Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015232.1 Kokia drynarioides strain JFW-HI SEQ_130277, whole genome shotgun sequence
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: 719139
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 336 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:358838 original size:15 final size:14
Alignment explanation
Indices: 358820--358957 Score: 99
Period size: 15 Copynumber: 9.6 Consensus size: 14
358810 TTGTTTGATT
358820 TTATTATTATTGTTA
1 TTATTATTATT-TTA
358835 TTATTATTA--TTA
1 TTATTATTATTTTA
* *
358847 TTATTATTCTGTTA
1 TTATTATTATTTTA
*
358861 TTTATTATTATTATTC
1 -TTATTATTATT-TTA
358877 TTATTATTATTTTA
1 TTATTATTATTTTA
*
358891 TATATTACTTATTTCCA
1 T-TATTA-TTATTT-TA
358908 TTTCCATT-TTATTTTA
1 -TT--ATTATTATTTTA
*
358924 TTTATTATTTTTTTA
1 -TTATTATTATTTTA
358939 -TATT-TTATTTTA
1 TTATTATTATTTTA
358951 TT-TTATT
1 TTATTATT
358958 TCTTATTTTT
Statistics
Matches: 101, Mismatches: 9, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
12 20 0.20
13 7 0.07
14 9 0.09
15 41 0.41
16 12 0.12
17 8 0.08
18 1 0.01
19 3 0.03
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:358923 original size:5 final size:5
Alignment explanation
Indices: 358913--358958 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
358903 TTCCATTTCC
358913 ATTTT ATTTT ATTTATT ATTTT -TTTAT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT A-TT-TT ATTTT ATTT-T ATTTT ATTTT ATTTT ATTT
358959 CTTATTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.08
5 24 0.65
6 7 0.19
7 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:358923 original size:33 final size:32
Alignment explanation
Indices: 358883--358956 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 32
358873 ATTCTTATTA
*
358883 TTATTTTATATATTACTTATTTCCATTTCCATT
1 TTATTTTATATATTACTTATTTACATTT-CATT
* * * * *
358916 TTATTTTATTTATTATTTTTTTATATTTTATT
1 TTATTTTATATATTACTTATTTACATTTCATT
358948 TTATTTTAT
1 TTATTTTAT
358957 TTCTTATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (32 bp):
TTATTTTATATATTACTTATTTACATTTCATT
Found at i:358931 original size:12 final size:12
Alignment explanation
Indices: 358916--358979 Score: 66
Period size: 12 Copynumber: 5.7 Consensus size: 12
358906 CATTTCCATT
358916 TTATTTTATTTA
1 TTATTTTATTTA
358928 TTATTTT-TTTA
1 TTATTTTATTTA
358939 -TATTTTA-TT-
1 TTATTTTATTTA
*
358948 TTATTTTATTTC
1 TTATTTTATTTA
*
358960 TTATTTT-TAGTA
1 TTATTTTAT-TTA
358972 TTATTTTA
1 TTATTTTA
358980 CTATTTGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 15 0.34
11 7 0.16
12 22 0.50
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (12 bp):
TTATTTTATTTA
Found at i:358958 original size:15 final size:16
Alignment explanation
Indices: 358782--358957 Score: 96
Period size: 17 Copynumber: 10.7 Consensus size: 16
358772 TCTTTTTTAA
*
358782 TTTATTATATTATT-T
1 TTTATTTTATTATTAT
* *
358797 ATTTAGGTTTATT-TTGT
1 -TTTA-TTTTATTATTAT
*
358814 TTGATTTTATTATTAT
1 TTTATTTTATTATTAT
358830 TGTTATTATTATTATTAT
1 T-TTATT-TTATTATTAT
* *
358848 TATTATTCTGTTATT-T
1 T-TTATTTTATTATTAT
* *
358864 ATTATTATTATTCTTAT
1 TTTATT-TTATTATTAT
358881 TATTATTTTATATATTA-
1 T-TTATTTTAT-TATTAT
* * *
358898 CTTATTTCCATT-TCCAT
1 TTTATTT-TATTAT-TAT
358915 TTTATTTTATTTATTAT
1 TTTATTTTA-TTATTAT
358932 TTT-TTTATATT-TTAT
1 TTTATTT-TATTATTAT
358947 TTTATTTTATT
1 TTTATTTTATT
358958 TCTTATTTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
15 23 0.19
16 36 0.29
17 38 0.31
18 26 0.21
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTATTTTATTATTAT
Found at i:358985 original size:32 final size:33
Alignment explanation
Indices: 358917--359016 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 33
358907 ATTTCCATTT
* * *
358917 TATTTTATTTATTATTTTT-TTA-TATTTTATTT
1 TATTTTATTTCTTATTTTTACTATTATTTTA-TC
*
358949 TATTTTATTTCTTATTTTTAGTATTATTTTA-C
1 TATTTTATTTCTTATTTTTACTATTATTTTATC
*
358981 TATTTGAATTATTCTTATTTTTACTATTATTCTTAT
1 TATTT-TA-T-TTCTTATTTTTACTATTATT-TTAT
359017 GTCTACTGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
32 23 0.41
33 3 0.05
34 8 0.14
35 19 0.34
36 3 0.05
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (33 bp):
TATTTTATTTCTTATTTTTACTATTATTTTATC
Found at i:359023 original size:18 final size:18
Alignment explanation
Indices: 358988--359023 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
358978 TACTATTTGA
* *
358988 ATTATTCTTATTTTTACT
1 ATTATTCTTATGTCTACT
359006 ATTATTCTTATGTCTACT
1 ATTATTCTTATGTCTACT
359024 GTAATGGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTATTCTTATGTCTACT
Found at i:361597 original size:63 final size:65
Alignment explanation
Indices: 361496--361623 Score: 233
Period size: 63 Copynumber: 2.0 Consensus size: 65
361486 TTGAAAAAAA
*
361496 AAAAAAGAAAANAAGAAGAAAGAAAGAAAATGTGGTTGAGATAGAATCATTAGAGTCGTATATTG
1 AAAAAAGAAAAAAAGAAGAAAGAAAGAAAATGTGGTTGAGATAGAATCATTAGAGTCGTATATTG
361561 -AAAAA-AAAAAAAGAAGAAAGAAAGAAAATGTGGTTGAGATAGAATCATTAGAGTCGTATATTG
1 AAAAAAGAAAAAAAGAAGAAAGAAAGAAAATGTGGTTGAGATAGAATCATTAGAGTCGTATATTG
361624 TTGAAAAGCT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 57 0.92
64 5 0.08
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.20
Consensus pattern (65 bp):
AAAAAAGAAAAAAAGAAGAAAGAAAGAAAATGTGGTTGAGATAGAATCATTAGAGTCGTATATTG
Found at i:369788 original size:19 final size:21
Alignment explanation
Indices: 369761--369800 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
369751 AATAACAATT
*
369761 GATTTATTGAT-TG-ATATTA
1 GATTAATTGATATGAATATTA
369780 GATTAATTGATATGAATATTA
1 GATTAATTGATATGAATATTA
369801 TTGTCAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (21 bp):
GATTAATTGATATGAATATTA
Found at i:370131 original size:18 final size:17
Alignment explanation
Indices: 370099--370132 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
370089 TTAAATCAAA
*
370099 TAAAATATTTTTTAATT
1 TAAAATATATTTTAATT
370116 TAAAATATAATTTTAAT
1 TAAAATAT-ATTTTAAT
370133 ATTATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATATATTTTAATT
Found at i:370849 original size:24 final size:24
Alignment explanation
Indices: 370809--370864 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
370799 GTTATGTGAC
* *
370809 AATTAAATTT-ATTTAAAATAAAA
1 AATTAAATTTAAATAAAAATAAAA
370832 ATATTAAATTTAAATAAAAAATAAAA
1 A-ATTAAATTTAAAT-AAAAATAAAA
370858 AATTAAA
1 AATTAAA
370865 GATTACAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 9 0.32
25 8 0.29
26 10 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTAAATTTAAATAAAAATAAAA
Found at i:370860 original size:20 final size:20
Alignment explanation
Indices: 370819--370861 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
370809 AATTAAATTT
**
370819 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATAAAAA
370839 ATTT-AAATAAAAAATAAAAA
1 ATTTAAAAT-AAAAATAAAAA
370859 ATT
1 ATT
370862 AAAGATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTAAAATAAAAATAAAAA
Found at i:371015 original size:18 final size:17
Alignment explanation
Indices: 370987--371021 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
370977 TATTCTTTGC
*
370987 AATTTTAAAAAATTATT
1 AATTTTAAAAAAATATT
371004 AATTTATAAAAAAATATT
1 AATTT-TAAAAAAATATT
371022 TACATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTTAAAAAAATATT
Found at i:381402 original size:29 final size:31
Alignment explanation
Indices: 381353--381411 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 31
381343 GTTGTAAGAA
381353 CTAAATTCCCAAAATT-AAA-AGTATAGGGG
1 CTAAATTCCCAAAATTAAAAGAGTATAGGGG
* *
381382 CTAAATT-CCACATTTATAAAGAGTATAGGG
1 CTAAATTCCCAAAATTA-AAAGAGTATAGGG
381412 ACATATGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.24
29 7 0.28
30 3 0.12
31 9 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (31 bp):
CTAAATTCCCAAAATTAAAAGAGTATAGGGG
Found at i:398329 original size:17 final size:18
Alignment explanation
Indices: 398307--398346 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
398297 ACCCATTTTT
398307 TTTAAATTCA-TTCTAAA
1 TTTAAATTCATTTCTAAA
* *
398324 TTTAAATTTATTTTTAAA
1 TTTAAATTCATTTCTAAA
398342 TTTAA
1 TTTAA
398347 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAAATTCATTTCTAAA
Found at i:398551 original size:7 final size:7
Alignment explanation
Indices: 398539--398572 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
398529 ATCTGACACA
398539 ACCACCG
1 ACCACCG
398546 ACCACCG
1 ACCACCG
398553 ACCACCG
1 ACCACCG
*
398560 ACCACCA
1 ACCACCG
398567 ACCACC
1 ACCACC
398573 ACATGATTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.32, C:0.59, G:0.09, T:0.00
Consensus pattern (7 bp):
ACCACCG
Found at i:399367 original size:24 final size:24
Alignment explanation
Indices: 399340--399392 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
399330 GGTGGATGGC
399340 GATGGTCGGACGCGACGGGGTCGT
1 GATGGTCGGACGCGACGGGGTCGT
399364 GATGGTCGGACGCGACGGGGTCGT
1 GATGGTCGGACGCGACGGGGTCGT
399388 GATGG
1 GATGG
399393 CCGAATAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (24 bp):
GATGGTCGGACGCGACGGGGTCGT
Found at i:400857 original size:18 final size:18
Alignment explanation
Indices: 400836--400893 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
400826 CTCTTCCTCT
400836 TCTTCCTTCTCCTTTTCC
1 TCTTCCTTCTCCTTTTCC
* *
400854 TCTTCCTTTTCCTCATTTTCA
1 TCTTCC--TT-CTCCTTTTCC
400875 TC-TCCTTCTTCCTTTTCC
1 TCTTCCTTC-TCCTTTTCC
400893 T
1 T
400894 TTTCTTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 1 0.03
18 16 0.50
20 5 0.16
21 10 0.31
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTTCCTTCTCCTTTTCC
Found at i:400916 original size:6 final size:6
Alignment explanation
Indices: 400907--400987 Score: 74
Period size: 6 Copynumber: 13.3 Consensus size: 6
400897 CTTCTTCTAG
* * * *
400907 GAGGAA GAGGAA GAGGAA AAGGAA GAGGAA AAGG-A GAAGGAA GAAGAG
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA G-AGGAA GAGGAA
* * *
400955 GAGGAA GAAGAAA GAGGAA AAAGAA GAGGAA GA
1 GAGGAA G-AGGAA GAGGAA GAGGAA GAGGAA GA
400988 AAAAGAAGAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
5 1 0.02
6 50 0.86
7 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:401002 original size:15 final size:15
Alignment explanation
Indices: 400959--401022 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
400949 GAAGAGGAGG
*
400959 AAGAAGAAAGAGGAAA
1 AAGAAG-AAGAAGAAA
*
400975 AAGAAGAGGAAGAAA
1 AAGAAGAAGAAGAAA
*
400990 AAGAAGAATAAGAAA
1 AAGAAGAAGAAGAAA
* *
401005 GAGAAGGAGAAGAGAA
1 AAGAAGAAGAAGA-AA
401021 AA
1 AA
401023 AATTAATATG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 30 0.77
16 9 0.23
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (15 bp):
AAGAAGAAGAAGAAA
Found at i:401009 original size:12 final size:13
Alignment explanation
Indices: 400917--401007 Score: 66
Period size: 12 Copynumber: 7.4 Consensus size: 13
400907 GAGGAAGAGG
*
400917 AAGAGG-AAAAGG
1 AAGAGGAAAAAGA
*
400929 AAGAGGAAAAGGA
1 AAGAGGAAAAAGA
* *
400942 GA-AGGAAGAAG-
1 AAGAGGAAAAAGA
* *
400953 AGGAGGAAGAAGA
1 AAGAGGAAAAAGA
400966 AAGAGGAAAAAG-
1 AAGAGGAAAAAGA
*
400978 AAGAGGAAGAA-A
1 AAGAGGAAAAAGA
* *
400990 AAGAAGAATAAGA
1 AAGAGGAAAAAGA
401003 AAGAG
1 AAGAG
401008 AAGGAGAAGA
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
12 41 0.67
13 20 0.33
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.01
Consensus pattern (13 bp):
AAGAGGAAAAAGA
Found at i:401126 original size:15 final size:15
Alignment explanation
Indices: 401106--401189 Score: 55
Period size: 15 Copynumber: 5.6 Consensus size: 15
401096 TTCATTTTTT
401106 CTCTT-CTCCTTCTTC
1 CTCTTCCTCC-TCTTC
401121 CTCTTCCTCCTCTTC
1 CTCTTCCTCCTCTTC
* * *
401136 CT-TCTCTTTCTCCTC
1 CTCT-TCCTCCTCTTC
* * *
401151 GTCTTCATCCTCATC
1 CTCTTCCTCCTCTTC
* **
401166 CTCTTCTTTATCTTC
1 CTCTTCCTCCTCTTC
401181 CTCTTCCTC
1 CTCTTCCTC
401190 TCCTTTTTCT
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
14 1 0.02
15 46 0.88
16 5 0.10
ACGTcount: A:0.04, C:0.45, G:0.01, T:0.50
Consensus pattern (15 bp):
CTCTTCCTCCTCTTC
Found at i:401142 original size:18 final size:18
Alignment explanation
Indices: 401121--401183 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
401111 CTCCTTCTTC
401121 CTCTTCCTCCTCTTCCTT
1 CTCTTCCTCCTCTTCCTT
* *
401139 CTCTTTCTCCTCGT-CTT
1 CTCTTCCTCCTCTTCCTT
* * *
401156 CATCCTCATCCTCTTCTTT
1 C-TCTTCCTCCTCTTCCTT
*
401175 ATCTTCCTC
1 CTCTTCCTC
401184 TTCCTCTCCT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
17 4 0.12
18 27 0.82
19 2 0.06
ACGTcount: A:0.05, C:0.44, G:0.02, T:0.49
Consensus pattern (18 bp):
CTCTTCCTCCTCTTCCTT
Found at i:401188 original size:21 final size:21
Alignment explanation
Indices: 401158--401201 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
401148 CTCGTCTTCA
*
401158 TCCTCATCCTCTTCTTTATCT
1 TCCTCATCCTCTCCTTTATCT
* *
401179 TCCTCTTCCTCTCCTTTTTCT
1 TCCTCATCCTCTCCTTTATCT
401200 TC
1 TC
401202 TTCTAGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.55
Consensus pattern (21 bp):
TCCTCATCCTCTCCTTTATCT
Found at i:401215 original size:6 final size:6
Alignment explanation
Indices: 401206--401306 Score: 64
Period size: 6 Copynumber: 16.8 Consensus size: 6
401196 TTCTTCTTCT
* * *
401206 AGGAAG AGG-A- A-GAAG AGGAAA AGGAAA AGGAAG AGTAGAAAG AGGAAA
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AG--G-AAG AGGAAG
* * * * * * *
401254 AGGAAG TGAAAG AGGAAG ATGAAG AAGAGG AGGAGG AGGAGG AGGAAG
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
401302 AGGAA
1 AGGAA
401307 AAAAAGGAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 2 0.03
6 64 0.84
7 1 0.01
8 1 0.01
9 5 0.07
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (6 bp):
AGGAAG
Found at i:401236 original size:21 final size:21
Alignment explanation
Indices: 401206--401270 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
401196 TTCTTCTTCT
*
401206 AGGAAGAGGAAGAAG-AGGAAA-
1 AGGAAAAGGAAG-AGTA-GAAAG
401227 AGGAAAAGGAAGAGTAGAAAG
1 AGGAAAAGGAAGAGTAGAAAG
401248 AGGAAAAGG-A-AGT-GAAAG
1 AGGAAAAGGAAGAGTAGAAAG
401266 AGGAA
1 AGGAA
401271 GATGAAGAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
18 10 0.24
19 3 0.07
20 7 0.17
21 21 0.51
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (21 bp):
AGGAAAAGGAAGAGTAGAAAG
Found at i:401509 original size:6 final size:6
Alignment explanation
Indices: 401474--401533 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
401464 TTTTCCTTTT
* * * * * *
401474 AGGAAA AGGAAT AGGAAG AGTAAA AGGAAG AGGAAG AAGAAG AAGAAG
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
*
401522 A-GAAG AAGAAG A
1 AGGAAG AGGAAG A
401534 AGAAAAAGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
5 5 0.11
6 41 0.89
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (6 bp):
AGGAAG
Found at i:401514 original size:3 final size:3
Alignment explanation
Indices: 401500--401558 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
401490 AGAGTAAAAG
* *
401500 GAA GAG GAA GAA GAA GAA GAA G-A GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
401547 GAA GAA GGA GAA
1 GAA GAA GAA GAA
401559 AGAGAAAGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:401564 original size:12 final size:12
Alignment explanation
Indices: 401549--401587 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
401539 AAGAAGAAGA
401549 AGAAGGAGAAAG
1 AGAAGGAGAAAG
* *
401561 AGAAAGAGAAAC
1 AGAAGGAGAAAG
401573 AGAAGGAG-AAG
1 AGAAGGAGAAAG
401584 AGAA
1 AGAA
401588 AAAATGGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.62, C:0.03, G:0.36, T:0.00
Consensus pattern (12 bp):
AGAAGGAGAAAG
Found at i:401626 original size:237 final size:233
Alignment explanation
Indices: 401243--401701 Score: 582
Period size: 237 Copynumber: 2.0 Consensus size: 233
401233 AGGAAGAGTA
* * * * * * * *
401243 GAAAGAGGAAAAGGAAGTGAAAGAGGAAGATGAAGAAGAGGAGGAGGAGGAGGAGGAAGAGGAAA
1 GAAAGAGGAAAAGGAAGAGAAAGAGGAAGAGGAAGAAGAAGAAGAAGAGGAAGAAGAAGAAGAAA
* * * * * *
401308 AAAAGGAAGAAGAAAAAGAATGAGAAAGAGAAGTAGAATAGATAAAATGGAGATGCCTCCAGTTT
66 AAAAGGAAGAAGAAAAAGAAAGAGAAACAGAAGGAGAAGAGAAAAAATGGAGATGCCTCCAATTT
* * * * ** *
401373 TCAAATGAATCACATATTGCATCTATGAGATTAATTTGAAAACTTTACGCATCTTTATTTTTTCT
131 TCAAATAAACCACATATTGCATCTATGAGATTAATTTGAAAACTTGACGAATCTCCATCTTTTCT
*
401438 CTTCACCTTCTTCATCTTCCTCTTCCTTTTCCTTTTAG
196 CTTCACCTTCTTCATCTTCCTCCTCCTTTTCCTTTTAG
*
401476 GAAA-AGGAATAGGAAGAGTAAA-AGGAAGAGGAAGAAGAAGAAGAAGA-GAAGAAGAAGAAGAA
1 GAAAGAGGAAAAGGAAGAG-AAAGAGGAAGAGGAAGAAGAAGAAGAAGAGGAAGAAGAAGAAGAA
*
401538 AAAGAAGAAGAAGAAGGAGAAAGAGAAAGAGAAACAGAAGGAGAAGAGAAAAAATGGATATGCCT
65 AAA-AAG--GAAGAA-GA-AAA-AGAAAGAGAAACAGAAGGAGAAGAGAAAAAATGGAGATGCCT
* *
401603 CTAATTTTCAAATAAACCACATATTGCATCTATGAGATTAATTTGAAAACTTGAGGAATCTCCAT
124 CCAATTTTCAAATAAACCACATATTGCATCTATGAGATTAATTTGAAAACTTGACGAATCTCCAT
* *
401668 CTTTTCTCTTCTCCTTCTTCCTCTTCCTCCTCCT
189 CTTTTCTCTTCACCTTCTTCATCTTCCTCCTCCT
401702 CCTCCTTCTC
Statistics
Matches: 191, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
231 15 0.08
232 36 0.19
233 7 0.04
234 6 0.03
235 2 0.01
236 3 0.02
237 122 0.64
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (233 bp):
GAAAGAGGAAAAGGAAGAGAAAGAGGAAGAGGAAGAAGAAGAAGAAGAGGAAGAAGAAGAAGAAA
AAAAGGAAGAAGAAAAAGAAAGAGAAACAGAAGGAGAAGAGAAAAAATGGAGATGCCTCCAATTT
TCAAATAAACCACATATTGCATCTATGAGATTAATTTGAAAACTTGACGAATCTCCATCTTTTCT
CTTCACCTTCTTCATCTTCCTCCTCCTTTTCCTTTTAG
Found at i:401698 original size:3 final size:3
Alignment explanation
Indices: 401686--401738 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
401676 TTCTCCTTCT
* * * * *
401686 TCC TCT TCC TCC TCC TCC TCC TTC TCC TCG TCC TCA TCC TCA TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
401734 TCC TC
1 TCC TC
401739 TTCTTTTTCT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.04, C:0.57, G:0.02, T:0.38
Consensus pattern (3 bp):
TCC
Found at i:401770 original size:6 final size:6
Alignment explanation
Indices: 401761--401869 Score: 68
Period size: 6 Copynumber: 18.2 Consensus size: 6
401751 TTCTATTTGT
* * * *
401761 AGAAGA AGAA-A AGGAAGA GGAAGA GGAAGA CGAGGA A-AAGGA A-AAGGA
1 AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAA-GA
401809 AG-AGTA A-AAGGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-AGAGA
1 AGAAG-A AGAAG-A AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGA-AGA
* *
401857 AGGAGA AAAAGA A
1 AGAAGA AGAAGA A
401870 CGAGAAGAGA
Statistics
Matches: 85, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
5 5 0.06
6 76 0.89
7 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.36, T:0.01
Consensus pattern (6 bp):
AGAAGA
Found at i:401874 original size:18 final size:18
Alignment explanation
Indices: 401815--401883 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
401805 AGGAAGAGTA
* *
401815 AAAG-GAAGAAGAAGAAG
1 AAAGAGAAGGAGAAAAAG
* *
401832 -AAGAAGAAGAAGAAGAAG
1 AAAG-AGAAGGAGAAAAAG
401850 AAAGAGAAGGAGAAAAAG
1 AAAGAGAAGGAGAAAAAG
*
401868 AACGAGAA-GAGAAAAA
1 AAAGAGAAGGAGAAAAA
401884 ATCGATATGC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.07
17 8 0.17
18 32 0.70
19 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (18 bp):
AAAGAGAAGGAGAAAAAG
Found at i:402023 original size:21 final size:21
Alignment explanation
Indices: 401999--402042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
401989 TTCCTCCTCG
401999 TCCTCATCCTCTT-CTTTATCT
1 TCCTCATCCTCTTCCTTT-TCT
*
402020 TCCTCTTCCTCTTCCTTTTCT
1 TCCTCATCCTCTTCCTTTTCT
402041 TC
1 TC
402043 TTCTACGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.55
Consensus pattern (21 bp):
TCCTCATCCTCTTCCTTTTCT
Found at i:402085 original size:18 final size:17
Alignment explanation
Indices: 402058--402122 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 17
402048 CGAGGAGGAG
402058 GAAGAGGAAAAAGAAGAA
1 GAAGA-GAAAAAGAAGAA
*
402076 GAAGAAGAAAAAAAAGAA
1 GAAG-AGAAAAAGAAGAA
* *
402094 GAATGAGAAAGAGAAGGA
1 GAA-GAGAAAAAGAAGAA
402112 GAAGAGAAAAA
1 GAAGAGAAAAA
402123 ATGGAGATGC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.17
18 31 0.77
19 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (17 bp):
GAAGAGAAAAAGAAGAA
Found at i:402265 original size:18 final size:18
Alignment explanation
Indices: 402225--402268 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
402215 CTTCCTATTC
* *
402225 CTCCTCCTCTTCCTCCTT
1 CTCCTCTTCTTCATCCTT
402243 CTCCTCTTCTTCATCC-T
1 CTCCTCTTCTTCATCCTT
402260 CATCCTCTT
1 C-TCCTCTT
402269 TTTTATCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.05, C:0.50, G:0.00, T:0.45
Consensus pattern (18 bp):
CTCCTCTTCTTCATCCTT
Found at i:402309 original size:3 final size:3
Alignment explanation
Indices: 402303--402356 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
402293 CTTCTTTTGT
* * *
402303 AGA AGA AGA AGA AGA AGA AGA AGA AG- AGA AGG AGA AGG AGA AGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
402350 AGG AGA A
1 AGA AGA A
402357 AGAGAAGGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:402361 original size:6 final size:6
Alignment explanation
Indices: 402306--402365 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
402296 CTTTTGTAGA
* * *
402306 AGAAGA AGAAGA AGAAGA AGAA-G AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
*
402353 AGAAAG AGAAGG A
1 AGAAGG AGAAGG A
402366 TAAGTGAAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
5 4 0.08
6 46 0.92
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:402608 original size:9 final size:9
Alignment explanation
Indices: 402596--402672 Score: 86
Period size: 9 Copynumber: 8.6 Consensus size: 9
402586 AAAGGAAAAG
*
402596 GAAGAGGAA
1 GAAGAAGAA
402605 GAAGAAGAA
1 GAAGAAGAA
402614 -AAGGAAGAA
1 GAA-GAAGAA
402623 GAAGAAGAA
1 GAAGAAGAA
402632 GAAGAAGAA
1 GAAGAAGAA
*
402641 GAAGAAGGA
1 GAAGAAGAA
*
402650 GAAGGAGAA
1 GAAGAAGAA
*
402659 -AGAGAAGGA
1 GA-AGAAGAA
402668 GAAGA
1 GAAGA
402673 GAAAAAATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.05
9 52 0.90
10 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (9 bp):
GAAGAAGAA
Found at i:402611 original size:12 final size:12
Alignment explanation
Indices: 402578--402673 Score: 65
Period size: 12 Copynumber: 8.0 Consensus size: 12
402568 TCTACAAATA
* *
402578 GAAGAAAAAAAG
1 GAAGAAGAAGAG
402590 GAA-AAGGAAGAG
1 GAAGAA-GAAGAG
402602 GAAGAAGAAGA-
1 GAAGAAGAAGAG
* *
402613 AAAGGAAGAAGAA
1 GAA-GAAGAAGAG
*
402626 GAAGAAGAAGAA
1 GAAGAAGAAGAG
402638 GAAGAAGAAG-G
1 GAAGAAGAAGAG
*
402649 AGAAGGAGAA-AG
1 -GAAGAAGAAGAG
*
402661 AGAAGGAGAAGAG
1 -GAAGAAGAAGAG
402674 AAAAAATAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
11 4 0.06
12 61 0.86
13 6 0.08
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGAG
Found at i:402626 original size:6 final size:6
Alignment explanation
Indices: 402596--402672 Score: 86
Period size: 6 Copynumber: 12.8 Consensus size: 6
402586 AAAGGAAAAG
*
402596 GAAGAG GAAGAA GAAGAA -AAGGAA GAAGAA GAAGAA GAAGAA GAAGAA
1 GAAGAA GAAGAA GAAGAA GAA-GAA GAAGAA GAAGAA GAAGAA GAAGAA
* * *
402644 GAAGGA GAAGGA GAA-AGA GAAGGA GAAGA
1 GAAGAA GAAGAA GAAGA-A GAAGAA GAAGA
402673 GAAAAAATAG
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
5 2 0.03
6 58 0.94
7 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (6 bp):
GAAGAA
Found at i:402780 original size:6 final size:6
Alignment explanation
Indices: 402771--402858 Score: 65
Period size: 6 Copynumber: 14.8 Consensus size: 6
402761 CTCTTCTCCT
* * * * *
402771 TCTTCC TCTTCC TCCTCTCC TCCTCC TCCTCC TCGTCC TCATCC TCATCC
1 TCTTCC TCTTCC T-CT-TCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
* * *
402821 TCTT-C T-TT-A TCTTCC TCTTCC TCTTCC TTTTCT TCTTC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
402859 TATTTGTAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
4 3 0.04
5 4 0.06
6 55 0.80
7 3 0.04
8 4 0.06
ACGTcount: A:0.03, C:0.48, G:0.01, T:0.48
Consensus pattern (6 bp):
TCTTCC
Found at i:402786 original size:3 final size:3
Alignment explanation
Indices: 402774--402822 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
402764 TTCTCCTTCT
* * * *
402774 TCC TCT TCC TCC T-C TCC TCC TCC TCC TCC TCG TCC TCA TCC TCA TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
402821 TC
1 TC
402823 TTCTTTATCT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.04, C:0.57, G:0.02, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:402854 original size:21 final size:21
Alignment explanation
Indices: 402812--402855 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
402802 CTCGTCCTCA
402812 TCCTCATCCTCTTCTTTATCT
1 TCCTCATCCTCTTCTTTATCT
*
402833 TCCTCTTCCTCTTCCTTT-TCT
1 TCCTCATCCTCTT-CTTTATCT
402854 TC
1 TC
402856 TTCTATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.55
Consensus pattern (21 bp):
TCCTCATCCTCTTCTTTATCT
Found at i:402892 original size:12 final size:12
Alignment explanation
Indices: 402867--402932 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
402857 TCTATTTGTA
* *
402867 GAAGAAGAAAAG
1 GAAGAGGAAGAG
402879 GAAGAGGAAGAG
1 GAAGAGGAAGAG
402891 GAAGATGAAGAAGAG
1 GAAGA-G--GAAGAG
* *
402906 GAAAAGGAAGAA
1 GAAGAGGAAGAG
* *
402918 GAGGAGGATGAG
1 GAAGAGGAAGAG
402930 GAA
1 GAA
402933 TAGAAAAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
12 30 0.71
13 1 0.02
14 1 0.02
15 10 0.24
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (12 bp):
GAAGAGGAAGAG
Found at i:402895 original size:21 final size:21
Alignment explanation
Indices: 402870--402922 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
402860 ATTTGTAGAA
*
402870 GAAGAAAAGGAAGAGGAAGAG
1 GAAGAAAAGGAAGAGGAAAAG
*
402891 GAAGATGAA-GAAGAGGAAAAG
1 GAAGA-AAAGGAAGAGGAAAAG
*
402912 GAAGAAGAGGA
1 GAAGAAAAGGA
402923 GGATGAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.02
Consensus pattern (21 bp):
GAAGAAAAGGAAGAGGAAAAG
Found at i:402903 original size:15 final size:15
Alignment explanation
Indices: 402885--402928 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
402875 AAAGGAAGAG
402885 GAAGAGGAAGATGAA
1 GAAGAGGAAGATGAA
* *
402900 GAAGAGGAAAAGGAA
1 GAAGAGGAAGATGAA
*
402915 GAAGAGGAGGATGA
1 GAAGAGGAAGATGA
402929 GGAATAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.43, T:0.05
Consensus pattern (15 bp):
GAAGAGGAAGATGAA
Found at i:403094 original size:6 final size:6
Alignment explanation
Indices: 403085--403169 Score: 59
Period size: 6 Copynumber: 14.2 Consensus size: 6
403075 CTCTTCTCCT
* * * *
403085 TCTTCC TCTTCC TCTTCC TCCTCC TCCTTCTCC TCGTCC TCATCC TCATCC
1 TCTTCC TCTTCC TCTTCC TCTTCC T-C-T-TCC TCTTCC TCTTCC TCTTCC
* * *
403136 TCTT-C T-TT-A TCTTTC TCTTCC TCTTCT TCTTCC T
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC T
403170 TTTTTTCTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.05
5 4 0.06
6 51 0.80
7 1 0.02
8 1 0.02
9 4 0.06
ACGTcount: A:0.04, C:0.46, G:0.01, T:0.49
Consensus pattern (6 bp):
TCTTCC
Found at i:403203 original size:6 final size:6
Alignment explanation
Indices: 403184--403280 Score: 83
Period size: 6 Copynumber: 16.3 Consensus size: 6
403174 TTCTTCTATA
* *
403184 GAAGAA GAAAAG GAAGAG GAAGAG GAAGAG GAAGAG G-A-A- GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
* * * * * *
403229 GAAAAG GAAAAAG GAAGAG TAAAAG GAAGAG GAAGAA GAAGAAG GAGGAG
1 GAAGAG G-AAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAG-AG GAAGAG
403279 GA
1 GA
403281 GGAAAAAGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 2 0.03
6 59 0.80
7 10 0.14
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.01
Consensus pattern (6 bp):
GAAGAG
Found at i:403256 original size:46 final size:47
Alignment explanation
Indices: 403191--403293 Score: 145
Period size: 46 Copynumber: 2.2 Consensus size: 47
403181 ATAGAAGAAG
* *
403191 AAAAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAA-GAGGAAAAGGA
1 AAAAGGAAGAGGAAAAGGAAGAGGAAGAAGAAGAAGGAGGAAAAGGA
* **
403237 AAAAGGAAGAGTAAAAGGAAGAGGAAGAAGAAGAAGGAGGAGGAGGA
1 AAAAGGAAGAGGAAAAGGAAGAGGAAGAAGAAGAAGGAGGAAAAGGA
403284 AAAAGAGAAG
1 AAAAG-GAAG
403294 GAGAAGAGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 32 0.64
47 14 0.28
48 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.01
Consensus pattern (47 bp):
AAAAGGAAGAGGAAAAGGAAGAGGAAGAAGAAGAAGGAGGAAAAGGA
Found at i:403304 original size:19 final size:22
Alignment explanation
Indices: 403197--403306 Score: 86
Period size: 21 Copynumber: 5.1 Consensus size: 22
403187 GAAGAAAAGG
* *
403197 AAGAGGAA-GAGGAAGAGGAAG
1 AAGAAGAAGGAGGAAGAGGAAA
* *
403218 AGGAAGAA-GAGGAAAAGGAAA
1 AAGAAGAAGGAGGAAGAGGAAA
** *
403239 AAGGAAGAGTAAAAGGAAGAGGAAG
1 AA-GAAGA--AGGAGGAAGAGGAAA
*
403264 AAGAAGAAGGAGGAGGAGGAAA
1 AAGAAGAAGGAGGAAGAGGAAA
403286 AAG-AGAAGGA-GAAGA-GAAA
1 AAGAAGAAGGAGGAAGAGGAAA
403305 AA
1 AA
403307 TGGATATGCC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
19 6 0.08
20 4 0.06
21 25 0.35
22 19 0.26
24 6 0.08
25 12 0.17
ACGTcount: A:0.58, C:0.00, G:0.41, T:0.01
Consensus pattern (22 bp):
AAGAAGAAGGAGGAAGAGGAAA
Found at i:403425 original size:21 final size:21
Alignment explanation
Indices: 403401--403440 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
403391 TTCTCCTTCT
* *
403401 TCCTCTTCCTCTTCCTCTTTC
1 TCCTCATCCTCATCCTCTTTC
403422 TCCTCATCCTCATCCTCTT
1 TCCTCATCCTCATCCTCTT
403441 CTTTAGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.47, G:0.00, T:0.47
Consensus pattern (21 bp):
TCCTCATCCTCATCCTCTTTC
Found at i:403454 original size:6 final size:6
Alignment explanation
Indices: 403445--403525 Score: 60
Period size: 6 Copynumber: 13.5 Consensus size: 6
403435 CCTCTTCTTT
* * * *
403445 AGAAGA AGAA-A AGGAAGA GGAAGA GGAAGA AGAGGA A-AAGGA AGAGGA
1 AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA
* *
403493 AGAAGA AGAAGA AGTAGA A-AGAGA AGGAGA AGA
1 AGAAGA AGAAGA AGAAGA AGA-AGA AGAAGA AGA
403526 GAAAAAATGT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 3 0.05
6 54 0.92
7 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.40, T:0.01
Consensus pattern (6 bp):
AGAAGA
Found at i:403474 original size:21 final size:21
Alignment explanation
Indices: 403449--403504 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
403439 TTCTTTAGAA
403449 GAAGAAAAGGAAGAGGAAGAG
1 GAAGAAAAGGAAGAGGAAGAG
* *
403470 GAAGAAGAGGAAAAGGAAGAG
1 GAAGAAAAGGAAGAGGAAGAG
403491 GAAGAAGAA-GAAGA
1 GAAGAA-AAGGAAGA
403505 AGTAGAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (21 bp):
GAAGAAAAGGAAGAGGAAGAG
Found at i:403476 original size:15 final size:15
Alignment explanation
Indices: 403458--403506 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
403448 AGAAGAAAAG
403458 GAAGAGGAAGAGGAA
1 GAAGAGGAAGAGGAA
*
403473 GAAGAGGAAAAGGAA
1 GAAGAGGAAGAGGAA
* * *
403488 GAGGAAGAAGAAGAA
1 GAAGAGGAAGAGGAA
403503 GAAG
1 GAAG
403507 TAGAAAGAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
GAAGAGGAAGAGGAA
Found at i:403482 original size:27 final size:27
Alignment explanation
Indices: 403445--403506 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
403435 CCTCTTCTTT
*
403445 AGAAGAAGAAAAGGAAGAGGAAGAGGA
1 AGAAGAAGAAAAGGAAGAGGAAGAAGA
*
403472 AGAAGAGGAAAAGGAAGAGGAAGAAGA
1 AGAAGAAGAAAAGGAAGAGGAAGAAGA
403499 AGAAGAAG
1 AGAAGAAG
403507 TAGAAAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (27 bp):
AGAAGAAGAAAAGGAAGAGGAAGAAGA
Found at i:403511 original size:9 final size:9
Alignment explanation
Indices: 403445--403525 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 9
403435 CCTCTTCTTT
403445 AGAAGAAGA
1 AGAAGAAGA
403454 A-AAGGAAGA
1 AGAA-GAAGA
* *
403463 GGAAGAGGA
1 AGAAGAAGA
*
403472 AGAAGAGGA
1 AGAAGAAGA
403481 A-AAGGAAGA
1 AGAA-GAAGA
*
403490 GGAAGAAGA
1 AGAAGAAGA
*
403499 AGAAGAAGT
1 AGAAGAAGA
403508 AGAA-AGAGA
1 AGAAGA-AGA
*
403517 AGGAGAAGA
1 AGAAGAAGA
403526 GAAAAAATGT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
8 5 0.09
9 47 0.82
10 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.40, T:0.01
Consensus pattern (9 bp):
AGAAGAAGA
Found at i:403562 original size:225 final size:229
Alignment explanation
Indices: 403242--403663 Score: 649
Period size: 225 Copynumber: 1.9 Consensus size: 229
403232 AAGGAAAAAG
*
403242 GAAGAGTAAAAGGAAGAGGAAGAAGAAGAAGGAGGAGGAGGAAAAAGAGAAGGAGAAGAGAAAAA
1 GAAGAGGAAAAGGAAGAGGAAGAAGAAGAAGGA-GAGGAGG-AAAAGAGAAGGAGAAGAGAAAAA
* * *
403307 TGGATATGCCTCCAATTTTTAAATCAATCACATATTGCATCTATGAGATTAATTTAAAAACTTGA
64 TGGAGATGCCTCCAATTTTCAAATCAATCACATATTACATCTATGAGATTAATTTAAAAACTTGA
* *
403372 GGCATCTCCGTTTTTTCTTTTCTCCTTCTTCCTCTTCCT-CTTCCTCTTTCTCCTCATCCTCATC
129 GGCATCTCCATTTTTTCCTTTCTCCTTCTTCCTCTTCCTGC-TCCTCTTTCTCCTCATCCTCATC
403436 CTCTTCTTTAGAAGAAGAAAAGGAAGAGGAAGAGGAA
193 CTCTTCTTTAGAAGAAGAAAAGGAAGAGGAAGAGGAA
*
403473 GAAGAGGAAAAGGAAGAGGAAGAAGAAGAA-GA-AGTA-G-AAAGAGAAGGAGAAGAGAAAAAAT
1 GAAGAGGAAAAGGAAGAGGAAGAAGAAGAAGGAGAGGAGGAAAAGAGAAGGAGAAGAG-AAAAAT
* * * * *
403534 GTAGAT-CCTCTAGTTTTCAAATCAATCACATATTACATCTATGAGATTTATTTGAAAACTTGAG
65 GGAGATGCCTCCAATTTTCAAATCAATCACATATTACATCTATGAGATTAATTTAAAAACTTGAG
*
403598 GCATCTCCATTTTTTCCTTTCTCCTTCTTCCTCTTCCTGCTCCTCTTTCTCCTCGTCCTCATCCT
130 GCATCTCCATTTTTTCCTTTCTCCTTCTTCCTCTTCCTGCTCCTCTTTCTCCTCATCCTCATCCT
403663 C
195 C
403664 ATCCTCATCC
Statistics
Matches: 176, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
225 130 0.74
226 11 0.06
227 1 0.01
228 3 0.02
230 2 0.01
231 29 0.16
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (229 bp):
GAAGAGGAAAAGGAAGAGGAAGAAGAAGAAGGAGAGGAGGAAAAGAGAAGGAGAAGAGAAAAATG
GAGATGCCTCCAATTTTCAAATCAATCACATATTACATCTATGAGATTAATTTAAAAACTTGAGG
CATCTCCATTTTTTCCTTTCTCCTTCTTCCTCTTCCTGCTCCTCTTTCTCCTCATCCTCATCCTC
TTCTTTAGAAGAAGAAAAGGAAGAGGAAGAGGAA
Found at i:403632 original size:6 final size:6
Alignment explanation
Indices: 403623--403699 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
403613 CCTTTCTCCT
* * *
403623 TCTTCC TCTTCC TGC-TCC TCTT-- TC-TCC TCGTCC TCATCC TCATCC
1 TCTTCC TCTTCC T-CTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
*
403668 TCATCC TCTTCC TTATCTTCC TCTTCC TCTTC
1 TCTTCC TCTTCC ---TCTTCC TCTTCC TCTTC
403700 GTTTTCTTCT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 3 0.05
6 48 0.79
7 1 0.02
9 6 0.10
ACGTcount: A:0.05, C:0.47, G:0.03, T:0.45
Consensus pattern (6 bp):
TCTTCC
Found at i:403695 original size:21 final size:21
Alignment explanation
Indices: 403665--403708 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
403655 CTCATCCTCA
403665 TCCTCATCCTCTTCCTTATCT
1 TCCTCATCCTCTTCCTTATCT
* * *
403686 TCCTCTTCCTCTTCGTTTTCT
1 TCCTCATCCTCTTCCTTATCT
403707 TC
1 TC
403709 TTCTACAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.02, T:0.52
Consensus pattern (21 bp):
TCCTCATCCTCTTCCTTATCT
Found at i:403739 original size:6 final size:6
Alignment explanation
Indices: 403730--403832 Score: 71
Period size: 6 Copynumber: 16.2 Consensus size: 6
403720 GAAAAAGAAA
* * * *
403730 AGGAAG AGGAAG AGAAATATG AAGAAG AGGAAA AGGAAG AGGAAG AGGAGG
1 AGGAAG AGGAAG AG-GA-A-G AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
* * * * *
403781 AGGAAA AGGAGGAG AAGGAGG AGGAAA AGGAAA AGGAAG AGGAAG ATGAAG
1 AGGAAG AGGA--AG -AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
403832 A
1 A
403833 AAAAGGAGAA
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
6 64 0.84
7 3 0.04
8 3 0.04
9 6 0.08
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (6 bp):
AGGAAG
Found at i:403774 original size:21 final size:21
Alignment explanation
Indices: 403732--403820 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
403722 AAAAGAAAAG
* * * *
403732 GAAGAGGAAGAGAAATATGAA
1 GAAGAGGAAAAGGAAGAGGAA
403753 GAAGAGGAAAAGGAAGAGGAA
1 GAAGAGGAAAAGGAAGAGGAA
*
403774 GAGGAGGAGGAAAAGGAGGA-GAA
1 GA--A-GAGGAAAAGGAAGAGGAA
* *
403797 GGAGGAGGAAAAGGAAAAGGAA
1 -GAAGAGGAAAAGGAAGAGGAA
403819 GA
1 GA
403821 GGAAGATGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
21 33 0.60
22 3 0.05
23 4 0.07
24 15 0.27
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (21 bp):
GAAGAGGAAAAGGAAGAGGAA
Found at i:403793 original size:33 final size:33
Alignment explanation
Indices: 403726--403820 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 33
403716 AATAGAAAAA
* * *
403726 GAAAAGGAAGAGGAAGAGAAATATGAAGAAGAG
1 GAAAAGGAAGAGGAAGAGGAAGAGGAAGAAGAG
*
403759 GAAAAGGAAGAGGAAGAGGAGGAGGAA-AAGGAG
1 GAAAAGGAAGAGGAAGAGGAAGAGGAAGAA-GAG
* * * *
403792 GAGAAGGAGGAGGAAAAGGAAAAGGAAGA
1 GAAAAGGAAGAGGAAGAGGAAGAGGAAGA
403821 GGAAGATGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.04
33 48 0.94
34 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (33 bp):
GAAAAGGAAGAGGAAGAGGAAGAGGAAGAAGAG
Found at i:403849 original size:18 final size:19
Alignment explanation
Indices: 403826--403869 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
403816 GAAGAGGAAG
*
403826 ATGAAGAAAAAG-GAGAAA
1 ATGAAGAAAAAGAGAAAAA
* *
403844 ATGAAGGAGAAGAGAAAAA
1 ATGAAGAAAAAGAGAAAAA
403863 ATGAAGA
1 ATGAAGA
403870 TGCCTCTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.07
Consensus pattern (19 bp):
ATGAAGAAAAAGAGAAAAA
Found at i:404661 original size:57 final size:57
Alignment explanation
Indices: 404588--404702 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
404578 AAGCTCAAAG
*
404588 GAACTTGAATGCTTGTCCAGCATGGCTTTCTCTTACAAAAACATCTCCAGATTCAAT
1 GAACTTGAATGCTTGTCCAGCATGGCTTTCTCTTACAAAAACATCTCCAAATTCAAT
* *
404645 GAACTTGGATGCTTGTCCAGCATGGCTTTCTCTTGCAAAAACATCTCCAAATTCAAT
1 GAACTTGAATGCTTGTCCAGCATGGCTTTCTCTTACAAAAACATCTCCAAATTCAAT
404702 G
1 G
404703 GTCTATTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (57 bp):
GAACTTGAATGCTTGTCCAGCATGGCTTTCTCTTACAAAAACATCTCCAAATTCAAT
Found at i:404771 original size:22 final size:23
Alignment explanation
Indices: 404738--404781 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
404728 TCATTCCATT
404738 TTTTCCTTCTTCTCCT-TTTCTTC
1 TTTTCCTTCTTCT-CTATTTCTTC
404761 TTTT-CTTCTTCTCTATTTCTT
1 TTTTCCTTCTTCTCTATTTCTT
404782 GAATTTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.10
22 14 0.70
23 4 0.20
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTCCTTCTTCTCTATTTCTTC
Found at i:405032 original size:21 final size:21
Alignment explanation
Indices: 405006--405046 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
404996 CAACGTGACA
405006 AGTTAACTAGCCACATCAACT
1 AGTTAACTAGCCACATCAACT
* *
405027 AGTTAACTTGCCGCATCAAC
1 AGTTAACTAGCCACATCAAC
405047 AACCCCGTTA
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:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
AGTTAACTAGCCACATCAACT
Found at i:405996 original size:6 final size:6
Alignment explanation
Indices: 405985--406014 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
405975 ACCAAAGCTC
405985 CCATCA CCATCA CCATCA CCATCA CCATCA
1 CCATCA CCATCA CCATCA CCATCA CCATCA
406015 TCTGAAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CCATCA
Found at i:407507 original size:33 final size:33
Alignment explanation
Indices: 407470--407540 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
407460 GGCGACTTTG
407470 AGCTCATCGGCCTTCTTGGAAGCTTCAAGAGCA
1 AGCTCATCGGCCTTCTTGGAAGCTTCAAGAGCA
* *
407503 AGCTCATCGGCTTTCTTGGAGGCTTCAAGAGCA
1 AGCTCATCGGCCTTCTTGGAAGCTTCAAGAGCA
407536 AGCTC
1 AGCTC
407541 CTTGGATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (33 bp):
AGCTCATCGGCCTTCTTGGAAGCTTCAAGAGCA
Found at i:407551 original size:33 final size:33
Alignment explanation
Indices: 407470--407554 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
407460 GGCGACTTTG
**
407470 AGCTCATCGGCCTTCTTGGAAGCTTCAAGAGCA
1 AGCTCATCGGATTTCTTGGAAGCTTCAAGAGCA
* *
407503 AGCTCATCGGCTTTCTTGGAGGCTTCAAGAGCA
1 AGCTCATCGGATTTCTTGGAAGCTTCAAGAGCA
* *
407536 AGCTCCTTGGATTTCTTGG
1 AGCTCATCGGATTTCTTGG
407555 CGGTTTCGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (33 bp):
AGCTCATCGGATTTCTTGGAAGCTTCAAGAGCA
Found at i:409040 original size:27 final size:28
Alignment explanation
Indices: 408984--409057 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
408974 TTAAGTTTTC
*
408984 TTAAAAATATTATATTATTTATTTTAATAT-
1 TTAAAAAT-TTATA-TA-TTCTTTTAATATA
409014 TTAATAAATTTATATATTCTTTT-ATATA
1 TTAA-AAATTTATATATTCTTTTAATATA
* *
409042 TTGAAAATTTTTATAT
1 TTAAAAATTTATATAT
409058 AATAATCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 15 0.38
28 9 0.23
29 2 0.05
30 9 0.23
31 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
TTAAAAATTTATATATTCTTTTAATATA
Found at i:411491 original size:15 final size:14
Alignment explanation
Indices: 411453--411500 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
411443 TGAAACTTGG
*
411453 ATTTTAAAATTTTA
1 ATTTTAAAATTTTT
*
411467 ATTTTGAAATTTATT
1 ATTTTAAAATTT-TT
*
411482 ATTTTTAAATTTTTT
1 A-TTTTAAAATTTTT
411497 ATTT
1 ATTT
411501 GAGAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 14 0.50
15 5 0.18
16 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
ATTTTAAAATTTTT
Found at i:415892 original size:41 final size:42
Alignment explanation
Indices: 415670--415888 Score: 196
Period size: 42 Copynumber: 5.2 Consensus size: 42
415660 CATTCTCATC
* * * * * * *
415670 TCTTCCTTTAAAACATAACCTCATACTCTTTTCAAGTCATGAG
1 TCTTCCTTT-TAACATAATCTCATGCTCATCTCGAGACATGAG
* * * **
415713 TATTCC-TTAAATCATAATCTCATGCTCTTCTCGAGACACAAG
1 TCTTCCTTTTAA-CATAATCTCATGCTCATCTCGAGACATGAG
415755 TCTTCCTTTTTAACATAATCTCATGCTCAT-TCGAGACATGAG
1 TCTTCC-TTTTAACATAATCTCATGCTCATCTCGAGACATGAG
* *
415797 TCTTCCTTTTTAACATAATGT-ATTTCTCATC-CGAGACATGAG
1 TCTTCC-TTTTAACATAATCTCA-TGCTCATCTCGAGACATGAG
* ** *
415839 TCTTCC-TTTAATATACCCTCATGCTCATCTCGAGACAGGAG
1 TCTTCCTTTTAACATAATCTCATGCTCATCTCGAGACATGAG
415880 TCTTCCTTT
1 TCTTCCTTT
415889 AATACGCATC
Statistics
Matches: 147, Mismatches: 21, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
40 16 0.11
41 21 0.14
42 85 0.58
43 21 0.14
44 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (42 bp):
TCTTCCTTTTAACATAATCTCATGCTCATCTCGAGACATGAG
Found at i:417597 original size:4 final size:4
Alignment explanation
Indices: 417588--417670 Score: 103
Period size: 4 Copynumber: 20.5 Consensus size: 4
417578 ATTTTACGAT
* * * *
417588 ATAA ATAA ATAA ATAA GTAA GTAA ATAA GTAA ATAA ATAA ATAC ATAAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA
* *
417637 ATAA ATAA ATAA ATAG ATAA ATAA CTAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
417671 TTAAAACTAG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
4 65 0.96
5 3 0.04
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:424012 original size:22 final size:22
Alignment explanation
Indices: 423987--424039 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 22
423977 TATTTATAAG
* *
423987 TTTTATTGATATTAGATATTTT
1 TTTTATTGATATTACATAGTTT
*
424009 TTTTGCATGGATATTACATAGTTT
1 TTTT--ATTGATATTACATAGTTT
*
424033 TCTTATT
1 TTTTATT
424040 TTTTTTATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
22 6 0.25
24 18 0.75
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.58
Consensus pattern (22 bp):
TTTTATTGATATTACATAGTTT
Found at i:426064 original size:2 final size:2
Alignment explanation
Indices: 426057--426089 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
426047 TGAAACTGCC
426057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
426090 GTGTCAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:427969 original size:18 final size:16
Alignment explanation
Indices: 427937--427980 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
427927 ATAGGACGAG
427937 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
427953 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
427967 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
427981 ACCTAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:428555 original size:31 final size:29
Alignment explanation
Indices: 428483--428556 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
428473 ACAAAATACT
* *
428483 AACATAAA-TGACTAAAATGTAACATTTCA
1 AACA-AAAGTGACTAAAATATAACATTGCA
* *
428512 AATATAAGTGACTAAAATATAACATTAAGCA
1 AACAAAAGTGACTAAAATATAACATT--GCA
428543 AACAAAAGTGACTA
1 AACAAAAGTGACTA
428557 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.06
29 20 0.56
31 14 0.39
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.24
Consensus pattern (29 bp):
AACAAAAGTGACTAAAATATAACATTGCA
Found at i:430191 original size:10 final size:9
Alignment explanation
Indices: 430177--430247 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
430167 TTTTTAATGC
430177 ATTTTTATA
1 ATTTTTATA
*
430186 ATTTTTATG
1 ATTTTTATA
*
430195 ACTTTTATAA
1 ATTTTTAT-A
* *
430205 ACTTTTACA
1 ATTTTTATA
430214 ATTTTT-T-
1 ATTTTTATA
*
430221 ATATTTTAAA
1 AT-TTTTATA
430231 GATTTTTATA
1 -ATTTTTATA
430241 ATTTTTA
1 ATTTTTA
430248 ATAAAATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 28 0.57
10 13 0.27
11 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:430277 original size:22 final size:21
Alignment explanation
Indices: 430238--430291 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
430228 AAAGATTTTT
430238 ATAATTTTTA-ATAAAATTTA
1 ATAATTTTTATATAAAATTTA
430258 A-ATATTTTTATATTAAAATTTA
1 ATA-ATTTTTATA-TAAAATTTA
430280 ATAATTTTTATA
1 ATAATTTTTATA
430292 ACTTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 8 0.27
21 1 0.03
22 19 0.63
23 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATAATTTTTATATAAAATTTA
Found at i:434977 original size:21 final size:21
Alignment explanation
Indices: 434953--435001 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
434943 GAAGCATGAT
*
434953 TTGTTTCAGTAGAAG-CTTCA
1 TTGTTTCAGTAGAAGTCTGCA
* *
434973 CTTGTATCGGTAGAAGTCTGCA
1 -TTGTTTCAGTAGAAGTCTGCA
434995 TTGTTTC
1 TTGTTTC
435002 TTGAATTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (21 bp):
TTGTTTCAGTAGAAGTCTGCA
Found at i:440870 original size:41 final size:41
Alignment explanation
Indices: 440825--440936 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
440815 GTAAAAAAAA
*
440825 TATACACACACCCTGGCACATGCCCATGTGCCCTAGAACAG
1 TATACACACACCCTGGCACAAGCCCATGTGCCCTAGAACAG
*
440866 TATACACACACCTTGGCACAAGCCCATGTGCCCTAGAACAG
1 TATACACACACCCTGGCACAAGCCCATGTGCCCTAGAACAG
* *
440907 TATACACACACCCTGACACACGCCCATGTG
1 TATACACACACCCTGGCACAAGCCCATGTG
440937 TCAACTCGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.17
Consensus pattern (41 bp):
TATACACACACCCTGGCACAAGCCCATGTGCCCTAGAACAG
Found at i:440967 original size:41 final size:41
Alignment explanation
Indices: 440922--441009 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
440912 ACACACCCTG
*
440922 ACACACGCCCATGTGTCAACTCGTGTGCC-CCAGAACAATAT
1 ACACACGCCCATGTGCCAACTCGTGTGCCTCCA-AACAATAT
* * * *
440963 ACACACGCTCGTGTGCCAACTTGTGTGCCTCCAAACAGTAT
1 ACACACGCCCATGTGCCAACTCGTGTGCCTCCAAACAATAT
441004 ACACAC
1 ACACAC
441010 ACCCTGACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 38 0.93
42 3 0.07
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.20
Consensus pattern (41 bp):
ACACACGCCCATGTGCCAACTCGTGTGCCTCCAAACAATAT
Found at i:441071 original size:41 final size:41
Alignment explanation
Indices: 440985--441072 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
440975 GTGCCAACTT
** ** **
440985 GTGTGCCTCCAAACAGTATACACACACCCTGACTTATGCTT
1 GTGTGCCTCCAAACAGTATACACACACCCTGACACACACAC
* * *
441026 GTGTGCCTCCAAATAGTATACACATACTCTGACACACACAC
1 GTGTGCCTCCAAACAGTATACACACACCCTGACACACACAC
441067 GTGTGC
1 GTGTGC
441073 TAGTCCATGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (41 bp):
GTGTGCCTCCAAACAGTATACACACACCCTGACACACACAC
Found at i:443449 original size:31 final size:31
Alignment explanation
Indices: 443411--443479 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
443401 CTTAAAACCC
* *
443411 TAGTGACTTAAAT-AATAACTTTTTAATAGTT
1 TAGTGACTTAAATGAA-AACTTTTGAATAATT
*
443442 TAGTGACTTGAATGAAAACTTTTGAATAATT
1 TAGTGACTTAAATGAAAACTTTTGAATAATT
*
443473 TATTGAC
1 TAGTGAC
443480 AACTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (31 bp):
TAGTGACTTAAATGAAAACTTTTGAATAATT
Found at i:445199 original size:27 final size:27
Alignment explanation
Indices: 445144--445200 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
445134 ATTCATTAAG
*
445144 AATCCAAAAGAATCATAAAAATAATAA
1 AATCCAAAAGAATCATAAAAATAAGAA
*
445171 AATCCAAAA-AATTATTAAAACAT-AGAA
1 AATCCAAAAGAATCA-TAAAA-ATAAGAA
445198 AAT
1 AAT
445201 GATAAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 20 0.77
28 2 0.08
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.21
Consensus pattern (27 bp):
AATCCAAAAGAATCATAAAAATAAGAA
Found at i:445353 original size:20 final size:19
Alignment explanation
Indices: 445322--445366 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
445312 ATTTTAGAAA
445322 ATTTTATAATTTTATGGGTTT
1 ATTTT-TAATTTTA-GGGTTT
445343 ATTTTTAATTTTAGGGTTT
1 ATTTTTAATTTTAGGGTTT
445362 -TTTTT
1 ATTTTT
445367 TTGCATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 6 0.25
20 8 0.33
21 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (19 bp):
ATTTTTAATTTTAGGGTTT
Found at i:445368 original size:20 final size:20
Alignment explanation
Indices: 445323--445367 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
445313 TTTTAGAAAA
*
445323 TTTTATAATTTTATGGGTTT
1 TTTTTTAATTTTATGGGTTT
*
445343 ATTTTTAATTTTA-GGGTTT
1 TTTTTTAATTTTATGGGTTT
445362 TTTTTT
1 TTTTTT
445368 TGCATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (20 bp):
TTTTTTAATTTTATGGGTTT
Found at i:445909 original size:22 final size:22
Alignment explanation
Indices: 445883--445924 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
445873 ATGGATTAGC
* *
445883 AGTTTAAGGTGTAAGGTTTATT
1 AGTTTAAGGTCTAAAGTTTATT
*
445905 AGTTTAGGGTCTAAAGTTTA
1 AGTTTAAGGTCTAAAGTTTA
445925 AAGAATGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (22 bp):
AGTTTAAGGTCTAAAGTTTATT
Found at i:450973 original size:38 final size:38
Alignment explanation
Indices: 450931--451022 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
450921 CCTATGGAAA
* *
450931 ACATGATAAGCATGTCTACTGTTAATGATGAATTGAAT
1 ACATGATAAACATGTCTACTGTTAATGATGAAGTGAAT
* * * *
450969 ACATGTTAAACATGTCTACTGTTAGTGTTGAAGTGAGT
1 ACATGATAAACATGTCTACTGTTAATGATGAAGTGAAT
* *
451007 ACATGTTATACATGTC
1 ACATGATAAACATGTC
451023 AACTACTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (38 bp):
ACATGATAAACATGTCTACTGTTAATGATGAAGTGAAT
Found at i:451033 original size:38 final size:38
Alignment explanation
Indices: 450959--451038 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
450949 CTGTTAATGA
* * **
450959 TGAATTGAATACATGTTAAACATGTCTACTGTTAGTGT
1 TGAAGTGAATACATGTTAAACATGTCAACTACTAGTGT
* *
450997 TGAAGTGAGTACATGTTATACATGTCAACTACTAGTGT
1 TGAAGTGAATACATGTTAAACATGTCAACTACTAGTGT
451035 TGAA
1 TGAA
451039 TTGTTTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (38 bp):
TGAAGTGAATACATGTTAAACATGTCAACTACTAGTGT
Found at i:451180 original size:44 final size:44
Alignment explanation
Indices: 451130--451378 Score: 153
Period size: 44 Copynumber: 5.7 Consensus size: 44
451120 AATCTTGTTG
* * *
451130 TGTATCCATAGCTCTGTGGCAAATTTTATCTGCGAATTTTTCTA
1 TGTATCCACAGCCCAGTGGCAAATTTTATCTGCGAATTTTTCTA
* * * ** *
451174 TGTATCCACAGCCCAGTGGTAGATTTTATTTGCGAATTTTGATG
1 TGTATCCACAGCCCAGTGGCAAATTTTATCTGCGAATTTTTCTA
* * ** * * * * *
451218 TGTACCCATAATCCAGTGGCAGATTTTATTTGCGATTTTTTTTG
1 TGTATCCACAGCCCAGTGGCAAATTTTATCTGCGAATTTTTCTA
* * ** * *
451262 TGTATCCACAACCCAGTGGTAGTTTTTATCTACGAATTTTGCTA
1 TGTATCCACAGCCCAGTGGCAAATTTTATCTGCGAATTTTTCTA
* ** * * * *
451306 TGTACCCACAGCTTAGTAG-AAGATTTTATCTGTGAATCTTGCTA
1 TGTATCCACAGCCCAGTGGCAA-ATTTTATCTGCGAATTTTTCTA
** * *
451350 TACATCCACAACCCAATGGC-AA-TTTATCT
1 TGTATCCACAGCCCAGTGGCAAATTTTATCT
451379 CCAAACTAGT
Statistics
Matches: 157, Mismatches: 46, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
42 7 0.04
43 2 0.01
44 148 0.94
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (44 bp):
TGTATCCACAGCCCAGTGGCAAATTTTATCTGCGAATTTTTCTA
Found at i:451266 original size:88 final size:88
Alignment explanation
Indices: 451110--451364 Score: 253
Period size: 88 Copynumber: 2.9 Consensus size: 88
451100 AGATTGGAAG
* * * * *
451110 TTTATTTGCAAATCTTGTTGTGTATCCATAGCTCTGTGGCAAATTTTATCTGCGAATTTTTCTAT
1 TTTATTTGCGAATTTTGATGTGTACCCATAGCTCAGTGGCAAATTTTATCTGCGAATTTTTCTAT
*
451175 GTATCCACAGCCCAGTGGTAGAT
66 GTATCCACAACCCAGTGGTAGAT
* * * * * *
451198 TTTATTTGCGAATTTTGATGTGTACCCATA-ATCCAGTGGCAGATTTTATTTGCGATTTTTTTTG
1 TTTATTTGCGAATTTTGATGTGTACCCATAGCT-CAGTGGCAAATTTTATCTGCGAATTTTTCTA
*
451262 TGTATCCACAACCCAGTGGTAGTT
65 TGTATCCACAACCCAGTGGTAGAT
* * * * * * * * * *
451286 TTTATCTACGAATTTTGCTATGTACCCACAGCTTAGTAG-AAGATTTTATCTGTGAATCTTGCTA
1 TTTATTTGCGAATTTTGATGTGTACCCATAGCTCAGTGGCAA-ATTTTATCTGCGAATTTTTCTA
**
451350 TACATCCACAACCCA
65 TGTATCCACAACCCA
451365 ATGGCAATTT
Statistics
Matches: 133, Mismatches: 31, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
87 2 0.02
88 130 0.98
89 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (88 bp):
TTTATTTGCGAATTTTGATGTGTACCCATAGCTCAGTGGCAAATTTTATCTGCGAATTTTTCTAT
GTATCCACAACCCAGTGGTAGAT
Found at i:458381 original size:7 final size:7
Alignment explanation
Indices: 458377--458418 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
458367 AAAAAAAATA
*
458377 AAAAAAC
1 AAAAAAG
458384 AAAAAAG
1 AAAAAAG
458391 AAAAGAA-
1 AAAA-AAG
458398 AAGAAAAG
1 AA-AAAAG
458406 AAAAAAG
1 AAAAAAG
458413 AAAAAA
1 AAAAAA
458419 AAAGAGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:458388 original size:17 final size:16
Alignment explanation
Indices: 458366--458440 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 16
458356 AGTATTTAAC
458366 CAAAAAAAATAAAAAAA
1 CAAAAAAAA-AAAAAAA
*
458383 CAAAAAAGAAAAGAAAA
1 CAAAAAA-AAAAAAAAA
* * *
458400 -GAAAAGAAAAAAGAA
1 CAAAAAAAAAAAAAAA
* *
458415 -AAAAAAAGAGAAAAA
1 CAAAAAAAAAAAAAAA
458430 CAAAAAGAAAA
1 CAAAAA-AAAA
458441 GGAGAGGTCA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
15 17 0.39
16 9 0.20
17 16 0.36
18 2 0.05
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.01
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAA
Found at i:458394 original size:5 final size:5
Alignment explanation
Indices: 458386--458441 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
458376 AAAAAAACAA
* *
458386 AAAAG AAAAG AAAAG AAAAG AAAAAAG AAAAA AAAAG AGAAA- AACA-
1 AAAAG AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG A-AAAG AAAAG
458432 AAAAG AAAAG
1 AAAAG AAAAG
458442 GAGAGGTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 5 0.12
5 30 0.70
6 3 0.07
7 5 0.12
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:458394 original size:12 final size:11
Alignment explanation
Indices: 458367--458440 Score: 78
Period size: 12 Copynumber: 6.4 Consensus size: 11
458357 GTATTTAACC
*
458367 AAAAAAAATAAA
1 AAAAAAAA-AAG
458379 AAAACAAAAAAG
1 AAAA-AAAAAAG
*
458391 -AAAAGAAAAG
1 AAAAAAAAAAG
458401 AAAAGAAAAAAG
1 AAAA-AAAAAAG
458413 AAAAAAAAAGAG
1 AAAAAAAAA-AG
458425 AAAAACAAAAAG
1 AAAAA-AAAAAG
458437 AAAA
1 AAAA
458441 GGAGAGGTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
10 6 0.11
11 11 0.20
12 29 0.54
13 8 0.15
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.01
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:458394 original size:22 final size:21
Alignment explanation
Indices: 458368--458440 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 21
458358 TATTTAACCA
458368 AAAAAAATAAAAAAACAAAAAAG
1 AAAAAAA-AAAAAAA-AAAAAAG
* *
458391 AAAAGAAAAGAAAAGAAAAAAG
1 AAAA-AAAAAAAAAAAAAAAAG
458413 AAAAAAAAAGAGAAAAACAAAAAG
1 AAAAAAAAA-A-AAAAA-AAAAAG
458437 AAAA
1 AAAA
458441 GGAGAGGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.10
22 12 0.29
23 13 0.31
24 13 0.31
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAAAAAG
Found at i:458399 original size:19 final size:18
Alignment explanation
Indices: 458376--458441 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 18
458366 CAAAAAAAAT
* *
458376 AAAAAAACAAAAAAG-AA
1 AAAAAAAGAAAAGAGAAA
*
458393 AAGAAAAGAAAAGA-AAA
1 AAAAAAAGAAAAGAGAAA
458410 AAGAAAAA-AAAAGAGAAA
1 AA-AAAAAGAAAAGAGAAA
458428 AACAAAAAGAAAAG
1 AA-AAAAAGAAAAG
458442 GAGAGGTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 21 0.52
18 14 0.35
19 5 0.12
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAGAGAAA
Found at i:459515 original size:98 final size:98
Alignment explanation
Indices: 459290--459990 Score: 474
Period size: 98 Copynumber: 7.3 Consensus size: 98
459280 GACCGAGTAA
* * *
459290 ACCAAATCCTATACCCTTGAAGTTGTC-GTGGGTCAAATT--AA-AAAT--CAGATCTTAATCTT
1 ACCAAATCCTATACCC-TGAAGTTG-CAGTGGATCAAATTAAAATAAATAACAGATCTCAATCTC
*
459349 CTTGAGGTTATAGTGGAATGGAGTGAAG------C
64 CTTGAGGTTACAGTGGAATGGAGTGAAGTTACAAC
* * ** * * * *
459378 ATCAAATCTTATATTTCTGAAGTTGCAGTGGATCGAATTAAAATGAGTAACGGATCTCAATCTCC
1 ACCAAATCCTATA-CCCTGAAGTTGCAGTGGATCAAATTAAAATAAATAACAGATCTCAATCTCC
* * *
459443 TTGAGGTAACAGTGGAATTGAGTGGAG-TACAAC
65 TTGAGGTTACAGTGGAATGGAGTGAAGTTACAAC
* * *
459476 ACCAAATCCTATACACCTGAAGTTGCAGTGGGTCAAATT---A-AAA-AGCAGATCTCAATAT-C
1 ACCAAATCCTATAC-CCTGAAGTTGCAGTGGATCAAATTAAAATAAATAACAGATCTCAATCTCC
* * * * *
459535 TTCGAGGTTACAAT--AA---AATAAAGTGA-AGC
65 TT-GAGGTTACAGTGGAATGGAGTGAAGTTACAAC
* * * ** * * * *
459564 ACCAAATTCTATATACCTAAAGTTATAATGGAT-AAGATTAAAATGAGTAAC-GAGTCTTAATCT
1 ACCAAATCCTATA-CCCTGAAGTTGCAGTGGATCAA-ATTAAAATAAATAACAGA-TCTCAATC-
* * *
459627 TCC-TCAGGTTATAGCGGAATGGAGTGAAG-TACAAC
62 TCCTTGAGGTTACAGTGGAATGGAGTGAAGTTACAAC
* * * * * *
459662 ATCAAATCCTATATCCTTGTAGTTGTAGTGGATCAGATTAAAATAAATAACGGATCTCAATCTCC
1 ACCAAATCCTATA-CCCTGAAGTTGCAGTGGATCAAATTAAAATAAATAACAGATCTCAATCTCC
* *
459727 TTGAGGTTACAGCGGAATGGAGTAAAGTTACAAC
65 TTGAGGTTACAGTGGAATGGAGTGAAGTTACAAC
* * *** * * *
459761 ACCAAATCCTATACCCCTGAGGTTGCAGTGGGTTGGATTAAAA-CAATAAAGCAGATCTTAATGT
1 ACCAAATCCTATA-CCCTGAAGTTGCAGTGGATCAAATTAAAATAAAT-AA-CAGATCTCAATCT
*
459825 CCCTGAGGTTACAGTGGAATGGAGTGAAGCTT-CAAC
63 CCTTGAGGTTACAGTGGAATGGAGTGAAG-TTACAAC
* * * * ** *
459861 ATCAAATCTTATATCCCTGAAGTTACAGTGGATCGAATTAAAATAAATAACAGATCTCAAAGTTC
1 ACCAAATCCTATA-CCCTGAAGTTGCAGTGGATCAAATTAAAATAAATAACAGATCTCAATCTCC
* * *
459926 TCGAGGTTACAGTGGAATGGAGTGAAGTTATAAT
65 TTGAGGTTACAGTGGAATGGAGTGAAGTTACAAC
*
459960 ACAAAATCCTATACCCCTGAAGTTGCAGTGG
1 ACCAAATCCTATA-CCCTGAAGTTGCAGTGG
459991 GTCGGATTAA
Statistics
Matches: 468, Mismatches: 105, Indels: 69
0.73 0.16 0.11
Matches are distributed among these distances:
87 3 0.01
88 63 0.13
89 2 0.00
90 2 0.00
91 5 0.01
92 6 0.01
93 71 0.15
94 3 0.01
95 4 0.01
97 4 0.01
98 113 0.24
99 110 0.24
100 77 0.16
101 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (98 bp):
ACCAAATCCTATACCCTGAAGTTGCAGTGGATCAAATTAAAATAAATAACAGATCTCAATCTCCT
TGAGGTTACAGTGGAATGGAGTGAAGTTACAAC
Found at i:459606 original size:186 final size:186
Alignment explanation
Indices: 459290--459704 Score: 448
Period size: 186 Copynumber: 2.2 Consensus size: 186
459280 GACCGAGTAA
* * *
459290 ACCAAATCCTATACCCTTGAAGTTGTCGTGGGTCAAATTAAAAATCAGATCTTAATCTTCTTGAG
1 ACCAAATCCTATACCCTTGAAGTTGTCGTGGGTCAAATTAAAAAGCAGATCTCAATCATCTTGAG
* * ** ** * ** * * * *
459355 GTTATAGTGGAATGGAGTGAAGCATCAAATCTTATATTTCTGAAGTTGCAGTGGATCGAATTAAA
66 GTTACAATAAAATAAAGTGAAGCACCAAATCTTATATACCTAAAGTTACAATGGATAGAATTAAA
* * * *
459420 ATGAGTAACG-GATCTCAATC-TCCTTGAGGTAACAGTGGAATTGAGTGGAGTACAAC
131 ATGAGTAACGAG-TCTCAATCTTCC-TCAGGTAACAGCGGAATGGAGTGAAGTACAAC
459476 ACCAAATCCTATACACC-TGAAGTTG-CAGTGGGTCAAATTAAAAAGCAGATCTCAAT-ATCTTC
1 ACCAAATCCTATAC-CCTTGAAGTTGTC-GTGGGTCAAATTAAAAAGCAGATCTCAATCATCTT-
*
459538 GAGGTTACAATAAAATAAAGTGAAGCACCAAAT-TCTATATACCTAAAGTTATAATGGATA-AGA
63 GAGGTTACAATAAAATAAAGTGAAGCACCAAATCT-TATATACCTAAAGTTACAATGGATAGA-A
* * *
459601 TTAAAATGAGTAACGAGTCTTAATCTTCCTCAGGTTATAGCGGAATGGAGTGAAGTACAAC
126 TTAAAATGAGTAACGAGTCTCAATCTTCCTCAGGTAACAGCGGAATGGAGTGAAGTACAAC
* * * * * *
459662 ATCAAATCCTATATCCTTGTAGTTGTAGTGGATCAGATTAAAA
1 ACCAAATCCTATACCCTTGAAGTTGTCGTGGGTCAAATTAAAA
459705 TAAATAACGG
Statistics
Matches: 190, Mismatches: 30, Indels: 18
0.80 0.13 0.08
Matches are distributed among these distances:
185 9 0.05
186 175 0.92
187 6 0.03
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (186 bp):
ACCAAATCCTATACCCTTGAAGTTGTCGTGGGTCAAATTAAAAAGCAGATCTCAATCATCTTGAG
GTTACAATAAAATAAAGTGAAGCACCAAATCTTATATACCTAAAGTTACAATGGATAGAATTAAA
ATGAGTAACGAGTCTCAATCTTCCTCAGGTAACAGCGGAATGGAGTGAAGTACAAC
Found at i:459803 original size:99 final size:99
Alignment explanation
Indices: 459394--460001 Score: 453
Period size: 99 Copynumber: 6.3 Consensus size: 99
459384 TCTTATATTT
* * * * * * *
459394 CTGAAGTTGCAGTGGATCGAATTAAAATGAGTAACGGATCTCAATCTCCTTGAGGTAACAGTGGA
1 CTGAAGTTGCAGTGGATCGGATTAAAATAAATAACAGATCTCAATGTCCTTGAGGTTACAGCGGA
* * *
459459 ATTGAGTGGAG-TACAACACCAAATCCTATACAC
66 ATGGAGTGAAGTTACAACACCAAATCCTATACCC
* * *
459492 CTGAAGTTGCAGT-G---GG-TCAAATTAAA-AAGCAGATCTCAATAT-CTTCGAGGTT--A-C-
1 CTGAAGTTGCAGTGGATCGGATTAAAATAAATAA-CAGATCTCAATGTCCTT-GAGGTTACAGCG
** * * * * * **
459546 -AATAAAATAAAGTGA-AGCACCAAATTCTATATAC
64 GAATGGAGTGAAGTTACAACACCAAATCCTATACCC
* ** * ** * * * * * *
459580 CTAAAGTTATAATGGATAAGATTAAAATGAGTAAC-GAGTCTTAATCTTCC-TCAGGTTATAGCG
1 CTGAAGTTGCAGTGGATCGGATTAAAATAAATAACAGA-TCTCAAT-GTCCTTGAGGTTACAGCG
* *
459643 GAATGGAGTGAAG-TACAACATCAAATCCTATATCC
64 GAATGGAGTGAAGTTACAACACCAAATCCTATACCC
* * * * * *
459678 TTGTAGTTGTAGTGGATCAGATTAAAATAAATAACGGATCTCAATCTCCTTGAGGTTACAGCGGA
1 CTGAAGTTGCAGTGGATCGGATTAAAATAAATAACAGATCTCAATGTCCTTGAGGTTACAGCGGA
*
459743 ATGGAGTAAAGTTACAACACCAAATCCTATACCC
66 ATGGAGTGAAGTTACAACACCAAATCCTATACCC
* * * * * * *
459777 CTGAGGTTGCAGTGGGTTGGATTAAAA-CAATAAAGCAGATCTTAATGTCCCTGAGGTTACAGTG
1 CTGAAGTTGCAGTGGATCGGATTAAAATAAAT-AA-CAGATCTCAATGTCCTTGAGGTTACAGCG
* * *
459841 GAATGGAGTGAAGCTT-CAACATCAAATCTTATATCC
64 GAATGGAGTGAAG-TTACAACACCAAATCCTATACCC
* * * * * *
459877 CTGAAGTTACAGTGGATCGAATTAAAATAAATAACAGATCTCAAAGTTCTCGAGGTTACAGTGGA
1 CTGAAGTTGCAGTGGATCGGATTAAAATAAATAACAGATCTCAATGTCCTTGAGGTTACAGCGGA
* * *
459942 ATGGAGTGAAGTTATAATACAAAATCCTATACCC
66 ATGGAGTGAAGTTACAACACCAAATCCTATACCC
*
459976 CTGAAGTTGCAGTGGGTCGGATTAAA
1 CTGAAGTTGCAGTGGATCGGATTAAA
460002 GTTACAAAAG
Statistics
Matches: 393, Mismatches: 91, Indels: 51
0.73 0.17 0.10
Matches are distributed among these distances:
88 32 0.08
89 2 0.01
91 1 0.00
92 8 0.02
93 40 0.10
94 5 0.01
95 2 0.01
96 1 0.00
97 5 0.01
98 97 0.25
99 118 0.30
100 77 0.20
101 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (99 bp):
CTGAAGTTGCAGTGGATCGGATTAAAATAAATAACAGATCTCAATGTCCTTGAGGTTACAGCGGA
ATGGAGTGAAGTTACAACACCAAATCCTATACCC
Found at i:459878 original size:50 final size:50
Alignment explanation
Indices: 459728--459892 Score: 147
Period size: 50 Copynumber: 3.3 Consensus size: 50
459718 TCAATCTCCT
* * *
459728 TGAGGTTACAGCGGAATGGAGTAAAG-TTACAACACCAAATCCTATACCCC
1 TGAGGTTACAGTGGAATGGAGTAAAGCTT-CAACACCAAATCTTATATCCC
* ** * * * * * *
459778 TGAGGTTGCAGTGGGTTGGATTAAAACAAT-AA-AGCAGATCTTAATGTCCC
1 TGAGGTTACAGTGGAATGGAGTAAAGC-TTCAACACCAAATCTT-ATATCCC
* *
459828 TGAGGTTACAGTGGAATGGAGTGAAGCTTCAACATCAAATCTTATATCCC
1 TGAGGTTACAGTGGAATGGAGTAAAGCTTCAACACCAAATCTTATATCCC
*
459878 TGAAGTTACAGTGGA
1 TGAGGTTACAGTGGA
459893 TCGAATTAAA
Statistics
Matches: 87, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
49 8 0.09
50 70 0.80
51 8 0.09
52 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (50 bp):
TGAGGTTACAGTGGAATGGAGTAAAGCTTCAACACCAAATCTTATATCCC
Found at i:459893 original size:199 final size:198
Alignment explanation
Indices: 459618--460001 Score: 536
Period size: 199 Copynumber: 1.9 Consensus size: 198
459608 GAGTAACGAG
* * * *
459618 TCTTAATCTTCCTCAGGTTATAGCGGAATGGAGTGAAGTACAACATCAAATCCTATATCCTTGTA
1 TCTTAATCTCCCTCAGGTTACAGCGGAATGGAGTGAAGTACAACATCAAATCCTATATCCCTGAA
** * * *
459683 GTTGTAGTGGATC-AGATTAAAATAAATAACGGATCTCAATCTCCTTGAGGTTACAGCGGAATGG
66 GTTACAGTGGATCGA-ATTAAAATAAATAACAGATCTCAAACTCCTCGAGGTTACAGCGGAATGG
* * *
459747 AGTAAAGTTACAACACCAAATCCTATACCCCTGAGGTTGCAGTGGGTTGGATTAAAACAATAAAG
130 AGTAAAGTTACAACACAAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAAACAATAAAG
459812 CAGA
195 CAGA
* * * * *
459816 TCTTAATGTCCCTGAGGTTACAGTGGAATGGAGTGAAGCTTCAACATCAAATCTTATATCCCTGA
1 TCTTAATCTCCCTCAGGTTACAGCGGAATGGAGTGAAG-TACAACATCAAATCCTATATCCCTGA
* * *
459881 AGTTACAGTGGATCGAATTAAAATAAATAACAGATCTCAAAGTTCTCGAGGTTACAGTGGAATGG
65 AGTTACAGTGGATCGAATTAAAATAAATAACAGATCTCAAACTCCTCGAGGTTACAGCGGAATGG
* * *
459946 AGTGAAGTTATAATACAAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAA
130 AGTAAAGTTACAACACAAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAA
460002 GTTACAAAAG
Statistics
Matches: 161, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
198 33 0.20
199 127 0.79
200 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (198 bp):
TCTTAATCTCCCTCAGGTTACAGCGGAATGGAGTGAAGTACAACATCAAATCCTATATCCCTGAA
GTTACAGTGGATCGAATTAAAATAAATAACAGATCTCAAACTCCTCGAGGTTACAGCGGAATGGA
GTAAAGTTACAACACAAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAAACAATAAAGC
AGA
Found at i:461126 original size:21 final size:21
Alignment explanation
Indices: 461093--461155 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
461083 GTTCAAGAAT
461093 AGTGTACACTTCTACCGATACA
1 AGTG-ACACTTCTACCGATACA
*
461115 AGTGACAGTTCTACCGATACA
1 AGTGACACTTCTACCGATACA
* **
461136 AGTGTCTTTTCTACCGATAC
1 AGTGACACTTCTACCGATAC
461156 TAAAAACTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 33 0.89
22 4 0.11
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (21 bp):
AGTGACACTTCTACCGATACA
Found at i:475815 original size:20 final size:20
Alignment explanation
Indices: 475790--475831 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
475780 ACTAAATGCC
475790 CACTTTCAACATTAAGCAAA
1 CACTTTCAACATTAAGCAAA
475810 CACTTTCAACATTAAGCAAA
1 CACTTTCAACATTAAGCAAA
475830 CA
1 CA
475832 TTCATAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (20 bp):
CACTTTCAACATTAAGCAAA
Found at i:476934 original size:17 final size:17
Alignment explanation
Indices: 476914--476961 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
476904 ACTACAATGC
476914 AAATGTGTTGACAAAT-A
1 AAATGTG-TGACAAATAA
476931 AAATGTAGTGAC-AATAA
1 AAATGT-GTGACAAATAA
476948 AAATGTGATGACAA
1 AAATGTG-TGACAA
476962 CTACATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.15
17 21 0.78
18 2 0.07
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (17 bp):
AAATGTGTGACAAATAA
Found at i:486709 original size:36 final size:36
Alignment explanation
Indices: 486669--486932 Score: 366
Period size: 36 Copynumber: 7.3 Consensus size: 36
486659 CTGTTGTGAA
* *
486669 AGTAAATATGTGGGTATGTTATTTATGCCATGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * * *
486705 AGTAAATATTTGGATATGTTATCCATGCCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
486741 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
*
486777 AATAAATATGTGGGTATGTTATTCATGCCATGAGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * * *
486813 AGTAAATATGTGGGTTTGTTATCCATGTCATGTGAC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* * * * *
486849 AGTAAATATGTGAGTTTGTTATTTATGCCATGTGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
* *
486885 AATAAATATGTGGGTATGTTATTCATGCCATGAGAT
1 AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
486921 AGTAAATATGTG
1 AGTAAATATGTG
486933 TTAATGCCAT
Statistics
Matches: 201, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 201 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (36 bp):
AGTAAATATGTGGGTATGTTATTCATGCCATGAGAC
Found at i:486807 original size:108 final size:108
Alignment explanation
Indices: 486671--486932 Score: 425
Period size: 108 Copynumber: 2.4 Consensus size: 108
486661 GTTGTGAAAG
* *
486671 TAAATATGTGGGTATGTTATTTATGCCATGAGATAGTAAATATTTGGATATGTTATCCATGCCAT
1 TAAATATGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTGGATATGTTATCCATGCCAT
*
486736 GTGACAGTAAATATGTGGGTATGTTATTCATGCCATGAGACAA
66 GTGACAGTAAATATGTGAGTATGTTATTCATGCCATGAGACAA
* * * *
486779 TAAATATGTGGGTATGTTATTCATGCCATGAGACAGTAAATATGTGGGTTTGTTATCCATGTCAT
1 TAAATATGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTGGATATGTTATCCATGCCAT
* * * *
486844 GTGACAGTAAATATGTGAGTTTGTTATTTATGCCATGTGATAA
66 GTGACAGTAAATATGTGAGTATGTTATTCATGCCATGAGACAA
486887 TAAATATGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTG
1 TAAATATGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTG
486933 TTAATGCCAT
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 142 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (108 bp):
TAAATATGTGGGTATGTTATTCATGCCATGAGATAGTAAATATGTGGATATGTTATCCATGCCAT
GTGACAGTAAATATGTGAGTATGTTATTCATGCCATGAGACAA
Found at i:490182 original size:45 final size:42
Alignment explanation
Indices: 490111--490200 Score: 108
Period size: 45 Copynumber: 2.1 Consensus size: 42
490101 TACTCTGATT
*
490111 TATATTAATTATTTAAAACACATTTAAAAAATTAGATTAATATTA
1 TATATTAAATATTTAAAACACATTT-AAAAATTAGATT-AT-TTA
* ** *
490156 TATATTAAATATTTAAAATATTTTTAAAATTTAGATTATTTA
1 TATATTAAATATTTAAAACACATTTAAAAATTAGATTATTTA
490198 TAT
1 TAT
490201 TTTATCTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 6 0.15
43 2 0.05
44 11 0.28
45 21 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (42 bp):
TATATTAAATATTTAAAACACATTTAAAAATTAGATTATTTA
Found at i:490249 original size:33 final size:33
Alignment explanation
Indices: 490211--490356 Score: 143
Period size: 34 Copynumber: 4.3 Consensus size: 33
490201 TTTATCTATC
* * *
490211 ATTTAAATATTTCATTTTTCATTGTATTAAATT
1 ATTTAAATATTTCATATATCATTATATTAAATT
* * *
490244 ATTTAAATATTATTTACAAATATCATTATAGTAAATG
1 ATTT-AA-A-TATTT-CATATATCATTATATTAAATT
* *
490281 ATTTAAATATTT-AT-TATTATTATATTTTAATT
1 ATTTAAATATTTCATATATCATTATA-TTAAATT
*
490313 ATTTAAAATATTTCATATATAATTATATTAAATT
1 ATTT-AAATATTTCATATATCATTATATTAAATT
490347 ATTTAAATAT
1 ATTTAAATAT
490357 ATTTTAAATT
Statistics
Matches: 92, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
31 9 0.10
32 9 0.10
33 18 0.20
34 19 0.21
35 11 0.12
36 7 0.08
37 19 0.21
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (33 bp):
ATTTAAATATTTCATATATCATTATATTAAATT
Found at i:490356 original size:24 final size:25
Alignment explanation
Indices: 490308--490375 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
490298 TATTATATTT
* *
490308 TAATTAT-TTAAAATATTTCATATA
1 TAATTATATTAAATTATTTCAAATA
490332 TAATTATATTAAATTATTT-AAATA
1 TAATTATATTAAATTATTTCAAATA
* * *
490356 TATTTTAAATTAATTTATTT
1 TA-ATTATATTAAATTATTT
490376 TTAATATTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 13 0.35
25 24 0.65
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATTATATTAAATTATTTCAAATA
Found at i:492060 original size:20 final size:20
Alignment explanation
Indices: 492037--492090 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
492027 AAAATTACAA
492037 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
492057 AAAAAATTTAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
* *
492077 -TAAAGTTCAAAATA
1 AAAAAATTCAAAATA
492091 TTTATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:492145 original size:10 final size:10
Alignment explanation
Indices: 492127--492176 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 10
492117 TTAAAATAAA
492127 TTATAAAAAT
1 TTATAAAAAT
*
492137 TTTTAAAAA-
1 TTATAAAAAT
*
492146 TAATAAAAAT
1 TTATAAAAAT
*
492156 ATAT-AAAAT
1 TTATAAAAAT
492165 TT-TAAAAAT
1 TTATAAAAAT
492174 TTA
1 TTA
492177 AAATAATGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
8 1 0.03
9 20 0.65
10 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:492162 original size:19 final size:19
Alignment explanation
Indices: 492124--492163 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
492114 TTTTTAAAAT
* * *
492124 AAATTATAAAAATTTTTAA
1 AAATAATAAAAATATATAA
492143 AAATAATAAAAATATATAA
1 AAATAATAAAAATATATAA
492162 AA
1 AA
492164 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATAAAAATATATAA
Found at i:494131 original size:12 final size:12
Alignment explanation
Indices: 494114--494138 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
494104 TGTTATTATG
494114 ATGAATGCTATT
1 ATGAATGCTATT
494126 ATGAATGCTATT
1 ATGAATGCTATT
494138 A
1 A
494139 ATTATTTAAT
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:495962 original size:39 final size:39
Alignment explanation
Indices: 495906--496005 Score: 155
Period size: 39 Copynumber: 2.6 Consensus size: 39
495896 AGTTCTCGAG
* * *
495906 TTACTGAATTGGTAGTGACACTGTAAACACTGCGATACA
1 TTACTGAACTGGCAGTGACACTGTAAACACTGCAATACA
*
495945 TTACTGAACTGGCAGTGACACTGTAAACACTGTAATACA
1 TTACTGAACTGGCAGTGACACTGTAAACACTGCAATACA
*
495984 TTACTGAACTAGCAGTGACACT
1 TTACTGAACTGGCAGTGACACT
496006 ATAACTAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (39 bp):
TTACTGAACTGGCAGTGACACTGTAAACACTGCAATACA
Found at i:498885 original size:12 final size:12
Alignment explanation
Indices: 498868--499062 Score: 155
Period size: 12 Copynumber: 15.9 Consensus size: 12
498858 TCCATAATTT
*
498868 ATATATATACAC
1 ATATATATATAC
*
498880 ATATATACATATAT
1 ATATAT--ATATAC
498894 ATATATATGTATAC
1 ATATATA--TATAC
* *
498908 ATATATACATAG
1 ATATATATATAC
*
498920 ATATACATATAC
1 ATATATATATAC
498932 --ATATATATAC
1 ATATATATATAC
*
498942 ATATACATATAC
1 ATATATATATAC
498954 ATATACATATATACAC
1 ATAT--ATATAT--AC
*
498970 ATATACATATAC
1 ATATATATATAC
*
498982 ATATACATATAC
1 ATATATATATAC
*
498994 ATACATATATAC
1 ATATATATATAC
*
499006 ATATACATATAC
1 ATATATATATAC
*
499018 ATATACATATAC
1 ATATATATATAC
*
499030 --ATACATATAC
1 ATATATATATAC
* **
499040 ATATACATATGT
1 ATATATATATAC
499052 ATATATATATA
1 ATATATATATA
499063 TAATCACTTT
Statistics
Matches: 151, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
10 19 0.13
12 95 0.63
14 31 0.21
16 6 0.04
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (12 bp):
ATATATATATAC
Found at i:498891 original size:6 final size:6
Alignment explanation
Indices: 498882--499049 Score: 204
Period size: 6 Copynumber: 28.7 Consensus size: 6
498872 ATATACACAT
* * * * *
498882 ATATAC ATATAT ATATAT ATGTATAC ATATAT ACATAG ATATAC ATATAC
1 ATATAC ATATAC ATATAC A--TATAC ATATAC ATATAC ATATAC ATATAC
*
498932 ATAT-- ATATAC ATATAC ATATAC ATATAC ATAT-- ATACAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* *
498976 ATATAC ATATAC ATATAC ATACAT ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
499024 ATATAC --ATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATAT
499050 GTATATATAT
Statistics
Matches: 141, Mismatches: 13, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
4 11 0.08
6 125 0.89
8 5 0.04
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.35
Consensus pattern (6 bp):
ATATAC
Found at i:498909 original size:28 final size:28
Alignment explanation
Indices: 498867--499064 Score: 197
Period size: 28 Copynumber: 7.1 Consensus size: 28
498857 GTCCATAATT
* *
498867 TATATATATACACATATATACATATATA
1 TATATACATATACATATATACATATATA
**
498895 TATATATGTATACATATATAC----ATA
1 TATATACATATACATATATACATATATA
* * *
498919 GATATACATATACATATATATACATATA
1 TATATACATATACATATATACATATATA
* *
498947 CATATACATATACATATATACACATATA
1 TATATACATATACATATATACATATATA
*
498975 CATATACATATACATATACATACATATATA
1 TATATACATATACATAT--ATACATATATA
* * * *
499005 CATATACATATACATATACATATACATA
1 TATATACATATACATATATACATATATA
* * *
499033 CATATACATATACATATGTATATATATA
1 TATATACATATACATATATACATATATA
499061 TATA
1 TATA
499065 ATCACTTTAA
Statistics
Matches: 148, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
24 20 0.14
28 101 0.68
30 27 0.18
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (28 bp):
TATATACATATACATATATACATATATA
Done.