Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 10 of 295
Found at i:3020887 original size:15 final size:15
Alignment explanation
Indices: 3020844--3020887 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
3020834 CAGTTCATTT
*
3020844 AAAT-AAAACATTAA
1 AAATAAAAAAATTAA
3020858 AAATAAAAAATATTAA
1 AAATAAAAAA-ATTAA
*
3020874 ACATAAAAAAATTA
1 AAATAAAAAAATTA
3020888 GTTCAACCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 14 0.54
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAAATTAA
Found at i:3021075 original size:21 final size:20
Alignment explanation
Indices: 3021051--3021107 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
3021041 TTTATGACTT
*
3021051 TTTTTTTATATTTTCAATATG
1 TTTTTTTA-ATTTTAAATATG
*
3021072 TTTTTATAAAATTTTAAATATG
1 TTTTT-T-TAATTTTAAATATG
*
3021094 TTTTATTAATTTTA
1 TTTTTTTAATTTTA
3021108 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 16 0.53
23 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTTTAATTTTAAATATG
Found at i:3021224 original size:19 final size:19
Alignment explanation
Indices: 3021202--3021283 Score: 87
Period size: 19 Copynumber: 4.3 Consensus size: 19
3021192 ATATTTAATA
* *
3021202 ATTTTTCTAATTTTTTTGT
1 ATTTTTATAATTTTTTTAT
*
3021221 ATTTTTGTAATTTTTTTAT
1 ATTTTTATAATTTTTTTAT
3021240 ATTTTTTATAA--TTTTTAT
1 A-TTTTTATAATTTTTTTAT
**
3021258 AGTTTTTATAATTTTTAAAT
1 A-TTTTTATAATTTTTTTAT
3021278 ATTTTT
1 ATTTTT
3021284 GTGGAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
18 17 0.31
19 23 0.43
20 14 0.26
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTATAATTTTTTTAT
Found at i:3021282 original size:9 final size:9
Alignment explanation
Indices: 3021142--3021274 Score: 85
Period size: 9 Copynumber: 14.6 Consensus size: 9
3021132 AATTCTTATA
3021142 TTTTATAAT
1 TTTTATAAT
*
3021151 ATTTATAAAT
1 TTTTAT-AAT
* *
3021161 TTATATCTAT
1 TTTTAT-AAT
*
3021171 TTTGAT-A-
1 TTTTATAAT
3021178 TTTT-TAAT
1 TTTTATAAT
3021186 TTTT-TAAT
1 TTTTATAAT
*
3021194 ATTTAATAAT
1 -TTTTATAAT
*
3021204 TTTTCTAAT
1 TTTTATAAT
* *
3021213 TTTTTTGTAT
1 TTTTAT-AAT
*
3021223 TTTTGTAATTT
1 TTTTATAA--T
*
3021234 TTTTATATT
1 TTTTATAAT
3021243 TTTTATAAT
1 TTTTATAAT
*
3021252 TTTTATAGT
1 TTTTATAAT
3021261 TTTTATAAT
1 TTTTATAAT
3021270 TTTTA
1 TTTTA
3021275 AATATTTTTG
Statistics
Matches: 96, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 9 0.09
9 51 0.53
10 24 0.25
11 7 0.07
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:3021282 original size:18 final size:17
Alignment explanation
Indices: 3021242--3021282 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
3021232 TTTTTTATAT
*
3021242 TTTTTATAATTTTTATAG
1 TTTTTATAATTTTTA-AA
3021260 TTTTTATAATTTTTAAA
1 TTTTTATAATTTTTAAA
3021277 TATTTT
1 T-TTTT
3021283 TGTGGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTTATAATTTTTAAA
Found at i:3022798 original size:16 final size:16
Alignment explanation
Indices: 3022779--3022817 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3022769 ATAAAGATAG
*
3022779 AATTTATTTATAAT-AA
1 AATTT-TTTAAAATGAA
3022795 AATTTTTTAAAATGAA
1 AATTTTTTAAAATGAA
3022811 AATTTTT
1 AATTTTT
3022818 GAAGAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTTTTTAAAATGAA
Found at i:3023037 original size:27 final size:27
Alignment explanation
Indices: 3022979--3023037 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3022969 TAAATATTCC
* * * *
3022979 TTATTTAAAACATATTTTTTGAATATA
1 TTATTTAAAACATAATATCTAAATATA
3023006 TTATTTAAAACATAATATCTAAAT-TA
1 TTATTTAAAACATAATATCTAAATATA
3023032 TGTATT
1 T-TATT
3023038 AAATTTTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (27 bp):
TTATTTAAAACATAATATCTAAATATA
Found at i:3026853 original size:17 final size:17
Alignment explanation
Indices: 3026818--3026851 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3026808 AAAGTTTTTT
*
3026818 ATTTTCATTGTATTAAA
1 ATTTTCATTATATTAAA
3026835 ATTTT-ATTATATTAAA
1 ATTTTCATTATATTAAA
3026851 A
1 A
3026852 ATAATGGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTTCATTATATTAAA
Found at i:3028631 original size:31 final size:31
Alignment explanation
Indices: 3028595--3028659 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
3028585 AGATTTATAA
3028595 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
1 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
3028626 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
1 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
3028657 TTT
1 TTT
3028660 TATAGTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.69
Consensus pattern (31 bp):
TTTAATTATTTTTTCCTTGTTTTTATAGTGT
Found at i:3032823 original size:16 final size:16
Alignment explanation
Indices: 3032802--3032832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3032792 TAACTAAGCT
*
3032802 CTGCTATTTTGTTTTG
1 CTGCTATGTTGTTTTG
3032818 CTGCTATGTTGTTTT
1 CTGCTATGTTGTTTT
3032833 AATGTGTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.19, T:0.61
Consensus pattern (16 bp):
CTGCTATGTTGTTTTG
Found at i:3035582 original size:27 final size:27
Alignment explanation
Indices: 3035544--3035599 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3035534 AAATTGAAAA
3035544 AATGAGAGAATTAGAGAGATGCAAGTT
1 AATGAGAGAATTAGAGAGATGCAAGTT
3035571 AATGAGAGAATTAGAGAGATGCAAGTT
1 AATGAGAGAATTAGAGAGATGCAAGTT
3035598 AA
1 AA
3035600 GGGTGCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.29, T:0.21
Consensus pattern (27 bp):
AATGAGAGAATTAGAGAGATGCAAGTT
Found at i:3038471 original size:1 final size:1
Alignment explanation
Indices: 3038465--3038489 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3038455 TCCAGATTGC
3038465 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3038490 CCCAGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3043266 original size:14 final size:12
Alignment explanation
Indices: 3043231--3043257 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3043221 AAATTACATA
3043231 TAATAAAATTTT
1 TAATAAAATTTT
3043243 TAATAAAATTTT
1 TAATAAAATTTT
3043255 TAA
1 TAA
3043258 AATAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATAAAATTTT
Found at i:3044192 original size:36 final size:36
Alignment explanation
Indices: 3044145--3044216 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3044135 TAGTATTAAG
3044145 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
1 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
3044181 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
1 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
3044217 TAAGATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (36 bp):
ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
Found at i:3048317 original size:58 final size:58
Alignment explanation
Indices: 3048184--3048318 Score: 180
Period size: 58 Copynumber: 2.3 Consensus size: 58
3048174 AACAAAACAA
* *
3048184 TTACAAATAGTATAAGTGTGCCTCTTTATTGATAGGTCAAGCTTTTACAATCAAAGGG
1 TTACAAATAGTATAAGTGTGCCTCTTTATTGATAGGTCAAACTTTTACAATCAAACGG
* * * * *
3048242 TTCCGAATGGTATAAGTGTGCCTTTTTATTGATAGGTCAAATTTTTACAATCAAACGG
1 TTACAAATAGTATAAGTGTGCCTCTTTATTGATAGGTCAAACTTTTACAATCAAACGG
* * *
3048300 TTATAAATAATAAAAGTGT
1 TTACAAATAGTATAAGTGT
3048319 ACAAATGGTT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (58 bp):
TTACAAATAGTATAAGTGTGCCTCTTTATTGATAGGTCAAACTTTTACAATCAAACGG
Found at i:3048323 original size:27 final size:27
Alignment explanation
Indices: 3048293--3048349 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3048283 TTTTTACAAT
*
3048293 CAAACGGTTATAAATAATAAAAGTGTA
1 CAAACGGTTATAAATAATAAAAGTATA
* * *
3048320 CAAATGGTTATAAATGATATAAGTATA
1 CAAACGGTTATAAATAATAAAAGTATA
3048347 CAA
1 CAA
3048350 TCTACACACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (27 bp):
CAAACGGTTATAAATAATAAAAGTATA
Found at i:3048534 original size:21 final size:20
Alignment explanation
Indices: 3048484--3048534 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
3048474 TTTTTTAGTT
3048484 TAAAATATTAAATTTTATTAA
1 TAAAAT-TTAAATTTTATTAA
*
3048505 AAAATATTTAAATTTTGA-TATA
1 TAAA-ATTTAAATTTT-ATTA-A
3048527 TAAAATTT
1 TAAAATTT
3048535 TTTGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAAATTTAAATTTTATTAA
Found at i:3053881 original size:21 final size:21
Alignment explanation
Indices: 3053855--3053898 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3053845 CCCTCTTTCA
3053855 ACTCCGACACAAACAAAAATG
1 ACTCCGACACAAACAAAAATG
*
3053876 ACTCCGACACTAACAAAAATG
1 ACTCCGACACAAACAAAAATG
3053897 AC
1 AC
3053899 AATAGCAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.30, G:0.09, T:0.11
Consensus pattern (21 bp):
ACTCCGACACAAACAAAAATG
Found at i:3060078 original size:33 final size:33
Alignment explanation
Indices: 3060041--3060120 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
3060031 GCAAGAGTAG
*
3060041 GAGTAGACA-AAACGGAAGCAAGAATGTCGGCTT
1 GAGTA-ACACAAACAGAAGCAAGAATGTCGGCTT
* **
3060074 GAGTAATACAAACATTAGCAAGAATGTCGGCTT
1 GAGTAACACAAACAGAAGCAAGAATGTCGGCTT
*
3060107 GAGTAATACAAACA
1 GAGTAACACAAACA
3060121 TTGGTGAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 2 0.05
33 40 0.95
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (33 bp):
GAGTAACACAAACAGAAGCAAGAATGTCGGCTT
Found at i:3060131 original size:33 final size:33
Alignment explanation
Indices: 3060057--3060122 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3060047 ACAAAACGGA
3060057 AGCAAGAATGTCGGCTTGAGTAATACAAACATT
1 AGCAAGAATGTCGGCTTGAGTAATACAAACATT
3060090 AGCAAGAATGTCGGCTTGAGTAATACAAACATT
1 AGCAAGAATGTCGGCTTGAGTAATACAAACATT
3060123 GGTGAGAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (33 bp):
AGCAAGAATGTCGGCTTGAGTAATACAAACATT
Found at i:3063805 original size:36 final size:34
Alignment explanation
Indices: 3063740--3063806 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
3063730 AATAAAAATT
3063740 TTAAATTTTAAAATTATAAAAATATATAAAAGAA
1 TTAAATTTTAAAATTATAAAAATATATAAAAGAA
* *
3063774 TTAAATATTTATAATATATATAAATATATAAAA
1 TTAAAT-TTTAAAAT-TATAAAAATATATAAAA
3063807 CAACTAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.21
35 7 0.24
36 16 0.55
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
TTAAATTTTAAAATTATAAAAATATATAAAAGAA
Found at i:3064162 original size:21 final size:22
Alignment explanation
Indices: 3064138--3064184 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3064128 GAAACAAAAA
3064138 TTATACATTTTT-TTTCTTAAT
1 TTATACATTTTTATTTCTTAAT
* *
3064159 TTATATATTTTTATTTTTTAAT
1 TTATACATTTTTATTTCTTAAT
3064181 TTAT
1 TTAT
3064185 GTTCACCACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATACATTTTTATTTCTTAAT
Found at i:3075993 original size:39 final size:39
Alignment explanation
Indices: 3075941--3076025 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
3075931 ATGTAAATTA
3075941 TTTTCAAGCAAACAAATACTGAAAAAACGAGGAAAACAT
1 TTTTCAAGCAAACAAATACTGAAAAAACGAGGAAAACAT
3075980 TTTTCAAGCAAACAAATACTGAAAAAACGAGGAAAACAT
1 TTTTCAAGCAAACAAATACTGAAAAAACGAGGAAAACAT
3076019 TTTTCAA
1 TTTTCAA
3076026 AAAATGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (39 bp):
TTTTCAAGCAAACAAATACTGAAAAAACGAGGAAAACAT
Found at i:3090671 original size:25 final size:25
Alignment explanation
Indices: 3090643--3090692 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3090633 TTATACGACC
3090643 TTAAAATGACCCTTATGCTGAATGA
1 TTAAAATGACCCTTATGCTGAATGA
3090668 TTAAAATGACCCTTATGCTGAATGA
1 TTAAAATGACCCTTATGCTGAATGA
3090693 CCCAAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (25 bp):
TTAAAATGACCCTTATGCTGAATGA
Found at i:3090699 original size:25 final size:25
Alignment explanation
Indices: 3090645--3090699 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
3090635 ATACGACCTT
**
3090645 AAAATGACCCTTATGCTGAATGATT
1 AAAATGACCCTTATGCTGAATGACC
3090670 AAAATGACCCTTATGCTGAATGACC
1 AAAATGACCCTTATGCTGAATGACC
*
3090695 CAAAT
1 AAAAT
3090700 TCAAAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCCTTATGCTGAATGACC
Found at i:3104025 original size:17 final size:17
Alignment explanation
Indices: 3103997--3104038 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3103987 AATTGAAATG
3103997 AATTTT-TTAAAATTAT
1 AATTTTATTAAAATTAT
* *
3104013 ATTTTTATTAAAATTTT
1 AATTTTATTAAAATTAT
3104030 AATTTTATT
1 AATTTTATT
3104039 TAATTTCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTATTAAAATTAT
Found at i:3104244 original size:17 final size:18
Alignment explanation
Indices: 3104222--3104255 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3104212 ACTTAGAGCT
3104222 TTTTTGG-TCTAATTGGC
1 TTTTTGGTTCTAATTGGC
3104239 TTTTTGGTTCTAATTGG
1 TTTTTGGTTCTAATTGG
3104256 TACTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.56
Consensus pattern (18 bp):
TTTTTGGTTCTAATTGGC
Found at i:3108872 original size:354 final size:358
Alignment explanation
Indices: 3108177--3108914 Score: 1041
Period size: 354 Copynumber: 2.1 Consensus size: 358
3108167 GAGGTTTATC
* *
3108177 TTCATAAGGAATGTGCTTAGTTAGAGTTAGCCCCCAGATTCAGTATGCCTTCCACCCCAAACACC
1 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAGATTCAGCATGCCTTCCACCCCAAACACC
* *
3108242 CTCTCACTCTTTTGCCAAAATCACCTTATTTTGGGGGCGCGGATTGTGCGACTTTTGTGGTAAGG
66 CTCTCACTCTTTTGCC--AAGCACCTTATTTT---GGCGCGGA-TGTGCGACTTTTGTGGCAAGG
** *
3108307 AATTAAGGGGATTTGTTTATAATTGTAATGATTGTATGTTCGATCTGCACATCAATTGTGCTTTG
125 AATTAAGGGGATTTGCATATAATTGTAATGATTGTAAGTTCGATCTGCACATCAATTGTGCTTTG
*
3108372 CTTCAATCATCCATTGCTGCTAATTTTCCTAATTCTTCGCACCCCCATCCATTGTTCTTCATTCA
190 CTTCAATCATCCATTGCTGCTAATTTTACTAATTCTTCGCACCCCCATCCATTGTTCTTCATTCA
* *
3108437 AAATCATAACAATGAAGTCAAGCCTGATTGCCCCGTGTGTCAAAAACCAATATCTGGTCCATTTT
255 AAACCATAACAATGAAGTCAAGCCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATTTT
* *
3108502 ACCACTGTTCAGATTGCACTTATCCTACA-TTGTTTAACA
320 ACCACTGTTCAGATTGCACATATCCTACAGTT-TATAACA
*
3108541 TTCATACGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCAT-CCTTTCCACCCCAAACA
1 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCC-AGATTCAGCATGCC-TTCCACCCCAAACA
3108605 CCCTCTCACTCTTTTGCC-AGCACCTTATTTT-G-G-GGA-GTGCGA-TTTGTGTGGCAAGGCAA
64 CCCTCTCACTCTTTTGCCAAGCACCTTATTTTGGCGCGGATGTGCGACTTT-TGTGGCAAGG-AA
* *
3108664 TT-TGGGGAATTT-CATATAATTGTTATGATTGTAAGTTC-AGTCTGCACATCAATTGTGCTTTG
127 TTAAGGGG-ATTTGCATATAATTGTAATGATTGTAAGTTCGA-TCTGCACATCAATTGTGCTTTG
* * *
3108726 CTTCAATCATCCATTGTTGCTAATTTTACTAGTTCTTTGCACCCCCATCCATTGTTCTTCATTCA
190 CTTCAATCATCCATTGCTGCTAATTTTACTAATTCTTCGCACCCCCATCCATTGTTCTTCATTCA
* **
3108791 AAACCATAACAATGAAGTCGATTCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATTTT
255 AAACCATAACAATGAAGTCAAGCCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATTTT
* * * *
3108856 ATCACTGCTT-AGATTGCAGATATCCTAGAGTTTATAACC
320 ACCACTG-TTCAGATTGCACATATCCTACAGTTTATAACA
3108895 TTCATAAGGAATGTGCTGAG
1 TTCATAAGGAATGTGCTGAG
3108915 CTACCCCTTG
Statistics
Matches: 340, Mismatches: 26, Indels: 26
0.87 0.07 0.07
Matches are distributed among these distances:
353 4 0.01
354 230 0.68
355 12 0.04
356 3 0.01
357 1 0.00
358 1 0.00
362 12 0.04
364 35 0.10
365 42 0.12
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (358 bp):
TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAGATTCAGCATGCCTTCCACCCCAAACACC
CTCTCACTCTTTTGCCAAGCACCTTATTTTGGCGCGGATGTGCGACTTTTGTGGCAAGGAATTAA
GGGGATTTGCATATAATTGTAATGATTGTAAGTTCGATCTGCACATCAATTGTGCTTTGCTTCAA
TCATCCATTGCTGCTAATTTTACTAATTCTTCGCACCCCCATCCATTGTTCTTCATTCAAAACCA
TAACAATGAAGTCAAGCCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATTTTACCACT
GTTCAGATTGCACATATCCTACAGTTTATAACA
Found at i:3121803 original size:21 final size:21
Alignment explanation
Indices: 3121777--3121817 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3121767 AGACGAGCAA
* *
3121777 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3121798 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3121818 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3128543 original size:114 final size:114
Alignment explanation
Indices: 3128219--3128543 Score: 447
Period size: 114 Copynumber: 2.9 Consensus size: 114
3128209 ATTTAAATGT
* * * *
3128219 CTTAATTCTTGGCTTAATGTTGTCCGGGTAGATGGAAGACTGTAAAGTCTCTGTTTGAAGATCAA
1 CTTAATTCATGGCTTAATGTTGTCCGGGTAGATGGAAGACTGCAAAATCTCCGTTTGAAGATCAA
* * * *
3128284 AGGAAATTGAGATGTCAATTGTGTTTGGAGTGGAATGGAGTTCTGATGC
66 AGGAAATTGAGATGCCAATTGTTTTTGGAGAGGAATGGAATTCTGATGC
* * *
3128333 TTTAATTCATGGCTTAATGTTGTCCGAGTAGATGGAAGACTGCGAAATCTCCGTTTGAAGATCAA
1 CTTAATTCATGGCTTAATGTTGTCCGGGTAGATGGAAGACTGCAAAATCTCCGTTTGAAGATCAA
* *
3128398 AGGAAATTGAGATGCCAATTGTTTGTCGAGAGGAATGGAATTCTGATGC
66 AGGAAATTGAGATGCCAATTGTTTTTGGAGAGGAATGGAATTCTGATGC
* * * ** *
3128447 CTTAATTCATGGCTTAATGTTGTCCGGGTGGATGCAAGACAT-CAAAATCTCCATTCAAAAATCA
1 CTTAATTCATGGCTTAATGTTGTCCGGGTAGATGGAAGAC-TGCAAAATCTCCGTTTGAAGATCA
3128511 AA-GAAATTTGAGATGCCAATTGTTTTTGGAGAG
65 AAGGAAA-TTGAGATGCCAATTGTTTTTGGAGAG
3128544 AGAGAAGGAG
Statistics
Matches: 185, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
113 4 0.02
114 180 0.97
115 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32
Consensus pattern (114 bp):
CTTAATTCATGGCTTAATGTTGTCCGGGTAGATGGAAGACTGCAAAATCTCCGTTTGAAGATCAA
AGGAAATTGAGATGCCAATTGTTTTTGGAGAGGAATGGAATTCTGATGC
Found at i:3129572 original size:22 final size:22
Alignment explanation
Indices: 3129547--3129589 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3129537 AATATCTAGT
*
3129547 ATTT-AAGTTTGACATTTTTTTA
1 ATTTGAAGTTT-AAATTTTTTTA
*
3129569 ATTTGATGTTTAAATTTTTTT
1 ATTTGAAGTTTAAATTTTTTT
3129590 TTATCTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.63
Consensus pattern (22 bp):
ATTTGAAGTTTAAATTTTTTTA
Found at i:3129875 original size:4 final size:4
Alignment explanation
Indices: 3129858--3129889 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
3129848 TTCATTATTT
*
3129858 TTAA TTAA TAAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
3129890 AACTAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:3132527 original size:16 final size:16
Alignment explanation
Indices: 3132506--3132536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3132496 AATATAGGTA
*
3132506 TATATATTGTATATTG
1 TATATATTATATATTG
3132522 TATATATTATATATT
1 TATATATTATATATT
3132537 ATGTACATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TATATATTATATATTG
Found at i:3132672 original size:14 final size:15
Alignment explanation
Indices: 3132655--3132716 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 15
3132645 ATTATACGTG
3132655 TATATATATA-TATT
1 TATATATATATTATT
3132669 TATATA-ATATTATT
1 TATATATATATTATT
*
3132683 TATATATATCATTATA
1 TATATATAT-ATTATT
*
3132699 TATTTATACCTATTATT
1 TATATATA--TATTATT
3132716 T
1 T
3132717 TCACTATTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 3 0.08
14 16 0.40
15 2 0.05
16 12 0.30
17 6 0.15
18 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATATATATTATT
Found at i:3132824 original size:19 final size:19
Alignment explanation
Indices: 3132791--3132851 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 19
3132781 TTTATTATTA
3132791 TTATTA-ATA-GTATATGT
1 TTATTATATATGTATATGT
*
3132808 TTATTATATATGTATATAT
1 TTATTATATATGTATATGT
*
3132827 CCTTAGTATATATGTATATGT
1 --TTATTATATATGTATATGT
3132848 TTAT
1 TTAT
3132852 GCAATGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 6 0.17
18 3 0.08
19 10 0.28
21 17 0.47
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (19 bp):
TTATTATATATGTATATGT
Found at i:3137571 original size:354 final size:359
Alignment explanation
Indices: 3136903--3137642 Score: 1036
Period size: 354 Copynumber: 2.1 Consensus size: 359
3136893 GAGGTTTATC
* * *
3136903 TTCATAAGGAATGTGCTTAGTTAGAGTTAGCCCCCCAGATTCAGTATGCCTTCCACCCCAAACAC
1 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCATGCCTTCCACCCCAAACAC
* *
3136968 CCTCTCACTCTTTTGCCAAAATCACCTTATTTTGGGGGGCGCGGATTGTGCGACTTTTGTGGTAA
66 CCTCTCACTCTTTTGCC--AAGCACCTTATTTT----GGCGCGGA-TGTGCGACTTTTGTGGCAA
** *
3137033 GGAATTAAGGGGATTTGTTTATAATTGTAATGATTGTATGTTCGATCTGCACATCAATTGTGCTT
124 GGAATTAAGGGGATTTGCATATAATTGTAATGATTGTAAGTTCGATCTGCACATCAATTGTGCTT
*
3137098 TGCTTCAATCATCCATTGCTGCTAATTTTCCTAATTCTTCGCACCCCCATCCATTGTTCTTCATT
189 TGCTTCAATCATCCATTGCTGCTAATTTTACTAATTCTTCGCACCCCCATCCATTGTTCTTCATT
* *
3137163 CAAAATCATAACAATGAAGTCAAGCCTGATTGCCCCGTGTGTCAAAAACCAATATCTGGTCCATT
254 CAAAACCATAACAATGAAGTCAAGCCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATT
* *
3137228 TTACCACTG-TTCAGATTGCACTTATCCTACA-TTGTTTAACA
319 TTACCACTGCTT-AGATTGCACATATCCTACAGTT-TATAACA
*
3137269 TTCATACGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCAT-CCTTTCCACCCCAAACA
1 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCATGCC-TTCCACCCCAAACA
3137333 CCCTCTCACTCTTTTGCC-AGCACCTTATTTT-G-G-GGA-GTGCGA-TTTGTGTGGCAAGGCAA
65 CCCTCTCACTCTTTTGCCAAGCACCTTATTTTGGCGCGGATGTGCGACTTT-TGTGGCAAGG-AA
* *
3137392 TT-TGGGGAATTT-CATATAATTGTTATGATTGTAAGTTC-AGTCTGCACATCAATTGTGCTTTG
128 TTAAGGGG-ATTTGCATATAATTGTAATGATTGTAAGTTCGA-TCTGCACATCAATTGTGCTTTG
* * *
3137454 CTTCAATCATCCATTGTTGCTAATTTTACTAGTTCTTTGCACCCCCATCCATTGTTCTTCATTCA
191 CTTCAATCATCCATTGCTGCTAATTTTACTAATTCTTCGCACCCCCATCCATTGTTCTTCATTCA
* **
3137519 AAACCATAACAATGAAGTCGATTCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATTTT
256 AAACCATAACAATGAAGTCAAGCCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATTTT
* * * *
3137584 ATCACTGCTTAGATTGCAGATATCCTAGAGTTTATAACC
321 ACCACTGCTTAGATTGCACATATCCTACAGTTTATAACA
3137623 TTCATAAGGAATGTGCTGAG
1 TTCATAAGGAATGTGCTGAG
3137643 CTACCCCTTG
Statistics
Matches: 340, Mismatches: 27, Indels: 26
0.87 0.07 0.07
Matches are distributed among these distances:
353 4 0.01
354 230 0.68
355 12 0.04
356 3 0.01
357 1 0.00
358 1 0.00
363 12 0.04
365 2 0.01
366 75 0.22
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (359 bp):
TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCATGCCTTCCACCCCAAACAC
CCTCTCACTCTTTTGCCAAGCACCTTATTTTGGCGCGGATGTGCGACTTTTGTGGCAAGGAATTA
AGGGGATTTGCATATAATTGTAATGATTGTAAGTTCGATCTGCACATCAATTGTGCTTTGCTTCA
ATCATCCATTGCTGCTAATTTTACTAATTCTTCGCACCCCCATCCATTGTTCTTCATTCAAAACC
ATAACAATGAAGTCAAGCCTGATTGCCCCGGGTGTCAAAAACCAATATCTGGTCCATTTTACCAC
TGCTTAGATTGCACATATCCTACAGTTTATAACA
Found at i:3140683 original size:32 final size:31
Alignment explanation
Indices: 3140636--3140724 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
3140626 TTAAGTTCTC
* * *
3140636 TCAAACTTTTTAAAAATTCTCATTAATTTTT
1 TCAAAATTTTTAAAAATTCTAATTAAATTTT
* *
3140667 TCAAAATTTTTAAAAAATTGTAATCAAAATTTT
1 TCAAAATTTTT-AAAAATTCTAAT-TAAATTTT
* *
3140700 T-AAAAGTTTTAAAAATTCTTATTAA
1 TCAAAATTTTTAAAAATTCTAATTAA
3140725 GCCCCAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
30 2 0.04
31 20 0.43
32 18 0.38
33 7 0.15
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (31 bp):
TCAAAATTTTTAAAAATTCTAATTAAATTTT
Found at i:3144371 original size:35 final size:35
Alignment explanation
Indices: 3144332--3144495 Score: 141
Period size: 35 Copynumber: 4.7 Consensus size: 35
3144322 TCCATGGCAA
* ** *
3144332 AGTTGTGAAACGTAGCTATGGTATCATTCATACTG
1 AGTTGTGAAACGTAGGTATGGTATCAACCATACCG
*
3144367 AGTTGTGAAACGTAGGTATGGTATTAACCATACCG
1 AGTTGTGAAACGTAGGTATGGTATCAACCATACCG
* * * * **
3144402 AGTTGTGAAACATAGGTATGGTATTATCGATATTG
1 AGTTGTGAAACGTAGGTATGGTATCAACCATACCG
* ** * * *
3144437 ACTTAAGAAATGTAGGTATGGCTTTC-CCCATACCG
1 AGTTGTGAAACGTAGGTATGG-TATCAACCATACCG
* *
3144472 AGTTGTAAAATGTAGGTATGGTAT
1 AGTTGTGAAACGTAGGTATGGTAT
3144496 TTCAATGAGG
Statistics
Matches: 102, Mismatches: 26, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
34 2 0.02
35 98 0.96
36 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (35 bp):
AGTTGTGAAACGTAGGTATGGTATCAACCATACCG
Found at i:3144410 original size:70 final size:70
Alignment explanation
Indices: 3144332--3144495 Score: 188
Period size: 70 Copynumber: 2.3 Consensus size: 70
3144322 TCCATGGCAA
* * **
3144332 AGTTGTGAAACGTAGCTATGGTATCATTC-ATACTGAGTTGTGAAACGTAGGTATGG-TATTAAC
1 AGTTGTGAAACGTAGGTATGGTATCA-TCGATACTGACTTAAGAAACGTAGGTATGGCT-TTAAC
3144395 CATACCG
64 CATACCG
* * * * **
3144402 AGTTGTGAAACATAGGTATGGTATTATCGATATTGACTTAAGAAATGTAGGTATGGCTTTCCCCA
1 AGTTGTGAAACGTAGGTATGGTATCATCGATACTGACTTAAGAAACGTAGGTATGGCTTTAACCA
3144467 TACCG
66 TACCG
* *
3144472 AGTTGTAAAATGTAGGTATGGTAT
1 AGTTGTGAAACGTAGGTATGGTAT
3144496 TTCAATGAGG
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
69 2 0.03
70 76 0.96
71 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (70 bp):
AGTTGTGAAACGTAGGTATGGTATCATCGATACTGACTTAAGAAACGTAGGTATGGCTTTAACCA
TACCG
Found at i:3146842 original size:11 final size:11
Alignment explanation
Indices: 3146802--3146843 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
3146792 TTGATGTGGA
3146802 TAAAAAAATAT
1 TAAAAAAATAT
3146813 GT-AAAAAA-AT
1 -TAAAAAAATAT
3146823 TATAAAAAATAT
1 TA-AAAAAATAT
3146835 TAAAAAAAT
1 TAAAAAAAT
3146844 GAACCTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.04
10 2 0.07
11 19 0.70
12 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAAAAAATAT
Found at i:3147683 original size:21 final size:21
Alignment explanation
Indices: 3147659--3147698 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3147649 AATATTAGCT
3147659 ATTTCAAAATTT-AAAATAAAA
1 ATTT-AAAATTTGAAAATAAAA
*
3147680 ATTTAATATTTGAAAATAA
1 ATTTAAAATTTGAAAATAA
3147699 TATCCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTTAAAATTTGAAAATAAAA
Found at i:3150994 original size:25 final size:26
Alignment explanation
Indices: 3150921--3150994 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 26
3150911 GTGTAACGAT
* * *
3150921 ATAATAATATGATGGTAATAAAAATACA
1 ATAATAATA--ATGATAATAATAACACA
* *
3150949 ATAATAAAAAT-ATATTAAATAACA-A
1 ATAATAATAATGATAAT-AATAACACA
3150974 ATAATAATAATGATAATAATA
1 ATAATAATAATGATAATAATA
3150995 TAGAAATATG
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
25 18 0.49
26 11 0.30
28 8 0.22
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (26 bp):
ATAATAATAATGATAATAATAACACA
Found at i:3151056 original size:2 final size:2
Alignment explanation
Indices: 3151049--3151123 Score: 50
Period size: 2 Copynumber: 39.5 Consensus size: 2
3151039 TAAAAATTAC
* * * * *
3151049 TA TA TA TA TA TA TA TA TC TA TG TA CA TA -A TA TA TC TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3151090 TG TA T- TA GA -A AA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3151124 GCATGCATTG
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3151310 original size:22 final size:22
Alignment explanation
Indices: 3151283--3151325 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3151273 ATACTAAGGC
*
3151283 TAATAAATAAT-AAGTATAATAA
1 TAAT-AATAATGAAATATAATAA
3151305 TAATAATAATGAAATATAATA
1 TAATAATAATGAAATATAATA
3151326 GTATGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
TAATAATAATGAAATATAATAA
Found at i:3155828 original size:50 final size:50
Alignment explanation
Indices: 3155704--3155952 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
3155694 GATAATAACA
* * ** * *
3155704 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
3155755 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
3155805 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
3155855 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
3155910 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
3155953 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:3155882 original size:100 final size:104
Alignment explanation
Indices: 3155703--3155952 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
3155693 TGATAATAAC
**
3155703 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
3155768 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
3155805 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
3155868 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
3155910 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3155953 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:3156068 original size:13 final size:13
Alignment explanation
Indices: 3156047--3156078 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3156037 GCTTGGATCA
*
3156047 TCATCAAATAAAT
1 TCATAAAATAAAT
3156060 TCATAAAATAAAT
1 TCATAAAATAAAT
3156073 TCATAA
1 TCATAA
3156079 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:3156325 original size:30 final size:30
Alignment explanation
Indices: 3156290--3156347 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3156280 CCTCGACTCT
*
3156290 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
3156320 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
3156348 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:3162600 original size:20 final size:19
Alignment explanation
Indices: 3162571--3162631 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 19
3162561 ATATAGTAAA
*
3162571 ATTTTGAACTGAAAATATAT
1 ATTTTAAACT-AAAATATAT
* *
3162591 ATTTTAAACTTAAATAGTAA
1 ATTTTAAACTAAAATA-TAT
*
3162611 ACTGTTAAACTTAAAATATAT
1 A-TTTTAAAC-TAAAATATAT
3162632 TATTAAGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.16
20 12 0.38
21 9 0.28
22 6 0.19
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (19 bp):
ATTTTAAACTAAAATATAT
Found at i:3167775 original size:9 final size:9
Alignment explanation
Indices: 3167761--3167818 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
3167751 ATAAGTATAA
3167761 AATTAACCG
1 AATTAACCG
3167770 AATTAACCG
1 AATTAACCG
*
3167779 AATTAATCG
1 AATTAACCG
3167788 AATTAACCG
1 AATTAACCG
* *
3167797 AATTACCCT
1 AATTAACCG
3167806 AATTAACCG
1 AATTAACCG
3167815 AATT
1 AATT
3167819 GTTTGTATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:3167850 original size:6 final size:6
Alignment explanation
Indices: 3167839--3167891 Score: 79
Period size: 6 Copynumber: 8.5 Consensus size: 6
3167829 AATTATATAT
*
3167839 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA
3167889 TTT
1 TTT
3167892 ATTAATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 34 0.79
7 8 0.19
8 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:3167874 original size:26 final size:26
Alignment explanation
Indices: 3167839--3167888 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3167829 AATTATATAT
3167839 TTTTTATTTTTATTTTTAGTTTTAGA
1 TTTTTATTTTTATTTTTAGTTTTAGA
*
3167865 TTTTTATTTTTATTTTTATTTTTA
1 TTTTTATTTTTATTTTTAGTTTTA
3167889 TTTATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (26 bp):
TTTTTATTTTTATTTTTAGTTTTAGA
Found at i:3167939 original size:18 final size:18
Alignment explanation
Indices: 3167916--3167953 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3167906 ATTTTTATGA
3167916 TTGGGTTCGGTAATTGGG
1 TTGGGTTCGGTAATTGGG
* *
3167934 TTGGGTTGGGTACTTGGG
1 TTGGGTTCGGTAATTGGG
3167952 TT
1 TT
3167954 AATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.05, G:0.45, T:0.42
Consensus pattern (18 bp):
TTGGGTTCGGTAATTGGG
Found at i:3175727 original size:64 final size:64
Alignment explanation
Indices: 3175626--3175755 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
3175616 CGCTGTGATT
3175626 TCAGTTTAGATGTAGGTTGTGCAACACTACCACTCGCTGCTTGTTACAAGTATGACAGGCATCC
1 TCAGTTTAGATGTAGGTTGTGCAACACTACCACTCGCTGCTTGTTACAAGTATGACAGGCATCC
3175690 TCAGTTTAGATGTAGGTTGTGCAACACTACCACTCGCTGCTTGTTACAAGTATGACAGGCATCC
1 TCAGTTTAGATGTAGGTTGTGCAACACTACCACTCGCTGCTTGTTACAAGTATGACAGGCATCC
3175754 TC
1 TC
3175756 TTACTTTGAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (64 bp):
TCAGTTTAGATGTAGGTTGTGCAACACTACCACTCGCTGCTTGTTACAAGTATGACAGGCATCC
Found at i:3176818 original size:13 final size:13
Alignment explanation
Indices: 3176800--3176826 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3176790 AAAAGACTAA
3176800 ATTCAATTTAGGC
1 ATTCAATTTAGGC
3176813 ATTCAATTTAGGC
1 ATTCAATTTAGGC
3176826 A
1 A
3176827 AAATGTCCCT
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:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTCAATTTAGGC
Found at i:3177047 original size:17 final size:17
Alignment explanation
Indices: 3177027--3177062 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3177017 AATTAATTAT
3177027 TTTTAAAAAATTAAAAA
1 TTTTAAAAAATTAAAAA
**
3177044 TTTTAAAATTTTAAAAA
1 TTTTAAAAAATTAAAAA
3177061 TT
1 TT
3177063 GACATCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAATTAAAAA
Found at i:3177575 original size:21 final size:21
Alignment explanation
Indices: 3177534--3177575 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3177524 TCAAATGAGA
**
3177534 GAAGATAATTTTTATTGAATT
1 GAAGATAATTTTTATACAATT
3177555 GAAGAATAA-TTTTATACAATT
1 GAAG-ATAATTTTTATACAATT
3177576 CTAGTCTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (21 bp):
GAAGATAATTTTTATACAATT
Found at i:3177695 original size:22 final size:22
Alignment explanation
Indices: 3177665--3177722 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3177655 AAGTTCTCTC
*
3177665 AAAACTTTTTAAAAATTCTCATT
1 AAAA-TTTTTAAAAATTCTAATT
* * *
3177688 AAAATTTTCAAAATTTGTAATT
1 AAAATTTTTAAAAATTCTAATT
3177710 AAAATTTTTAAAA
1 AAAATTTTTAAAA
3177723 GTTTTAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATTTTTAAAAATTCTAATT
Found at i:3179972 original size:12 final size:12
Alignment explanation
Indices: 3179955--3179980 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3179945 TCAAGAATAC
3179955 TTCTTTTTTTTT
1 TTCTTTTTTTTT
3179967 TTCTTTTTTTTT
1 TTCTTTTTTTTT
3179979 TT
1 TT
3179981 TACAGTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:3186016 original size:32 final size:31
Alignment explanation
Indices: 3185980--3186046 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
3185970 AAATTTTTAT
*
3185980 TTAAATTCTCTC-AATTTTTTAAAAAGTTCTCA
1 TTAAATT-TCTCAAAATTTTTAAAAA-TTCTCA
* *
3186012 TTAAATTTTTCAAAATTTTTAAAAATTCTTA
1 TTAAATTTCTCAAAATTTTTAAAAATTCTCA
3186043 TTAA
1 TTAA
3186047 GCCCCAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (31 bp):
TTAAATTTCTCAAAATTTTTAAAAATTCTCA
Found at i:3189293 original size:47 final size:49
Alignment explanation
Indices: 3189175--3189353 Score: 232
Period size: 47 Copynumber: 3.8 Consensus size: 49
3189165 TGTAACCCGC
* *
3189175 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGG--GC-GTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCAGTTCACAT
3189221 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-C-AGTTCACAT
* *
3189271 -C-TCA-TGAACTCGGACTCAACTCAACGAGTTCGGA--CATTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCAGTTCACAT
*
3189315 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
3189354 TTCAACCATC
Statistics
Matches: 116, Mismatches: 6, Indels: 19
0.82 0.04 0.13
Matches are distributed among these distances:
43 3 0.03
44 5 0.04
45 1 0.01
46 36 0.31
47 59 0.51
48 3 0.03
49 2 0.02
50 4 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (49 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCAGTTCACAT
Found at i:3189342 original size:94 final size:93
Alignment explanation
Indices: 3189182--3189353 Score: 290
Period size: 94 Copynumber: 1.8 Consensus size: 93
3189172 CGCCCATAAG
* *
3189182 TGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCA
*
3189247 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACAAGTTCGGATGCCTAGTTACATCTCA
* *
3189275 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTCACATCCATAAGTGAACTCGGACTCAACTC
1 TGAACTCGGACTCAACTCAACGAGCTCGGAC-GTTCACATCCATAAGTGAACTCGGACTCAACTC
3189340 AACAAGTTCGGATG
65 AACAAGTTCGGATG
3189354 TTCAACCATC
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
93 28 0.38
94 45 0.62
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATCTCA
Found at i:3198713 original size:17 final size:17
Alignment explanation
Indices: 3198691--3198725 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3198681 CAACCAATCA
3198691 AAAAGTGTCATGTCACT
1 AAAAGTGTCATGTCACT
3198708 AAAAGTGTCATGTCACT
1 AAAAGTGTCATGTCACT
3198725 A
1 A
3198726 TCTCATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (17 bp):
AAAAGTGTCATGTCACT
Found at i:3198771 original size:25 final size:25
Alignment explanation
Indices: 3198741--3198801 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
3198731 TTAAAATATA
** *
3198741 ATTAAATAAAAATTTTTATTTTAAT
1 ATTAAATAAAAATAATTATATTAAT
*
3198766 ATTAAATAAAAATAATTGTATTAAT
1 ATTAAATAAAAATAATTATATTAAT
3198791 ATTAAATAAAA
1 ATTAAATAAAA
3198802 TAAAAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTAAATAAAAATAATTATATTAAT
Found at i:3205097 original size:23 final size:22
Alignment explanation
Indices: 3205021--3205172 Score: 137
Period size: 23 Copynumber: 6.5 Consensus size: 22
3205011 GACTTACCAT
3205021 AGCTCATATGAGCTTACCGATATATC
1 AGCTCATA-GAGCTTACCG-T-T-TC
** *
3205047 AGCTTGTAAGAGCTTACTGTTTTC
1 AGCTCAT-AGAGCTTACCG-TTTC
3205071 AGCTCATTAGAGCTTACCGTTTC
1 AGCTCA-TAGAGCTTACCGTTTC
*
3205094 AGCTCGTATGAGCTTA-C-TATTC
1 AGCTCATA-GAGCTTACCGT-TTC
3205116 AGCTCGATAGAGCTTACCGTTTC
1 AGCTC-ATAGAGCTTACCGTTTC
*
3205139 AGCTCGATAGAGCTTACCGTTTT
1 AGCTC-ATAGAGCTTACCGTTTC
3205162 AGCTCAATAGA
1 AGCTC-ATAGA
3205173 TTATTGCTCA
Statistics
Matches: 108, Mismatches: 11, Indels: 17
0.79 0.08 0.12
Matches are distributed among these distances:
21 1 0.01
22 18 0.17
23 54 0.50
24 17 0.16
25 2 0.02
26 15 0.14
27 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (22 bp):
AGCTCATAGAGCTTACCGTTTC
Found at i:3205129 original size:45 final size:45
Alignment explanation
Indices: 3205021--3205172 Score: 157
Period size: 45 Copynumber: 3.2 Consensus size: 45
3205011 GACTTACCAT
* * *
3205021 AGCTCATATGAGCTTACCGATATATCAGCTTGTAAGAGCTTACTGTTTTC
1 AGCTCATA-GAGCTTACCG-T-T-TCAGCTCGTATGAGCTTAC-GTATTC
3205071 AGCTCATTAGAGCTTACCGTTTCAGCTCGTATGAGCTTAC-TATTC
1 AGCTCA-TAGAGCTTACCGTTTCAGCTCGTATGAGCTTACGTATTC
*
3205116 AGCTCGATAGAGCTTACCGTTTCAGCTCG-ATAGAGCTTACCGT-TTT
1 AGCTC-ATAGAGCTTACCGTTTCAGCTCGTAT-GAGCTTA-CGTATTC
3205162 AGCTCAATAGA
1 AGCTC-ATAGA
3205173 TTATTGCTCA
Statistics
Matches: 92, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
44 2 0.02
45 38 0.41
46 14 0.15
47 18 0.20
48 1 0.01
49 1 0.01
50 16 0.17
51 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
AGCTCATAGAGCTTACCGTTTCAGCTCGTATGAGCTTACGTATTC
Found at i:3227828 original size:14 final size:15
Alignment explanation
Indices: 3227804--3227838 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3227794 TATATATATT
3227804 ACCATATAAATACTA
1 ACCATATAAATACTA
3227819 ACCATA-AAATACTA
1 ACCATATAAATACTA
3227833 ATCCAT
1 A-CCAT
3227839 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:3228710 original size:123 final size:123
Alignment explanation
Indices: 3228506--3228813 Score: 503
Period size: 123 Copynumber: 2.5 Consensus size: 123
3228496 CTATATAAAA
* ** * * *
3228506 CACCGGCATAAAGCCTGCTAGGCACAAAGCCTG-ATTCATTTCACCGGCA-CAAAGCCTGCTAGA
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAAT-AATCCACCGGCATC-AAGCCTGCTAGA
* *
3228569 CATAAAGTCGGAATTAATTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
64 CATAAAGTCGAAAATAATTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
3228629 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGACA
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGACA
*
3228694 TAAAGTCTAAAATAATTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
66 TAAAGTCGAAAATAATTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
3228752 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAG
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAG
3228814 GCATTAAGCC
Statistics
Matches: 174, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
123 171 0.98
124 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (123 bp):
CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGACA
TAAAGTCGAAAATAATTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
Found at i:3228828 original size:41 final size:41
Alignment explanation
Indices: 3228506--3228828 Score: 416
Period size: 41 Copynumber: 7.9 Consensus size: 41
3228496 CTATATAAAA
* * * * *
3228506 CACCGGCATAAAGCCTGCTAGGCACAAAGCCTG-ATTCATTT
1 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAAT-AATT
* * *
3228547 CACCGGCA-CAAAGCCTGCTAGACATAAAGTCGGAATTAATT
1 CACCGGCATC-AAGCCTGCTAGACATAAAGCCTGAAATAATT
* *
3228588 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAATAATT
* * *
3228629 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAATAATT
* *
3228670 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAATAATT
* *
3228711 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAATAATT
* * *
3228752 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAATAATT
* *
3228793 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
1 CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAA
3228829 ATCTCATATA
Statistics
Matches: 255, Mismatches: 24, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
41 251 0.98
42 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGCCTGAAATAATT
Found at i:3229061 original size:64 final size:63
Alignment explanation
Indices: 3228943--3229123 Score: 262
Period size: 64 Copynumber: 2.9 Consensus size: 63
3228933 GCAAACAAAC
*
3228943 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
3229004 T
63 T
3229005 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
3229069 ATTTGAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTT
3229124 AAATATATAT
Statistics
Matches: 110, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
62 17 0.15
63 6 0.05
64 77 0.70
65 10 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (63 bp):
ATTCGAACCACATATGTAATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:3233622 original size:15 final size:15
Alignment explanation
Indices: 3233599--3233633 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3233589 ATAACTTAAA
*
3233599 TTCAGTACTTAAATT
1 TTCAATACTTAAATT
3233614 TTCAATACTTAAATT
1 TTCAATACTTAAATT
3233629 TTCAA
1 TTCAA
3233634 CCCTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (15 bp):
TTCAATACTTAAATT
Found at i:3233639 original size:15 final size:15
Alignment explanation
Indices: 3233605--3233639 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3233595 TAAATTCAGT
*
3233605 ACTTAAATTTTCAAT
1 ACTTAAATTTTCAAC
3233620 ACTTAAATTTTCAAC
1 ACTTAAATTTTCAAC
*
3233635 CCTTA
1 ACTTA
3233640 TTTTTTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (15 bp):
ACTTAAATTTTCAAC
Found at i:3236916 original size:57 final size:57
Alignment explanation
Indices: 3236758--3236921 Score: 215
Period size: 57 Copynumber: 2.9 Consensus size: 57
3236748 CATGTTAGAA
* * *
3236758 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATGATATATCATGTCTGAC
1 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATAATTTATTATGTCTGAC
* * * * *
3236815 ATATGAAGAAATGATTG-CCTAAAATGGA-TGCTGTTTCCAGAATTTATTATGTCTGAC
1 ATTTGAAGAAATGGTTGTCC-AAAAT-GACTGTTGTTTTCATAATTTATTATGTCTGAC
*
3236872 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTTATAATTTATTAT
1 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATAATTTATTAT
3236922 CAAAGCTCAC
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
56 4 0.04
57 81 0.91
58 4 0.04
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (57 bp):
ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATAATTTATTATGTCTGAC
Found at i:3238807 original size:20 final size:21
Alignment explanation
Indices: 3238782--3238825 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3238772 AGGTTTATTG
3238782 TTTTTATT-TCTTTTCTTCCT
1 TTTTTATTATCTTTTCTTCCT
* *
3238802 TTTTTATTATTTTTTCTTTCT
1 TTTTTATTATCTTTTCTTCCT
3238823 TTT
1 TTT
3238826 CAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTATTATCTTTTCTTCCT
Found at i:3239552 original size:3 final size:3
Alignment explanation
Indices: 3239533--3239947 Score: 116
Period size: 3 Copynumber: 139.7 Consensus size: 3
3239523 TGGTTTAATG
* * *
3239533 TTA TTA -TA TTTA CTA TTA TTA TT- TTA CTA TTA TTA -TA TAA TATA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * * * *
3239577 TTT TTA TTA TCA TAA TTT TTA TTA TT- TTA CTA TTA TAA CTTAA CGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TT-A -TTA
* * * **
3239624 TTA TTA CTA TTA TTT TTA TTT TTA TTA CCA TTA TTA TTA TTA -TA CTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * ** *
3239671 GTA TT- TATA TTTA TT- TTA TT- CTA ATA CCA TTA TTG TTA TTA CTT-
1 TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * *
3239715 CTA TTA TT- TTT TTAA CTA TTA TTA TT- TATA TATA TATA TTA TTA TT-
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA
* * * * * * *
3239761 TGTA TCA TTG TTA TTA TTA CTG TTA TTA ATA -TA CTTA TTA TTG CTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* *
3239807 TTA TTA TTT TTA TTA TTA TTA CTA TT- TTA TT- TT- TTA CTT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * * *
3239849 TTA TTA ATA TTA TTA TTA TTA TCA -TC TTA TT- TTA TTA CTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * *
3239895 TTG TTG TAA TTA CTA TTA CTA GTA TTA TTA TT- TTT TTAA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
3239940 TTA TTA TT
1 TTA TTA TT
3239948 GGTGGTAGTA
Statistics
Matches: 295, Mismatches: 83, Indels: 68
0.66 0.19 0.15
Matches are distributed among these distances:
2 34 0.12
3 230 0.78
4 27 0.09
5 4 0.01
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3239560 original size:14 final size:15
Alignment explanation
Indices: 3239533--3239570 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
3239523 TGGTTTAATG
3239533 TTATTATATTTACTA
1 TTATTATATTTACTA
3239548 TTATTAT-TTTACTA
1 TTATTATATTTACTA
3239562 TTATTATAT
1 TTATTATAT
3239571 AATATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATATTTACTA
Found at i:3239614 original size:23 final size:22
Alignment explanation
Indices: 3239546--3239614 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
3239536 TTATATTTAC
*
3239546 TATTATTATTTTACTATTATTA
1 TATTATTATTTTACTATTATAA
* * *
3239568 TATAATATATTTTTATTATCATAA
1 TATTAT-TA-TTTTACTATTATAA
*
3239592 TTTTTATTATTTTACTATTATAA
1 -TATTATTATTTTACTATTATAA
3239615 CTTAACGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 5 0.14
23 14 0.39
24 13 0.36
25 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATTTTACTATTATAA
Found at i:3239884 original size:22 final size:21
Alignment explanation
Indices: 3239814--3239896 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 21
3239804 CTATTATTAT
3239814 TTTTATTATTATTA-CTATTTTA
1 TTTTATTATTATTATC-A-TTTA
* *
3239836 TTTT-TTACTT-TTATTATTAA
1 TTTTATTA-TTATTATCATTTA
*
3239856 TATTATTATTATTATCATCTTA
1 TTTTATTATTATTATCAT-TTA
*
3239878 TTTTATTACTATTATCATT
1 TTTTATTATTATTATCATT
3239897 GTTGTAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
20 8 0.16
21 17 0.35
22 24 0.49
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTATTATTATCATTTA
Found at i:3240279 original size:24 final size:27
Alignment explanation
Indices: 3240230--3240281 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
3240220 TAACATTATT
3240230 AATATTTCTAATATGTATATACTATGTA
1 AATATTTCTAATATGTATATA-TATGTA
3240258 AATATTTC-AATAT-TATAT-TATGTA
1 AATATTTCTAATATGTATATATATGTA
3240282 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.25
26 5 0.21
27 5 0.21
28 8 0.33
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (27 bp):
AATATTTCTAATATGTATATATATGTA
Found at i:3243393 original size:19 final size:20
Alignment explanation
Indices: 3243345--3243388 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3243335 TATAAGTTAC
3243345 TTAGCAAATTAAATATTTTT
1 TTAGCAAATTAAATATTTTT
3243365 TTAGCAAATTAAATATTTTT
1 TTAGCAAATTAAATATTTTT
3243385 TTAG
1 TTAG
3243389 TAATTTCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TTAGCAAATTAAATATTTTT
Found at i:3248816 original size:90 final size:90
Alignment explanation
Indices: 3248663--3248831 Score: 232
Period size: 90 Copynumber: 1.9 Consensus size: 90
3248653 AATGCTCAAG
* *
3248663 CCTAGTTCAAGCACTAACATGAGATCAATTACCAAGTTTAGGGATTAACTTGAACAAAAAAAAGT
1 CCTAGTTCAAGCACTAACATGAGAACAATTACCAAGTTTAGAGATTAACTTGAACAAAAAAAAGT
*
3248728 CCATACCCCAATGTAGGAACAATTA
66 CCAAACCCCAATGTAGGAACAATTA
* * * * *
3248753 CCTAGTTCAAGC-CTTAACATGTGAACAATTGCCAAGTTTATAGATTAATTTGGACAAAAAAAAG
1 CCTAGTTCAAGCAC-TAACATGAGAACAATTACCAAGTTTAGAGATTAACTTGAACAAAAAAAAG
**
3248817 TTGAAACCCCAATGT
65 TCCAAACCCCAATGT
3248832 GAGAATTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
89 1 0.01
90 67 0.99
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (90 bp):
CCTAGTTCAAGCACTAACATGAGAACAATTACCAAGTTTAGAGATTAACTTGAACAAAAAAAAGT
CCAAACCCCAATGTAGGAACAATTA
Found at i:3250392 original size:27 final size:28
Alignment explanation
Indices: 3250362--3250426 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
3250352 AAATCACTAT
3250362 ATAAAAAAATT-TCAATAAATAAAA-AAA
1 ATAAAAAAATTATCAAT-AATAAAATAAA
* *
3250389 AT-AAAAAATTATTAATATTAAAATAAA
1 ATAAAAAAATTATCAATAATAAAATAAA
3250416 ATAAAATAAAT
1 ATAAAA-AAAT
3250427 ATAATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 14 0.44
27 11 0.34
28 3 0.09
29 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAAAAAAATTATCAATAATAAAATAAA
Found at i:3261063 original size:20 final size:20
Alignment explanation
Indices: 3261038--3261077 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3261028 AGCCTTGAAC
*
3261038 CTTTGAATCTAAAA-CCCAAA
1 CTTTGAA-CCAAAATCCCAAA
3261058 CTTTGAACCAAAATCCCAAA
1 CTTTGAACCAAAATCCCAAA
3261078 ACCCAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.23
Consensus pattern (20 bp):
CTTTGAACCAAAATCCCAAA
Found at i:3264912 original size:31 final size:31
Alignment explanation
Indices: 3264877--3264947 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
3264867 GTTTAGGTTA
* *
3264877 GGACTAAAATTTTA-AAATTCATAAAGTATAG
1 GGACTAAAA-TTTACAAATTCAAAAAGTACAG
* * *
3264908 GGACTACAATTTACCAATTCAAAAAGTACAT
1 GGACTAAAATTTACAAATTCAAAAAGTACAG
3264939 GGACTAAAA
1 GGACTAAAA
3264948 AGATATGCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.27
Consensus pattern (31 bp):
GGACTAAAATTTACAAATTCAAAAAGTACAG
Found at i:3275029 original size:10 final size:10
Alignment explanation
Indices: 3275014--3275038 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3275004 ATGTACTTAA
3275014 AATATAGATT
1 AATATAGATT
3275024 AATATAGATT
1 AATATAGATT
3275034 AATAT
1 AATAT
3275039 TTTTAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
AATATAGATT
Found at i:3279044 original size:26 final size:25
Alignment explanation
Indices: 3279015--3279070 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
3279005 AAATTTAAAT
*
3279015 TTTAATTAGAATATATTAAAAGAAAA
1 TTTAATTAAAATATATTAAAA-AAAA
*
3279041 TTTATTTAAAATATATTAAAAAAAA
1 TTTAATTAAAATATATTAAAAAAAA
*
3279066 GTTAA
1 TTTAA
3279071 AATGTTCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
TTTAATTAAAATATATTAAAAAAAA
Found at i:3279418 original size:31 final size:31
Alignment explanation
Indices: 3279344--3279410 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
3279334 CTTTAATTTG
*
3279344 AAAAATAGTAAAATTTTGCATTCTGACTTTTT
1 AAAAATA-TAAAATTTTGCATTCTAACTTTTT
*
3279376 AAAAATGATAAAATTTTG-ATT-TAATTTTTT
1 AAAAAT-ATAAAATTTTGCATTCTAACTTTTT
3279406 AAAAA
1 AAAAA
3279411 ACTATAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 12 0.38
31 3 0.09
32 16 0.50
33 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (31 bp):
AAAAATATAAAATTTTGCATTCTAACTTTTT
Found at i:3282894 original size:22 final size:22
Alignment explanation
Indices: 3282859--3282904 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3282849 CAATTTTGGC
* * *
3282859 CCCTTTATATTAAACTCCAAAA
1 CCCTTCATACTAAACCCCAAAA
3282881 CCCTTCATACTAAACCCCAAAA
1 CCCTTCATACTAAACCCCAAAA
3282903 CC
1 CC
3282905 TAACACATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (22 bp):
CCCTTCATACTAAACCCCAAAA
Found at i:3284249 original size:26 final size:26
Alignment explanation
Indices: 3284210--3284317 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
3284200 TGATACAAAT
*
3284210 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3284236 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3284262 TTATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3284288 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3284314 TGAT
1 TGAT
3284318 GGGAATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3288494 original size:12 final size:12
Alignment explanation
Indices: 3288479--3288503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3288469 TGATTTATTT
3288479 GACCAACTTAGA
1 GACCAACTTAGA
3288491 GACCAACTTAGA
1 GACCAACTTAGA
3288503 G
1 G
3288504 GAGTTTCGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (12 bp):
GACCAACTTAGA
Found at i:3291398 original size:26 final size:26
Alignment explanation
Indices: 3291369--3291473 Score: 165
Period size: 26 Copynumber: 4.0 Consensus size: 26
3291359 TGATACAAAT
*
3291369 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3291395 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3291421 TTATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3291447 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3291473 T
1 T
3291474 TATGAGAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3291433 original size:52 final size:52
Alignment explanation
Indices: 3291371--3291476 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
3291361 ATACAAATTG
*
3291371 ATAATGGGTTAGGTAAATGTTTCATGATAATGGATTAGGTAAATATTCCATT
1 ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATT
* *
3291423 ATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCATT
1 ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATT
3291475 AT
1 AT
3291477 GAGAATTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.39
Consensus pattern (52 bp):
ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATT
Found at i:3294288 original size:15 final size:15
Alignment explanation
Indices: 3294268--3294297 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3294258 CCTTCCTTTT
3294268 TTTATTTGCAAATCC
1 TTTATTTGCAAATCC
3294283 TTTATTTGCAAATCC
1 TTTATTTGCAAATCC
3294298 GCCCCAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
TTTATTTGCAAATCC
Found at i:3294398 original size:3 final size:3
Alignment explanation
Indices: 3294392--3294601 Score: 76
Period size: 3 Copynumber: 73.3 Consensus size: 3
3294382 ATATTGCTAT
* *
3294392 TTA TTA -TA TTA TTA CTA TTA TCA TTA TTA TTA TT- TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
3294437 TTA -TG TTA -TA TTTA GTA TTA TT- TT- TTA ATA TTA -CA TT- TT-
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
3294476 TTA CTA TTA -TA TTA CTA TTA TCT- TTG TTA TT- TTC TCTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA
* **
3294520 TTTA TTA CTCTA TTT TTA ACA TTA TTA TTA -TA TTA -TA TT- TT- TTA
1 -TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
3294564 TATC TTA TTA TTA TTG CTA GTA TTA TTA TTA TTA TTA T
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3294602 ATACAATATT
Statistics
Matches: 153, Mismatches: 33, Indels: 42
0.67 0.14 0.18
Matches are distributed among these distances:
2 31 0.20
3 109 0.71
4 11 0.07
5 2 0.01
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3294409 original size:18 final size:18
Alignment explanation
Indices: 3294374--3294425 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
3294364 AGATTAAGTT
*
3294374 TTTATTATA-TATTGCTA
1 TTTATTATATTATTACTA
3294391 TTTATTATATTATTACTA
1 TTTATTATATTATTACTA
3294409 TTATCATTATTATTATT
1 TT-T-ATTA-TATTATT
3294426 TTATATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 9 0.30
18 9 0.30
19 1 0.03
20 4 0.13
21 7 0.23
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATTATATTATTACTA
Found at i:3294862 original size:26 final size:26
Alignment explanation
Indices: 3294798--3294867 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
3294788 TTTTAATACC
*
3294798 CTATATAT-TGTGTATATTCTTAATA
1 CTATATATATATGTATATTCTTAATA
* *
3294823 CTATATAGTGTATGTATTTTCTTAATAA
1 CTATATA-TATATGTATATTCTTAAT-A
3294851 CTATAT-TATATGTATAT
1 CTATATATATATGTATAT
3294868 ATATACTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 7 0.18
26 10 0.26
27 14 0.37
28 7 0.18
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (26 bp):
CTATATATATATGTATATTCTTAATA
Found at i:3297728 original size:21 final size:23
Alignment explanation
Indices: 3297681--3297734 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
3297671 CATTCAAGAT
**
3297681 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
3297704 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
3297725 AAAAT-ATATA
1 AAAATAATATA
3297735 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:3297772 original size:25 final size:23
Alignment explanation
Indices: 3297744--3297805 Score: 54
Period size: 25 Copynumber: 2.5 Consensus size: 23
3297734 AATGTGTAAA
*
3297744 AAAAGTTTGAAATATATAATATAT
1 AAAA-TTTGAAATAAATAATATAT
*
3297768 GAAAATATT-AAAGTAAATAATGTAT
1 -AAAAT-TTGAAA-TAAATAATATAT
3297793 AAAAATTTGAAAT
1 -AAAATTTGAAAT
3297806 GAGCATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (23 bp):
AAAATTTGAAATAAATAATATAT
Found at i:3297969 original size:15 final size:15
Alignment explanation
Indices: 3297945--3297990 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3297935 ATATAAATAG
*
3297945 AAATAAAAATATAAT
1 AAATAGAAATATAAT
3297960 AAATAGAAATATAAT
1 AAATAGAAATATAAT
3297975 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
3297991 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:3298038 original size:23 final size:23
Alignment explanation
Indices: 3297937--3298039 Score: 92
Period size: 23 Copynumber: 4.7 Consensus size: 23
3297927 ATATTAGTAT
3297937 ATAAATAGAAATA-AA-AATATA
1 ATAAATAGAAATAGAATAATATA
*
3297958 ATAAATAGAAATATAATAATAGT-
1 ATAAATAGAAATAGAATAATA-TA
* *
3297981 AGAAATATAAATAG-ATAA-ATA
1 ATAAATAGAAATAGAATAATATA
* * * *
3298002 A-AAATAGTATTAGAATAACAAA
1 ATAAATAGAAATAGAATAATATA
3298024 ATAAATAGAAATAGAA
1 ATAAATAGAAATAGAA
3298040 ACATAAAAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
20 10 0.15
21 19 0.29
22 9 0.14
23 27 0.41
24 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.24
Consensus pattern (23 bp):
ATAAATAGAAATAGAATAATATA
Found at i:3300236 original size:33 final size:32
Alignment explanation
Indices: 3300193--3300255 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
3300183 AAATTGAAAT
3300193 GAAATGGAAAAGAAAATAATTCAATTCCAATA
1 GAAATGGAAAAGAAAATAATTCAATTCCAATA
* *
3300225 GAAATAGGAAAAGAGAATAATTTAATTCCAA
1 GAAAT-GGAAAAGAAAATAATTCAATTCCAA
3300256 ATTGGAGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (32 bp):
GAAATGGAAAAGAAAATAATTCAATTCCAATA
Found at i:3305000 original size:10 final size:10
Alignment explanation
Indices: 3304985--3305016 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3304975 TAATTTATGG
3304985 TACAAATTGA
1 TACAAATTGA
3304995 TACAAATTGA
1 TACAAATTGA
*
3305005 TGCAAATTGA
1 TACAAATTGA
3305015 TA
1 TA
3305017 ATAGGTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (10 bp):
TACAAATTGA
Found at i:3305049 original size:26 final size:26
Alignment explanation
Indices: 3305012--3305095 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
3305002 TGATGCAAAT
* *
3305012 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3305038 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
3305064 TGATAATGGGTTAGGTAAATGTTTTA
1 TGATAATGGGTTAGGTAAATGTTTCA
3305090 TGATAA
1 TGATAA
3305096 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:3306607 original size:26 final size:26
Alignment explanation
Indices: 3306577--3306629 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3306567 TTTATAGTTT
*
3306577 TACCCTTAGGAGATAAATT-ACCAAAA
1 TACCCCTAGG-GATAAATTGACCAAAA
* *
3306603 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCAAAA
3306629 T
1 T
3306630 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCAAAA
Found at i:3314672 original size:26 final size:26
Alignment explanation
Indices: 3314641--3314696 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
3314631 TGAAATGCCC
*
3314641 ATCATGGAACATTTAGCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
3314667 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
3314693 ATCA
1 ATCA
3314697 ATTTGTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:3315328 original size:22 final size:22
Alignment explanation
Indices: 3315297--3315338 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3315287 ATATAAGTAC
* *
3315297 AATAATAATAATGGTAATAAAA
1 AATAAAAATAATAGTAATAAAA
3315319 AATAAAAATAATAGTAATAA
1 AATAAAAATAATAGTAATAA
3315339 TAGCACATTA
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:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
AATAAAAATAATAGTAATAAAA
Found at i:3315536 original size:12 final size:12
Alignment explanation
Indices: 3315492--3315539 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
3315482 TGTTCATGCG
*
3315492 TAAATATAAAGA
1 TAAATATAAACA
**
3315504 TAGGTATAATACA
1 TAAATATAA-ACA
3315517 TAAAATATAAACA
1 T-AAATATAAACA
3315530 TAAATATAAA
1 TAAATATAAA
3315540 GAGATAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 16 0.55
13 7 0.24
14 6 0.21
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (12 bp):
TAAATATAAACA
Found at i:3316289 original size:24 final size:22
Alignment explanation
Indices: 3316261--3316310 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 22
3316251 CAAATTCGAA
3316261 AATAAAATAAAAAGGAAAAATAAT
1 AATAAAATAAAAA-G-AAAATAAT
*
3316285 AAT-AAATAGAAAGAAAATAAT
1 AATAAAATAAAAAGAAAATAAT
3316306 AATAA
1 AATAA
3316311 TGTAATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 8 0.33
24 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (22 bp):
AATAAAATAAAAAGAAAATAAT
Found at i:3316311 original size:24 final size:23
Alignment explanation
Indices: 3316265--3316311 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3316255 TTCGAAAATA
*
3316265 AAATAAAAAGGAAAAATAATAAT
1 AAATAAAAAGAAAAAATAATAAT
*
3316288 AAATAGAAAGAAAATAATAATAAT
1 AAATAAAAAGAAAA-AATAATAAT
3316312 GTAATATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (23 bp):
AAATAAAAAGAAAAAATAATAAT
Found at i:3319268 original size:30 final size:30
Alignment explanation
Indices: 3319228--3319288 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3319218 TTACAAAGGC
*
3319228 ATTGGTGGTCTAGG-GGGTTTAGGCGGTGGA
1 ATTGGAGGTCTAGGTGGG-TTAGGCGGTGGA
*
3319258 ATTGGAGGTCTAGGTGGGTTAGGGGGTGGA
1 ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA
3319288 A
1 A
3319289 CTGGTGGCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.16, C:0.05, G:0.51, T:0.28
Consensus pattern (30 bp):
ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA
Found at i:3319314 original size:42 final size:42
Alignment explanation
Indices: 3319260--3319355 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
3319250 GCGGTGGAAT
*
3319260 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACTGGTGGCGGAGG
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
* *
3319302 TGGAGGTCTAGGTGGTTTAGGGGGTGGAACCGGTGGCGGAGT
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
3319344 TGGAGGTCTAGG
1 TGGAGGTCTAGG
3319356 CGGTGGGACC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.15, C:0.08, G:0.54, T:0.23
Consensus pattern (42 bp):
TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
Found at i:3319361 original size:33 final size:33
Alignment explanation
Indices: 3319319--3319394 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
3319309 CTAGGTGGTT
* *
3319319 TAGGGGGTGGAACCGGTGGCGGAGTTGGAGGTC
1 TAGGCGGTGGAACCGGGGGCGGAGTTGGAGGTC
*
3319352 TAGGCGGTGGGACCGGGGGCGGAGTTGGAGGTC
1 TAGGCGGTGGAACCGGGGGCGGAGTTGGAGGTC
*
3319385 TAGGTGGTGG
1 TAGGCGGTGG
3319395 TGGTTGTCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.13, C:0.12, G:0.57, T:0.18
Consensus pattern (33 bp):
TAGGCGGTGGAACCGGGGGCGGAGTTGGAGGTC
Found at i:3319472 original size:57 final size:57
Alignment explanation
Indices: 3319372--3319508 Score: 199
Period size: 57 Copynumber: 2.5 Consensus size: 57
3319362 GACCGGGGGC
* *
3319372 GGAGTTGGAGGTCTA---GGTGGTGGTGGTTGTCCAGGTACAGGTGGTGTAGGCAGT
1 GGAGCTGGAGGTCTAGGTGGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGT
* * *
3319426 GGAGGTGGAGGTCTAGGTGGTGGTGGTGGTTGTCCAGATACCGGTGGTGTAGGCGGT
1 GGAGCTGGAGGTCTAGGTGGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGT
*
3319483 GGAGCTGGAGGTATAGGTGGTGGTGG
1 GGAGCTGGAGGTCTAGGTGGTGGTGG
3319509 CAGCGGCGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
54 14 0.19
57 60 0.81
ACGTcount: A:0.14, C:0.09, G:0.51, T:0.26
Consensus pattern (57 bp):
GGAGCTGGAGGTCTAGGTGGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGT
Found at i:3320700 original size:30 final size:29
Alignment explanation
Indices: 3320657--3320714 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3320647 TAAAGCATTA
* **
3320657 AATTTATCGTTTTTATTTATTTTTAAAAAT
1 AATTTAGCGTTTTT-TAGATTTTTAAAAAT
*
3320687 AATTTAGCTTTTTTTAGATTTTTAAAAA
1 AATTTAGCGTTTTTTAGATTTTTAAAAA
3320715 AAAAATTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (29 bp):
AATTTAGCGTTTTTTAGATTTTTAAAAAT
Found at i:3320881 original size:68 final size:66
Alignment explanation
Indices: 3320785--3320920 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 66
3320775 ATGGTTTATA
* * * *
3320785 AATATTTTAATTTTTTATAATTTTTTAAGGGACCTATTTGCATATTTTCGAGACTGTCAATTACC
1 AATATTTTAATTTTTTATAATTTTTTAAGGGACCAATTTACATATTTTCGAAACTATCAATTACC
3320850 C
66 C
* *
3320851 AATATTTTGACTTTTTTGATAATTTTTTAAGGGACCAATTTACATTTTTTCGAAACTATCAATTA
1 AATATTTT-AATTTTTT-ATAATTTTTTAAGGGACCAATTTACATATTTTCGAAACTATCAATTA
3320916 CCC
64 CCC
3320919 AA
1 AA
3320921 GAAATATTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
66 8 0.13
67 7 0.11
68 47 0.76
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.46
Consensus pattern (66 bp):
AATATTTTAATTTTTTATAATTTTTTAAGGGACCAATTTACATATTTTCGAAACTATCAATTACC
C
Found at i:3322414 original size:47 final size:47
Alignment explanation
Indices: 3322357--3322450 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
3322347 TTACTCCGCC
3322357 CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
1 CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
*
3322404 CTGTTCTAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
1 CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
3322451 ATGTGGGTGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (47 bp):
CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
Found at i:3334916 original size:19 final size:18
Alignment explanation
Indices: 3334873--3334916 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3334863 ATTTAAAATG
3334873 TTTA-TTAAAAATAAAAA
1 TTTATTTAAAAATAAAAA
*
3334890 TATAATTTAAAAATAAAAAA
1 T-TTATTTAAAAAT-AAAAA
3334910 TTTATTT
1 TTTATTT
3334917 GGACAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.05
18 2 0.09
19 13 0.59
20 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTATTTAAAAATAAAAA
Found at i:3336825 original size:23 final size:23
Alignment explanation
Indices: 3336798--3336843 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3336788 TAAGATAAGT
*
3336798 GGATTCAAATAATTTTGGGTTTA
1 GGATTCAAATAATTTTGGATTTA
* *
3336821 GGATTTAATTAATTTTGGATTTA
1 GGATTCAAATAATTTTGGATTTA
3336844 AATCTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (23 bp):
GGATTCAAATAATTTTGGATTTA
Found at i:3339664 original size:11 final size:11
Alignment explanation
Indices: 3339650--3339690 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3339640 TGTTTTCTCC
3339650 CTATTTTGCTA
1 CTATTTTGCTA
*
3339661 CTATTTTACTA
1 CTATTTTGCTA
* *
3339672 TTATGTTGCTA
1 CTATTTTGCTA
3339683 CTATTTTG
1 CTATTTTG
3339691 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:3339943 original size:12 final size:12
Alignment explanation
Indices: 3339913--3339945 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3339903 TATATATTTT
3339913 AAAATT-ATATA
1 AAAATTAATATA
3339924 AAAA-TAATATA
1 AAAATTAATATA
3339935 AAAATTAATAT
1 AAAATTAATAT
3339946 GGACAGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Done.