Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 111 of 325
Found at i:35288004 original size:12 final size:12
Alignment explanation
Indices: 35287903--35288019 Score: 94
Period size: 12 Copynumber: 9.3 Consensus size: 12
35287893 CCTTTTTCTC
*
35287903 TTTTCTTTTCTT
1 TTTTCTTTTTTT
*
35287915 TTCTCTTTTGTTT
1 TTTTCTTTT-TTT
**
35287928 TTATT-TTTTGCT
1 TT-TTCTTTTTTT
35287940 TTTTCTTTTCCTTT
1 TTTTCTTTT--TTT
*
35287954 TATTTCTTTTTTA
1 T-TTTCTTTTTTT
*
35287967 TTTTCTTTTTGT
1 TTTTCTTTTTTT
*
35287979 TTTTCTTTTCTT
1 TTTTCTTTTTTT
35287991 TTTTCTTTTTTT
1 TTTTCTTTTTTT
35288003 TTATT-TTTTTATT
1 TT-TTCTTTTT-TT
35288016 TTTT
1 TTTT
35288020 TAAGGTGAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
11 2 0.02
12 54 0.64
13 17 0.20
14 3 0.04
15 8 0.10
ACGTcount: A:0.04, C:0.11, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:35288017 original size:17 final size:16
Alignment explanation
Indices: 35287951--35288021 Score: 70
Period size: 17 Copynumber: 4.3 Consensus size: 16
35287941 TTTCTTTTCC
* *
35287951 TTTTATTTCTTTTTTA
1 TTTTATTTTTTTTTTT
* *
35287967 TTTTCTTTTTGTTTTTC
1 TTTTATTTTT-TTTTTT
*
35287984 TTTTCTTTTTTCTTTTT
1 TTTTATTTTTT-TTTTT
*
35288001 TTTTATTTTTTTATTT
1 TTTTATTTTTTTTTTT
35288017 TTTTA
1 TTTTA
35288022 AGGTGAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.38
17 29 0.62
ACGTcount: A:0.07, C:0.07, G:0.01, T:0.85
Consensus pattern (16 bp):
TTTTATTTTTTTTTTT
Found at i:35288019 original size:7 final size:8
Alignment explanation
Indices: 35287960--35288021 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
35287950 CTTTTATTTC
35287960 TTTTTTAT
1 TTTTTTAT
35287968 TTTCTTT-T
1 TTT-TTTAT
*
35287976 TGTTTTTCT
1 T-TTTTTAT
*
35287985 TTTCTT-T
1 TTTTTTAT
*
35287992 TTTCTT-T
1 TTTTTTAT
35287999 TTTTTTAT
1 TTTTTTAT
35288007 TTTTTTAT
1 TTTTTTAT
35288015 TTTTTTA
1 TTTTTTA
35288022 AGGTGAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
7 13 0.27
8 28 0.58
9 7 0.15
ACGTcount: A:0.06, C:0.06, G:0.02, T:0.85
Consensus pattern (8 bp):
TTTTTTAT
Found at i:35294081 original size:289 final size:290
Alignment explanation
Indices: 35293560--35294145 Score: 953
Period size: 289 Copynumber: 2.0 Consensus size: 290
35293550 CCCCTAAAGG
* *
35293560 GGTAAGTTTACAATTACGCCCCTTGAGGGTAAATAACTGTTCTTACGCTATAATCTGATTGTCTT
1 GGTAAGTTTACAATTACGCCCCTCGAAGGTAAATAACTGTTCTTACGCTATAATCTGATTGTCTT
* * * *
35293625 TCTGAAGCATGCCTTGTTAATTATATATATATTATGCATACATGTTATACTGCATGGGGTTGGGT
66 TCTAAAGCATGCCTTGTTAATTATATATATATTATGCATACATGTCATACTGCATAGGGTTGAGT
* *
35293690 TTTGTTATAGAGGAAGAACCCGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTGCT
131 TTTATTATAGAGGAAGAACCCGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTACT
* *
35293755 GCGGATTATAGTTAGTGCCGCAACTGGTGCTAACACTGTAAGTGTAGGGATGGCGTGGGTGATTT
196 GCGGATTATAGTTAGTGCCACAACCGGTGCTAACACTGTAAGTGTAGGGATGGCGTGGGTGATTT
35293820 ATTCCCCACAGGAAGTGTAGGGATGGACGGA
261 ATTCCCCACAGGAAGTGTAGGG-TGGACGGA
* * * *
35293851 GGTAAGTTTACGATTACGCCTCTCGAAGGTAAATAATTGTTCTTACGCTATAATCTG-TCTGTGT
1 GGTAAGTTTACAATTACGCCCCTCGAAGGTAAATAACTGTTCTTACGCTATAATCTGAT-TGTCT
*
35293915 TTCTAAAGCATGCCTTGTTAA-T-TATATATATTCTGCATACATGTCATACTGCATAGGGTTGAG
65 TTCTAAAGCATGCCTTGTTAATTATATATATATTATGCATACATGTCATACTGCATAGGGTTGAG
*
35293978 TTTTATTATGGAGGAAGAACCCGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTAC
130 TTTTATTATAGAGGAAGAACCCGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTAC
* *
35294043 TGTGGATTATAGTTAGTGCCACAACCGGTGGTAACACTGTAAGTGTAGGGATGGCGTGGGTGATT
195 TGCGGATTATAGTTAGTGCCACAACCGGTGCTAACACTGTAAGTGTAGGGATGGCGTGGGTGATT
* *
35294108 TATTCCTCATAGGAAGTGTAGGGTGGACGGA
260 TATTCCCCACAGGAAGTGTAGGGTGGACGGA
35294139 GGTAAGT
1 GGTAAGT
35294146 GCAGGGTTGG
Statistics
Matches: 274, Mismatches: 20, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
288 15 0.05
289 181 0.66
290 2 0.01
291 76 0.28
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (290 bp):
GGTAAGTTTACAATTACGCCCCTCGAAGGTAAATAACTGTTCTTACGCTATAATCTGATTGTCTT
TCTAAAGCATGCCTTGTTAATTATATATATATTATGCATACATGTCATACTGCATAGGGTTGAGT
TTTATTATAGAGGAAGAACCCGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTACT
GCGGATTATAGTTAGTGCCACAACCGGTGCTAACACTGTAAGTGTAGGGATGGCGTGGGTGATTT
ATTCCCCACAGGAAGTGTAGGGTGGACGGA
Found at i:35297751 original size:8 final size:8
Alignment explanation
Indices: 35297740--35297784 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
35297730 CTAGATTGGC
*
35297740 AAAAGCTG
1 AAAAGCCG
35297748 AAAAGCCG
1 AAAAGCCG
*
35297756 AAAAGCTG
1 AAAAGCCG
35297764 AAAAGCCG
1 AAAAGCCG
*
35297772 AAATGCCG
1 AAAAGCCG
35297780 AAAAG
1 AAAAG
35297785 TCGGTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.51, C:0.18, G:0.24, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:35297761 original size:16 final size:16
Alignment explanation
Indices: 35297740--35297784 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
35297730 CTAGATTGGC
35297740 AAAAGCTGAAAAGCCG
1 AAAAGCTGAAAAGCCG
35297756 AAAAGCTGAAAAGCCG
1 AAAAGCTGAAAAGCCG
* *
35297772 AAATGCCGAAAAG
1 AAAAGCTGAAAAG
35297785 TCGGTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.24, T:0.07
Consensus pattern (16 bp):
AAAAGCTGAAAAGCCG
Found at i:35300686 original size:21 final size:22
Alignment explanation
Indices: 35300661--35300715 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
35300651 ATAAATAAGA
* *
35300661 AAAAATAATAAGGGCAA-GAAT
1 AAAAATAATAAGGCCAATAAAT
*
35300682 AAAAATAA-ACAAGCCAATAAAT
1 AAAAATAATA-AGGCCAATAAAT
35300704 AAAAATAATAAG
1 AAAAATAATAAG
35300716 AAAAAACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.04
21 13 0.48
22 12 0.44
23 1 0.04
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAATAAGGCCAATAAAT
Found at i:35300905 original size:13 final size:13
Alignment explanation
Indices: 35300868--35300912 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
35300858 AATTTTATAT
35300868 AAAAGAT-ATAAC
1 AAAAGATAATAAC
*
35300880 TAAATAAATAATAAC
1 -AAA-AGATAATAAC
35300895 AAAAGATAATAAC
1 AAAAGATAATAAC
35300908 AAAAG
1 AAAAG
35300913 TGAGGATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 17 0.61
14 6 0.21
15 5 0.18
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (13 bp):
AAAAGATAATAAC
Found at i:35302475 original size:39 final size:38
Alignment explanation
Indices: 35302378--35302524 Score: 177
Period size: 39 Copynumber: 3.7 Consensus size: 38
35302368 CGAATTTTCG
* * *
35302378 CACACTAAGTGCCAATACATAGTCGAAGCTATTTTAATC
1 CACACTAAGTGCC-ATACATAGCCGAAGCTATCTCAATC
* *
35302417 CTGTACACTAAATGCCATACATAGCCAAAGCTATCTCAATC
1 C---ACACTAAGTGCCATACATAGCCGAAGCTATCTCAATC
*
35302458 ACACACTAAGTGCCATACATAACCGAAGCTATCTCAAATC
1 -CACACTAAGTGCCATACATAGCCGAAGCTATCTC-AATC
35302498 GCACACTAAGTGCCATACATAGCCGAA
1 -CACACTAAGTGCCATACATAGCCGAA
35302525 TTGTCGTCAA
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
39 31 0.33
40 29 0.31
41 21 0.23
42 12 0.13
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.22
Consensus pattern (38 bp):
CACACTAAGTGCCATACATAGCCGAAGCTATCTCAATC
Found at i:35302514 original size:40 final size:39
Alignment explanation
Indices: 35302375--35302524 Score: 192
Period size: 40 Copynumber: 3.7 Consensus size: 39
35302365 ACTCGAATTT
* * *
35302375 TCGCACACTAAGTGCCAATACATAGTCGAAGCTATTTTAA
1 TCGCACACTAAGTGCC-ATACATAGCCGAAGCTATCTCAA
* * *
35302415 TCCTGTACACTAAATGCCATACATAGCCAAAGCTATCTCAA
1 T-C-GCACACTAAGTGCCATACATAGCCGAAGCTATCTCAA
* *
35302456 TCACACACTAAGTGCCATACATAACCGAAGCTATCTCAAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTC-AA
35302496 TCGCACACTAAGTGCCATACATAGCCGAA
1 TCGCACACTAAGTGCCATACATAGCCGAA
35302525 TTGTCGTCAA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 30 0.32
40 31 0.33
41 21 0.22
42 12 0.13
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.23
Consensus pattern (39 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCAA
Found at i:35304658 original size:20 final size:20
Alignment explanation
Indices: 35304629--35304674 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
35304619 AAGATAGTGG
*
35304629 CTTGTTACACGCCTTGGAGC
1 CTTGTCACACGCCTTGGAGC
35304649 CTTGTCACACGCCTTGGAGC
1 CTTGTCACACGCCTTGGAGC
35304669 CTTGTC
1 CTTGTC
35304675 CTGTTTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.33, G:0.24, T:0.30
Consensus pattern (20 bp):
CTTGTCACACGCCTTGGAGC
Found at i:35306093 original size:3 final size:3
Alignment explanation
Indices: 35306085--35306142 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
35306075 CATGCATATT
35306085 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
35306133 ATA ATA ATA A
1 ATA ATA ATA A
35306143 ACATACTATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35307037 original size:30 final size:31
Alignment explanation
Indices: 35307003--35307064 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
35306993 GATTCATCCA
*
35307003 TGGAAAAT-AAAATAAAGAAAATGATGA-AAT
1 TGGAAAATGAAAAAAAAGAAAA-GATGATAAT
* *
35307033 TGGAAAGTGAAAAAAAATAAAAGATGATAAT
1 TGGAAAATGAAAAAAAAGAAAAGATGATAAT
35307064 T
1 T
35307065 AATTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (31 bp):
TGGAAAATGAAAAAAAAGAAAAGATGATAAT
Found at i:35313350 original size:14 final size:15
Alignment explanation
Indices: 35313326--35313354 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35313316 TTATGCATGT
35313326 TATGATTTGATATGA
1 TATGATTTGATATGA
35313341 TATG-TTTGATATGA
1 TATGATTTGATATGA
35313355 CCTAGCATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
TATGATTTGATATGA
Found at i:35316877 original size:15 final size:16
Alignment explanation
Indices: 35316836--35316881 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
35316826 TTTATGTCAT
* *
35316836 TTTTATAATAATAAAA
1 TTTTATAATTATTAAA
35316852 TTTTCATAATTATTAAA
1 TTTT-ATAATTATTAAA
35316869 -TTTATAATTATTA
1 TTTTATAATTATTA
35316882 TATAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 10 0.37
16 7 0.26
17 10 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTATAATTATTAAA
Found at i:35318986 original size:30 final size:30
Alignment explanation
Indices: 35318952--35319014 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
35318942 ATTTAACAAG
*
35318952 CAAATGCCTCTAAAATAATAAAAAAATTAA
1 CAAATACCTCTAAAATAATAAAAAAATTAA
* *
35318982 CAAATACCTTTAAAATAATAAGAAAATTAA
1 CAAATACCTCTAAAATAATAAAAAAATTAA
35319012 CAA
1 CAA
35319015 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAAAAAAATTAA
Found at i:35320867 original size:27 final size:26
Alignment explanation
Indices: 35320836--35320892 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
35320826 AGAAAAAGAA
*
35320836 AAAAAAGAA-AACTAAAGGGAAAAATACG
1 AAAAAAGAAGAA-GAAA-GGAAAAATA-G
35320864 AAAAAAGAAGAAGAAAGGAAAAATAG
1 AAAAAAGAAGAAGAAAGGAAAAATAG
35320890 AAA
1 AAA
35320893 GTAAAAGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 9 0.33
28 12 0.44
29 2 0.07
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.05
Consensus pattern (26 bp):
AAAAAAGAAGAAGAAAGGAAAAATAG
Found at i:35320868 original size:28 final size:26
Alignment explanation
Indices: 35320827--35320892 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
35320817 ATTGAATGAA
* * *
35320827 GAAAAAGAAAAAAAAGAA-AACTAAAGG
1 GAAAAATAGAAAAAAGAAGAA-GAAA-G
35320854 GAAAAATACGAAAAAAGAAGAAGAAAG
1 GAAAAATA-GAAAAAAGAAGAAGAAAG
35320881 GAAAAATAGAAA
1 GAAAAATAGAAA
35320893 GTAAAAGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 4 0.12
27 16 0.47
28 12 0.35
29 2 0.06
ACGTcount: A:0.73, C:0.03, G:0.20, T:0.05
Consensus pattern (26 bp):
GAAAAATAGAAAAAAGAAGAAGAAAG
Found at i:35323770 original size:64 final size:64
Alignment explanation
Indices: 35323650--35323770 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 64
35323640 ACACACAGTC
* * * ***
35323650 GTGTCCTTCACCCTTGTGATCATTATTTTGTAATCAGTGAGTTACACGGTTGGGACAGATGCCT
1 GTGTCCTTAACCCGTGTGATCATTATATTGTAATCAGTGAGTTACACGGCCAGGACAGATGCCT
* *
35323714 GTGTCCTTAACCCGTGTGCTCATTATATTGTAATTAGTGAGTTACACGGCCAGGACA
1 GTGTCCTTAACCCGTGTGATCATTATATTGTAATCAGTGAGTTACACGGCCAGGACA
35323771 CACACCCGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (64 bp):
GTGTCCTTAACCCGTGTGATCATTATATTGTAATCAGTGAGTTACACGGCCAGGACAGATGCCT
Found at i:35323798 original size:64 final size:64
Alignment explanation
Indices: 35323640--35323785 Score: 166
Period size: 64 Copynumber: 2.3 Consensus size: 64
35323630 ACATGGCCTA
** * * * * ***
35323640 ACACACAGTCGTGTCCTTCACCCTTGTGATCATTATTTTGTAATCAGTGAGTTACACGGTTGGG
1 ACACACACCCGTGTCCTTAACCCGTGTGCTCATTATATTGTAATCAGTGAGTTACACGGCCAGG
* ** * *
35323704 ACAGATGCCTGTGTCCTTAACCCGTGTGCTCATTATATTGTAATTAGTGAGTTACACGGCCAGG
1 ACACACACCCGTGTCCTTAACCCGTGTGCTCATTATATTGTAATCAGTGAGTTACACGGCCAGG
35323768 ACACACACCCGTGTCCTT
1 ACACACACCCGTGTCCTT
35323786 GGCTCGTGTG
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (64 bp):
ACACACACCCGTGTCCTTAACCCGTGTGCTCATTATATTGTAATCAGTGAGTTACACGGCCAGG
Found at i:35338432 original size:6 final size:6
Alignment explanation
Indices: 35338418--35338451 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
35338408 CATACACAGT
* *
35338418 CAGAAA CAGATA CAGATA CAGATA TAGATA CAGA
1 CAGATA CAGATA CAGATA CAGATA CAGATA CAGA
35338452 GTTGGGATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (6 bp):
CAGATA
Found at i:35341006 original size:21 final size:21
Alignment explanation
Indices: 35340980--35341060 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
35340970 TATGAGGAAG
35340980 GGCACATAGCCGTGTGGCTGA
1 GGCACATAGCCGTGTGGCTGA
* *
35341001 GGCACAT-GCCCGTGTGAAG-AGG
1 GGCACATAG-CCGTGTG--GCTGA
* *
35341023 GGCACATGGCCGTGTGACTGA
1 GGCACATAGCCGTGTGGCTGA
*
35341044 GGCACACAGCCGTGTGG
1 GGCACATAGCCGTGTGG
35341061 ACTAGGAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
20 1 0.02
21 29 0.62
22 15 0.32
23 2 0.04
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.16
Consensus pattern (21 bp):
GGCACATAGCCGTGTGGCTGA
Found at i:35341823 original size:4 final size:4
Alignment explanation
Indices: 35341814--35341839 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35341804 ATCATAGACA
35341814 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
35341840 CTATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:35343597 original size:29 final size:29
Alignment explanation
Indices: 35343556--35343624 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
35343546 ACACCAGGGG
35343556 ACACACGGCTGTGTACTTAACCGTGTATC
1 ACACACGGCTGTGTACTTAACCGTGTATC
35343585 ACACACGGCTGTGTACTTAACCGTGTATC
1 ACACACGGCTGTGTACTTAACCGTGTATC
35343614 ACACACGGCTG
1 ACACACGGCTG
35343625 AGACACACGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (29 bp):
ACACACGGCTGTGTACTTAACCGTGTATC
Found at i:35347061 original size:42 final size:42
Alignment explanation
Indices: 35347014--35347159 Score: 114
Period size: 42 Copynumber: 3.5 Consensus size: 42
35347004 ATGAGTTTTC
* * *
35347014 GTTTAACGCTAATAGGTTTTAGTTCAGCTCTCTCGAGCTTCA
1 GTTTAACCCTAATAGGTTTCAGTTCAACTCTCTCGAGCTTCA
** * *
35347056 GTTTAACCCTTCTAGGTTTCAGTTCAACTCTGTTGAGCTTCA
1 GTTTAACCCTAATAGGTTTCAGTTCAACTCTCTCGAGCTTCA
** * * ** * *
35347098 AATTAACCCTTATGGGTTTTTGTTCAACTC-CTATGAGCTTCT
1 GTTTAACCCTAATAGGTTTCAGTTCAACTCTCT-CGAGCTTCA
* * *
35347140 GTTTATCCCTTATGGGTTTC
1 GTTTAACCCTAATAGGTTTC
35347160 CGTTTAGCAC
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 1 0.01
42 83 0.99
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (42 bp):
GTTTAACCCTAATAGGTTTCAGTTCAACTCTCTCGAGCTTCA
Found at i:35352470 original size:24 final size:24
Alignment explanation
Indices: 35352443--35352562 Score: 93
Period size: 24 Copynumber: 5.0 Consensus size: 24
35352433 AGCTTCTGTT
35352443 ATATGGCTCTTTATGAGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
* * * *
35352467 ATATGGTTATTTGTGAACTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
*
35352491 ATTATGGCTC-TTATGAGCTTTCCG
1 A-TATGGCTCTTTATGAGCTTCCCG
* * ** *
35352515 TTATATAGC-ATAAATAAGCTTCCCG
1 --ATATGGCTCTTTATGAGCTTCCCG
*
35352540 ATA-GGCTCTTTATGGGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
35352563 TTACATGGCT
Statistics
Matches: 70, Mismatches: 21, Indels: 11
0.69 0.21 0.11
Matches are distributed among these distances:
22 2 0.03
23 14 0.20
24 32 0.46
25 21 0.30
26 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (24 bp):
ATATGGCTCTTTATGAGCTTCCCG
Found at i:35353610 original size:42 final size:40
Alignment explanation
Indices: 35353544--35353627 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 40
35353534 GTTCAAAATT
*
35353544 TGTCACACAGGCAGAGACATAGGCGTGTGTCTTAGCCGTG
1 TGTCACACAGGCAGAGACACAGGCGTGTGTCTTAGCCGTG
*
35353584 TGTCACACACGGCTTAGA-ACACAGGCGTGTGTCTTGGCCGTG
1 TGTCACACA-GGC--AGAGACACAGGCGTGTGTCTTAGCCGTG
35353626 TG
1 TG
35353628 AAACCTGCAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 9 0.23
41 3 0.08
42 24 0.62
43 3 0.08
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (40 bp):
TGTCACACAGGCAGAGACACAGGCGTGTGTCTTAGCCGTG
Found at i:35358083 original size:13 final size:13
Alignment explanation
Indices: 35358065--35358091 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35358055 GATATAGATT
35358065 CAGATTCAAATAA
1 CAGATTCAAATAA
35358078 CAGATTCAAATAA
1 CAGATTCAAATAA
35358091 C
1 C
35358092 TGATATGAAA
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:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (13 bp):
CAGATTCAAATAA
Found at i:35359323 original size:31 final size:31
Alignment explanation
Indices: 35359282--35359345 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
35359272 CCTTTTCATA
*
35359282 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
35359313 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
35359344 TT
1 TT
35359346 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:35359589 original size:24 final size:24
Alignment explanation
Indices: 35359553--35359656 Score: 167
Period size: 23 Copynumber: 4.4 Consensus size: 24
35359543 CTGGAGGCCT
*
35359553 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
*
35359578 AGCCCTTTTAATAGCTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
35359602 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
35359625 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
35359648 AGCCCTTTT
1 AGCCCTTTT
35359657 GCACTCCCTC
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
23 45 0.60
24 26 0.35
25 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:35359726 original size:9 final size:9
Alignment explanation
Indices: 35359712--35359770 Score: 64
Period size: 9 Copynumber: 6.1 Consensus size: 9
35359702 ACATCTCATG
35359712 TACATATCA
1 TACATATCA
35359721 TACATATCA
1 TACATATCA
35359730 TGTACATATCA
1 --TACATATCA
*
35359741 TACATGTCA
1 TACATATCA
*
35359750 TGTGCATATCA
1 --TACATATCA
35359761 TACATATCA
1 TACATATCA
35359770 T
1 T
35359771 GTTTATCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 26 0.62
11 16 0.38
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (9 bp):
TACATATCA
Found at i:35359730 original size:20 final size:20
Alignment explanation
Indices: 35359702--35359772 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
35359692 GCATTTATGA
*
35359702 ACATCTCATGTACATATCAT
1 ACATATCATGTACATATCAT
35359722 ACATATCATGTACATATCAT
1 ACATATCATGTACATATCAT
* *
35359742 ACATGTCATGTGCATATCAT
1 ACATATCATGTACATATCAT
35359762 ACATATCATGT
1 ACATATCATGT
35359773 TTATCAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (20 bp):
ACATATCATGTACATATCAT
Found at i:35359837 original size:25 final size:25
Alignment explanation
Indices: 35359809--35359856 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35359799 ATATATAAAC
* * *
35359809 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGAAAAACGGTCATTTTTA
35359834 CCTAGGGGAAAAACGGTCATTTT
1 CCTAGGGGAAAAACGGTCATTTT
35359857 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGAAAAACGGTCATTTTTA
Found at i:35361151 original size:27 final size:27
Alignment explanation
Indices: 35361121--35361173 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
35361111 GGGTGTTTTG
35361121 GTAAATCTATAAACCAAGGGTATTTCA
1 GTAAATCTATAAACCAAGGGTATTTCA
* * * *
35361148 GTAATTTTGTAAACCAATGGTATTTC
1 GTAAATCTATAAACCAAGGGTATTTC
35361174 TATAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (27 bp):
GTAAATCTATAAACCAAGGGTATTTCA
Found at i:35361179 original size:27 final size:27
Alignment explanation
Indices: 35361130--35361238 Score: 89
Period size: 27 Copynumber: 4.0 Consensus size: 27
35361120 GGTAAATCTA
35361130 TAAACCAAGGGTATTTCAGTAATTTTG
1 TAAACCAAGGGTATTTCAGTAATTTTG
*
35361157 TAAACCAATGGTATTTCTA-TAATTTT-
1 TAAACCAAGGGTATTTC-AGTAATTTTG
* * *
35361183 TAGAAAGTCAAGGGTATTTCTGTAACTTTG
1 T--AAA-CCAAGGGTATTTCAGTAATTTTG
* **
35361213 TAAATC-AGAGGTATTTTGGTAATTTT
1 TAAACCAAG-GGTATTTCAGTAATTTT
35361239 ACAAATTGAG
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
26 3 0.04
27 39 0.58
28 7 0.10
29 17 0.25
30 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.41
Consensus pattern (27 bp):
TAAACCAAGGGTATTTCAGTAATTTTG
Found at i:35361244 original size:27 final size:27
Alignment explanation
Indices: 35361219--35361319 Score: 125
Period size: 27 Copynumber: 3.7 Consensus size: 27
35361209 TTTGTAAATC
35361219 AGAGGTATTTTGGTAATTTTACAAA-T
1 AGAGGTATTTTGGTAATTTTACAAACT
* * * *
35361245 TGAGGGTATTTCGATAATTTCACAAACT
1 AGA-GGTATTTTGGTAATTTTACAAACT
*
35361273 AGTGGTATTTTGGTAATTTTACAAACT
1 AGAGGTATTTTGGTAATTTTACAAACT
35361300 AG-GAGTATTTTGGTAATTTT
1 AGAG-GTATTTTGGTAATTTT
35361320 GTAAATCGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.05
27 58 0.92
28 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.43
Consensus pattern (27 bp):
AGAGGTATTTTGGTAATTTTACAAACT
Found at i:35361342 original size:27 final size:27
Alignment explanation
Indices: 35361311--35361495 Score: 235
Period size: 27 Copynumber: 6.9 Consensus size: 27
35361301 GGAGTATTTT
*
35361311 GGTAATTTTGTAAATCGAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAAC
* * * * *
35361338 AGTAATTCTATAAATCAATGGTAAAAT
1 GGTAATTCTGTAAATCGAGGGTAAAAC
*
35361365 GGTAATTTTGTAAATCGAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAAC
* * *
35361392 GGTAATTCTATAAGTCGAGGGGAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAAC
* *
35361419 GGTAATTATGTAAATCGGGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAAC
* *
35361446 GGTAATTATGTAAATCGGGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAAC
*
35361473 GGTAATTCTGTAAATCGGGGGTA
1 GGTAATTCTGTAAATCGAGGGTA
35361496 CTTTCATAAT
Statistics
Matches: 136, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 136 1.00
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.28
Consensus pattern (27 bp):
GGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:35361522 original size:54 final size:53
Alignment explanation
Indices: 35361311--35361522 Score: 180
Period size: 54 Copynumber: 3.9 Consensus size: 53
35361301 GGAGTATTTT
* * * * *
35361311 GGTAATTTTGTAAATCGAGGGTAAAAC-AGTAATTCTATAAA-TCAATGGTAAAAT
1 GGTAATTATGTAAATCGGGGGTAAAACGA-TAATT-T-TAAAGTCGAGGGTAAAAC
* * * * *
35361365 GGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATAAGTCGAGGGGAAAAC
1 GGTAATTATGTAAATCGGGGGTAAAACGATAATTTTA-AAGTCGAGGGTAAAAC
* *
35361419 GGTAATTATGTAAATCGGGGGTAAAACGGTAATTATGTAAA-TCGGGGGTAAAAC
1 GGTAATTATGTAAATCGGGGGTAAAACGATAATT-T-TAAAGTCGAGGGTAAAAC
* ***
35361473 GGTAATTCTGTAAATCGGGGGTACTTTC-ATAATTTTACAAGTCGAGGGTA
1 GGTAATTATGTAAATCGGGGGTA-AAACGATAATTTTA-AAGTCGAGGGTA
35361523 TTTCAGTAAT
Statistics
Matches: 133, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
52 4 0.03
53 5 0.04
54 119 0.89
55 3 0.02
56 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (53 bp):
GGTAATTATGTAAATCGGGGGTAAAACGATAATTTTAAAGTCGAGGGTAAAAC
Found at i:35363183 original size:18 final size:18
Alignment explanation
Indices: 35363160--35363195 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35363150 AACAGAAACG
*
35363160 TCAAAATAGAAGAAAATA
1 TCAAAATAAAAGAAAATA
*
35363178 TCAAAATAAAATAAAATA
1 TCAAAATAAAAGAAAATA
35363196 AAAACCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (18 bp):
TCAAAATAAAAGAAAATA
Found at i:35367598 original size:42 final size:42
Alignment explanation
Indices: 35367552--35367673 Score: 117
Period size: 42 Copynumber: 2.9 Consensus size: 42
35367542 CAGCTCTCTC
*
35367552 GAGCTTCAATTTAACCCTTCTGGGTTTCAATTTAGCACGT-TT
1 GAGCTTCAATTTAACCCTTCTGGGTTTC-ATTTAGCACCTATT
* * * *
35367594 GAGCTTTAGA-TTAACCCTTATGGGTTTCTGTTTAGCTCCTATT
1 GAGCTTCA-ATTTAACCCTTCTGGGTTTC-ATTTAGCACCTATT
*
35367637 -AGCTTCCATTTAACCCTTAC-GGGTTTTCATTTAGCAC
1 GAGCTTCAATTTAACCCTT-CTGGG-TTTCATTTAGCAC
35367674 TTATATGCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.02
42 56 0.88
43 7 0.11
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (42 bp):
GAGCTTCAATTTAACCCTTCTGGGTTTCATTTAGCACCTATT
Found at i:35376169 original size:30 final size:31
Alignment explanation
Indices: 35376135--35376194 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
35376125 AAACTTTTCA
35376135 TTTTCCCCCT-AAATTTTTACTCCC-TCCCAC
1 TTTT-CCCCTAAAATTTTTACTCCCTTCCCAC
35376165 TTTTCCCCTAAAATTTTTACTCCCTTCCCA
1 TTTTCCCCTAAAATTTTTACTCCCTTCCCA
35376195 TCCCATCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 5 0.18
30 18 0.64
31 5 0.18
ACGTcount: A:0.18, C:0.40, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAATTTTTACTCCCTTCCCAC
Found at i:35376198 original size:5 final size:5
Alignment explanation
Indices: 35376185--35376230 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
35376175 AAATTTTTAC
*
35376185 TCCCT TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA -CCC- TCCCA TCC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCCCA TCC
35376231 AACCCCCCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
4 6 0.16
5 32 0.84
ACGTcount: A:0.15, C:0.63, G:0.00, T:0.22
Consensus pattern (5 bp):
TCCCA
Found at i:35376241 original size:12 final size:13
Alignment explanation
Indices: 35376195--35376241 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
35376185 TCCCTTCCCA
*
35376195 TCCCATCCCATCCC
1 TCCCAT-CCAACCC
*
35376209 ATCCCATCCCACCC
1 -TCCCATCCAACCC
35376223 TCCCATCCAACCC
1 TCCCATCCAACCC
35376236 -CCCATC
1 TCCCATC
35376242 TACCCCAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 6 0.21
13 12 0.41
14 5 0.17
15 6 0.21
ACGTcount: A:0.19, C:0.64, G:0.00, T:0.17
Consensus pattern (13 bp):
TCCCATCCAACCC
Found at i:35376642 original size:38 final size:38
Alignment explanation
Indices: 35376591--35376667 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
35376581 ATACATAATT
35376591 AGAAGATAATTGAAGTGACTAAGTAAGCAAAGAAGCTA
1 AGAAGATAATTGAAGTGACTAAGTAAGCAAAGAAGCTA
35376629 AGAAGATAATTGAAGTGACTAAGTAAGCAAAGAAGCTA
1 AGAAGATAATTGAAGTGACTAAGTAAGCAAAGAAGCTA
35376667 A
1 A
35376668 CTCATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.23, T:0.18
Consensus pattern (38 bp):
AGAAGATAATTGAAGTGACTAAGTAAGCAAAGAAGCTA
Found at i:35377799 original size:10 final size:10
Alignment explanation
Indices: 35377784--35377833 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
35377774 TAATTTTAGG
35377784 ATTTAT-TTT
1 ATTTATCTTT
35377793 CATTTATCTTT
1 -ATTTATCTTT
*
35377804 AATTATCTTT
1 ATTTATCTTT
35377814 ATTTAT-TTAT
1 ATTTATCTT-T
35377824 ATTTATCTTT
1 ATTTATCTTT
35377834 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:35378617 original size:39 final size:39
Alignment explanation
Indices: 35378569--35378643 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
35378559 AATTTCAATC
* *
35378569 AAAACTTTTAATTCTATTTTATTT-TATT-TTTTCCAGATA
1 AAAAATTTTAATGCTATTTT-TTTAT-TTCTTTTCCAGATA
35378608 AAAAATTTTAATGCTATTTTTTTATTTCTTTTCCAG
1 AAAAATTTTAATGCTATTTTTTTATTTCTTTTCCAG
35378644 GTACGCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.56
Consensus pattern (39 bp):
AAAAATTTTAATGCTATTTTTTTATTTCTTTTCCAGATA
Found at i:35381588 original size:19 final size:19
Alignment explanation
Indices: 35381537--35381591 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
35381527 GAAACCCAAT
35381537 TTTTATTTATTTTTATTATTA
1 TTTTA-TTA-TTTTATTATTA
35381558 TTCTT-TCT-TTTTATTATTA
1 TT-TTAT-TATTTTATTATTA
35381577 TTTTATTATTTTATT
1 TTTTATTATTTTATT
35381592 TTTTAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 3 0.10
19 21 0.70
20 1 0.03
21 3 0.10
22 2 0.07
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTATTTTATTATTA
Found at i:35382795 original size:96 final size:97
Alignment explanation
Indices: 35382669--35382851 Score: 271
Period size: 96 Copynumber: 1.9 Consensus size: 97
35382659 TTTTTAAGAA
* * *
35382669 TATGTCGGCCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCCCGTCAAAAGGTTCG
1 TATGTCGGCCTGAGTAACCGAGGTGAGGTGCTTGGCTATCATCTCTCTTCCCGTCAAAAGGTTCA
*
35382734 ATATGTTCTTAAG-AAAAATAAAAATTAGGAG
66 ATATATTCTTAAGCAAAAATAAAAATTAGGAG
* * *
35382765 TATGTTGGGCTGAGTAACCGAGGT-AGGGTGCTTGGCTATCATCTCTCTTCGCGTCAAAAGGTTC
1 TATGTCGGCCTGAGTAACCGAGGTGA-GGTGCTTGGCTATCATCTCTCTTCCCGTCAAAAGGTTC
*
35382829 AATATATTCTTAAGCAACAATAA
65 AATATATTCTTAAGCAAAAATAA
35382852 GTAAATAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 1 0.01
96 69 0.90
97 7 0.09
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (97 bp):
TATGTCGGCCTGAGTAACCGAGGTGAGGTGCTTGGCTATCATCTCTCTTCCCGTCAAAAGGTTCA
ATATATTCTTAAGCAAAAATAAAAATTAGGAG
Found at i:35384273 original size:31 final size:31
Alignment explanation
Indices: 35384201--35384274 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
35384191 CATACTAGGT
* *
35384201 CGAAGCCTTTACATTTTTCATATCACTGGGC
1 CGAAGCCTTTTCATTATTCATATCACTGGGC
35384232 CGAAGCCTTTTCATTATTCATATCACTGGGC
1 CGAAGCCTTTTCATTATTCATATCACTGGGC
35384263 CGAAGCCTTTTC
1 CGAAGCCTTTTC
35384275 TGTAACAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (31 bp):
CGAAGCCTTTTCATTATTCATATCACTGGGC
Found at i:35384517 original size:24 final size:25
Alignment explanation
Indices: 35384479--35384586 Score: 112
Period size: 24 Copynumber: 4.4 Consensus size: 25
35384469 CTGGAGGCCT
* *
35384479 AGCCTTTTTTAAT-AACTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAA
* **
35384503 ATCCCTTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTCAATAAACTGGGGC-AA
35384529 AGCCCTTTTCAATAAACTGGGGCAA
1 AGCCCTTTTCAATAAACTGGGGCAA
** * *
35384554 AGCCCTTTTCGGT-AATTGGGGCAT
1 AGCCCTTTTCAATAAACTGGGGCAA
35384578 AGCCCTTTT
1 AGCCCTTTT
35384587 GCACTTCCTC
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
24 28 0.39
25 22 0.31
26 22 0.31
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (25 bp):
AGCCCTTTTCAATAAACTGGGGCAA
Found at i:35384534 original size:26 final size:25
Alignment explanation
Indices: 35384479--35384562 Score: 116
Period size: 26 Copynumber: 3.4 Consensus size: 25
35384469 CTGGAGGCCT
*
35384479 AGCCTTTTTTAAT-AACTGGGGCAA
1 AGCCCTTTTTAATAAACTGGGGCAA
* *
35384503 ATCCCTTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTTAATAAACTGGGGC-AA
*
35384529 AGCCCTTTTCAATAAACTGGGGCAA
1 AGCCCTTTTTAATAAACTGGGGCAA
35384554 AGCCCTTTT
1 AGCCCTTTT
35384563 CGGTAATTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
24 10 0.19
25 20 0.38
26 22 0.42
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (25 bp):
AGCCCTTTTTAATAAACTGGGGCAA
Found at i:35384563 original size:25 final size:24
Alignment explanation
Indices: 35384456--35384586 Score: 109
Period size: 24 Copynumber: 5.2 Consensus size: 24
35384446 AGCATAACTG
**
35384456 CTTTATCATATAACTGGAGGCCTAGCC
1 CTTT-TCA-ATAACTGG-GGCAAAGCC
* * *
35384483 TTTTTTAATAACTGGGGCAAATCC
1 CTTTTCAATAACTGGGGCAAAGCC
**
35384507 CTTTTTGATAAACTGGGGCAAAAGCC
1 CTTTTCAAT-AACTGGGGC-AAAGCC
35384533 CTTTTCAATAAACTGGGGCAAAGCC
1 CTTTTCAAT-AACTGGGGCAAAGCC
** * *
35384558 CTTTTCGGTAATTGGGGCATAGCC
1 CTTTTCAATAACTGGGGCAAAGCC
35384582 CTTTT
1 CTTTT
35384587 GCACTTCCTC
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
24 31 0.35
25 30 0.34
26 24 0.27
27 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
CTTTTCAATAACTGGGGCAAAGCC
Found at i:35384650 original size:11 final size:11
Alignment explanation
Indices: 35384634--35384681 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
35384624 TATATGAATT
35384634 TATCATGTGCA
1 TATCATGTGCA
*
35384645 TATCA--TACA
1 TATCATGTGCA
35384654 TATCATGTGCA
1 TATCATGTGCA
35384665 TATCATGT-CA
1 TATCATGTGCA
*
35384675 AATCATG
1 TATCATG
35384682 CATATCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.25
10 8 0.25
11 16 0.50
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (11 bp):
TATCATGTGCA
Found at i:35385910 original size:20 final size:20
Alignment explanation
Indices: 35385885--35385934 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
35385875 AAAGAAGAAA
35385885 AGAATAAAACTATGGTTTAC
1 AGAATAAAACTATGGTTTAC
35385905 AGAATAAAACTATGGTTTAC
1 AGAATAAAACTATGGTTTAC
*
35385925 AGAAGAAAAC
1 AGAATAAAAC
35385935 GGCACAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (20 bp):
AGAATAAAACTATGGTTTAC
Found at i:35388462 original size:51 final size:49
Alignment explanation
Indices: 35388402--35388591 Score: 227
Period size: 51 Copynumber: 3.8 Consensus size: 49
35388392 CTAGGTCGCA
* * *
35388402 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-TT-GGTCACG
* * * *
35388453 TGTGTAGTACTAAGTGCAGACTACTATGTGTATCAAGATAGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CCAGATAATT-GGTCACG
* * * * * *
35388504 TGTGTAGTACTAAGTGCAGGCTATTACGTGTACCAAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCACG
35388553 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
35388592 GTTTGGCTAC
Statistics
Matches: 118, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 40 0.34
50 7 0.06
51 66 0.56
52 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTCACG
Found at i:35390928 original size:40 final size:41
Alignment explanation
Indices: 35390883--35390968 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
35390873 TGTTATTTTA
* *
35390883 ATTTTAATTTTCGGGATTT-CA-ATCAAAACTTTTAATTCT
1 ATTTTTATTTTAGGGATTTCCAGATCAAAACTTTTAATTCT
* ****
35390922 GTTTTTATTTTATTTTTTTCCAGATCAAAACTTTTAATTCT
1 ATTTTTATTTTAGGGATTTCCAGATCAAAACTTTTAATTCT
35390963 ATTTTT
1 ATTTTT
35390969 TTATTTCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
39 12 0.32
40 2 0.05
41 23 0.62
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.56
Consensus pattern (41 bp):
ATTTTTATTTTAGGGATTTCCAGATCAAAACTTTTAATTCT
Found at i:35407345 original size:29 final size:29
Alignment explanation
Indices: 35407294--35407428 Score: 96
Period size: 30 Copynumber: 4.6 Consensus size: 29
35407284 AAAACTTCTG
* **
35407294 GGGTT-AAATGTAATTTTTAGAAAATTTA
1 GGGTTAAAATGAAATTTAAAGAAAATTTA
* * *
35407322 GGATTAAAATGAAATTTAATGAAAGTTTA
1 GGGTTAAAATGAAATTTAAAGAAAATTTA
* *
35407351 GGGGTCT-AAGTGAAATTTAAAGAAAGTTTAA
1 -GGGT-TAAAATGAAATTTAAAGAAAATTT-A
* *
35407382 GGGTCAAAATGAAATTT-AGGAAAAGTTTA
1 GGGTTAAAATGAAATTTAAAGAAAA-TTTA
* *
35407411 GGGGTCAAAATGCAATTT
1 -GGGTTAAAATGAAATTT
35407429 TTATTTTTTA
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
28 4 0.05
29 24 0.28
30 56 0.65
31 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (29 bp):
GGGTTAAAATGAAATTTAAAGAAAATTTA
Found at i:35407367 original size:30 final size:30
Alignment explanation
Indices: 35407327--35407428 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
35407317 ATTTAGGATT
*
35407327 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
35407357 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
35407387 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
35407417 AAAATGCAATTT
1 AAAATGAAATTT
35407429 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:35407884 original size:54 final size:54
Alignment explanation
Indices: 35407699--35408078 Score: 592
Period size: 54 Copynumber: 7.1 Consensus size: 54
35407689 CACGTGAGCC
* *
35407699 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AA
* *
35407754 AAGGCTCAACTCTCCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
35407804 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
35407858 AAGGCTCAACTCACCTCTCGCAATATG-GTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
35407911 AAGGCTCAACTCACCTCTCGCAATATTAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
35407965 AAGGCTCAACTCACCTCTCACAATATGAGTTGGTTTTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAAAAACAGAAATTAA
35408021 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AA
35408076 AAG
1 AAG
35408079 TAGAAATTGA
Statistics
Matches: 302, Mismatches: 14, Indels: 18
0.90 0.04 0.05
Matches are distributed among these distances:
50 47 0.16
52 1 0.00
53 50 0.17
54 103 0.34
55 44 0.15
56 57 0.19
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:35408052 original size:110 final size:109
Alignment explanation
Indices: 35407699--35408078 Score: 596
Period size: 107 Copynumber: 3.5 Consensus size: 109
35407689 CACGTGAGCC
* *
35407699 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAAAAGGCTCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AAAAGGCTCAA
* *
35407763 CTCTCCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AA
65 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
35407804 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGGCTCAAC
35407868 TCACCTCTCGCAATATG-GTTGATTTTTGAAAAACAGAAATTAA
66 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
35407911 AAGGCTCAACTCACCTCTCGCAATATTAGTTGATTTTTGAAAAACAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGGCTCAAC
* *
35407975 TCACCTCTCACAATATGAGTTGGTTTTTTTGAAAAACAGAAATTAA
66 TCACCTCTCGCAATATGAGTT-G-ATTTTTGAAAAACAGAAATTAA
35408021 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAG
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAG
35408079 TAGAAATTGA
Statistics
Matches: 254, Mismatches: 12, Indels: 12
0.91 0.04 0.04
Matches are distributed among these distances:
103 18 0.07
104 28 0.11
105 38 0.15
106 10 0.04
107 79 0.31
108 3 0.01
109 1 0.00
110 72 0.28
111 5 0.02
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (109 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGGCTCAAC
TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:35408076 original size:14 final size:14
Alignment explanation
Indices: 35408057--35408091 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35408047 GAGTTGATTT
35408057 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
35408071 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
35408085 TTGAAAA
1 TTGAAAA
35408092 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:35408298 original size:192 final size:179
Alignment explanation
Indices: 35408025--35408679 Score: 605
Period size: 192 Copynumber: 3.6 Consensus size: 179
35408015 AATTAAAAGG
* *
35408025 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAGTAGAAATTGAA
1 CTCAACTCACCTCTTGCAATATGAGTTGA-TTTTGAAAAATAG-AATTGAAAAGTAGAAATTGAA
*
35408090 AATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTGAAAC
64 AATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTG-AA-
* *
35408155 ACAGCAATTAAAAAAACAGAAATTAAAAACAGAATTTGAAAAGACCTCAGCGTGTG-GCCTGAGA
126 A-AGC-A-T----AAACAG-AA--AAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGA
* * *
35408219 CTCAACTCACCTCTTGCAATATGAGTTGA-TTTGAAAAGTAGAATTAGTAAAGCAGAAATTGAAA
1 CTCAACTCACCTCTTGCAATATGAGTTGATTTTGAAAAATAGAATT-GAAAAGTAGAAATTGAAA
*
35408283 ATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA---TTTTTGAAAAGC
65 ATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGC
* ** * * *
35408345 ATAGATTGAAAAAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGG
130 ATAAACAGAAAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGA
* * *
35408395 CTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAATATAGGTTGGAAAAAATAGAAATTG
1 CTCAACTCACCTCTTGCAATATGAGTTGA-TTTTGAAAAATAGA-ATT-G-AAAAGTAGAAATTG
*
35408460 AAAATACCTCAGCGTGTCC-TGAGGCTTAACTCACCTCTCGCAATATGAGTTGA-----TTT-AA
62 AAAATACCTCAGCGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAA
* ** * * * * * *
35408518 AAACAGT---CA-CTAAGAACAGAAATTAAAAATACCTCAGC--GTG-TCCTAAGG
126 AAGCA-TAAACAGAAAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGA
* * ** *
35408567 CTCAACTCACCTCTCGCAATATGAATTGATTTTTGCAAAATATA-AATTGAAAAACATAAATTGA
1 CTCAACTCACCTCTTGCAATATGAGTTGA-TTTTG-AAAA-ATAGAATTGAAAAGTAGAAATTGA
*
35408631 AATTACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATGAGT
63 AAATACCTCAGCGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
35408680 CAACTTTTTT
Statistics
Matches: 409, Mismatches: 41, Indels: 46
0.82 0.08 0.09
Matches are distributed among these distances:
170 60 0.15
171 3 0.01
172 41 0.10
173 5 0.01
174 27 0.07
176 60 0.15
177 9 0.02
178 17 0.04
179 6 0.01
180 59 0.14
181 2 0.00
183 1 0.00
184 1 0.00
185 3 0.01
186 1 0.00
187 2 0.00
188 6 0.01
191 4 0.01
192 74 0.18
194 28 0.07
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (179 bp):
CTCAACTCACCTCTTGCAATATGAGTTGATTTTGAAAAATAGAATTGAAAAGTAGAAATTGAAAA
TACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCA
TAAACAGAAAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGA
Found at i:35408343 original size:87 final size:86
Alignment explanation
Indices: 35408179--35408679 Score: 536
Period size: 87 Copynumber: 5.7 Consensus size: 86
35408169 AACAGAAATT
* * * *
35408179 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAG
35408244 TTGA--TTTGAAAAGTAGAATTAG
64 TTGATTTTTGAAAA-TAGAATTAG
* * *
35408266 TAAAGCAGAAATTGAAAATACCTCAGCGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATAAGT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATGAGT
*
35408330 TGATTTTTGAAAAGCATAG-ATTGAA
65 TGATTTTTG-AAA--ATAGAATT-AG
* * *
35408355 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
35408419 GTTGATTTTTGAAAAATATAGGTTGG
63 GTTGATTTTTG-AAAATAGA-ATTAG
* *
35408445 AAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTTAACTCACCTCTCGCAATATGAGT
1 -AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * *
35408510 TGA--TTT-AAAA-ACAGTCACT
65 TGATTTTTGAAAATAGAATTA-G
* * * *
35408529 AAGAACAGAAATTAAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAATT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
35408594 GATTTTTGCAAAATATAAATT-G
66 GATTTTTG-AAAATA-GAATTAG
* *
35408616 AAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
35408680 CAACTTTTTT
Statistics
Matches: 350, Mismatches: 42, Indels: 44
0.80 0.10 0.10
Matches are distributed among these distances:
83 63 0.18
84 4 0.01
85 38 0.11
87 95 0.27
88 9 0.03
89 67 0.19
90 1 0.00
91 71 0.20
93 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (86 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAATAGAATTAG
Found at i:35408372 original size:15 final size:16
Alignment explanation
Indices: 35408339--35408372 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35408329 TTGATTTTTG
* *
35408339 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
35408355 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
35408371 AA
1 AA
35408373 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:35408625 original size:14 final size:14
Alignment explanation
Indices: 35408603--35408632 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35408593 TGATTTTTGC
*
35408603 AAAATATAAATTGA
1 AAAACATAAATTGA
35408617 AAAACATAAATTGA
1 AAAACATAAATTGA
35408631 AA
1 AA
35408633 TTACCTCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAACATAAATTGA
Found at i:35420917 original size:17 final size:17
Alignment explanation
Indices: 35420895--35420955 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
35420885 ACAATAATAT
35420895 AAAATA-ATGATATGTAC
1 AAAATATAT-ATATGTAC
35420912 AAAATATATATATGTAC
1 AAAATATATATATGTAC
*
35420929 ATAATATAGT-TA--TA-
1 AAAATATA-TATATGTAC
35420943 AAAATATATATAT
1 AAAATATATATAT
35420956 TAAATTCGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.03
14 9 0.24
15 2 0.05
17 23 0.61
18 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (17 bp):
AAAATATATATATGTAC
Found at i:35422063 original size:30 final size:30
Alignment explanation
Indices: 35422008--35422124 Score: 139
Period size: 30 Copynumber: 3.9 Consensus size: 30
35421998 TGTAATTTTT
* *
35422008 AGAAAATTTA-GGGTTAAAATGAAATTTAA
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
* * *
35422037 TGAAAGTTTAGGGGTCTAAGTGAAATTTAA
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
*
35422067 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
* *
35422096 GGAAAAGTTTAGGGGTCAAAATGTAATTT
1 AG-AAAGTTTAGGGGTCAAAATGAAATTT
35422125 TTATTTTTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.14
30 64 0.86
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (30 bp):
AGAAAGTTTAGGGGTCAAAATGAAATTTAA
Found at i:35422124 original size:60 final size:59
Alignment explanation
Indices: 35421995--35422124 Score: 163
Period size: 60 Copynumber: 2.2 Consensus size: 59
35421985 TTCTGGAGAT
** * * *
35421995 AAATGTAATTTTTAGAAAATTTAGGGTTAAAATGAAATTTAATGAAAGTTTAGGGGTCT
1 AAATGTAATTTAAAGAAAATTTAGGGTCAAAATGAAATTTAAGGAAAGTTTAGGGGTCA
* * *
35422054 AAGTGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTAGGGGTCA
1 AAATGTAATTTAAAGAAAATTT-AGGGTCAAAATGAAATTTAAGG-AAAGTTTAGGGGTCA
35422114 AAATGTAATTT
1 AAATGTAATTT
35422125 TTATTTTTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 19 0.32
60 40 0.68
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (59 bp):
AAATGTAATTTAAAGAAAATTTAGGGTCAAAATGAAATTTAAGGAAAGTTTAGGGGTCA
Found at i:35422139 original size:14 final size:15
Alignment explanation
Indices: 35422120--35422154 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
35422110 GTCAAAATGT
35422120 AATTTTTATTTTT-A
1 AATTTTTATTTTTGA
*
35422134 AATTTTTTTTTTTGA
1 AATTTTTATTTTTGA
35422149 AATTTT
1 AATTTT
35422155 GAAAATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTTTGA
Found at i:35425287 original size:10 final size:10
Alignment explanation
Indices: 35425274--35425307 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
35425264 AATGGATTAT
35425274 AAAAAATTTAA
1 AAAAAATTT-A
35425285 AAAAAATTTA
1 AAAAAATTTA
35425295 AAAAAATTTA
1 AAAAAATTTA
35425305 AAA
1 AAA
35425308 GATTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:35425290 original size:11 final size:11
Alignment explanation
Indices: 35425274--35425307 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
35425264 AATGGATTAT
35425274 AAAAAATTTAA
1 AAAAAATTTAA
35425285 AAAAAATTT-A
1 AAAAAATTTAA
35425295 AAAAAATTTAA
1 AAAAAATTTAA
35425306 AA
1 AA
35425308 GATTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAAATTTAA
Found at i:35427498 original size:19 final size:20
Alignment explanation
Indices: 35427460--35427500 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
35427450 TAATATATTT
35427460 ATAAATTTAGAAACAATTAA
1 ATAAATTTAGAAACAATTAA
35427480 ATAATATTTA-AAA-AATTAA
1 ATAA-ATTTAGAAACAATTAA
35427499 AT
1 AT
35427501 TTTAAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAAATTTAGAAACAATTAA
Found at i:35427609 original size:13 final size:14
Alignment explanation
Indices: 35427576--35427609 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
35427566 CTTATATATT
35427576 AAATT-AATTTATA
1 AAATTAAATTTATA
35427589 AAATTAAATTT-TA
1 AAATTAAATTTATA
35427602 AAATTAAA
1 AAATTAAA
35427610 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTAAATTTATA
Found at i:35427616 original size:17 final size:18
Alignment explanation
Indices: 35427594--35427637 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
35427584 TTATAAAATT
35427594 AAATTTTAAAAT-TAAAA
1 AAATTTTAAAATATAAAA
35427611 AAATTTTAAAATATAAAA
1 AAATTTTAAAATATAAAA
35427629 ATAATTTTA
1 A-AATTTTA
35427638 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 12 0.48
18 6 0.24
19 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTTAAAATATAAAA
Found at i:35427646 original size:19 final size:19
Alignment explanation
Indices: 35427580--35427665 Score: 68
Period size: 20 Copynumber: 4.4 Consensus size: 19
35427570 TATATTAAAT
35427580 TAATTTATAAAATTAAATTTTA
1 TAATTTA-AAAA-T-AATTTTA
*
35427602 -AAATTAAAAA-AATTTTA
1 TAATTTAAAAATAATTTTA
* *
35427619 AAATATAAAAATAATTTTA
1 TAATTTAAAAATAATTTTA
* *
35427638 TATTTTAAAATTTAATTTTA
1 TAATTTAAAA-ATAATTTTA
*
35427658 TAAATTAA
1 TAATTTAA
35427666 TGTAATATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
17 7 0.13
18 8 0.15
19 14 0.27
20 18 0.35
21 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATTTAAAAATAATTTTA
Found at i:35435289 original size:17 final size:18
Alignment explanation
Indices: 35435248--35435287 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35435238 ACCCAGTTCG
35435248 TGTTTTCAGAAAAGCTTT
1 TGTTTTCAGAAAAGCTTT
*
35435266 TGTTTTCATAAAA-C-TT
1 TGTTTTCAGAAAAGCTTT
35435282 TGTTTT
1 TGTTTT
35435288 TCGTCAATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (18 bp):
TGTTTTCAGAAAAGCTTT
Found at i:35436685 original size:16 final size:18
Alignment explanation
Indices: 35436649--35436686 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35436639 GACAGATCTA
35436649 AAAATAGAAGAAAGTAAC
1 AAAATAGAAGAAAGTAAC
*
35436667 AAAATAGATG-AAG-AAC
1 AAAATAGAAGAAAGTAAC
35436683 AAAA
1 AAAA
35436687 GAACAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAATAGAAGAAAGTAAC
Found at i:35446651 original size:28 final size:27
Alignment explanation
Indices: 35446619--35446685 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
35446609 ATTTTTTTCT
*
35446619 TTTCTTTTTCCTTCTCTTTTTTTCTCCC
1 TTTCTTTTTCCTTAT-TTTTTTTCTCCC
* ***
35446647 TTTCTTCTTTCTTTATTTTTTTTCTTTT
1 TTTCTT-TTTCCTTATTTTTTTTCTCCC
35446675 TTTCTTTTTCC
1 TTTCTTTTTCC
35446686 CTCTTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 4 0.12
28 21 0.66
29 7 0.22
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTCTTTTTCCTTATTTTTTTTCTCCC
Found at i:35446672 original size:13 final size:14
Alignment explanation
Indices: 35446647--35446684 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
35446637 TTTTTCTCCC
35446647 TTTCTTCTTTCTTTA
1 TTTCTT-TTTCTTTA
*
35446662 TTT-TTTTTCTTTT
1 TTTCTTTTTCTTTA
35446675 TTTCTTTTTC
1 TTTCTTTTTC
35446685 CCTCTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 10 0.48
14 8 0.38
15 3 0.14
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTCTTTA
Found at i:35446679 original size:25 final size:26
Alignment explanation
Indices: 35446610--35446681 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
35446600 TTCTTTTCCA
* *
35446610 TTTTTTTCTTTTCTTT-TTCCTTCTCT
1 TTTTTTTCTTTT-TTTCTTTCTTCTAT
* *
35446636 TTTTTTCTCCCTTTCTTCTTTCTT-TAT
1 TTTTTT-T-CTTTTTTTCTTTCTTCTAT
35446663 TTTTTTTCTTTTTTTCTTT
1 TTTTTTTCTTTTTTTCTTT
35446682 TTCCCTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
25 10 0.27
26 7 0.19
27 11 0.30
28 9 0.24
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTTTCTTTTTTTCTTTCTTCTAT
Found at i:35457456 original size:15 final size:15
Alignment explanation
Indices: 35457436--35457464 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35457426 ATAATCCTAA
35457436 TAATTATCTTAATAT
1 TAATTATCTTAATAT
35457451 TAATTATCTTAATA
1 TAATTATCTTAATA
35457465 AAATGGAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATCTTAATAT
Found at i:35458709 original size:13 final size:13
Alignment explanation
Indices: 35458691--35458717 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35458681 GAAGCTATCG
35458691 CACATGGGCGTGT
1 CACATGGGCGTGT
35458704 CACATGGGCGTGT
1 CACATGGGCGTGT
35458717 C
1 C
35458718 CCTGTCGAGC
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:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (13 bp):
CACATGGGCGTGT
Found at i:35466039 original size:22 final size:22
Alignment explanation
Indices: 35466014--35466056 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35466004 TATTCAAACA
35466014 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
35466036 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
35466057 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:35468841 original size:14 final size:14
Alignment explanation
Indices: 35468808--35468835 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35468798 TTGAAATTTA
35468808 TGAAAAGTTTAGGG
1 TGAAAAGTTTAGGG
35468822 TGAAAAGTTTAGGG
1 TGAAAAGTTTAGGG
35468836 GCAAAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
TGAAAAGTTTAGGG
Found at i:35475073 original size:18 final size:18
Alignment explanation
Indices: 35475043--35475094 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 18
35475033 TGGGATCGAA
35475043 CATA-GCCTGTGACACGGG
1 CATATGCCT-TGACACGGG
35475061 CATATGCCTTGACCACACGGG
1 CATATGCCTTG---ACACGGG
*
35475082 CATGTGCCTTGAC
1 CATATGCCTTGAC
35475095 CACGCGGGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 8 0.28
19 4 0.14
21 17 0.59
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.21
Consensus pattern (18 bp):
CATATGCCTTGACACGGG
Found at i:35475108 original size:21 final size:21
Alignment explanation
Indices: 35475054--35475108 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
35475044 ATAGCCTGTG
*
35475054 ACACGGGCATATGCCTTGACC
1 ACACGGGCATGTGCCTTGACC
35475075 ACACGGGCATGTGCCTTGACC
1 ACACGGGCATGTGCCTTGACC
* *
35475096 ACGCGGGCGTGTG
1 ACACGGGCATGTG
35475109 TGCCCTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.31, G:0.33, T:0.18
Consensus pattern (21 bp):
ACACGGGCATGTGCCTTGACC
Found at i:35486870 original size:13 final size:13
Alignment explanation
Indices: 35486852--35486877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35486842 AATAAAGAAT
35486852 GTGGAGGTGTTTG
1 GTGGAGGTGTTTG
35486865 GTGGAGGTGTTTG
1 GTGGAGGTGTTTG
35486878 AATTCCACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.54, T:0.38
Consensus pattern (13 bp):
GTGGAGGTGTTTG
Found at i:35487164 original size:30 final size:30
Alignment explanation
Indices: 35487130--35487188 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
35487120 TTGAGCCTAG
*
35487130 TGATTGTGTGGGTACTGTTGATGGGCCCGA
1 TGATTGTGTAGGTACTGTTGATGGGCCCGA
**
35487160 TGATTGTGTAGGTGTTGTTGATGGGCCCG
1 TGATTGTGTAGGTACTGTTGATGGGCCCG
35487189 TCCCATCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.41, T:0.36
Consensus pattern (30 bp):
TGATTGTGTAGGTACTGTTGATGGGCCCGA
Found at i:35487695 original size:7 final size:7
Alignment explanation
Indices: 35487685--35487716 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
35487675 TTATATACAT
35487685 AATACTA
1 AATACTA
35487692 AATACTA
1 AATACTA
35487699 AATACTA
1 AATACTA
*
35487706 AGTACTA
1 AATACTA
35487713 AATA
1 AATA
35487717 TGAAACGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:35497860 original size:17 final size:18
Alignment explanation
Indices: 35497838--35497871 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
35497828 TATGAATTTT
35497838 ATTAAAATAT-AAAATAA
1 ATTAAAATATGAAAATAA
35497855 ATTAAAATATGAAAATA
1 ATTAAAATATGAAAATA
35497872 CAAAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTAAAATATGAAAATAA
Found at i:35498488 original size:23 final size:23
Alignment explanation
Indices: 35498439--35498497 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
35498429 TTATCAGATT
**
35498439 TTAATTTATAATAAAGTGCAATT
1 TTAATTTATAATAAAGTGCAACA
*
35498462 TTAATTTATATATAAA-TGTAACA
1 TTAATTTATA-ATAAAGTGCAACA
35498485 TTAA-TTA-AATAAA
1 TTAATTTATAATAAA
35498498 AATTAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.16
21 1 0.03
22 3 0.09
23 18 0.56
24 5 0.16
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (23 bp):
TTAATTTATAATAAAGTGCAACA
Found at i:35499184 original size:29 final size:29
Alignment explanation
Indices: 35499150--35499222 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
35499140 ATAAGGATTG
* * *
35499150 GATCAAATTAGTCTTTCTATTATTAAATA
1 GATCAAATTAGTCTCTATATTATTAAACA
* *
35499179 GATCAATTTAGTCCCTATATTATTAAACA
1 GATCAAATTAGTCTCTATATTATTAAACA
*
35499208 GAATCAAATAAGTCT
1 G-ATCAAATTAGTCT
35499223 AAATTTTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (29 bp):
GATCAAATTAGTCTCTATATTATTAAACA
Found at i:35503902 original size:60 final size:59
Alignment explanation
Indices: 35503782--35503918 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
35503772 CAGTGTTAAC
* *
35503782 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATAT
* * *
35503843 TGGGCCTAGCCCATATCAGTGTCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATAT
* *
35503903 TGGGTCTTGCCCATAT
1 TGGGCCTAGCCCATAT
35503919 TAACACAGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 4 0.06
60 51 0.77
61 11 0.17
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTATAT
Found at i:35503954 original size:19 final size:20
Alignment explanation
Indices: 35503911--35503966 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
35503901 ATTGGGTCTT
35503911 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
35503931 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
* *
35503950 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
35503967 CTCATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:35508675 original size:12 final size:11
Alignment explanation
Indices: 35508643--35508687 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
35508633 ATTTTTATGT
35508643 AAAATTAT-AA
1 AAAATTATAAA
*
35508653 AAAATT-CAAA
1 AAAATTATAAA
35508663 AAAATTATTAAA
1 AAAATTA-TAAA
35508675 AAAATTATAAA
1 AAAATTATAAA
35508686 AA
1 AA
35508688 TACAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 14 0.47
11 6 0.20
12 10 0.33
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:35508686 original size:20 final size:19
Alignment explanation
Indices: 35508643--35508714 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 19
35508633 ATTTTTATGT
35508643 AAAATTAT-AAAAAATTCAAA
1 AAAATTATAAAAAAATT--AA
35508663 AAAATTATTAAAAAAATTATA
1 AAAATTA-TAAAAAAATTA-A
*
35508684 AAAA-TACAAAAAAAAGTTAA
1 AAAATTA-TAAAAAAA-TTAA
35508704 AAAATTA-AAAA
1 AAAATTATAAAA
35508715 CTTTCTACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
19 4 0.09
20 22 0.49
21 11 0.24
22 8 0.18
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (19 bp):
AAAATTATAAAAAAATTAA
Found at i:35513370 original size:3 final size:3
Alignment explanation
Indices: 35513353--35513451 Score: 119
Period size: 3 Copynumber: 32.7 Consensus size: 3
35513343 TGCAAAAGCA
* *
35513353 AAG AGAG AA- AAG AAG AAG AAG AAG AAG AAA AAA AAG AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * *
35513398 AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG GAG GAG AAAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
35513447 AAG AA
1 AAG AA
35513452 AAAAATGTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.02
3 78 0.92
4 5 0.06
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35513387 original size:24 final size:24
Alignment explanation
Indices: 35513360--35513429 Score: 131
Period size: 24 Copynumber: 2.9 Consensus size: 24
35513350 GCAAAGAGAG
35513360 AAAAGAAGAAGAAGAAGAAGAAAA
1 AAAAGAAGAAGAAGAAGAAGAAAA
35513384 AAAAGAAGAAGAAGAAGAAGAAAA
1 AAAAGAAGAAGAAGAAGAAGAAAA
*
35513408 AGAAGAAGAAGAAGAAGAAGAA
1 AAAAGAAGAAGAAGAAGAAGAA
35513430 GGAGAAGGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AAAAGAAGAAGAAGAAGAAGAAAA
Found at i:35514542 original size:11 final size:11
Alignment explanation
Indices: 35514507--35514534 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
35514497 GAGAGTAAGA
35514507 AATTTTAATGT
1 AATTTTAATGT
35514518 AATTTTAATGT
1 AATTTTAATGT
35514529 AATTTT
1 AATTTT
35514535 GATATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTAATGT
Found at i:35516161 original size:6 final size:6
Alignment explanation
Indices: 35516150--35516182 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
35516140 ACCAACTCCG
35516150 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAG
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAG
35516183 GCAGTGCCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.30, G:0.36, T:0.00
Consensus pattern (6 bp):
GAGCCA
Found at i:35519690 original size:19 final size:17
Alignment explanation
Indices: 35519667--35519708 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
35519657 TAAAATATAA
* *
35519667 TAAAATAATAATATT-T
1 TAAAAAAATTATATTAT
35519683 TAAAAAAATTATATTAT
1 TAAAAAAATTATATTAT
35519700 TAAAAAAAT
1 TAAAAAAAT
35519709 GGGTCGCGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAAATTATATTAT
Found at i:35520418 original size:54 final size:51
Alignment explanation
Indices: 35520354--35520471 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 51
35520344 TCCTAAGGGT
*
35520354 AACAGTAACAGTAACAGT-AGCGGTACACAAAGTACCTCATCGGAACAAATCTGG
1 AACAGTAACAGTAACAGTCA--GGT--ACAAAGTACCTCATCGGAACAAATCCGG
* ** * *
35520408 AACAGTAACAGTAATAGTCAGGTACGGAGTACCTCTTCGGAACGAATCCGG
1 AACAGTAACAGTAACAGTCAGGTACAAAGTACCTCATCGGAACAAATCCGG
*
35520459 AACAGTCACAGTA
1 AACAGTAACAGTA
35520472 GTCGACACAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
51 35 0.62
53 3 0.05
54 17 0.30
55 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (51 bp):
AACAGTAACAGTAACAGTCAGGTACAAAGTACCTCATCGGAACAAATCCGG
Found at i:35520762 original size:3 final size:3
Alignment explanation
Indices: 35520754--35520788 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35520744 ATTCAATACC
35520754 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
35520789 GATGATGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:35521438 original size:17 final size:19
Alignment explanation
Indices: 35521404--35521441 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
35521394 AAACCTTTAA
35521404 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTTCTTCTTTC
35521423 TTTTCTC-TTT-TTCTTTC
1 TTTTCTCTTTTCTTCTTTC
35521440 TT
1 TT
35521442 CCTTCCCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTCTTTC
Found at i:35523883 original size:43 final size:41
Alignment explanation
Indices: 35523835--35523991 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 41
35523825 CAACGCCAAC
** *
35523835 GTCCCAGACGTAATCTTACATGTAATCAAATAACGATGCCACT
1 GTCCCAGACGTGGTCTTACATGAAATCAAAT-ACGATGCCA-T
35523878 GTCCCAGACAG-GGTCTTACATGAAATCAAATACGATGCCGAT
1 GTCCCAGAC-GTGGTCTTACATGAAATCAAATACGATGCC-AT
* ** *
35523920 GTCCCAAACACGGTCTTACACGTAAATTTCAAAT-CGATGCCAAT
1 GTCCCAGACGTGGTCTTACATG-AAA--TCAAATACGATGCC-AT
35523964 GTCCCAGACGTGGTCTTACATGAAATCA
1 GTCCCAGACGTGGTCTTACATGAAATCA
35523992 CATATCGGAA
Statistics
Matches: 97, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
41 3 0.03
42 27 0.28
43 33 0.34
44 28 0.29
45 6 0.06
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
GTCCCAGACGTGGTCTTACATGAAATCAAATACGATGCCAT
Found at i:35523935 original size:42 final size:41
Alignment explanation
Indices: 35523848--35523991 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 41
35523838 CCAGACGTAA
* *
35523848 TCTTACATGTAATCAAATAACGATGCCACTGTCCCAGACAGGG
1 TCTTACATGAAATCAAAT-ACGATGCCA-TGTCCCAGACACGG
*
35523891 TCTTACATGAAATCAAATACGATGCCGATGTCCCAAACACGG
1 TCTTACATGAAATCAAATACGATGCC-ATGTCCCAGACACGG
* **
35523933 TCTTACACGTAAATTTCAAAT-CGATGCCAATGTCCCAGACGTGG
1 TCTTACATG-AAA--TCAAATACGATGCC-ATGTCCCAGACACGG
35523977 TCTTACATGAAATCA
1 TCTTACATGAAATCA
35523992 CATATCGGAA
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
41 3 0.03
42 28 0.32
43 24 0.27
44 27 0.31
45 6 0.07
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
TCTTACATGAAATCAAATACGATGCCATGTCCCAGACACGG
Found at i:35526926 original size:20 final size:20
Alignment explanation
Indices: 35526901--35526960 Score: 57
Period size: 26 Copynumber: 2.6 Consensus size: 20
35526891 GAGAAGTATT
35526901 ATAAAAATTTCTATTGATAA
1 ATAAAAATTTCTATTGATAA
35526921 ATAAAAATGCATATTTCTATTGATAA
1 AT--AAA---A-ATTTCTATTGATAA
35526947 ATAAAAATTCTCTA
1 ATAAAAATT-TCTA
35526961 GCAAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
20 5 0.15
21 5 0.15
22 3 0.09
24 3 0.09
25 1 0.03
26 16 0.48
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (20 bp):
ATAAAAATTTCTATTGATAA
Found at i:35529782 original size:3 final size:3
Alignment explanation
Indices: 35529774--35529804 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35529764 GCGCAAGACA
35529774 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35529805 TATTCGTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35529899 original size:3 final size:3
Alignment explanation
Indices: 35529891--35529922 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
35529881 TTTATTTCTC
*
35529891 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35529923 CATTGTCGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:35530044 original size:13 final size:13
Alignment explanation
Indices: 35530028--35530053 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35530018 ATTTTCCTTA
35530028 ATATTTATTTATT
1 ATATTTATTTATT
35530041 ATATTTATTTATT
1 ATATTTATTTATT
35530054 TATCCCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTTATTTATT
Found at i:35536859 original size:44 final size:44
Alignment explanation
Indices: 35536795--35536945 Score: 153
Period size: 44 Copynumber: 3.5 Consensus size: 44
35536785 CACCATCCTA
*
35536795 TCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTACAGATCTTG
* * ** * ** * * *
35536839 TCTCCCTAAGCAGTAATGGAGCAGATTTAAG-CCAC-CATCCTA
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTACAGATCTTG
* **
35536881 TCTCCTTAAGCAGTAGTGGAGTAGGCTAAAGATTGTAGATCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTACAGATCTTG
*
35536925 TCTCTCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAG
35536946 CAGGTTTAAG
Statistics
Matches: 80, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
42 29 0.36
43 2 0.03
44 49 0.61
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTACAGATCTTG
Found at i:35536901 original size:42 final size:42
Alignment explanation
Indices: 35536757--35536901 Score: 173
Period size: 42 Copynumber: 3.4 Consensus size: 42
35536747 ATCTTGTCTT
35536757 CCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTC
1 CCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTC
* ** * ** * * *
35536799 CCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTTGTCTC
1 CCTAAGCAGTAGTGGAGCAGATTTAAG-CCAC-CATCCTATCTC
*
35536843 CCTAAGCAGTAATGGAGCAGATTTAAGCCACCATCCTATCTC
1 CCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTC
*
35536885 CTTAAGCAGTAGTGGAG
1 CCTAAGCAGTAGTGGAG
35536902 TAGGCTAAAG
Statistics
Matches: 80, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
42 46 0.57
43 4 0.05
44 30 0.38
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (42 bp):
CCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTC
Found at i:35536987 original size:86 final size:86
Alignment explanation
Indices: 35536747--35536969 Score: 358
Period size: 86 Copynumber: 2.6 Consensus size: 86
35536737 AATACGGTGA
*
35536747 ATCTTGTCT-TCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAG
1 ATCTTGTCTCT-CTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCTTAAGCAGTAG
*
35536811 TGGAGTAGGCTGAAGATTACAG
65 TGGAGTAGGCTAAAGATTACAG
* *
35536833 ATCTTGTCTCCCTAAGCAGTAATGGAGCAGATTTAAGCCACCATCCTATCTCCTTAAGCAGTAGT
1 ATCTTGTCTCTCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCTTAAGCAGTAGT
**
35536898 GGAGTAGGCTAAAGATTGTAG
66 GGAGTAGGCTAAAGATTACAG
* *
35536919 ATCTTGTCTCTCTAAGCAGTAGTGGAGCAGGTTTAAGCCACCGTCCTATCT
1 ATCTTGTCTCTCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCT
35536970 TTTTGAGTAG
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
86 126 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (86 bp):
ATCTTGTCTCTCTAAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCTTAAGCAGTAGT
GGAGTAGGCTAAAGATTACAG
Found at i:35537155 original size:88 final size:88
Alignment explanation
Indices: 35537001--35537505 Score: 751
Period size: 88 Copynumber: 5.8 Consensus size: 88
35536991 GTTAAAATCA
* * * * *
35537001 ACAATTCTTATCTCCTTGAAATTCTAGCGGAGTAGGTCGAAGTTACAAATCTCTTCTCCCTAAAA
1 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
35537066 TGGTATTGGATCGGCTCGAAGCC
66 TGGCATTGGAGCGGCTCGAAGCC
* * * * *
35537089 ACAATTCGTCTCTCCTTGAAGTTCCAGCGGAGTAGATTGAAGTTACAAATCTCTTATCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
35537154 TGGTATTGGAGCGGCTCAAAGCC
66 TGGCATTGGAGCGGCTCGAAGCC
* *
35537177 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTTTTCTCCCTAAAA
1 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
35537242 TGGCATTGGAGCGGCTCGAAGCC
66 TGGCATTGGAGCGGCTCGAAGCC
*
35537265 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCTCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
*
35537330 TGGCAATGGAGCGGCTCGAAGCC
66 TGGCATTGGAGCGGCTCGAAGCC
* * * * *
35537353 ATAATTCATATCTCTTTGAAGTTCCAGCGGAGTAGATCGAAACTACAAATCTCTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
35537418 TGGCATTGAAGCGGCTCGTAGCC
66 TGGCATTGGAGCGGCTCGAAGCC
* * *
35537441 ACAATTCGTATCTCCTTGAAGTTTTAGC-GAGTAGATCGAAGCTAGAAATCTCTTCTTCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
35537505 T
66 T
35537506 TACAATGGAA
Statistics
Matches: 377, Mismatches: 40, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
87 34 0.09
88 343 0.91
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (88 bp):
ACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
TGGCATTGGAGCGGCTCGAAGCC
Found at i:35537263 original size:44 final size:44
Alignment explanation
Indices: 35537213--35537351 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 44
35537203 GCGGAGTAGA
* *
35537213 TCGAAGCTACAAATCTTTTCTCCCTAAAATGGCATTGGAGCGGC
1 TCGAAGCTACAAATCTTTTCTCCCTGAAATGGCAATGGAGCGGC
* * * * * * * ** ** *
35537257 TCGAAGCCACAATTCGTATCTCCTTGAAGT-TCTAGCGGAGTAGA
1 TCGAAGCTACAAATCTTTTCTCCCTGAAATGGC-AATGGAGCGGC
* *
35537301 TCGAAGCTACAAATCTCTTCTCTCTGAAATGGCAATGGAGCGGC
1 TCGAAGCTACAAATCTTTTCTCCCTGAAATGGCAATGGAGCGGC
35537345 TCGAAGC
1 TCGAAGC
35537352 CATAATTCAT
Statistics
Matches: 66, Mismatches: 27, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
43 1 0.02
44 64 0.97
45 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.26
Consensus pattern (44 bp):
TCGAAGCTACAAATCTTTTCTCCCTGAAATGGCAATGGAGCGGC
Found at i:35537393 original size:44 final size:42
Alignment explanation
Indices: 35537257--35537393 Score: 105
Period size: 44 Copynumber: 3.1 Consensus size: 42
35537247 TTGGAGCGGC
* *
35537257 TCGAAGCCACAATTCGTATCTCCTTGAAGTTCTAGCGGAGTAGA
1 TCGAAGCCA-AATTC-TATCTCTTTGAAGTTCCAGCGGAGTAGA
* * ** ** ** *
35537301 TCGAAGCTACAAATCTCT-TCTCTCTGAAATGGCAATGGAGCGGC
1 TCGAAGC--CAAAT-TCTATCTCTTTGAAGTTCCAGCGGAGTAGA
35537345 TCGAAGCCATAATTCATATCTCTTTGAAGTTCCAGCGGAGTAGA
1 TCGAAGCCA-AATTC-TATCTCTTTGAAGTTCCAGCGGAGTAGA
35537389 TCGAA
1 TCGAA
35537394 ACTACAAATC
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
42 4 0.06
43 4 0.06
44 51 0.76
45 4 0.06
46 4 0.06
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (42 bp):
TCGAAGCCAAATTCTATCTCTTTGAAGTTCCAGCGGAGTAGA
Found at i:35539830 original size:3 final size:3
Alignment explanation
Indices: 35539822--35539846 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35539812 GCGCAAGACA
35539822 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
35539847 TATTCGTCCA
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:35539939 original size:3 final size:3
Alignment explanation
Indices: 35539931--35539962 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
35539921 TTTATTTCTC
*
35539931 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35539963 CATTGTCGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:35540084 original size:13 final size:13
Alignment explanation
Indices: 35540068--35540093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35540058 ATTTTCCTTA
35540068 ATATTTATTTATT
1 ATATTTATTTATT
35540081 ATATTTATTTATT
1 ATATTTATTTATT
35540094 TATCCCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTTATTTATT
Found at i:35550380 original size:15 final size:15
Alignment explanation
Indices: 35550360--35550388 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35550350 AGTACTCCAG
35550360 CCGAAATTCAAGACT
1 CCGAAATTCAAGACT
35550375 CCGAAATTCAAGAC
1 CCGAAATTCAAGAC
35550389 GCTGTCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (15 bp):
CCGAAATTCAAGACT
Done.