Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 11 of 221
Found at i:3593837 original size:30 final size:28
Alignment explanation
Indices: 3593802--3593880 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 28
3593792 ACTTATAAAA
3593802 ATAAAAATATGTATATGTATATAGATATAT
1 ATAAAAA-AT-TATATGTATATAGATATAT
* *
3593832 ATAAAAAGA-AATATGAGTATATATATATAT
1 ATAAAAA-ATTATAT--GTATATAGATATAT
3593862 ATTAAACAAATTATATGTA
1 A-TAAA-AAATTATATGTA
3593881 AAATATATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
28 4 0.10
30 25 0.62
31 5 0.12
32 6 0.15
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (28 bp):
ATAAAAAATTATATGTATATAGATATAT
Found at i:3594004 original size:3 final size:3
Alignment explanation
Indices: 3593993--3594056 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
3593983 CAATAATACC
* * *
3593993 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
3594038 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
3594057 GCAAAAGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3595482 original size:18 final size:19
Alignment explanation
Indices: 3595449--3595487 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3595439 ATGTTTTAAT
3595449 AAATAAAAATTATTTTGAA
1 AAATAAAAATTATTTTGAA
* *
3595468 AAATATAAA-TATTTTTAA
1 AAATAAAAATTATTTTGAA
3595486 AA
1 AA
3595488 GTTTTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATAAAAATTATTTTGAA
Found at i:3601972 original size:22 final size:22
Alignment explanation
Indices: 3601947--3602014 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
3601937 CACTTAAAAG
3601947 TTTAATCTGGTTTAACTCTAAA
1 TTTAATCTGGTTTAACTCTAAA
3601969 TTTAA------TTAACT-TAAAA
1 TTTAATCTGGTTTAACTCT-AAA
3601985 GTTTAATCTGGTTTAACTCTAAA
1 -TTTAATCTGGTTTAACTCTAAA
3602008 TTTAATC
1 TTTAATC
3602015 AAGAATAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 18
0.67 0.00 0.33
Matches are distributed among these distances:
15 1 0.03
16 9 0.24
17 5 0.14
22 12 0.32
23 9 0.24
24 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTAATCTGGTTTAACTCTAAA
Found at i:3601992 original size:39 final size:39
Alignment explanation
Indices: 3601938--3602013 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
3601928 ATATTCTCTC
3601938 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAATTA
1 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAATTA
3601977 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAAT
1 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAAT
3602014 CAAGAATAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (39 bp):
ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAATTA
Found at i:3609778 original size:27 final size:27
Alignment explanation
Indices: 3609731--3609789 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3609721 ATTAAATTAG
* * * *
3609731 TTTATAAATTCACATATTTTAATAA-T
1 TTTATAAATTAAAATAATTTAAAAACT
3609757 TTTATAAAATTAAAATAATTTAAAAACT
1 TTTAT-AAATTAAAATAATTTAAAAACT
3609785 TTTAT
1 TTTAT
3609790 TATATATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.19
27 16 0.59
28 6 0.22
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTATAAATTAAAATAATTTAAAAACT
Found at i:3611810 original size:20 final size:20
Alignment explanation
Indices: 3611768--3611812 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3611758 AAATTTTGTT
*
3611768 ATAATTTTAATACTTTTTTAA
1 ATAATTTTAATAC-TTTTAAA
3611789 ATAATTTTAATGA-TTTTAAA
1 ATAATTTTAAT-ACTTTTAAA
3611809 ATAA
1 ATAA
3611813 AAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 11 0.50
22 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAATTTTAATACTTTTAAA
Found at i:3611857 original size:26 final size:25
Alignment explanation
Indices: 3611803--3611857 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
3611793 TTTTAATGAT
* * * *
3611803 TTTAAAATAAAAAATTATTTTATTT
1 TTTAAAATAAAAAATTAATTAAATG
3611828 TTTAAAATTAAAAAATTAATTAAATG
1 TTTAAAA-TAAAAAATTAATTAAATG
3611854 TTTA
1 TTTA
3611858 TGTGGAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAAAATAAAAAATTAATTAAATG
Found at i:3611888 original size:22 final size:22
Alignment explanation
Indices: 3611863--3611905 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3611853 GTTTATGTGG
3611863 AATTCACGTGGCAATCCATGTA
1 AATTCACGTGGCAATCCATGTA
3611885 AATTCACGTGGCAATCCATGT
1 AATTCACGTGGCAATCCATGT
3611906 GAATGTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (22 bp):
AATTCACGTGGCAATCCATGTA
Found at i:3619635 original size:42 final size:40
Alignment explanation
Indices: 3619576--3619656 Score: 144
Period size: 42 Copynumber: 2.0 Consensus size: 40
3619566 CCCGCGATCA
3619576 TGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTGT
1 TGTTAGAATAAACTACCCCTTTAGTA--CTGTCATTTATTGT
3619618 TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTG
1 TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTG
3619657 GTGTAATCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 13 0.33
42 26 0.67
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (40 bp):
TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTGT
Found at i:3624058 original size:42 final size:42
Alignment explanation
Indices: 3624006--3624096 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
3623996 TTACGTTAGC
*
3624006 AATTAATATAAATGTTTGTAGTACATGAGGTTAAATTGAACA
1 AATTCATATAAATGTTTGTAGTACATGAGGTTAAATTGAACA
3624048 AATTCATATAAATGTTTGTAGTACATGAGGTTAAATTGAACA
1 AATTCATATAAATGTTTGTAGTACATGAGGTTAAATTGAACA
3624090 AATTCAT
1 AATTCAT
3624097 GTTAAAAGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (42 bp):
AATTCATATAAATGTTTGTAGTACATGAGGTTAAATTGAACA
Found at i:3625412 original size:144 final size:144
Alignment explanation
Indices: 3625149--3625434 Score: 448
Period size: 144 Copynumber: 2.0 Consensus size: 144
3625139 TGTTCTTTAT
* *
3625149 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGTTATTGAGTGAGCTTTAT
1 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGTCATTGAGCGAGCTTTAT
** *
3625214 CATTGTAATATCTTCCTTGAGAGGTGTCTTTAATCATTGTTATTATTTAACATATTTGTAAGGGG
66 CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGGG
3625279 TTGCTTAAGGTTAC
131 TTGCTTAAGGTTAC
* * * *
3625293 ACACACTTGGGTAACCATCTCTTTTATTCTTTTCAATTGTTGTATT-TCCATTGAGCGAGCTTTA
1 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGT-CATTGAGCGAGCTTTA
* *
3625357 TCATTGTAATATCTTCCTTGCGAGACGTCTTCAATCATTGTTATTATTTATCATATTTGTAAGGG
65 TCATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGG
*
3625422 TTTGCTTAAGGTT
130 GTTGCTTAAGGTT
3625435 TTTGAGTAGA
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
143 1 0.01
144 128 0.99
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (144 bp):
ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGTCATTGAGCGAGCTTTAT
CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGGG
TTGCTTAAGGTTAC
Found at i:3626618 original size:22 final size:23
Alignment explanation
Indices: 3626577--3626619 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3626567 ATTTTATGTT
*
3626577 AATAATATATTTTAGCATTTTTA
1 AATAATATATTTTAACATTTTTA
*
3626600 AATAATAT-TTTTAATATTTT
1 AATAATATATTTTAACATTTT
3626620 ATTGAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
AATAATATATTTTAACATTTTTA
Found at i:3626619 original size:21 final size:22
Alignment explanation
Indices: 3626577--3626620 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3626567 ATTTTATGTT
3626577 AATAATATATTTTAGCATTTTTA
1 AATAATATATTTTA-CATTTTTA
3626600 AATAATAT-TTTTA-ATATTTTA
1 AATAATATATTTTACAT-TTTTA
3626621 TTGAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 5 0.25
22 5 0.25
23 8 0.40
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
AATAATATATTTTACATTTTTA
Found at i:3632346 original size:18 final size:19
Alignment explanation
Indices: 3632309--3632346 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3632299 TAATTAAATA
* *
3632309 AAAAATTAAATTTATTTAT
1 AAAAATAAAATTTATATAT
3632328 AAAAATAAAATTT-TATAT
1 AAAAATAAAATTTATATAT
3632346 A
1 A
3632347 CATTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATAAAATTTATATAT
Found at i:3639368 original size:14 final size:14
Alignment explanation
Indices: 3639349--3639383 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3639339 CCCATTCTGT
*
3639349 TGCGGTGTTCCACG
1 TGCGGTGTTCCACC
3639363 TGCGGTGTTCCACC
1 TGCGGTGTTCCACC
3639377 TGCGGTG
1 TGCGGTG
3639384 AAGTGCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.29, G:0.37, T:0.29
Consensus pattern (14 bp):
TGCGGTGTTCCACC
Found at i:3651204 original size:15 final size:15
Alignment explanation
Indices: 3651184--3651226 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
3651174 TCACCACTCT
3651184 TAATTATAAAAAAAA
1 TAATTATAAAAAAAA
*
3651199 TAATTATAATAAAAA
1 TAATTATAAAAAAAA
*
3651214 TAATAATAAAAAA
1 TAATTATAAAAAA
3651227 TCTTAGGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATTATAAAAAAAA
Found at i:3662184 original size:60 final size:60
Alignment explanation
Indices: 3662092--3662218 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
3662082 CTAAAACTAA
* * ** * *
3662092 AAAAAATCAATAAATTTAGCCATTAATGTTTACAAAATTTGTCATTTGAGTTTGAATTCT
1 AAAAATTCAATAAATTTAGCCATCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
* *
3662152 AAAAATTCAATAAATTTAGCGC-TCAACATTTACAAAATTTATCATTTTAATTTTAATTCT
1 AAAAATTCAATAAATTTAGC-CATCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
3662212 AAAAATT
1 AAAAATT
3662219 TTTAAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (60 bp):
AAAAATTCAATAAATTTAGCCATCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
Found at i:3663076 original size:60 final size:60
Alignment explanation
Indices: 3662944--3663060 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
3662934 TTAGAAACAA
* * * * * *
3662944 AACTAAATTAACAAATTTTATAAATGTTGAGGGCTAAATCTATTGATTTTTTTGAATTAG
1 AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATCTATTGATATTTTTAAATTAG
* *
3663004 AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATTTTTTGA-ATTTTTAAATT
1 AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATCTATTGATATTTTTAAATT
3663061 TAGGATCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 9 0.18
60 40 0.82
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (60 bp):
AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATCTATTGATATTTTTAAATTAG
Found at i:3666979 original size:12 final size:12
Alignment explanation
Indices: 3666962--3666990 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3666952 GAGTTGACTC
3666962 TGGTGATGGTGG
1 TGGTGATGGTGG
3666974 TGGTGATGGTGG
1 TGGTGATGGTGG
3666986 TGGTG
1 TGGTG
3666991 GTGAAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.59, T:0.34
Consensus pattern (12 bp):
TGGTGATGGTGG
Found at i:3666983 original size:18 final size:18
Alignment explanation
Indices: 3666906--3666993 Score: 58
Period size: 18 Copynumber: 5.1 Consensus size: 18
3666896 CTTAGATGGG
* * *
3666906 GGTGGTGGTGACGGTGGC
1 GGTGATGGTGATGGTGGT
3666924 GGTGATGGTGATGGTGG-
1 GGTGATGGTGATGGTGGT
* * *
3666941 GG-G-TGGCGATGGAGTT
1 GGTGATGGTGATGGTGGT
* *
3666957 GACT-CTGGTGATGGTGGT
1 G-GTGATGGTGATGGTGGT
*
3666975 GGTGATGGTGGTGGTGGT
1 GGTGATGGTGATGGTGGT
3666993 G
1 G
3666994 AAGAAGAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
15 9 0.17
16 2 0.04
17 3 0.06
18 39 0.74
ACGTcount: A:0.09, C:0.06, G:0.57, T:0.28
Consensus pattern (18 bp):
GGTGATGGTGATGGTGGT
Found at i:3670562 original size:21 final size:21
Alignment explanation
Indices: 3670521--3670562 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3670511 TGTTGAAGTC
* *
3670521 GTAATTAGTTATTAGTTGATT
1 GTAATTAGTTATCAGTCGATT
3670542 GTAATTA-TTATCAGTACGATT
1 GTAATTAGTTATCAGT-CGATT
3670563 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (21 bp):
GTAATTAGTTATCAGTCGATT
Found at i:3687383 original size:6 final size:7
Alignment explanation
Indices: 3687353--3687381 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3687343 TAGAAACACA
3687353 GAGAAAG
1 GAGAAAG
3687360 GAGAAAG
1 GAGAAAG
3687367 GAGAAAG
1 GAGAAAG
3687374 GA-AAAG
1 GAGAAAG
3687380 GA
1 GA
3687382 AAGCGTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
GAGAAAG
Found at i:3688980 original size:18 final size:18
Alignment explanation
Indices: 3688938--3688980 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3688928 TTAGGATTCA
3688938 ATGATTTTTGAAGTTTAGG
1 ATGA-TTTTGAAGTTTAGG
3688957 ATTGATTTTG-AGTTTAGGG
1 A-TGATTTTGAAGTTTA-GG
3688976 ATGAT
1 ATGAT
3688981 AATGGAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (18 bp):
ATGATTTTGAAGTTTAGG
Found at i:3701972 original size:17 final size:17
Alignment explanation
Indices: 3701939--3701972 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3701929 AAAATTTATT
* *
3701939 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
3701956 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
3701973 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:3701983 original size:41 final size:41
Alignment explanation
Indices: 3701910--3702016 Score: 142
Period size: 41 Copynumber: 2.6 Consensus size: 41
3701900 ATTTATTTAA
* **
3701910 AAAATTAAAACAAAAATAAAAAATTTATTTTAAAAATATTTT
1 AAAATTAAAA-AAATATAAAAAAAGTATTTTAAAAATATTTT
* *
3701952 AAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAGTATTTT
1 AAAATTAAAAAAATATAAAAAAAGTATTTTAAAAATATTTT
*
3701993 AAAATTTAAAAAAATAAAAAAAAA
1 AAAA-TTAAAAAAATATAAAAAAA
3702017 AATAAAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 30 0.53
42 27 0.47
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (41 bp):
AAAATTAAAAAAATATAAAAAAAGTATTTTAAAAATATTTT
Found at i:3702017 original size:12 final size:12
Alignment explanation
Indices: 3702000--3702024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3701990 TTTAAAATTT
3702000 AAAAAAATAAAA
1 AAAAAAATAAAA
3702012 AAAAAAATAAAA
1 AAAAAAATAAAA
3702024 A
1 A
3702025 TTATTGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:3703062 original size:22 final size:20
Alignment explanation
Indices: 3703033--3703072 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3703023 TTAAGAGGTT
*
3703033 TAATAGAAATTTTTAAAAAAG
1 TAATAG-AATTTTCAAAAAAG
3703054 TAATGAGAATTTTCAAAAA
1 TAAT-AGAATTTTCAAAAA
3703073 TTTTGAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
TAATAGAATTTTCAAAAAAG
Found at i:3709572 original size:34 final size:34
Alignment explanation
Indices: 3709497--3709574 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
3709487 ACAATAATAA
* *
3709497 ATATTTTATAAAATAAATTTATATTAATATTTAT
1 ATATTTTATAAAATAAATTTAAATAAATATTTAT
*
3709531 ATATTTTATAAATTAAATTTAAATAAA-ATATTAT
1 ATATTTTATAAAATAAATTTAAATAAATAT-TTAT
3709565 -TATTTT-TAAA
1 ATATTTTATAAA
3709575 CAATAACTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.10
33 8 0.20
34 28 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTTTATAAAATAAATTTAAATAAATATTTAT
Found at i:3713401 original size:31 final size:32
Alignment explanation
Indices: 3713366--3713429 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3713356 TCCGCCTATA
* *
3713366 TTAATTTTTAATTA-TTTTAT-TTTATTTTATT
1 TTAATATTTAATAATTTTTATATTT-TTTTATT
3713397 TTAATATTTAATAATTTTTATATTTTTTTATT
1 TTAATATTTAATAATTTTTATATTTTTTTATT
3713429 T
1 T
3713430 ATTGGAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 12 0.41
32 14 0.48
33 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (32 bp):
TTAATATTTAATAATTTTTATATTTTTTTATT
Found at i:3720142 original size:15 final size:16
Alignment explanation
Indices: 3720111--3720144 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3720101 TTCCAAAACA
3720111 TAAAATGTGAATCAAG
1 TAAAATGTGAATCAAG
*
3720127 TAAAATGT-ATTCAAG
1 TAAAATGTGAATCAAG
3720142 TAA
1 TAA
3720145 GCTCATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (16 bp):
TAAAATGTGAATCAAG
Found at i:3723124 original size:67 final size:67
Alignment explanation
Indices: 3723016--3723152 Score: 220
Period size: 67 Copynumber: 2.0 Consensus size: 67
3723006 TCCAAGATTT
* * * *
3723016 TATTTGTTATACTTGATGAACCTACATAATGGGACATCTATTTAGAATAACTCATGTCAAACTTC
1 TATTTGTTAAACCTCATGAACCTACATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
3723081 TC
66 TC
* *
3723083 TATTTGTTAAACCTCATGAACCTATATGATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
1 TATTTGTTAAACCTCATGAACCTACATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
3723148 TC
66 TC
3723150 TAT
1 TAT
3723153 AAAATTCGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (67 bp):
TATTTGTTAAACCTCATGAACCTACATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
TC
Found at i:3728094 original size:13 final size:14
Alignment explanation
Indices: 3728076--3728109 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3728066 TGGAATTCTT
*
3728076 AAAAATTGGGC-TG
1 AAAAATTGGGCAAG
3728089 AAAAATTGGGCAAG
1 AAAAATTGGGCAAG
3728103 AAAAATT
1 AAAAATT
3728110 TTAAAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.21
Consensus pattern (14 bp):
AAAAATTGGGCAAG
Found at i:3741689 original size:70 final size:70
Alignment explanation
Indices: 3741576--3741716 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
3741566 AGATATCACT
*
3741576 AGTCACTTTAAGTTTGTTGAGCATAATCAGAAGGTGGATGAACTCATTTCCTAAGGATTTAATAA
1 AGTCACTTTAAGTTTGTTGAGCATAATCAGAAGCTGGATGAACTCATTTCCTAAGGATTTAATAA
3741641 TTAAC
66 TTAAC
3741646 AGTCACTTTAAGTTTGTTGAGCATAATCAGAAGCTGGATGAACTCATTTCCTAAGGATTTAATAA
1 AGTCACTTTAAGTTTGTTGAGCATAATCAGAAGCTGGATGAACTCATTTCCTAAGGATTTAATAA
3741711 TTAAC
66 TTAAC
3741716 A
1 A
3741717 AAAATCCCAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (70 bp):
AGTCACTTTAAGTTTGTTGAGCATAATCAGAAGCTGGATGAACTCATTTCCTAAGGATTTAATAA
TTAAC
Found at i:3761918 original size:5 final size:5
Alignment explanation
Indices: 3761908--3761933 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3761898 AAATTTAAAA
3761908 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
3761934 AATAATGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:3765511 original size:24 final size:24
Alignment explanation
Indices: 3765475--3765525 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3765465 TAAAAAATTA
3765475 TTTATATTATTTTAATTTAAT-ATT
1 TTTATATTATTTT-ATTTAATGATT
* *
3765499 TTTATATTTTTTTATTTATTGATT
1 TTTATATTATTTTATTTAATGATT
3765523 TTT
1 TTT
3765526 TTATATAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTATATTATTTTATTTAATGATT
Found at i:3776155 original size:17 final size:17
Alignment explanation
Indices: 3776135--3776168 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3776125 ATTTTTAATT
3776135 TTTTAATATTT-TTTTAA
1 TTTTAAT-TTTATTTTAA
3776152 TTTTAATTTTATTTTAA
1 TTTTAATTTTATTTTAA
3776169 CCCTCCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTATTTTAA
Found at i:3777438 original size:17 final size:17
Alignment explanation
Indices: 3777416--3777469 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
3777406 ATTAAATATT
3777416 AAATTATTTAAAAAATA
1 AAATTATTTAAAAAATA
* *
3777433 AAATTATGTAACAAAT-
1 AAATTATTTAAAAAATA
3777449 AAATATATCTATAAAAAATA
1 AAAT-TAT-T-TAAAAAATA
3777469 A
1 A
3777470 TATAAACTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 4 0.14
17 17 0.59
19 7 0.24
20 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (17 bp):
AAATTATTTAAAAAATA
Found at i:3778204 original size:22 final size:23
Alignment explanation
Indices: 3778175--3778249 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
3778165 TTTAAATTGA
3778175 TTAT-ATAATTTATTAAAAT-AT
1 TTATAATAATTTATTAAAATAAT
**
3778196 TTATAATAAAATATTAGAAGATACAT
1 TTATAATAATTTATTA-AA-ATA-AT
* *
3778222 TT-TAATATTTTATTAAATTAAT
1 TTATAATAATTTATTAAAATAAT
3778244 TTATAA
1 TTATAA
3778250 ATTCACATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 4 0.10
22 13 0.31
23 7 0.17
24 4 0.10
25 10 0.24
26 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (23 bp):
TTATAATAATTTATTAAAATAAT
Found at i:3778423 original size:21 final size:21
Alignment explanation
Indices: 3778399--3778450 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3778389 CATTATTTTT
*
3778399 AATCTCACTGCTACAGTATCC
1 AATCTCACTGCTACAGTAACC
*
3778420 AATCTCA-TAGCTACAGTAACT
1 AATCTCACT-GCTACAGTAACC
3778441 AATCTCACTG
1 AATCTCACTG
3778451 TCACAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (21 bp):
AATCTCACTGCTACAGTAACC
Found at i:3778585 original size:21 final size:21
Alignment explanation
Indices: 3778559--3778611 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
3778549 AACAGCGGTG
3778559 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTGGGTACTGTA
3778580 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTGGGTACTGTA
3778601 GCGGTGAGATT
1 GCGGTGAGATT
3778612 AGAAACAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.09, G:0.43, T:0.28
Consensus pattern (21 bp):
GCGGTGAGATTGGGTACTGTA
Found at i:3778585 original size:27 final size:27
Alignment explanation
Indices: 3778552--3778606 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 27
3778542 GGTTAAAAAC
3778552 AGCGGTGGCGGTGAGATTGGGTACTGT
1 AGCGGTGGCGGTGAGATTGGGTACTGT
3778579 A------GCGGTGAGATTGGGTACTGT
1 AGCGGTGGCGGTGAGATTGGGTACTGT
3778600 AGCGGTG
1 AGCGGTG
3778607 AGATTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 12
0.65 0.00 0.35
Matches are distributed among these distances:
21 21 0.95
27 1 0.05
ACGTcount: A:0.16, C:0.11, G:0.47, T:0.25
Consensus pattern (27 bp):
AGCGGTGGCGGTGAGATTGGGTACTGT
Found at i:3778926 original size:22 final size:22
Alignment explanation
Indices: 3778875--3778926 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
3778865 TTTTATAGTT
*
3778875 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
3778898 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
3778920 ATAATAA
1 ATAATAA
3778927 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:3782279 original size:64 final size:64
Alignment explanation
Indices: 3782178--3782324 Score: 285
Period size: 64 Copynumber: 2.3 Consensus size: 64
3782168 ATGTTATATT
3782178 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
*
3782242 AGTTCGAATCCTTTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
3782306 AGTTCGAATCCTCTAATTT
1 AGTTCGAATCCTCTAATTT
3782325 AAATACTATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (64 bp):
AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
Found at i:3782977 original size:15 final size:15
Alignment explanation
Indices: 3782957--3782988 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3782947 TGTAAGTTTC
3782957 TTAGAAATAAAATGA
1 TTAGAAATAAAATGA
*
3782972 TTAGAAATAAGATGA
1 TTAGAAATAAAATGA
3782987 TT
1 TT
3782989 GGGGAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (15 bp):
TTAGAAATAAAATGA
Found at i:3783671 original size:379 final size:379
Alignment explanation
Indices: 3782972--3784094 Score: 2203
Period size: 379 Copynumber: 3.0 Consensus size: 379
3782962 AATAAAATGA
*
3782972 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTAGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
3783037 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
3783102 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
3783167 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
3783232 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
3783297 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
326 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
3783351 TTAGAAATAAGATGATTGGGGAAATTTAGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTAGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
3783416 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
3783481 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
3783546 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
3783611 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
3783676 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
326 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
3783730 TTAGAAATAAGATGATTGGGGAAATTTAGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTAGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
3783795 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
*
3783860 GACCAAAAGAGTGAGCTC-TTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
*
3783924 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGATTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
3783989 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
*
3784054 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGC
326 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGC
3784095 TATTGAATGC
Statistics
Matches: 740, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
378 215 0.29
379 525 0.71
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.42
Consensus pattern (379 bp):
TTAGAAATAAGATGATTGGGGAAATTTAGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
Found at i:3789032 original size:24 final size:26
Alignment explanation
Indices: 3789005--3789054 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
3788995 AAGGCTCCAT
3789005 TTTAGAAAATA-TTTTC-TATTTTTA
1 TTTAGAAAATAGTTTTCGTATTTTTA
* *
3789029 TTTAGAATATAGTTTTCGTTTTTTTA
1 TTTAGAAAATAGTTTTCGTATTTTTA
3789055 AAATTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 5 0.23
26 7 0.32
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (26 bp):
TTTAGAAAATAGTTTTCGTATTTTTA
Found at i:3789278 original size:17 final size:17
Alignment explanation
Indices: 3789256--3789289 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3789246 ATAAATAAAA
3789256 AATAAAAA-AAATATTTT
1 AATAAAAATAAA-ATTTT
3789273 AATAAAAATAAAATTTT
1 AATAAAAATAAAATTTT
3789290 CATTACAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAAAATAAAATTTT
Found at i:3789868 original size:14 final size:14
Alignment explanation
Indices: 3789834--3789862 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3789824 TATGCAATAT
3789834 CCAAATAATAACAA
1 CCAAATAATAACAA
3789848 CCAAATAATAACAA
1 CCAAATAATAACAA
3789862 C
1 C
3789863 ATAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (14 bp):
CCAAATAATAACAA
Found at i:3796945 original size:46 final size:46
Alignment explanation
Indices: 3796875--3796996 Score: 163
Period size: 46 Copynumber: 2.7 Consensus size: 46
3796865 ATAAGTGCCA
* * *
3796875 CACTGATATGTAGCCGAAGCTACCACTGATATGAAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGTTACCACTGATATGAAGCCATAGCTAC
* * *
3796921 CACTGAAATGTAGCCAAAGTTACCACTGATATGTAGCCATAGTTAC
1 CACTGAAATGTAGCCGAAGTTACCACTGATATGAAGCCATAGCTAC
* * *
3796967 CACTGAAATTTAGCCGAAGTTGCCATTGAT
1 CACTGAAATGTAGCCGAAGTTACCACTGAT
3796997 CAATAACACT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGTTACCACTGATATGAAGCCATAGCTAC
Found at i:3796987 original size:23 final size:23
Alignment explanation
Indices: 3796875--3796996 Score: 138
Period size: 23 Copynumber: 5.3 Consensus size: 23
3796865 ATAAGTGCCA
*
3796875 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGTTAC
* * *
3796898 CACTGATATGAAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGTTAC
* *
3796921 CACTGAAATGTAGCCAAAGTTAC
1 CACTGATATGTAGCCGAAGTTAC
3796944 CACTGATATGTAGCC-ATAGTTAC
1 CACTGATATGTAGCCGA-AGTTAC
* * *
3796967 CACTGAAATTTAGCCGAAGTTGC
1 CACTGATATGTAGCCGAAGTTAC
*
3796990 CATTGAT
1 CACTGAT
3796997 CAATAACACT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 1 0.01
23 82 0.98
24 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGTTAC
Found at i:3798901 original size:21 final size:21
Alignment explanation
Indices: 3798877--3798918 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3798867 TTTTTTGTTC
*
3798877 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
3798898 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
3798919 TACTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:3800923 original size:21 final size:21
Alignment explanation
Indices: 3800882--3800924 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3800872 AAACTTTCAT
*
3800882 TGTACAAATTAATTTTTTTTA
1 TGTACAAATTAATTTTATTTA
*
3800903 TGTATAAATTTAA-TTTATTTA
1 TGTACAAA-TTAATTTTATTTA
3800924 T
1 T
3800925 TGAATAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (21 bp):
TGTACAAATTAATTTTATTTA
Found at i:3801875 original size:6 final size:6
Alignment explanation
Indices: 3801858--3801918 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
3801848 TTCAACGCAG
* * * * *
3801858 AGAGAG AGAGAA AGAGAA ATATAA ATAG-A ATAGAA AGAGAA AGAGAA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA
3801905 AGAGAA AGAGAA AG
1 AGAGAA AGAGAA AG
3801919 GCAGAGGGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
5 5 0.10
6 44 0.90
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.07
Consensus pattern (6 bp):
AGAGAA
Found at i:3801910 original size:23 final size:23
Alignment explanation
Indices: 3801866--3801910 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3801856 AGAGAGAGAG
* * *
3801866 AGAAAGAGAAATATAAATAGAAT
1 AGAAAGAGAAAGAGAAAGAGAAT
3801889 AGAAAGAGAAAGAGAAAGAGAA
1 AGAAAGAGAAAGAGAAAGAGAA
3801911 AGAGAAAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (23 bp):
AGAAAGAGAAAGAGAAAGAGAAT
Found at i:3810766 original size:8 final size:9
Alignment explanation
Indices: 3810749--3810776 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3810739 AAAACCCAAC
3810749 AAAATAAAA
1 AAAATAAAA
3810758 AAAATAAAA
1 AAAATAAAA
3810767 AAAATAAAA
1 AAAATAAAA
3810776 A
1 A
3810777 CTGAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAATAAAA
Found at i:3815245 original size:50 final size:49
Alignment explanation
Indices: 3815187--3815380 Score: 167
Period size: 50 Copynumber: 3.9 Consensus size: 49
3815177 CATTGAGATT
* *
3815187 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCAA
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCACCAA
** * * * *
3815236 GATGAGAGGTCCCCCGTAAGACCATGTTTGGGACAT-AGCATGGGCACCGAT
1 -ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGA-CATTGGCACC-AA
** * * **
3815287 ATGAGAACTCCCATGTAAGACCATATATGGGATATGACATTGGCAGTATA
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCACCA-A
* ** * *
3815337 A-GAAACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCA
3815381 TGTTATTATC
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
49 37 0.32
50 75 0.66
51 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCACCAA
Found at i:3820706 original size:56 final size:51
Alignment explanation
Indices: 3820489--3820736 Score: 222
Period size: 50 Copynumber: 4.9 Consensus size: 51
3820479 TGATAATAAC
* * * *
3820489 ATGCCAAAGCCATGTCCCAGAAATGGTCTTACATGGGA-TGT-T--TCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
* * * * * * *
3820536 TACTGCCAATGCCATATCCCAGATATAGTCTTACATGAGAGT-TCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
* * * **
3820588 GTGCCCATGCCATATCCCAGACATGGTCTTACGGGGGAC-CTCTAATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
* *
3820638 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CTCTC-TAATCTC---G
3820694 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCT
3820737 TTACCCAAAT
Statistics
Matches: 164, Mismatches: 24, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
48 1 0.01
49 33 0.20
50 74 0.45
51 1 0.01
52 6 0.04
53 8 0.05
54 4 0.02
56 37 0.23
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (51 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
Found at i:3823866 original size:19 final size:20
Alignment explanation
Indices: 3823817--3823866 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
3823807 TAAAATATAA
* *
3823817 ATTTTGGAATTTTTATAAAT
1 ATTTTAGAATTTTGATAAAT
*
3823837 ATTTTAAAATTTTGA-AAATT
1 ATTTTAGAATTTTGATAAA-T
3823857 ATTTT-GAATT
1 ATTTTAGAATT
3823867 ATTTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTTTAGAATTTTGATAAAT
Found at i:3824007 original size:13 final size:13
Alignment explanation
Indices: 3823989--3824023 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
3823979 ATTCAACTCG
3823989 ACTTGAACTCGAA
1 ACTTGAACTCGAA
3824002 ACTTGAACTCGAA
1 ACTTGAACTCGAA
3824015 ACTTGAACT
1 ACTTGAACT
3824024 ACTTATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (13 bp):
ACTTGAACTCGAA
Found at i:3824804 original size:21 final size:20
Alignment explanation
Indices: 3824764--3824810 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
3824754 TTTACAGGAA
3824764 AATT-ATTTTAATTTTTTAT
1 AATTAATTTTAATTTTTTAT
*
3824783 AATTAATTTTAGTTTATTTAT
1 AATTAATTTTAATTT-TTTAT
*
3824804 AACTAAT
1 AATTAAT
3824811 ACGAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 9 0.38
21 11 0.46
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTAATTTTAATTTTTTAT
Found at i:3824888 original size:33 final size:33
Alignment explanation
Indices: 3824851--3824924 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 33
3824841 TTATGTTAGT
*
3824851 GTTTTATAAAATTAAATCAAATATATTTATAAA
1 GTTTTATAAAATTAAATCAAAAATATTTATAAA
** *
3824884 G-TTT-TAAAATTGTATTAAAAATATTTATAAA
1 GTTTTATAAAATTAAATCAAAAATATTTATAAA
* *
3824915 ATCTTATAAA
1 GTTTTATAAA
3824925 GTTGAGAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 23 0.70
32 5 0.15
33 5 0.15
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (33 bp):
GTTTTATAAAATTAAATCAAAAATATTTATAAA
Found at i:3826796 original size:13 final size:13
Alignment explanation
Indices: 3826778--3826824 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3826768 GGTTGGTTTG
3826778 ATTAATTGATTCT
1 ATTAATTGATTCT
3826791 ATTAATTGATT-T
1 ATTAATTGATTCT
* * *
3826803 GATCAACTGATTCC
1 -ATTAATTGATTCT
3826817 ATTAATTG
1 ATTAATTG
3826825 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 1 0.04
13 26 0.96
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (13 bp):
ATTAATTGATTCT
Found at i:3826803 original size:26 final size:26
Alignment explanation
Indices: 3826774--3826824 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3826764 TAGTGGTTGG
* * *
3826774 TTTGATTAATTGATTCTATTAATTGA
1 TTTGATCAACTGATTCCATTAATTGA
3826800 TTTGATCAACTGATTCCATTAATTG
1 TTTGATCAACTGATTCCATTAATTG
3826825 TTTATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (26 bp):
TTTGATCAACTGATTCCATTAATTGA
Found at i:3827474 original size:21 final size:20
Alignment explanation
Indices: 3827436--3827483 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
3827426 ATGCATGTTA
* *
3827436 AAAAATTGACTAATAGGGAGG
1 AAAAATTGACTAACAGGG-GC
* *
3827457 AAAAATTGATTTACAGGGGC
1 AAAAATTGACTAACAGGGGC
3827477 AAAAATT
1 AAAAATT
3827484 TTCGACAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (20 bp):
AAAAATTGACTAACAGGGGC
Found at i:3828540 original size:36 final size:36
Alignment explanation
Indices: 3828499--3828571 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
3828489 TTAATGCACT
* *
3828499 TTAATTCACCTCATTTTATATTTATAACGATACCAA
1 TTAATTCACCTCATTTTACATTCATAACGATACCAA
* *
3828535 TTAATTCACGTTATTTTACATTCATAACGATACCAA
1 TTAATTCACCTCATTTTACATTCATAACGATACCAA
3828571 T
1 T
3828572 ATCAATCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41
Consensus pattern (36 bp):
TTAATTCACCTCATTTTACATTCATAACGATACCAA
Found at i:3831265 original size:14 final size:14
Alignment explanation
Indices: 3831242--3831271 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3831232 TGGGTGTAGT
3831242 TTACCCTTGAAATA
1 TTACCCTTGAAATA
*
3831256 TTACCTTTGAAATA
1 TTACCCTTGAAATA
3831270 TT
1 TT
3831272 TCATAGTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (14 bp):
TTACCCTTGAAATA
Found at i:3836291 original size:22 final size:22
Alignment explanation
Indices: 3836233--3836293 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
3836223 ATGAGGGTAG
* *
3836233 GATATGATATGATATGAAATGT
1 GATATGATAAGATATGAAATAT
* * *
3836255 GCTACGACATA-ATATGAAATAT
1 GATATGATA-AGATATGAAATAT
3836277 GATATGATAAGATATGA
1 GATATGATAAGATATGA
3836294 TAAAAGATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (22 bp):
GATATGATAAGATATGAAATAT
Found at i:3843426 original size:15 final size:15
Alignment explanation
Indices: 3843395--3843444 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
3843385 TTTTAAGATT
3843395 TTTTTGTAAAGAATATA
1 TTTTT-TAAA-AATATA
3843412 TTTTTTAAAAATATA
1 TTTTTTAAAAATATA
*
3843427 TCTTTTTATAATATATA
1 T-TTTTTA-AAAATATA
3843444 T
1 T
3843445 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 7 0.23
16 10 0.33
17 13 0.43
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (15 bp):
TTTTTTAAAAATATA
Found at i:3846081 original size:170 final size:171
Alignment explanation
Indices: 3845786--3846101 Score: 483
Period size: 170 Copynumber: 1.9 Consensus size: 171
3845776 GACCATCAGG
* *
3845786 AACAGTGAGCGGCAGCAACAGAAAGTTCACATCAAAGATAAATGAAATCCATATACGGTAAGTAT
1 AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
*
3845851 AATCATAATTAAAAATGAAATCCAAATATGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
66 AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
*
3845916 AAGATTTAATC-TAAATCCAATTAATCTTAAATTGGAAATGC
131 AA-AGTTAATCTTAAATCCAATTAATCTTAAATTGGAAATGC
* * * *
3845957 AACAG-GAGTGGCAGCAACAGAAAGTTAATATCAAAGAAAAATGAAATCCATATATGGTGAGTAT
1 AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
* ** ** *
3846021 AATCATAATTAAAACTGAAATCCGTATACGCTTTTTTGAATGACCAAACCTCACTAAAAGGGAAA
66 AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
3846086 AAAGTTAATCTTAAAT
131 AAAGTTAATCTTAAAT
3846102 TAAGATGTAG
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
169 7 0.05
170 118 0.91
171 5 0.04
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (171 bp):
AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
AAAGTTAATCTTAAATCCAATTAATCTTAAATTGGAAATGC
Found at i:3854937 original size:15 final size:16
Alignment explanation
Indices: 3854917--3854947 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3854907 GTTGCTCTCC
3854917 TATTTCTA-TTATTTT
1 TATTTCTATTTATTTT
3854932 TATTTCTATTTATTTT
1 TATTTCTATTTATTTT
3854948 ATAACACGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTCTATTTATTTT
Found at i:3855954 original size:21 final size:21
Alignment explanation
Indices: 3855930--3855972 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3855920 TTTTCAATGA
3855930 TAATTATTAAGTAAGTTTTTC
1 TAATTATTAAGTAAGTTTTTC
**
3855951 TAATTATTAAGTTTGTTTTTC
1 TAATTATTAAGTAAGTTTTTC
3855972 T
1 T
3855973 CCAGAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (21 bp):
TAATTATTAAGTAAGTTTTTC
Found at i:3856806 original size:225 final size:224
Alignment explanation
Indices: 3856415--3856858 Score: 816
Period size: 225 Copynumber: 2.0 Consensus size: 224
3856405 TCATTGAAGC
*
3856415 TTGTTTTAGCTAACCCATGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
1 TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
3856480 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
66 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
*****
3856545 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAATTTTTTTTTG
131 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAA-AAAAATTTG
3856610 TAAAATTTTGGTATAAATAGAGAGTTGTCA
195 TAAAATTTTGGTATAAATAGAGAGTTGTCA
3856640 TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
1 TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
*
3856705 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGACTAGAT
66 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
3856770 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAAAAAAATTTGT
131 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAAAAAAATTTGT
3856835 AAAATTTTGGTATAAATAGAGAGT
196 AAAATTTTGGTATAAATAGAGAGT
3856859 AGAGGGTTTG
Statistics
Matches: 212, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
224 29 0.14
225 183 0.86
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.39
Consensus pattern (224 bp):
TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAAAAAAATTTGT
AAAATTTTGGTATAAATAGAGAGTTGTCA
Found at i:3860644 original size:24 final size:24
Alignment explanation
Indices: 3860612--3860664 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3860602 ACTAAGGTTT
3860612 AACA-TATACTTCAAGAGTATGTA
1 AACATTATACTTCAAGAGTATGTA
3860635 AACATTATACTTCAAGAGTATGTA
1 AACATTATACTTCAAGAGTATGTA
3860659 AACATT
1 AACATT
3860665 CTCTTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (24 bp):
AACATTATACTTCAAGAGTATGTA
Found at i:3868837 original size:15 final size:15
Alignment explanation
Indices: 3868817--3868852 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3868807 TCAAAATCAA
3868817 TATTTTTACAATATT
1 TATTTTTACAATATT
*
3868832 TATTTTTATAATATT
1 TATTTTTACAATATT
*
3868847 AATTTT
1 TATTTT
3868853 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTTACAATATT
Found at i:3871617 original size:21 final size:22
Alignment explanation
Indices: 3871565--3871623 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
3871555 CTCATACTAT
*
3871565 GAGTTATTTTCTTTAGATAATTAC
1 GAGTTATTTT-TTTA-ATAATTAA
*
3871589 G-TTTATTTTTTTAA-AATTAA
1 GAGTTATTTTTTTAATAATTAA
3871609 GAGTTATTTTTTTAA
1 GAGTTATTTTTTTAA
3871624 CTTCATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.19
21 13 0.42
22 4 0.13
23 7 0.23
24 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (22 bp):
GAGTTATTTTTTTAATAATTAA
Found at i:3872819 original size:21 final size:20
Alignment explanation
Indices: 3872795--3872839 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3872785 AAGAATATTA
*
3872795 TATTAATAATAATAATAATTT
1 TATTAATAAT-ATAATAATAT
*
3872816 TATTTAATAATTTAATAATAT
1 TA-TTAATAATATAATAATAT
3872837 TAT
1 TAT
3872840 CTTATACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.05
21 12 0.57
22 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAATAATATAATAATAT
Found at i:3873039 original size:12 final size:13
Alignment explanation
Indices: 3873022--3873054 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
3873012 ATCTCGAACA
3873022 TTAAAAAAATTT-
1 TTAAAAAAATTTC
3873034 TT-AAAAAATTTC
1 TTAAAAAAATTTC
3873046 TTAAAAAAA
1 TTAAAAAAA
3873055 ATCAATCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 4 0.21
13 6 0.32
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAAAATTTC
Found at i:3876275 original size:19 final size:17
Alignment explanation
Indices: 3876251--3876285 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3876241 TATTATATGA
3876251 TGAATTGACGAATTGATGT
1 TGAATTGA-GAA-TGATGT
3876270 TGAATTGAGAATGATG
1 TGAATTGAGAATGATG
3876286 GAATGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (17 bp):
TGAATTGAGAATGATGT
Found at i:3886849 original size:3 final size:3
Alignment explanation
Indices: 3886841--3886879 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3886831 CCGTCATGGA
*
3886841 GAT GAT GAT GTT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3886880 TGGTTCAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (3 bp):
GAT
Found at i:3896435 original size:24 final size:24
Alignment explanation
Indices: 3896399--3896485 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
3896389 AAAAATAATC
* *
3896399 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGCTTATTTG
*
3896423 TTTCAATTTAACTCTGCTTATTTG
1 TTTCAATTAAACTCTGCTTATTTG
*
3896447 TTTCAATTAAACTCTGCTTATTTA
1 TTTCAATTAAACTCTGCTTATTTG
*
3896471 TTTCAATCAAACTCT
1 TTTCAATTAAACTCT
3896486 AATTAGTCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (24 bp):
TTTCAATTAAACTCTGCTTATTTG
Found at i:3897340 original size:14 final size:14
Alignment explanation
Indices: 3897321--3897347 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3897311 TGTGCTGTTT
3897321 ACACCATTATCAAA
1 ACACCATTATCAAA
3897335 ACACCATTATCAA
1 ACACCATTATCAA
3897348 GCCACTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (14 bp):
ACACCATTATCAAA
Found at i:3897677 original size:21 final size:21
Alignment explanation
Indices: 3897653--3897693 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3897643 CATATAAAAT
*
3897653 TGACATATTTCTTATTTATCG
1 TGACATATTTATTATTTATCG
*
3897674 TGACGTATTTATTATTTATC
1 TGACATATTTATTATTTATC
3897694 ATGTTCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (21 bp):
TGACATATTTATTATTTATCG
Found at i:3906282 original size:72 final size:72
Alignment explanation
Indices: 3906124--3906266 Score: 241
Period size: 72 Copynumber: 2.0 Consensus size: 72
3906114 TCTCGGATTT
* * * *
3906124 AAAAAATGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCATTTAAAA
1 AAAAAAAGGATCATGCCCAGTAAATTAGGACACGATCTCTTCTTAATTCCCAAGATCATTTAAAA
3906189 CTTGAGA
66 CTTGAGA
*
3906196 AAAAAAAGGATCATGCCCAGTAAATTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAA
1 AAAAAAAGGATCATGCCCAGTAAATTAGGACACGATCTCTTCTTAATTCCCAAGATCATTTAAAA
3906261 CTTGAG
66 CTTGAG
3906267 TTTGAAAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (72 bp):
AAAAAAAGGATCATGCCCAGTAAATTAGGACACGATCTCTTCTTAATTCCCAAGATCATTTAAAA
CTTGAGA
Found at i:3906821 original size:3 final size:3
Alignment explanation
Indices: 3906813--3906849 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3906803 TAAGTGAGTA
3906813 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3906850 CAAGGTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3907290 original size:12 final size:12
Alignment explanation
Indices: 3907273--3907298 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3907263 GGAGCCGGTC
3907273 GGGTCGCACGCG
1 GGGTCGCACGCG
3907285 GGGTCGCACGCG
1 GGGTCGCACGCG
3907297 GG
1 GG
3907299 TCGGCGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.54, T:0.08
Consensus pattern (12 bp):
GGGTCGCACGCG
Found at i:3907299 original size:11 final size:11
Alignment explanation
Indices: 3907272--3907301 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
3907262 TGGAGCCGGT
3907272 CGGGTCGCACG
1 CGGGTCGCACG
3907283 CGGGGTCGCACG
1 C-GGGTCGCACG
3907295 CGGGTCG
1 CGGGTCG
3907302 GCGTTAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.07, C:0.33, G:0.50, T:0.10
Consensus pattern (11 bp):
CGGGTCGCACG
Found at i:3908868 original size:10 final size:10
Alignment explanation
Indices: 3908828--3908890 Score: 51
Period size: 9 Copynumber: 6.6 Consensus size: 10
3908818 AATTTTTCAT
*
3908828 ATTTTCTAAA
1 ATTTTATAAA
*
3908838 ATTTTA-AAT
1 ATTTTATAAA
**
3908847 ATTTT-TTGA
1 ATTTTATAAA
3908856 ATTTTATAAA
1 ATTTTATAAA
3908866 ATTTTA-AAA
1 ATTTTATAAA
* *
3908875 ATATTATATA
1 ATTTTATAAA
3908885 ATTTTA
1 ATTTTA
3908891 GGAATTTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
9 20 0.50
10 20 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:3909078 original size:17 final size:16
Alignment explanation
Indices: 3909041--3909101 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
3909031 AAACTTATCC
3909041 AATTAATTTAAGTTATTTA
1 AATTAATTTAA---ATTTA
*
3909060 AATTAGTTTAAATTTTA
1 AATTAATTTAAA-TTTA
* *
3909077 AAATAATTTAAACTTA
1 AATTAATTTAAATTTA
3909093 AATTAATTT
1 AATTAATTT
3909102 TACCTCAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 12 0.33
17 14 0.39
19 10 0.28
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (16 bp):
AATTAATTTAAATTTA
Found at i:3911703 original size:21 final size:21
Alignment explanation
Indices: 3911685--3912037 Score: 283
Period size: 21 Copynumber: 16.4 Consensus size: 21
3911675 ACCACCACTA
*
3911685 CCACCGGTCCACTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
*
3911706 CCACCAGTGCACTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3911727 CCACCCGTCCACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
* ** * *
3911748 CCACCCGTCTTCTCACCACCA
1 CCACCAGTCCACTCCCCACCC
* *
3911769 CCACCAGTGCACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
* * *
3911790 CCACCCGTCTACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
* *
3911811 CCACCACCCGTCTACTCACCACCCCC
1 CCACCA---GTCCACTC-CC-CACCC
* *
3911837 ACCACCAGTGCACTCACCACCC
1 -CCACCAGTCCACTCCCCACCC
* * * *
3911859 CCACCCGTCTACTCACCACCA
1 CCACCAGTCCACTCCCCACCC
* *
3911880 CCACCAGTGCACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
* * *
3911901 CCACCCGTCTACTCACCACCC
1 CCACCAGTCCACTCCCCACCC
* * *
3911922 CCACCCGTCTACTCCCCACCA
1 CCACCAGTCCACTCCCCACCC
* * *
3911943 CCACCCGTCTACTCACCACCACCA
1 CCACCAGTCCACT--CC-CCACCC
*
3911967 CCACCAGTCCAGTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
* * *
3911988 CCACCCGTCCACTCACCACCA
1 CCACCAGTCCACTCCCCACCC
*
3912009 CCACCAGTCCAGTCCCCACCC
1 CCACCAGTCCACTCCCCACCC
3912030 CCACCAGT
1 CCACCAGT
3912038 ACAATCTCCA
Statistics
Matches: 275, Mismatches: 48, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
21 225 0.82
22 6 0.02
23 3 0.01
24 30 0.11
25 1 0.00
26 4 0.01
27 6 0.02
ACGTcount: A:0.21, C:0.61, G:0.07, T:0.12
Consensus pattern (21 bp):
CCACCAGTCCACTCCCCACCC
Found at i:3911767 original size:63 final size:63
Alignment explanation
Indices: 3911677--3912037 Score: 429
Period size: 63 Copynumber: 5.6 Consensus size: 63
3911667 CCTAAATCAC
* * * * * *
3911677 CACCACTACCACCGGTCCACTCCCCACCCCCACCAGTGCACTCCCCACCCCCACCCGTCCACT
1 CACCACCACCACCCGTCTACTCACCACCCCCACCAGTGCACTCACCACCCCCACCCGTCTACT
* * *
3911740 CACCACCCCCACCCGTCTTCTCACCACCACCACCAGTGCACTCACCACCCCCACCCGTCTACT
1 CACCACCACCACCCGTCTACTCACCACCCCCACCAGTGCACTCACCACCCCCACCCGTCTACT
3911803 CACCACCCCCACCACCCGTCTACTCACCACCCCCACCACCAGTGCACTCACCACCCCCACCCGTC
1 CACCA---CCACCACCCGTCTACTCACCA--CCC-CCACCAGTGCACTCACCACCCCCACCCGTC
3911868 TACT
60 TACT
* *
3911872 CACCACCACCACCAGTGC-ACTCACCACCCCCACCCGT-CTACTCACCACCCCCACCCGTCTACT
1 CACCACCACCACCCGT-CTACTCACCACCCCCACCAGTGC-ACTCACCACCCCCACCCGTCTACT
* * * * *
3911935 CCCCACCACCACCCGTCTACTCACCACCACCACCACCAGTCCAGTCCCCACCCCCACCCGTCCAC
1 CACCACCACCACCCGTCTACTCACCA-C-CC-CCACCAGTGCACTCACCACCCCCACCCGTCTAC
3912000 T
63 T
* * * *
3912001 CACCACCACCACCAGTCCAGTCCCCACCCCCACCAGT
1 CACCACCACCACCCGTCTACTCACCACCCCCACCAGT
3912038 ACAATCTCCA
Statistics
Matches: 260, Mismatches: 25, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
62 2 0.01
63 120 0.46
64 6 0.02
65 3 0.01
66 86 0.33
67 2 0.01
68 2 0.01
69 39 0.15
ACGTcount: A:0.21, C:0.60, G:0.07, T:0.12
Consensus pattern (63 bp):
CACCACCACCACCCGTCTACTCACCACCCCCACCAGTGCACTCACCACCCCCACCCGTCTACT
Found at i:3911858 original size:111 final size:106
Alignment explanation
Indices: 3911685--3912034 Score: 409
Period size: 108 Copynumber: 3.2 Consensus size: 106
3911675 ACCACCACTA
* * * *
3911685 CCACCGGTCCACTCCCCACCCCCACCAGTGC-ACTCCCCACCCCCA-CCCGTCCACTCACCACCC
1 CCACCCGTCTACTCACCACCCCCACCCGT-CTACTCCCCACCCCCACCCCGTCCACTCACCACCC
*
3911748 CCACCCGTCTTCTCACCACCACCACCAGTGCACTCACCACCC
65 CCACCCGTCTACTCACCACCACCACCAGTGCACTCACCACCC
* *
3911790 CCACCCGTCTACTCACCACCCCCACCACCCGTCTACTCACCACCCCCACCACCAGTGCACTCACC
1 CCACCCGTCTACTCACCA--CCC-CCACCCGTCTACTCCCCACCCCCACC-CC-GTCCACTCACC
3911855 ACCCCCACCCGTCTACTCACCACCACCACCAGTGCACTCACCACCC
61 ACCCCCACCCGTCTACTCACCACCACCACCAGTGCACTCACCACCC
* *
3911901 CCACCCGTCTACTCACCACCCCCACCCGTCTACTCCCCACCACCA-CCCGTCTACTCACCACCAC
1 CCACCCGTCTACTCACCACCCCCACCCGTCTACTCCCCACCCCCACCCCGTCCACTCACCA-C-C
* * * * * * * *
3911965 CACCACCAGTCCAGTCCCCACCCCCACCCGTCCACTCACCACCA
64 C-CCACCCGTCTACTCACCACCACCACCAGTGCACTCACCACCC
* * * *
3912009 CCACCAGTCCAGTCCCCACCCCCACC
1 CCACCCGTCTACTCACCACCCCCACC
3912035 AGTACAATCT
Statistics
Matches: 212, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
105 25 0.12
106 3 0.01
107 7 0.03
108 98 0.46
109 4 0.02
110 2 0.01
111 73 0.34
ACGTcount: A:0.21, C:0.61, G:0.07, T:0.11
Consensus pattern (106 bp):
CCACCCGTCTACTCACCACCCCCACCCGTCTACTCCCCACCCCCACCCCGTCCACTCACCACCCC
CACCCGTCTACTCACCACCACCACCAGTGCACTCACCACCC
Found at i:3912049 original size:42 final size:42
Alignment explanation
Indices: 3911685--3912034 Score: 351
Period size: 42 Copynumber: 8.1 Consensus size: 42
3911675 ACCACCACTA
* * * * *
3911685 CCACCGGTCCACTCCCCACCCCCACCAGTGCACTCCCCACCC
1 CCACCCGTCTACTCACCACCACCACCAGTCCACTCCCCACCC
* * * ** * *
3911727 CCACCCGTCCACTCACCACCCCCACCCGTCTTCTCACCACCA
1 CCACCCGTCTACTCACCACCACCACCAGTCCACTCCCCACCC
* * * * *
3911769 CCACCAGTGC-ACTCACCACCCCCACCCGTCTACTCACCACCCCC
1 CCACCCGT-CTACTCACCACCACCACCAGTCCACTC-CC-CACCC
* *
3911813 ACCACCCGTCTACTCACCACCCCCACCACCAGTGCACTCACCACCC
1 -CCACCCGTCTACTCACCA---CCACCACCAGTCCACTCCCCACCC
* *
3911859 CCACCCGTCTACTCACCACCACCACCAGTGCACTCACCACCC
1 CCACCCGTCTACTCACCACCACCACCAGTCCACTCCCCACCC
* * * *
3911901 CCACCCGTCTACTCACCACCCCCACCCGTCTACTCCCCACCA
1 CCACCCGTCTACTCACCACCACCACCAGTCCACTCCCCACCC
*
3911943 CCACCCGTCTACTCACCACCACCACCACCAGTCCAGTCCCCACCC
1 CCACCCGTCTACT---CACCACCACCACCAGTCCACTCCCCACCC
* *
3911988 CCACCCGTCCACTCACCACCACCACCAGTCCAGTCCCCACCC
1 CCACCCGTCTACTCACCACCACCACCAGTCCACTCCCCACCC
3912030 CCACC
1 CCACC
3912035 AGTACAATCT
Statistics
Matches: 265, Mismatches: 32, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
42 172 0.65
43 2 0.01
44 4 0.02
45 69 0.26
46 4 0.02
47 1 0.00
48 13 0.05
ACGTcount: A:0.21, C:0.61, G:0.07, T:0.11
Consensus pattern (42 bp):
CCACCCGTCTACTCACCACCACCACCAGTCCACTCCCCACCC
Found at i:3913111 original size:20 final size:20
Alignment explanation
Indices: 3913075--3913112 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3913065 TCTCCAAACT
*
3913075 CTAAAACTTTTTATTTTCCC
1 CTAAAACTTGTTATTTTCCC
3913095 CTAAAAC-TGTTACTTTTC
1 CTAAAACTTGTTA-TTTTC
3913113 ATCATATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (20 bp):
CTAAAACTTGTTATTTTCCC
Found at i:3913906 original size:14 final size:13
Alignment explanation
Indices: 3913874--3913907 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3913864 TAATACTTAA
3913874 TTTTTTATTAAAT
1 TTTTTTATTAAAT
*
3913887 TTTTTTGATTAATT
1 TTTTTT-ATTAAAT
3913901 TTTTTTA
1 TTTTTTA
3913908 GAAAAAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTATTAAAT
Found at i:3915663 original size:21 final size:20
Alignment explanation
Indices: 3915627--3915721 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 20
3915617 AGCACCGGTT
* *
3915627 CCACCTCCACCAGTCCCTTCC
1 CCACCACCACCCGTCCC-TCC
* *
3915648 CTACCACCACCCGTCCAATCC
1 CCACCACCACCCGTCC-CTCC
*
3915669 CCACCACCACCTGTGCCCTCC
1 CCACCACCACCCGT-CCCTCC
* *
3915690 CCACCCCCACCCGTCCACTCA
1 CCACCACCACCCGTCC-CTCC
3915711 CCACCACCACC
1 CCACCACCACC
3915722 ACCACCACCA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.19, C:0.63, G:0.05, T:0.13
Consensus pattern (20 bp):
CCACCACCACCCGTCCCTCC
Found at i:3915673 original size:42 final size:42
Alignment explanation
Indices: 3915627--3916096 Score: 164
Period size: 42 Copynumber: 11.3 Consensus size: 42
3915617 AGCACCGGTT
* * *
3915627 CCACCTCCACCAGT-CCCTTCCCTACCACCACCCGTCCAATCC
1 CCACCACCACCAGTGCCC-TCCCCACCACCACCCGTCCAATCA
* * *
3915669 CCACCACCACCTGTGCCCTCCCCACCCCCACCCGTCCACTCA
1 CCACCACCACCAGTGCCCTCCCCACCACCACCCGTCCAATCA
* *
3915711 CCACCACCACCA---------CCACCACCACCGGTTCC-TTCA
1 CCACCACCACCAGTGCCCTCCCCACCACCACCCG-TCCAATCA
* * **** * * *
3915744 CCCCCACCAGCAGTAAAATCCCCACCTCCACCGGTGCC-CTCA
1 CCACCACCACCAGTGCCCTCCCCACCACCACCCGT-CCAATCA
* * * ** *
3915786 CCACCACCACCATCGGTTCCTTCACCC-CCACCACCAGTAAAATCC
1 CCACCACCACCA---GTGCCCTC-CCCACCACCACCCGTCCAATCA
* * * * *
3915831 CCACCTCCACCGGTGACCTCACCACCACCACCATCGGTTCC-TTCA
1 CCACCACCACCAGTGCCCTCCCCACCACCACC--C-G-TCCAATCA
* **** * * *
3915876 CCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCC-CTCA
1 CCACCACCACCAGTGCCCTCCCCACCACCACCCGT-CCAATCA
* * * * ** *
3915918 CCACCACCACCTGTGCCATCTCCACCCCCACCCGTCCGCTCC
1 CCACCACCACCAGTGCCCTCCCCACCACCACCCGTCCAATCA
* * * * ** *
3915960 CCACCCCCACCTGTGCCCTCTCCACCCCCACCCGTCCTCTCC
1 CCACCACCACCAGTGCCCTCCCCACCACCACCCGTCCAATCA
* * * **
3916002 CCACCCCCACCAGTGCACTCACCACCACCACCCGTCCTTTCA
1 CCACCACCACCAGTGCCCTCCCCACCACCACCCGTCCAATCA
* * * **
3916044 CCACCACCACCCGT-CCTCTCCCCACC-CCACCAGTGCGCTCA
1 CCACCACCACCAGTGCC-CTCCCCACCACCACCCGTCCAATCA
3916085 CCACCACCACCA
1 CCACCACCACCA
3916097 CCACCCGTCT
Statistics
Matches: 329, Mismatches: 74, Indels: 51
0.72 0.16 0.11
Matches are distributed among these distances:
33 24 0.07
34 3 0.01
41 29 0.09
42 214 0.65
43 3 0.01
45 52 0.16
46 4 0.01
ACGTcount: A:0.20, C:0.58, G:0.08, T:0.14
Consensus pattern (42 bp):
CCACCACCACCAGTGCCCTCCCCACCACCACCCGTCCAATCA
Found at i:3915717 original size:3 final size:3
Alignment explanation
Indices: 3915704--3915733 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3915694 CCCCACCCGT
3915704 CCA CTCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA C-CA CCA CCA CCA CCA CCA CCA CCA CC
3915734 GGTTCCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.67, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:3915745 original size:21 final size:21
Alignment explanation
Indices: 3915721--3916095 Score: 91
Period size: 21 Copynumber: 17.6 Consensus size: 21
3915711 CCACCACCAC
3915721 CACCACCACCACCGGTTCCTT
1 CACCACCACCACCGGTTCCTT
* * * ****
3915742 CACCCCCACCAGCAGTAAAAT
1 CACCACCACCACCGGTTCCTT
* * * *
3915763 CCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCGGTTCCTT
3915784 CACCACCACCACCATCGGTTCCTT
1 CACCACCACCA-C--CGGTTCCTT
* * ****
3915808 CACCCCCACCACCAGTAAAAT
1 CACCACCACCACCGGTTCCTT
* * *
3915829 CCCCACCTCCACCGGTGACC-T
1 CACCACCACCACCGGT-TCCTT
3915850 CACCACCACCACCATCGGTTCCTT
1 CACCACCACCA-C--CGGTTCCTT
* * ****
3915874 CACCCCCACCACCAGTAAAAT
1 CACCACCACCACCGGTTCCTT
* * * *
3915895 CCCCACCTCCACCGGTGCCCT
1 CACCACCACCACCGGTTCCTT
* * *
3915916 CACCACCACCACCTGTGCCAT
1 CACCACCACCACCGGTTCCTT
* * * *
3915937 CTCCACCCCCACCCG-TCCGCT
1 CACCACCACCACCGGTTCC-TT
* * * * *
3915958 CCCCACCCCCACCTGTGCCCT
1 CACCACCACCACCGGTTCCTT
* * *
3915979 CTCCACCCCCACCCG-TCCTCT
1 CACCACCACCACCGGTTCCT-T
* * * *
3916000 CCCCACCCCCACCAGTGCAC-T
1 CACCACCACCACCGGTTC-CTT
*
3916021 CACCACCACCACCCG-TCCTTT
1 CACCACCACCACCGGTTCC-TT
*
3916042 CACCACCACCACCCG-TCCTCT
1 CACCACCACCACCGGTTCCT-T
* * *
3916063 CCCCACC-CCACCAGTGCGC-T
1 CACCACCACCACCGGTTC-CTT
3916083 CACCACCACCACC
1 CACCACCACCACC
3916096 ACCACCCGTC
Statistics
Matches: 259, Mismatches: 76, Indels: 38
0.69 0.20 0.10
Matches are distributed among these distances:
19 1 0.00
20 19 0.07
21 195 0.75
22 7 0.03
23 5 0.02
24 32 0.12
ACGTcount: A:0.20, C:0.57, G:0.09, T:0.14
Consensus pattern (21 bp):
CACCACCACCACCGGTTCCTT
Found at i:3915745 original size:24 final size:23
Alignment explanation
Indices: 3915718--3915887 Score: 70
Period size: 24 Copynumber: 7.6 Consensus size: 23
3915708 TCACCACCAC
*
3915718 CACCACCACCACCACCGGTTCCTT
1 CACC-CCACCACCACCGGTACCTT
* * ***
3915742 CA-CCC-CCACCAGCAGTAAAAT
1 CACCCCACCACCACCGGTACCTT
* * *
3915763 C--CCCACCTCCACCGGTGCCCT
1 CACCCCACCACCACCGGTACCTT
* *
3915784 CACCACCACCACCATCGGTTCCTT
1 CACC-CCACCACCACCGGTACCTT
* ***
3915808 CA-CCC-CCACCACCAGTAAAAT
1 CACCCCACCACCACCGGTACCTT
*
3915829 --CCCCACCTCCACCGGTGACC-T
1 CACCCCACCACCACCGGT-ACCTT
* *
3915850 CACCACCACCACCATCGGTTCCTT
1 CACC-CCACCACCACCGGTACCTT
3915874 CACCCCCACCACCA
1 CA-CCCCACCACCA
3915888 GTAAAATCCC
Statistics
Matches: 104, Mismatches: 30, Indels: 24
0.66 0.19 0.15
Matches are distributed among these distances:
20 6 0.06
21 41 0.39
22 5 0.05
23 7 0.07
24 43 0.41
25 2 0.02
ACGTcount: A:0.24, C:0.54, G:0.09, T:0.14
Consensus pattern (23 bp):
CACCCCACCACCACCGGTACCTT
Found at i:3915805 original size:66 final size:66
Alignment explanation
Indices: 3915718--3915928 Score: 395
Period size: 66 Copynumber: 3.2 Consensus size: 66
3915708 TCACCACCAC
* *
3915718 CACCACCACCACCACCGGTTCCTTCACCCCCACCAGCAGTAAAATCCCCACCTCCACCGGTGCCC
1 CACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCC
3915783 T
66 T
*
3915784 CACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGACC
1 CACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCC
3915849 T
66 T
3915850 CACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCC
1 CACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCC
3915915 T
66 T
3915916 CACCACCACCACC
1 CACCACCACCACC
3915929 TGTGCCATCT
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 141 1.00
ACGTcount: A:0.24, C:0.54, G:0.09, T:0.14
Consensus pattern (66 bp):
CACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCC
T
Found at i:3916096 original size:21 final size:21
Alignment explanation
Indices: 3915897--3916095 Score: 150
Period size: 21 Copynumber: 9.5 Consensus size: 21
3915887 AGTAAAATCC
* * *
3915897 CCACCTCCACCGGTGCCCTCA
1 CCACCACCACCCGTGCTCTCA
* *
3915918 CCACCACCACCTGTGC-CATCT
1 CCACCACCACCCGTGCTC-TCA
* * * *
3915939 CCACCCCCACCCGTCCGCTCC
1 CCACCACCACCCGTGCTCTCA
* * * *
3915960 CCACCCCCACCTGTGCCCTCT
1 CCACCACCACCCGTGCTCTCA
* * *
3915981 CCACCCCCACCCGTCCTCTCC
1 CCACCACCACCCGTGCTCTCA
* * *
3916002 CCACCCCCACCAGTGCACTCA
1 CCACCACCACCCGTGCTCTCA
* *
3916023 CCACCACCACCCGTCCTTTCA
1 CCACCACCACCCGTGCTCTCA
* *
3916044 CCACCACCACCCGTCCTCTCC
1 CCACCACCACCCGTGCTCTCA
* *
3916065 CCACC-CCACCAGTGCGCTCA
1 CCACCACCACCCGTGCTCTCA
3916085 CCACCACCACC
1 CCACCACCACC
3916096 ACCACCCGTC
Statistics
Matches: 145, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.12
21 127 0.88
22 1 0.01
ACGTcount: A:0.16, C:0.62, G:0.09, T:0.14
Consensus pattern (21 bp):
CCACCACCACCCGTGCTCTCA
Found at i:3916142 original size:21 final size:21
Alignment explanation
Indices: 3915914--3916143 Score: 83
Period size: 21 Copynumber: 10.7 Consensus size: 21
3915904 CACCGGTGCC
* *
3915914 CTCACCACCACCACCTGTGCCA
1 CTCACCACCACCACCCGT-CAA
* * **
3915936 -TCTCCACCCCCACCCGTCCG
1 CTCACCACCACCACCCGTCAA
* * * *
3915956 CTCCCCACCCCCACCTGTGC-C
1 CTCACCACCACCACCCGT-CAA
* * **
3915977 CTCTCCACCCCCACCCGTCCT
1 CTCACCACCACCACCCGTCAA
* * *
3915998 CTCCCCACCCCCACCAGTGC-A
1 CTCACCACCACCACCCGT-CAA
**
3916019 CTCACCACCACCACCCGTCCT
1 CTCACCACCACCACCCGTCAA
* **
3916040 TTCACCACCACCACCCGTCCT
1 CTCACCACCACCACCCGTCAA
*
3916061 CTCCCCACC-CCACCAGTGCGCTCACCA
1 CTCACCACCACCACC----CG-TCA--A
*
3916088 C-CACCACCACCACCCGTCTA
1 CTCACCACCACCACCCGTCAA
* *
3916108 CTCACCGCCTCCACCCGTCAA
1 CTCACCACCACCACCCGTCAA
* *
3916129 GTCTCCACCACCACC
1 CTCACCACCACCACC
3916144 AGTAAAATCC
Statistics
Matches: 163, Mismatches: 31, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
20 11 0.07
21 130 0.80
22 4 0.02
23 2 0.01
24 2 0.01
25 2 0.01
26 6 0.04
27 6 0.04
ACGTcount: A:0.17, C:0.61, G:0.08, T:0.14
Consensus pattern (21 bp):
CTCACCACCACCACCCGTCAA
Found at i:3917477 original size:190 final size:191
Alignment explanation
Indices: 3917139--3917487 Score: 506
Period size: 190 Copynumber: 1.8 Consensus size: 191
3917129 AAGTAATAAG
**
3917139 TAATGTACTACTATTATATATGTCTATTATTATAATATAGATTATAATAAAAGATATAGATTTAC
1 TAATGTACTACTATTATATATAACTATTATTATAATATAGATTATAATAAAAGATATAGATTTAC
* * * * *
3917204 ATGATATTATAATGTTTAATTATATATAAACTATTAATATATTATATAATATGATATAGCATTAC
66 ATAATATTATAATATTTAATTATATATAAACTATTAATATATTAAATAATATGACATAACATTAC
* *
3917269 ATGATACAATAGGAGGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTCGAGCATATT
131 ATAATACAATAAGAGGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTCGAGCATATT
* *
3917330 TAATGTACTACTATTATATATAACTATTATTA-AATTATAGATTATAAT-AAAGGTAT-GGTATT
1 TAATGTACTACTATTATATATAACTATTATTATAA-TATAGATTATAATAAAAGATATAGAT-TT
* * *
3917392 GCATAATATTATAATATTTAATTATATATAAACTATTAATATATTAAATGATATGACATAACTTT
64 ACATAATATTATAATATTTAATTATATATAAACTATTAATATATTAAATAATATGACATAACATT
* * *
3917457 ATATAATATAGTAAGAGGGTTAACTTTCAAA
129 ACATAATACAATAAGAGGGTTAACTTTCAAA
3917488 AGGATTTAGA
Statistics
Matches: 139, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
189 2 0.01
190 94 0.68
191 43 0.31
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (191 bp):
TAATGTACTACTATTATATATAACTATTATTATAATATAGATTATAATAAAAGATATAGATTTAC
ATAATATTATAATATTTAATTATATATAAACTATTAATATATTAAATAATATGACATAACATTAC
ATAATACAATAAGAGGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTCGAGCATATT
Found at i:3917530 original size:16 final size:17
Alignment explanation
Indices: 3917511--3917543 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3917501 TATATAATGT
*
3917511 ACTATTGTTAT-ATATA
1 ACTATTATTATAATATA
3917527 ACTATTATTATAATATA
1 ACTATTATTATAATATA
3917544 GATTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
ACTATTATTATAATATA
Found at i:3919887 original size:24 final size:24
Alignment explanation
Indices: 3919852--3919947 Score: 147
Period size: 24 Copynumber: 4.0 Consensus size: 24
3919842 GACTTGGCTA
* *
3919852 ATTTGCCGTCAATTCATCTTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
* *
3919876 ATTTTCCATCAATTCATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
3919900 ATTTACCGTCAATTCATCCTTTAC
1 ATTTACCGTCAATTCATCCTTTGC
3919924 ATTTACCGTCAATTCATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
3919948 CACAAAACAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (24 bp):
ATTTACCGTCAATTCATCCTTTGC
Found at i:3927096 original size:19 final size:21
Alignment explanation
Indices: 3927054--3927102 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
3927044 ATGTTTTACT
*
3927054 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACAAGC
3927075 TTCTGTTCAGCT-TT-CAAGC
1 TTCTGTTCAGCTCTTACAAGC
3927094 TTCTGTTCA
1 TTCTGTTCA
3927103 CGATGTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
21 12 0.44
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACAAGC
Found at i:3931006 original size:21 final size:21
Alignment explanation
Indices: 3930982--3931034 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3930972 AAATATAATT
3930982 AAATA-TAATAATAACAATAAA
1 AAATAGTAATAA-AACAATAAA
* *
3931003 AAATAGTGATAAAATAAT-AA
1 AAATAGTAATAAAACAATAAA
*
3931023 AAATAGCAATAA
1 AAATAGTAATAA
3931035 TAATAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.44
21 10 0.37
22 5 0.19
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAGTAATAAAACAATAAA
Found at i:3931018 original size:18 final size:19
Alignment explanation
Indices: 3930991--3931043 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3930981 TAAATATAAT
*
3930991 AATAACAATAAAAAATAGT
1 AATAACAATAAAAAATAGC
*
3931010 GATAA-AATAATAAAAATAGC
1 AATAACAAT-A-AAAAATAGC
*
3931030 AATAATAATAAAAA
1 AATAACAATAAAAA
3931044 TAATTAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 13 0.46
21 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (19 bp):
AATAACAATAAAAAATAGC
Found at i:3940945 original size:18 final size:18
Alignment explanation
Indices: 3940919--3940953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3940909 CACATATCAA
* *
3940919 TTAAGTACCTAATTAAAC
1 TTAAATACCAAATTAAAC
3940937 TTAAATACCAAATTAAA
1 TTAAATACCAAATTAAA
3940954 TATTAAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAAATACCAAATTAAAC
Found at i:3945025 original size:45 final size:44
Alignment explanation
Indices: 3944890--3945087 Score: 120
Period size: 43 Copynumber: 4.5 Consensus size: 44
3944880 GAGCGGGTTA
* * *
3944890 AAGATAGTAGATCTTGCCCTCCTGCATAGACAGTGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCT-CGTAGACAGTGAAGCAGATCG
* * * * * * *
3944935 AAGACA-CAG-CCTTGCCTCCCTCGGTTG-CAGTGGAGCAGGTTG
1 AAGATAGCAGATCTTGCCTTCCTC-GTAGACAGTGAAGCAGATCG
**
3944977 AAGATAGCAGATCTTGCCTTCCTACGTAGACAACGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCT-CGTAGACAGTGAAGCAGATCG
* * * * * * * *
3945022 AAGACACCAG-CCTCG-CTTCCCTCGGTTG-CAGTGGAGCAGGTTG
1 AAGATAGCAGATCTTGCCTT-CCTC-GTAGACAGTGAAGCAGATCG
*
3945065 AAGATAGCAGATCTTGTCTTCCT
1 AAGATAGCAGATCTTGCCTTCCT
3945088 GTACTGATGG
Statistics
Matches: 111, Mismatches: 33, Indels: 19
0.68 0.20 0.12
Matches are distributed among these distances:
42 18 0.16
43 36 0.32
44 30 0.27
45 27 0.24
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (44 bp):
AAGATAGCAGATCTTGCCTTCCTCGTAGACAGTGAAGCAGATCG
Found at i:3945070 original size:88 final size:87
Alignment explanation
Indices: 3944678--3945088 Score: 534
Period size: 87 Copynumber: 4.7 Consensus size: 87
3944668 AAATCGAAAG
* * *
3944678 CAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTCGCCTTCCTGCAT
1 CAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCAT
*
3944743 GGACAGCGAAGCAGATCAAAAA
66 AGACAGCGAAGCAGATCAAAAA
* * * * * * *
3944765 CAAAGCCTTGCCTCCATTGGTTGCAGTGGAACGGGTTAAAGATAGCAAACCTTGCCTTTCTGCAT
1 CAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCAT
* *
3944830 TGACAGCGAAGTAGATCAAAAA
66 AGACAGCGAAGCAGATCAAAAA
* * *
3944852 CAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGTAGATCTTGCCCTCCTGCAT
1 CAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCAT
* * *
3944917 AGACAGTGAAGCAGATCGAAGA
66 AGACAGCGAAGCAGATCAAAAA
* * * *
3944939 CACAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACGT
1 CAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCAT
* * *
3945004 AGACAACGAAGCAGATCGAAGA
66 AGACAGCGAAGCAGATCAAAAA
* * * * *
3945026 CACCAGCCTCGCTTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGTCTTCCTG
1 CA-AAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTG
3945089 TACTGATGGC
Statistics
Matches: 288, Mismatches: 35, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
87 232 0.81
88 56 0.19
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (87 bp):
CAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCAT
AGACAGCGAAGCAGATCAAAAA
Found at i:3945313 original size:44 final size:45
Alignment explanation
Indices: 3945245--3945339 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
3945235 ATCGCTTCAG
* * *
3945245 GTCTTATCTCCCTGAGGTTACAATGGAGCAGGCTGAGAA-AGCAA
1 GTCTTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAA
* * *
3945289 GTCTTATCCCCCTGAAGTTGCAATGGGGCAGATTGAGAATAGCAA
1 GTCTTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAA
*
3945334 ATCTTA
1 GTCTTA
3945340 CTGCCCAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 33 0.77
45 10 0.23
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (45 bp):
GTCTTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAA
Found at i:3955868 original size:6 final size:6
Alignment explanation
Indices: 3955857--3955882 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3955847 TTTTAGCTCA
3955857 ATTGAT ATTGAT ATTGAT ATTGAT AT
1 ATTGAT ATTGAT ATTGAT ATTGAT AT
3955883 CTGTATAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATTGAT
Found at i:3960033 original size:14 final size:13
Alignment explanation
Indices: 3960009--3960058 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
3959999 ATTTGAAAGA
*
3960009 TTAAAAAAATTAT
1 TTAAGAAAATTAT
3960022 TTATAGAAAATT-T
1 TTA-AGAAAATTAT
3960035 TTAAAGAACAATTAT
1 TT-AAGAA-AATTAT
3960050 TTAAGAAAA
1 TTAAGAAAA
3960059 AAACATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 12 0.38
14 17 0.53
15 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (13 bp):
TTAAGAAAATTAT
Found at i:3963650 original size:23 final size:22
Alignment explanation
Indices: 3963595--3963650 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
3963585 AATAGAAAAC
3963595 ATAAATTAATTTTAAAAATAAA
1 ATAAATTAATTTTAAAAATAAA
* * *
3963617 AGATATTTAATTTTAAAACTAAA
1 ATA-AATTAATTTTAAAAATAAA
3963640 ATAAATGTAAT
1 ATAAAT-TAAT
3963651 CAAAATTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAAATTAATTTTAAAAATAAA
Found at i:3976978 original size:233 final size:238
Alignment explanation
Indices: 3976409--3977021 Score: 724
Period size: 233 Copynumber: 2.6 Consensus size: 238
3976399 TTATTATCCC
* * ** * ** * *
3976409 TAGCAAATTTAAAGTGAATATTAGTTCTTGAATATCCAAAATGGCTTGAACTAGCAATGGCCGAC
1 TAGCAAATTCAAAATGAATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCCAC
* * * * *
3976474 CTAAAAATCCTAGACTCAAACTACTTGAGCCCAAAA-AACTCGAACACAAAATTAATTCAAACCC
66 TTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
* * * *
3976538 TTCTCCAAGTAGTGCAGATTTGAATATTTGTAAATATCTAACTTGCTTTTTAGGATTCAGATATT
131 TTCTCCAAGTAGTGCAGATTCGAATATTTGCAAATATCTAACTTGCTTTTGAAGATTCAGATATT
* *
3976603 GTAGATTCGAATGATATTTAAATTCGGATTTTCTAATTACTATTCT
196 G-AGATTCG-A-GATATTTAAATTCGAATTTTCTAATTACCATTCT
* ** *
3976649 TAGTAAATTCAAAATGAATATTAGTTCTCGTATATCCAAAATGGCTTGAACTAATAATGACCCAC
1 TAGCAAATTCAAAATGAATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCCAC
* *
3976714 TTAAAAATCCTTGACTCAAACCACATGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
66 TTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
* * *
3976779 TTCTTCAAGTAGTGTAGATTCGAATATTTGCAAATATCTAACTTGCCTTTTGAAGATT-GGATAT
131 TTCTCCAAGTAGTGCAGATTCGAATATTTGCAAATATCTAACTTG-CTTTTGAAGATTCAGATAT
*
3976843 TG-GA-T-G-G-TATTTAAATTTGAATATTT-TAATTACCATT-T
195 TGAGATTCGAGATATTTAAATTCGAAT-TTTCTAATTACCATTCT
* ** * * * *
3976881 CTAGCATATTTGAAGT-AGATATTAGCCCTCGAATATCCAAAATGGCTTGAATTAATAGTGTCCC
1 -TAGCAAATTCAAAATGA-ATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCC
* * * *
3976945 ACTTAAAAATTCAAGACTCAAGCCACTTGAACCCAAAACAACTTGAACACAAAATTGATCCAAAC
64 ACTTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAAC
3977010 CCTTCTCCAAGT
129 CCTTCTCCAAGT
3977022 TTGCATTTGT
Statistics
Matches: 324, Mismatches: 44, Indels: 17
0.84 0.11 0.04
Matches are distributed among these distances:
232 2 0.01
233 143 0.44
234 4 0.01
237 1 0.00
238 1 0.00
239 2 0.01
240 87 0.27
241 74 0.23
242 10 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (238 bp):
TAGCAAATTCAAAATGAATATTAGCCCTCGAATATCCAAAATGGCTTGAACTAATAATGACCCAC
TTAAAAATCCTAGACTCAAACCACTTGAACCCAAAACAACTCGAACACAAAATTGATCCAAACCC
TTCTCCAAGTAGTGCAGATTCGAATATTTGCAAATATCTAACTTGCTTTTGAAGATTCAGATATT
GAGATTCGAGATATTTAAATTCGAATTTTCTAATTACCATTCT
Found at i:3981943 original size:37 final size:37
Alignment explanation
Indices: 3981891--3981982 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
3981881 ACATCATCAC
** **
3981891 TTTCATAGATGATTGTATTTGGAAGACATTGAGCTAT
1 TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
* * *
3981928 TTTCATAGATCATTGTAGTCAGAAGACAAGGATCTAT
1 TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
3981965 TTTCATAGATGATTGTAT
1 TTTCATAGATGATTGTAT
3981983 CAACCCTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (37 bp):
TTTCATAGATGATTGTATTCAGAAGACAAGGAGCTAT
Found at i:3986176 original size:15 final size:15
Alignment explanation
Indices: 3986156--3986187 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3986146 AACATCTCTA
3986156 TTAAAAAATTGTGGG
1 TTAAAAAATTGTGGG
3986171 TTAAAAAATTGTGGG
1 TTAAAAAATTGTGGG
3986186 TT
1 TT
3986188 TAGGTTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (15 bp):
TTAAAAAATTGTGGG
Found at i:3986720 original size:19 final size:18
Alignment explanation
Indices: 3986696--3986740 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3986686 TTATATTTAA
* *
3986696 AAAAAATATTAATTACTAT
1 AAAAAATATT-AGTACGAT
3986715 AAAAAATTATTAGTACGAT
1 AAAAAA-TATTAGTACGAT
3986734 AAAAAAT
1 AAAAAAT
3986741 CTAAACAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 18 0.78
20 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAAATATTAGTACGAT
Done.