Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 9 of 226
Found at i:3276843 original size:211 final size:211
Alignment explanation
Indices: 3276426--3276922 Score: 834
Period size: 211 Copynumber: 2.4 Consensus size: 211
3276416 ATAACTCGCA
* * * * *
3276426 CAATGCC-ATATCCCAGATATGGTCTTACATGCTATCATATATCGATGCTAATGTCCCAGACATG
1 CAATGCCAATGTCCCAGACATGGTCTTACACG-AATCATATA-CGATGCCAATGTCCCAGACATG
3276490 GTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGA
64 GTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGA
* *
3276555 TGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCGGACATGATC
129 TGCCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCCAGACATGATC
3276620 TTACAAGTAATCTCATAT
194 TTACAAGTAATCTCATAT
3276638 CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
* *
3276703 CTTACACGTAATCTCATATCGATGCCAATGTCCCAGGCATGGTCTTACACGAATCATATACGATG
66 CTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGATG
* *
3276768 CCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCTAGACATGGTCTT
131 CCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCCAGACATGATCTT
*
3276833 ACACGTAATCTCATAT
196 ACAAGTAATCTCATAT
* * *
3276849 CGATGCCAATGTCCTAGACATGGTCTTACACGAATCATATACGATGCCAATGTCTCAGACATGGT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
3276914 CTTACACGT
66 CTTACACGT
3276923 TCGAAATTCT
Statistics
Matches: 269, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
211 233 0.87
212 15 0.06
213 21 0.08
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (211 bp):
CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
CTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGATG
CCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCCAGACATGATCTT
ACAAGTAATCTCATAT
Found at i:3277094 original size:31 final size:31
Alignment explanation
Indices: 3277053--3277253 Score: 183
Period size: 31 Copynumber: 6.5 Consensus size: 31
3277043 CAACAATATA
* *
3277053 TATATTCATATACGAATCAAATTCGGCAACG
1 TATAATCATATACGAATCAAATTCGGCAATG
* *
3277084 TATAATCATATACAAATC-AATTTGGCAATG
1 TATAATCATATACGAATCAAATTCGGCAATG
* *
3277114 TATAACCATATATGAATCAAATTCGGCAATG
1 TATAATCATATACGAATCAAATTCGGCAATG
**
3277145 TATAATCATATACGAATC-AATTCGGCAACC
1 TATAATCATATACGAATCAAATTCGGCAATG
** * ** * **
3277175 TATTTTCTTATATAAATCAACTTCGATAATG
1 TATAATCATATACGAATCAAATTCGGCAATG
* * **
3277206 TATAACCATATACAAAT-AAATTTTAGCAATG
1 TATAATCATATACGAATCAAA-TTCGGCAATG
*
3277237 TATAATTATATACGAAT
1 TATAATCATATACGAAT
3277254 TAATTCAGCA
Statistics
Matches: 132, Mismatches: 35, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
30 50 0.38
31 82 0.62
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (31 bp):
TATAATCATATACGAATCAAATTCGGCAATG
Found at i:3277131 original size:61 final size:61
Alignment explanation
Indices: 3277053--3277289 Score: 208
Period size: 61 Copynumber: 3.9 Consensus size: 61
3277043 CAACAATATA
*
3277053 TATATTCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATG
1 TATAATCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATG
* * * * * **
3277114 TATAACCATATATGAATCAAATTCGGCAATGTATAATCATATACGAATCAATTCGGCAACC
1 TATAATCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATG
** * ** * ** * * * *
3277175 TATTTTCTTATATAAATCAACTTCGATAATGTATAACCATATACAAATAAATTTTAGCAATG
1 TATAATCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAA-TTTGGCAATG
* * * * * *
3277237 TATAATTATATACGAAT-TAATTCAGCAACTTAT-ATCCACATACAATTCAATTT
1 TATAATCATATACGAATCAAATTCGGCAACGTATAAT-CATATACAAATCAATTT
3277290 CAACAACTTT
Statistics
Matches: 134, Mismatches: 40, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
60 4 0.03
61 113 0.84
62 17 0.13
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.34
Consensus pattern (61 bp):
TATAATCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATG
Found at i:3277206 original size:92 final size:91
Alignment explanation
Indices: 3277053--3277288 Score: 251
Period size: 92 Copynumber: 2.6 Consensus size: 91
3277043 CAACAATATA
* * * *
3277053 TATATTCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATGTATA
1 TATAATCATATACGAATC-AATTCGGCAACCTATAATCATATACAAATCAATTCGACAATGTATA
** *
3277118 ACCATATATGAATCAAA-TTCGGCAATG
65 ACCATATACAAAT-AAATTTCAGCAATG
** * * *
3277145 TATAATCATATACGAATCAATTCGGCAACCTATTTTCTTATATAAATCAACTTCGATAATGTATA
1 TATAATCATATACGAATCAATTCGGCAACCTATAATCATATACAAATCAA-TTCGACAATGTATA
*
3277210 ACCATATACAAATAAATTTTAGCAATG
65 ACCATATACAAATAAATTTCAGCAATG
* * * * * *
3277237 TATAATTATATACGAATTAATTCAGCAACTTAT-ATCCACATACAATTCAATT
1 TATAATCATATACGAATCAATTCGGCAACCTATAAT-CATATACAAATCAATT
3277289 TCAACAACTT
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
91 33 0.28
92 86 0.72
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (91 bp):
TATAATCATATACGAATCAATTCGGCAACCTATAATCATATACAAATCAATTCGACAATGTATAA
CCATATACAAATAAATTTCAGCAATG
Found at i:3286839 original size:22 final size:22
Alignment explanation
Indices: 3286799--3286854 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3286789 AATAAAATTG
*
3286799 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
3286819 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* *
3286841 TATTAATAAATTAT
1 AAATAATAAATTAT
3286855 TATATGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 9 0.29
21 2 0.06
22 20 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:3293026 original size:15 final size:15
Alignment explanation
Indices: 3293002--3293032 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3292992 GCATCCTCTG
3293002 TTCCAATTATACATA
1 TTCCAATTATACATA
*
3293017 TTCCAGTTATACATA
1 TTCCAATTATACATA
3293032 T
1 T
3293033 ATGGGTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.42
Consensus pattern (15 bp):
TTCCAATTATACATA
Found at i:3298664 original size:16 final size:16
Alignment explanation
Indices: 3298643--3298710 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
3298633 TTTGGTTCGC
3298643 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3298659 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
3298675 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
3298691 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3298707 TGTA
1 TGTA
3298711 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3298966 original size:16 final size:16
Alignment explanation
Indices: 3298926--3298980 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
3298916 TTAATCATAT
*
3298926 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
3298942 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
3298957 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
3298975 -TAAAAT
1 TTAAAAT
3298981 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:3298973 original size:18 final size:17
Alignment explanation
Indices: 3298946--3298980 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3298936 TTTTTATTAA
*
3298946 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3298964 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3298981 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3299093 original size:18 final size:17
Alignment explanation
Indices: 3299066--3299100 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3299056 TTACTATTAA
*
3299066 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3299084 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3299101 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3299146 original size:61 final size:60
Alignment explanation
Indices: 3298961--3299151 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
3298951 TTTTAATTAA
* *
3298961 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
3299022 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
3299080 A
60 T
*
3299081 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
3299142 AATATATAAT
1 AATATATAAT
3299152 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Found at i:3299229 original size:120 final size:120
Alignment explanation
Indices: 3298924--3299207 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
3298914 ATTTAATCAT
*
3298924 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAAT-
* * * *
3298989 ATT-AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
64 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
3299045 AATTAACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
3299110 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
3299165 ATTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
3299208 TTTTCAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 133 0.89
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:3308743 original size:15 final size:15
Alignment explanation
Indices: 3308723--3308753 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3308713 TTTACAAACC
3308723 AAACCCAATCCAATT
1 AAACCCAATCCAATT
*
3308738 AAACCCAATTCAATT
1 AAACCCAATCCAATT
3308753 A
1 A
3308754 CAAAACCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACCCAATCCAATT
Found at i:3309601 original size:8 final size:8
Alignment explanation
Indices: 3309582--3309618 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
3309572 TTTCCTTATA
3309582 TATATATTT
1 TATAT-TTT
3309591 TATATTTT
1 TATATTTT
3309599 TATATTTT
1 TATATTTT
3309607 TACTATTTT
1 TA-TATTTT
3309616 TAT
1 TAT
3309619 TTATCCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (8 bp):
TATATTTT
Found at i:3309602 original size:17 final size:17
Alignment explanation
Indices: 3309582--3309618 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3309572 TTTCCTTATA
3309582 TATATATTTTA-TATTTT
1 TATAT-TTTTACTATTTT
3309599 TATATTTTTACTATTTT
1 TATATTTTTACTATTTT
3309616 TAT
1 TAT
3309619 TTATCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TATATTTTTACTATTTT
Found at i:3310873 original size:12 final size:13
Alignment explanation
Indices: 3310848--3310878 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3310838 ATAAAAATAG
3310848 AAAATTAATAAAA
1 AAAATTAATAAAA
3310861 AAAATTAATAAAA
1 AAAATTAATAAAA
3310874 AAAAT
1 AAAAT
3310879 AATGATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATTAATAAAA
Found at i:3317002 original size:31 final size:32
Alignment explanation
Indices: 3316964--3317025 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
3316954 ACTCTTGTAT
*
3316964 AGAAAGCCC-TTAATTATAAATGGACTTATTA
1 AGAAAGCCCATTAATTATAAACGGACTTATTA
* *
3316995 AGAAAGCCCATTAGTTATAAACGGGCTTATT
1 AGAAAGCCCATTAATTATAAACGGACTTATT
3317026 CTGACCCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (32 bp):
AGAAAGCCCATTAATTATAAACGGACTTATTA
Found at i:3337897 original size:19 final size:19
Alignment explanation
Indices: 3337860--3337897 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3337850 ATTGCCATTT
*
3337860 TTTGTTGTTGTTGTTTTGA
1 TTTGTTGTTGTGGTTTTGA
3337879 TTTGTT-TTGTGGTTATTGA
1 TTTGTTGTTGTGGTT-TTGA
3337898 ATCTGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.08, C:0.00, G:0.26, T:0.66
Consensus pattern (19 bp):
TTTGTTGTTGTGGTTTTGA
Found at i:3345815 original size:2 final size:2
Alignment explanation
Indices: 3345808--3345832 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3345798 TTCTTCTTCT
3345808 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3345833 TCATGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3359696 original size:17 final size:18
Alignment explanation
Indices: 3359668--3359701 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3359658 GTTAGCAATA
3359668 AAATATTTTTAAAAAAAT
1 AAATATTTTTAAAAAAAT
3359686 AAATA-TTTTAAAAAAA
1 AAATATTTTTAAAAAAA
3359702 GAGATACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATATTTTTAAAAAAAT
Found at i:3360258 original size:25 final size:24
Alignment explanation
Indices: 3360211--3360260 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3360201 ACTCCCCCAT
* *
3360211 ATATAAAATCTATACAATTTAAAA
1 ATATAAAATCTATAAAATGTAAAA
*
3360235 ATATAAAATATTATAAAATGTAAAA
1 ATATAAAAT-CTATAAAATGTAAAA
3360260 A
1 A
3360261 AAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
ATATAAAATCTATAAAATGTAAAA
Found at i:3361590 original size:3 final size:3
Alignment explanation
Indices: 3361582--3361606 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3361572 CAACGGTAAT
3361582 AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC A
3361607 GTGTTATAAT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3393761 original size:40 final size:40
Alignment explanation
Indices: 3393717--3393797 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
3393707 GTTTTACTTG
* *
3393717 ACCGGTGATATTTATACTTATATATTAAAGTAAGGTTCAA
1 ACCGGTGATATCTATACTTATATATTAAAGTAAGATTCAA
*
3393757 ACCGGTGATGTCTATACTTATATATTAAAGTAAGATTCAA
1 ACCGGTGATATCTATACTTATATATTAAAGTAAGATTCAA
3393797 A
1 A
3393798 GGTTCTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (40 bp):
ACCGGTGATATCTATACTTATATATTAAAGTAAGATTCAA
Found at i:3393989 original size:29 final size:29
Alignment explanation
Indices: 3393956--3394011 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3393946 TTTGGTCTCT
**
3393956 ATATTTTGATAATGTTATTAATTAGTTTA
1 ATATTTTGATAATGCAATTAATTAGTTTA
*
3393985 ATATTTTTATAATGCAATTAATTAGTT
1 ATATTTTGATAATGCAATTAATTAGTT
3394012 CAAATAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.54
Consensus pattern (29 bp):
ATATTTTGATAATGCAATTAATTAGTTTA
Found at i:3395132 original size:17 final size:17
Alignment explanation
Indices: 3395108--3395181 Score: 73
Period size: 16 Copynumber: 4.5 Consensus size: 17
3395098 GAAACCCCAC
3395108 GCGAACCCCACATATAT
1 GCGAACCCCACATATAT
* *
3395125 GTGAACCCC-CATGTAT
1 GCGAACCCCACATATAT
* *
3395141 GCGAGCCTCACATATA-
1 GCGAACCCCACATATAT
*
3395157 GACGAACCCC-CATATAG
1 G-CGAACCCCACATATAT
3395174 GCGAACCC
1 GCGAACCC
3395182 TTATGTATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
16 26 0.57
17 20 0.43
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.16
Consensus pattern (17 bp):
GCGAACCCCACATATAT
Found at i:3395295 original size:30 final size:30
Alignment explanation
Indices: 3395259--3395327 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3395249 GTGAACCCCC
* **
3395259 ATGTGCGAAAGCTATATGTGTGAACCTTAT
1 ATGTGCGAAAGCTATATGCGCAAACCTTAT
** *
3395289 ATGTGCGAACTCTGTATGCGCAAACCTTAT
1 ATGTGCGAAAGCTATATGCGCAAACCTTAT
3395319 ATGTGCGAA
1 ATGTGCGAA
3395328 CTCTAAATGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (30 bp):
ATGTGCGAAAGCTATATGCGCAAACCTTAT
Found at i:3395306 original size:15 final size:15
Alignment explanation
Indices: 3395259--3395332 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
3395249 GTGAACCCCC
**
3395259 ATGTGCGAAAGCTAT
1 ATGTGCGAACTCTAT
*
3395274 ATGTGTGAAC-CTTAT
1 ATGTGCGAACTC-TAT
*
3395289 ATGTGCGAACTCTGT
1 ATGTGCGAACTCTAT
* *
3395304 ATGCGCAAAC-CTTAT
1 ATGTGCGAACTC-TAT
3395319 ATGTGCGAACTCTA
1 ATGTGCGAACTCTA
3395333 AATGCGAACC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
14 2 0.04
15 42 0.91
16 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (15 bp):
ATGTGCGAACTCTAT
Found at i:3395338 original size:30 final size:30
Alignment explanation
Indices: 3395281--3395338 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3395271 TATATGTGTG
**
3395281 AACCTTATATGTGCGAACTCTGTATGCGCA
1 AACCTTATATGTGCGAACTCTAAATGCGCA
3395311 AACCTTATATGTGCGAACTCTAAATGCG
1 AACCTTATATGTGCGAACTCTAAATGCG
3395339 AACCCATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (30 bp):
AACCTTATATGTGCGAACTCTAAATGCGCA
Found at i:3397987 original size:22 final size:23
Alignment explanation
Indices: 3397951--3398015 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 23
3397941 GGTCGTAGGG
* *
3397951 AAGAAGGAAAGAAAAAACAT-G-A
1 AAGAA-GAAAAAAAAAAAATGGAA
3397973 AAGAAGAAAAAAAAAAGAATGGAA
1 AAGAAGAAAAAAAAAA-AATGGAA
*
3397997 AAAAAGGAAAAAAAAAAAA
1 AAGAA-GAAAAAAAAAAAA
3398016 CAAGTGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 10 0.28
22 7 0.19
23 1 0.03
24 7 0.19
25 11 0.31
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (23 bp):
AAGAAGAAAAAAAAAAAATGGAA
Found at i:3424179 original size:36 final size:34
Alignment explanation
Indices: 3424138--3424205 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
3424128 TTTTTTATAA
*
3424138 TAAACTAAATTTTGTTAATAAAAATATTAAAATTTT
1 TAAACTAAATTTT-TTAATAAAAAT-TAAAAATTTT
***
3424174 TAAACTTGCTTTTTTAATAAAAATTAAAAATT
1 TAAACTAAATTTTTTAATAAAAATTAAAAATT
3424206 AAAAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 7 0.25
35 11 0.39
36 10 0.36
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (34 bp):
TAAACTAAATTTTTTAATAAAAATTAAAAATTTT
Found at i:3424655 original size:22 final size:22
Alignment explanation
Indices: 3424629--3424696 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
3424619 TTCACAAACA
3424629 AATTCCTTTCAAAAATTCTCTC
1 AATTCCTTTCAAAAATTCTCTC
* *
3424651 AATTCCCTTCAAAATTTCTCTC
1 AATTCCTTTCAAAAATTCTCTC
* *
3424673 AATTTCTTTCCAAAATTCTCTC
1 AATTCCTTTCAAAAATTCTCTC
3424695 AA
1 AA
3424697 ACTCTCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTCCTTTCAAAAATTCTCTC
Found at i:3424702 original size:30 final size:30
Alignment explanation
Indices: 3424668--3424726 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3424658 TTCAAAATTT
* * *
3424668 CTCTCAATTTCTTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
3424698 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
3424727 TTTCCTTCAA
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:0.31, C:0.34, G:0.00, T:0.36
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:3424712 original size:52 final size:51
Alignment explanation
Indices: 3424646--3424748 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
3424636 TTCAAAAATT
* * * *
3424646 CTCTCAATTCCCTT-CAAAATTTCTCTCAATTTCTTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
3424698 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
3424749 TCCATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:3424737 original size:21 final size:22
Alignment explanation
Indices: 3424698--3424739 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3424688 TTCTCTCAAA
3424698 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
3424720 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
3424740 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:3424835 original size:30 final size:28
Alignment explanation
Indices: 3424781--3424836 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
3424771 ATTAAATTTC
3424781 ATTTTTTAAGAAAATTTTAAATTTTTTT
1 ATTTTTTAAGAAAATTTTAAATTTTTTT
*
3424809 ATTTTTTATA-AATAATTTTAAAATTTTT
1 ATTTTTTA-AGAA-AATTTTAAATTTTTT
3424837 AATATTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
ATTTTTTAAGAAAATTTTAAATTTTTTT
Found at i:3424837 original size:28 final size:28
Alignment explanation
Indices: 3424781--3424837 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
3424771 ATTAAATTTC
*
3424781 ATTTTTTAAGAAAATTTTAAATTTTTTT
1 ATTTTTTAAGAAAATTTTAAATATTTTT
3424809 ATTTTTTATA-AATAATTTTAAA-ATTTTT
1 ATTTTTTA-AGAA-AATTTTAAATATTTTT
3424837 A
1 A
3424838 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTTTAAGAAAATTTTAAATATTTTT
Found at i:3424989 original size:24 final size:23
Alignment explanation
Indices: 3424934--3424989 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
3424924 TATATTTTAA
*
3424934 ATTTTTTTAAGATATTTTTATTT
1 ATTTTTTTAAGATATTTTTATAT
3424957 ATGTATTTTT-AGATATTTATTAATAT
1 AT-T-TTTTTAAGATATTT-TT-ATAT
3424983 ATTTTTT
1 ATTTTTT
3424990 GTTATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
ATTTTTTTAAGATATTTTTATAT
Found at i:3427143 original size:23 final size:24
Alignment explanation
Indices: 3427107--3427181 Score: 91
Period size: 23 Copynumber: 3.2 Consensus size: 24
3427097 ACATTATTTG
* *
3427107 ATTAAAATCTCTAACCCT-ACTTA
1 ATTAAAAACCCTAACCCTAACTTA
*
3427130 ATTAAAAACCCTAA-CCTAATTTA
1 ATTAAAAACCCTAACCCTAACTTA
* *
3427153 ATTAAAAACCCAAACCCTAACCTA
1 ATTAAAAACCCTAACCCTAACTTA
3427177 ATTAA
1 ATTAA
3427182 TTAAATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 3 0.07
23 29 0.66
24 12 0.27
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (24 bp):
ATTAAAAACCCTAACCCTAACTTA
Found at i:3427167 original size:29 final size:29
Alignment explanation
Indices: 3427135--3427420 Score: 251
Period size: 32 Copynumber: 9.8 Consensus size: 29
3427125 ACTTAATTAA
3427135 AAACCCTAACCTAATTTAATTAAAAACCC
1 AAACCCTAACCTAATTTAATTAAAAACCC
3427164 AAACCCTAACCTAATTAATTAAATTAAAAACCC
1 AAACCCTAACCTAA-T--TT-AATTAAAAACCC
* *
3427197 TAA-CCTAACTTAATTTAAATAATTAAAAACCC
1 AAACCCTAACCTAA-TT---TAATTAAAAACCC
* *
3427229 TAACCCTAACCTAACTTAATT---AA---
1 AAACCCTAACCTAATTTAATTAAAAACCC
3427252 AAACCCTAACCTAATTTAATTAAAAACCC
1 AAACCCTAACCTAATTTAATTAAAAACCC
3427281 AAACCCTAACCTAATTAATTAAATTAAAAACCC
1 AAACCCTAACCTAA-T--TT-AATTAAAAACCC
* *
3427314 TAA-CCTAACTTAATTTAAATAATTAAAAACCC
1 AAACCCTAACCTAA-TT---TAATTAAAAACCC
* *
3427346 TAACCCTAACCTAACTTAATT---AA---
1 AAACCCTAACCTAATTTAATTAAAAACCC
3427369 AAACCCTAACCTAATTTAATTAAAAACCC
1 AAACCCTAACCTAATTTAATTAAAAACCC
3427398 AAACCCTAACCTAA-TTAATTAAA
1 AAACCCTAACCTAATTTAATTAAA
3427421 TTGGAAACTC
Statistics
Matches: 217, Mismatches: 12, Indels: 57
0.76 0.04 0.20
Matches are distributed among these distances:
23 38 0.18
26 8 0.04
28 9 0.04
29 52 0.24
30 4 0.02
32 58 0.27
33 48 0.22
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (29 bp):
AAACCCTAACCTAATTTAATTAAAAACCC
Found at i:3427199 original size:56 final size:56
Alignment explanation
Indices: 3427129--3427422 Score: 376
Period size: 56 Copynumber: 5.1 Consensus size: 56
3427119 AACCCTACTT
3427129 AATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAATTA
1 AATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAATTA
* *** *
3427185 AATTAAAAACCCTAACCTAACTTAATTTAAATAATTAAAAACCCTAACCCTAACCTAACTT-
1 AATTAAAAACCCTAACCTAATTTAA-TTAAA-AA-CCCAAACCCTAA-CCTAA-TTAA-TTA
3427246 AATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAATTA
1 AATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAATTA
* *** *
3427302 AATTAAAAACCCTAACCTAACTTAATTTAAATAATTAAAAACCCTAACCCTAACCTAACTT-
1 AATTAAAAACCCTAACCTAATTTAA-TTAAA-AA-CCCAAACCCTAA-CCTAA-TTAA-TTA
3427363 AATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAATTA
1 AATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAATTA
3427419 AATT
1 AATT
3427423 GGAAACTCTA
Statistics
Matches: 204, Mismatches: 20, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
55 4 0.02
56 58 0.28
57 20 0.10
58 22 0.11
59 22 0.11
60 20 0.10
61 54 0.26
62 4 0.02
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (56 bp):
AATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAATTA
Found at i:3427251 original size:61 final size:62
Alignment explanation
Indices: 3427151--3427389 Score: 323
Period size: 61 Copynumber: 3.9 Consensus size: 62
3427141 TAACCTAATT
* *
3427151 TAATTAAAAACCCAAACCCTAACCTAATTAATTAAATTAAAAACCCTAACCTAACTTAATTTAAA
1 TAATTAAAAACCCTAACCCTAACCT-A--ACTTAAATTAAAAACCCTAACCTAACTTAATTTAAA
*
3427216 TAATTAAAAACCCTAACCCTAACCTAACTT-AATTAAAAACCCTAACCTAATTTAA-TTAAA
1 TAATTAAAAACCCTAACCCTAACCTAACTTAAATTAAAAACCCTAACCTAACTTAATTTAAA
*** *
3427276 -AA-CCCAAACCCTAA-CCTAA-TTAA-TTAAATTAAAAACCCTAACCTAACTTAATTTAAA
1 TAATTAAAAACCCTAACCCTAACCTAACTTAAATTAAAAACCCTAACCTAACTTAATTTAAA
*
3427333 TAATTAAAAACCCTAACCCTAACCTAACTT-AATTAAAAACCCTAACCTAATTTAATT
1 TAATTAAAAACCCTAACCCTAACCTAACTTAAATTAAAAACCCTAACCTAACTTAATT
3427390 AAAAACCCAA
Statistics
Matches: 154, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
55 2 0.01
56 27 0.18
57 10 0.06
58 11 0.07
59 11 0.07
60 10 0.06
61 53 0.34
62 5 0.03
64 1 0.01
65 24 0.16
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (62 bp):
TAATTAAAAACCCTAACCCTAACCTAACTTAAATTAAAAACCCTAACCTAACTTAATTTAAA
Found at i:3427256 original size:23 final size:23
Alignment explanation
Indices: 3427230--3427298 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3427220 TAAAAACCCT
3427230 AACCCTAACCTAACTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
*
3427253 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
* *
3427276 AACCCAAACCCTAACCTAATTAA
1 AACCCTAA-CCTAACTTAATTAA
3427299 TTAAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 29 0.71
24 12 0.29
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.25
Consensus pattern (23 bp):
AACCCTAACCTAACTTAATTAAA
Found at i:3427373 original size:23 final size:23
Alignment explanation
Indices: 3427347--3427415 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3427337 TAAAAACCCT
3427347 AACCCTAACCTAACTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
*
3427370 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
* *
3427393 AACCCAAACCCTAACCTAATTAA
1 AACCCTAA-CCTAACTTAATTAA
3427416 TTAAATTGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 29 0.71
24 12 0.29
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.25
Consensus pattern (23 bp):
AACCCTAACCTAACTTAATTAAA
Found at i:3427434 original size:117 final size:117
Alignment explanation
Indices: 3427117--3427422 Score: 596
Period size: 117 Copynumber: 2.6 Consensus size: 117
3427107 ATTAAAATCT
3427117 CTAACCCT-ACTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTA
1 CTAA-CCTAACTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTA
3427181 ATTAAATTAAAAACCCTAACCTAACTTAATTTAAATAATTAAAAACCCTAACC
65 ATTAAATTAAAAACCCTAACCTAACTTAATTTAAATAATTAAAAACCCTAACC
3427234 CTAACCTAACTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAA
1 CTAACCTAACTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAA
3427299 TTAAATTAAAAACCCTAACCTAACTTAATTTAAATAATTAAAAACCCTAACC
66 TTAAATTAAAAACCCTAACCTAACTTAATTTAAATAATTAAAAACCCTAACC
3427351 CTAACCTAACTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAA
1 CTAACCTAACTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAA
3427416 TTAAATT
66 TTAAATT
3427423 GGAAACTCTA
Statistics
Matches: 188, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
116 3 0.02
117 185 0.98
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (117 bp):
CTAACCTAACTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCAAACCCTAACCTAATTAA
TTAAATTAAAAACCCTAACCTAACTTAATTTAAATAATTAAAAACCCTAACC
Found at i:3428625 original size:125 final size:125
Alignment explanation
Indices: 3428393--3428617 Score: 319
Period size: 125 Copynumber: 1.8 Consensus size: 125
3428383 CAAACTTGCT
* * * *
3428393 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTA
1 ACTGTAGCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTA
** * * *
3428458 TCAGCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAAATTATTTCTCACATGACC
66 GAAGCGATTTCACACTATTTACTCAGAAAACGTCAAAAAAAAATTATTTCTCACATGACC
* *
3428518 ACTGTAGCGAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTA
1 ACTGTAGCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTA
*
3428583 GAAGCGATTTCCCACTATTTAAC-CAG-AAACGTCAA
66 GAAGCGATTTCACACTATTT-ACTCAGAAAACGTCAA
3428618 CTCAAAAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
124 9 0.10
125 77 0.89
126 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (125 bp):
ACTGTAGCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTA
GAAGCGATTTCACACTATTTACTCAGAAAACGTCAAAAAAAAATTATTTCTCACATGACC
Found at i:3437541 original size:19 final size:20
Alignment explanation
Indices: 3437519--3437564 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
3437509 TTGGGTTCAA
3437519 GGTTCGAGCTCA-AGTTAAG
1 GGTTCGAGCTCAGAGTTAAG
* * *
3437538 GGTTC-AGGTTAGAGTTTAG
1 GGTTCGAGCTCAGAGTTAAG
3437557 GGTTCGAG
1 GGTTCGAG
3437565 ATTCGAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.18
19 16 0.73
20 2 0.09
ACGTcount: A:0.22, C:0.11, G:0.37, T:0.30
Consensus pattern (20 bp):
GGTTCGAGCTCAGAGTTAAG
Found at i:3444044 original size:36 final size:36
Alignment explanation
Indices: 3443997--3444066 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
3443987 ATGATAATGG
*
3443997 TAAAACTGAATTCGTTTTTGTGAGCATGAAATTTGT
1 TAAAACTGAATTCGTGTTTGTGAGCATGAAATTTGT
3444033 TAAAACTGAATTCGTGTTTGTGAGCATGAAATTT
1 TAAAACTGAATTCGTGTTTGTGAGCATGAAATTT
3444067 ATATGCAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (36 bp):
TAAAACTGAATTCGTGTTTGTGAGCATGAAATTTGT
Found at i:3447350 original size:173 final size:173
Alignment explanation
Indices: 3447055--3447923 Score: 1666
Period size: 173 Copynumber: 5.0 Consensus size: 173
3447045 GAAGTCGGTA
* *** *
3447055 AACACCGAAGAAGTCTCCTTTTTGGGTCCAAAAGCAGGAGTCAATTTTGCAATATCCTCCTTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447120 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
3447185 CATAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
131 CATAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
3447228 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447293 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
3447358 CATAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
131 CATAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
3447401 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447466 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
3447531 CAGTAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
131 CA-TAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
3447575 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447640 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
3447705 CATAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
131 CATAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
3447748 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447813 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
*
3447878 CAGTAAAGAAAAGAAAATAGAGAAAAGCTAAAAGAAAGCAAATC
131 CA-TAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
3447922 AA
1 AA
3447924 TACGTATTAT
Statistics
Matches: 688, Mismatches: 6, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
173 473 0.69
174 215 0.31
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (173 bp):
AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
CATAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATC
Found at i:3447695 original size:347 final size:347
Alignment explanation
Indices: 3447055--3447923 Score: 1677
Period size: 347 Copynumber: 2.5 Consensus size: 347
3447045 GAAGTCGGTA
* *** *
3447055 AACACCGAAGAAGTCTCCTTTTTGGGTCCAAAAGCAGGAGTCAATTTTGCAATATCCTCCTTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447120 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
3447185 CA-TAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATCAACACTGAAGAAGTCTCCTTT
131 CAGTAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATCAACACTGAAGAAGTCTCCTTT
3447249 TTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATTTGATTCCGTGGAAAAAGAAAT
196 TTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATTTGATTCCGTGGAAAAAGAAAT
3447314 GCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAGCATAAAGAAAAGAAAATAGAG
261 GCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAGCATAAAGAAAAGAAAATAGAG
3447379 AAAAGTTAAAAGAAAGCAAATC
326 AAAAGTTAAAAGAAAGCAAATC
3447401 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447466 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
3447531 CAGTAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATCAACACTGAAGAAGTCTCCTTT
131 CAGTAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATCAACACTGAAGAAGTCTCCTTT
3447596 TTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATTTGATTCCGTGGAAAAAGAAAT
196 TTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATTTGATTCCGTGGAAAAAGAAAT
3447661 GCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAGCATAAAGAAAAGAAAATAGAG
261 GCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAGCATAAAGAAAAGAAAATAGAG
3447726 AAAAGTTAAAAGAAAGCAAATC
326 AAAAGTTAAAAGAAAGCAAATC
3447748 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
1 AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
3447813 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
66 TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
*
3447878 CAGTAAAGAAAAGAAAATAGAGAAAAGCTAAAAGAAAGCAAATCAA
131 CAGTAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATCAA
3447924 TACGTATTAT
Statistics
Matches: 516, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
346 127 0.25
347 389 0.75
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (347 bp):
AACACTGAAGAAGTCTCCTTTTTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATT
TGATTCCGTGGAAAAAGAAATGCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAG
CAGTAAAGAAAAGAAAATAGAGAAAAGTTAAAAGAAAGCAAATCAACACTGAAGAAGTCTCCTTT
TTGGGTCCATGCGCAGGAGTCAATTTTGCAATATCCTCCCTATTTGATTCCGTGGAAAAAGAAAT
GCTTTGATTATTTTGTTCATATGTAGTGATGATATGGAATACAGCATAAAGAAAAGAAAATAGAG
AAAAGTTAAAAGAAAGCAAATC
Found at i:3455494 original size:14 final size:15
Alignment explanation
Indices: 3455474--3455516 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
3455464 AATCGAAACT
3455474 GTACAAAATAAATTA
1 GTACAAAATAAATTA
3455489 -TACAAAAATATAATTA
1 GTAC-AAAATA-AATTA
*
3455505 GTACAAGATAAA
1 GTACAAAATAAA
3455517 CCATAGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 3 0.12
15 8 0.33
16 10 0.42
17 3 0.12
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (15 bp):
GTACAAAATAAATTA
Found at i:3455498 original size:15 final size:17
Alignment explanation
Indices: 3455474--3455510 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
3455464 AATCGAAACT
3455474 GTAC-AAAATA-AATTA
1 GTACAAAAATATAATTA
3455489 -TACAAAAATATAATTA
1 GTACAAAAATATAATTA
3455505 GTACAA
1 GTACAA
3455511 GATAAACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 6 0.32
16 5 0.26
17 5 0.26
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (17 bp):
GTACAAAAATATAATTA
Found at i:3457110 original size:42 final size:40
Alignment explanation
Indices: 3457050--3457171 Score: 110
Period size: 42 Copynumber: 3.0 Consensus size: 40
3457040 CGGCCCGAAT
3457050 TATATATTAAA-AT-T-TA-TTTTTATTTTTAATCAAATA
1 TATATATTAAATATATATATTTTTTATTTTTAATCAAATA
* * *
3457086 TACTTTTTATTAAATATATATATTTTTTGGACTTTTAATCCGAAT-
1 TA---TATATTAAATATATATATTTTTT--ATTTTTAAT-CAAATA
* *
3457131 TATATATTAAATATTTTTATTTTTTATTTTTAATCAAATA
1 TATATATTAAATATATATATTTTTTATTTTTAATCAAATA
3457171 T
1 T
3457172 GGGCCGGGTT
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
36 2 0.03
39 12 0.18
40 11 0.16
41 1 0.01
42 22 0.33
43 5 0.07
45 10 0.15
46 4 0.06
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (40 bp):
TATATATTAAATATATATATTTTTTATTTTTAATCAAATA
Found at i:3458203 original size:24 final size:21
Alignment explanation
Indices: 3458155--3458203 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
3458145 GGGGATATGT
* *
3458155 AATTATTATATTTTTTTGGTT
1 AATTATTATATTTTTGTGGTA
3458176 AATTATTATATTTTGTGTGTGTGA
1 AATTATTATATTTT-TGTG-GT-A
3458200 AATT
1 AATT
3458204 GTGATTCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.61
22 3 0.13
23 2 0.09
24 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (21 bp):
AATTATTATATTTTTGTGGTA
Found at i:3460181 original size:13 final size:13
Alignment explanation
Indices: 3460163--3460191 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3460153 AAAATAAAAA
3460163 ATATATTTATTAT
1 ATATATTTATTAT
3460176 ATATATTTATTAT
1 ATATATTTATTAT
3460189 ATA
1 ATA
3460192 AATACTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATATTTATTAT
Found at i:3461202 original size:24 final size:23
Alignment explanation
Indices: 3461174--3461222 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
3461164 TATAATAGTG
*
3461174 AAATAATAGTAAAAAAGTGAAAAA
1 AAATAATAGCAAAAAAGT-AAAAA
* *
3461198 AAATAGTAGCAAAACAGTAAAAA
1 AAATAATAGCAAAAAAGTAAAAA
3461221 AA
1 AA
3461223 TAACTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.14
Consensus pattern (23 bp):
AAATAATAGCAAAAAAGTAAAAA
Found at i:3461204 original size:21 final size:22
Alignment explanation
Indices: 3461178--3461222 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
3461168 ATAGTGAAAT
3461178 AATAGTA-AAAA-AGTGAAAAAA
1 AATAGTACAAAACAGT-AAAAAA
3461199 AATAGTAGCAAAACAGTAAAAAA
1 AATAGTA-CAAAACAGTAAAAAA
3461222 A
1 A
3461223 TAACTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.13
Consensus pattern (22 bp):
AATAGTACAAAACAGTAAAAAA
Found at i:3462509 original size:31 final size:31
Alignment explanation
Indices: 3462471--3462547 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
3462461 AAAAACACTT
*
3462471 AATAGTTTAGTGACTTAAAT-AAAAATATTTG
1 AATAGTTTAGTGACTTAAATGAAAAAT-TTTA
* * *
3462502 AATAGTTTACTAACTTAAATGAAAACTTTTA
1 AATAGTTTAGTGACTTAAATGAAAAATTTTA
3462533 AATAGTTTAGTGACT
1 AATAGTTTAGTGACT
3462548 ATTTTATAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 34 0.87
32 5 0.13
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (31 bp):
AATAGTTTAGTGACTTAAATGAAAAATTTTA
Found at i:3463753 original size:25 final size:25
Alignment explanation
Indices: 3463719--3463770 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3463709 TTTAATTGGG
3463719 TTGATATGTGTTTTAAAAGCCCTTT
1 TTGATATGTGTTTTAAAAGCCCTTT
3463744 TTGATATGTGTTTTAAAAGCCCTTT
1 TTGATATGTGTTTTAAAAGCCCTTT
3463769 TT
1 TT
3463771 AAAGACTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (25 bp):
TTGATATGTGTTTTAAAAGCCCTTT
Found at i:3465083 original size:21 final size:20
Alignment explanation
Indices: 3465039--3465084 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
3465029 TAAAATATTT
*
3465039 TTATATAAATTTAATTATAA
1 TTATATAAATTTAATTAAAA
3465059 -TATATATAA-TTAATATAAAA
1 TTATATA-AATTTAAT-TAAAA
3465079 TTATAT
1 TTATAT
3465085 TTATGCCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATATAAATTTAATTAAAA
Found at i:3475408 original size:31 final size:31
Alignment explanation
Indices: 3475373--3475432 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3475363 CTAAATGATT
3475373 ATTGAACTATTCT-AAACTTTTTATTTAAATC
1 ATTGAACTATT-TGAAACTTTTTATTTAAATC
* *
3475404 ATTGAATTATTTGAAAGTTTTTATTTAAA
1 ATTGAACTATTTGAAACTTTTTATTTAAA
3475433 GTATTGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (31 bp):
ATTGAACTATTTGAAACTTTTTATTTAAATC
Found at i:3475439 original size:31 final size:30
Alignment explanation
Indices: 3475372--3475439 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
3475362 ACTAAATGAT
3475372 TATTGAACTATTCTAAACTTTTTATTTAAA
1 TATTGAACTATTCTAAACTTTTTATTTAAA
* *
3475402 TCATTGAATTATT-TGAAAGTTTTTATTTAAA
1 T-ATTGAACTATTCT-AAACTTTTTATTTAAA
3475433 GTATTGA
1 -TATTGA
3475440 GTTGTTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 30 0.91
32 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (30 bp):
TATTGAACTATTCTAAACTTTTTATTTAAA
Found at i:3475724 original size:31 final size:30
Alignment explanation
Indices: 3475689--3475748 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
3475679 AAAGATGTGA
* * *
3475689 TTTTAATAGCTCAGTAACTTAAATGAAAATT
1 TTTTAACAGCCCAATAACTTAAAT-AAAATT
*
3475720 TTTTAACAGCCCAATAATTTAAATAAAAT
1 TTTTAACAGCCCAATAACTTAAATAAAAT
3475749 AAAAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTTAACAGCCCAATAACTTAAATAAAATT
Found at i:3477582 original size:17 final size:16
Alignment explanation
Indices: 3477555--3477589 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3477545 TTGGGTTATC
*
3477555 ATATAAATAATCTATA
1 ATATAAATAATATATA
3477571 ATATATAATAATATATA
1 ATATA-AATAATATATA
3477588 AT
1 AT
3477590 CTTTCATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAATAATATATA
Found at i:3481618 original size:67 final size:68
Alignment explanation
Indices: 3481536--3481666 Score: 237
Period size: 68 Copynumber: 1.9 Consensus size: 68
3481526 GTTACAAAAT
*
3481536 AATAATAATAAAACAT-AAGTTTGTTTTACTAATCAAATGTTAAATTTTGTTACAACAATTAATA
1 AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAAATTTTGTTACAACAATTAATA
3481600 CAA
66 CAA
*
3481603 AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAAT
1 AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAAATTTTGTTACAACAATTAAT
3481667 TTAATTAATT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
67 16 0.26
68 45 0.74
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (68 bp):
AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAAATTTTGTTACAACAATTAATA
CAA
Found at i:3481693 original size:93 final size:92
Alignment explanation
Indices: 3481589--3481759 Score: 229
Period size: 93 Copynumber: 1.8 Consensus size: 92
3481579 ATTTTGTTAC
* * *
3481589 AACAATTAATACAA-AATA-ATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTT
1 AACAATTAATACAACAATACA-AATAAAA-AT-AAGATAATTTTACTAATCAAATGTTAGACTTT
3481652 GTTACAACAATTAATTTAATTAATTCAATT
63 GTTACAACAATTAATTTAATTAATTCAATT
* * **
3481682 AACAATTAATACAATCAATACAATTAATAATTTGATAATTTTACTAATCAAATGTTAGACTTTGT
1 AACAATTAATACAA-CAATACAAATAAAAATAAGATAATTTTACTAATCAAATGTTAGACTTTGT
3481747 TACAACAATTAAT
65 TACAACAATTAAT
3481760 ACAATTAACA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
93 56 0.82
94 2 0.03
95 9 0.13
96 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.38
Consensus pattern (92 bp):
AACAATTAATACAACAATACAAATAAAAATAAGATAATTTTACTAATCAAATGTTAGACTTTGTT
ACAACAATTAATTTAATTAATTCAATT
Found at i:3481705 original size:25 final size:25
Alignment explanation
Indices: 3481657--3481713 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
3481647 ATTTTGTTAC
** * *
3481657 AACAATTAATTTAATTAATTCAATT
1 AACAATTAATACAATCAATACAATT
3481682 AACAATTAATACAATCAATACAATT
1 AACAATTAATACAATCAATACAATT
*
3481707 AATAATT
1 AACAATT
3481714 TGATAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (25 bp):
AACAATTAATACAATCAATACAATT
Found at i:3481710 original size:9 final size:9
Alignment explanation
Indices: 3481658--3481710 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
3481648 TTTTGTTACA
3481658 ACAATTAAT
1 ACAATTAAT
**
3481667 TTAATTAAT
1 ACAATTAAT
*
3481676 TCAATT-A-
1 ACAATTAAT
3481683 ACAATTAAT
1 ACAATTAAT
*
3481692 ACAATCAAT
1 ACAATTAAT
3481701 ACAATTAAT
1 ACAATTAAT
3481710 A
1 A
3481711 ATTTGATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 5 0.14
8 2 0.06
9 29 0.81
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (9 bp):
ACAATTAAT
Found at i:3481804 original size:16 final size:16
Alignment explanation
Indices: 3481783--3481824 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
3481773 AATAATTTGA
*
3481783 TAATTTTATTAACAAT
1 TAATTTTAATAACAAT
3481799 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
3481815 TAATTTTAAT
1 TAATTTTAAT
3481825 TTTATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:3481808 original size:22 final size:23
Alignment explanation
Indices: 3481798--3481853 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
3481788 TTATTAACAA
* *
3481798 TTAATTTTAAT-AACAATTAATT
1 TTAATTTTAATAAAAAAATAATT
*
3481820 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
3481843 TTAATTTTAAT
1 TTAATTTTAAT
3481854 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:3483688 original size:29 final size:29
Alignment explanation
Indices: 3483596--3483699 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 29
3483586 AAACCCGCAT
3483596 CAACTTAGTTGAGTAAACAATGTTAATAG
1 CAACTTAGTTGAGTAAACAATGTTAATAG
* * * * **
3483625 CAAC-TATTTTG-CTAAA-TATATT-ATTC
1 CAACTTA-GTTGAGTAAACAATGTTAATAG
**
3483651 CTTTCTTAGTTGAGTAAACAATGTTAATAG
1 C-AACTTAGTTGAGTAAACAATGTTAATAG
3483681 CAACTTAGTTGAGTAAACA
1 CAACTTAGTTGAGTAAACA
3483700 GTAGTAATCA
Statistics
Matches: 53, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
26 3 0.06
27 8 0.15
28 12 0.23
29 27 0.51
30 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (29 bp):
CAACTTAGTTGAGTAAACAATGTTAATAG
Found at i:3486806 original size:31 final size:31
Alignment explanation
Indices: 3486739--3486807 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3486729 ATTAACAGTC
*
3486739 TAATGACTTAAATAAAAACTTTTGAATAATA
1 TAATGACTCAAATAAAAACTTTTGAATAATA
* * * * *
3486770 CAATGACTCAAATGAACATTTTTGAATAATT
1 TAATGACTCAAATAAAAACTTTTGAATAATA
3486801 TAATGAC
1 TAATGAC
3486808 CATTTGTGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (31 bp):
TAATGACTCAAATAAAAACTTTTGAATAATA
Found at i:3516244 original size:38 final size:38
Alignment explanation
Indices: 3516190--3516266 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
3516180 CTTCAATAGA
* *
3516190 TAATCAAGCTCGTGATCATGTCTAATTGTAACTGCTTT
1 TAATCAAGCCCATGATCATGTCTAATTGTAACTGCTTT
* *
3516228 TAATCAAGCCCATGATCATGTTTAATTGTAACTGTTTT
1 TAATCAAGCCCATGATCATGTCTAATTGTAACTGCTTT
3516266 T
1 T
3516267 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (38 bp):
TAATCAAGCCCATGATCATGTCTAATTGTAACTGCTTT
Found at i:3532732 original size:43 final size:43
Alignment explanation
Indices: 3532670--3532817 Score: 217
Period size: 43 Copynumber: 3.4 Consensus size: 43
3532660 TGTCCCAGAC
** ** *
3532670 ATGGTCTTACATAAAAATCTCGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCTAGCT
*
3532714 ATGGTCTTACACGAAATCTCAAATTGATGCCAATAGCCTAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCTAGCT
3532757 ATGGTCTTACAC-AGAATCTCAAATCGATGCCAATAGCCTAGCT
1 ATGGTCTTACACGA-AATCTCAAATCGATGCCAATAGCCTAGCT
3532800 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGAAATC
3532818 ACACCTCGGA
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
42 1 0.01
43 82 0.86
44 12 0.13
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCTAGCT
Found at i:3532976 original size:31 final size:31
Alignment explanation
Indices: 3532935--3533203 Score: 355
Period size: 31 Copynumber: 8.7 Consensus size: 31
3532925 ATCCAATGCT
* * *
3532935 CAAATC-AATTCGACAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
3532965 CGAATCAAATTCGGCAATGTATATCTACATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
3532996 CAAAT-TAATTTGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
3533026 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
3533057 CAAATCAAATTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
3533088 CAATTCAAATTCGGCAATGTATATCTATATG
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
3533119 CAAATCAAATTCGACAATGTATATCTATA-A
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
3533149 AAAATTCAAATTTGCCAATGTATATCTATATA
1 CAAA-TCAAATTCGGCAATGTATATCTATATA
3533181 CAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
3533204 AAACATATAT
Statistics
Matches: 207, Mismatches: 28, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
30 34 0.16
31 169 0.82
32 4 0.02
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:3533945 original size:18 final size:19
Alignment explanation
Indices: 3533908--3533945 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3533898 CATATAATTC
*
3533908 TTAAGTTATTTTATCATTA
1 TTAAGTTATTTTACCATTA
*
3533927 TTAA-TTATTTTACCTTTA
1 TTAAGTTATTTTACCATTA
3533945 T
1 T
3533946 AACCTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (19 bp):
TTAAGTTATTTTACCATTA
Found at i:3538204 original size:28 final size:27
Alignment explanation
Indices: 3538132--3538205 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
3538122 TTTTTTTATT
*
3538132 AAATA-AT-TTATTATTATATTTTTAA
1 AAATATATATTATTATTATATTATTAA
* *
3538157 AAATATTTATGTGTTATTATATATATTAA
1 AAATATATAT-TATTATTATAT-TATTAA
3538186 AAAT-TATATTATTATT-TATT
1 AAATATATATTATTATTATATT
3538206 GTCAACGATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
25 6 0.15
26 4 0.10
27 7 0.17
28 14 0.35
29 9 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
AAATATATATTATTATTATATTATTAA
Found at i:3538253 original size:23 final size:23
Alignment explanation
Indices: 3538220--3538266 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3538210 ACGATATTAT
*
3538220 TTTATTTTTATATATTTTT-AAAA
1 TTTATTATTATAT-TTTTTGAAAA
3538243 TTTATTATTATATTTTTTGAAAA
1 TTTATTATTATATTTTTTGAAAA
3538266 T
1 T
3538267 AATTATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTATTATTATATTTTTTGAAAA
Found at i:3538288 original size:52 final size:52
Alignment explanation
Indices: 3538130--3538288 Score: 162
Period size: 52 Copynumber: 3.0 Consensus size: 52
3538120 AATTTTTTTA
* * * *
3538130 TTAAATAATTTATTATTATA-TTTTTAAAAATATTTATGTGTTATTATATATA
1 TTAAA-AATTTATTATTATATTTTTTAAAAATAATTATGTATTTTTATATATT
* ** *
3538182 TTAAAAATTATATTATTAT-TTATTGTCAACGAT-ATTATTTTATTTTTATATATT
1 TTAAAAATT-TATTATTATATT-TT-TTAAAAATAATTA-TGTATTTTTATATATT
* *
3538236 TTTAAAATTTATTATTATATTTTTTGAAAATAATTATGTATTTTTATATATT
1 TTAAAAATTTATTATTATATTTTTTAAAAATAATTATGTATTTTTATATATT
3538288 T
1 T
3538289 CTTTGAATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
51 4 0.05
52 35 0.41
53 20 0.23
54 27 0.31
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (52 bp):
TTAAAAATTTATTATTATATTTTTTAAAAATAATTATGTATTTTTATATATT
Found at i:3546156 original size:43 final size:44
Alignment explanation
Indices: 3546106--3546193 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
3546096 AAATAGAATC
* *
3546106 TCTCTCTT-AAGTGTTACATTGTACATAGAAAAAAATATACATA
1 TCTCTCTTAAAATGTTACATTGTACAAAGAAAAAAATATACATA
3546149 TCTCTCTTAAAATGTTACATTGTACAAAGAAAAAAATATACATA
1 TCTCTCTTAAAATGTTACATTGTACAAAGAAAAAAATATACATA
3546193 T
1 T
3546194 AATAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 8 0.19
44 34 0.81
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (44 bp):
TCTCTCTTAAAATGTTACATTGTACAAAGAAAAAAATATACATA
Found at i:3552453 original size:25 final size:25
Alignment explanation
Indices: 3552420--3552480 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
3552410 TTAACCGACT
* *
3552420 TTATTTTTTTA-T-CAATTTAATCC
1 TTATTTTTTTAGTAAAATTTAATCA
3552443 TTAATTATTTTTAGTAAAATTTAATCA
1 TT-ATT-TTTTTAGTAAAATTTAATCA
3552470 TTATTTTTTTA
1 TTATTTTTTTA
3552481 AATAGTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 3 0.09
25 12 0.38
26 4 0.12
27 11 0.34
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTTTTTTAGTAAAATTTAATCA
Found at i:3552638 original size:26 final size:25
Alignment explanation
Indices: 3552601--3552665 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
3552591 TAAAATTTTA
* *
3552601 AAAATTATAAAAATATTCAAAA-ATT
1 AAAATTAAAAAAATA-TAAAAAGATT
*
3552626 AAAATTCAAAAAATTATAAAAAGATT
1 AAAATT-AAAAAAATATAAAAAGATT
*
3552652 ATAATTTAAAAAAA
1 A-AAATTAAAAAAA
3552666 ATGTATGATG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 11 0.34
26 17 0.53
27 4 0.12
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATTAAAAAAATATAAAAAGATT
Found at i:3554657 original size:19 final size:19
Alignment explanation
Indices: 3554633--3554674 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3554623 TCTTTAGAAT
3554633 TTTTTTAAAAAAAT-TATAA
1 TTTTTTAAAAAAATATA-AA
*
3554652 TTTTTTTAAAAAATATAAA
1 TTTTTTAAAAAAATATAAA
3554671 TTTT
1 TTTT
3554675 AGAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTTAAAAAAATATAAA
Found at i:3554687 original size:19 final size:20
Alignment explanation
Indices: 3554665--3554702 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3554655 TTTTAAAAAA
3554665 TATAAAT-TTTAGAATTTTT
1 TATAAATATTTAGAATTTTT
*
3554684 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
3554703 AATTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TATAAATATTTAGAATTTTT
Found at i:3554709 original size:27 final size:25
Alignment explanation
Indices: 3554643--3554710 Score: 64
Period size: 28 Copynumber: 2.6 Consensus size: 25
3554633 TTTTTTAAAA
*
3554643 AAATTATAATTTTTTTAAAAAATAT
1 AAATTTTAATTTTTTTAAAAAATAT
* * *
3554668 AAATTTTAGAATTTTTTATAAATATTTT
1 AAATTTT--AATTTTTT-TAAAAAATAT
*
3554696 GAATTTTAATTTTTT
1 AAATTTTAATTTTTT
3554711 GAGAAAGACC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 6 0.17
26 8 0.23
27 8 0.23
28 13 0.37
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
AAATTTTAATTTTTTTAAAAAATAT
Found at i:3555060 original size:23 final size:23
Alignment explanation
Indices: 3555030--3555084 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
3555020 ATTTTTAAAT
3555030 CTGAAAAATAGACGATCATATTC
1 CTGAAAAATAGACGATCATATTC
*
3555053 CTGAAAAATAGACGGTCATATTC
1 CTGAAAAATAGACGATCATATTC
3555076 CTGAAAAAT
1 CTGAAAAAT
3555085 TAAAATAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (23 bp):
CTGAAAAATAGACGATCATATTC
Found at i:3556707 original size:4 final size:4
Alignment explanation
Indices: 3556698--3556724 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3556688 TATGACCCAT
3556698 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3556725 TGGATTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3559184 original size:24 final size:24
Alignment explanation
Indices: 3559157--3559206 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3559147 TCATCAACAG
* * *
3559157 ATTTTACTATCATCGAAACCATCC
1 ATTTTACTATCACCAAAACCAACC
3559181 ATTTTACTATCACCAAAACCAACC
1 ATTTTACTATCACCAAAACCAACC
3559205 AT
1 AT
3559207 CCTTCCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (24 bp):
ATTTTACTATCACCAAAACCAACC
Found at i:3559204 original size:28 final size:28
Alignment explanation
Indices: 3559173--3559240 Score: 73
Period size: 32 Copynumber: 2.3 Consensus size: 28
3559163 CTATCATCGA
3559173 AACCATCCATTTTACTATCACCAAAACC
1 AACCATCCATTTTACTATCACCAAAACC
* **
3559201 AACCATCCTTCCCTTTTACTATCACTGAAACC
1 AACCA----TCCATTTTACTATCACCAAAACC
3559233 AACCATCC
1 AACCATCC
3559241 TTATCATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
28 8 0.24
32 25 0.76
ACGTcount: A:0.34, C:0.38, G:0.01, T:0.26
Consensus pattern (28 bp):
AACCATCCATTTTACTATCACCAAAACC
Found at i:3559221 original size:32 final size:32
Alignment explanation
Indices: 3559182--3559242 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3559172 AAACCATCCA
3559182 TTTTACTATCACCAAAACCAACCATCCTTCCC
1 TTTTACTATCACCAAAACCAACCATCCTTCCC
**
3559214 TTTTACTATCACTGAAACCAACCATCCTT
1 TTTTACTATCACCAAAACCAACCATCCTT
3559243 ATCATTGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (32 bp):
TTTTACTATCACCAAAACCAACCATCCTTCCC
Found at i:3568341 original size:12 final size:12
Alignment explanation
Indices: 3568324--3568361 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3568314 TTATTGAGAA
3568324 GAAAAAAAAAAG
1 GAAAAAAAAAAG
3568336 GAAAAAAGAAAA-
1 GAAAAAA-AAAAG
3568348 GAAAAAAAAAAG
1 GAAAAAAAAAAG
3568360 GA
1 GA
3568362 GTTTGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAG
Found at i:3571600 original size:15 final size:13
Alignment explanation
Indices: 3571571--3571595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3571561 TGTAAAACGG
3571571 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
3571584 AAAAAAAAAAAG
1 AAAAAAAAAAAG
3571596 TGAAAGGTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:3593878 original size:37 final size:37
Alignment explanation
Indices: 3593837--3593913 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
3593827 TTTATTAGAC
*
3593837 TTAGATATCCAAAATCGATAATTGATCAAATAAACAT
1 TTAGATATCCAAAATCAATAATTGATCAAATAAACAT
*
3593874 TTAGATATCCAAAATTAATAATTGATCAAATAAACAT
1 TTAGATATCCAAAATCAATAATTGATCAAATAAACAT
3593911 TTA
1 TTA
3593914 AATTAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.32
Consensus pattern (37 bp):
TTAGATATCCAAAATCAATAATTGATCAAATAAACAT
Found at i:3595275 original size:102 final size:102
Alignment explanation
Indices: 3595099--3595306 Score: 373
Period size: 102 Copynumber: 2.0 Consensus size: 102
3595089 ATTGAGCTGT
3595099 TTTTCTTTAAGAAAAGTCACGAGTCTTTGGAGAAGTCTTCTGGATTGGGTAAATTTCAGTAATAG
1 TTTTCTTTAAGAAAAGTCACGAGTCTTTGGAGAAGTCTTCTGGATTGGGTAAATTTCAGTAATAG
3595164 TCACCCAATTATTAATTTTAAATATATTTACCATATG
66 TCACCCAATTATTAATTTTAAATATATTTACCATATG
* *
3595201 TTTTCTTTAA-AAAACGTCGCGAGTTTTTGGAGAAGTCTTCTGGATTGGGTAAATTTCAGTAATA
1 TTTTCTTTAAGAAAA-GTCACGAGTCTTTGGAGAAGTCTTCTGGATTGGGTAAATTTCAGTAATA
*
3595265 GTCACCCAATTATTAATTTTAAATATATTTACTATATG
65 GTCACCCAATTATTAATTTTAAATATATTTACCATATG
3595303 TTTT
1 TTTT
3595307 TATTATATAC
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 4 0.04
102 98 0.96
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (102 bp):
TTTTCTTTAAGAAAAGTCACGAGTCTTTGGAGAAGTCTTCTGGATTGGGTAAATTTCAGTAATAG
TCACCCAATTATTAATTTTAAATATATTTACCATATG
Found at i:3603821 original size:14 final size:14
Alignment explanation
Indices: 3603783--3603825 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
3603773 TAAAATGTAC
3603783 AATATAATTAAA-T
1 AATATAATTAAATT
3603796 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
3603811 AA-ATAATTTAATT
1 AATATAATTAAATT
3603824 AA
1 AA
3603826 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:3607427 original size:16 final size:16
Alignment explanation
Indices: 3607406--3607440 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3607396 ATTTCAAGTC
3607406 TTACAGCCTATTAATT
1 TTACAGCCTATTAATT
3607422 TTACAGCCTATTAATT
1 TTACAGCCTATTAATT
3607438 TTA
1 TTA
3607441 GTCAAAGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (16 bp):
TTACAGCCTATTAATT
Found at i:3612994 original size:15 final size:15
Alignment explanation
Indices: 3612974--3613005 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3612964 AAATACAAAT
*
3612974 AAAAGAATTATTAGA
1 AAAAGAATTAATAGA
3612989 AAAAGAATTAATAGA
1 AAAAGAATTAATAGA
3613004 AA
1 AA
3613006 CAACTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (15 bp):
AAAAGAATTAATAGA
Found at i:3616248 original size:8 final size:8
Alignment explanation
Indices: 3616235--3616261 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3616225 AGCTCAACCT
3616235 AAATTTTA
1 AAATTTTA
3616243 AAATTTTA
1 AAATTTTA
3616251 AAATTTTA
1 AAATTTTA
3616259 AAA
1 AAA
3616262 ATAAAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTTA
Found at i:3617153 original size:24 final size:25
Alignment explanation
Indices: 3617108--3617167 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
3617098 ATTATATTTT
3617108 ATTTTTT-AAAATTAAATTAAAT-TA
1 ATTTTTTAAAAATTAAA-TAAATATA
3617132 ATTTTTTAAAAATTATAA-AAATATA
1 ATTTTTTAAAAATTA-AATAAATATA
* *
3617157 AATTATTAAAA
1 ATTTTTTAAAA
3617168 CAATAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 11 0.35
25 18 0.58
26 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTTTTAAAAATTAAATAAATATA
Found at i:3623605 original size:15 final size:16
Alignment explanation
Indices: 3623585--3623621 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3623575 ACAAAATCAA
3623585 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
3623600 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
3623616 ATAAAA
1 ATAAAA
3623622 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:3623813 original size:60 final size:60
Alignment explanation
Indices: 3623739--3623860 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
3623729 ATACTAAACT
* * * * *
3623739 AAACACAACAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
3623799 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
3623859 AA
1 AA
3623861 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:3623885 original size:23 final size:23
Alignment explanation
Indices: 3623854--3623964 Score: 131
Period size: 23 Copynumber: 4.8 Consensus size: 23
3623844 TTATAAAATA
3623854 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
* *
3623877 ATTATAATATCCATAC--A-AA-
1 ATTACAATATTCATACAAACAAT
3623896 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
*
3623919 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--ACAAT
3623946 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
3623965 ATACTAATCA
Statistics
Matches: 75, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
19 14 0.19
20 2 0.03
21 2 0.03
22 2 0.03
23 31 0.41
25 4 0.05
27 20 0.27
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (23 bp):
ATTACAATATTCATACAAACAAT
Found at i:3623910 original size:42 final size:42
Alignment explanation
Indices: 3623853--3623944 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
3623843 ATTATAAAAT
*
3623853 AATTACAATATTCATACAAACAATATTATAATATCCATACAA
1 AATTACAATATTCATACAAACAATATTACAATATCCATACAA
*
3623895 AATTACAATATTCATACAAACAATATTACAATATTCATACAA
1 AATTACAATATTCATACAAACAATATTACAATATCCATACAA
3623937 AATTACAA
1 AATTACAA
3623945 AATTACAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.30
Consensus pattern (42 bp):
AATTACAATATTCATACAAACAATATTACAATATCCATACAA
Found at i:3623952 original size:27 final size:27
Alignment explanation
Indices: 3623890--3623966 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
3623880 ATAATATCCA
3623890 TACAAAATTACAATATTCATAC--AA-
1 TACAAAATTACAATATTCATACAAAAT
*
3623914 -ACAATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
3623940 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
3623967 ACTAATCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
23 20 0.43
25 2 0.04
27 25 0.53
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:3623962 original size:19 final size:19
Alignment explanation
Indices: 3623853--3624171 Score: 132
Period size: 19 Copynumber: 16.3 Consensus size: 19
3623843 ATTATAAAAT
3623853 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
* *
3623875 ATATTATAATATCCATACAA
1 A-ATTACAATATTCATACAA
3623895 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
3623917 ATATTACAATATTCATACAA
1 A-ATTACAATATTCATACAA
*
3623937 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* * *
3623953 TATTCATACAAAATAC-TAATCAA
1 -AAT--TACAATATTCAT-A-CAA
**
3623976 AA--AC--TATAAATACAA
1 AATTACAATATTCATACAA
*
3623991 AATT---A-ATT-ATAAAA
1 AATTACAATATTCATACAA
*
3624005 TAATTACAATATTCATAAAA
1 -AATTACAATATTCATACAA
3624025 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
3624046 AATTACACTATTCATACAA
1 AATTACAATATTCATACAA
* * *
3624065 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
3624085 AA-TACAAAATGAATT-ATAAAA
1 AATTAC--AAT--ATTCATACAA
3624106 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
*
3624126 AATTATAATATTCATACAAA
1 AATTACAATATTCATAC-AA
*
3624146 AAGTTACAATATACATACAA
1 AA-TTACAATATTCATACAA
3624166 AATTAC
1 AATTAC
3624172 CCATTGGCGC
Statistics
Matches: 233, Mismatches: 27, Indels: 77
0.69 0.08 0.23
Matches are distributed among these distances:
14 5 0.02
15 11 0.05
16 9 0.04
17 6 0.03
18 11 0.05
19 73 0.31
20 30 0.13
21 39 0.17
22 9 0.04
23 38 0.16
25 2 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:3624063 original size:101 final size:101
Alignment explanation
Indices: 3623895--3624168 Score: 395
Period size: 101 Copynumber: 2.6 Consensus size: 101
3623885 ATCCATACAA
3623895 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCAT--AAA-AA-ATTACAATATTCATAC---A--A-AAAATTACAATATTCAT
*
3623960 ACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAAT
56 ACAAAATACTAATCAAAAACTATAAATACAAAATGAATTATAAAAT
*
3624006 AATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTACACTATTCATACAAAATACT
1 AATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACT
*
3624071 AATCCAAAACTATAAATACAAAATGAATTATAAAAT
66 AATCAAAAACTATAAATACAAAATGAATTATAAAAT
* * * *
3624107 AATTACAATATTCATACAAAATTATAATATTCATACAAAAAGTTACAATATACATACAAAAT
1 AATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAAT
3624169 TACCCATTGG
Statistics
Matches: 155, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
101 117 0.75
102 1 0.01
104 1 0.01
107 16 0.10
108 2 0.01
109 3 0.02
111 15 0.10
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.30
Consensus pattern (101 bp):
AATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACT
AATCAAAAACTATAAATACAAAATGAATTATAAAAT
Found at i:3624217 original size:27 final size:26
Alignment explanation
Indices: 3624176--3624248 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 26
3624166 AATTACCCAT
3624176 TGGCGCCTTCCTATGAGGCACTTTTAA
1 TGGCGCC-TCCTATGAGGCACTTTTAA
3624203 TGGCGCCTCCTTATGAGGCACTTTTAA
1 TGGCGCCTCC-TATGAGGCACTTTTAA
*
3624230 TGGTGCCTCCCTATGAGGC
1 TGGCGCCT-CCTATGAGGC
3624249 GCCACCCGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 3 0.07
27 38 0.88
28 2 0.05
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.32
Consensus pattern (26 bp):
TGGCGCCTCCTATGAGGCACTTTTAA
Found at i:3624882 original size:28 final size:29
Alignment explanation
Indices: 3624842--3624902 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3624832 GGTTTAATAT
*
3624842 AAAAAATTAAAATT-ATTTTATAAAATTC
1 AAAAAATTAAAATTAATTTTATAAAAGTC
* * *
3624870 AAAAATTTTAAATTAATTTTATACAAGTC
1 AAAAAATTAAAATTAATTTTATAAAAGTC
3624899 AAAA
1 AAAA
3624903 TTGTGATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAAAATTAAAATTAATTTTATAAAAGTC
Found at i:3625963 original size:30 final size:30
Alignment explanation
Indices: 3625922--3625978 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
3625912 TGAATTTTTC
*
3625922 TTAC-AATTTTTTATATTATTTTTATAACTT
1 TTACAAATTTTTTATATT-TTTTAATAACTT
3625952 TTACAAATTTTTTATATTTTTTAATAA
1 TTACAAATTTTTTATATTTTTTAATAA
3625979 TATTATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.61
Consensus pattern (30 bp):
TTACAAATTTTTTATATTTTTTAATAACTT
Found at i:3626078 original size:18 final size:19
Alignment explanation
Indices: 3626055--3626094 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3626045 TTTTTCTAGA
3626055 TTATATATATTTGA-ATTT
1 TTATATATATTTGATATTT
* *
3626073 TTATATATTTTTTATATTT
1 TTATATATATTTGATATTT
3626092 TTA
1 TTA
3626095 AATGTGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATATATATTTGATATTT
Found at i:3634791 original size:16 final size:16
Alignment explanation
Indices: 3634754--3634793 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3634744 TTAATAAAAT
* *
3634754 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3634770 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3634786 TAAAATTA
1 TAAAATTA
3634794 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3634876 original size:68 final size:68
Alignment explanation
Indices: 3634800--3634974 Score: 341
Period size: 68 Copynumber: 2.6 Consensus size: 68
3634790 ATTATCAAAT
3634800 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAA
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAA
3634865 TTG
66 TTG
3634868 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAA
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAA
3634933 TTG
66 TTG
*
3634936 TATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAA
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAA
3634975 CACTAGTCAA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 106 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAA
TTG
Found at i:3634883 original size:9 final size:9
Alignment explanation
Indices: 3634850--3634877 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3634840 TTTATCAAAT
3634850 TATTAATTG
1 TATTAATTG
3634859 TATTAATTG
1 TATTAATTG
3634868 TATTAATTG
1 TATTAATTG
3634877 T
1 T
3634878 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3634930 original size:9 final size:9
Alignment explanation
Indices: 3634918--3634945 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3634908 TTTATCAAAT
3634918 TATTAATTG
1 TATTAATTG
3634927 TATTAATTG
1 TATTAATTG
3634936 TATTAATTG
1 TATTAATTG
3634945 T
1 T
3634946 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3638403 original size:11 final size:11
Alignment explanation
Indices: 3638387--3638417 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3638377 TATATATATT
3638387 TAAAAATTATA
1 TAAAAATTATA
*
3638398 TAAAAATAATA
1 TAAAAATTATA
3638409 TAAAAATTA
1 TAAAAATTA
3638418 ATACGCCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:3640776 original size:41 final size:41
Alignment explanation
Indices: 3640717--3640859 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
3640707 AGATGATTCA
* *
3640717 GACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATATTTCG
1 GACTTTACGTCTAACAGGCTTGATGCCAGTGAAATATTTCG
* * * *
3640758 GGCTTTACGTCTAGCAGGCTTGATGCCAGTGAAATGTTTCA
1 GACTTTACGTCTAACAGGCTTGATGCCAGTGAAATATTTCG
** * *
3640799 GACTTTATATCCAACAGGCTTGATGCCAGTGAAATATTTTG
1 GACTTTACGTCTAACAGGCTTGATGCCAGTGAAATATTTCG
3640840 GACTTTACGTCTAACAGGCT
1 GACTTTACGTCTAACAGGCT
3640860 AATTGCCGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
GACTTTACGTCTAACAGGCTTGATGCCAGTGAAATATTTCG
Found at i:3640899 original size:82 final size:83
Alignment explanation
Indices: 3640709--3640900 Score: 187
Period size: 82 Copynumber: 2.3 Consensus size: 83
3640699 TGAAAGTAAG
* * * * * *
3640709 ATGATTCAGACTTTA-CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCGGGCTTTACGTCTAGC
1 ATGAATCAGACTTTATAGCCTAGCAGGCTTGATGCCAGTGAAATATTTCGGACTTTACGTCTAAC
*
3640773 AGGCTTGATGCCAGTGAA
66 AGGCTTAATGCCAGTGAA
** * * *
3640791 ATGTTTCAGACTTTATATCC-AACAGGCTTGATGCCAGTGAAATATTTTGGACTTTACGTCTAAC
1 ATGAATCAGACTTTATAGCCTAGCAGGCTTGATGCCAGTGAAATATTTCGGACTTTACGTCTAAC
*
3640855 AGGC-TAATTGCC-GATGTA
66 AGGCTTAA-TGCCAG-TGAA
* **
3640873 CTGAATCAGGTTTTA-AGCCTAGCAGGCT
1 ATGAATCAGACTTTATAGCCTAGCAGGCT
3640901 AAGTGCCGGT
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
81 6 0.07
82 81 0.92
83 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (83 bp):
ATGAATCAGACTTTATAGCCTAGCAGGCTTGATGCCAGTGAAATATTTCGGACTTTACGTCTAAC
AGGCTTAATGCCAGTGAA
Found at i:3641382 original size:71 final size:70
Alignment explanation
Indices: 3641307--3641463 Score: 181
Period size: 71 Copynumber: 2.2 Consensus size: 70
3641297 GATAAATACA
* * * *
3641307 TATATACATTTGGTTATAATATTTGTTAAG-TATATGTATATATATGCATTCGGCTATTCATGTT
1 TATATACATTTGGTTATAATATCTGTTAAGATATATGTATACA-A-GCATTCGACTATTCATATT
3641371 CAAAGTG
64 CAAAGTG
*** *
3641378 TATATACATTTGGAGCTAATATCTGTTAAGCATATATGTATACAAGCATTCGACTATTCATATTT
1 TATATACATTTGGTTATAATATCTGTTAAG-ATATATGTATACAAGCATTCGACTATTCATATTC
*
3641443 ATAGTG
65 AAAGTG
* *
3641449 AATATACATTCGGTT
1 TATATACATTTGGTT
3641464 TTAAGAGTTG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
71 59 0.83
72 1 0.01
73 11 0.15
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (70 bp):
TATATACATTTGGTTATAATATCTGTTAAGATATATGTATACAAGCATTCGACTATTCATATTCA
AAGTG
Found at i:3646588 original size:30 final size:31
Alignment explanation
Indices: 3646513--3646595 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
3646503 TTAGACTCCC
* * * *
3646513 AAAATTTTAAAAATGTTAGTTAA-ACTTTTA
1 AAAATTTTGAAAATTTTAATTAATTCTTTTA
* *
3646543 AAATTTTTGAAAATTTTCATTAATTCTTTTA
1 AAAATTTTGAAAATTTTAATTAATTCTTTTA
3646574 AAAATTTT-AAAATTTTAATTAA
1 AAAATTTTGAAAATTTTAATTAA
3646596 GCCCTTCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 31 0.70
31 13 0.30
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (31 bp):
AAAATTTTGAAAATTTTAATTAATTCTTTTA
Found at i:3651445 original size:24 final size:23
Alignment explanation
Indices: 3651415--3651459 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
3651405 AAGAATTTTA
*
3651415 AAAAATAAAAAAGTCTAAATATTC
1 AAAAATAAAAAA-TATAAATATTC
3651439 AAAAATAAAAAATATAAATAT
1 AAAAATAAAAAATATAAATAT
3651460 AAATATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAAATAAAAAATATAAATATTC
Found at i:3651448 original size:23 final size:24
Alignment explanation
Indices: 3651415--3651459 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3651405 AAGAATTTTA
* *
3651415 AAAAATAAAAAAGTCTAAATATTC
1 AAAAATAAAAAAATATAAATATTC
3651439 AAAAAT-AAAAAATATAAATAT
1 AAAAATAAAAAAATATAAATAT
3651460 AAATATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAATAAAAAAATATAAATATTC
Done.