at i:25177641 original size:13 final size:15
Alignment explanation
Indices: 25177622--25177662 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
25177612 CATATAAGTT
25177622 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
25177636 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
25177650 TTATGTAAGTTAT
1 -TATGTAAGTTAT
25177663 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:25177657 original size:16 final size:16
Alignment explanation
Indices: 25177186--25177699 Score: 139
Period size: 16 Copynumber: 30.4 Consensus size: 16
25177176 GTTACATAAT
* *
25177186 TTATGTATTAAGTAAA
1 TTATGTATTATGTAAG
*
25177202 TTATGTAAGTTATGTACG
1 TTATGT-A-TTATGTAAG
*
25177220 TGTAT-AAGTTATGTAAG
1 T-TATGTA-TTATGTAAG
* *
25177237 TCATGTATTAAGTAAG
1 TTATGTATTATGTAAG
* *
25177253 CTATGTAAATTGTGT-A-
1 TTATGT--ATTATGTAAG
25177269 TTATGTAACTTATGTAAG
1 TTATGT-A-TTATGTAAG
** * *
25177287 TTATCAAAGTAATGTATG
1 TTAT-GTA-TTATGTAAG
*
25177305 TTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
*
25177321 TTATGTATTATGTAAC
1 TTATGTATTATGTAAG
** *
25177337 TTATGTAAGTTA-CCAAA
1 TTATGT-A-TTATGTAAG
*
25177354 TTAATGTCTGTTATGTAAG
1 TT-ATG--TATTATGTAAG
25177373 -T-TGTAAGTTATGT-A-
1 TTATGT-A-TTATGTAAG
25177387 TTATGTAACTTATGTAAG
1 TTATGT-A-TTATGTAAG
*** *
25177405 TTACCAAATTAATGTATG
1 TTA-TGTATT-ATGTAAG
*
25177423 TTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
*
25177439 TTATTATATATTATGTAAG
1 ---TTATGTATTATGTAAG
25177458 TTATGTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
25177476 TTATGTATTATGTAGG
1 TTATGTATTATGTAAG
*
25177492 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
25177510 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
25177528 TTTTGTATTATGTAAG
1 TTATGTATTATGTAAG
25177544 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
*
25177560 TTATGTAAGTTTATATAA-
1 TTATGT-A--TTATGTAAG
** *
25177578 AAAT-T-TTATATAAG
1 TTATGTATTATGTAAG
25177592 TTATGTATTATGTAAGG
1 TTATGTATTATGTAA-G
25177609 TAACATATAAGT-TTATGTAAG
1 T----TAT--GTATTATGTAAG
25177630 TTATG-A--ATGTAAG
1 TTATGTATTATGTAAG
25177643 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
25177659 TTATTTAAATTATTTAAG
1 TTATGT--ATTATGTAAG
* *
25177677 TTGTGTATTAAGTAAG
1 TTATGTATTATGTAAG
*
25177693 TCATGTA
1 TTATGTA
25177700 GGCTATGTGT
Statistics
Matches: 370, Mismatches: 71, Indels: 114
0.67 0.13 0.21
Matches are distributed among these distances:
13 20 0.05
14 4 0.01
15 8 0.02
16 149 0.40
17 39 0.11
18 117 0.32
19 17 0.05
20 1 0.00
21 5 0.01
22 8 0.02
23 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:25177773 original size:19 final size:20
Alignment explanation
Indices: 25177751--25177797 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25177741 TTTTTCAAAT
* *
25177751 ATATATAAAATTTTA-ATAA
1 ATATATAAAACTGTATATAA
25177770 ATATATTAAAACTGTATATAA
1 ATATA-TAAAACTGTATATAA
25177791 ATATATA
1 ATATATA
25177798 TATCAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATATAAAACTGTATATAA
Found at i:25177773 original size:21 final size:22
Alignment explanation
Indices: 25177747--25177799 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
25177737 TAAATTTTTC
* *
25177747 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAACTGTATAT
25177768 AAATATAT-TAAAACTGTATAT
1 AAATATATATAAAACTGTATAT
25177789 AAATATATATA
1 AAATATATATA
25177800 TCAAAGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATATAAAACTGTATAT
Found at i:25179655 original size:11 final size:11
Alignment explanation
Indices: 25179620--25179657 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
25179610 TTACTCAACC
25179620 AGTAATATGAA
1 AGTAATATGAA
*
25179631 AGGAATATGAA
1 AGTAATATGAA
25179642 AGTAATATGAA
1 AGTAATATGAA
25179653 AGTAA
1 AGTAA
25179658 ATTAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (11 bp):
AGTAATATGAA
Found at i:25180584 original size:27 final size:27
Alignment explanation
Indices: 25180536--25180587 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
25180526 TCTTACATTT
*
25180536 AAATAAATAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
**
25180563 AAATAAATAATTACTTACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
25180588 TTTGTTTATT
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:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:25182458 original size:14 final size:14
Alignment explanation
Indices: 25182439--25182506 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
25182429 ATGACCGTTG
25182439 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
25182453 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
25182468 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
25182481 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
25182494 AAACCTTAAATCT
1 AAACCCTAAATCT
25182507 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:25182462 original size:15 final size:15
Alignment explanation
Indices: 25182442--25182479 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
25182432 ACCGTTGAAA
25182442 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
25182457 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
25182472 CCCTAAAT
1 CCCTAAAT
25182480 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:25183012 original size:41 final size:41
Alignment explanation
Indices: 25182967--25183245 Score: 199
Period size: 41 Copynumber: 6.8 Consensus size: 41
25182957 GCGGCGTAGA
* *
25182967 ATTAGTGGCGCTCAAATAAAAACATCACTAAAGATCCGAGC
1 ATTAGCGGCGCTCAAATAAAAACACCACTAAAGATCCGAGC
* * * * * * * *
25183008 ATTAGCGACGCTTAGACAAAAACGCCGCTAAAG-GCCAGAGG
1 ATTAGCGGCGCTCAAATAAAAACACCACTAAAGATCC-GAGC
* * * * *
25183049 ATTAGTGGCGCTGAGATAAAAACGCCACTAAAGCTCCGAGC
1 ATTAGCGGCGCTCAAATAAAAACACCACTAAAGATCCGAGC
* * * * * * *
25183090 CTTAGCGGCGCTTAGACAAAAACGCCGCTAAAG-GCCAGAG-
1 ATTAGCGGCGCTCAAATAAAAACACCACTAAAGATCC-GAGC
* * * *
25183130 ATTTAGCGGCGCTCATATAAAAACACCGCTAAAGATCGGAGT
1 A-TTAGCGGCGCTCAAATAAAAACACCACTAAAGATCCGAGC
* *
25183172 ATTAGCAGCGC-CAAGATAAAAACGA-CACTAAAGATCCAAGC
1 ATTAGCGGCGCTCAA-ATAAAAAC-ACCACTAAAGATCCGAGC
* * *
25183213 ATTAGCGGCGCACAAATAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTCAAATAAAAACACCACTAAAG
25183246 TTTTAAAAAT
Statistics
Matches: 189, Mismatches: 39, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
40 6 0.03
41 175 0.93
42 8 0.04
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.15
Consensus pattern (41 bp):
ATTAGCGGCGCTCAAATAAAAACACCACTAAAGATCCGAGC
Found at i:25183104 original size:82 final size:81
Alignment explanation
Indices: 25182967--25183245 Score: 301
Period size: 82 Copynumber: 3.4 Consensus size: 81
25182957 GCGGCGTAGA
*
25182967 ATTAGTGGCGCTCAAATAAAAACATCACTAAAGATCCGAGCATTAGCGACGCTTAGACAAAAACG
1 ATTAGTGGCGCTCAAATAAAAACACCACTAAAGATCCGAGCATTAGCGACGCTTAGACAAAAACG
25183032 CCGCTAAAGGCCAGAGG
66 CCGCTAAAGGCCAGA-G
* * * * * *
25183049 ATTAGTGGCGCTGAGATAAAAACGCCACTAAAGCTCCGAGCCTTAGCGGCGCTTAGACAAAAACG
1 ATTAGTGGCGCTCAAATAAAAACACCACTAAAGATCCGAGCATTAGCGACGCTTAGACAAAAACG
25183114 CCGCTAAAGGCCAGAG
66 CCGCTAAAGGCCAGAG
* * * * * ** *
25183130 ATTTAGCGGCGCTCATATAAAAACACCGCTAAAGATCGGAGTATTAGC-AGCGCCAAGATAAAAA
1 A-TTAGTGGCGCTCAAATAAAAACACCACTAAAGATCCGAGCATTAGCGA-CGCTTAGACAAAAA
* * *
25183194 CGACACTAAAGATCCA-AG
64 CGCCGCTAAAG-GCCAGAG
* * * *
25183212 CATTAGCGGCGCACAAATAAAAACGCCGCTAAAG
1 -ATTAGTGGCGCTCAAATAAAAACACCACTAAAG
25183246 TTTTAAAAAT
Statistics
Matches: 167, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
81 2 0.01
82 161 0.96
83 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.15
Consensus pattern (81 bp):
ATTAGTGGCGCTCAAATAAAAACACCACTAAAGATCCGAGCATTAGCGACGCTTAGACAAAAACG
CCGCTAAAGGCCAGAG
Found at i:25185798 original size:15 final size:14
Alignment explanation
Indices: 25185756--25185800 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
25185746 GATTACAAGA
25185756 TTCTTTTTTTTTGT
1 TTCTTTTTTTTTGT
*
25185770 CTTCTTGTTTTTTGT
1 -TTCTTTTTTTTTGT
*
25185785 TTGTTTTTTCTTTGT
1 TTCTTTTTT-TTTGT
25185800 T
1 T
25185801 GTCCCCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (14 bp):
TTCTTTTTTTTTGT
Found at i:25189752 original size:24 final size:23
Alignment explanation
Indices: 25189692--25189752 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
25189682 CTCGTTGACA
25189692 TTAGATTAGCATCA-TTACATGTT
1 TTAGATTAG-ATCATTTACATGTT
* *
25189715 TTA-ATTACCA-CATTTATTATGTT
1 TTAGATTA-GATCATTTA-CATGTT
25189738 TTAGATTAGATCATT
1 TTAGATTAGATCATT
25189753 GTTCTAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 12 0.40
24 8 0.27
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (23 bp):
TTAGATTAGATCATTTACATGTT
Done.