Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 181 of 279
Found at i:59317125 original size:99 final size:99
Alignment explanation
Indices: 59317012--59317203 Score: 375
Period size: 99 Copynumber: 1.9 Consensus size: 99
59317002 ATTATGTTTC
*
59317012 TTCATTTTTTTATGATTTTTCAAAGTCAGAACAGGGGAACCCAAATTCATTCTGACCTTGTCTTA
1 TTCAATTTTTTATGATTTTTCAAAGTCAGAACAGGGGAACCCAAATTCATTCTGACCTTGTCTTA
59317077 CAAAATTCATTATATCTCAAAATTTACATTTTTA
66 CAAAATTCATTATATCTCAAAATTTACATTTTTA
59317111 TTCAATTTTTTATGATTTTTCAAAGTCAGAACAGGGGAACCCAAATTCATTCTGACCTTGTCTTA
1 TTCAATTTTTTATGATTTTTCAAAGTCAGAACAGGGGAACCCAAATTCATTCTGACCTTGTCTTA
59317176 CAAAATTCATTATATCTCAAAATTTACA
66 CAAAATTCATTATATCTCAAAATTTACA
59317204 AATCCATTGC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (99 bp):
TTCAATTTTTTATGATTTTTCAAAGTCAGAACAGGGGAACCCAAATTCATTCTGACCTTGTCTTA
CAAAATTCATTATATCTCAAAATTTACATTTTTA
Found at i:59322732 original size:22 final size:23
Alignment explanation
Indices: 59322707--59322752 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
59322697 CAACCAAATC
59322707 AATTCA-ACATATTT-TAGAGATA
1 AATTCATACATATTTATA-AGATA
*
59322729 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
59322752 A
1 A
59322753 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 13 0.62
24 2 0.10
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:59322758 original size:23 final size:23
Alignment explanation
Indices: 59322714--59322758 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
59322704 ATCAATTCAA
*
59322714 CATATTTTAGAGATAAATTCATG
1 CATATTTTAGAGATAAAGTCATG
*
59322737 CATATTTATA-AGATAACGTCAT
1 CATATTT-TAGAGATAAAGTCAT
59322759 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (23 bp):
CATATTTTAGAGATAAAGTCATG
Found at i:59325039 original size:21 final size:20
Alignment explanation
Indices: 59325000--59325058 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 20
59324990 GTAAATAGTA
59325000 TATATATTAT-TTATATATTAT
1 TATATATT-TGTT-TATATTAT
59325021 CTATCATA-TTGTTTATATTAT
1 -TAT-ATATTTGTTTATATTAT
59325042 TATATATTTTGTTTATA
1 TATATA-TTTGTTTATA
59325059 AATTTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 18 0.55
22 6 0.18
23 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TATATATTTGTTTATATTAT
Found at i:59325386 original size:7 final size:7
Alignment explanation
Indices: 59325374--59325445 Score: 54
Period size: 7 Copynumber: 9.3 Consensus size: 7
59325364 TTTAAATATC
59325374 TTTATTT
1 TTTATTT
59325381 TTTATTT
1 TTTATTT
*
59325388 TTGACTGATAT
1 TT---T-ATTT
59325399 TTTATATT
1 TTTAT-TT
*
59325407 TTTATAT
1 TTTATTT
*
59325414 TTTGTTT
1 TTTATTT
59325421 ATTTATTT
1 -TTTATTT
59325429 TTGTATTT
1 TT-TATTT
59325437 TTTATTT
1 TTTATTT
59325444 TT
1 TT
59325446 AGTATTGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
7 26 0.50
8 20 0.38
10 1 0.02
11 5 0.10
ACGTcount: A:0.18, C:0.01, G:0.06, T:0.75
Consensus pattern (7 bp):
TTTATTT
Found at i:59325415 original size:15 final size:15
Alignment explanation
Indices: 59325395--59325444 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
59325385 TTTTTGACTG
*
59325395 ATATTTTATATTTTT
1 ATATTTTGTATTTTT
59325410 ATATTTTGT-TTATTT
1 ATATTTTGTATT-TTT
59325425 AT-TTTTGTATTTTT
1 ATATTTTGTATTTTT
59325439 -TATTTT
1 ATATTTT
59325445 TAGTATTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.03
14 15 0.48
15 15 0.48
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (15 bp):
ATATTTTGTATTTTT
Found at i:59325445 original size:15 final size:15
Alignment explanation
Indices: 59325405--59325457 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
59325395 ATATTTTATA
59325405 TTTTTATATTTTGT-T
1 TTTTTAT-TTTTGTAT
*
59325420 TATTTATTTTTGTAT
1 TTTTTATTTTTGTAT
59325435 TTTTTATTTTTAGTAT
1 TTTTTATTTTT-GTAT
59325451 TGTTTTA
1 T-TTTTA
59325458 GTAGGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 6 0.18
15 17 0.52
16 5 0.15
17 5 0.15
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (15 bp):
TTTTTATTTTTGTAT
Found at i:59325451 original size:28 final size:28
Alignment explanation
Indices: 59325376--59325452 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
59325366 TAAATATCTT
*
59325376 TATTTTTTATTTTTG-ACTGATATTTTA
1 TATTTTTTATTTTTGTATTGATATTTTA
* * *
59325403 TATTTTTATATTTTGTTTATTTAT-TTTTG
1 TATTTTT-TATTTT-TGTATTGATATTTTA
59325432 TATTTTTTATTTTTAGTATTG
1 TATTTTTTATTTTT-GTATTG
59325453 TTTTAGTAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
27 8 0.20
28 16 0.40
29 12 0.30
30 4 0.10
ACGTcount: A:0.19, C:0.01, G:0.08, T:0.71
Consensus pattern (28 bp):
TATTTTTTATTTTTGTATTGATATTTTA
Found at i:59330546 original size:16 final size:16
Alignment explanation
Indices: 59330512--59330553 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
59330502 TGGGACCAAA
*
59330512 AAATTATATTATTTAAT
1 AAATTA-ATTACTTAAT
*
59330529 AAATTAATTACTTGAT
1 AAATTAATTACTTAAT
59330545 AAATTAATT
1 AAATTAATT
59330554 TCAATACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AAATTAATTACTTAAT
Found at i:59331873 original size:31 final size:32
Alignment explanation
Indices: 59331833--59331899 Score: 127
Period size: 31 Copynumber: 2.1 Consensus size: 32
59331823 TTTTCCTGAC
59331833 CGCTCTAAACTTTTTTACATTTTACATTTTTT
1 CGCTCTAAACTTTTTTACATTTTACATTTTTT
59331865 CGCT-TAAACTTTTTTACATTTTACATTTTTT
1 CGCTCTAAACTTTTTTACATTTTACATTTTTT
59331896 CGCT
1 CGCT
59331900 ATCTCTTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.55
Consensus pattern (32 bp):
CGCTCTAAACTTTTTTACATTTTACATTTTTT
Found at i:59333792 original size:12 final size:12
Alignment explanation
Indices: 59333775--59333808 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
59333765 CCGACCTGCC
59333775 TATATTAATTTT
1 TATATTAATTTT
59333787 TATATT-ATTTT
1 TATATTAATTTT
59333798 TATA-TAATTTT
1 TATATTAATTTT
59333809 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:59334046 original size:22 final size:22
Alignment explanation
Indices: 59334020--59334062 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59334010 TATTCAAACA
*
59334020 ATAATAACAAAGTAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
**
59334042 ATAATAGTAAAATAGTAGCAA
1 ATAATAACAAAATAGTAGCAA
59334063 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:59334316 original size:14 final size:15
Alignment explanation
Indices: 59334297--59334325 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59334287 GTTATTGCTT
59334297 TTTTACATT-TTTTA
1 TTTTACATTATTTTA
59334311 TTTTACATTATTTTA
1 TTTTACATTATTTTA
59334326 CATTATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTACATTATTTTA
Found at i:59334321 original size:10 final size:10
Alignment explanation
Indices: 59334308--59334332 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59334298 TTTACATTTT
59334308 TTATTTTACA
1 TTATTTTACA
59334318 TTATTTTACA
1 TTATTTTACA
59334328 TTATT
1 TTATT
59334333 AATTATAAAA
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:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTTTACA
Found at i:59334738 original size:5 final size:6
Alignment explanation
Indices: 59334707--59334735 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
59334697 GAGGAAATGT
59334707 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
59334736 GAAGGCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:59340168 original size:30 final size:30
Alignment explanation
Indices: 59340132--59340231 Score: 139
Period size: 30 Copynumber: 3.3 Consensus size: 30
59340122 CTTAGCTTTT
59340132 TCCACCACCAACTCCACTAGCCACACATT-C
1 TCCACCACCAACTCCACTAGCCACAC-TTGC
*
59340162 TCCACCACCAAATCCACTAGCCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
** * *
59340192 TCCATTACCTACTCCACTAACCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
59340222 TCCACCACCA
1 TCCACCACCA
59340232 CTTGTACCTA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.29, C:0.48, G:0.04, T:0.19
Consensus pattern (30 bp):
TCCACCACCAACTCCACTAGCCACACTTGC
Found at i:59340602 original size:27 final size:27
Alignment explanation
Indices: 59340564--59340712 Score: 78
Period size: 25 Copynumber: 5.6 Consensus size: 27
59340554 TTTTAAATTT
59340564 TATATT-TCGTATATATATATTTTATAC
1 TATATTAT-GTATATATATATTTTATAC
* * * *
59340591 TATTTTATG--TATATATCTTTAATAT
1 TATATTATGTATATATATATTTTATAC
* *
59340616 TATATTATTTATATATATATTTTTTTTTAC
1 TATATTATGTATATATATA---TTTTATAC
* * * *
59340646 -ATGTTATCTTATGTATATATCTTA-AC
1 TATATTAT-GTATATATATATTTTATAC
* * *
59340672 TATATTATGTATGTAT-T-TTTAACAC
1 TATATTATGTATATATATATTTTATAC
*
59340697 TATATTATGTACATAT
1 TATATTATGTATATAT
59340713 TTTTAATATT
Statistics
Matches: 93, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
24 3 0.03
25 37 0.40
26 9 0.10
27 22 0.24
28 1 0.01
29 6 0.06
30 15 0.16
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (27 bp):
TATATTATGTATATATATATTTTATAC
Found at i:59340702 original size:25 final size:25
Alignment explanation
Indices: 59340670--59340718 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
59340660 ATATATCTTA
**
59340670 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
59340695 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
59340719 TATTATCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:59340723 original size:20 final size:20
Alignment explanation
Indices: 59340698--59340753 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
59340688 TTTTAACACT
59340698 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
* * *
59340718 ATATTAT-CACTTATTTTTT
1 ATATTATGTACATATTTTTA
*
59340737 TTATATATGTACATATT
1 ATAT-TATGTACATATT
59340754 GATGTAGTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:59340896 original size:16 final size:15
Alignment explanation
Indices: 59340872--59340919 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
59340862 TAATTATTAT
*
59340872 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
59340888 TATTTTAATATTTTA
1 TATTTTAATATTTTA
59340903 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
59340919 T
1 T
59340920 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:59340907 original size:7 final size:8
Alignment explanation
Indices: 59340872--59340923 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
59340862 TAATTATTAT
*
59340872 TATTCTAA
1 TATTTTAA
*
59340880 TATTTTGA
1 TATTTTAA
59340888 TATTTTAA
1 TATTTTAA
59340896 TATTTT-A
1 TATTTTAA
59340903 TATTTTATA
1 TATTTTA-A
*
59340912 TATTTTAT
1 TATTTTAA
59340920 TATT
1 TATT
59340924 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:59353940 original size:27 final size:27
Alignment explanation
Indices: 59353900--59354049 Score: 96
Period size: 25 Copynumber: 5.6 Consensus size: 27
59353890 ATTTTAAATT
59353900 CTATATTACGTGTATATATATATTTTATA
1 CTATATTA--TGTATATATATATTTTATA
* * *
59353929 CTATTTTATG--TATATATCTTTAATA
1 CTATATTATGTATATATATATTTTATA
* * *
59353954 TTATATTATTTATATATATATTTTTTTA
1 CTATATTATGTATATATATA-TTTTATA
* * * *
59353982 C-ATGTTATCTTATGTATATATCTTA-A
1 CTATATTAT-GTATATATATATTTTATA
* * *
59354008 CTATATTATGTATGTAT-T-TTTAACA
1 CTATATTATGTATATATATATTTTATA
*
59354033 CTATATTATGTACATAT
1 CTATATTATGTATATAT
59354050 TTTTAATATT
Statistics
Matches: 95, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
24 3 0.03
25 37 0.39
26 9 0.09
27 24 0.25
28 15 0.16
29 7 0.07
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (27 bp):
CTATATTATGTATATATATATTTTATA
Found at i:59353962 original size:25 final size:25
Alignment explanation
Indices: 59353841--59354057 Score: 92
Period size: 25 Copynumber: 8.5 Consensus size: 25
59353831 TTGTTATTAT
*
59353841 TATATTTCTTAATATTATATTA--TA
1 TATATTT-TTAATACTATATTATGTA
* *
59353865 TATATTCTTT--TAATATATTA-G-G
1 TATATT-TTTAATACTATATTATGTA
* * *
59353887 TACATTTTAAATTCTATATTACGTGTA
1 TATATTTTTAATACTATATTA--TGTA
* *
59353914 TATATATATTTTATACTATTTTATGTA
1 TATAT-T-TTTAATACTATATTATGTA
* * *
59353941 TATATCTTTAATATTATATTATTTATATA
1 TATATTTTTAATA--CTA-TA-TTATGTA
** *
59353970 TATATTTTTTTACATGTTATCTTATGTA
1 TATA--TTTTTA-ATACTATATTATGTA
*
59353998 TATA-TCTT-A-ACTATATTATGTA
1 TATATTTTTAATACTATATTATGTA
* *
59354020 TGTATTTTTAACACTATATTATGTA
1 TATATTTTTAATACTATATTATGTA
*
59354045 CATATTTTTAATA
1 TATATTTTTAATA
59354058 TTATCACGTA
Statistics
Matches: 142, Mismatches: 31, Indels: 39
0.67 0.15 0.18
Matches are distributed among these distances:
21 2 0.01
22 27 0.19
23 12 0.08
24 9 0.06
25 33 0.23
26 1 0.01
27 15 0.11
28 12 0.08
29 22 0.15
30 2 0.01
31 5 0.04
32 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (25 bp):
TATATTTTTAATACTATATTATGTA
Found at i:59353964 original size:30 final size:30
Alignment explanation
Indices: 59353924--59354005 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
59353914 TATATATATT
*
59353924 TTATACTATTTTATGTATATATCTTTAATA
1 TTATATTATTTTATGTATATATCTTTAATA
* **
59353954 TTATATTA-TTTATATATATAT-TTTTTTA
1 TTATATTATTTTATGTATATATCTTTAATA
* * *
59353982 -CATGTTATCTTATGTATATATCTT
1 TTATATTATTTTATGTATATATCTT
59354006 AACTATATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 5 0.12
28 16 0.38
29 14 0.33
30 7 0.17
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (30 bp):
TTATATTATTTTATGTATATATCTTTAATA
Found at i:59354259 original size:9 final size:8
Alignment explanation
Indices: 59354212--59354258 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
59354202 TAATTATTAT
*
59354212 TATTCTAA
1 TATTTTAA
**
59354220 TATTTGGA
1 TATTTTAA
59354228 TATTTTAA
1 TATTTTAA
59354236 TA-TTTAA
1 TATTTTAA
59354243 TATTTTATA
1 TATTTTA-A
59354252 TATTTTA
1 TATTTTA
59354259 TTGTTCACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
7 7 0.22
8 17 0.53
9 8 0.25
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (8 bp):
TATTTTAA
Found at i:59367539 original size:22 final size:22
Alignment explanation
Indices: 59367511--59367556 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
59367501 TTTTTCTAGA
*
59367511 AAACACTCATGATGATCGGATT
1 AAACACTCACGATGATCGGATT
59367533 AAACACTCACGATGATCGGATT
1 AAACACTCACGATGATCGGATT
59367555 AA
1 AA
59367557 TCATTAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
AAACACTCACGATGATCGGATT
Found at i:59370186 original size:43 final size:43
Alignment explanation
Indices: 59370120--59370205 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
59370110 TCACCCAACA
* *
59370120 ATGAAAAGTTACAAATGGCAACCCAATTATTTAATATTGTATT
1 ATGAAAAGTTACAAATGGCAACCCAACTATTCAATATTGTATT
*
59370163 ATGAAAAGTTACAAATGGTAACCCAACTATTCAATATTGTATT
1 ATGAAAAGTTACAAATGGCAACCCAACTATTCAATATTGTATT
59370206 TTTTGGTCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (43 bp):
ATGAAAAGTTACAAATGGCAACCCAACTATTCAATATTGTATT
Found at i:59371600 original size:3 final size:3
Alignment explanation
Indices: 59371592--59371625 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
59371582 AGTTAAATGC
59371592 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
59371626 AGGAAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:59374400 original size:7 final size:7
Alignment explanation
Indices: 59374388--59374415 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
59374378 AAAACACTAT
59374388 GCAAAAG
1 GCAAAAG
59374395 GCAAAAG
1 GCAAAAG
59374402 GCAAAAG
1 GCAAAAG
59374409 GCAAAAG
1 GCAAAAG
59374416 TCCCAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00
Consensus pattern (7 bp):
GCAAAAG
Found at i:59380837 original size:27 final size:26
Alignment explanation
Indices: 59380785--59380838 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
59380775 CCTTATGTAT
**
59380785 ATTTATTTTCCCATTTTTGTACCTAA
1 ATTTATTTTCCCATTTTAATACCTAA
* *
59380811 ATTTTTTTATCCCATTTTAATATCTAA
1 ATTTATTT-TCCCATTTTAATACCTAA
59380838 A
1 A
59380839 GTATCAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.28, C:0.17, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTATTTTCCCATTTTAATACCTAA
Found at i:59382707 original size:20 final size:21
Alignment explanation
Indices: 59382682--59382721 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
59382672 CAAAATGAGC
59382682 CTCTC-ATAAATG-ACTTTTCT
1 CTCTCAAT-AATGTACTTTTCT
59382702 CTCTCAATAATGTACTTTTC
1 CTCTCAATAATGTACTTTTC
59382722 AAAGTGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.45
Consensus pattern (21 bp):
CTCTCAATAATGTACTTTTCT
Found at i:59383503 original size:29 final size:29
Alignment explanation
Indices: 59383470--59383525 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
59383460 AAAGGTAACA
*
59383470 AATGATCTATTTCGATAATTAATTTATAG
1 AATGATCTATTTCAATAATTAATTTATAG
* *
59383499 AATGATCTATTTTAATATTTAATTTAT
1 AATGATCTATTTCAATAATTAATTTAT
59383526 TTTTTGGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (29 bp):
AATGATCTATTTCAATAATTAATTTATAG
Found at i:59386001 original size:41 final size:41
Alignment explanation
Indices: 59385950--59386092 Score: 150
Period size: 41 Copynumber: 3.4 Consensus size: 41
59385940 TAATATTAAA
*
59385950 AAATGTATATACATAATATACAAAAGAAGATATATGCATGT
1 AAATATATATACATAATATACAAAAGAAGATATATGCATGT
* * *
59385991 AAATATATATACATAAGAT-CGTATAA-AA-ATATATAACTATGAT
1 AAATATATATACATAATATAC--AAAAGAAGATATAT-GC-ATG-T
59386034 ATTAA-AGTATATACATAATATACAAAAGAAGATATATGCATGT
1 A--AATA-TATATACATAATATACAAAAGAAGATATATGCATGT
59386077 AAATATATATACATAA
1 AAATATATATACATAA
59386093 GATCGTATAA
Statistics
Matches: 83, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
40 7 0.08
41 33 0.40
42 7 0.08
43 4 0.05
44 7 0.08
45 18 0.22
46 7 0.08
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (41 bp):
AAATATATATACATAATATACAAAAGAAGATATATGCATGT
Found at i:59386047 original size:45 final size:45
Alignment explanation
Indices: 59385996--59386137 Score: 165
Period size: 45 Copynumber: 3.2 Consensus size: 45
59385986 CATGTAAATA
59385996 TATATACATAAGATCGTATAAAAATATATAACTATGATATTAAAG
1 TATATACATAAGATCGTATAAAAATATATAACTATGATATTAAAG
* * *
59386041 TATATACATAATATAC--A-AAAGAAGATATATGC-ATG-TA--AATA-
1 TATATACATAAGAT-CGTATAAA-AATATATA-ACTATGATATTAA-AG
59386082 TATATACATAAGATCGTATAAAAATATATAACTATGATATTAAAG
1 TATATACATAAGATCGTATAAAAATATATAACTATGATATTAAAG
59386127 TATATACATAA
1 TATATACATAA
59386138 TATATATGAA
Statistics
Matches: 79, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
40 1 0.01
41 16 0.20
42 12 0.15
43 10 0.13
44 12 0.15
45 27 0.34
46 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.32
Consensus pattern (45 bp):
TATATACATAAGATCGTATAAAAATATATAACTATGATATTAAAG
Found at i:59386070 original size:86 final size:86
Alignment explanation
Indices: 59385954--59386141 Score: 376
Period size: 86 Copynumber: 2.2 Consensus size: 86
59385944 ATTAAAAAAT
59385954 GTATATACATAATATACAAAAGAAGATATATGCATGTAAATATATATACATAAGATCGTATAAAA
1 GTATATACATAATATACAAAAGAAGATATATGCATGTAAATATATATACATAAGATCGTATAAAA
59386019 ATATATAACTATGATATTAAA
66 ATATATAACTATGATATTAAA
59386040 GTATATACATAATATACAAAAGAAGATATATGCATGTAAATATATATACATAAGATCGTATAAAA
1 GTATATACATAATATACAAAAGAAGATATATGCATGTAAATATATATACATAAGATCGTATAAAA
59386105 ATATATAACTATGATATTAAA
66 ATATATAACTATGATATTAAA
59386126 GTATATACATAATATA
1 GTATATACATAATATA
59386142 TATGAAAACA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 102 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (86 bp):
GTATATACATAATATACAAAAGAAGATATATGCATGTAAATATATATACATAAGATCGTATAAAA
ATATATAACTATGATATTAAA
Found at i:59386575 original size:15 final size:15
Alignment explanation
Indices: 59386543--59386582 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
59386533 TAATAATACC
59386543 AATA-AAAATA-AAT
1 AATAGAAAATATAAT
59386556 AATAGAAAATATAAT
1 AATAGAAAATATAAT
59386571 AATAGAAAATAT
1 AATAGAAAATAT
59386583 CAAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 4 0.16
14 6 0.24
15 15 0.60
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
AATAGAAAATATAAT
Found at i:59387594 original size:16 final size:16
Alignment explanation
Indices: 59387575--59387611 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
59387565 GCCAGGGGAT
59387575 GGTGCTGGTCG-ACCTA
1 GGTGCTGG-CGTACCTA
59387591 GGTGC-GGCGTACCTA
1 GGTGCTGGCGTACCTA
59387606 GGTGCT
1 GGTGCT
59387612 AGGGGCCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.11
15 12 0.63
16 5 0.26
ACGTcount: A:0.11, C:0.24, G:0.41, T:0.24
Consensus pattern (16 bp):
GGTGCTGGCGTACCTA
Found at i:59388588 original size:75 final size:73
Alignment explanation
Indices: 59388414--59388876 Score: 517
Period size: 73 Copynumber: 6.3 Consensus size: 73
59388404 AACACATAAA
* * * * *
59388414 TTGAAAAGCAGAAATTAAAAATACCTCAGTGTGCCCTGATGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
59388479 GTTGATTT
66 GTTGATTT
* * * * * *
59388487 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCCCAACTCACCTCTCGCAATGTAA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
59388552 GTTAATTTTT
66 GTTGA--TTT
* *
59388562 TTGAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
59388627 GTTGATTT
66 GTTGATTT
* * * *
59388635 TTGAAAAACAGAAATTGAAATTACCTCAGCCTGTCTTGAGGCCCAACTCACCTCTCGCAA-ATGT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG-
59388699 AAGTTGA---
65 -AGTTGATTT
** * *
59388706 TT-AAAAACAGATTTTGAAAATACCTC-GACGTGAGACCCGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAG-CGT--GTCCTGAGGCTCAACTCACCTCTCGCAATA
59388769 TGAGTTGATTTTT
63 TGAGTTGA--TTT
* * * * *
59388782 TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGAGCC-AATGCTCAACTCATCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAATA
*
59388846 TGAGTCGATTT
63 TGAGTTGATTT
59388857 TTGAAAAACAGAAATTGAAA
1 TTGAAAAACAGAAATTGAAA
59388877 CATCAGAGTA
Statistics
Matches: 327, Mismatches: 45, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
69 1 0.00
70 23 0.07
71 8 0.02
72 27 0.08
73 118 0.36
74 6 0.02
75 87 0.27
76 2 0.01
77 53 0.16
78 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (73 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:59388682 original size:148 final size:144
Alignment explanation
Indices: 59388412--59388809 Score: 552
Period size: 148 Copynumber: 2.7 Consensus size: 144
59388402 AAAACACATA
* * *
59388412 AATTGAAAAGCAGAAATTAAAAATACCTCAGTGTGCCCTGATGCTCAACTCACCTCTCGCAATAT
1 AATTGAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
* *
59388477 GAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCCCAACTCACCTCT
66 GAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCCTGTCCTAAGGCCCAACTCACCTCT
59388542 CGC-AATGTAAGTT
131 CGCAAATGTAAGTT
59388555 AATTTTTTTGAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGC
1 AA-----TTGAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGC
* *
59388620 AATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCCTGTCTTGAGGCCCAACTCA
61 AATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCCTGTCCTAAGGCCCAACTCA
59388685 CCTCTCGCAAATGTAAGTT
126 CCTCTCGCAAATGTAAGTT
* * **
59388704 GATT-AAAAACAGATTTTGAAAATACCTC-GACGTGAGACCC-GAGGCTCAACTCACCTCTCGCA
1 AATTGAAAAGCAGAAATTGAAAATACCTCAG-CGT--G-CCCTGAGGCTCAACTCACCTCTCGCA
* *
59388766 ATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTCA
62 ATATGAGTTGA--TTTTTGAAAAACAGAAATTGAAATTACCTCA
59388810 ACGTGTGAGC
Statistics
Matches: 230, Mismatches: 13, Indels: 20
0.87 0.05 0.08
Matches are distributed among these distances:
142 1 0.00
143 26 0.11
144 2 0.01
145 34 0.15
146 3 0.01
147 29 0.13
148 124 0.54
149 11 0.05
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (144 bp):
AATTGAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCCTGTCCTAAGGCCCAACTCACCTCT
CGCAAATGTAAGTT
Found at i:59389073 original size:18 final size:16
Alignment explanation
Indices: 59389043--59389082 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
59389033 AACCCAAAAT
59389043 AAAAAATAAAAAAAGA
1 AAAAAATAAAAAAAGA
59389059 AAAAAATGAAGAAAAAGA
1 AAAAAAT-AA-AAAAAGA
59389077 AAAAAA
1 AAAAAA
59389083 CCTAACCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.32
17 2 0.09
18 13 0.59
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (16 bp):
AAAAAATAAAAAAAGA
Found at i:59398698 original size:14 final size:14
Alignment explanation
Indices: 59398679--59398706 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59398669 ATGCAGGGAA
59398679 GACTTCAGTGCCTT
1 GACTTCAGTGCCTT
59398693 GACTTCAGTGCCTT
1 GACTTCAGTGCCTT
59398707 CTATCGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (14 bp):
GACTTCAGTGCCTT
Found at i:59403318 original size:41 final size:41
Alignment explanation
Indices: 59403263--59403405 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 41
59403253 TAATATTAAA
*
59403263 AAATTTATATACATAATATACAAAAGAAGATATATGCATGT
1 AAATATATATACATAATATACAAAAGAAGATATATGCATGT
* * * *
59403304 AAATATATGTACATAAGAT-CGTATAA-AA-ATATATAACTATGAT
1 AAATATATATACATAATATAC--AAAAGAAGATATAT-GC-ATG-T
59403347 ATTAA-AGTATATACATAATATACAAAAGAAGATATATGCATGT
1 A--AATA-TATATACATAATATACAAAAGAAGATATATGCATGT
*
59403390 AAATATATGTACATAA
1 AAATATATATACATAA
59403406 GATCGTATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
40 7 0.09
41 31 0.39
42 7 0.09
43 4 0.05
44 7 0.09
45 17 0.21
46 7 0.09
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (41 bp):
AAATATATATACATAATATACAAAAGAAGATATATGCATGT
Found at i:59403364 original size:45 final size:45
Alignment explanation
Indices: 59403313--59403450 Score: 148
Period size: 45 Copynumber: 3.2 Consensus size: 45
59403303 TAAATATATG
59403313 TACATAAGATCGTATAAAAATATATAACTATGATATTAAAGTATA
1 TACATAAGATCGTATAAAAATATATAACTATGATATTAAAGTATA
* * * *
59403358 TACATAATATAC--A-AAAGAAGATATATGC-ATG-TA--AATA-TATG
1 TACATAAGAT-CGTATAAA-AATATATA-ACTATGATATTAA-AGTATA
59403399 TACATAAGATCGTATAAAAATATATAACTATGATATTAAAGTATA
1 TACATAAGATCGTATAAAAATATATAACTATGATATTAAAGTATA
59403444 TACATAA
1 TACATAA
59403451 TATATATGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
40 1 0.01
41 15 0.21
42 12 0.16
43 10 0.14
44 12 0.16
45 22 0.30
46 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.32
Consensus pattern (45 bp):
TACATAAGATCGTATAAAAATATATAACTATGATATTAAAGTATA
Found at i:59403383 original size:86 final size:86
Alignment explanation
Indices: 59403268--59403454 Score: 374
Period size: 86 Copynumber: 2.2 Consensus size: 86
59403258 TTAAAAAATT
59403268 TATATACATAATATACAAAAGAAGATATATGCATGTAAATATATGTACATAAGATCGTATAAAAA
1 TATATACATAATATACAAAAGAAGATATATGCATGTAAATATATGTACATAAGATCGTATAAAAA
59403333 TATATAACTATGATATTAAAG
66 TATATAACTATGATATTAAAG
59403354 TATATACATAATATACAAAAGAAGATATATGCATGTAAATATATGTACATAAGATCGTATAAAAA
1 TATATACATAATATACAAAAGAAGATATATGCATGTAAATATATGTACATAAGATCGTATAAAAA
59403419 TATATAACTATGATATTAAAG
66 TATATAACTATGATATTAAAG
59403440 TATATACATAATATA
1 TATATACATAATATA
59403455 TATGAAAATA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 101 1.00
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (86 bp):
TATATACATAATATACAAAAGAAGATATATGCATGTAAATATATGTACATAAGATCGTATAAAAA
TATATAACTATGATATTAAAG
Found at i:59403855 original size:3 final size:3
Alignment explanation
Indices: 59403849--59403903 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
59403839 AATAAAACAT
** * * *
59403849 ATA ATA ATA ATA ATA ATA ATA CCA ATA ACA ATAA ATA ATA GTA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
59403895 ATA ATA ATA
1 ATA ATA ATA
59403904 GAAAATATCA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:59404906 original size:16 final size:16
Alignment explanation
Indices: 59404887--59404923 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
59404877 GCTAGGGGAT
59404887 GGTGCTGGTCG-ACCTA
1 GGTGCTGG-CGCACCTA
59404903 GGTGC-GGCGCACCTA
1 GGTGCTGGCGCACCTA
59404918 GGTGCT
1 GGTGCT
59404924 AGGGGGCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.11
15 12 0.63
16 5 0.26
ACGTcount: A:0.11, C:0.27, G:0.41, T:0.22
Consensus pattern (16 bp):
GGTGCTGGCGCACCTA
Found at i:59405114 original size:23 final size:23
Alignment explanation
Indices: 59405087--59405149 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
59405077 GGGCTTATGT
** *
59405087 TGTAAATGGGTTTTGGGGTTTAG
1 TGTAAATGGGTCATGGGATTTAG
59405110 TGTAAATGGGTCATGGGATTTAG
1 TGTAAATGGGTCATGGGATTTAG
59405133 TGTAAATGGGTCATGGG
1 TGTAAATGGGTCATGGG
59405150 GAAAAATTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.03, G:0.38, T:0.37
Consensus pattern (23 bp):
TGTAAATGGGTCATGGGATTTAG
Found at i:59411253 original size:16 final size:16
Alignment explanation
Indices: 59411225--59411265 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
59411215 GAAATTATAA
59411225 AATATTAATT-TTTTT
1 AATATTAATTATTTTT
59411240 AA-ATTAATTATTTTT
1 AATATTAATTATTTTT
59411255 AATATTAATTA
1 AATATTAATTA
59411266 AAAAAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.29
15 9 0.38
16 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTAATTATTTTT
Found at i:59413734 original size:38 final size:38
Alignment explanation
Indices: 59413692--59413767 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
59413682 TTGTAGATGG
59413692 GTTTGAAGGAGGTGGAATTTGAGGAGGTTATCTTGGGT
1 GTTTGAAGGAGGTGGAATTTGAGGAGGTTATCTTGGGT
59413730 GTTTGAAGGAGGTGGAATTTGAGGAGGTTATCTTGGGT
1 GTTTGAAGGAGGTGGAATTTGAGGAGGTTATCTTGGGT
59413768 TTTATAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.34
Consensus pattern (38 bp):
GTTTGAAGGAGGTGGAATTTGAGGAGGTTATCTTGGGT
Found at i:59418672 original size:75 final size:75
Alignment explanation
Indices: 59418549--59418698 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
59418539 GTATTCCAGT
59418549 TTCTACATTTTGTTGTATATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTA
1 TTCTACATTTTGTTGTATATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTA
59418614 TTTCTAATGC
66 TTTCTAATGC
59418624 TTCTACATTTTGTTGTATATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTA
1 TTCTACATTTTGTTGTATATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTA
59418689 TTTCTAATGC
66 TTTCTAATGC
59418699 ATGAATTTCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.49
Consensus pattern (75 bp):
TTCTACATTTTGTTGTATATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTA
TTTCTAATGC
Found at i:59419177 original size:394 final size:394
Alignment explanation
Indices: 59418567--59419356 Score: 1571
Period size: 394 Copynumber: 2.0 Consensus size: 394
59418557 TTTGTTGTAT
59418567 ATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAATGCTTCTACAT
1 ATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAATGCTTCTACAT
*
59418632 TTTGTTGTATATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAAT
66 TTTGTTGTAGATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAAT
59418697 GCATGAATTTCTCAGAAGTTTTATGTACATTGTGGCACTTTTTTTCTATATGGTTGTGTGCTTCA
131 GCATGAATTTCTCAGAAGTTTTATGTACATTGTGGCACTTTTTTTCTATATGGTTGTGTGCTTCA
59418762 TCTTTTCCTTTCTTACAGGGGATGAGCGATCTGCTATCTCTAATTTTGTTTGTGATGAAGGATGA
196 TCTTTTCCTTTCTTACAGGGGATGAGCGATCTGCTATCTCTAATTTTGTTTGTGATGAAGGATGA
59418827 GTCAGAATCATTTTGGTGTTTTGTGGCACTAATAGAACGCTTTGGGCCCAATTTTAATCGTGATC
261 GTCAGAATCATTTTGGTGTTTTGTGGCACTAATAGAACGCTTTGGGCCCAATTTTAATCGTGATC
59418892 AAAACGACATGCATTCTCAGCTTTTTGCATTATCTAAGGCCTCTCTCTCTCTTTCACAGACGCAC
326 AAAACGACATGCATTCTCAGCTTTTTGCATTATCTAAGGCCTCTCTCTCTCTTTCACAGACGCAC
59418957 ACTC
391 ACTC
59418961 ATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAATGCTTCTACAT
1 ATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAATGCTTCTACAT
59419026 TTTGTTGTAGATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAAT
66 TTTGTTGTAGATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAAT
59419091 GCATGAATTTCTCAGAAGTTTTATGTACATTGTGGCACTTTTTTTCTATATGGTTGTGTGCTTCA
131 GCATGAATTTCTCAGAAGTTTTATGTACATTGTGGCACTTTTTTTCTATATGGTTGTGTGCTTCA
59419156 TCTTTTCCTTTCTTACAGGGGATGAGCGATCTGCTATCTCTAATTTTGTTTGTGATGAAGGATGA
196 TCTTTTCCTTTCTTACAGGGGATGAGCGATCTGCTATCTCTAATTTTGTTTGTGATGAAGGATGA
59419221 GTCAGAATCATTTTGGTGTTTTGTGGCACTAATAGAACGCTTTGGGCCCAATTTTAATCGTGATC
261 GTCAGAATCATTTTGGTGTTTTGTGGCACTAATAGAACGCTTTGGGCCCAATTTTAATCGTGATC
59419286 AAAACGACATGCATTCTCAGCTTTTTGCATTATCTAAGGCCTCTCTCTCTCTTTCACAGACGCAC
326 AAAACGACATGCATTCTCAGCTTTTTGCATTATCTAAGGCCTCTCTCTCTCTTTCACAGACGCAC
59419351 ACTC
391 ACTC
59419355 AT
1 AT
59419357 ACACACAAAC
Statistics
Matches: 395, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
394 395 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (394 bp):
ATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAATGCTTCTACAT
TTTGTTGTAGATCATTTGATCAGGCGTGTAAATGTTTAGGCTTATAGCTTGTTTTTATTTCTAAT
GCATGAATTTCTCAGAAGTTTTATGTACATTGTGGCACTTTTTTTCTATATGGTTGTGTGCTTCA
TCTTTTCCTTTCTTACAGGGGATGAGCGATCTGCTATCTCTAATTTTGTTTGTGATGAAGGATGA
GTCAGAATCATTTTGGTGTTTTGTGGCACTAATAGAACGCTTTGGGCCCAATTTTAATCGTGATC
AAAACGACATGCATTCTCAGCTTTTTGCATTATCTAAGGCCTCTCTCTCTCTTTCACAGACGCAC
ACTC
Found at i:59421687 original size:16 final size:16
Alignment explanation
Indices: 59421668--59421720 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
59421658 ATTACAACTT
*
59421668 TATTCTATTACAGCCC
1 TATTCCATTACAGCCC
* *
59421684 TATTCCATTATAGCTC
1 TATTCCATTACAGCCC
59421700 TATTCCATTACAGCCC
1 TATTCCATTACAGCCC
59421716 TATTC
1 TATTC
59421721 TATTCCAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.06, T:0.40
Consensus pattern (16 bp):
TATTCCATTACAGCCC
Found at i:59428650 original size:23 final size:23
Alignment explanation
Indices: 59428620--59428671 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
59428610 ACCCCTATTA
59428620 ACTTGACTCGGACTCGAACGAAT
1 ACTTGACTCGGACTCGAACGAAT
59428643 ACTTGACTCGGACTCGAACGAAT
1 ACTTGACTCGGACTCGAACGAAT
59428666 ACTTGA
1 ACTTGA
59428672 ATCGTCCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
ACTTGACTCGGACTCGAACGAAT
Found at i:59428796 original size:19 final size:19
Alignment explanation
Indices: 59428771--59428816 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
59428761 TACAAAACAT
59428771 ATCTTGGTACACAAAGTGC
1 ATCTTGGTACACAAAGTGC
* * **
59428790 ATTTTGGCACGTAAAGTGC
1 ATCTTGGTACACAAAGTGC
59428809 ATCTTGGT
1 ATCTTGGT
59428817 GCATAAGCGC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (19 bp):
ATCTTGGTACACAAAGTGC
Found at i:59433481 original size:26 final size:26
Alignment explanation
Indices: 59433426--59433482 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
59433416 TTTAATTCTT
* *
59433426 TTAAATAATTTTATATTTAAAAAATA
1 TTAAATAATTTTACATTAAAAAAATA
* *
59433452 TTAAATAATTTTCCA-TAAAAAGAATC
1 TTAAATAATTTTACATTAAAAA-AATA
59433478 TTAAA
1 TTAAA
59433483 CAATCAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (26 bp):
TTAAATAATTTTACATTAAAAAAATA
Found at i:59434740 original size:27 final size:27
Alignment explanation
Indices: 59434710--59434761 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
59434700 ATTGTACTGC
59434710 GAGAAAGATAGTGGATCATTACTCTAG
1 GAGAAAGATAGTGGATCATTACTCTAG
*
59434737 GAGAAATATAGTGGATCATTACTCT
1 GAGAAAGATAGTGGATCATTACTCT
59434762 GGGCAAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (27 bp):
GAGAAAGATAGTGGATCATTACTCTAG
Found at i:59440144 original size:38 final size:39
Alignment explanation
Indices: 59440060--59440153 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
59440050 ACCAATATGG
*
59440060 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
59440099 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* *
59440137 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
59440154 AATCTATCTG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
38 19 0.40
39 25 0.53
40 3 0.06
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:59441184 original size:5 final size:5
Alignment explanation
Indices: 59441174--59441223 Score: 84
Period size: 5 Copynumber: 10.0 Consensus size: 5
59441164 AATAATTAAG
59441174 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAAT TATA- TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT
59441224 AAAAGAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.09
5 34 0.79
6 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:59441291 original size:31 final size:30
Alignment explanation
Indices: 59441256--59441316 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
59441246 GAAACAGAAT
*
59441256 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
59441287 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
59441317 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:59442892 original size:39 final size:40
Alignment explanation
Indices: 59442785--59442892 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 40
59442775 GACCTCGAGT
* **
59442785 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGATAGAGC
** ** *
59442826 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
59442864 CGATGAGACACTGGGTGTCAACTATTACT
1 CGATGAGACACTGGGTGTCAACTATTACT
59442893 ACAAACTATC
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
38 19 0.36
39 16 0.30
40 1 0.02
41 15 0.28
42 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
Found at i:59446185 original size:3 final size:3
Alignment explanation
Indices: 59446177--59446209 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
59446167 TAAACGATAT
*
59446177 GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
59446210 TGGATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:59450916 original size:68 final size:68
Alignment explanation
Indices: 59450843--59451008 Score: 190
Period size: 67 Copynumber: 2.5 Consensus size: 68
59450833 ACCTCAACTC
* **
59450843 TCATGTTATTTTTGGATGCAACTACCATGTTGATTATGGGTCTCATATATATGGAGCTTCGGCTC
1 TCATGTTATTTTTGGATGCAACTACCATGTTGATTATGGGTCTCATATATATGAAGCTTCAACTC
*
59450908 TTT
66 TCT
** * * * * * * *
59450911 TCATGTTATTTTTCAAT-TAATTACTATGTTGATTTTGGGTTTCATATATGTGAATCTTCAACTC
1 TCATGTTATTTTTGGATGCAACTACCATGTTGATTATGGGTCTCATATATATGAAGCTTCAACTC
59450975 TCT
66 TCT
* *
59450978 TCATGTTGTTTTTGGATGCAACTATCATGTT
1 TCATGTTATTTTTGGATGCAACTACCATGTT
59451009 AATTGTAAGT
Statistics
Matches: 77, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
67 53 0.69
68 24 0.31
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (68 bp):
TCATGTTATTTTTGGATGCAACTACCATGTTGATTATGGGTCTCATATATATGAAGCTTCAACTC
TCT
Found at i:59468660 original size:8 final size:8
Alignment explanation
Indices: 59468647--59468713 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
59468637 GAAAGAAAAA
59468647 AAAAGAAG
1 AAAAGAAG
59468655 AAAAGAA-
1 AAAAGAAG
*
59468662 AAGA-AAG
1 AAAAGAAG
59468669 AAAAGAA-
1 AAAAGAAG
*
59468676 AAAGAGAAA
1 AAA-AGAAG
59468685 AAAAGAAAG
1 AAAAG-AAG
59468694 AGAAA-AAG
1 A-AAAGAAG
*
59468702 AAAAAAAG
1 AAAAGAAG
59468710 AAAA
1 AAAA
59468714 ATGGAGAGGC
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
6 2 0.04
7 12 0.24
8 26 0.53
9 6 0.12
10 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:59468660 original size:22 final size:23
Alignment explanation
Indices: 59468628--59468712 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 23
59468618 TCTATTTCAA
*
59468628 AAAAAAAAAG-AAAGAAA-AAA-
1 AAAAAAGAAGAAAAGAAAGAAAG
*
59468648 AAAGAAGAAAAGAAAAGAAAGAAA-
1 AAA-AA-AGAAGAAAAGAAAGAAAG
59468672 AGAAAAAG-AGAAAA-AAAGAAAG
1 A-AAAAAGAAGAAAAGAAAGAAAG
*
59468694 AGAAAAAGAAAAAAAGAAA
1 A-AAAAAGAAGAAAAGAAA
59468713 AATGGAGAGG
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.05
21 9 0.16
22 19 0.35
23 13 0.24
24 9 0.16
25 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAGAAAAGAAAGAAAG
Found at i:59468666 original size:27 final size:27
Alignment explanation
Indices: 59468628--59468713 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
59468618 TCTATTTCAA
*
59468628 AAAAAAAAAGAAAGAAAAAAAAAGAAG
1 AAAAGAAAAGAAAGAAAAAAAAAGAAG
59468655 AAAAGAAAAGAAAGAAAAGAAAAAG-AG
1 AAAAGAAAAGAAAGAAAA-AAAAAGAAG
* *
59468682 -AAA-AAAAGAAAG--AGAAAAAGAAA
1 AAAAGAAAAGAAAGAAAAAAAAAGAAG
59468705 AAAAGAAAA
1 AAAAGAAAA
59468714 ATGGAGAGGC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
22 6 0.12
23 2 0.04
24 3 0.06
25 13 0.25
26 3 0.06
27 19 0.37
28 6 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (27 bp):
AAAAGAAAAGAAAGAAAAAAAAAGAAG
Found at i:59468713 original size:14 final size:13
Alignment explanation
Indices: 59468626--59468714 Score: 97
Period size: 14 Copynumber: 6.3 Consensus size: 13
59468616 CTTCTATTTC
59468626 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
59468639 AAGAAAAAAAAAGA
1 AA-AAAAAAAAAGA
* *
59468653 AGAAAAGAAAAGA
1 AAAAAAAAAAAGA
59468666 AAGAAAAGAAAAAGA
1 AA-AAAA-AAAAAGA
59468681 GAAAAAAAGAAAGAGA
1 -AAAAAAA-AAA-AGA
59468697 AAAAGAAAAAAAGA
1 AAAA-AAAAAAAGA
59468711 AAAA
1 AAAA
59468715 TGGAGAGGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
13 13 0.20
14 24 0.37
15 20 0.31
16 8 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:59468714 original size:27 final size:27
Alignment explanation
Indices: 59468626--59468714 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 27
59468616 CTTCTATTTC
*
59468626 AAAAAA-AAAAAGAAAGAA-AAAAAAAG
1 AAAAAAGAAAGAGAAA-AAGAAAAAAAG
* *
59468652 AAGAAAAGAAAAGAAAGAAAAGAAAAAGAG
1 AA-AAAAG-AAAGAGA-AAAAGAAAAAAAG
59468682 AAAAAAAGAAAGAGAAAAAGAAAAAAAG
1 -AAAAAAGAAAGAGAAAAAGAAAAAAAG
59468710 AAAAA
1 AAAAA
59468715 TGGAGAGGCC
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
26 2 0.04
27 9 0.17
28 12 0.23
29 13 0.25
30 14 0.27
31 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAAGAGAAAAAGAAAAAAAG
Found at i:59469788 original size:38 final size:38
Alignment explanation
Indices: 59469654--59469788 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 38
59469644 CACCTTAATC
*
59469654 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTT-CA----CAGATCTTATCT
* * *
59469697 CCCTAAGCAGTAGTGG-AGCA-GATCAAAGACTCACCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGTTCACAGA-T---CTT-ATCT
59469738 CCCTAAGCAGTAGGGTAACAGGTTCACAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTCACAGATCTTATCT
59469776 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
59469789 CAGAGCAGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 23
0.72 0.07 0.22
Matches are distributed among these distances:
37 6 0.08
38 17 0.22
40 2 0.03
41 21 0.28
42 12 0.16
43 16 0.21
44 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (38 bp):
CCCTAAGCAGTAGGGTAACAGGTTCACAGATCTTATCT
Found at i:59469841 original size:82 final size:83
Alignment explanation
Indices: 59469646--59470055 Score: 496
Period size: 82 Copynumber: 4.9 Consensus size: 83
59469636 AAATTCAGCA
*
59469646 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTT-CA--T-CAGATCTTATCTCCCTAAGCAGTAGT
*
59469711 GGAGCAGATC-A--AAGACTCA
62 GGAGCAGATCGACGAAGACTCG
**
59469730 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCA-CAGATCTTATCTCCCTAAGCAGTAGCAGAG
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCATCAGATCTTATCTCCCTAAGCAGTAGTGGAG
*
59469794 CAGATCGACGAAGACCCG
66 CAGATCGACGAAGACTCG
* * *
59469812 CCTTAATCCCCTAACCAGTAGGGTAACAGGTTAAATTTGTAGATCTTATTCTCCCTAAGCAGTAG
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTT-CA--T-CAGATCTTA-TCTCCCTAAGCAGTAG
59469877 TGGAGCAGAT---CGAAGACTCG
61 TGGAGCAGATCGACGAAGACTCG
* * * *
59469897 CCTTAATCCCTTAAGCAGTAGGGTAACAGGTTCGT-AGATCTTATCTCCCTAAGCAGTAGCGGAA
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCATCAGATCTTATCTCCCTAAGCAGTAGTGGAG
* *
59469961 CAGATCGATGACGACTCG
66 CAGATCGACGAAGACTCG
*
59469979 CCTTAATCCCTTAAGCAGTAGGGTAACAGG-TCAAAATTGCAGATCTTATCTCCCTAAGCAGTAG
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTC---A-T-CAGATCTTATCTCCCTAAGCAGTAG
59470043 TGGAGCAGATCGA
61 TGGAGCAGATCGA
59470056 AGGTGCGCCT
Statistics
Matches: 286, Mismatches: 22, Indels: 33
0.84 0.06 0.10
Matches are distributed among these distances:
79 58 0.20
80 9 0.03
81 2 0.01
82 76 0.27
83 2 0.01
84 32 0.11
85 40 0.14
87 43 0.15
88 24 0.08
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (83 bp):
CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCATCAGATCTTATCTCCCTAAGCAGTAGTGGAG
CAGATCGACGAAGACTCG
Found at i:59469921 original size:167 final size:166
Alignment explanation
Indices: 59469646--59470094 Score: 704
Period size: 167 Copynumber: 2.7 Consensus size: 166
59469636 AAATTCAGCA
59469646 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
* * *
59469711 GGAGCAGATCAAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCACAGATCTTATCT
66 GGAGCAGATCGAAGACTCGCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTCACAGATCTTATCT
*
59469776 CCCTAAGCAGTAGCAGAGCAGATCGACGAAGACCCG
131 CCCTAAGCAGTAGCAGAACAGATCGACGAAGACCCG
* *
59469812 CCTTAATCCCCTAACCAGTAGGGTAACAGGTTAAATTTGTAGATCTTATTCTCCCTAAGCAGTAG
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTA-TCTCCCTAAGCAGTAG
**
59469877 TGGAGCAGATCGAAGACTCGCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTCGTAGATCTTATC
65 TGGAGCAGATCGAAGACTCGCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTCACAGATCTTATC
* * * *
59469942 TCCCTAAGCAGTAGCGGAACAGATCGATGACGACTCG
130 TCCCTAAGCAGTAGCAGAACAGATCGACGAAGACCCG
* * *
59469979 CCTTAATCCCTTAAGCAGTAGGGTAACAGGTCAAAATTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
* *
59470044 GGAGCAGATCGAAG-GTGCGCCTTAA-CCCTTTAAGTAGTAGGGTAACAGGTT
66 GGAGCAGATCGAAGACT-CGCCTTAATCCC-TTAAGCAGTAGGGTAACAGGTT
59470095 AAAGTATAGC
Statistics
Matches: 261, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
165 4 0.02
166 106 0.41
167 151 0.58
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (166 bp):
CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGACTCGCCTTAATCCCTTAAGCAGTAGGGTAACAGGTTCACAGATCTTATCT
CCCTAAGCAGTAGCAGAACAGATCGACGAAGACCCG
Found at i:59470007 original size:44 final size:42
Alignment explanation
Indices: 59469863--59470007 Score: 130
Period size: 38 Copynumber: 3.5 Consensus size: 42
59469853 GATCTTATTC
* *
59469863 TCCC-TAAGCAGTAGTGGAGCAGATCGA-AGACTCGCCTTAA
1 TCCCTTAAGCAGTAGCGGAACAGATCGATAGACTCGCCTTAA
*
59469903 TCCCTTAAGCAGTAG-GGTAACAGGTTCG-TAGA-T---CTT-A
1 TCCCTTAAGCAGTAGCGG-AACA-GATCGATAGACTCGCCTTAA
*
59469940 TCTCCCTAAGCAGTAGCGGAACAGATCGATGACGACTCGCCTTAA
1 TC-CCTTAAGCAGTAGCGGAACAGATCGAT-A-GACTCGCCTTAA
59469985 TCCCTTAAGCAGTAG-GGTAACAG
1 TCCCTTAAGCAGTAGCGG-AACAG
59470008 GTCAAAATTG
Statistics
Matches: 85, Mismatches: 5, Indels: 26
0.73 0.04 0.22
Matches are distributed among these distances:
37 7 0.08
38 20 0.24
39 3 0.04
40 8 0.09
41 15 0.18
42 7 0.08
43 2 0.02
44 20 0.24
45 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (42 bp):
TCCCTTAAGCAGTAGCGGAACAGATCGATAGACTCGCCTTAA
Found at i:59470577 original size:207 final size:206
Alignment explanation
Indices: 59470222--59470935 Score: 1167
Period size: 207 Copynumber: 3.5 Consensus size: 206
59470212 TGGAGAGCAG
* *
59470222 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTATGCTGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
59470287 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
59470352 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGTAAGATCCAAGATGGTTTGGCATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAG-AAGATCCAAGATGGTTTGGCATCCTTGTGCT
59470417 TACAAGGAACAA
195 TACAAGGAACAA
* *
59470429 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
* * * *
59470494 TCTCTATACTGTCAGAGAACGAATCGAAGTTTGGCGTCTCCATATTCGATGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
59470559 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAG-AAGATCCAAGATGGTTTGGCATCCTTGTGCT
59470624 TACAAGGAACAA
195 TACAAGGAACAA
* * * * *
59470636 ATTGAAGACATAGTTGTTTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
* * * *
59470701 TCTCTGTATTGTCAGAGAACAAATTGAAGTTTTGCGTCTCCATATTCGACGGAGGACAGACATAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
** * * * *
59470766 AGCAGATCTAACCTTCAGATGATTAAACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGAAGATCCAAGATGGTTTGGCATCCTTGTGCTT
*
59470831 ACAAGGAGCAA
196 ACAAGGAACAA
*
59470842 ATCGAAGACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
* *
59470907 TCTCTGTATTGTCAGTGAACAAATTGAAG
66 TCTCTGTATTGTCAGAGAACAAATCGAAG
59470936 AAACAGATTT
Statistics
Matches: 473, Mismatches: 34, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
206 127 0.27
207 346 0.73
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (206 bp):
ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
AGCAGATCTGGCCTTCAGATGTTTATACTGAAGAAGATCCAAGATGGTTTGGCATCCTTGTGCTT
ACAAGGAACAA
Found at i:59471325 original size:19 final size:19
Alignment explanation
Indices: 59471300--59471388 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
59471290 ATAATCTTCA
59471300 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
59471319 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
59471338 ATGAT-T-CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
59471355 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
59471373 ATGATATACAATCTTA
1 ATGATATGCAATCTTA
59471389 AAAGATATGA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
17 17 0.26
18 17 0.26
19 31 0.48
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:59471340 original size:14 final size:15
Alignment explanation
Indices: 59471321--59471375 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 15
59471311 TCTTAGATGT
59471321 GATATG-CAATCTTA
1 GATATGTCAATCTTA
59471335 GATATGATTCAATCTTA
1 GATATG--TCAATCTTA
59471352 GATATGATTGCAATCTTA
1 GATATG--T-CAATCTTA
59471370 GATATG
1 GATATG
59471376 ATATACAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.16
17 17 0.46
18 14 0.38
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (15 bp):
GATATGTCAATCTTA
Found at i:59471370 original size:35 final size:38
Alignment explanation
Indices: 59471300--59471388 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 38
59471290 ATAATCTTCA
* *
59471300 ATGATATGCAATCTTAGATGTGATATGCAATCTTAGAT
1 ATGATATACAATCTTAGATATGATATGCAATCTTAGAT
59471338 ATGAT-T-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATATACAATCTTAGATATGATATGCAATCTTAGAT
59471373 ATGATATACAATCTTA
1 ATGATATACAATCTTA
59471389 AAAGATATGA
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
35 18 0.38
36 16 0.33
37 9 0.19
38 5 0.10
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (38 bp):
ATGATATACAATCTTAGATATGATATGCAATCTTAGAT
Found at i:59476675 original size:10 final size:10
Alignment explanation
Indices: 59476625--59476675 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
59476615 TTAAACTTAA
59476625 TTAATTAAAGG
1 TTAATTAAA-G
59476636 TT-ATTAAA-
1 TTAATTAAAG
59476644 TTAATT-AAG
1 TTAATTAAAG
59476653 ATTAATTATAAG
1 -TTAATTA-AAG
59476665 TTAATTAAAG
1 TTAATTAAAG
59476675 T
1 T
59476676 ACATCAGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
8 4 0.11
9 3 0.09
10 16 0.46
11 9 0.26
12 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (10 bp):
TTAATTAAAG
Found at i:59478921 original size:19 final size:19
Alignment explanation
Indices: 59478897--59478934 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
59478887 AACTAGTTTG
**
59478897 ATTAAAAAACTATTAAAAA
1 ATTAAAAAAAAATTAAAAA
59478916 ATTAAAAAAAAATTAAAAA
1 ATTAAAAAAAAATTAAAAA
59478935 TTTAGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
ATTAAAAAAAAATTAAAAA
Found at i:59480430 original size:21 final size:21
Alignment explanation
Indices: 59480387--59480431 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
59480377 TTCACATTCG
* *
59480387 TTTTTACTATTTCAATATGGT
1 TTTTTACTAGTTAAATATGGT
59480408 TTTTCTACTAGTTAAATAT-GT
1 TTTT-TACTAGTTAAATATGGT
59480429 TTT
1 TTT
59480432 AGACCAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTTTACTAGTTAAATATGGT
Found at i:59481666 original size:6 final size:6
Alignment explanation
Indices: 59481655--59481683 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
59481645 GATCCAAGAA
59481655 ACAATG ACAATG ACAATG ACAATG ACAAT
1 ACAATG ACAATG ACAATG ACAATG ACAAT
59481684 AGGATAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (6 bp):
ACAATG
Found at i:59490479 original size:86 final size:86
Alignment explanation
Indices: 59490334--59490495 Score: 290
Period size: 86 Copynumber: 1.9 Consensus size: 86
59490324 ATTGGTATAC
* *
59490334 AAAATACGAGTTTTAAAAAAAAAAATTTTGGGTGCTGGTCTGCAATGGCCGGCACCCAGTATAAC
1 AAAATACGAGTTTTAAAAAAAAAAATTTTGGGTGCTGGCCTGCAATGGCCGGCACCCAGTACAAC
59490399 AAAAAAAAATTTTGCTCTCTA
66 AAAAAAAAATTTTGCTCTCTA
59490420 AAAATACGAGTTTTAAAAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA
1 AAAATACGAGTTTTAAAAAAAAAAATTTTGGGTGCTGGCCTG-CAATGGCCGGCACCCAGTACAA
59490484 CAAAAAAAAATT
65 CAAAAAAAAATT
59490496 CGAATTTTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
85 15 0.21
86 58 0.79
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (86 bp):
AAAATACGAGTTTTAAAAAAAAAAATTTTGGGTGCTGGCCTGCAATGGCCGGCACCCAGTACAAC
AAAAAAAAATTTTGCTCTCTA
Found at i:59490588 original size:107 final size:108
Alignment explanation
Indices: 59490408--59490795 Score: 594
Period size: 106 Copynumber: 3.6 Consensus size: 108
59490398 CAAAAAAAAA
59490408 TTTTGCTCTCTAAAAATACGAGTTTTAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGC
1 TTTTGCTCTCTAAAAATACGAGTTTT-AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGC
59490473 ACCCAGTACAACAAAAAAAAATTCGAATTTTTTTTCAAAATTTTT
65 ACCCAGTACAAC-AAAAAAAATTCGAATTTTTTTTCAAAATTTTT
*
59490518 TTTTGCTCTCTAAAAATACGAGTTTT-AAAAAAAAATTT-GGTGCTGGCTTGTCAATGGCCGGCA
1 TTTTGCTCTCTAAAAATACGAGTTTTAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCA
59490581 CCCAGTACAACAAAAAAAA-TCGAATTTTTTTTTC-AAA-TTTT
66 CCCAGTACAACAAAAAAAATTCGAA-TTTTTTTTCAAAATTTTT
* * * *
59490622 TTTTGCTCTTTAAAAATACGAATTTTAAAAAAAAAAATTTGGGTGGTGGCCTGTCAAT-GCCGAC
1 TTTTGCTCTCTAAAAATACGAGTTTT-AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGC
*
59490686 ACCCAGTACAACAAAAAAAATTTGAATTTTTTTTCAAAATTTTTT
65 ACCCAGTACAACAAAAAAAATTCGAATTTTTTTTCAAAA-TTTTT
* * *
59490731 TTTTGCTCTCTAAAAATACGAG-TTT-AAAAAAAAATTTGAGTGCTGCCCTGTCATTGGCCGGCA
1 TTTTGCTCTCTAAAAATACGAGTTTTAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCA
59490794 CC
66 CC
59490796 AAACCTTATA
Statistics
Matches: 255, Mismatches: 14, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
104 28 0.11
105 8 0.03
106 89 0.35
107 65 0.25
108 15 0.06
109 24 0.09
110 26 0.10
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (108 bp):
TTTTGCTCTCTAAAAATACGAGTTTTAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCA
CCCAGTACAACAAAAAAAATTCGAATTTTTTTTCAAAATTTTT
Found at i:59490791 original size:213 final size:214
Alignment explanation
Indices: 59490408--59490795 Score: 665
Period size: 213 Copynumber: 1.8 Consensus size: 214
59490398 CAAAAAAAAA
* *
59490408 TTTTGCTCTCTAAAAATACGAGTTTTAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGC
1 TTTTGCTCTCTAAAAATACGAATTTTAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGAC
59490473 ACCCAGTACAACAAAAAAAAATTCGAATTTTTTTTCAAAATTTTTTTTTGCTCTCTAAAAATACG
66 ACCCAGTACAACAAAAAAAAATTCGAATTTTTTTTCAAAATTTTTTTTTGCTCTCTAAAAATACG
* *
59490538 AGTTTTAAAAAAAAATTTGGTGCTGGCTTGTCAATGGCCGGCACCCAGTACAACAAAAAAAATCG
131 AGTTTTAAAAAAAAATTTGGTGCTGCCCTGTCAATGGCCGGCACCCAGTACAACAAAAAAAATCG
59490603 AATTTTTTTTTCAAATTTT
196 AATTTTTTTTTCAAATTTT
* *
59490622 TTTTGCTCTTTAAAAATACGAATTTTAAAAAAAAAAATTTGGGTGGTGGCCTGTCAAT-GCCGAC
1 TTTTGCTCTCTAAAAATACGAATTTTAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGAC
*
59490686 ACCCAGTACAAC-AAAAAAAATTTGAATTTTTTTTCAAAATTTTTTTTTTGCTCTCTAAAAATAC
66 ACCCAGTACAACAAAAAAAAATTCGAATTTTTTTTCAAAA-TTTTTTTTTGCTCTCTAAAAATAC
*
59490750 GAG-TTTAAAAAAAAATTTGAGTGCTGCCCTGTCATTGGCCGGCACC
130 GAGTTTTAAAAAAAAATTTG-GTGCTGCCCTGTCAATGGCCGGCACC
59490796 AAACCTTATA
Statistics
Matches: 164, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
212 42 0.26
213 67 0.41
214 55 0.34
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (214 bp):
TTTTGCTCTCTAAAAATACGAATTTTAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGAC
ACCCAGTACAACAAAAAAAAATTCGAATTTTTTTTCAAAATTTTTTTTTGCTCTCTAAAAATACG
AGTTTTAAAAAAAAATTTGGTGCTGCCCTGTCAATGGCCGGCACCCAGTACAACAAAAAAAATCG
AATTTTTTTTTCAAATTTT
Found at i:59492129 original size:53 final size:53
Alignment explanation
Indices: 59491988--59492138 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
59491978 GTAAGTGTGC
* **
59491988 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
59492041 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
59492094 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
59492139 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:59493952 original size:31 final size:31
Alignment explanation
Indices: 59493900--59493980 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
59493890 AATATTAAAA
* ** *
59493900 AACAGAATAATTTCATTATAAAAG-AAATATT
1 AACAGAATAATTTTAAAAT-AAAGTAAAAATT
*
59493931 TACAGAATAATTTTAAAATAAAGTAAAAATT
1 AACAGAATAATTTTAAAATAAAGTAAAAATT
* *
59493962 AACAGAAAAAATTTAAAAT
1 AACAGAATAATTTTAAAAT
59493981 TGTTGCGATC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 4 0.10
31 37 0.90
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30
Consensus pattern (31 bp):
AACAGAATAATTTTAAAATAAAGTAAAAATT
Found at i:59496185 original size:109 final size:110
Alignment explanation
Indices: 59495961--59496234 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 110
59495951 TCATAAATTT
*
59495961 GGTGCCGGCCATTGACAGGCCAGCACCC-AAATTTTTTTTTAAACTCGTATTTTTAGAGAGCAAA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTAAAACTCGTATTTTTAGAGAGC-AA
*
59496025 AAAAAAAAATTTTGAAAAAAAATTTGAATTTTTTTTTGTTGTACTG
65 AAAAAAAAATTTTGAAAAAAAATTTGAAATTTTTTTTGTTGTACTG
*
59496071 GGTGCCGGCCATTGACAAGCCAGCACCCAAAATTTTTTTTAAAACTCGTATTTTTAGAGAGC-AA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTAAAACTCGTATTTTTAGAGAGCAAA
59496135 AAAAAAAATTTTG-AAAAAAATTTCGAAATTTTTTTTGTTGTACTG
66 AAAAAAAATTTTGAAAAAAAATTT-GAAATTTTTTTTGTTGTACTG
**
59496180 GGTGCCGGCCATTGACAGGCCAGCACCCAATTTTTTTTTTTAAAACTCGTATTTT
1 GGTGCCGGCCATTGACAGGCCAGCACCCAA-AATTTTTTTTAAAACTCGTATTTT
59496235 GTATACCAAT
Statistics
Matches: 155, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
108 10 0.06
109 64 0.41
110 49 0.32
111 32 0.21
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (110 bp):
GGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTAAAACTCGTATTTTTAGAGAGCAAA
AAAAAAAATTTTGAAAAAAAATTTGAAATTTTTTTTGTTGTACTG
Found at i:59498220 original size:24 final size:22
Alignment explanation
Indices: 59498168--59498222 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
59498158 ATTTTACTTG
*
59498168 TTTATTTTTTAAATTTATTAAA
1 TTTATATTTTAAATTTATTAAA
* *
59498190 TAATATATTTTATAATTTTTTAAAA
1 T-TTATATTTTA-AATTTATT-AAA
59498215 TTTATATT
1 TTTATATT
59498223 ATGAGAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 8 0.31
24 13 0.50
25 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTATATTTTAAATTTATTAAA
Found at i:59502962 original size:24 final size:24
Alignment explanation
Indices: 59502907--59502962 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
59502897 GAATTATAAA
59502907 ATATAT-AAAATATGTACATATAT
1 ATATATAAAAATATGTACATATAT
* **
59502930 ATATGTAAAAATATGTATTTATAT
1 ATATATAAAAATATGTACATATAT
*
59502954 ATTTATAAA
1 ATATATAAA
59502963 GGTTAGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (24 bp):
ATATATAAAAATATGTACATATAT
Found at i:59504910 original size:22 final size:22
Alignment explanation
Indices: 59504880--59504927 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
59504870 TTAATAAAAC
59504880 ACATGCAAAATTATAAATAAAT
1 ACATGCAAAATTATAAATAAAT
*
59504902 ACATTCAAAATTATAAATAAAT
1 ACATGCAAAATTATAAATAAAT
59504924 ACAT
1 ACAT
59504928 ACTTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.29
Consensus pattern (22 bp):
ACATGCAAAATTATAAATAAAT
Found at i:59505521 original size:20 final size:20
Alignment explanation
Indices: 59505498--59505535 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59505488 TTGTTTTACG
*
59505498 TATAAGATTATTATTTTATT
1 TATAAAATTATTATTTTATT
*
59505518 TATAAAATTTTTATTTTA
1 TATAAAATTATTATTTTA
59505536 AGAAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TATAAAATTATTATTTTATT
Found at i:59505681 original size:7 final size:7
Alignment explanation
Indices: 59505665--59505698 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
59505655 TTTTAAATAA
59505665 TTTT-AT
1 TTTTAAT
59505671 TTTTAAT
1 TTTTAAT
*
59505678 TTTTAAA
1 TTTTAAT
59505685 TTTTAAT
1 TTTTAAT
59505692 TTTTAAT
1 TTTTAAT
59505699 AATCAAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:59518326 original size:21 final size:21
Alignment explanation
Indices: 59518300--59518340 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59518290 AGACAAGCGA
* *
59518300 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
59518321 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
59518341 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:59520027 original size:46 final size:44
Alignment explanation
Indices: 59519923--59520030 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
59519913 TGTCTTTGAC
** * * *
59519923 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
59519967 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
59520013 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
59520031 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:59520925 original size:16 final size:16
Alignment explanation
Indices: 59520906--59520938 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59520896 TTCTATTCTG
*
59520906 TTTCTTTTCTTTCTTT
1 TTTCTATTCTTTCTTT
59520922 TTTCTATTCTTTCTTT
1 TTTCTATTCTTTCTTT
59520938 T
1 T
59520939 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTATTCTTTCTTT
Found at i:59520960 original size:5 final size:5
Alignment explanation
Indices: 59520947--59521019 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
59520937 TTGTTTTATG
59520947 TATACA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
59520995 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
59521020 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:59520983 original size:19 final size:18
Alignment explanation
Indices: 59520955--59520990 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
59520945 TGTATACATA
59520955 TAATATAATATAATATAT
1 TAATATAATATAATATAT
59520973 TAATAATAATATAATATA
1 TAAT-ATAATATAATATA
59520991 AAAACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATAATATAATATAT
Found at i:59521000 original size:24 final size:25
Alignment explanation
Indices: 59520954--59521018 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
59520944 ATGTATACAT
* *
59520954 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
59520978 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
59521003 TTACTATAATATAATA
1 ATAATATAATATAATA
59521019 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:59523019 original size:26 final size:26
Alignment explanation
Indices: 59522983--59523035 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
59522973 CTCCCAAAAG
**
59522983 AAAGAATTTTTTTTTATCATCCTTTA
1 AAAGAATTTTTTTCAATCATCCTTTA
59523009 AAAGAATTTTTTTCAATCATCCTTTA
1 AAAGAATTTTTTTCAATCATCCTTTA
59523035 A
1 A
59523036 TTCTTGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (26 bp):
AAAGAATTTTTTTCAATCATCCTTTA
Found at i:59524848 original size:18 final size:18
Alignment explanation
Indices: 59524825--59524869 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
59524815 TTACTAAAAT
*
59524825 AATTATTGTTTAAAATTA
1 AATTATTATTTAAAATTA
59524843 AATTATTATTTAAAATTA
1 AATTATTATTTAAAATTA
59524861 AATTATTAT
1 AATTATTAT
59524870 ATTTCTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATTATTATTTAAAATTA
Found at i:59526095 original size:16 final size:18
Alignment explanation
Indices: 59526056--59526089 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59526046 TAAGTTTATA
59526056 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
59526073 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
59526090 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:59528728 original size:21 final size:22
Alignment explanation
Indices: 59528702--59528748 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
59528692 CTCTGCTCAA
*
59528702 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
59528723 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
59528745 ACTC
1 ACTC
59528749 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:59533372 original size:13 final size:13
Alignment explanation
Indices: 59533356--59533388 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
59533346 TCTCAAAAGT
59533356 ACTTTTCCATAGC
1 ACTTTTCCATAGC
59533369 ACTTTTCCATAGC
1 ACTTTTCCATAGC
59533382 ACTTTTC
1 ACTTTTC
59533389 AAAAGCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.30, G:0.06, T:0.42
Consensus pattern (13 bp):
ACTTTTCCATAGC
Found at i:59533395 original size:13 final size:13
Alignment explanation
Indices: 59533330--59533395 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
59533320 TTTAAACCAA
*
59533330 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
*
59533343 A-TTTCTCAAAAGT
1 ACTTT-TCAAAAGC
* *
59533356 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
* *
59533369 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
59533382 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
59533395 A
1 A
59533396 TTGTCAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.07
13 38 0.86
14 3 0.07
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:59535980 original size:33 final size:33
Alignment explanation
Indices: 59535938--59536010 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
59535928 ACTCTGTTTA
*
59535938 GTGTGTTGGT-TGGATTAGCTCTTATGAGCATTG
1 GTGTGTTGGTCT-GATTAACTCTTATGAGCATTG
59535971 GTGTGTTGGTCTGATTAACTCTTATGAGCATTG
1 GTGTGTTGGTCTGATTAACTCTTATGAGCATTG
59536004 GTGTGTT
1 GTGTGTT
59536011 AGAGGGATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 37 0.97
34 1 0.03
ACGTcount: A:0.15, C:0.10, G:0.32, T:0.44
Consensus pattern (33 bp):
GTGTGTTGGTCTGATTAACTCTTATGAGCATTG
Found at i:59543298 original size:19 final size:19
Alignment explanation
Indices: 59543274--59543311 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
59543264 CTCTCAACAT
59543274 GTTAATTAATTTTATTAAA
1 GTTAATTAATTTTATTAAA
59543293 GTTAATTAATTTTATTAAA
1 GTTAATTAATTTTATTAAA
59543312 CACTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
GTTAATTAATTTTATTAAA
Found at i:59549999 original size:60 final size:60
Alignment explanation
Indices: 59549904--59550116 Score: 313
Period size: 60 Copynumber: 3.6 Consensus size: 60
59549894 GTCGCTTAAA
* *
59549904 TATTAGTAAATTTCTTTTTTGATCACTCAACTATGAATAGTTACAAAATGATCACTCAAC
1 TATTAGTCAATTTCTTTTTTGATCACCCAACTATGAATAGTTACAAAATGATCACTCAAC
* * *
59549964 TATTAGTCAATTTCTTTTTTGATCACCCAATTATGAATAGTTACAAAAT-AGTCACCCAAT
1 TATTAGTCAATTTCTTTTTTGATCACCCAACTATGAATAGTTACAAAATGA-TCACTCAAC
* * * *
59550024 TATTAGTCAATTTCTTTTTTGGTCACCCAGCTATGAATAGTTACAAAATGGTCACTGAAC
1 TATTAGTCAATTTCTTTTTTGATCACCCAACTATGAATAGTTACAAAATGATCACTCAAC
*
59550084 TATTAGTCAATTTTTTTTTTG-TCACCCAACTAT
1 TATTAGTCAATTTCTTTTTTGATCACCCAACTAT
59550117 CTTGGATTTT
Statistics
Matches: 137, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
59 12 0.09
60 125 0.91
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (60 bp):
TATTAGTCAATTTCTTTTTTGATCACCCAACTATGAATAGTTACAAAATGATCACTCAAC
Found at i:59569466 original size:20 final size:20
Alignment explanation
Indices: 59569441--59569486 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
59569431 TGTTCAAATG
59569441 ATTAACCGAA-TGAAACTAGT
1 ATTAACCGAATTG-AACTAGT
59569461 ATTAACCGAATTGAACTAGT
1 ATTAACCGAATTGAACTAGT
59569481 ATTAAC
1 ATTAAC
59569487 TGAACTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTAACCGAATTGAACTAGT
Found at i:59571621 original size:14 final size:14
Alignment explanation
Indices: 59571602--59571629 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59571592 GACATCAAAC
59571602 GCAAATAAAGTAAT
1 GCAAATAAAGTAAT
59571616 GCAAATAAAGTAAT
1 GCAAATAAAGTAAT
59571630 AAAGCGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
GCAAATAAAGTAAT
Found at i:59579488 original size:17 final size:17
Alignment explanation
Indices: 59579466--59579500 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
59579456 GACCCTCTTA
59579466 GTTGCGCAATCCAAACT
1 GTTGCGCAATCCAAACT
59579483 GTTGCGCAATCCAAACT
1 GTTGCGCAATCCAAACT
59579500 G
1 G
59579501 ACTCGGTACT
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:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (17 bp):
GTTGCGCAATCCAAACT
Found at i:59580215 original size:5 final size:6
Alignment explanation
Indices: 59580179--59580248 Score: 79
Period size: 6 Copynumber: 11.2 Consensus size: 6
59580169 CAACCCAATC
*
59580179 ATAAAA ATTAAAA A-AAAA TTAATAA ATAAAA ATAAAA ATAAAA ATTTAAAA
1 ATAAAA A-TAAAA ATAAAA ATAA-AA ATAAAA ATAAAA ATAAAA A--TAAAA
*
59580230 CTAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA A
59580249 ACATATAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
5 4 0.07
6 35 0.64
7 11 0.20
8 5 0.09
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (6 bp):
ATAAAA
Found at i:59580221 original size:26 final size:26
Alignment explanation
Indices: 59580179--59580248 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
59580169 CAACCCAATC
*
59580179 ATAAAAATTAAAA-AAAAA-TTAATAA
1 ATAAAAATAAAAATAAAAATTTAA-AA
59580204 ATAAAAATAAAAATAAAAATTTAAAA
1 ATAAAAATAAAAATAAAAATTTAAAA
*
59580230 CTAAAAATAAAAATAAAAA
1 ATAAAAATAAAAATAAAAA
59580249 ACATATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.29
26 25 0.61
27 4 0.10
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (26 bp):
ATAAAAATAAAAATAAAAATTTAAAA
Found at i:59580286 original size:9 final size:9
Alignment explanation
Indices: 59580268--59580362 Score: 118
Period size: 9 Copynumber: 10.6 Consensus size: 9
59580258 TTTATACAAA
*
59580268 TAATTTGGT
1 TAATTCGGT
59580277 TAATTCGGT
1 TAATTCGGT
59580286 TAATTCGGT
1 TAATTCGGT
* *
59580295 TAATTTGGG
1 TAATTCGGT
*
59580304 TAATTCGGG
1 TAATTCGGT
*
59580313 TAATTCGGG
1 TAATTCGGT
*
59580322 TAATTCTGT
1 TAATTCGGT
*
59580331 TAATTCGAT
1 TAATTCGGT
*
59580340 TAATTAGGT
1 TAATTCGGT
59580349 TAATTCGGT
1 TAATTCGGT
59580358 TAATT
1 TAATT
59580363 TTATACTTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 75 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (9 bp):
TAATTCGGT
Found at i:59584116 original size:7 final size:7
Alignment explanation
Indices: 59584104--59584133 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
59584094 CAATTCTCTA
59584104 TCAAGAT
1 TCAAGAT
59584111 TCAAGAT
1 TCAAGAT
59584118 TCAAGAT
1 TCAAGAT
59584125 TCAAGAT
1 TCAAGAT
59584132 TC
1 TC
59584134 CAAACTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (7 bp):
TCAAGAT
Found at i:59589046 original size:30 final size:30
Alignment explanation
Indices: 59588990--59589046 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
59588980 CATAGGCTGG
* * *
59588990 CACATGGGCGTGTGGCCAGTCTGTGTGGCT
1 CACACGGGCGTGTGGCCAGCCCGTGTGGCT
59589020 CACACGGGCGTGT-GCCAAGCCCGTGTG
1 CACACGGGCGTGTGGCC-AGCCCGTGTG
59589047 AAAATGTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.12, C:0.28, G:0.39, T:0.21
Consensus pattern (30 bp):
CACACGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:59590617 original size:13 final size:13
Alignment explanation
Indices: 59590599--59590641 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
59590589 GTGCAAATTA
*
59590599 AAAGAAAAAGAAG
1 AAAGAAAAAAAAG
59590612 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
59590625 AAA-AATAAATAAAG
1 AAAGAA-AAA-AAAG
59590639 AAA
1 AAA
59590642 AGAAGGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 2 0.07
13 18 0.67
14 7 0.26
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:59590642 original size:22 final size:22
Alignment explanation
Indices: 59590598--59590642 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
59590588 CGTGCAAATT
*
59590598 AAAAGAAAAAGAAGAAAGAAAA
1 AAAAGAAAAAAAAGAAAGAAAA
*
59590620 AAAAGAAAAATAAATAAAGAAAA
1 AAAAGAAAAA-AAAGAAAGAAAA
59590643 GAAGGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAAAAAGAAAGAAAA
Found at i:59607960 original size:70 final size:71
Alignment explanation
Indices: 59607886--59608076 Score: 219
Period size: 70 Copynumber: 2.7 Consensus size: 71
59607876 TAATGTTGCG
* *
59607886 AAGTTTAGAATCGGCCCTCCTCTAGTCACGTTGAAGTTGCAAAAGTTCTTCCCTT-CATGTTGAA
1 AAGTTTAGAATAGGCCCTCCTCTAGTCATGTTGAAGTTGCAAAAGTTCTTCCCTTCCATGTTGAA
59607950 GTTACA
66 GTTACA
* ** *
59607956 AAG-TTCGAGATAGGTTCTCCTCTCA-TCATGTTGAAGTTGCAAAAGTTCTT-TCTTCCATGTTG
1 AAGTTTAGA-ATAGGCCCTCCTCT-AGTCATGTTGAAGTTGCAAAAGTTCTTCCCTTCCATGTTG
* *
59608018 ATGTTGCA
64 AAGTTACA
** * * *
59608026 AAGTTCGGAATGGGCCCTCCTCTAGCCATGTTGAAGTTGCAAAAGCTCTTC
1 AAGTTTAGAATAGGCCCTCCTCTAGTCATGTTGAAGTTGCAAAAGTTCTTC
59608077 TCGCCATTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
69 8 0.08
70 88 0.88
71 4 0.04
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (71 bp):
AAGTTTAGAATAGGCCCTCCTCTAGTCATGTTGAAGTTGCAAAAGTTCTTCCCTTCCATGTTGAA
GTTACA
Found at i:59608223 original size:42 final size:43
Alignment explanation
Indices: 59608177--59608283 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
59608167 GTCTCTACCT
*
59608177 TACCATGTCGATGTTAAAAAAAAAAAGAATTGA-TCTCCATTG
1 TACCATGTCGATGTTAAAAAAAAAAAGAATTAATTCTCCATTG
* * * **
59608219 TACCATGTTGATGTTGAAAAAAAATAAGGATTAATTCTCTGTTG
1 TACCATGTCGATGTT-AAAAAAAAAAAGAATTAATTCTCCATTG
* *
59608263 TACCACGTCGATGTTGAAAAA
1 TACCATGTCGATGTTAAAAAA
59608284 TCGAAATTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
42 14 0.26
43 20 0.37
44 20 0.37
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (43 bp):
TACCATGTCGATGTTAAAAAAAAAAAGAATTAATTCTCCATTG
Found at i:59608241 original size:44 final size:44
Alignment explanation
Indices: 59608177--59608283 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
59608167 GTCTCTACCT
*
59608177 TACCATGTCGATGTT-AAAAAAAAAAAGAATTGA-TCTCCATTG
1 TACCATGTCGATGTTGAAAAAAAAAAAGAATTAATTCTCCATTG
* * * **
59608219 TACCATGTTGATGTTGAAAAAAAATAAGGATTAATTCTCTGTTG
1 TACCATGTCGATGTTGAAAAAAAAAAAGAATTAATTCTCCATTG
*
59608263 TACCACGTCGATGTTGAAAAA
1 TACCATGTCGATGTTGAAAAA
59608284 TCGAAATTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 14 0.25
43 15 0.27
44 26 0.47
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (44 bp):
TACCATGTCGATGTTGAAAAAAAAAAAGAATTAATTCTCCATTG
Found at i:59608542 original size:14 final size:15
Alignment explanation
Indices: 59608514--59608546 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
59608504 TGATGAGACT
*
59608514 AAAAAAATGACCAAA
1 AAAAAAAGGACCAAA
59608529 AAAAAAAGGA-CAAA
1 AAAAAAAGGACCAAA
59608543 AAAA
1 AAAA
59608547 GCGCAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.03
Consensus pattern (15 bp):
AAAAAAAGGACCAAA
Found at i:59611235 original size:17 final size:18
Alignment explanation
Indices: 59611199--59611235 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
59611189 TTCATAATGT
59611199 AATAGGAAAACATCACAAA
1 AATAGGAAAACA-CACAAA
59611218 AATAGGAAAACA-ACAAA
1 AATAGGAAAACACACAAA
59611235 A
1 A
59611236 CATAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.14, G:0.11, T:0.08
Consensus pattern (18 bp):
AATAGGAAAACACACAAA
Done.