Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 182 of 190
Found at i:53551886 original size:29 final size:29
Alignment explanation
Indices: 53551854--53551919 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
53551844 TTTAAAATAG
** *
53551854 TTTTAATATTTTTTTATA-ATTCTTAATCA
1 TTTTAATATAATTTTATATATTCTTAA-AA
*
53551883 TTTTAAAATAATTTTATATATTCTTAAAA
1 TTTTAATATAATTTTATATATTCTTAAAA
53551912 TTTTAATA
1 TTTTAATA
53551920 ATTCTTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTAATATAATTTTATATATTCTTAAAA
Found at i:53551893 original size:21 final size:19
Alignment explanation
Indices: 53551844--53551912 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 19
53551834 TTTATTGTAA
*
53551844 TTTAAAATAGTTTTAATAT
1 TTTAAAATAATTTTAATAT
***
53551863 TTTTTTATAATTCTTAATCAT
1 TTTAAAATAATT-TTAAT-AT
53551884 TTTAAAATAATTTTATATAT
1 TTTAAAATAATTTTA-ATAT
53551904 TCTTAAAAT
1 T-TTAAAAT
53551913 TTTAATAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 8 0.21
20 11 0.28
21 20 0.51
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (19 bp):
TTTAAAATAATTTTAATAT
Found at i:53561621 original size:2 final size:2
Alignment explanation
Indices: 53561614--53561663 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
53561604 AGAATAGAAA
53561614 AT 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 AT
53561656 AT AT AT AT
1 AT AT AT AT
53561664 GTAAGTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53562995 original size:23 final size:20
Alignment explanation
Indices: 53562941--53562992 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
53562931 ATCAGTATAT
*
53562941 GACACATAAGTGCCTGAAAC
1 GACACATAAGTACCTGAAAC
*
53562961 GACACACGAAGTACCTGAAATAC
1 GACACA-TAAGTACCTG-AA-AC
53562984 GACACATAA
1 GACACATAA
53562993 AGTTACTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 6 0.23
21 8 0.31
22 4 0.15
23 8 0.31
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
GACACATAAGTACCTGAAAC
Found at i:53563924 original size:15 final size:15
Alignment explanation
Indices: 53563888--53563918 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53563878 TATATAAAAC
*
53563888 AAAAGAAAGAATAGA
1 AAAAGAAAGAAAAGA
53563903 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
53563918 A
1 A
53563919 GCAGAATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:53565041 original size:25 final size:24
Alignment explanation
Indices: 53565013--53565123 Score: 120
Period size: 25 Copynumber: 4.6 Consensus size: 24
53565003 GAGCTTTAGT
*
53565013 GTGCTCTCTGATTATTAGCACGTTG
1 GTGCTCTCTGA-TATTAGCACGTTA
*
53565038 GTGCTCTCTGATTATTAGCACGTTT
1 GTGCTCTCTGA-TATTAGCACGTTA
*
53565063 GTGCTCTCTGATATTTAGCACGTCA
1 GTGCTCTCTGATA-TTAGCACGTTA
* * *
53565088 GTGCTCTTTG-T-TTAGCACATTC
1 GTGCTCTCTGATATTAGCACGTTA
53565110 GTGCTCTCTG-TATT
1 GTGCTCTCTGATATT
53565124 TGATCCGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
22 18 0.24
23 2 0.03
24 3 0.04
25 53 0.70
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (24 bp):
GTGCTCTCTGATATTAGCACGTTA
Found at i:53566198 original size:17 final size:18
Alignment explanation
Indices: 53566168--53566201 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53566158 GAATTTTATT
53566168 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
53566186 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
53566202 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:53566916 original size:25 final size:25
Alignment explanation
Indices: 53566885--53566956 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
53566875 AGCACTCTCT
* *
53566885 CGAGCCATATAACAGGATGCTCATG
1 CGAGCCATATAACAGGAAGCTCATC
* * *
53566910 TGAGCCATGTAACAGGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTCATC
53566935 CGAG-C-TATAACAGGAAGCTCAT
1 CGAGCCATATAACAGGAAGCTCAT
53566957 TAAGCTTAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 23 0.59
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTCATC
Found at i:53567188 original size:25 final size:24
Alignment explanation
Indices: 53567160--53567229 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
53567150 TAATACCGAT
*
53567160 TGGGATGCTCGCAAGAACTATATAA
1 TGGGATGCTCG-AAGAGCTATATAA
*
53567185 TGGGAAGCTCGAGAGAGCT-TATAA
1 TGGGATGCTCGA-AGAGCTATATAA
**
53567209 CAGGATGCTCGTAAGAGCTAT
1 TGGGATGCTCG-AAGAGCTAT
53567230 GGTGTGTCCG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 20 0.54
25 17 0.46
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (24 bp):
TGGGATGCTCGAAGAGCTATATAA
Found at i:53567772 original size:410 final size:410
Alignment explanation
Indices: 53567012--53568239 Score: 2179
Period size: 410 Copynumber: 3.0 Consensus size: 410
53567002 AGCGAACCAC
* * * *
53567012 ATCAGGAAGCTCACAAGGAGCCTATATCATGACGCTCATAAATAGCTGCGGTATGTCCGCATTAT
1 ATCAGGAAGCTCACAAAGAGTCTATATCATGACGCTCATAAATAGCTGCGGTATGTCTGCTTTAT
* ** * *
53567077 ATGTAGGATCCATACCGATCTTATAACATTACGCTCACAAAGAGTTGCGGTATGACTGTAACACA
66 ATGTAGGATCCATACCGATCATATAACAGGACGCTCACAAAGAGTTGCGGTATGACTGCAACATA
* * * * * *
53567142 TGCATGGTTAATACCGATTGGGATGCTCGCAAGAACTATATAATGGGAAGCTCGAGAGAGCTTAT
131 TGCAGGGTCAATACCGATTGGGATGCTTGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTAT
* * * *
53567207 AACAGGATGCTCGTAAGAGCTATGGTGTGTCCGCAACATATGCAGAACCACAACCAATATGGGAA
196 AACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGCAGAACCACAACCAATACGAGAA
* *
53567272 ATCCTGTTTCCATCGAATTTCATTAATTCAAAC-AGGACATATTACTTATCAGGCATTATTGAAC
261 ATCATGTTTCCATCGAATTTCATTAATTCAAACGA-GACATATTACTTATCGGGCATTATTGAAC
*
53567336 ATGCGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAA
325 ATGTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAA
53567401 CATATAAATATACACAAATAT
390 CATATAAATATACACAAATAT
*
53567422 ATCAGGAAGCTCACAAAGAGTCTATATCATGACGCTCATAAATAGCTGCTGTATGTCTGCTTTAT
1 ATCAGGAAGCTCACAAAGAGTCTATATCATGACGCTCATAAATAGCTGCGGTATGTCTGCTTTAT
*
53567487 ATGTAGGATCCATACCGATCATATAACAGGACGCTCACAAAGAGCTGCGGTATGACTGCAACATA
66 ATGTAGGATCCATACCGATCATATAACAGGACGCTCACAAAGAGTTGCGGTATGACTGCAACATA
53567552 TGCAGGGTCAATACCGATTGGGATGCTTGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTAT
131 TGCAGGGTCAATACCGATTGGGATGCTTGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTAT
*
53567617 AACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGTAGAACCACAACCAATACGAGAA
196 AACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGCAGAACCACAACCAATACGAGAA
53567682 ATCATGTTTCCATCGAATTTCATTAATTCAAACGAGACATATTACTTATCGGGCATTATTGAACA
261 ATCATGTTTCCATCGAATTTCATTAATTCAAACGAGACATATTACTTATCGGGCATTATTGAACA
53567747 TGTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAAC
326 TGTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAAC
53567812 ATATAAATATACACAAATAT
391 ATATAAATATACACAAATAT
*
53567832 ATCAGGAAGCTCACAAAGAGTTTATATCATGACGCTCATAAATAGCTGCGGTATGTCTGCTTTAT
1 ATCAGGAAGCTCACAAAGAGTCTATATCATGACGCTCATAAATAGCTGCGGTATGTCTGCTTTAT
53567897 ATGTAGGATCCATACCGATCATATAACAGGACGCTCACAAAGAGTTGCGGTATGACTGCAACATA
66 ATGTAGGATCCATACCGATCATATAACAGGACGCTCACAAAGAGTTGCGGTATGACTGCAACATA
*
53567962 TGCAGGGTCAATACCGATTGGGATGCTTGCAAGAACCATATAACAGAAAGCTCGAGAGAGCTTAT
131 TGCAGGGTCAATACCGATTGGGATGCTTGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTAT
53568027 AACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGCAGAACCACAACCAATACGAGAA
196 AACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGCAGAACCACAACCAATACGAGAA
*
53568092 ATCATGTTTCCATCGAATTTCATTAATTCAAACGGGACATATTACTTATCGGGCATTATTGAACA
261 ATCATGTTTCCATCGAATTTCATTAATTCAAACGAGACATATTACTTATCGGGCATTATTGAACA
53568157 TGTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAAC
326 TGTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAAC
*
53568222 ATACAAATATACACAAAT
391 ATATAAATATACACAAAT
53568240 TAGTTACACA
Statistics
Matches: 785, Mismatches: 32, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
410 784 1.00
411 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (410 bp):
ATCAGGAAGCTCACAAAGAGTCTATATCATGACGCTCATAAATAGCTGCGGTATGTCTGCTTTAT
ATGTAGGATCCATACCGATCATATAACAGGACGCTCACAAAGAGTTGCGGTATGACTGCAACATA
TGCAGGGTCAATACCGATTGGGATGCTTGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTAT
AACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGCAGAACCACAACCAATACGAGAA
ATCATGTTTCCATCGAATTTCATTAATTCAAACGAGACATATTACTTATCGGGCATTATTGAACA
TGTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAAC
ATATAAATATACACAAATAT
Found at i:53568038 original size:24 final size:24
Alignment explanation
Indices: 53568000--53568047 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53567990 GCAAGAACCA
53568000 TATAACAGAAAGCTCG-AGAGAGCT
1 TATAACAGAAAGCTCGTA-AGAGCT
* *
53568024 TATAACAGGATGCTCGTAAGAGCT
1 TATAACAGAAAGCTCGTAAGAGCT
53568048 ATGGTGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (24 bp):
TATAACAGAAAGCTCGTAAGAGCT
Found at i:53578480 original size:52 final size:52
Alignment explanation
Indices: 53578423--53578527 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
53578413 AAAACTTTGT
*
53578423 TAGGTGCTGGTAGATTGGATTGGGTTTTTAGATTATGGTTAGAATTGATTAG
1 TAGGTGCTGGTAGATTGGATTGGATTTTTAGATTATGGTTAGAATTGATTAG
* *
53578475 TAGGTGTTGGTAGATTGGATTGGATTTTTAGGTTATGGTTAGAATTGATTAG
1 TAGGTGCTGGTAGATTGGATTGGATTTTTAGATTATGGTTAGAATTGATTAG
53578527 T
1 T
53578528 CTAATTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.44
Consensus pattern (52 bp):
TAGGTGCTGGTAGATTGGATTGGATTTTTAGATTATGGTTAGAATTGATTAG
Found at i:53578513 original size:28 final size:28
Alignment explanation
Indices: 53578430--53578513 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
53578420 TGTTAGGTGC
* *
53578430 TGGTAGATTGGATTGGGTTTTTAGATTA
1 TGGTAGATTGGATTGGATTTTTAGGTTA
**
53578458 TGGTTAGA----ATT-GATTAGTAGGTGT-
1 TGG-TAGATTGGATTGGATTTTTAGGT-TA
53578482 TGGTAGATTGGATTGGATTTTTAGGTTA
1 TGGTAGATTGGATTGGATTTTTAGGTTA
53578510 TGGT
1 TGGT
53578514 TAGAATTGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
23 4 0.10
24 10 0.24
25 4 0.10
27 4 0.10
28 16 0.38
29 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (28 bp):
TGGTAGATTGGATTGGATTTTTAGGTTA
Found at i:53580221 original size:2 final size:2
Alignment explanation
Indices: 53580209--53580239 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
53580199 CATTTCCTTT
*
53580209 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53580240 GTTTAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:53582045 original size:5 final size:5
Alignment explanation
Indices: 53582037--53582068 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
53582027 TATTAGTATT
53582037 TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TT
1 TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TT
53582069 AGTATTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCTA
Found at i:53593728 original size:19 final size:18
Alignment explanation
Indices: 53593692--53593731 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53593682 TTTCCACTCG
*
53593692 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
53593710 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
53593729 TTT
1 TTT
53593732 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:53593863 original size:18 final size:20
Alignment explanation
Indices: 53593818--53593866 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
53593808 CTTTCTCCAA
53593818 TCTTTTTCTCTTTTTCAATT
1 TCTTTTTCTCTTTTTCAATT
*
53593838 T-TTGTTTCT-TTTTT-AGTT
1 TCTT-TTTCTCTTTTTCAATT
53593856 TCTTTTTCTCT
1 TCTTTTTCTCT
53593867 CGTCACTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.36
19 10 0.40
20 6 0.24
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.73
Consensus pattern (20 bp):
TCTTTTTCTCTTTTTCAATT
Found at i:53594808 original size:13 final size:13
Alignment explanation
Indices: 53594790--53594824 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
53594780 TAGCTTCTTC
53594790 TTTTTTTTCACGA
1 TTTTTTTTCACGA
53594803 -TTTTTTTCACGA
1 TTTTTTTTCACGA
53594815 TTTTTTTTCA
1 TTTTTTTTCA
53594825 ACTTGATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.66
Consensus pattern (13 bp):
TTTTTTTTCACGA
Found at i:53598801 original size:2 final size:2
Alignment explanation
Indices: 53598791--53598833 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
53598781 TATTCACTTA
53598791 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53598834 TCCAGTTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53606223 original size:22 final size:22
Alignment explanation
Indices: 53606198--53606241 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53606188 ACTTTGAAGA
53606198 TTCATTCAGGAAAAAGAAAGGG
1 TTCATTCAGGAAAAAGAAAGGG
53606220 TTCATTCAGGAAAAAGAAAGGG
1 TTCATTCAGGAAAAAGAAAGGG
53606242 GCTTCAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.18
Consensus pattern (22 bp):
TTCATTCAGGAAAAAGAAAGGG
Found at i:53610319 original size:2 final size:2
Alignment explanation
Indices: 53610312--53610341 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53610302 TTTTGAATTA
53610312 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
53610342 CACTCGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53626067 original size:27 final size:27
Alignment explanation
Indices: 53626016--53626070 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
53626006 CATTCCTCTA
53626016 AAACCCTCGGTTTTCCATATATATTTT
1 AAACCCTCGGTTTTCCATATATATTTT
*
53626043 AAACCCT-GGATTGTTCCAT-TGTATTTT
1 AAACCCTCGG-TT-TTCCATATATATTTT
53626070 A
1 A
53626071 TACCATGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 17 0.68
28 6 0.24
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (27 bp):
AAACCCTCGGTTTTCCATATATATTTT
Found at i:53628673 original size:20 final size:19
Alignment explanation
Indices: 53628639--53628677 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
53628629 GAGTTTAGAG
*
53628639 TTTATGATTTTATTATTTA
1 TTTATAATTTTATTATTTA
53628658 TTTATAATTATTATTATTTA
1 TTTATAATT-TTATTATTTA
53628678 GTTGTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATAATTTTATTATTTA
Found at i:53635561 original size:17 final size:16
Alignment explanation
Indices: 53635535--53635570 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
53635525 TAATCTAATT
53635535 TATTTAATATATTTAAA
1 TATTTAATATA-TTAAA
*
53635552 TATTTTATATATTAAA
1 TATTTAATATATTAAA
53635568 TAT
1 TAT
53635571 CGATAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAATATATTAAA
Found at i:53638992 original size:21 final size:21
Alignment explanation
Indices: 53638944--53639002 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 21
53638934 AAATATAACT
53638944 ATTAACATTTATATTTTTTATTA
1 ATTAAC-TTTA-ATTTTTTATTA
53638967 ATTAATCTTTAATTTTTT-TTA
1 ATTAA-CTTTAATTTTTTATTA
* *
53638988 GTTAAGTTTAATTTT
1 ATTAACTTTAATTTT
53639003 CAATATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 9 0.27
21 7 0.21
22 7 0.21
23 9 0.27
24 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
ATTAACTTTAATTTTTTATTA
Found at i:53640497 original size:22 final size:22
Alignment explanation
Indices: 53640463--53640507 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53640453 GGCTTCAAAA
53640463 TTCAGTTTCATACCTAAGTTTT
1 TTCAGTTTCATACCTAAGTTTT
* * * *
53640485 TTCATTTTGATACTTGAGTTTT
1 TTCAGTTTCATACCTAAGTTTT
53640507 T
1 T
53640508 ATTTTTTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (22 bp):
TTCAGTTTCATACCTAAGTTTT
Found at i:53646918 original size:40 final size:40
Alignment explanation
Indices: 53646867--53646953 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
53646857 AATTATGGAA
* * *
53646867 TACTGAATATTGTTTTG-AGTACTG-AGTTGAATTGTGAAGT
1 TACTGAATATTGTTATGTA-TACTGCA-TTGAACTGTGAAAT
53646907 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
53646947 TACTGAA
1 TACTGAA
53646954 GTAATGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
Found at i:53647218 original size:45 final size:45
Alignment explanation
Indices: 53647153--53647385 Score: 310
Period size: 45 Copynumber: 5.2 Consensus size: 45
53647143 ATATGCCGAC
* *
53647153 TACTGTTA-TGTTACTATTACCGATTTGACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAA
*
53647197 TACTGTTACTGTTACTGTTACCGAATCGACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAA
* * *
53647242 TACTATTACTGTTACTGTTATCGATTCGACACTTTGTGTGGCGAA
1 TACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAA
* * * *
53647287 TACTGTTACCGTTACTATTACCGATTTGGCACTTTGTGTG-CTGAA
1 TACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTC-GAA
* * * *
53647332 TACTGTTCCCG-TACTGTTACAGATTCGACACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAA
53647376 TACTGTTACT
1 TACTGTTACT
53647386 ATCACTACTA
Statistics
Matches: 165, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
44 44 0.27
45 121 0.73
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAA
Found at i:53648885 original size:20 final size:20
Alignment explanation
Indices: 53648860--53648902 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
53648850 AATGGTTTAA
53648860 AAATTA-ATTTAGTAATATTT
1 AAATTATATTTA-TAATATTT
*
53648880 AAATTATATTTATAATTTTT
1 AAATTATATTTATAATATTT
53648900 AAA
1 AAA
53648903 AAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTATATTTATAATATTT
Found at i:53648912 original size:20 final size:20
Alignment explanation
Indices: 53648855--53648913 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
53648845 CTGATAATGG
*
53648855 TTTAAAAATTAATTTAGTAATA
1 TTTAAAAAATAA-TTA-TAATA
** * *
53648877 TTTAAATTATATTTATAATT
1 TTTAAAAAATAATTATAATA
53648897 TTTAAAAAATAATTATA
1 TTTAAAAAATAATTATA
53648914 TAGATTTTCT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 18 0.62
21 3 0.10
22 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAAAAATAATTATAATA
Found at i:53658255 original size:15 final size:14
Alignment explanation
Indices: 53658234--53658269 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
53658224 ATAATCCTTA
*
53658234 ATAATTATCTTAAT
1 ATAATTATCCTAAT
53658248 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
53658263 ATAATTA
1 ATAATTA
53658270 AAACAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:53661234 original size:13 final size:13
Alignment explanation
Indices: 53661218--53661244 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53661208 CCATATTAGT
53661218 TTTTTATATATAA
1 TTTTTATATATAA
53661231 TTTTTATATATAA
1 TTTTTATATATAA
53661244 T
1 T
53661245 ACATCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTATATATAA
Found at i:53663531 original size:6 final size:6
Alignment explanation
Indices: 53663520--53663546 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53663510 TAGGTATAAT
53663520 ATTAAG ATTAAG ATTAAG ATTAAG ATT
1 ATTAAG ATTAAG ATTAAG ATTAAG ATT
53663547 TCACTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (6 bp):
ATTAAG
Found at i:53664214 original size:2 final size:2
Alignment explanation
Indices: 53664207--53664240 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53664197 AATTCCATCC
53664207 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
53664241 TTGCTTCGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53667673 original size:2 final size:2
Alignment explanation
Indices: 53667666--53667697 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53667656 CAAAAGTAGA
53667666 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
53667698 TTGTAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53675703 original size:25 final size:25
Alignment explanation
Indices: 53675649--53675715 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
53675639 AACCCTAATT
*
53675649 TTTCATTTCTTTCTT-TCCCTTCTTCT
1 TTTC-TTTCTTT-TTCTCCCTTCTTCG
53675675 TTTCTTTCTTTTTCTCCCTGT-TTCG
1 TTTCTTTCTTTTTCTCCCT-TCTTCG
*
53675700 TTTCTATTCTGTTTCT
1 TTTCT-TTCTTTTTCT
53675716 TTTATTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 2 0.06
25 20 0.56
26 14 0.39
ACGTcount: A:0.03, C:0.27, G:0.04, T:0.66
Consensus pattern (25 bp):
TTTCTTTCTTTTTCTCCCTTCTTCG
Found at i:53675750 original size:7 final size:7
Alignment explanation
Indices: 53675738--53675801 Score: 51
Period size: 7 Copynumber: 8.6 Consensus size: 7
53675728 ATTTACTTAT
53675738 TATAATA
1 TATAATA
53675745 TATAATA
1 TATAATA
53675752 TA-ATATA
1 TATA-ATA
53675759 TACTTAATA
1 TA--TAATA
*
53675768 -ATTAAGA
1 TA-TAATA
53675775 TATAATA
1 TATAATA
53675782 TTATAATA
1 -TATAATA
53675790 TTATAATA
1 -TATAATA
53675798 TATA
1 TATA
53675802 TTTTTTAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
6 1 0.02
7 27 0.55
8 17 0.35
9 3 0.06
10 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:53675788 original size:8 final size:8
Alignment explanation
Indices: 53675735--53675798 Score: 55
Period size: 8 Copynumber: 8.4 Consensus size: 8
53675725 TATATTTACT
53675735 TATTATAA
1 TATTATAA
53675743 TA-TATAA
1 TATTATAA
*
53675750 TATAATATA
1 TATTATA-A
*
53675759 TACT-TAA
1 TATTATAA
*
53675766 TAAT-TAA
1 TATTATAA
*
53675773 GA-TATAA
1 TATTATAA
53675780 TATTATAA
1 TATTATAA
53675788 TATTATAA
1 TATTATAA
53675796 TAT
1 TAT
53675799 ATATTTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 1 0.02
7 19 0.41
8 23 0.50
9 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (8 bp):
TATTATAA
Found at i:53676376 original size:39 final size:39
Alignment explanation
Indices: 53676322--53676400 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
53676312 TAAAAAGAAG
*
53676322 ATCAAATCGGTCCACGTACGATAGATGAATGATTAAATT
1 ATCAAATCGGTCCACGTACGATAGATGAACGATTAAATT
53676361 ATCAAATCGGTCCACGTACGATAGATGAACGATTAAATT
1 ATCAAATCGGTCCACGTACGATAGATGAACGATTAAATT
53676400 A
1 A
53676401 GTCACTCTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (39 bp):
ATCAAATCGGTCCACGTACGATAGATGAACGATTAAATT
Found at i:53678700 original size:25 final size:26
Alignment explanation
Indices: 53678671--53678721 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
53678661 AAACTTATTA
*
53678671 TTTAAGTATAA-AATTAAAACCAAAT
1 TTTAAATATAATAATTAAAACCAAAT
*
53678696 TTTAAATATAATAATTAAAATCAAAT
1 TTTAAATATAATAATTAAAACCAAAT
53678722 CTTATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (26 bp):
TTTAAATATAATAATTAAAACCAAAT
Found at i:53691233 original size:23 final size:22
Alignment explanation
Indices: 53691180--53691238 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
53691170 TAAATATTAG
*
53691180 TTTATTAATATTTTAATTTGAT
1 TTTATTAATATATTAATTTGAT
* *
53691202 TTTTTTAATGATATT-ATTTTAT
1 TTTATTAAT-ATATTAATTTGAT
*
53691224 TGTTATTAATTTATT
1 T-TTATTAATATATT
53691239 TAGTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTATTAATATATTAATTTGAT
Found at i:53694092 original size:18 final size:18
Alignment explanation
Indices: 53694071--53694122 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
53694061 ACCACTATGT
53694071 GGCCCAATACCATCC-TTC
1 GGCCCAATACCA-CCATTC
*
53694089 GGCCCAACACCACCATTC
1 GGCCCAATACCACCATTC
*
53694107 GGCCCAATAGCACCAT
1 GGCCCAATACCACCAT
53694123 CAATCCCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 28 0.93
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.15
Consensus pattern (18 bp):
GGCCCAATACCACCATTC
Found at i:53694308 original size:19 final size:18
Alignment explanation
Indices: 53694278--53694343 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 18
53694268 AGCAAACCAT
53694278 TTTTGACC-ACAATCATAA
1 TTTTGACCAACAAT-ATAA
53694296 TTTTGACCAACAATATAA
1 TTTTGACCAACAATATAA
*
53694314 TTTTGACCACTTCCAATATAA
1 TTTTGACCA---ACAATATAA
53694335 TTTTGACCA
1 TTTTGACCA
53694344 CTTTCAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 21 0.49
19 5 0.12
21 17 0.40
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (18 bp):
TTTTGACCAACAATATAA
Found at i:53694332 original size:21 final size:21
Alignment explanation
Indices: 53694306--53694364 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
53694296 TTTTGACCAA
53694306 CAATATAATTTTGACCACTTC
1 CAATATAATTTTGACCACTTC
*
53694327 CAATATAATTTTGACCACTTT
1 CAATATAATTTTGACCACTTC
*
53694348 CAAAATAATTTTGACCA
1 CAATATAATTTTGACCA
53694365 GGGTTAGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (21 bp):
CAATATAATTTTGACCACTTC
Found at i:53697046 original size:3 final size:3
Alignment explanation
Indices: 53697038--53697069 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53697028 ATGAAATTTG
53697038 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
53697070 GTTCATTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:53699973 original size:46 final size:46
Alignment explanation
Indices: 53699909--53700002 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
53699899 CTTCACTCAT
53699909 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
1 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
*
53699955 CACACACAACAACCTTGATGCTGCTAAGAGGGACCCAGATTATTCA
1 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
53700001 CA
1 CA
53700003 TTCTTTTGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (46 bp):
CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
Found at i:53701972 original size:23 final size:22
Alignment explanation
Indices: 53701942--53701985 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53701932 AAAAAAAGAA
53701942 AGTATTTTTAGAAAAAGCATAC
1 AGTATTTTTAGAAAAAGCATAC
53701964 AGTATTTTTAGAAAAAGCATAC
1 AGTATTTTTAGAAAAAGCATAC
53701986 CAGGTGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (22 bp):
AGTATTTTTAGAAAAAGCATAC
Found at i:53703371 original size:12 final size:12
Alignment explanation
Indices: 53703354--53703401 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
53703344 AAGCTGCTCA
53703354 TATTAGTTGTTT
1 TATTAGTTGTTT
*
53703366 TATTAGTTATTCT
1 TATTAGTTGTT-T
* *
53703379 TGTTAGCTGTTT
1 TATTAGTTGTTT
53703391 TATTAGTTGTT
1 TATTAGTTGTT
53703402 AATGATGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (12 bp):
TATTAGTTGTTT
Found at i:53729840 original size:7 final size:7
Alignment explanation
Indices: 53729828--53729856 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
53729818 ATCCAAACGA
53729828 CATTGAT
1 CATTGAT
53729835 CATTGAT
1 CATTGAT
53729842 CATTGAT
1 CATTGAT
53729849 CATTGAT
1 CATTGAT
53729856 C
1 C
53729857 GTGAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (7 bp):
CATTGAT
Found at i:53742635 original size:23 final size:23
Alignment explanation
Indices: 53742592--53742636 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53742582 CTCAAATTTA
*
53742592 AATTTTAAAAAATATTTTTATAC
1 AATTTTAAAAAATATTATTATAC
*
53742615 AATTTATAAAAATTA-TATTATA
1 AATTT-TAAAAAATATTATTATA
53742637 AACATGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTTAAAAAATATTATTATAC
Found at i:53743216 original size:29 final size:28
Alignment explanation
Indices: 53743184--53743244 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
53743174 AAAAGCCCTT
53743184 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
53743213 TTTTTTGATTATTTATCGGAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
53743241 TTTT
1 TTTT
53743245 CCGCGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:53744125 original size:40 final size:41
Alignment explanation
Indices: 53744081--53744170 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 41
53744071 TCCCCTAGGG
53744081 CGCGATTTCCAT-CCATGT-CAGC-AAATCGCGCTGACGTGGA
1 CGCGATTTCC-TGCCATGTAC-GCGAAATCGCGCTGACGTGGA
* * *
53744121 CGCGATGTCCTGCCATGTACTCTGACATCGCGCTGACGTGGA
1 CGCGATTTCCTGCCATGTACGC-GAAATCGCGCTGACGTGGA
*
53744163 TGCGATTT
1 CGCGATTT
53744171 TACGGAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
39 1 0.02
40 16 0.39
41 1 0.02
42 23 0.56
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.26
Consensus pattern (41 bp):
CGCGATTTCCTGCCATGTACGCGAAATCGCGCTGACGTGGA
Found at i:53751907 original size:3 final size:3
Alignment explanation
Indices: 53751899--53751955 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
53751889 TTAAAAGAGT
* *
53751899 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53751947 ATA ATA ATA
1 ATA ATA ATA
53751956 TGAAATTTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53752740 original size:20 final size:20
Alignment explanation
Indices: 53752711--53752754 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53752701 CAGTTACGAA
*
53752711 AAAAGAAAAAA-AATAAAGAG
1 AAAAGAAAAAATAAAAAAG-G
*
53752731 AAAAGTAAAAATAAAAAAGG
1 AAAAGAAAAAATAAAAAAGG
53752751 AAAA
1 AAAA
53752755 TAGAACTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAAATAAAAAAGG
Found at i:53753484 original size:40 final size:40
Alignment explanation
Indices: 53753440--53753551 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 40
53753430 ACACTGCGCT
*
53753440 TTAGGGAAATAAGACTTGATGCGATCTGCTCCACTACTGC
1 TTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGC
* * *
53753480 TTAGGGAGATAAGATCTGGTTTCTTTTG-TCTGCTCCACTACTGC
1 TTAGGGAGATAAGA-CTTGATGC----GATCTGCTCCACTACTGC
*
53753524 TTAGGGAGATAATACTTGATGCGATCTG
1 TTAGGGAGATAAGACTTGATGCGATCTG
53753552 TGGTTTTAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
39 1 0.02
40 17 0.29
41 5 0.09
43 5 0.09
44 29 0.50
45 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (40 bp):
TTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGC
Found at i:53753867 original size:174 final size:172
Alignment explanation
Indices: 53753555--53754243 Score: 626
Period size: 174 Copynumber: 4.0 Consensus size: 172
53753545 CGATCTGTGG
53753555 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAA
1 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGATTA-TGTCTTCGATCTGCTCCGCTGTAA
* * *
53753619 CCTCAGGGGGATAAGATCTGAAATTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCT
65 CCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCT
*
53753684 GGCGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTTT
130 GGCGCGATCTGCTCTACTGTAAC-TCAGAGAGATAAGATCCTGT
* * * *
53753728 ATTTTAAACCGTTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAA
1 -TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGATTATGTCTTCGATCTGCTCCGCTGTAA
53753793 CCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCT
65 CCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCT
* *
53753858 GGTGCGATCTGCTCTACTGTAACTCAGAGAGATAAGTTCCTGT
130 GGCGCGATCTGCTCTACTGTAACTCAGAGAGATAAGATCCTGT
* ** * * * * * * *
53753901 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGT
1 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGAT-T--ATGTCTTCGATCTGCTCCGCTGT
* * * * * * *
53753966 AACCTCAGGGAGATAAGACCTG---G--TGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGAT
63 AACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-
****** * * * **
53754026 CCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGATTATGT
127 CC--TGGCGCGATCTGCTCTACTGTAAC-TCAGAGAGATAAGATCCTGT
* * * * * * * * *
53754075 CTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGT
1 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGAT-T--ATGTCTTCGATCTGCTCCGCTGT
* * * * * *
53754140 AACCTCAGGGAGATAAGACCTG--A---TGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT
63 AACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-
* * * ** *
53754200 CCTGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGATC
127 CCTGGC-GCGATCTGCTCTACTGTAA-CTCAGAGAGATAAGATC
53754244 TGAAAGTCTT
Statistics
Matches: 452, Mismatches: 52, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
170 30 0.07
171 2 0.00
172 32 0.07
173 65 0.14
174 282 0.62
175 41 0.09
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (172 bp):
TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGATTATGTCTTCGATCTGCTCCGCTGTAAC
CTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG
GCGCGATCTGCTCTACTGTAACTCAGAGAGATAAGATCCTGT
Found at i:53754142 original size:303 final size:304
Alignment explanation
Indices: 53753570--53754417 Score: 1412
Period size: 303 Copynumber: 2.8 Consensus size: 304
53753560 ATCCGCTCCG
* * ** *
53753570 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGGGATAAGA
1 CTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
* *
53753635 TCTGAAATTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGCGCGATCTGCTCTA
66 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
* *
53753700 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAACCGTTCCACTGTAACTTCAGGGAGATAGG
131 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAACTTCAGGGAGATAAG
53753765 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
196 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
* *
53753830 CCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
261 CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
*
53753874 CTGTAAC-TCAGAGAGATAAGTTCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
1 CTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
*
53753938 TCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
66 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
*
53754003 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAG
131 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAACTTCAGGGAGATAAG
53754068 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
196 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
53754133 CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
261 CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
*
53754177 CTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGA
1 CTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
53754242 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
66 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
* * * ** * *
53754307 CTGTAACTTTAGAGAGATAAGATCCTGT-CTTCGATCTGTTCCACTGTAACCTCAGGGAGATAAG
131 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAACTTCAGGGAGATAAG
* ** * *
53754371 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA
196 AT-T--ATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
53754418 CCTGGTGCGA
Statistics
Matches: 510, Mismatches: 30, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
303 321 0.63
304 153 0.30
306 36 0.07
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (304 bp):
CTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAACTTCAGGGAGATAAG
ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
Found at i:53754206 original size:130 final size:130
Alignment explanation
Indices: 53754041--53754462 Score: 736
Period size: 130 Copynumber: 3.2 Consensus size: 130
53754031 ATTTTAATCC
* * ** *
53754041 GCTCCACTGTAACTTCAGGGAGATAAGATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAG
1 GCTCTACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
*
53754106 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCT
66 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCT
* *
53754171 ACTCTACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTACTCCGCTGTAACCTCAGGGAG
1 GCTCTACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
*
53754236 ATAAGATCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCT
66 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCT
* * *
53754301 GCTCTACTGTAACTTTAGAGAGATAAGATCCTGTCTTCGATCTGTTCCACTGTAACCTCAGGGAG
1 GCTCTACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
53754366 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCT
66 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCT
53754431 GCTCTACTGTAACTTCAGAGAGATAAGATCCT
1 GCTCTACTGTAACTTCAGAGAGATAAGATCCT
53754463 TTATTTTAAA
Statistics
Matches: 276, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 276 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (130 bp):
GCTCTACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCT
Found at i:53754437 original size:46 final size:42
Alignment explanation
Indices: 53753565--53754458 Score: 394
Period size: 46 Copynumber: 20.6 Consensus size: 42
53753555 TTTTAATCCG
* * * * *
53753565 CTCCGCTGTAACTTCAGGGAGATAGGA--TAGTGTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCT-G-GTCATCG-TCTA
* * * * *
53753608 CTCCGCTGTAACCTCAGGGGGATAAGATCTGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTG---GTCATC-GTCTA
* * *
53753654 CTCTACTGTAACCTCAGGGAGATAAGACCTGG-C-GCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGGTCATCG-TCTA
* * * * ** **
53753695 CTCTACTGTAACTTCAGAGAGATAAGATCCT--TTATTTTAAA
1 CTCCACTGTAACCTCAGGGAGATAAGA-CCTGGTCATCGTCTA
* * * * * * *
53753736 CCGTTCCACTGTAACTTCAGGGAGATAGGA-TTATGTCTTCAATCTG
1 -C--TCCACTGTAACCTCAGGGAGATAAGACCT-GGTCATC-GTCTA
* * *
53753782 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTG---GTCATC-GTCTA
* *
53753828 CTCCACTGTAACCTCAGGGAGATAAGACCTGGT--GCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGGTCATCG-TCTA
* * * * *
53753869 CTCTACTGTAA-CTCAGAGAGATAAGTTCCT-GTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAG-ACCTGGTCATCG-TCTA
* * *
53753911 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTG---GTCATC-GTCTA
* *
53753957 CTCCACTGTAACCTCAGGGAGATAAGACCTGGT--GCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGGTCATCG-TCTA
* * * ** ** ** **
53753998 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGA-CC-TGGTCATCGTCTA
* * * * * *
53754042 CTCCACTGTAACTTCAGGGAGATAAGA-TTATGTCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCT-GGTCATC-GTCTA
* * *
53754085 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTG---GTCATC-GTCTA
53754131 CTCCACTGTAACCTCAGGGAGATAAGACCT-G--ATGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGGTCAT-CG-TCTA
* * * *
53754172 CTCTACTGTAACTTCAGAGAGATAAGATCCT-GTCTTCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGA-CCTGGTCATCG-TCTA
* * *
53754215 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTG---GTCATC-GTCTA
* * *
53754261 CTCTACTGTAACCTCAGGGAGATAAGACCTGGT--GCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGGTCATCG-TCTA
* * * * * *
53754302 CTCTACTGTAACTTTAGAGAGATAAGATCCT-GTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA-CCTGGTCATCG-TCTA
* * *
53754345 TTCCACTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTG---GTCATC-GTCTA
* *
53754391 CTCCACTGTAACCTCAGGGAGATAAGACCTGGT--GCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGGTCATCG-TCTA
* * *
53754432 CTCTACTGTAACTTCAGAGAGATAAGA
1 CTCCACTGTAACCTCAGGGAGATAAGA
53754459 TCCTTTATTT
Statistics
Matches: 673, Mismatches: 117, Indels: 124
0.74 0.13 0.14
Matches are distributed among these distances:
40 22 0.03
41 163 0.24
42 42 0.06
43 158 0.23
44 55 0.08
45 4 0.01
46 225 0.33
47 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
CTCCACTGTAACCTCAGGGAGATAAGACCTGGTCATCGTCTA
Found at i:53754463 original size:434 final size:434
Alignment explanation
Indices: 53753743--53754559 Score: 1431
Period size: 434 Copynumber: 1.9 Consensus size: 434
53753733 AAACCGTTCC
* * * *
53753743 ACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAG
1 ACTGTAACTTCAGAGAGATAAGATCATGTCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAG
53753808 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
66 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
* *
53753873 ACTGTAACTCAGAGAGATAAGTTCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
131 ACTGTAACTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGA
53753938 TCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
196 TCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
* *
53754003 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAA
261 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAACCGCTCCACTATAATC-TCAGGGAGATAA
**
53754067 GATTA-TGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
325 GATTACTAACTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
53754131 CTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCT
390 CTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCT
* *
53754176 ACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAG
1 ACTGTAACTTCAGAGAGATAAGATCATGTCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAG
*
53754241 ATCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
66 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
* *
53754306 ACTGTAACTTTAGAGAGATAAGATCCTGTCTTCGATCTGTTCCACTGTAACCTCAGGGAGATAAG
131 ACTGTAAC-TCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAG
53754371 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
195 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
* *
53754436 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAACCGTTCCACTATAATCTCAGGGAGATAG
260 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAACCGCTCCACTATAATCTCAGGGAGATAA
* *
53754501 GATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTC
325 GATTACTAACTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTC
53754560 AGCCAGCTCC
Statistics
Matches: 362, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
433 131 0.36
434 181 0.50
435 50 0.14
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (434 bp):
ACTGTAACTTCAGAGAGATAAGATCATGTCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAG
ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
ACTGTAACTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGA
TCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAACCGCTCCACTATAATCTCAGGGAGATAAG
ATTACTAACTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTAC
TCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCT
Found at i:53754634 original size:87 final size:86
Alignment explanation
Indices: 53754554--53755166 Score: 815
Period size: 86 Copynumber: 7.1 Consensus size: 86
53754544 AGATCTGAAA
* * * * * * * *
53754554 TTCTTCAGCCAGCTCCACTACAACCGA-GAGAGGTAAGG-TTCGTCTTCGACCTGCTTCGCTGTC
1 TTCTTCAACCAGCTCCACTGCAACCAATGA-AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
* * *
53754617 AATGCAAGAAGGCAAGATCTGT
65 AACGCAGGAAGGCAAGATCTGC
* *
53754639 TGTCTTCAACCAGCTCCA-T-C-ACAAATGAGGGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCG
1 T-TCTTCAACCAGCTCCACTGCAACCAATGA---AGGCAAGGCTTTGT-T-TTCGATCTGCTTCG
* * **
53754700 CTGTCAATGCAGGAAGGCAAGATCTTT
60 CTGTTAACGCAGGAAGGCAAGATCTGC
53754727 TGTCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
1 T-TCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
53754792 AACGCAGGAAGGCAAGATCTGC
65 AACGCAGGAAGGCAAGATCTGC
*
53754814 TTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
1 TTCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
53754879 ACGCAGGAAGGCAAGATCTGC
66 ACGCAGGAAGGCAAGATCTGC
* * *
53754900 TTCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTA
1 TTCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
*
53754965 ACGCAGGAATGCAAGATCTGC
66 ACGCAGGAAGGCAAGATCTGC
* *
53754986 TTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTA
1 TTCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
*
53755051 ACGCAGGAAGGCAATATCTGC
66 ACGCAGGAAGGCAAGATCTGC
* * * *
53755072 TATCTTCAACCAGCTCCACTGCAACCGATGGAGGCAAGGATTTGTTTTCGATCTGCTTCACTGTT
1 T-TCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
* *
53755137 AATGCAGGAAGGCAAGATCTGA
65 AACGCAGGAAGGCAAGATCTGC
53755159 TGTCTTCA
1 T-TCTTCA
53755167 TTGATCTGTT
Statistics
Matches: 484, Mismatches: 33, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
83 3 0.01
84 3 0.01
85 2 0.00
86 276 0.57
87 120 0.25
88 66 0.14
89 6 0.01
90 1 0.00
91 7 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (86 bp):
TTCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
ACGCAGGAAGGCAAGATCTGC
Found at i:53754675 original size:44 final size:44
Alignment explanation
Indices: 53754616--53754744 Score: 129
Period size: 44 Copynumber: 2.9 Consensus size: 44
53754606 GCTTCGCTGT
*
53754616 CAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCA
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCA
* * * * * **
53754660 CAAATG-AGGGAGGCAAGGTTTG-TGTCTTCGACCTGCTTCGC-TGT
1 C-AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGC-TC-CATCA
*
53754704 CAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCA
53754745 CTGCAACCAA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
43 17 0.26
44 31 0.48
45 17 0.26
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (44 bp):
CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCA
Found at i:53754807 original size:43 final size:43
Alignment explanation
Indices: 53754756--53755064 Score: 195
Period size: 43 Copynumber: 7.2 Consensus size: 43
53754746 TGCAACCAAT
*
53754756 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAG
* * * * * * * * *
53754799 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CAAT
1 GAAGGCAAGGCTTTG-TT-TTCAATCTGCTTCGCTGTTAACGC-AG
*
53754842 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAG
* * * * * * * *
53754885 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-TAAC-CAAT
1 GAAGGCAAGGCTTTG-TT-TTCAATCTGCTTCGCTGTTAACGC-AG
* *
53754928 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAG
* * * * * * * * * *
53754971 GAATGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CAAT
1 GAAGGCAAGGCTTTG-TT-TTCAATCTGCTTCGCTGTTAACGC-AG
53755014 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAG
53755057 GAAGGCAA
1 GAAGGCAA
53755065 TATCTGCTAT
Statistics
Matches: 187, Mismatches: 61, Indels: 36
0.66 0.21 0.13
Matches are distributed among these distances:
42 48 0.26
43 92 0.49
44 47 0.25
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (43 bp):
GAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAG
Found at i:53755151 original size:43 final size:42
Alignment explanation
Indices: 53754756--53755152 Score: 164
Period size: 43 Copynumber: 9.2 Consensus size: 42
53754746 TGCAACCAAT
* * *
53754756 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGATTTGTTTTCAATCTGCTTCACTGTTAA-GCAG
* * * * * * * *
53754799 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAACCAAT
1 GAAGGCAAGGATTTG-TT-TTCAATCTGCTTCACTGTTAAGC-AG
* * *
53754842 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGATTTGTTTTCAATCTGCTTCACTGTTAA-GCAG
* * * * * * *
53754885 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-TAACCAAT
1 GAAGGCAAGGATTTG-TT-TTCAATCTGCTTCACTGTTAAGC-AG
* * **
53754928 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAACGCAG
1 GAAGGCAAGGATTTGTTTTCAATCTGCTTCACTGTTAA-GCAG
* * * * * * * * *
53754971 GAATGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAACCAAT
1 GAAGGCAAGGATTTG-TT-TTCAATCTGCTTCACTGTTAAGC-AG
* *
53755014 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGATTTGTTTTCAATCTGCTTCACTGTTAA-GCAG
* * * * * * *
53755057 GAAGGCAA-TATCTGCTATCTTCAACCAGCTCCACTG-CAACCGATG
1 GAAGGCAAGGATTTG-T-T-TTCAATCTGCTTCACTGTTAAGC-A-G
*
53755102 G-AGGCAAGGATTTGTTTTCGATCTGCTTCACTGTTAATGCAG
1 GAAGGCAAGGATTTGTTTTCAATCTGCTTCACTGTTAA-GCAG
53755144 GAAGGCAAG
1 GAAGGCAAG
53755153 ATCTGATGTC
Statistics
Matches: 243, Mismatches: 84, Indels: 54
0.64 0.22 0.14
Matches are distributed among these distances:
42 66 0.27
43 99 0.41
44 59 0.24
45 19 0.08
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (42 bp):
GAAGGCAAGGATTTGTTTTCAATCTGCTTCACTGTTAAGCAG
Found at i:53756403 original size:13 final size:13
Alignment explanation
Indices: 53756387--53756411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53756377 TTTTTCATTT
53756387 TTTCATTTTTTTA
1 TTTCATTTTTTTA
53756400 TTTCATTTTTTT
1 TTTCATTTTTTT
53756412 GACTCAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCATTTTTTTA
Found at i:53760876 original size:3 final size:3
Alignment explanation
Indices: 53760868--53760924 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
53760858 TTAAAAGAGT
* *
53760868 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53760916 ATA ATA ATA
1 ATA ATA ATA
53760925 TGAAATTTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53765062 original size:6 final size:6
Alignment explanation
Indices: 53765051--53765082 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
53765041 AAGTTATAAC
53765051 TCACAT TCACAT TCACAT TCACAT TCACAT TC
1 TCACAT TCACAT TCACAT TCACAT TCACAT TC
53765083 CACAAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
TCACAT
Found at i:53768878 original size:33 final size:35
Alignment explanation
Indices: 53768817--53768882 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
53768807 TAACAGTCTG
*
53768817 TGATTCTCAAAAAGAAAATCACTAACAAATTTCGA
1 TGATTCTCAAAAAGAAAATCACGAACAAATTTCGA
*
53768852 TGATTCTC-AAAAG-AAATCACGGACAAATTTC
1 TGATTCTCAAAAAGAAAATCACGAACAAATTTC
53768883 AGCCACTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 16 0.55
34 5 0.17
35 8 0.28
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (35 bp):
TGATTCTCAAAAAGAAAATCACGAACAAATTTCGA
Found at i:53770551 original size:2 final size:2
Alignment explanation
Indices: 53770544--53770574 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
53770534 TTACATGTTC
*
53770544 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53770575 GTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53776504 original size:30 final size:32
Alignment explanation
Indices: 53776451--53776509 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
53776441 TTTAATTTGA
53776451 TTAAATTTAGTCATTATACTTTTT-GAATGGG
1 TTAAATTTAGTCATTATACTTTTTCGAATGGG
* *
53776482 TTAATTTTAGTTATTATA-TTTTTCGAAT
1 TTAAATTTAGTCATTATACTTTTTCGAAT
53776510 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (32 bp):
TTAAATTTAGTCATTATACTTTTTCGAATGGG
Found at i:53776518 original size:30 final size:31
Alignment explanation
Indices: 53776451--53776524 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
53776441 TTTAATTTGA
*
53776451 TTAAA-TTTAGTCATTATACTTTTTGAATGGG
1 TTAAATTTTAGTTATTATACTTTTTGAAT-GG
*
53776482 TT-AATTTTAGTTATTATA-TTTTTCGAAT-T
1 TTAAATTTTAGTTATTATACTTTTT-GAATGG
53776511 TTAAATTTTCAGTT
1 TTAAATTTT-AGTT
53776525 TTAACTGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 2 0.05
30 13 0.35
31 22 0.59
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.55
Consensus pattern (31 bp):
TTAAATTTTAGTTATTATACTTTTTGAATGG
Found at i:53784079 original size:31 final size:31
Alignment explanation
Indices: 53784044--53784111 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
53784034 AAAAAACTTT
*
53784044 AATAGTCCAATAACTTAAAT-AAATTTTTTTG
1 AATAGTCCAATAACTTAAATGAAA-ATTTTTG
** * *
53784075 AATAGTTTAATGATTTAAATGAAAATTTTTG
1 AATAGTCCAATAACTTAAATGAAAATTTTTG
53784106 AATAGT
1 AATAGT
53784112 TTAAGTGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (31 bp):
AATAGTCCAATAACTTAAATGAAAATTTTTG
Found at i:53805164 original size:7 final size:7
Alignment explanation
Indices: 53805154--53805193 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
53805144 AAATGAAAAG
53805154 TTGTTAA
1 TTGTTAA
53805161 TTGTTAA
1 TTGTTAA
53805168 TTGTTAA
1 TTGTTAA
*
53805175 TTATTAA
1 TTGTTAA
*
53805182 TTATTTAA
1 TT-GTTAA
53805190 TTGT
1 TTGT
53805194 ATTTGATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (7 bp):
TTGTTAA
Found at i:53805917 original size:17 final size:17
Alignment explanation
Indices: 53805895--53805938 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
53805885 ACAAATCTAC
53805895 TCTTAATTA-ATAATAAA
1 TCTTAATTATAT-ATAAA
53805912 TCTTAAAATTATATATAAA
1 TCTT--AATTATATATAAA
53805931 TCTTAATT
1 TCTTAATT
53805939 CAATTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 8 0.33
19 14 0.58
20 2 0.08
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
TCTTAATTATATATAAA
Found at i:53808853 original size:95 final size:95
Alignment explanation
Indices: 53808750--53808988 Score: 374
Period size: 96 Copynumber: 2.5 Consensus size: 95
53808740 AACAACTAGT
*
53808750 TTTATTTGATTTTTCCTTAAAAACCCTAAATACTAAA-CCTCAATCTGATTTTTTT-AAATTTAT
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCT-AATCT-ATTTTTTTAAAATTTAT
*
53808813 AATTAATTTACTCAAGTAACTCTAAACCCTAA
64 AATTAATTTACTCAAGTAACCCTAAACCCTAA
53808845 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTATTTTTTTAAAAATTTATA
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTATTTTTTT-AAAATTTATA
*
53808910 ATTAATTTTCTCAAGTAACCCTAAACCCTAA
65 ATTAATTTACTCAAGTAACCCTAAACCCTAA
* * *
53808941 TTTATTTAATTTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTA
1 TTTATTTGA-TTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTA
53808989 AAATTTATAA
Statistics
Matches: 134, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
94 8 0.06
95 41 0.31
96 49 0.37
97 36 0.27
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (95 bp):
TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTATTTTTTTAAAATTTATAA
TTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:53808946 original size:96 final size:94
Alignment explanation
Indices: 53808750--53809051 Score: 377
Period size: 88 Copynumber: 3.2 Consensus size: 94
53808740 AACAACTAGT
*
53808750 TTTATTTGATTTTTCCTTAAAAACCCTAAATACTAAA-CCTCAATCTGATTTTTTTAAATTTATA
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCT-AATCT-ATTTTTTTAAATTTATA
*
53808814 ATTAATTTACTCAAGTAACTCTAAACCCTAA
64 ATTAATTTACTCAAGTAACCCTAAACCCTAA
53808845 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTATTTTTTTAAAAATTTATA
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTATTTTTTT--AAATTTATA
*
53808910 ATTAATTTTCTCAAGTAACCCTAAACCCTAA
64 ATTAATTTACTCAAGTAACCCTAAACCCTAA
* * *
53808941 TTTATTTAATTTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTA-------AAATTTATAA
1 TTTATTTGA-TTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTATTTTTTTAAATTTATAA
* * * * * *
53808999 CTAATTTAATTAAGAAACCTTAAACCCTTA
65 TTAATTTACTCAAGTAACCCTAAACCCTAA
*
53809029 TTTATTTAATTTTTTCCTTAAAA
1 TTTATTTGA-TTTTTCCTTAAAA
53809052 TCCTAAAATT
Statistics
Matches: 189, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
88 55 0.29
94 8 0.04
95 41 0.22
96 49 0.26
97 36 0.19
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (94 bp):
TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTATTTTTTTAAATTTATAAT
TAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:53809212 original size:40 final size:40
Alignment explanation
Indices: 53809153--53809274 Score: 165
Period size: 40 Copynumber: 3.0 Consensus size: 40
53809143 GGAAGTACTT
*
53809153 TGTCCACGTGGACATAAAGCGCTCCCTCAAGGAAGCGTTTTC
1 TGTCCACGTGGAC--AAAGCGCTTCCTCAAGGAAGCGTTTTC
* * **
53809195 TGTTCACGTGGACAAAGCGCTTCATTGAGGAAGCGGTTTT-
1 TGTCCACGTGGACAAAGCGCTTCCTCAAGGAAGC-GTTTTC
53809235 TGTCCACGTGGACAAAGCGCTTCCTCAAGGAAGCGTTTTC
1 TGTCCACGTGGACAAAGCGCTTCCTCAAGGAAGCGTTTTC
53809275 CTGCTTTATC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
39 5 0.07
40 47 0.68
41 5 0.07
42 12 0.17
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (40 bp):
TGTCCACGTGGACAAAGCGCTTCCTCAAGGAAGCGTTTTC
Found at i:53809503 original size:19 final size:19
Alignment explanation
Indices: 53809472--53809528 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
53809462 AAAAATATAA
*
53809472 AAAAATTATAAATATTT-T
1 AAAAATTTTAAATATTTAT
*
53809490 TAAAATTTTCAAATATTTAT
1 AAAAATTTT-AAATATTTAT
53809510 AAAAATTTTAAAT-TTTAT
1 AAAAATTTTAAATATTTAT
53809528 A
1 A
53809529 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 13 0.38
19 12 0.35
20 9 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAATTTTAAATATTTAT
Found at i:53809550 original size:17 final size:18
Alignment explanation
Indices: 53809530--53809600 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
53809520 AATTTTATAT
53809530 TTAAAAAAATAT-AAATA
1 TTAAAAAAATATAAAATA
* *
53809547 TTAAAAATAT-TAAAATT
1 TTAAAAAAATATAAAATA
* *
53809564 TCTAAAAAAATAAAAAAAA
1 T-TAAAAAAATATAAAATA
* * *
53809583 TTTAAAAACTCTAAAATA
1 TTAAAAAAATATAAAATA
53809601 ATATTTTTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
16 1 0.03
17 14 0.35
18 20 0.50
19 5 0.12
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAAAAAAATATAAAATA
Found at i:53809589 original size:28 final size:29
Alignment explanation
Indices: 53809549--53809603 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
53809539 TATAAATATT
**
53809549 AAAAATATTAAAATTTCTAAAAAAATAAA
1 AAAAATATTAAAAACTCTAAAAAAATAAA
*
53809578 AAAAAT-TTAAAAACTCTAAAATAATA
1 AAAAATATTAAAAACTCTAAAAAAATA
53809604 TTTTTTGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAATATTAAAAACTCTAAAAAAATAAA
Found at i:53810034 original size:21 final size:21
Alignment explanation
Indices: 53810004--53810067 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
53809994 TTAAAAACTG
* *
53810004 TAAATTTATTCTATTTTGGTT
1 TAAATATATTCTATTTTAGTT
*
53810025 TAAATATATT-TATTTAAGTT
1 TAAATATATTCTATTTTAGTT
* *
53810045 T-AATATATACTAATTTTAATT
1 TAAATATATTCT-ATTTTAGTT
53810066 TA
1 TA
53810068 TCGTATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 7 0.21
20 10 0.29
21 17 0.50
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (21 bp):
TAAATATATTCTATTTTAGTT
Found at i:53810933 original size:7 final size:7
Alignment explanation
Indices: 53810921--53810945 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53810911 TTAATATCTT
53810921 TTATTTA
1 TTATTTA
53810928 TTATTTA
1 TTATTTA
53810935 TTATTTA
1 TTATTTA
53810942 TTAT
1 TTAT
53810946 GTATCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:53819061 original size:9 final size:9
Alignment explanation
Indices: 53819047--53819105 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
53819037 AAGTTTTTCT
53819047 TATTGATGA
1 TATTGATGA
53819056 TA-T--TGA
1 TATTGATGA
53819062 TATTGATGA
1 TATTGATGA
* *
53819071 TAGTGACGA
1 TATTGATGA
*
53819080 TATTGATGC
1 TATTGATGA
* *
53819089 TAGTGATGC
1 TATTGATGA
53819098 TATTGATG
1 TATTGATG
53819106 GTGACCTTGA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
6 5 0.12
7 1 0.03
8 1 0.03
9 33 0.82
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.41
Consensus pattern (9 bp):
TATTGATGA
Found at i:53819081 original size:18 final size:18
Alignment explanation
Indices: 53819060--53819105 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
53819050 TGATGATATT
53819060 GATATTGATGATAGTGAC
1 GATATTGATGATAGTGAC
* *
53819078 GATATTGATGCTAGTGAT
1 GATATTGATGATAGTGAC
*
53819096 GCTATTGATG
1 GATATTGATG
53819106 GTGACCTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (18 bp):
GATATTGATGATAGTGAC
Found at i:53822393 original size:31 final size:31
Alignment explanation
Indices: 53822358--53822420 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
53822348 AATTTAGGTG
* * *
53822358 CCAAATTAGGAAAAAATACCAAGTTTAAGTA
1 CCAAATTAGAAAAAAAAACCAAGTTCAAGTA
*
53822389 CCAAATTAGAAAAAAAAATCAAGTTCAAGTA
1 CCAAATTAGAAAAAAAAACCAAGTTCAAGTA
53822420 C
1 C
53822421 TGAATGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (31 bp):
CCAAATTAGAAAAAAAAACCAAGTTCAAGTA
Found at i:53826190 original size:22 final size:22
Alignment explanation
Indices: 53826165--53826212 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
53826155 TGGTCTGTAG
53826165 TTTTTGAATTTATT-AATTTTAA
1 TTTTT-AATTTATTAAATTTTAA
* *
53826187 TTTTTTATTTTTTAAATTTTAA
1 TTTTTAATTTATTAAATTTTAA
53826209 TTTT
1 TTTT
53826213 GATCAGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTAATTTATTAAATTTTAA
Found at i:53831736 original size:13 final size:13
Alignment explanation
Indices: 53831701--53831738 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
53831691 GAGATATTTG
*
53831701 TAATTTGAAATCT
1 TAATTTGAAAACT
53831714 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
53831728 TAATTTGAAAA
1 TAATTTGAAAA
53831739 TTTGGAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:53834910 original size:20 final size:23
Alignment explanation
Indices: 53834875--53834919 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
53834865 GAACAAATTG
53834875 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
53834897 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
53834918 TT
1 TT
53834920 CTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:53834975 original size:21 final size:23
Alignment explanation
Indices: 53834951--53834993 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
53834941 TTAATTTTTT
*
53834951 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
*
53834972 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
53834994 TGATTACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:53844937 original size:12 final size:12
Alignment explanation
Indices: 53844920--53844944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53844910 ATCCTTGTTT
53844920 TCGTTGTTATTG
1 TCGTTGTTATTG
53844932 TCGTTGTTATTG
1 TCGTTGTTATTG
53844944 T
1 T
53844945 TTTTCTTGTT
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:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TCGTTGTTATTG
Found at i:53847071 original size:25 final size:25
Alignment explanation
Indices: 53847036--53847103 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
53847026 TTTTTATACT
*
53847036 TTTTAATAAATTTAATTATATTT-AG
1 TTTTAAAAAATTTAATTAT-TTTAAG
* *
53847061 TTTTAAAAAATTGAATT-TTTTAAAT
1 TTTTAAAAAATTTAATTATTTT-AAG
*
53847086 TTTTAAAAAAATTAATTA
1 TTTTAAAAAATTTAATTA
53847104 AATGCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.09
24 1 0.03
25 31 0.89
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (25 bp):
TTTTAAAAAATTTAATTATTTTAAG
Found at i:53850783 original size:31 final size:30
Alignment explanation
Indices: 53850719--53850846 Score: 145
Period size: 30 Copynumber: 4.2 Consensus size: 30
53850709 TTTTTTTTAT
*
53850719 TTTTTTAATTTTAAAATACTTTTATTAAAT--
1 TTTTTTAATTTTAAAATA-TTTT-TAAAATAC
*
53850749 TTTTTAAATTTTAAAAT-TTTTCTAAAATAC
1 TTTTTTAATTTTAAAATATTTT-TAAAATAC
53850779 TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTTAAAATAC
** *
53850809 TTTTTTAATTTTAATTTTAATTTTTAAAATAA
1 TTTTTTAATTTTAA-AAT-ATTTTTAAAATAC
53850841 TTTTTT
1 TTTTTT
53850847 GGTATTTATT
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
28 9 0.10
30 54 0.63
31 5 0.06
32 18 0.21
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:53896015 original size:21 final size:21
Alignment explanation
Indices: 53895989--53896031 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53895979 TAGTTTGTTC
53895989 TGAAATGAAACAAAAAAGTTT
1 TGAAATGAAACAAAAAAGTTT
53896010 TGAAATGAAACAAAAAAGTTT
1 TGAAATGAAACAAAAAAGTTT
53896031 T
1 T
53896032 CTTTGTGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (21 bp):
TGAAATGAAACAAAAAAGTTT
Found at i:53903497 original size:18 final size:17
Alignment explanation
Indices: 53903464--53903502 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53903454 TTTTATAAAT
53903464 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
53903482 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
53903499 TGTG
1 TGTG
53903503 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:53906159 original size:11 final size:11
Alignment explanation
Indices: 53906119--53906193 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
53906109 TTTTTTATCA
53906119 TTTT-AATAAT
1 TTTTAAATAAT
* *
53906129 TCTTATATAACT
1 TTTTAAATAA-T
53906141 TTTT-AATAAT
1 TTTTAAATAAT
53906151 TTTTAAAT-A-
1 TTTTAAATAAT
*
53906160 TTTTAAATAAA
1 TTTTAAATAAT
**
53906171 TTTTCTATAAT
1 TTTTAAATAAT
53906182 TTTTAAAATAAT
1 TTTT-AAATAAT
53906194 ATATAATATA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
9 8 0.16
10 10 0.20
11 23 0.46
12 9 0.18
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAATAAT
Found at i:53906541 original size:20 final size:21
Alignment explanation
Indices: 53906516--53906555 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53906506 AATATTTTTT
*
53906516 AAATATTTAAGC-CTTTTAAA
1 AAATATATAAGCACTTTTAAA
*
53906536 AAATATATAATCACTTTTAA
1 AAATATATAAGCACTTTTAA
53906556 TTATATATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATATATAAGCACTTTTAAA
Found at i:53908133 original size:12 final size:11
Alignment explanation
Indices: 53908111--53908141 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
53908101 TCCTTTTCCT
53908111 TCTTTTTTCTC
1 TCTTTTTTCTC
53908122 TCTTTTTCTCTC
1 TCTTTTT-TCTC
53908134 TCTTTTTT
1 TCTTTTTT
53908142 TGTTTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:53908758 original size:2 final size:2
Alignment explanation
Indices: 53908751--53908798 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
53908741 CCGAATCCTG
53908751 AT 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 AT
53908793 AT AT AT
1 AT AT AT
53908799 TGTTCGGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53916481 original size:13 final size:13
Alignment explanation
Indices: 53916451--53916485 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
53916441 AGAGTTATGA
53916451 AAATAAAATA-AT
1 AAATAAAATATAT
53916463 -AATAAAATATAT
1 AAATAAAATATAT
53916475 AAATAAAATAT
1 AAATAAAATAT
53916486 GAACATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATATAT
Found at i:53916559 original size:3 final size:3
Alignment explanation
Indices: 53916551--53916621 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
53916541 GCCTATATGT
53916551 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
53916599 ATA ATA ATA ATA ATA ATG ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
53916622 TCAATTGAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53917541 original size:15 final size:15
Alignment explanation
Indices: 53917529--53917557 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53917519 GAAGAGAATG
53917529 AAAAAAA-AAAGAAA
1 AAAAAAAGAAAGAAA
53917543 AAAAAAAGAAAGAAA
1 AAAAAAAGAAAGAAA
53917558 GTTAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAGAAA
Found at i:53917545 original size:10 final size:11
Alignment explanation
Indices: 53917528--53917553 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53917518 AGAAGAGAAT
53917528 GAAAAAAAAAA
1 GAAAAAAAAAA
53917539 GAAAAAAAAAA
1 GAAAAAAAAAA
53917550 GAAA
1 GAAA
53917554 GAAAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:53949824 original size:17 final size:18
Alignment explanation
Indices: 53949788--53949825 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
53949778 ATACTGTTAC
* *
53949788 TATTTTATTTAATATGAA
1 TATTTTAATTAATATAAA
53949806 TATTTTAATT-ATATAAA
1 TATTTTAATTAATATAAA
53949823 TAT
1 TAT
53949826 AAATATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TATTTTAATTAATATAAA
Found at i:53950113 original size:14 final size:15
Alignment explanation
Indices: 53950073--53950114 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53950063 TTCCTAAAAA
*
53950073 AAAAATT-ATTTTCC
1 AAAAATTGATTTTTC
53950087 AAAAATTGATTTTTC
1 AAAAATTGATTTTTC
*
53950102 AAAAGTTG-TTTTT
1 AAAAATTGATTTTT
53950115 AGTGAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
AAAAATTGATTTTTC
Found at i:53952239 original size:17 final size:17
Alignment explanation
Indices: 53952217--53952249 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53952207 AATGGATCAT
53952217 GGTTTATCTTTAGTTCC
1 GGTTTATCTTTAGTTCC
53952234 GGTTTATCTTTAGTTC
1 GGTTTATCTTTAGTTC
53952250 TCAATTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (17 bp):
GGTTTATCTTTAGTTCC
Found at i:53953038 original size:43 final size:43
Alignment explanation
Indices: 53952969--53953067 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
53952959 TAGCTCTCTC
*
53952969 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAGCGTGG
1 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
* * * *
53953012 TTATGATTACCATTAGTGTTG-TTTAATTGGACATTTAACGTTG
1 TTATAACTACCATTAGTG-TGCCTTAATTGGACATTTAACGTGG
53953055 TTATAACTACCAT
1 TTATAACTACCAT
53953068 CAAACTTTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 46 0.96
44 2 0.04
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (43 bp):
TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
Found at i:53954085 original size:18 final size:17
Alignment explanation
Indices: 53954057--53954091 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53954047 ATTATTAAGA
*
53954057 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53954074 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53954092 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53954367 original size:16 final size:16
Alignment explanation
Indices: 53954324--53954376 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
53954314 TTGAATTGCT
*
53954324 ATTACGCCTCTACTCC
1 ATTACGCCTCTATTCC
*
53954340 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
** *
53954356 ATTGTGCCTCTATTCA
1 ATTACGCCTCTATTCC
53954372 ATTAC
1 ATTAC
53954377 AGCGAACCAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:53955584 original size:20 final size:20
Alignment explanation
Indices: 53955559--53955599 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
53955549 ATATTTTTTA
53955559 TTTTTAATCAAATATATATT
1 TTTTTAATCAAATATATATT
*
53955579 TTTTTAATCAAATATTTATT
1 TTTTTAATCAAATATATATT
53955599 T
1 T
53955600 AATATGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAATCAAATATATATT
Found at i:53957462 original size:30 final size:30
Alignment explanation
Indices: 53957426--53957485 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53957416 CTTGTAATAT
53957426 AAAAAAAAAAAAAACACTCTAATCAAGTTA
1 AAAAAAAAAAAAAACACTCTAATCAAGTTA
53957456 AAAAAAAAAAAAAACACTCTAATCAAGTTA
1 AAAAAAAAAAAAAACACTCTAATCAAGTTA
53957486 CATAAGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.17
Consensus pattern (30 bp):
AAAAAAAAAAAAAACACTCTAATCAAGTTA
Found at i:53957838 original size:24 final size:23
Alignment explanation
Indices: 53957806--53957857 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
53957796 TTCTTGGAGT
53957806 TTTTTTTTTCCTCCAAGAAAGCAA
1 TTTTTTTTT-CTCCAAGAAAGCAA
53957830 TTTTTTTTTCTCCAAGAAAGCAA
1 TTTTTTTTTCTCCAAGAAAGCAA
*
53957853 CTTTT
1 TTTTT
53957858 AGTGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (23 bp):
TTTTTTTTTCTCCAAGAAAGCAA
Found at i:53958340 original size:17 final size:19
Alignment explanation
Indices: 53958320--53958355 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
53958310 TTTCTAATTT
53958320 TTAAAAAT-AAA-AAAAAA
1 TTAAAAATCAAATAAAAAA
53958337 TTAAAAATCAAATAAAAAA
1 TTAAAAATCAAATAAAAAA
53958356 ATTCTGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (19 bp):
TTAAAAATCAAATAAAAAA
Found at i:53964282 original size:21 final size:21
Alignment explanation
Indices: 53964246--53964285 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
53964236 CTTATTCAAG
53964246 TTATTTTGAATCTGAATTATT
1 TTATTTTGAATCTGAATTATT
53964267 TTATATTTGAAT-TGAATTA
1 TTAT-TTTGAATCTGAATTA
53964286 ATTTCGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (21 bp):
TTATTTTGAATCTGAATTATT
Found at i:53968859 original size:17 final size:18
Alignment explanation
Indices: 53968826--53968880 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
53968816 AAATTCAAAA
*
53968826 AAAAATGTAAAAGTTATTT
1 AAAAAT-TAAAAATTATTT
53968845 AAAAA-TAAAAATTA-TT
1 AAAAATTAAAAATTATTT
53968861 AAAAATTCTAAAAATTATTT
1 AAAAA-T-TAAAAATTATTT
53968881 TGTTAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.23
17 8 0.26
19 14 0.45
20 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (18 bp):
AAAAATTAAAAATTATTT
Found at i:53970036 original size:43 final size:43
Alignment explanation
Indices: 53969967--53970303 Score: 458
Period size: 43 Copynumber: 7.8 Consensus size: 43
53969957 TTTTAGGAAT
* *
53969967 AAACGCCGCTATAGATCATGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * **
53970010 AAACGCCGCTATAGATCAAGAGCTTTAACGGCGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
53970053 AAACGCCGCTAGAGATCAAGACCTTTAGCGGCGCTTCTCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* **
53970096 AAACGCCGCTATAGATCAAGAGCTTTAGCGGCGCTTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
53970139 AAACGCCTCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
53970182 AAACGCCGCTATAGCTCAAGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
53970225 AAACGCCGCTATAGCTCGAGGCCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
53970268 AAACGCCGCTATAGCTCGAGACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
53970304 CTTGTAAAAA
Statistics
Matches: 261, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 261 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:53971636 original size:2 final size:2
Alignment explanation
Indices: 53971629--53971673 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
53971619 CCAACAACTT
53971629 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
53971671 GA G
1 GA G
53971674 GGGGGGGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53971891 original size:20 final size:20
Alignment explanation
Indices: 53971866--53971905 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53971856 TAAAATAATA
53971866 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
53971886 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
53971906 GTACTTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAATAAATTAATAACAC
Found at i:53975033 original size:15 final size:15
Alignment explanation
Indices: 53975013--53975087 Score: 70
Period size: 15 Copynumber: 5.1 Consensus size: 15
53975003 CCGGCCCCTG
53975013 AATCCCTAAACCTTA
1 AATCCCTAAACCTTA
53975028 AATCCCT-AACTCTT-
1 AATCCCTAAAC-CTTA
*
53975042 AACCCCTAAACCCTT-
1 AATCCCTAAA-CCTTA
53975057 AA-CCACTAAACCTTA
1 AATCC-CTAAACCTTA
*
53975072 AATCCC-AACCCTTA
1 AATCCCTAAACCTTA
53975086 AA
1 AA
53975088 CCATAATCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
14 24 0.46
15 25 0.48
16 3 0.06
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (15 bp):
AATCCCTAAACCTTA
Found at i:53975073 original size:22 final size:22
Alignment explanation
Indices: 53975017--53975137 Score: 67
Period size: 22 Copynumber: 5.6 Consensus size: 22
53975007 CCCCTGAATC
53975017 CCTAAACCTTAAATCCCTAACT
1 CCTAAACCTTAAATCCCTAACT
* * *
53975039 CTTAACCCCTAAA-CCCTTAAC-
1 CCTAAACCTTAAATCCC-TAACT
53975060 CACTAAACCTTAAATCCC-AAC-
1 C-CTAAACCTTAAATCCCTAACT
* *
53975081 CCTTAAACCAT-AATCCCTTA-T
1 CC-TAAACCTTAAATCCCTAACT
* * *
53975102 CCATAATCCCTAAATCCAT-ACT
1 CC-TAAACCTTAAATCCCTAACT
*
53975124 CCCTAATCCTTAAA
1 -CCTAAACCTTAAA
53975138 ATATGAGCTC
Statistics
Matches: 77, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
20 7 0.09
21 25 0.32
22 40 0.52
23 5 0.06
ACGTcount: A:0.36, C:0.37, G:0.00, T:0.26
Consensus pattern (22 bp):
CCTAAACCTTAAATCCCTAACT
Found at i:53975105 original size:14 final size:14
Alignment explanation
Indices: 53975088--53975132 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
53975078 AACCCTTAAA
*
53975088 CCATAATCCCTTAT
1 CCATAATCCCTAAT
53975102 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
53975117 CCATACTCCCTAAT
1 CCATAATCCCTAAT
53975131 CC
1 CC
53975133 TTAAAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Done.