Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 85 of 230
Found at i:23599415 original size:50 final size:48
Alignment explanation
Indices: 23599308--23599645 Score: 230
Period size: 56 Copynumber: 6.6 Consensus size: 48
23599298 TGCGAAAGCT
* * * * *
23599308 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-CTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGAT-TCTCATCTAGGTGCC-ATGCC
* * * *
23599357 ATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGTCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA-TTCTCATCTAGGTG-CCATGCC
* * * * **
23599407 ATGTCCCAGACATGGTCTTAC-GGGGACCTCTCATCTTGGTGCGAACACC
1 ATGTCCCAGACATGGTCTTACATGGGA-TTCTCATCTAGGTGC-CATGCC
*
23599456 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGAT-TCTCATCTAGGTGCC-ATGCC
** * *
23599506 ATGTCCTTGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA--T-TC-TCATCT--A-GGTGCC-ATGCC
* *
23599562 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA--T-TC-TCATCT--A-GGTGCC-ATGCC
**
23599618 ATGTCCCAGACATATTCTTACATGGGAT
1 ATGTCCCAGACATGGTCTTACATGGGAT
23599646 CTCTTTACCC
Statistics
Matches: 242, Mismatches: 34, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
48 1 0.00
49 67 0.28
50 72 0.30
51 2 0.01
52 4 0.02
53 5 0.02
54 1 0.00
56 90 0.37
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (48 bp):
ATGTCCCAGACATGGTCTTACATGGGATTCTCATCTAGGTGCCATGCC
Found at i:23599479 original size:99 final size:102
Alignment explanation
Indices: 23599355--23599649 Score: 276
Period size: 99 Copynumber: 2.8 Consensus size: 102
23599345 ACTGCCAATG
* *
23599355 CCATATCCCAGATATGGTCTTACATGAGAGT-TCTCATATAGGTGTCC-ATGCCATGTCCCAGAC
1 CCATGTCCCAGACATGGTCTTACATGAGA-TCTCTCATATAGGTG-CCAATGCCATGTCCCAGAC
* *
23599418 ATGGTCTTAC-GGGGACCTCTC-ATCT-TGGTGCGAACA
64 ATGGTCTTACAGGGGACCTCTCAATCTATGATGCCAACA
* * * **
23599454 CCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAATGCCATGTCCTTGACAT
1 CCATGTCCCAGACATGGTCTTACATGAGATCTCTCATATAGGTGCCAATGCCATGTCCCAGACAT
* **
23599519 GGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATG
66 GGTCTTACAGGGGACCTCTC--AATCT--ATGATGCCAACA
* * *
23599560 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCC
1 CCATGTCCCAGACATGGTCTTACATGAGATCTCTCAT-A--T--A-GGTGCCAATGCCATGTCCC
** * *
23599625 AGACATATTCTTACATGGGATCTCT
60 AGACATGGTCTTACAGGGGACCTCT
23599650 TTACCCAAAT
Statistics
Matches: 160, Mismatches: 21, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
98 3 0.02
99 61 0.38
100 10 0.06
103 4 0.03
106 43 0.27
109 1 0.01
112 38 0.24
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (102 bp):
CCATGTCCCAGACATGGTCTTACATGAGATCTCTCATATAGGTGCCAATGCCATGTCCCAGACAT
GGTCTTACAGGGGACCTCTCAATCTATGATGCCAACA
Found at i:23599562 original size:56 final size:56
Alignment explanation
Indices: 23599496--23599649 Score: 263
Period size: 56 Copynumber: 2.8 Consensus size: 56
23599486 CTCATCTCGG
**
23599496 TGCCAATGCCATGTCCTTGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
23599552 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
** *
23599608 TGCCAATGCCATGTCCCAGACATATTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
23599650 TTACCCAAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 93 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (56 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
Found at i:23608728 original size:17 final size:17
Alignment explanation
Indices: 23608706--23608738 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23608696 ATAAGTATAC
23608706 ATTGTCATTACATTTTT
1 ATTGTCATTACATTTTT
*
23608723 ATTGTCATTACCTTTT
1 ATTGTCATTACATTTT
23608739 AGTGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:23616490 original size:24 final size:20
Alignment explanation
Indices: 23616445--23616485 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
23616435 CAAGACAAGC
23616445 ATACAAATCAAATATTCCTT
1 ATACAAATCAAATATTCCTT
23616465 ATACAAATCAAATATTCCTT
1 ATACAAATCAAATATTCCTT
23616485 A
1 A
23616486 CTTATTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (20 bp):
ATACAAATCAAATATTCCTT
Found at i:23620774 original size:42 final size:42
Alignment explanation
Indices: 23620677--23620774 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
23620667 GAAATGGGCA
* * *
23620677 TACTCACACGAGATGTGGGTCAAAATGTGAGCTGCACGATAC
1 TACTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATAC
** * * *
23620719 TGTTAACACGAGCTGTGGGTCAAAATGTAAGCTACATGATGC
1 TACTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATAC
*
23620761 TACTCACATGAGCT
1 TACTCACACGAGCT
23620775 ATTGAGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (42 bp):
TACTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATAC
Found at i:23624650 original size:23 final size:23
Alignment explanation
Indices: 23624621--23624669 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
23624611 ACCTTAGGAC
23624621 TGGATGATGAACTAAAGTGAGAT
1 TGGATGATGAACTAAAGTGAGAT
23624644 TGGATGATGAACTAAAGTGAGAT
1 TGGATGATGAACTAAAGTGAGAT
23624667 TGG
1 TGG
23624670 TTAACTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.27
Consensus pattern (23 bp):
TGGATGATGAACTAAAGTGAGAT
Found at i:23632176 original size:20 final size:20
Alignment explanation
Indices: 23632124--23632178 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
23632114 ATATGTATGA
* *
23632124 ATACCCTGAATGAAGTATCG
1 ATACCTTGACTGAAGTATCG
* *
23632144 ATACTTTGGCTGAAGTATCG
1 ATACCTTGACTGAAGTATCG
*
23632164 ATGCCTTGACTGAAG
1 ATACCTTGACTGAAG
23632179 CATCAATACA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
ATACCTTGACTGAAGTATCG
Found at i:23635055 original size:18 final size:18
Alignment explanation
Indices: 23635025--23635072 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
23635015 TTTCTATCAC
*
23635025 TTTT-AATACTTTTTAAT
1 TTTTAAATAATTTTTAAT
*
23635042 TTTTAAATAATTTTTTATT
1 TTTTAAATAA-TTTTTAAT
23635061 TTTTAAA-AATTT
1 TTTTAAATAATTT
23635073 AAAAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAAATAATTTTTAAT
Found at i:23635058 original size:19 final size:18
Alignment explanation
Indices: 23635034--23635072 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
23635024 CTTTTAATAC
23635034 TTTTTAATTTTTAAATAAT
1 TTTTTAATTTTTAAA-AAT
*
23635053 TTTTTATTTTTTAAAAAT
1 TTTTTAATTTTTAAAAAT
23635071 TT
1 TT
23635073 AAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTAATTTTTAAAAAT
Found at i:23637807 original size:88 final size:90
Alignment explanation
Indices: 23637704--23637885 Score: 260
Period size: 88 Copynumber: 2.0 Consensus size: 90
23637694 TCCTCTTTTT
* * *
23637704 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGTATCAAAAAGGCCCTTAAAC-CTTTT
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTCTTTT
*
23637768 C-AAAAAAAGCAATTAAGCCCCTAC
66 CAAAAAAAAACAATTAAGCCCCTAC
* * * * *
23637792 TTTTTTTGCATTCAATTGGGTACTTGAACTTTCAAAATATATCAAAAAGACCCTCAAACTTTTTT
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTCTTTT
*
23637857 CAAAAAAAAATAATTAAGCCCCTAC
66 CAAAAAAAAACAATTAAGCCCCTAC
23637882 TTTT
1 TTTT
23637886 ATTAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 52 0.63
89 5 0.06
90 25 0.30
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.34
Consensus pattern (90 bp):
TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTCTTTT
CAAAAAAAAACAATTAAGCCCCTAC
Found at i:23637912 original size:9 final size:9
Alignment explanation
Indices: 23637900--23638010 Score: 86
Period size: 9 Copynumber: 12.1 Consensus size: 9
23637890 AAAATTAGAA
23637900 AAAATATAT
1 AAAATATAT
23637909 AAAA-ATATT
1 AAAATATA-T
*
23637918 AAAAAATAT
1 AAAATATAT
23637927 AAAA-ATAT
1 AAAATATAT
* *
23637935 AAAAATTTGT
1 -AAAATATAT
*
23637945 AAAATTTTAT
1 AAAA-TATAT
23637955 AAAA-ATCAT
1 AAAATAT-AT
23637964 AAAATATTAT
1 AAAATA-TAT
23637974 AAAATATAT
1 AAAATATAT
*
23637983 AGAAATATAA
1 A-AAATATAT
23637993 AAAAT-TAT
1 AAAATATAT
*
23638001 AAAATTTAT
1 AAAATATAT
23638010 A
1 A
23638011 GTCATTAGAA
Statistics
Matches: 86, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
8 15 0.17
9 40 0.47
10 30 0.35
11 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATATAT
Found at i:23637913 original size:20 final size:19
Alignment explanation
Indices: 23637888--23637932 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
23637878 CTACTTTTAT
23637888 TAAAAATTAGAAAAAATATA
1 TAAAAATTAGAAAAAA-ATA
**
23637908 TAAAAA-TATTAAAAAATA
1 TAAAAATTAGAAAAAAATA
23637926 TAAAAAT
1 TAAAAAT
23637933 ATAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAATTAGAAAAAAATA
Found at i:23637924 original size:10 final size:9
Alignment explanation
Indices: 23637888--23638004 Score: 69
Period size: 10 Copynumber: 12.6 Consensus size: 9
23637878 CTACTTTTAT
*
23637888 TAAAAATTA
1 TAAAAAATA
*
23637897 GAAAAAATA
1 TAAAAAATA
23637906 TATAAAAATA
1 TA-AAAAATA
23637916 TTAAAAAATA
1 -TAAAAAATA
23637926 T-AAAAATA
1 TAAAAAATA
*
23637934 T-AAAAATT
1 TAAAAAATA
* * *
23637942 TGTAAAATTT
1 T-AAAAAATA
23637952 TATAAAAATCA
1 TA-AAAAAT-A
*
23637963 TAAAATAT-
1 TAAAAAATA
*
23637971 TATAAAATA
1 TAAAAAATA
*
23637980 TATAGAAATA
1 TA-AAAAATA
23637990 TAAAAAATTA
1 TAAAAAA-TA
23638000 TAAAA
1 TAAAA
23638005 TTTATAGTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
8 21 0.25
9 15 0.18
10 45 0.53
11 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAAATA
Found at i:23637938 original size:46 final size:47
Alignment explanation
Indices: 23637888--23638004 Score: 125
Period size: 46 Copynumber: 2.5 Consensus size: 47
23637878 CTACTTTTAT
23637888 TAAAAATTAGAAAAAATATATAAAAAT-ATTAAAA-AATATAAAA-ATA
1 TAAAAATTAGAAAAAAT-TATAAAAATCA-TAAAATAATATAAAATATA
* ** *
23637934 TAAAAATTTGTAAAATTTTATAAAAATCATAAAATATTATAAAATATA
1 TAAAAATTAG-AAAAAATTATAAAAATCATAAAATAATATAAAATATA
* *
23637982 TAGAAA-TATAAAAAATTATAAAA
1 TAAAAATTAGAAAAAATTATAAAA
23638005 TTTATAGTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
46 35 0.60
47 15 0.26
48 8 0.14
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (47 bp):
TAAAAATTAGAAAAAATTATAAAAATCATAAAATAATATAAAATATA
Found at i:23638034 original size:56 final size:55
Alignment explanation
Indices: 23637910--23638049 Score: 149
Period size: 56 Copynumber: 2.5 Consensus size: 55
23637900 AAAATATATA
* * *
23637910 AAAATATTAAAAAATATAA-AAATATAAAAATTTGTAAAATTTTATAAAAATCAT
1 AAAATATTAAAAAATATAAGAAATATAAAAAATTATAAAATTTTATAAAAATCAG
* *** *
23637964 AAAATATTATAAAATATATAGAAATATAAAAAATTATAAAA-TTTATAGTCATTAG
1 AAAATATTAAAAAATATA-AGAAATATAAAAAATTATAAAATTTTATAAAAATCAG
* *
23638019 AAAATTATAAAAAAATGTAAAGAAATATAAA
1 AAAA-TATTAAAAAATAT-AAGAAATATAAA
23638050 TTTCGTAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
54 17 0.24
55 14 0.20
56 39 0.55
57 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (55 bp):
AAAATATTAAAAAATATAAGAAATATAAAAAATTATAAAATTTTATAAAAATCAG
Found at i:23638237 original size:10 final size:10
Alignment explanation
Indices: 23638224--23638249 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23638214 TTTTTCTAAT
23638224 TTTTATAAAA
1 TTTTATAAAA
23638234 TTTTATAAAA
1 TTTTATAAAA
23638244 TTTTAT
1 TTTTAT
23638250 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:23638312 original size:20 final size:20
Alignment explanation
Indices: 23638289--23638349 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
23638279 TTAATAAATT
23638289 TTAAATTTTTTATATTTTTA
1 TTAAATTTTTTATATTTTTA
* * *
23638309 TTAAA-ATTTAATAATTTTTC
1 TTAAATTTTTTAT-ATTTTTA
* *
23638329 TAAAATTTATTAT-TTTTTA
1 TTAAATTTTTTATATTTTTA
23638348 TT
1 TT
23638350 TTTATAAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 5
0.68 0.20 0.11
Matches are distributed among these distances:
19 11 0.37
20 15 0.50
21 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAAATTTTTTATATTTTTA
Found at i:23638324 original size:47 final size:47
Alignment explanation
Indices: 23638234--23638380 Score: 155
Period size: 46 Copynumber: 3.2 Consensus size: 47
23638224 TTTTATAAAA
*
23638234 TTTT-ATAAAATTT-T-ATTTTTTATTTTTAT-AAAAAAATTCTAAT
1 TTTTAATAAAATTTATAATTTTTTATTTTTATAAAAAAAATTATAAT
* ** *
23638277 TTTTAATAAATTTTA-AATTTTTTATATTTT-TATTAAAATTTAATAAT
1 TTTTAATAAAATTTATAATTTTTTAT-TTTTATAAAAAAAATT-ATAAT
* * *
23638324 TTTT-CTAAAATTTATTATTTTTTATTTTTATAAAAAAAATTCTAAT
1 TTTTAATAAAATTTATAATTTTTTATTTTTATAAAAAAAATTATAAT
23638370 TTTTAATAAAA
1 TTTTAATAAAA
23638381 GTAGGGGCTT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
43 4 0.05
44 8 0.10
45 10 0.12
46 30 0.37
47 30 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (47 bp):
TTTTAATAAAATTTATAATTTTTTATTTTTATAAAAAAAATTATAAT
Found at i:23638345 original size:18 final size:19
Alignment explanation
Indices: 23638297--23638345 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
23638287 TTTTAAATTT
*
23638297 TTTA-TATTTTTATTAAAA
1 TTTATTATTTTTACTAAAA
*
23638315 TTTAATAATTTTT-CTAAAA
1 TTT-ATTATTTTTACTAAAA
23638334 TTTATTATTTTT
1 TTTATTATTTTT
23638346 TATTTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 11 0.42
19 9 0.35
20 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTATTTTTACTAAAA
Found at i:23638345 original size:19 final size:17
Alignment explanation
Indices: 23638297--23638346 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
23638287 TTTTAAATTT
23638297 TTTATATTTTTATTAAAA
1 TTTATATTTTT-TTAAAA
*
23638315 TTTAATAATTTTTCTAAAA
1 TTT-AT-ATTTTTTTAAAA
23638334 TTTATTATTTTTT
1 TTTA-TATTTTTT
23638347 ATTTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATATTTTTTTAAAA
Found at i:23642548 original size:3 final size:3
Alignment explanation
Indices: 23642534--23642573 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
23642524 ACAAAATTTA
*
23642534 AAT AAC 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 AAT A
23642574 CTATCAACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:23643919 original size:187 final size:184
Alignment explanation
Indices: 23643660--23644204 Score: 869
Period size: 187 Copynumber: 2.9 Consensus size: 184
23643650 AAAAAGGCGG
** *
23643660 AACCAAATTAGTGAAAAAAATTAAGTAACAATAGAATATTTAAGTAGAGCAAATCTGCAATTAGA
1 AACCAAATTAGTGAAAAAAA-CGAGT-A-AATAGAATATTTAAGTAGAGCAAATCTGCAATGAGA
*
23643725 ACAGAGATCTTCAACATCAACTAAACAGCTT-ATGCATTTTCTCTTCACATTGATCTACTCTTTC
63 ACAGAGATCTTCAACATCAACTAAACAGCTTAATGCA-TTTCTCTTCACATTGATCTACTCTTAC
23643789 CTAAAATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
127 CTAAAATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
* * *
23643847 AACCAAATTAGTGAAAAGAAACGAGTAAGACTAGAAGATTTAAGTAGAGCACATCTGCAACGAGA
1 AACCAAATTAGTGAAAA-AAACGAGTAA-A-TAGAATATTTAAGTAGAGCAAATCTGCAATGAGA
* * *
23643912 ACAGAGATCTTCAACATCAACTAAACAGCTTAACGCATTTCTTTTCACATTGATCTACTATTACC
63 ACAGAGATCTTCAACATCAACTAAACAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACC
* *
23643977 TAAAATCAAACATGAAATTCCCACTCTTTCTCAGGAAACAAACAAACACTAAACACT
128 TAAAATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
* *
23644034 AACCAAAGTAGTGAAAAAAACGAGT-AATAGATTATTTAAGTAGAGCAAATCTGCAATGAGAACA
1 AACCAAATTAGTGAAAAAAACGAGTAAATAGAATATTTAAGTAGAGCAAATCTGCAATGAGAACA
*
23644098 GAGATCTTCAACATCAACTAAGCAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACCTAA
66 GAGATCTTCAACATCAACTAAACAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACCTAA
*
23644163 AATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAGACAA
131 AATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAA
23644205 GCAACAATTT
Statistics
Matches: 331, Mismatches: 23, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
183 134 0.40
184 1 0.00
185 2 0.01
186 10 0.03
187 177 0.53
188 7 0.02
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (184 bp):
AACCAAATTAGTGAAAAAAACGAGTAAATAGAATATTTAAGTAGAGCAAATCTGCAATGAGAACA
GAGATCTTCAACATCAACTAAACAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACCTAA
AATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
Found at i:23647106 original size:10 final size:10
Alignment explanation
Indices: 23647091--23647117 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
23647081 AAAGTGAATA
23647091 ATTCAAATTT
1 ATTCAAATTT
23647101 ATTCAAATTT
1 ATTCAAATTT
23647111 ATTCAAA
1 ATTCAAA
23647118 CCAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTCAAATTT
Found at i:23651434 original size:50 final size:50
Alignment explanation
Indices: 23651371--23651500 Score: 152
Period size: 50 Copynumber: 2.6 Consensus size: 50
23651361 AGGTCCCATG
* * ** *
23651371 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCA
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAAGAGAACTCCCACA
* * * **
23651421 TAAGACCATGTCTGAGACATGGCATGGGCACCGATAAGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAAGAGAACTCCCACA
* *
23651471 TAAGACCATATCTGGGATATGGCATTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
23651501 GTACAGAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAAGAGAACTCCCACA
Found at i:23653835 original size:25 final size:25
Alignment explanation
Indices: 23653786--23653835 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
23653776 TTCATACTAT
* *
23653786 TTTTTGAAATTTTTTATAATTTTTA
1 TTTTTAAAATTTTTTATAATATTTA
23653811 TTTTTAAAATATTTTTATAA-ATTTA
1 TTTTTAAAAT-TTTTTATAATATTTA
23653836 ATATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTTAAAATTTTTTATAATATTTA
Found at i:23654877 original size:30 final size:30
Alignment explanation
Indices: 23654843--23654902 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
23654833 ACTTAACAAG
*
23654843 TAAATGTCTCTAAAATAATAACAAAATTAA
1 TAAATGCCTCTAAAATAATAACAAAATTAA
* *
23654873 TAAATGCCTTTAAAATAATAATAAAATTAA
1 TAAATGCCTCTAAAATAATAACAAAATTAA
23654903 CAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (30 bp):
TAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:23654912 original size:17 final size:17
Alignment explanation
Indices: 23654882--23654914 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23654872 ATAAATGCCT
23654882 TTAAAATAATAATAAAA
1 TTAAAATAATAATAAAA
23654899 TTAACAATAA-AATAAA
1 TTAA-AATAATAATAAA
23654915 TTTTATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAAATAATAATAAAA
Found at i:23654960 original size:22 final size:22
Alignment explanation
Indices: 23654935--23654977 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23654925 TATCCAAACA
23654935 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
23654957 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
23654978 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:23656417 original size:25 final size:23
Alignment explanation
Indices: 23656370--23656417 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
23656360 ATACTTTTAC
* *
23656370 ATATTCATATTTTTTATTTTTTT
1 ATATTCATATTTTTAATTATTTT
23656393 ATATTCATATTTTTGCAATTATTTT
1 ATATTCATATTTTT--AATTATTTT
23656418 TAACCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (23 bp):
ATATTCATATTTTTAATTATTTT
Found at i:23659150 original size:21 final size:21
Alignment explanation
Indices: 23659124--23659167 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
23659114 TTGACCAATC
*
23659124 AAGGAGACAAGACATGAAGAG
1 AAGGAGACAAAACATGAAGAG
23659145 AAGGAGACAAAACATGAAGAG
1 AAGGAGACAAAACATGAAGAG
23659166 AA
1 AA
23659168 TGTTTGCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.30, T:0.05
Consensus pattern (21 bp):
AAGGAGACAAAACATGAAGAG
Found at i:23669374 original size:25 final size:24
Alignment explanation
Indices: 23669324--23669374 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
23669314 GGGTATCAAC
*
23669324 AAAAAAAATATCAAATTAAAATAT
1 AAAAAAAATATCAAATTAAAACAT
* **
23669348 AAAAATAAATATTAAATTTTAACAT
1 AAAAA-AAATATCAAATTAAAACAT
23669373 AA
1 AA
23669375 TTCACTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAAAAATATCAAATTAAAACAT
Found at i:23669469 original size:74 final size:73
Alignment explanation
Indices: 23669331--23669469 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 73
23669321 AACAAAAAAA
* * * **
23669331 ATATCAAATTAAAATATAAAAATAAATATTAAATTTTAACATAATTCACTAATAATTAGTCAAAA
1 ATATCAAATTAAAATATAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAAA
23669396 ATTTATAT
66 ATTTATAT
23669404 ATATCAAATTAAAATATAAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAA
1 ATATCAAATTAAAATAT-AAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAA
23669469 A
65 A
23669470 GCTAATCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
73 17 0.28
74 43 0.72
ACGTcount: A:0.58, C:0.09, G:0.01, T:0.32
Consensus pattern (73 bp):
ATATCAAATTAAAATATAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAAA
ATTTATAT
Found at i:23677318 original size:3 final size:3
Alignment explanation
Indices: 23677310--23677334 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23677300 GGCCCCGCCA
23677310 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
23677335 TCTCTACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:23679503 original size:34 final size:34
Alignment explanation
Indices: 23679460--23679527 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
23679450 TTTTTCGAGT
23679460 TAGTTCACACACACTTGATGATAATTCTAATAAC
1 TAGTTCACACACACTTGATGATAATTCTAATAAC
23679494 TAGTTCACACACACTTGATGATAATTCTAATAAC
1 TAGTTCACACACACTTGATGATAATTCTAATAAC
23679528 CCACACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (34 bp):
TAGTTCACACACACTTGATGATAATTCTAATAAC
Found at i:23680011 original size:15 final size:17
Alignment explanation
Indices: 23679982--23680013 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
23679972 AGAAAATTGT
23679982 GAAAAGAAAACAAAAGA
1 GAAAAGAAAACAAAAGA
23679999 GAAAA-AAAA-AAAAGA
1 GAAAAGAAAACAAAAGA
23680014 AAACGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAACAAAAGA
Found at i:23682285 original size:25 final size:25
Alignment explanation
Indices: 23682249--23682330 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
23682239 CGAGTTGAAT
* * *
23682249 TCGAGCTGAATATCAGTAAGCTCATG
1 TCGAGCTAAATATCGGTAAGCTC-TC
23682275 T-GAGCTAAATATCGGTAAGCTCTC
1 TCGAGCTAAATATCGGTAAGCTCTC
*
23682299 TCGAGCTAAATATCGGTAACCTCTC
1 TCGAGCTAAATATCGGTAAGCTCTC
*
23682324 TTGAGCT
1 TCGAGCT
23682331 GAGAATCAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
24 2 0.04
25 47 0.94
26 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (25 bp):
TCGAGCTAAATATCGGTAAGCTCTC
Found at i:23685689 original size:42 final size:43
Alignment explanation
Indices: 23685642--23685750 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 43
23685632 ATATTCGTAT
* *
23685642 ACAAGCTACCATGTAGGTTGTGGATAAACGA-AAAATTTGCAG
1 ACAAGCTACCATGTAGGTTGTGGATAAACCACAAAATTTGCAA
* * * *
23685684 ACAAGCTACCTTGTAGGTTATGGATAAACCACCAATTTTGCAA
1 ACAAGCTACCATGTAGGTTGTGGATAAACCACAAAATTTGCAA
* *
23685727 AGAAGCTGCCATGTAGGTTGTGGA
1 ACAAGCTACCATGTAGGTTGTGGA
23685751 CGAAGCCACA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 28 0.50
43 28 0.50
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (43 bp):
ACAAGCTACCATGTAGGTTGTGGATAAACCACAAAATTTGCAA
Found at i:23692195 original size:41 final size:41
Alignment explanation
Indices: 23692136--23692221 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
23692126 CATGTTATCA
** * *
23692136 CATATCGATGCCTCTGTCCTAGACA-GGGTCTTACAC-GAAT
1 CATATCGATGCCAATGTCCCAGA-ATGGGTCTTACACAAAAT
*
23692176 CATATACGATGCCAATGTCCCAGAATTGGTCTTACACAAAAT
1 CATAT-CGATGCCAATGTCCCAGAATGGGTCTTACACAAAAT
23692218 CATA
1 CATA
23692222 CCTCAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
40 6 0.16
41 25 0.66
42 7 0.18
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (41 bp):
CATATCGATGCCAATGTCCCAGAATGGGTCTTACACAAAAT
Found at i:23700975 original size:39 final size:39
Alignment explanation
Indices: 23700886--23701157 Score: 270
Period size: 39 Copynumber: 7.1 Consensus size: 39
23700876 TGCTATTGGA
*
23700886 GTATCGAAGTACAACCA--GGCACGTAAGTGCAATTAGGG
1 GTATCGAAGTACAA-CAGGGGCACGTAAGTGCAATCAGGG
* * ** *
23700924 GTA-CCAAGGTACAACAAGGGCATATAAGTGCAATTAGGG
1 GTATCGAA-GTACAACAGGGGCACGTAAGTGCAATCAGGG
* * * **
23700963 GTATTGAAGTACAATAGGGGCACGTAAGAGTGATCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* *
23701002 GTATCAAAGTACAACAGGGGCACGTAAGTGCGATCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* * * *
23701041 GTACCGAAGTAAAATAGGGGCACGTAAGTGC-GTCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* * *
23701079 GTATCGAAGTACAACAGGGGCACGTAGGTGCGATCAAGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* * *
23701118 GTACCAAAGTAC-A-A-GGGCACGTAAGTGCCATCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
23701154 GTAT
1 GTAT
23701158 AATTATATAA
Statistics
Matches: 194, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
36 22 0.11
37 6 0.03
38 43 0.22
39 121 0.62
40 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (39 bp):
GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
Found at i:23701030 original size:19 final size:19
Alignment explanation
Indices: 23701008--23701104 Score: 72
Period size: 19 Copynumber: 5.1 Consensus size: 19
23700998 AGGGGTATCA
23701008 AAGTACAACAGGGGCACGT
1 AAGTACAACAGGGGCACGT
* * *
23701027 AAGTGCGATCAGGGGTACCG-
1 AAGTAC-AACAGGGGCA-CGT
* *
23701047 AAGTAAAATAGGGGCACGT
1 AAGTACAACAGGGGCACGT
* ** *
23701066 AAGTGCGTCAGGGGTATCG-
1 AAGTACAACAGGGGCA-CGT
23701085 AAGTACAACAGGGGCACGT
1 AAGTACAACAGGGGCACGT
23701104 A
1 A
23701105 GGTGCGATCA
Statistics
Matches: 55, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
18 4 0.07
19 35 0.64
20 14 0.25
21 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.35, T:0.14
Consensus pattern (19 bp):
AAGTACAACAGGGGCACGT
Found at i:23702812 original size:16 final size:17
Alignment explanation
Indices: 23702781--23702813 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23702771 AAAAATAATT
23702781 TAATTTGATATAATTTA
1 TAATTTGATATAATTTA
*
23702798 TAATTT-ATTTAATTTA
1 TAATTTGATATAATTTA
23702814 ATTGTCGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TAATTTGATATAATTTA
Found at i:23703865 original size:24 final size:22
Alignment explanation
Indices: 23703833--23703882 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
23703823 ATCTTAAAAT
*
23703833 AAAATCATTAATTAAAAATTAATA
1 AAAAACATTAATT-AAAA-TAATA
**
23703857 AAAAACATTTCTTAAAATAATA
1 AAAAACATTAATTAAAATAATA
23703879 AAAA
1 AAAA
23703883 TGTGTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 4 0.17
24 10 0.43
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAACATTAATTAAAATAATA
Found at i:23703959 original size:23 final size:23
Alignment explanation
Indices: 23703932--23703976 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
23703922 ATATATTTTA
23703932 ATTAAATT-TTAAAAATAATTAAT
1 ATTAAATTCTTAAAAAT-ATTAAT
*
23703955 ATTAATTTCTTAAAAATATTAA
1 ATTAAATTCTTAAAAATATTAA
23703977 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTAAATTCTTAAAAATATTAAT
Found at i:23704207 original size:26 final size:26
Alignment explanation
Indices: 23704178--23704229 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
23704168 AAACCAAACA
*
23704178 TTTCAAAAGTACTTCT-CAAAAGCAAT
1 TTTCAAAAGCACTT-TGCAAAAGCAAT
* *
23704204 TTTCCATAGCACTTTGCAAAAGCAAT
1 TTTCAAAAGCACTTTGCAAAAGCAAT
23704230 GCTAAACTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (26 bp):
TTTCAAAAGCACTTTGCAAAAGCAAT
Found at i:23707351 original size:16 final size:15
Alignment explanation
Indices: 23707332--23707365 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
23707322 AAAGTTGATA
*
23707332 ATAATTAATATATATT
1 ATAATAAATATA-ATT
23707348 ATAATAAATATAATT
1 ATAATAAATATAATT
23707363 ATA
1 ATA
23707366 TACTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:23715099 original size:10 final size:10
Alignment explanation
Indices: 23715080--23715127 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
23715070 GAATTTGTCA
*
23715080 AAAATAAATC
1 AAAATTAATC
23715090 AAAATTAATC
1 AAAATTAATC
*
23715100 AAAATTTAATAT
1 AAAA-TTAAT-C
*
23715112 AAAATTAATT
1 AAAATTAATC
23715122 AAAATT
1 AAAATT
23715128 CAACATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 20 0.59
11 10 0.29
12 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTAATC
Found at i:23718521 original size:47 final size:46
Alignment explanation
Indices: 23718453--23718541 Score: 133
Period size: 47 Copynumber: 1.9 Consensus size: 46
23718443 TTGTAATGGT
* *
23718453 ATGTCGTTGGGAGAGCTCAATCACAATATTATAGTGAAATGATTTG
1 ATGTCATTGGGAGAGCTCAATCACAATACTATAGTGAAATGATTTG
* *
23718499 ATGTCATTGGGGAGAGCTCAATCACAATGCTATAGTGGAATGA
1 ATGTCATT-GGGAGAGCTCAATCACAATACTATAGTGAAATGA
23718542 CTTGGTGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 7 0.18
47 31 0.82
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (46 bp):
ATGTCATTGGGAGAGCTCAATCACAATACTATAGTGAAATGATTTG
Found at i:23720048 original size:25 final size:25
Alignment explanation
Indices: 23720014--23720091 Score: 138
Period size: 25 Copynumber: 3.1 Consensus size: 25
23720004 TAGGACATAA
*
23720014 ATGTAATTTTTCCAAAAAAGATTCC
1 ATGTAATTTTTCCAAAAAGGATTCC
*
23720039 ATGTAATTTTTCTAAAAAGGATTCC
1 ATGTAATTTTTCCAAAAAGGATTCC
23720064 ATGTAATTTTTCCAAAAAGGATTCC
1 ATGTAATTTTTCCAAAAAGGATTCC
23720089 ATG
1 ATG
23720092 GCGAAGAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (25 bp):
ATGTAATTTTTCCAAAAAGGATTCC
Found at i:23729426 original size:26 final size:26
Alignment explanation
Indices: 23729397--23729454 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
23729387 AATTTTCTTG
*
23729397 AAATTTTATCGAGGGTAAAATTGTCA
1 AAATTTTACCGAGGGTAAAATTGTCA
* *
23729423 AAATTTTACCGTGTGTAAAATTGTCA
1 AAATTTTACCGAGGGTAAAATTGTCA
23729449 AAATTT
1 AAATTT
23729455 AACTGGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (26 bp):
AAATTTTACCGAGGGTAAAATTGTCA
Found at i:23729465 original size:25 final size:26
Alignment explanation
Indices: 23729409--23729470 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
23729399 ATTTTATCGA
*
23729409 GGGTAAAATTGTCAAAATTTTACCGT
1 GGGTAAAATTGTCAAAATTTAACCGT
* *
23729435 GTGTAAAATTGTCAAAATTTAACTG-
1 GGGTAAAATTGTCAAAATTTAACCGT
*
23729460 GGGTAACATTG
1 GGGTAAAATTG
23729471 GGGTGAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (26 bp):
GGGTAAAATTGTCAAAATTTAACCGT
Found at i:23744836 original size:27 final size:26
Alignment explanation
Indices: 23744784--23744842 Score: 109
Period size: 26 Copynumber: 2.2 Consensus size: 26
23744774 TATATATAAT
23744784 ATATATATTTGATTAAAAATAAAAAA
1 ATATATATTTGATTAAAAATAAAAAA
23744810 ATATATATTTGATTAAAAATTAAAAAA
1 ATATATATTTGATTAAAAA-TAAAAAA
23744837 ATATAT
1 ATATAT
23744843 TTAATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
ATATATATTTGATTAAAAATAAAAAA
Found at i:23755045 original size:10 final size:10
Alignment explanation
Indices: 23755032--23755265 Score: 102
Period size: 10 Copynumber: 23.4 Consensus size: 10
23755022 TCCTTCCCTC
23755032 TTCTTCTTCT
1 TTCTTCTTCT
* *
23755042 TTCTTTTTTT
1 TTCTTCTTCT
*
23755052 TCTCTTCTCCT
1 T-TCTTCTTCT
*
23755063 TTCCTT-TTTT
1 TT-CTTCTTCT
23755073 TTCCTTCTT-T
1 TT-CTTCTTCT
*
23755083 TTCTTTCTTTT
1 TTC-TTCTTCT
23755094 TTCTTC-TCAT
1 TTCTTCTTC-T
23755104 TTCCTT-TTCT
1 TT-CTTCTTCT
*
23755114 TTCCTCTT-T
1 TTCTTCTTCT
*
23755123 TTCTTTCTTTT
1 TTC-TTCTTCT
23755134 TTCTTC-TCAT
1 TTCTTCTTC-T
23755144 TTCCTT-TTCT
1 TT-CTTCTTCT
*
23755154 TTCCTCTT-T
1 TTCTTCTTCT
*
23755163 TTCTTTCTTTT
1 TTC-TTCTTCT
*
23755174 TTCTTCTCCT
1 TTCTTCTTCT
23755184 TTCCTT-TTCT
1 TT-CTTCTTCT
23755194 TTC--CTTCT
1 TTCTTCTTCT
23755202 TT-TTCTTTCT
1 TTCTTC-TTCT
* *
23755212 TTCCTCTCCT
1 TTCTTCTTCT
23755222 TTCCTT-TTCT
1 TT-CTTCTTCT
*
23755232 TTCTT-TTCC
1 TTCTTCTTCT
*
23755241 TTCAT-TTCT
1 TTCTTCTTCT
23755250 TTCTTTCTTTCT
1 TTC-TTC-TTCT
23755262 TTCT
1 TTCT
23755266 CTCTCCTTCT
Statistics
Matches: 173, Mismatches: 24, Indels: 53
0.69 0.10 0.21
Matches are distributed among these distances:
8 6 0.03
9 33 0.19
10 85 0.49
11 42 0.24
12 7 0.04
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:23755106 original size:17 final size:18
Alignment explanation
Indices: 23755089--23755191 Score: 57
Period size: 18 Copynumber: 5.3 Consensus size: 18
23755079 CTTTTTCTTT
23755089 CTTTTTTCTTCTCATTTC
1 CTTTTTTCTTCTCATTTC
* *
23755107 CTTTTCTT-TCCTCTTTTTC
1 CTTTT-TTCTTCTC-ATTTC
23755126 TTTCTTTTTTCTTCTCATTTC
1 ---CTTTTTTCTTCTCATTTC
* *
23755147 CTTTTCTT-TCCTCTTTTTC
1 CTTTT-TTCTTCTC-ATTTC
*
23755166 TTTCTTTTTTCTTCTCCTTTC
1 ---CTTTTTTCTTCTCATTTC
23755187 CTTTT
1 CTTTT
23755192 CTTTCCTTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 24
0.67 0.08 0.25
Matches are distributed among these distances:
18 23 0.35
19 12 0.18
21 12 0.18
22 18 0.28
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTTTTTCTTCTCATTTC
Found at i:23755133 original size:40 final size:41
Alignment explanation
Indices: 23755034--23755262 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 41
23755024 CTTCCCTCTT
*
23755034 CTTCTTCTTTCTTT-TTTTTCTCTTCTCCTTTCCTTTTTTTTC
1 CTTCTT-TTTCTTTCTTTTT-TCTTCTCCTTTCCTTTTCTTTC
*
23755076 CTTCTTTTTCTTTCTTTTTTCTTCTCATTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
*
23755117 C-TCTTTTTCTTTCTTTTTTCTTCTCATTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
23755157 C-TCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
*
23755197 CTTCTTTTTCTTTC---TTTCCTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
*
23755235 TTTTCCTTCATTTCTTTCTTTCTTTCTT
1 -CTT-CTT--TTTCTTTCTTT-TTTCTT
23755263 TCTCTCTCCT
Statistics
Matches: 171, Mismatches: 6, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
38 23 0.13
39 2 0.01
40 82 0.48
41 40 0.23
42 19 0.11
46 5 0.03
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (41 bp):
CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
Found at i:23755190 original size:5 final size:5
Alignment explanation
Indices: 23755180--23755242 Score: 58
Period size: 5 Copynumber: 13.0 Consensus size: 5
23755170 TTTTTTCTTC
* * * *
23755180 TCCTT TCCTT TTCTT TCC-T TCTTT TTCTT T-CTT TCCTC TCCTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
* *
23755228 TTCTT TCTTT TCCTT
1 TCCTT TCCTT TCCTT
23755243 CATTTCTTTC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 7 0.16
5 38 0.84
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TCCTT
Found at i:23755347 original size:27 final size:27
Alignment explanation
Indices: 23755317--23755380 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
23755307 CTGGTGCCAT
23755317 CAATGACTTTGGCACCATCGGTGTCGC
1 CAATGACTTTGGCACCATCGGTGTCGC
* * *
23755344 CAATCACTTTGGCACCTTTGGTGTCGC
1 CAATGACTTTGGCACCATCGGTGTCGC
23755371 CAATGACTTT
1 CAATGACTTT
23755381 CCCTCCACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (27 bp):
CAATGACTTTGGCACCATCGGTGTCGC
Found at i:23759253 original size:14 final size:14
Alignment explanation
Indices: 23759213--23759255 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
23759203 AAATAATATT
* *
23759213 AAAATTACTATATA
1 AAAATTAATAAATA
23759227 AAAATTCAATAAATA
1 AAAATT-AATAAATA
*
23759242 AAAATTATTAAATA
1 AAAATTAATAAATA
23759256 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATTAATAAATA
Found at i:23759266 original size:21 final size:22
Alignment explanation
Indices: 23759236--23759279 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
23759226 AAAAATTCAA
*
23759236 TAAATAAAAATTAT-TAAATAT
1 TAAATAAAAATAATATAAATAT
*
23759257 TAAATTAAAATAATATAAATAT
1 TAAATAAAAATAATATAAATAT
23759279 T
1 T
23759280 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATAAAAATAATATAAATAT
Found at i:23769396 original size:18 final size:18
Alignment explanation
Indices: 23769340--23769396 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
23769330 TGGCACCTCG
* *
23769340 GTTTTTACATATATCTCT
1 GTTTATACATATATCTGT
* *
23769358 GTGTATAGATATATCCATGT
1 GTTTATACATATAT-C-TGT
*
23769378 GTTTCTACATATATCTGT
1 GTTTATACATATATCTGT
23769396 G
1 G
23769397 CAATTATGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 15 0.50
19 2 0.07
20 13 0.43
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (18 bp):
GTTTATACATATATCTGT
Found at i:23775990 original size:18 final size:19
Alignment explanation
Indices: 23775969--23776012 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
23775959 TATTATTACT
23775969 TAATTTTTTAAAATGA-GG
1 TAATTTTTTAAAATGATGG
* * *
23775987 TAATATTTTAGAGTGATGG
1 TAATTTTTTAAAATGATGG
23776006 TAATTTT
1 TAATTTT
23776013 AAATTATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (19 bp):
TAATTTTTTAAAATGATGG
Found at i:23785866 original size:85 final size:85
Alignment explanation
Indices: 23785723--23785892 Score: 304
Period size: 85 Copynumber: 2.0 Consensus size: 85
23785713 TTAGAGTAGA
*
23785723 GGTTTAGGCTATTTCTAAATTCCCAAATAACGTAATGAATCATGTCTACAAGCAGCGATTCCAAA
1 GGTTTAGGCTATTTCTAAATTCCCAAATAACGCAATGAATCATGTCTACAAGCAGCGATTCCAAA
*
23785788 CAGTCACCAATTACTTTCGC
66 CACTCACCAATTACTTTCGC
* *
23785808 GGTTTAGGCTATTTCTAAATTCTCAAATAACGCATTGAATCATGTCTACAAGCAGCGATTCCAAA
1 GGTTTAGGCTATTTCTAAATTCCCAAATAACGCAATGAATCATGTCTACAAGCAGCGATTCCAAA
23785873 CACTCACCAATTACTTTCGC
66 CACTCACCAATTACTTTCGC
23785893 CTAGACTCCG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (85 bp):
GGTTTAGGCTATTTCTAAATTCCCAAATAACGCAATGAATCATGTCTACAAGCAGCGATTCCAAA
CACTCACCAATTACTTTCGC
Found at i:23794098 original size:89 final size:89
Alignment explanation
Indices: 23793027--23794098 Score: 1566
Period size: 89 Copynumber: 12.1 Consensus size: 89
23793017 AAATCCGCCA
* * *
23793027 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
23793092 AGTACATGAAGACAAGATCTGCTT
66 AGTACATGAAGACAAGATCTGCTT
* * * * *
23793116 TCTTCGAACTGCTTCACCACCAGTATGGGAAGGCAAGATATGTTATCTTTGATCTACTCCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
23793181 AGTACATGAAGACAAGATCTGCTT
66 AGTACATGAAGACAAGATCTGCTT
** * * * *
23793205 TCTCCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACACC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
23793270 AGTACATGAAGACAAGATCTGCTT
66 AGTACATGAAGACAAGATCTGCTT
* * * * *
23793294 TCTTTGACCTGCTTCGCCACCAGTATGGGAATGCAAGATCTATTATCTCTGATCTATTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
23793359 AGTACATGAAGACAAGATCTGCTT
66 AGTACATGAAGACAAGATCTGCTT
* * *
23793383 TCTTTGACCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
23793448 AGTACATGAAGACAAGATCTGCTT
66 AGTACATGAAGACAAGATCTGCTT
* * *
23793472 TCTTTGACCTGCTTCACCACCAGTATGGGAAGGCGAAG-TCTGTTATCTCTGATCTACTTCACGC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGC-AAGATCTGTTATCTTTGATCTACTTCACGC
**
23793536 CAGTACATGAAGACAAGATCTATTT
65 CAGTACATGAAGACAAGATCTGCTT
* * *
23793561 TCTTTGATCCGCTTTGCCACTAGTATGGGAAGGCAAGATCTGTTATCTCTT-ATCTACTTCACGC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCT-TTGATCTACTTCACGC
*
23793625 CAGTACATGAAGACAAGATTTGCTT
65 CAGTACATGAAGACAAGATCTGCTT
* *
23793650 TCTTTGATCTG-TCTCGCCACTAGTATGGGAA-G--A-CTCTGTTATCTTTGATCTACTTCACGC
1 TCTTTGATCTGCT-TCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGC
23793710 CAGTACATGAAGACAAGATCTGCTT
65 CAGTACATGAAGACAAGATCTGCTT
* * * * *
23793735 TCTTCGATCTGTTTCGCCACCAATATGGGAAGACAAGATCTGTTACCTTTGATCTACTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
*
23793800 AGTACATGAAGACAAGATCTGTTTTT
66 AGTACATGAAGACAAGATCTG--CTT
* * *
23793826 TCCTTCGATCTACTTCGCCACCAGTATGGGAAGGCGAGATCTGTTATCTTTGATCTACTTCACGC
1 T-CTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGC
*
23793891 CAGTACATGAAGACAAGATCTGTTT
65 CAGTACATGAAGACAAGATCTGCTT
* * *
23793916 TCTTCGATCCGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
*
23793981 AGTACATGAAGACAAGATCTACTT
66 AGTACATGAAGACAAGATCTGCTT
* * *
23794005 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCAAGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
*
23794070 AGTACATGAAAACAAGATCTG-TT
66 AGTACATGAAGACAAGATCTGCTT
23794093 ATCTTT
1 -TCTTT
23794099 CCACCTGCTC
Statistics
Matches: 893, Mismatches: 76, Indels: 28
0.90 0.08 0.03
Matches are distributed among these distances:
84 2 0.00
85 73 0.08
86 2 0.00
88 8 0.01
89 718 0.80
90 8 0.01
91 3 0.00
92 79 0.09
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (89 bp):
TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCC
AGTACATGAAGACAAGATCTGCTT
Found at i:23815898 original size:3 final size:3
Alignment explanation
Indices: 23815890--23815949 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
23815880 GTAAACAATG
* * *
23815890 TAA TAA TAA TGA T-A TAA TGA TAAA TAAA TAAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA T-AA T-AA TAA TAA TAA TAA TAA
*
23815937 TGA TAA TAA TAA T
1 TAA TAA TAA TAA T
23815950 GGACTAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 36 0.75
4 10 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23815942 original size:18 final size:18
Alignment explanation
Indices: 23815886--23815950 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
23815876 GATAGTAAAC
23815886 AATG-TAATAATAATGATAT
1 AATGATAATAATAATG--AT
23815905 AATGAT-A-AATAA--AT
1 AATGATAATAATAATGAT
23815919 AA--ATAATAATAATGAT
1 AATGATAATAATAATGAT
23815935 AATGATAATAATAATG
1 AATGATAATAATAATG
23815951 GACTAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
12 2 0.05
13 1 0.03
14 9 0.23
16 4 0.10
18 17 0.44
19 5 0.13
20 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (18 bp):
AATGATAATAATAATGAT
Found at i:23817057 original size:16 final size:16
Alignment explanation
Indices: 23817032--23817062 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23817022 TTTAAGTGAA
23817032 TTGAAATACTATATGT
1 TTGAAATACTATATGT
*
23817048 TTGAATTACTATATG
1 TTGAAATACTATATG
23817063 ATATGGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (16 bp):
TTGAAATACTATATGT
Found at i:23820236 original size:24 final size:24
Alignment explanation
Indices: 23820209--23820256 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
23820199 TTTAATGTTC
*
23820209 AATTTGATA-TATGTGTTTTTTTTT
1 AATTTGATACT-TGAGTTTTTTTTT
*
23820233 AATTTGGTACTTGAGTTTTTTTTT
1 AATTTGATACTTGAGTTTTTTTTT
23820257 CTCAATTAAG
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:0.19, C:0.02, G:0.15, T:0.65
Consensus pattern (24 bp):
AATTTGATACTTGAGTTTTTTTTT
Found at i:23823680 original size:12 final size:12
Alignment explanation
Indices: 23823663--23823688 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23823653 TGATAAGTGA
23823663 TTCTATTTTCTT
1 TTCTATTTTCTT
23823675 TTCTATTTTCTT
1 TTCTATTTTCTT
23823687 TT
1 TT
23823689 GTGTGTTTTA
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:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTATTTTCTT
Found at i:23824788 original size:63 final size:63
Alignment explanation
Indices: 23824689--23824817 Score: 215
Period size: 63 Copynumber: 2.0 Consensus size: 63
23824679 CAACCTGATT
*
23824689 TATAACTTAAATTTTGTAATTCAAAATCTATTAAGATGCGCCTCATT-CTCGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAAATCTATTAAGATGCGCCTCATTCCT-GATGTGATAAGAA
* *
23824752 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGTGCCTCATTCCTGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAAATCTATTAAGATGCGCCTCATTCCTGATGTGATAAGAA
23824815 TAT
1 TAT
23824818 CTCTTTGTGA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 60 0.97
64 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (63 bp):
TATAACTTAAATTTGGTAATTCAAAATCTATTAAGATGCGCCTCATTCCTGATGTGATAAGAA
Found at i:23825746 original size:35 final size:34
Alignment explanation
Indices: 23825692--23825764 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 34
23825682 AGACCAAGAG
* *
23825692 GATTGAAGGCCAGGGGAGTATGGAAAGTGATTTA
1 GATTGAAGACCAGGGGAGTATGGAAAGTGATTCA
23825726 GATTGAAGACCATGGGGAGTATGGAAAGTGATTCA
1 GATTGAAGACCA-GGGGAGTATGGAAAGTGATTCA
23825761 GATT
1 GATT
23825765 CAGATTGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 11 0.31
35 25 0.69
ACGTcount: A:0.33, C:0.07, G:0.36, T:0.25
Consensus pattern (34 bp):
GATTGAAGACCAGGGGAGTATGGAAAGTGATTCA
Found at i:23828735 original size:16 final size:17
Alignment explanation
Indices: 23828703--23828736 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23828693 TAATAGTGGT
*
23828703 TTGAAATGTTAACTTAA
1 TTGAAATATTAACTTAA
23828720 TTGAAATATT-ACTTAA
1 TTGAAATATTAACTTAA
23828736 T
1 T
23828737 GACTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (17 bp):
TTGAAATATTAACTTAA
Found at i:23836389 original size:35 final size:35
Alignment explanation
Indices: 23836303--23836391 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
23836293 AGTACATCGA
* *
23836303 TAATCCAACCATAACACGCCAGATGCTCATACGAGC
1 TAATCCAACCA-AACACGCCAGATGCTCAAAAGAGC
* **
23836339 CAATCCCTCCAAAACACGCCA-ATGCTCAAAAGAGC
1 TAATCCAACC-AAACACGCCAGATGCTCAAAAGAGC
23836374 TAATCCAACCGAAACACG
1 TAATCCAACC-AAACACG
23836392 TCAAACAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
35 26 0.60
36 16 0.37
37 1 0.02
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.13
Consensus pattern (35 bp):
TAATCCAACCAAACACGCCAGATGCTCAAAAGAGC
Found at i:23839006 original size:17 final size:19
Alignment explanation
Indices: 23838984--23839020 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
23838974 TTTAGGGAAT
23838984 AAATT-GAATAAAAT-ACA
1 AAATTGGAATAAAATGACA
*
23839001 AAATTGGTATAAAATGACA
1 AAATTGGAATAAAATGACA
23839020 A
1 A
23839021 TTGACTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.24
Consensus pattern (19 bp):
AAATTGGAATAAAATGACA
Found at i:23844740 original size:20 final size:19
Alignment explanation
Indices: 23844717--23844821 Score: 84
Period size: 20 Copynumber: 5.3 Consensus size: 19
23844707 TAAGTGCGTT
23844717 CAGGGGTACTGAAGTACAAA
1 CAGGGGTAC-GAAGTACAAA
* * ** *
23844737 CAGGGGCACGTATGTGTAAT
1 CAGGGGTACG-AAGTACAAA
23844757 CAGGGGTACGAAGTACAAA
1 CAGGGGTACGAAGTACAAA
* * * *
23844776 CAGGGGCACGTATGTGCAAT
1 CAGGGGTACG-AAGTACAAA
23844796 CAGGGGTACCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
*
23844816 TAGGGG
1 CAGGGG
23844822 CATGTATGTG
Statistics
Matches: 63, Mismatches: 19, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
19 15 0.24
20 46 0.73
21 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.34, T:0.16
Consensus pattern (19 bp):
CAGGGGTACGAAGTACAAA
Found at i:23844829 original size:79 final size:81
Alignment explanation
Indices: 23844697--23844876 Score: 247
Period size: 79 Copynumber: 2.2 Consensus size: 81
23844687 AGAGTATAAT
* * ** * * *
23844697 CAGGGGCACTTAAGTGCGTTCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGTAA-TCAGG
1 CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAAG
23844761 GGTAC-GAAGTACAAA
66 GGTACTGAAGTACAAA
* *
23844776 CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATAGGGGCATGTATGTGCAATTCAAG
1 CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAAG
23844841 GGTACTGAAGTACAAA
66 GGTACTGAAGTACAAA
* *
23844857 TAGGGACACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
23844877 TCATGCAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 51 0.58
80 9 0.10
81 28 0.32
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (81 bp):
CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAAG
GGTACTGAAGTACAAA
Found at i:23844856 original size:41 final size:41
Alignment explanation
Indices: 23844697--23844879 Score: 248
Period size: 40 Copynumber: 4.6 Consensus size: 41
23844687 AGAGTATAAT
* * *
23844697 CAGGGGCACTTAAGTGC-GTTCAGGGGTACTGAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
*
23844737 CAGGGGCACGTATGTGTAA-TCAGGGGTAC-GAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
*
23844776 CAGGGGCACGTATGTGCAA-TCAGGGGTACCGAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
* * *
23844816 TAGGGGCATGTATGTGCAATTCAAGGGTACTGAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
* *
23844857 TAGGGACACGTATGTGCAATTCA
1 CAGGGGCACGTATGTGCAATTCA
23844880 TGCAATAATT
Statistics
Matches: 129, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 38 0.29
40 51 0.40
41 40 0.31
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.20
Consensus pattern (41 bp):
CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
Found at i:23847702 original size:34 final size:34
Alignment explanation
Indices: 23847613--23847729 Score: 101
Period size: 34 Copynumber: 3.4 Consensus size: 34
23847603 TTCTGATCTT
* * * * * * *
23847613 ATATGAAATTCTAATCTGACATATGCTTCTAGAA
1 ATATGAAATTTTGATCTGATATATGTTTTTGGTA
* * * *
23847647 ATATGACATTCTAATCCGATATATGTTTTTGG-A
1 ATATGAAATTTTGATCTGATATATGTTTTTGGTA
**
23847680 ATTATGGCATTTTGATCTGATATATGTTTTTGGTA
1 A-TATGAAATTTTGATCTGATATATGTTTTTGGTA
23847715 ATATGAAATTTTGAT
1 ATATGAAATTTTGAT
23847730 ATTATATTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 2 0.03
34 65 0.94
35 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (34 bp):
ATATGAAATTTTGATCTGATATATGTTTTTGGTA
Found at i:23850590 original size:17 final size:17
Alignment explanation
Indices: 23850568--23850600 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
23850558 CCATCACATT
23850568 AAAGGCACATAAATGTG
1 AAAGGCACATAAATGTG
23850585 AAAGGCACATAAATGT
1 AAAGGCACATAAATGT
23850601 AAGACCCGAA
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:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
AAAGGCACATAAATGTG
Found at i:23852288 original size:20 final size:20
Alignment explanation
Indices: 23852221--23852287 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
23852211 ATATTAAATA
*
23852221 TTTAAAATAAAGAATAACAT
1 TTTAAAATAAAGATTAACAT
* * * * *
23852241 TATAAAAGTAAAAATAAAGAA
1 TTTAAAA-TAAAGATTAACAT
23852262 TTTAAATATAAAGATTAA-AT
1 TTTAAA-ATAAAGATTAACAT
23852282 TTTAAA
1 TTTAAA
23852288 TTTAAATATA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
20 13 0.37
21 21 0.60
22 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (20 bp):
TTTAAAATAAAGATTAACAT
Found at i:23856218 original size:3 final size:3
Alignment explanation
Indices: 23856210--23856252 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
23856200 CTATCTTGTC
23856210 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
23856253 AACTACTCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:23856922 original size:30 final size:30
Alignment explanation
Indices: 23856862--23856931 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
23856852 TTAAATTATT
* ** *
23856862 AATGATAAAATTGTACTTTAATTTTTTAAA
1 AATGATAAAATTGTAATTTAATCCTCTAAA
*
23856892 AATGATAAAATTTTAATTTAATCCTCTAAA
1 AATGATAAAATTGTAATTTAATCCTCTAAA
* *
23856922 AGTTATAAAA
1 AATGATAAAA
23856932 ATTAATATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (30 bp):
AATGATAAAATTGTAATTTAATCCTCTAAA
Found at i:23856946 original size:25 final size:23
Alignment explanation
Indices: 23856918--23856983 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
23856908 TTTAATCCTC
23856918 TAAAAGTTATAAAAATTAATATTAT
1 TAAAA-TTATAAAAATT-ATATTAT
* *
23856943 TAAAATAAT-AAAATTATATTTT
1 TAAAATTATAAAAATTATATTAT
**
23856965 TATTATTATAAAAA-TATAT
1 TAAAATTATAAAAATTATAT
23856984 CATTTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 17 0.49
23 10 0.29
24 3 0.09
25 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAAATTATAAAAATTATATTAT
Found at i:23858472 original size:20 final size:21
Alignment explanation
Indices: 23858447--23858486 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
23858437 AAAAAAAGGA
*
23858447 ATTACACTTGAAATA-AAAAT
1 ATTACACTTCAAATATAAAAT
*
23858467 ATTACATTTCAAATATAAAA
1 ATTACACTTCAAATATAAAA
23858487 AATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
ATTACACTTCAAATATAAAAT
Found at i:23860700 original size:33 final size:33
Alignment explanation
Indices: 23860658--23860725 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
23860648 CAACCGAAGT
23860658 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
1 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
23860691 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
1 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
23860724 TA
1 TA
23860726 ACATTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.13
Consensus pattern (33 bp):
TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
Found at i:23867091 original size:35 final size:30
Alignment explanation
Indices: 23867052--23867125 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 30
23867042 TAATTTTAAT
23867052 AATTAAATTTACATTATTAAATCAAAAAATAGAAA-
1 AATTAAATTTAC-TTA--AAAT--AAAAATA-AAAG
23867087 AATTAAA-TTACTTAAAATAAAAATAAAAG
1 AATTAAATTTACTTAAAATAAAAATAAAAG
23867116 AATTAAATTT
1 AATTAAATTT
23867126 CAAATATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
28 3 0.08
29 14 0.38
30 2 0.05
31 4 0.11
33 3 0.08
34 4 0.11
35 7 0.19
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (30 bp):
AATTAAATTTACTTAAAATAAAAATAAAAG
Found at i:23867138 original size:29 final size:28
Alignment explanation
Indices: 23867076--23867138 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
23867066 TATTAAATCA
*
23867076 AAAAATAGAAAAATTAAATTACTTAAAAT
1 AAAAATAGAAAAATTAAATTA-TCAAAAT
23867105 AAAAATA-AAAGAATTAAATT-TCAAATAT
1 AAAAATAGAAA-AATTAAATTATCAAA-AT
23867133 ACAAAA
1 A-AAAA
23867139 AAGTGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.13
28 6 0.20
29 20 0.67
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAAATAGAAAAATTAAATTATCAAAAT
Found at i:23868679 original size:28 final size:27
Alignment explanation
Indices: 23868621--23868679 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
23868611 GATTTCGCGG
23868621 AAAATGGCCCATTCCGGTAAATAATTAA
1 AAAATGGCCCATTCCGGTAAAT-ATTAA
* *
23868649 AAAAGTGGCCTATTTCGGTAAAT-TTAA
1 AAAA-TGGCCCATTCCGGTAAATATTAA
23868676 AAAA
1 AAAA
23868680 AAGGGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 4 0.14
29 16 0.57
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (27 bp):
AAAATGGCCCATTCCGGTAAATATTAA
Found at i:23869973 original size:63 final size:63
Alignment explanation
Indices: 23869872--23870000 Score: 150
Period size: 63 Copynumber: 2.0 Consensus size: 63
23869862 TCACAAGTAT
* * * * * * **
23869872 CATAGCATGCACACTCATTCCCCGCATCATCACCTTCAGCTTTGGTTTATTTTACAAAACCAC
1 CATAGCACGCACAATCATTCCCCACATCAACACATTCAGCATAAGTTTATTTTACAAAACCAC
* * * *
23869935 CATAGCACGCACAATTATTCCCTACATCAACACATTCAGCATAAGTTTATTTTACACAAGCAC
1 CATAGCACGCACAATCATTCCCCACATCAACACATTCAGCATAAGTTTATTTTACAAAACCAC
23869998 CAT
1 CAT
23870001 CGTACATGCA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.29
Consensus pattern (63 bp):
CATAGCACGCACAATCATTCCCCACATCAACACATTCAGCATAAGTTTATTTTACAAAACCAC
Found at i:23874136 original size:17 final size:17
Alignment explanation
Indices: 23874114--23874147 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23874104 AAATTAAAAC
23874114 TTAAATCATAATTACCT
1 TTAAATCATAATTACCT
**
23874131 TTAAATTTTAATTACCT
1 TTAAATCATAATTACCT
23874148 ACCAATAACT
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:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATCATAATTACCT
Found at i:23877648 original size:17 final size:18
Alignment explanation
Indices: 23877616--23877652 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
23877606 TGAAATTTAT
*
23877616 CAAGTTTTATTTTAAAAA
1 CAAGTTTTAGTTTAAAAA
23877634 CAAGTTTT-GTTTAAAAA
1 CAAGTTTTAGTTTAAAAA
23877651 CA
1 CA
23877653 TTATATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (18 bp):
CAAGTTTTAGTTTAAAAA
Found at i:23879664 original size:20 final size:20
Alignment explanation
Indices: 23879635--23879744 Score: 86
Period size: 20 Copynumber: 5.5 Consensus size: 20
23879625 AAATTCGAAG
* *
23879635 GTATCGATACTTTTAGTGAA
1 GTATCAATACTTTTAGTAAA
* *
23879655 GTATCAATAC-TTTACCTTAA
1 GTATCAATACTTTTA-GTAAA
*
23879675 GTATCAATA-TTTT-TTAAAA
1 GTATCAATACTTTTAGT-AAA
* *
23879694 CTATCAATAC-TTTAGCTTAA
1 GTATCAATACTTTTAG-TAAA
23879714 GTATCAATACTTTT-GTTAAA
1 GTATCAATACTTTTAG-TAAA
23879734 GTATCAATACT
1 GTATCAATACT
23879745 GCAATGCCCA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
18 1 0.01
19 17 0.24
20 50 0.69
21 4 0.06
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (20 bp):
GTATCAATACTTTTAGTAAA
Found at i:23879699 original size:39 final size:40
Alignment explanation
Indices: 23879656--23879744 Score: 137
Period size: 39 Copynumber: 2.2 Consensus size: 40
23879646 TTTAGTGAAG
23879656 TATCAATACTTTACCTTAAGTATCAATA-TTTT-TTAAAAC
1 TATCAATACTTTACCTTAAGTATCAATACTTTTGTT-AAAC
* *
23879695 TATCAATACTTTAGCTTAAGTATCAATACTTTTGTTAAAG
1 TATCAATACTTTACCTTAAGTATCAATACTTTTGTTAAAC
23879735 TATCAATACT
1 TATCAATACT
23879745 GCAATGCCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 27 0.59
40 17 0.37
41 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (40 bp):
TATCAATACTTTACCTTAAGTATCAATACTTTTGTTAAAC
Found at i:23887832 original size:68 final size:71
Alignment explanation
Indices: 23887690--23887834 Score: 156
Period size: 68 Copynumber: 2.1 Consensus size: 71
23887680 TATTAAATCT
* * *
23887690 TATTAAATTAATAAAATATTTTTCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAATTAATAAAATATCTATCTA-AAGATAAACATTAAATTAAATTTAATATTAAGATAATA
**
23887755 AGTTGAA
65 AAATGAA
** *
23887762 TATTAAATTAATAAAATA-CTAT-T-AAGATAAGTATTAAATTAAATTTAATGTTAA-ATATATT
1 TATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATATTAAGATA-A-T
23887823 AAAAT-AA
64 AAAATGAA
23887830 TATTA
1 TATTA
23887835 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
67 3 0.05
68 36 0.57
69 3 0.05
70 1 0.02
71 2 0.03
72 18 0.29
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (71 bp):
TATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATATTAAGATAATAA
AATGAA
Found at i:23888236 original size:19 final size:19
Alignment explanation
Indices: 23888212--23888254 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
23888202 AAAACATCAT
* *
23888212 ATTAATTTTAATTAATTTG
1 ATTAATTTAAATTAACTTG
*
23888231 ATTAATTTAAATTTACTTG
1 ATTAATTTAAATTAACTTG
23888250 ATTAA
1 ATTAA
23888255 AATTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTAATTTAAATTAACTTG
Found at i:23889753 original size:22 final size:22
Alignment explanation
Indices: 23889726--23889792 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 22
23889716 CGAATAAACT
**
23889726 GAGAGCAAAAATGTGCTAATCA
1 GAGAGCACTAATGTGCTAATCA
*
23889748 GAGAGCACTAACGTGCTAATAGTCA
1 GAGAGCACTAATGTGCT-A-A-TCA
23889773 GAGAGCACTAATGTGCTAAT
1 GAGAGCACTAATGTGCTAAT
23889793 AATCAGAGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 15 0.39
23 2 0.05
24 2 0.05
25 19 0.50
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (22 bp):
GAGAGCACTAATGTGCTAATCA
Found at i:23889777 original size:25 final size:25
Alignment explanation
Indices: 23889742--23889800 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
23889732 AAAAATGTGC
23889742 TAATCAGAGAGCACTAACGTGCTAA
1 TAATCAGAGAGCACTAACGTGCTAA
* *
23889767 TAGTCAGAGAGCACTAATGTGCTAA
1 TAATCAGAGAGCACTAACGTGCTAA
23889792 TAATCAGAG
1 TAATCAGAG
23889801 CACGCGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (25 bp):
TAATCAGAGAGCACTAACGTGCTAA
Found at i:23896692 original size:12 final size:11
Alignment explanation
Indices: 23896677--23896792 Score: 74
Period size: 12 Copynumber: 9.5 Consensus size: 11
23896667 CAATTTCACA
23896677 AAAAAAAGAAAG
1 AAAAAAA-AAAG
23896689 AAAAGAAAAAAG
1 AAAA-AAAAAAG
23896701 AAAAAAAAACA-
1 AAAAAAAAA-AG
*
23896712 AAAGAAAAAAG
1 AAAAAAAAAAG
23896723 AAAAATCAAAGTCAA-
1 AAAAA--AAA---AAG
23896738 AATACAAAAAAATG
1 AA-A-AAAAAAA-G
23896752 AAAATAAAAAAG
1 AAAA-AAAAAAG
*
23896764 AAAAAGAAAAG
1 AAAAAAAAAAG
23896775 AAAAAGAAAAAAG
1 -AAAA-AAAAAAG
23896788 AAAAA
1 AAAAA
23896793 GGAGAGGCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 31
0.71 0.03 0.26
Matches are distributed among these distances:
10 1 0.01
11 24 0.28
12 29 0.34
13 19 0.22
14 2 0.02
15 5 0.06
16 3 0.04
17 2 0.02
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.04
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:23896694 original size:9 final size:8
Alignment explanation
Indices: 23896677--23896792 Score: 67
Period size: 9 Copynumber: 13.6 Consensus size: 8
23896667 CAATTTCACA
23896677 AAAAAAAG
1 AAAAAAAG
23896685 AAAGAAAAG
1 AAA-AAAAG
23896694 -AAAAAAG
1 AAAAAAAG
23896701 AAAAAAA-
1 AAAAAAAG
*
23896708 AACAAAAG
1 AAAAAAAG
23896716 -AAAAAAG
1 AAAAAAAG
23896723 AAAAATCAAAG
1 -AAAA--AAAG
* * *
23896734 TCAAAATAC
1 -AAAAAAAG
23896743 AAAAAAATG
1 AAAAAAA-G
*
23896752 AAAATAAAA
1 AAAA-AAAG
23896761 AAGAAAAAG
1 AA-AAAAAG
*
23896770 AAAAGAAAA
1 AAAA-AAAG
23896779 AGAAAAAAG
1 A-AAAAAAG
23896788 AAAAA
1 AAAAA
23896793 GGAGAGGCCA
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
7 17 0.20
8 22 0.27
9 29 0.35
10 8 0.10
11 7 0.08
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:23896701 original size:7 final size:7
Alignment explanation
Indices: 23896678--23896727 Score: 64
Period size: 7 Copynumber: 6.7 Consensus size: 7
23896668 AATTTCACAA
23896678 AAAAAAG
1 AAAAAAG
23896685 AAAGAAAAG
1 -AA-AAAAG
23896694 AAAAAAG
1 AAAAAAG
*
23896701 AAAAAAA
1 AAAAAAG
23896708 AACAAAAG
1 AA-AAAAG
23896716 AAAAAAG
1 AAAAAAG
23896723 AAAAA
1 AAAAA
23896728 TCAAAGTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
7 23 0.61
8 10 0.26
9 5 0.13
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:23896767 original size:5 final size:6
Alignment explanation
Indices: 23896745--23896793 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
23896735 CAAAATACAA
23896745 AAAAATG AAAATA- AAAAAG AAAAAG -AAAAG AAAAAG AAAAAAG AAAAAG
1 AAAAA-G AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG
23896794 GAGAGGCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 6 0.16
6 21 0.55
7 10 0.26
8 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:23897630 original size:60 final size:57
Alignment explanation
Indices: 23897557--23897667 Score: 177
Period size: 60 Copynumber: 1.9 Consensus size: 57
23897547 GACAAGGGAT
* *
23897557 CAAGGTGAAAACCCGCAAAGGGCGCTTTGATTCCTAAAAATAATAATAATAAAAAAAGAC
1 CAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCC-AAAAA-AATAA-AATAAAAAAAGAC
23897617 CAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCCAAAAAAATAAAATAAAA
1 CAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCCAAAAAAATAAAATAAAA
23897668 TAAATAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
57 7 0.14
58 5 0.10
59 5 0.10
60 32 0.65
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.16
Consensus pattern (57 bp):
CAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCCAAAAAAATAAAATAAAAAAAGAC
Found at i:23899192 original size:131 final size:132
Alignment explanation
Indices: 23899024--23899309 Score: 416
Period size: 131 Copynumber: 2.2 Consensus size: 132
23899014 AATAACAGAT
* **
23899024 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGG
* * *
23899089 GAAGCAAATTTAAGCCATTTGTCCTATCTCCCTGGACAGCAGGGGAATAGGTGGAAGATTGT-AA
66 GAAGCAAATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAGATTGTGAA
23899153 GC
131 GC
*
23899155 CTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGG
* * * * *
23899220 GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAATAGTGGAATAGGTTGAAGGTTGTGAA
66 GAAGCAAATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAGATTGTGAA
*
23899285 TC
131 GC
*
23899287 C-TATCTCCCT-GGTCAGTAGTGGA
1 CTTATCTCCCTAAG-CAGTAGTGGA
23899310 ATAGGTTGAA
Statistics
Matches: 138, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
130 1 0.01
131 133 0.96
132 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (132 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGG
GAAGCAAATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAGATTGTGAA
GC
Found at i:23899336 original size:44 final size:43
Alignment explanation
Indices: 23899241--23899353 Score: 127
Period size: 44 Copynumber: 2.6 Consensus size: 43
23899231 AAGCCACTAG
* ** ***
23899241 TCCTATCTCCCTGGACAATAGTGGAATAGGTTGAAGGTTGTGAA
1 TCCTATCTCCCTGG-CAGTAGTGGAATAGGTTGAAAATTACAAA
23899285 TCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAAATTACAAA
1 TCCTATCTCCCTGG-CAGTAGTGGAATAGGTTGAAAATTACAAA
* *
23899329 TCTTATCTCCCTAAGCAGTAGTGGA
1 TCCTATCTCCCT-GGCAGTAGTGGA
23899354 GCAGATCGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 58 0.98
45 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (43 bp):
TCCTATCTCCCTGGCAGTAGTGGAATAGGTTGAAAATTACAAA
Found at i:23899701 original size:44 final size:44
Alignment explanation
Indices: 23899653--23900052 Score: 150
Period size: 44 Copynumber: 9.1 Consensus size: 44
23899643 CTTGGTCAGC
*
23899653 AGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAAT
1 AGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAGT
** * * ** *
23899697 AGTGGAGCAGATCGAAGAA-GGCAAATCTTATCTTCCCT-AGGAGT
1 AGTGGAATAGGTTGAA-AATTACAAATCTTATC-TCCCTAAGCAGT
* * * * * * * * * **
23899741 AG-GGAAGCAGATT-TAAGTCACTAGTCCTATCTCCCT-GGACAAC
1 AGTGGAA-TAGGTTGAAAATTACAAATCTTATCTCCCTAAG-CAGT
* * * ** **
23899784 AGGGGAATAGGTGGAAGATTGTAAGCCTTATCTCCCTAAGCAGT
1 AGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAGT
* * *
23899828 AGTGGAGTAGGTTGAAAATTACAGATCTTATATCCCTAAGCAGT
1 AGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAGT
** * * ***** * * *
23899872 AGTGGAGCAGATTGAAGACGGTGAATCTTATTTTCCC-CAGAAGT
1 AGTGGAATAGGTTGAAAATTACAAATCTTA-TCTCCCTAAGCAGT
* * *** * * * ** *
23899916 AG-GGAAGCAGGTT-TAAGCCACTAGTCCTATCTCCCTGGGCAGC
1 AGTGGAA-TAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAGT
* ** ** *
23899959 AGTGGAATAGGTTGAAGATTGTAAGCCTTACCTCCCTAAGCAGT
1 AGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAGT
* *
23900003 AGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAGT
23900047 AGTGGA
1 AGTGGA
23900053 GCAGATAAAA
Statistics
Matches: 246, Mismatches: 97, Indels: 26
0.67 0.26 0.07
Matches are distributed among these distances:
42 12 0.05
43 38 0.15
44 183 0.74
45 13 0.05
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (44 bp):
AGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAGT
Found at i:23899873 original size:131 final size:131
Alignment explanation
Indices: 23899634--23899884 Score: 283
Period size: 131 Copynumber: 1.9 Consensus size: 131
23899624 AGGTTGTGAA
* * * * * *
23899634 TCCTATCTCCTTGGTCAGCAGTGGAATAGGTTGAAAATTACAAATCTTATCTCCCTAAGCAATAG
1 TCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAAATTACAAACCTTATCTCCCTAAGCAATAG
* * *
23899699 TGGAGCAGATCGAAGAAGGCAAATCTTATCTTCCCTAGGAGTAG-GGAAGCAGATTTAAGTCACT
66 TGGAGCAGATCGAAGAAGACAAATCTTATCATCCCTAGCAGTAGTGG-AGCAGATTTAAGTCACT
23899763 AG
130 AG
* ** * *
23899765 TCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAGATTGTAAGCCTTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAAATTACAAACCTTATCTCCCTAAGCAATAG
* * * * *
23899830 TGGAGTAGGTTGAA-AATTACAGATCTTAT-ATCCCTAAGCAGTAGTGGAGCAGATT
66 TGGAGCAGATCGAAGAA-GACAAATCTTATCATCCCT-AGCAGTAGTGGAGCAGATT
23899885 GAAGACGGTG
Statistics
Matches: 98, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
130 7 0.07
131 89 0.91
132 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (131 bp):
TCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAAATTACAAACCTTATCTCCCTAAGCAATAG
TGGAGCAGATCGAAGAAGACAAATCTTATCATCCCTAGCAGTAGTGGAGCAGATTTAAGTCACTA
G
Found at i:23900053 original size:44 final size:44
Alignment explanation
Indices: 23899810--23900053 Score: 171
Period size: 44 Copynumber: 5.6 Consensus size: 44
23899800 GATTGTAAGC
23899810 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
* * * ** *
23899854 CTTATATCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGT-GA-AT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAA-A-ATTACAGAT
* * * * * ***
23899898 CTTATTTTCCC-CAGAAGTAG-GGAAGCAGGTT-TAAGCCACTAG-T
1 CTTA-TCTCCCTAAGCAGTAGTGG-AGTAGGTTGAAAATTAC-AGAT
* ** * * * *
23899941 CCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAAGATTGTA-AG-C
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAA-AAT-TACAGAT
*
23899985 CTTACCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
23900029 CTTATCTCCCTAAGCAGTAGTGGAG
1 CTTATCTCCCTAAGCAGTAGTGGAG
23900054 CAGATAAAAA
Statistics
Matches: 150, Mismatches: 36, Indels: 28
0.70 0.17 0.13
Matches are distributed among these distances:
41 1 0.01
42 8 0.05
43 23 0.15
44 108 0.72
45 8 0.05
46 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
Found at i:23900075 original size:44 final size:44
Alignment explanation
Indices: 23899985--23900067 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
23899975 GATTGTAAGC
* * *
23899985 CTTACCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTACCTCCCTAAGCAGTAGTGGAGCAGGATGAAAATAACAGAT
*
23900029 CTTATCTCCCTAAGCAGTAGTGGAGCA-GAT-AAAA-AACAG
1 CTTACCTCCCTAAGCAGTAGTGGAGCAGGATGAAAATAACAG
23900068 TGAATCTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 4 0.11
42 4 0.11
43 2 0.06
44 25 0.71
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (44 bp):
CTTACCTCCCTAAGCAGTAGTGGAGCAGGATGAAAATAACAGAT
Found at i:23900075 original size:175 final size:175
Alignment explanation
Indices: 23899155--23900058 Score: 1341
Period size: 175 Copynumber: 5.2 Consensus size: 175
23899145 GATTGTAAGC
* **
23899155 CTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCCAGGAGTAGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGG
* *
23899220 GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAATAGTGGAATAGGTTGAAGGTTGTGAA
66 GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGT-AA
* * * *
23899285 TCC-TATCTCCCT-GGTCAGTAGTGGAATAGGTTGAAAATTACAAAT
130 GCCTTATCTCCCTAAG-CAGTAGTGGAGTAGGTTGAAAATTACAGAT
*
23899330 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTT-CTCAGGAGTAGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGG
* * * * *
23899394 GAAGCAGATTTAAACCACTAGTCCTATCTCCCTGGACAGCAGGGGAATAGGTGGAAGATTGTATG
66 GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
*
23899459 CCTTAGCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
131 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
* * *
23899504 CTTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTGAATCTTATTTTCCCCAAGAGTAGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGG
* * *
23899569 GAAGTAGATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGTGGAATATGTTGAAGGTTGTGAA
66 GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGT-AA
* ** * * *
23899634 TCC-TATCT-CCTTGGTCAGCAGTGGAATAGGTTGAAAATTACAAAT
130 GCCTTATCTCCCTAAG-CAGTAGTGGAGTAGGTTGAAAATTACAGAT
* * ** *
23899679 CTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGAAGGCAAATCTTATCTTCCCTAGGAGTAGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGG
* * *
23899744 GAAGCAGATTTAAGTCACTAGTCCTATCTCCCTGGACAACAGGGGAATAGGTGGAAGATTGTAAG
66 GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
23899809 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
131 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
* * * *
23899854 CTTATATCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGTGAATCTTATTTTCCCCAGAAGTAGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGG
* * *
23899919 GAAGCAGGTTTAAGCCACTAGTCCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAAGATTGTAAG
66 GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
*
23899984 CCTTACCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
131 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
23900029 CTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGAT
23900059 AAAAAACAGT
Statistics
Matches: 650, Mismatches: 72, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
173 3 0.00
174 161 0.25
175 479 0.74
176 7 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (175 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGG
GAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGAT
Found at i:23908177 original size:17 final size:17
Alignment explanation
Indices: 23908155--23908188 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23908145 CTTAGAAGAA
23908155 CTTAGTCCAACAAACTT
1 CTTAGTCCAACAAACTT
*
23908172 CTTAGTCCAACATACTT
1 CTTAGTCCAACAAACTT
23908189 TTTAACATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (17 bp):
CTTAGTCCAACAAACTT
Found at i:23917338 original size:28 final size:27
Alignment explanation
Indices: 23917273--23917338 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
23917263 CATCTTTCAG
**
23917273 TTTTAAATTTTGTCTATTTATTCATTT
1 TTTTAAATTTTGAATATTTATTCATTT
*
23917300 TTTTATTATTTTGAATATTTATTC-TTAGT
1 TTTTA-AATTTTGAATATTTATTCATT--T
23917329 TTTTAAATTT
1 TTTTAAATTT
23917339 ATTCTTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.22
28 19 0.59
29 6 0.19
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTTAAATTTTGAATATTTATTCATTT
Found at i:23923426 original size:44 final size:44
Alignment explanation
Indices: 23923376--23923460 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
23923366 AATTAATTAT
23923376 AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGTTAC
1 AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGTTAC
*
23923420 AGAAAATACTTACTAATCTAATCGAGTCATGAATTAGTAGT
1 AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGT
23923461 ATGAATCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (44 bp):
AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGTTAC
Found at i:23924164 original size:9 final size:9
Alignment explanation
Indices: 23924088--23924163 Score: 82
Period size: 9 Copynumber: 8.4 Consensus size: 9
23924078 GTAGTGATTC
*
23924088 AATTTGGTT
1 AATTCGGTT
*
23924097 AATTCGGGT
1 AATTCGGTT
**
23924106 AATTCAATT
1 AATTCGGTT
*
23924115 AATTCGATT
1 AATTCGGTT
23924124 AATTCAGG-T
1 AATTC-GGTT
23924133 AATTCGGTT
1 AATTCGGTT
23924142 AATTCGGTT
1 AATTCGGTT
*
23924151 AATTTGGTT
1 AATTCGGTT
23924160 AATT
1 AATT
23924164 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
8 2 0.04
9 54 0.95
10 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:23936235 original size:35 final size:35
Alignment explanation
Indices: 23936189--23936356 Score: 126
Period size: 35 Copynumber: 5.1 Consensus size: 35
23936179 TGGGCAAGAC
23936189 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
1 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
* ** * ***
23936224 TTTTATAAAGAATTAT-CATTGG--G-CAA--AAC
1 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
23936253 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
1 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
* ** * ***
23936288 TTTTATAAAGAATTAT-CATTGG--G-CAA--GAC
1 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
23936317 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
1 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
23936352 TTTTA
1 TTTTA
23936357 AAAAATGTTT
Statistics
Matches: 93, Mismatches: 28, Indels: 24
0.64 0.19 0.17
Matches are distributed among these distances:
29 32 0.34
30 6 0.06
31 4 0.04
32 4 0.04
33 4 0.04
34 6 0.06
35 37 0.40
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (35 bp):
TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
Found at i:23936247 original size:64 final size:64
Alignment explanation
Indices: 23936170--23936356 Score: 365
Period size: 64 Copynumber: 2.9 Consensus size: 64
23936160 CCAGGTGTCA
23936170 AATTATCATTGGGCAAGACTTTTATAAAGAATTATAAAAAGGTTGTTAATTTTGTTTTATAAAG
1 AATTATCATTGGGCAAGACTTTTATAAAGAATTATAAAAAGGTTGTTAATTTTGTTTTATAAAG
*
23936234 AATTATCATTGGGCAAAACTTTTATAAAGAATTATAAAAAGGTTGTTAATTTTGTTTTATAAAG
1 AATTATCATTGGGCAAGACTTTTATAAAGAATTATAAAAAGGTTGTTAATTTTGTTTTATAAAG
23936298 AATTATCATTGGGCAAGACTTTTATAAAGAATTATAAAAAGGTTGTTAATTTTGTTTTA
1 AATTATCATTGGGCAAGACTTTTATAAAGAATTATAAAAAGGTTGTTAATTTTGTTTTA
23936357 AAAAATGTTT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 121 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (64 bp):
AATTATCATTGGGCAAGACTTTTATAAAGAATTATAAAAAGGTTGTTAATTTTGTTTTATAAAG
Found at i:23936266 original size:29 final size:29
Alignment explanation
Indices: 23936224--23936332 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 29
23936214 GTTAATTTTG
23936224 TTTTATAAAGAATTATCATTGGGCAAAAC
1 TTTTATAAAGAATTATCATTGGGCAAAAC
* ** * ***
23936253 TTTTATAAAGAATTATAAAAAGGTTGTTAATTTTG
1 TTTTATAAAGAATTAT-CATTGG--G-CAA--AAC
*
23936288 TTTTATAAAGAATTATCATTGGGCAAGAC
1 TTTTATAAAGAATTATCATTGGGCAAAAC
23936317 TTTTATAAAGAATTAT
1 TTTTATAAAGAATTAT
23936333 AAAAAGGTTG
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
29 32 0.53
30 3 0.05
31 2 0.03
32 2 0.03
33 2 0.03
34 3 0.05
35 16 0.27
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (29 bp):
TTTTATAAAGAATTATCATTGGGCAAAAC
Found at i:23936529 original size:13 final size:13
Alignment explanation
Indices: 23936495--23936522 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23936485 ACCTTAAAAT
23936495 ATATATTATATAC
1 ATATATTATATAC
23936508 ATATATTATATAC
1 ATATATTATATAC
23936521 AT
1 AT
23936523 CAATTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATTATATAC
Found at i:23936611 original size:54 final size:54
Alignment explanation
Indices: 23936544--23936661 Score: 218
Period size: 54 Copynumber: 2.1 Consensus size: 54
23936534 TGCCTTCAAA
23936544 TTTTTAATGTTAGAATTCATATCGTAACATGATCGAGTACTAAAATCTTGAATATG
1 TTTTT-AT-TTAGAATTCATATCGTAACATGATCGAGTACTAAAATCTTGAATATG
23936600 TTTTTATTTAGAATTCATATCGTAACATGATCGAGTACTAAAATCTTGAATATG
1 TTTTTATTTAGAATTCATATCGTAACATGATCGAGTACTAAAATCTTGAATATG
23936654 TTTTTATT
1 TTTTTATT
23936662 AATTAAATAC
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
54 55 0.89
55 2 0.03
56 5 0.08
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (54 bp):
TTTTTATTTAGAATTCATATCGTAACATGATCGAGTACTAAAATCTTGAATATG
Found at i:23940284 original size:50 final size:50
Alignment explanation
Indices: 23940148--23940389 Score: 258
Period size: 50 Copynumber: 4.8 Consensus size: 50
23940138 ATTTGGGTAA
* * *
23940148 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
23940204 AGAGGTCCCATGT----CCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
23940250 AGAGGTTCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
23940300 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
23940350 AGAACTCCCATGTAAGACCATATCTGAGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
23940390 TAGTACAAGA
Statistics
Matches: 163, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
46 15 0.09
49 4 0.02
50 108 0.66
51 1 0.01
52 23 0.14
56 12 0.07
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:23940430 original size:49 final size:49
Alignment explanation
Indices: 23940217--23940440 Score: 155
Period size: 50 Copynumber: 4.5 Consensus size: 49
23940207 GGTCCCATGT
* * * * ** * *
23940217 CCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTTCCATGTAAGA
1 CCATGTCTGGGATATGGCATTGGCAC-GACAAGAGAACTCCCATATAAGA
* * * * ** ***
23940267 CCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGA
1 CCATGTCTGGGATATGGCATTGGCA-CGACAAGAGAACTCCCATATAAGA
* * * * *
23940317 CCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGA
1 CCATGTCTGGGATATGGCATTGGCA-CGACAAGAGAACTCCCATATAAGA
* * *
23940367 CCATATCTGAGATATGGCATTGGTA-GTACAAGA-AACATCCCATATAAGA
1 CCATGTCTGGGATATGGCATTGGCACG-ACAAGAGAAC-TCCCATATAAGA
*
23940416 CCATGTCTGGGATATGGCTTTGGCA
1 CCATGTCTGGGATATGGCATTGGCA
23940441 TGTTATTATT
Statistics
Matches: 149, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
48 4 0.03
49 36 0.24
50 108 0.72
51 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (49 bp):
CCATGTCTGGGATATGGCATTGGCACGACAAGAGAACTCCCATATAAGA
Found at i:23942416 original size:18 final size:18
Alignment explanation
Indices: 23942393--23942435 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
23942383 TACCAAGTGC
*
23942393 GTATCCTAGCCATTATAT
1 GTATCCTAACCATTATAT
*
23942411 GTATCCTAACCCTTATAT
1 GTATCCTAACCATTATAT
*
23942429 GTTTCCT
1 GTATCCT
23942436 TTTCCTAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCATTATAT
Done.