Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004973.1 Hibiscus syriacus cultivar Beakdansim tig00011168_pilon, 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: 108597
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:563 original size:4 final size:4
Alignment explanation
Indices: 554--592 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
544 AATTGTTTAC
554 TATT TATT TATT TA-T TATT TATT TATT TA-T TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT T
593 TTTTTGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.18
4 27 0.82
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:572 original size:15 final size:15
Alignment explanation
Indices: 549--592 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
539 ATTTAAATTG
*
549 TTTACTATTTATTTA
1 TTTATTATTTATTTA
564 TTTATTATTTATTTA
1 TTTATTATTTATTTA
579 TTTATTATTTATTT
1 TTTATTATTTATTT
593 TTTTTGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:592 original size:11 final size:11
Alignment explanation
Indices: 557--591 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
547 TGTTTACTAT
557 TTATTTATTTA
1 TTATTTATTTA
568 TTATTTATTTA
1 TTATTTATTTA
579 TT-TATTATTTA
1 TTAT-TTATTTA
590 TT
1 TT
592 TTTTTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 1 0.04
11 22 0.96
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:820 original size:56 final size:56
Alignment explanation
Indices: 754--860 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
744 TAGGTGCAAC
* *
754 TGCTTTTACATTTACTG-TTTTTCATTAATTATCATGAATTTCAACAAGCATGTTAT
1 TGCTTTTACATTTACTGCTTTTTCA-TAATTATCATAAATTGCAACAAGCATGTTAT
* * *
810 TGCTTTTACATTTACTGCTTTTTGATAATTTTCATAAATTGCAGCAAGCAT
1 TGCTTTTACATTTACTGCTTTTTCATAATTATCATAAATTGCAACAAGCAT
861 ATAAATGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 39 0.87
57 6 0.13
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (56 bp):
TGCTTTTACATTTACTGCTTTTTCATAATTATCATAAATTGCAACAAGCATGTTAT
Found at i:1789 original size:15 final size:15
Alignment explanation
Indices: 1713--1789 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
1703 GTCTTTTATC
1713 CACATAGAACACTTT
1 CACATAGAACACTTT
** * *
1728 TGCATAGAGCATTTT
1 CACATAGAACACTTT
* **
1743 CACGTAGAACACAGT
1 CACATAGAACACTTT
1758 CACATA-AAGCACTTT
1 CACATAGAA-CACTTT
*
1773 CACATAGAACACATT
1 CACATAGAACACTTT
1788 CA
1 CA
1790 TATATAATAA
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:3535 original size:24 final size:24
Alignment explanation
Indices: 3459--3567 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
3449 AAACGGAGAT
*
3459 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
3483 ATCAGATATCATAATAGAA-TCTAG
1 ATCAGAAATCAGAACAGAATTC-AG
*
3507 ATCATAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
3531 GTCATG-TATCAGAACATAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
3554 AGTAAGAAATCAGA
1 A-TCAGAAATCAGA
3568 TAAAATATTC
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
23 3 0.05
24 61 0.92
25 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:8305 original size:17 final size:18
Alignment explanation
Indices: 8283--8321 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
8273 TTTTATTAAT
8283 ATTTATGTATG-TGTGGC
1 ATTTATGTATGATGTGGC
*
8300 ATTTATGTATGATGTGGT
1 ATTTATGTATGATGTGGC
8318 ATTT
1 ATTT
8322 TTCTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:8552 original size:31 final size:31
Alignment explanation
Indices: 8517--8577 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
8507 TAAAGCAGAT
* *
8517 GGAATATTTGTTTTATTT-AATTATAATTTTG
1 GGAATATTTATTTGATTTCAA-TATAATTTTG
*
8548 GGAATGTTTATTTGATTTCAATATAATTTT
1 GGAATATTTATTTGATTTCAATATAATTTT
8578 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.56
Consensus pattern (31 bp):
GGAATATTTATTTGATTTCAATATAATTTTG
Found at i:11292 original size:29 final size:29
Alignment explanation
Indices: 11255--11407 Score: 168
Period size: 29 Copynumber: 5.3 Consensus size: 29
11245 CATTTTACAG
* * *
11255 AAATGGCACCATTTTTAAAATAATTACCA
1 AAATAGCACCATTTTTGAATTAATTACCA
* * *
11284 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTACCA
*
11313 AAATAGCACCATTTTTGAATTAATT-CCC
1 AAATAGCACCATTTTTGAATTAATTACCA
* *
11341 AAATATCACCA-TTTTGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTACCA
* *
11369 AAATAGCACC-TATTTCGAATAAATTACCA
1 AAATAGCACCAT-TTTTGAATTAATTACCA
*
11398 AAATACCACC
1 AAATAGCACC
11408 CGGTCAACGT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
27 13 0.12
28 23 0.22
29 69 0.66
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCATTTTTGAATTAATTACCA
Found at i:11376 original size:56 final size:58
Alignment explanation
Indices: 11255--11407 Score: 186
Period size: 56 Copynumber: 2.7 Consensus size: 58
11245 CATTTTACAG
* *
11255 AAATGGCACCATTTTTAAAATAATTACCAAAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTTAAAATAATTACCAAAATAGCACCATTTTCGAATTAATTCCCA
* * * *
11313 AAATAGCACCATTTTTGAATTAATT-CCCAAATATCACCATTTT-GAATTAATTCCCA
1 AAATAGCACCATTTTTAAAATAATTACCAAAATAGCACCATTTTCGAATTAATTCCCA
* ** *
11369 AAATAGCACC-TATTTCGAATAAATTACCAAAATACCACC
1 AAATAGCACCATTTTTAAAAT-AATTACCAAAATAGCACC
11408 CGGTCAACGT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
55 6 0.07
56 27 0.33
57 26 0.32
58 22 0.27
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.31
Consensus pattern (58 bp):
AAATAGCACCATTTTTAAAATAATTACCAAAATAGCACCATTTTCGAATTAATTCCCA
Found at i:12684 original size:4 final size:4
Alignment explanation
Indices: 12670--12700 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
12660 ATTTAAATTG
*
12670 TTTA CTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
12701 TTTGCTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:12925 original size:57 final size:57
Alignment explanation
Indices: 12863--12971 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
12853 GGGGTGCAAC
*
12863 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATGAATTTCAGCAAGCATGTTAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
*
12920 TGCTTTTACATTTACTGCTTTTTGATTAATTTTCATAAATTTCAGCAAGCAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCAT
12972 ATAAATGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.49
Consensus pattern (57 bp):
TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
Found at i:13721 original size:25 final size:25
Alignment explanation
Indices: 13679--13729 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
13669 AACCGCACAG
13679 AATTTGTCTCGAAGGACCACGTAGA
1 AATTTGTCTCGAAGGACCACGTAGA
* *
13704 AATTTGTC-CTGAATGACCGCGTAGA
1 AATTTGTCTC-GAAGGACCACGTAGA
13729 A
1 A
13730 CCCTCGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
AATTTGTCTCGAAGGACCACGTAGA
Found at i:13908 original size:15 final size:15
Alignment explanation
Indices: 13832--13908 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
13822 GTTCTTTATC
13832 CACATAGAACACTTT
1 CACATAGAACACTTT
** * *
13847 TGCATAGAGCATTTT
1 CACATAGAACACTTT
* **
13862 CACGTAGAACACAGT
1 CACATAGAACACTTT
13877 CACATA-AAGCACTTT
1 CACATAGAA-CACTTT
*
13892 CACATAGAACACATT
1 CACATAGAACACTTT
13907 CA
1 CA
13909 TATATTAACA
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:15617 original size:24 final size:25
Alignment explanation
Indices: 15590--15659 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 25
15580 AAACGGAGAT
15590 ATCAGAAATCAAAACAGAATTCT-G
1 ATCAGAAATCAAAACAGAATTCTAG
* * *
15614 ATCAGATATCATAATAGAA-TCTAG
1 ATCAGAAATCAAAACAGAATTCTAG
* * *
15638 ATCATAAATCAGAACATAATTC
1 ATCAGAAATCAAAACAGAATTC
15660 AGGTCATGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 3 0.08
24 31 0.86
25 2 0.06
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.26
Consensus pattern (25 bp):
ATCAGAAATCAAAACAGAATTCTAG
Found at i:15666 original size:24 final size:24
Alignment explanation
Indices: 15639--15698 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
15629 AGAATCTAGA
*
15639 TCATAAATCAGAACATAATTCAGG
1 TCATAAATCAGAACATAATTCAAG
** *
15663 TCATGTATCATAACATAATTCAAG
1 TCATAAATCAGAACATAATTCAAG
*
15687 TCAGAAATCAGA
1 TCATAAATCAGA
15699 TAAAATATTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (24 bp):
TCATAAATCAGAACATAATTCAAG
Found at i:15695 original size:48 final size:48
Alignment explanation
Indices: 15590--15698 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
15580 AAACGGAGAT
* * * *
15590 ATCAGAAATCAAAACAGAATTCTGATCAGATATCATAATAGAATCTAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCATAACAGAATCAAG
* * * *
15638 ATCATAAATCAGAACATAATTCAGGTCATG-TATCATAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATCA-GATATCATAACAGAA-TCAAG
15687 -TCAGAAATCAGA
1 ATCAGAAATCAGA
15699 TAAAATATTC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCATAACAGAATCAAG
Found at i:20107 original size:17 final size:17
Alignment explanation
Indices: 20085--20134 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
20075 TAGTTTGCCC
20085 AAAATTTTAAAATAATA
1 AAAATTTTAAAATAATA
20102 AAAATTTTAAAAT-ATA
1 AAAATTTTAAAATAATA
*
20118 ATAAATATCTAAAATAA
1 A-AAAT-TTTAAAATAA
20135 GAAGATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.14
17 17 0.59
18 7 0.24
19 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTTTAAAATAATA
Found at i:20528 original size:17 final size:18
Alignment explanation
Indices: 20506--20544 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
20496 TTTTATTAAT
20506 ATTTATGTATG-TGTGGC
1 ATTTATGTATGATGTGGC
*
20523 ATTTATGTATGATGTGGT
1 ATTTATGTATGATGTGGC
20541 ATTT
1 ATTT
20545 TTCTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:20769 original size:30 final size:31
Alignment explanation
Indices: 20735--20794 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20725 TAAAGCAGAT
*
20735 GGAATATTT-TTTTATTT-AATTATAATTTTG
1 GGAATATTTATTTGATTTCAA-TATAATTTTG
*
20765 GGAATGTTTATTTGATTTCAATATAATTTT
1 GGAATATTTATTTGATTTCAATATAATTTT
20795 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 16 0.62
32 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.57
Consensus pattern (31 bp):
GGAATATTTATTTGATTTCAATATAATTTTG
Found at i:23517 original size:29 final size:29
Alignment explanation
Indices: 23480--23634 Score: 179
Period size: 29 Copynumber: 5.4 Consensus size: 29
23470 CATTTTACAG
* * * *
23480 AAATTGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* *
23509 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
23538 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* *
23567 AAATATCA-CCATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* * *
23595 AAATAGTA-CCTATTTCGAATAAATTCCCA
1 AAATAGCACCCT-TTTTGAATTAATTCCCA
23624 AAATAGCACCC
1 AAATAGCACCC
23635 GGTCAACGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
28 26 0.24
29 80 0.74
30 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCTTTTTGAATTAATTCCCA
Found at i:23611 original size:57 final size:58
Alignment explanation
Indices: 23480--23633 Score: 213
Period size: 57 Copynumber: 2.7 Consensus size: 58
23470 CATTTTACAG
* ** * *
23480 AAATTGCACCCTTTTTAAAATAATTACCAAAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCGAATTAATTCCCAAAATAGCACCATTTTCGAATTAATTCCCA
*
23538 AAATAGCACCCTTTTCGAATTAATTCCCAAAATATCACCATTTT-GAATTAATTCCCA
1 AAATAGCACCCTTTTCGAATTAATTCCCAAAATAGCACCATTTTCGAATTAATTCCCA
* *
23595 AAATAGTA-CCTATTTCGAATAAATTCCCAAAATAGCACC
1 AAATAGCACCCT-TTTCGAATTAATTCCCAAAATAGCACC
23634 CGGTCAACGG
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
56 3 0.03
57 45 0.52
58 38 0.44
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (58 bp):
AAATAGCACCCTTTTCGAATTAATTCCCAAAATAGCACCATTTTCGAATTAATTCCCA
Found at i:26000 original size:25 final size:25
Alignment explanation
Indices: 25958--26008 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
25948 AACCGCACAG
25958 AATTTGTCTCGAAGGACCACGTAGA
1 AATTTGTCTCGAAGGACCACGTAGA
* *
25983 AATTTGTC-CTGAATGACCGCGTAGA
1 AATTTGTCTC-GAAGGACCACGTAGA
26008 A
1 A
26009 CCCTCGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
AATTTGTCTCGAAGGACCACGTAGA
Found at i:26189 original size:15 final size:15
Alignment explanation
Indices: 26141--26189 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
26131 ATAAAGCATT
*
26141 TTCACGTAGAACACA
1 TTCACATAGAACACA
* *
26156 GTCACATA-AAGCACT
1 TTCACATAGAA-CACA
26171 TTCACATAGAACACA
1 TTCACATAGAACACA
26186 TTCA
1 TTCA
26190 TATATTAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.07
15 23 0.85
16 2 0.07
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (15 bp):
TTCACATAGAACACA
Found at i:28263 original size:17 final size:18
Alignment explanation
Indices: 28241--28279 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
28231 TTTTATTAAT
28241 ATTTATGTATG-TGTGGC
1 ATTTATGTATGATGTGGC
*
28258 ATTTATGTATGATGTGGT
1 ATTTATGTATGATGTGGC
28276 ATTT
1 ATTT
28280 TTCTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:28512 original size:31 final size:31
Alignment explanation
Indices: 28477--28537 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
28467 TAAAGCAGAT
*
28477 GGAATATTTTTTTAATTT-AATTATAATTTTG
1 GGAATATTTATTTAATTTCAA-TATAATTTTG
* *
28508 GGAATGTTTATTTGATTTCAATATAATTTT
1 GGAATATTTATTTAATTTCAATATAATTTT
28538 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (31 bp):
GGAATATTTATTTAATTTCAATATAATTTTG
Found at i:28851 original size:22 final size:22
Alignment explanation
Indices: 28823--28989 Score: 109
Period size: 22 Copynumber: 7.7 Consensus size: 22
28813 TATATGGCTT
28823 ATATATAGTTTATATTAATAAA
1 ATATATAGTTTATATTAATAAA
* *
28845 ATATATAATTTATAATT-AT-AC
1 ATATATAGTTTAT-ATTAATAAA
*
28866 ATAGTATA---TATATAAATATAA
1 ATA-TATAGTTTATATTAATA-AA
* **
28887 ATTATATAGTTTATATATAGT-TC
1 A-TATATAGTTTATAT-TAATAAA
28910 ATATATAGTTTATA-T-ATAAA
1 ATATATAGTTTATATTAATAAA
* *
28930 CTATATAATTTATATTAATAAA
1 ATATATAGTTTATATTAATAAA
* **
28952 TTATATAGTTTATA-TATATAGT
1 ATATATAGTTTATATTA-ATAAA
*
28974 ATATAGAGTTTATATT
1 ATATATAGTTTATATT
28990 TATATTATAT
Statistics
Matches: 111, Mismatches: 19, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
18 2 0.02
19 6 0.05
20 13 0.12
21 13 0.12
22 65 0.59
23 5 0.05
24 5 0.05
25 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
ATATATAGTTTATATTAATAAA
Found at i:28905 original size:11 final size:11
Alignment explanation
Indices: 28889--28988 Score: 73
Period size: 11 Copynumber: 9.3 Consensus size: 11
28879 AAATATAAAT
28889 TATATAGTTTA
1 TATATAGTTTA
*
28900 TATATAGTTCA
1 TATATAGTTTA
28911 TATATAGTTTA
1 TATATAGTTTA
***
28922 TATATAAACTA
1 TATATAGTTTA
28933 TATA-A-TTTA
1 TATATAGTTTA
* **
28942 TAT-TAATAAA
1 TATATAGTTTA
28952 TTATATAGTTTA
1 -TATATAGTTTA
*
28964 TATATA-TAGTA
1 TATATAGT-TTA
*
28975 TATAGAGTTTA
1 TATATAGTTTA
28986 TAT
1 TAT
28989 TTATATTATA
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
9 6 0.09
10 4 0.06
11 53 0.78
12 5 0.07
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:28993 original size:22 final size:22
Alignment explanation
Indices: 28777--29028 Score: 108
Period size: 22 Copynumber: 11.7 Consensus size: 22
28767 ATATATAAAC
*
28777 TATATAGTTTATACATAGTAGTA
1 TATATAGTTTATATATA-TAGTA
* * *
28800 TATA-AGTATAAATTATATGGCTTA
1 TATATAGTTTATA-TATATAG--TA
**
28824 TATATAGTTTATAT-TAATAAAA
1 TATATAGTTTATATAT-ATAGTA
*
28846 TATATAATTTATAATTATACATAGTA
1 TATATAGTTTAT-A-TAT--ATAGTA
* *
28872 TATATA---TAAATATA-AAT-
1 TATATAGTTTATATATATAGTA
28889 TATATAG-TT-TATATATAGTTCA
1 TATATAGTTTATATATATAG-T-A
* *
28911 TATATAGTTTATATATAAACTA
1 TATATAGTTTATATATATAGTA
*
28933 TATA-A-TTTATAT-TAATA-AA
1 TATATAGTTTATATAT-ATAGTA
28952 TTATATAGTTTATATATATAGTA
1 -TATATAGTTTATATATATAGTA
*
28975 TATAGAGTTTATAT-T-TA-TA
1 TATATAGTTTATATATATAGTA
*
28994 T-TATA-TTTATATATATACTA
1 TATATAGTTTATATATATAGTA
* **
29014 TGTATAAATTATATA
1 TATATAGTTTATATA
29029 GTTTATTAAT
Statistics
Matches: 176, Mismatches: 25, Indels: 57
0.68 0.10 0.22
Matches are distributed among these distances:
17 13 0.07
18 11 0.06
19 10 0.06
20 19 0.11
21 10 0.06
22 63 0.36
23 16 0.09
24 17 0.10
25 7 0.04
26 10 0.06
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (22 bp):
TATATAGTTTATATATATAGTA
Found at i:29053 original size:11 final size:11
Alignment explanation
Indices: 29001--29338 Score: 76
Period size: 11 Copynumber: 31.5 Consensus size: 11
28991 ATATTATATT
*
29001 TATATATATAC
1 TATATATAAAC
* *
29012 TATGTATAAAT
1 TATATATAAAC
** *
29023 TATATAGTTTAT
1 TATATA-TAAAC
29035 TA-ATATAAAC
1 TATATATAAAC
*
29045 TATATATAAGTC
1 TATATATAA-AC
* *
29057 ATATAGTTTATAC
1 -TATA-TATAAAC
*
29070 T-TATATACTAC
1 TATATATA-AAC
*
29081 TATGTATAAAC
1 TATATATAAAC
29092 TATATATAAA-
1 TATATATAAAC
29102 TCATATAT--AC
1 T-ATATATAAAC
*
29112 TATATATAAATTA
1 TATATATAAA--C
29125 TATATATAAAC
1 TATATATAAAC
29136 TA-A-ATAAA-
1 TATATATAAAC
***
29144 T-TATATAGTT
1 TATATATAAAC
* *
29154 TACATATGAAC
1 TATATATAAAC
29165 TATATATATAA-
1 TATATATA-AAC
*
29176 -ACTA-ATAGAC
1 TA-TATATAAAC
* *
29186 --TATAGAAAT
1 TATATATAAAC
29195 TATATATAAAC
1 TATATATAAAC
*
29206 TATTTATAAAC
1 TATATATAAAC
**
29217 TATATAGTTTATATT
1 TATATA---TA-AAC
*
29232 TATATATATAC
1 TATATATAAAC
29243 TATATAT--A-
1 TATATATAAAC
29251 -AT-TATAAA-
1 TATATATAAAC
* *
29259 T-TATATATAT
1 TATATATAAAC
* *
29269 TATGTATAAAT
1 TATATATAAAC
** *
29280 TATATAGTTTAT
1 TATATA-TAAAC
29292 TA-ATATAAAC
1 TATATATAAAC
29302 TATATATAAAC
1 TATATATAAAC
*
29313 CATATAT--AC
1 TATATATAAAC
*
29322 TATATGTAAAC
1 TATATATAAAC
29333 TATATA
1 TATATA
29339 GTATATATAG
Statistics
Matches: 236, Mismatches: 54, Indels: 74
0.65 0.15 0.20
Matches are distributed among these distances:
6 3 0.01
7 2 0.01
8 6 0.03
9 32 0.14
10 20 0.08
11 125 0.53
12 21 0.09
13 15 0.06
14 5 0.02
15 7 0.03
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (11 bp):
TATATATAAAC
Found at i:29134 original size:33 final size:34
Alignment explanation
Indices: 29004--29134 Score: 101
Period size: 33 Copynumber: 3.9 Consensus size: 34
28994 TTATATTTAT
* * *
29004 ATATATACTATGTATAAATTATATAGT-TTATTA
1 ATATATACTATATATAAATTATATAGTATAAATA
* * * * * *
29037 ATATAAACTATATATAAGTCATATAGTTTATACTT
1 ATATATACTATATATAAATTATATAGTATA-AATA
* * *
29072 ATATACTACTATGTATAAA--CTATA-TATAAATC
1 ATATA-TACTATATATAAATTATATAGTATAAATA
29104 ATATATACTATATATAAATTATATA-TATAAA
1 ATATATACTATATATAAATTATATAGTATAAA
29135 CTAAATAAAT
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
31 12 0.16
32 7 0.09
33 36 0.47
34 5 0.06
35 7 0.09
36 10 0.13
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (34 bp):
ATATATACTATATATAAATTATATAGTATAAATA
Found at i:29178 original size:13 final size:13
Alignment explanation
Indices: 29112--29250 Score: 70
Period size: 13 Copynumber: 10.5 Consensus size: 13
29102 TCATATATAC
*
29112 TATATATAAATTA
1 TATATATAAACTA
29125 TATATATAAACTAAA
1 TATATATAAACT--A
* * * *
29140 TAAATTATATAGTT
1 TATA-TATAAACTA
* *
29154 TACATATGAACTA
1 TATATATAAACTA
29167 TATATATAAACTAA
1 TATATATAAACT-A
* *
29181 TAGACTATAGAAAT-
1 TATA-TATA-AACTA
29195 TATATATAAACTA
1 TATATATAAACTA
29208 T-T-TATAAACTA
1 TATATATAAACTA
* * *
29219 TATAGTTTATA-TT
1 TATA-TATAAACTA
*
29232 TATATATATACTA
1 TATATATAAACTA
29245 TATATA
1 TATATA
29251 ATTATAAATT
Statistics
Matches: 94, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
11 10 0.11
12 10 0.11
13 43 0.46
14 14 0.15
15 8 0.09
16 9 0.10
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:29284 original size:63 final size:60
Alignment explanation
Indices: 29191--29310 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 60
29181 TAGACTATAG
* *
29191 AAATTATATATAAACTATTTATAAACTATATAGTTTATATTTATATATATACTATATATAATTAT
1 AAATTATATAT-AACTATGTATAAACTATATAG-TT-TA-TTA-ATATAAACTATATATAATTAT
* *
29256 AAATTATATAT-ATTATGTATAAATTATATAGTTTATTAATATAAACTATATATAA
1 AAATTATATATAACTATGTATAAACTATATAGTTTATTAATATAAACTATATATAA
29311 ACCATATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
59 16 0.31
60 3 0.06
61 2 0.04
62 2 0.04
63 17 0.33
65 11 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (60 bp):
AAATTATATATAACTATGTATAAACTATATAGTTTATTAATATAAACTATATATAATTAT
Found at i:29940 original size:23 final size:23
Alignment explanation
Indices: 29914--29957 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29904 ATATTATAAA
*
29914 GTATAATATATATATATGTGTGT
1 GTATAAGATATATATATGTGTGT
29937 GTATAAGATATATATATGTGT
1 GTATAAGATATATATATGTGT
29958 AGGACTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (23 bp):
GTATAAGATATATATATGTGTGT
Found at i:29950 original size:2 final size:2
Alignment explanation
Indices: 28845--29930 Score: 263
Period size: 2 Copynumber: 544.0 Consensus size: 2
28835 TATTAATAAA
* * *
28845 AT AT AT A- AT TT AT A- AT -T AT AC AT AGT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
28885 AA AT -T AT AT AGT TT AT AT AT AGT -T CAT AT AT AGT TT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT A-T AT -AT AT AT A-T AT AT AT AT
* * * *
28927 AA ACT AT AT A- AT TT AT AT -T A- AT AA AT -T AT AT AGT TT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
28967 AT AT AGT AT AT AG AGT TT AT AT TT AT AT -T AT AT TT AT AT AT AT
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
29010 ACT AT GT AT AA AT -T AT AT AGT TT AT -T A- AT AT AA ACT AT AT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT
* * *
29050 AT A- AGT CAT AT AGT TT AT ACT -T AT AT ACT ACT AT GT AT AA ACT
1 AT AT A-T -AT AT A-T AT AT A-T AT AT AT A-T A-T AT AT AT AT A-T
* * *
29093 AT AT AT AA AT CAT AT AT ACT AT AT AT AA AT -T AT AT AT AT AA ACT
1 AT AT AT AT AT -AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
29137 AA AT AA AT -T AT AT AGT TT AC AT AT GA- ACT AT AT AT AT AA ACT
1 AT AT AT AT AT AT AT A-T AT AT AT AT -AT A-T AT AT AT AT AT A-T
* * * * * *
29179 A- AT AG ACT AT AG AA AT -T AT AT AT AA ACT AT TT AT AA ACT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
* * *
29220 AT AGT TT AT AT TT AT AT AT AT ACT AT AT AT A- AT -T AT AA AT -T
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * *
29261 AT AT AT AT -T AT GT AT AA AT -T AT AT AGT TT AT -T A- AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * *
29300 ACT AT AT AT AA ACC AT AT AT ACT AT AT GT AA ACT AT AT AGT AT AT
1 A-T AT AT AT AT A-T AT AT AT A-T AT AT AT AT A-T AT AT A-T AT AT
* * * * *
29345 AT AGT TT AC AT AT GA- AC A- AT AT AT AT AA AT -T AT A- AA ACT
1 AT A-T AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
29384 AT AT ACT AT AGT TT AT AT TT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
29428 -T AT AGT TT TT GT TT AT AT A- AT AT AT AC AT A- AA AT AT AT AC
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29468 AT -T AT ACT -T AT AT A- AGT AT AT A- AT AT A- AGT GT AT A- AGT
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T
* * * * * *
29506 AT AT AT AT -T TT AA AT GT AT AT AT AT -T GT AT AT AT AT GT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
29546 ACT -T AT AT AA AC A- AT AC AT -T AT A- AGT AT AT A- AGT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT
* * * * * *
29584 AT CT AT AT AT AA AGT AT AT AT A- AA AGC AT AT A- AA AGC AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT A-T AT AT
29625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
29708 AG A- AGT AT AT A- AT AT AT AT AT AT AT AT A- AGT AT AC AT -T AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
29748 AC GT AT A- AGT AT A- AGT AT AT A- AT AT AA AT AT AT A- AGT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * * *
29787 AA AGT AC AT AT -T CAT AT GACT AA AT -T AA AT AT GT AT AA AT AT
1 AT A-T AT AT AT AT -AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
29829 AT AT AA AA AT AT AT A- AA AT GT AT A- AA AT AT -T AA AGT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
29868 AT AT -T AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29909 AT AA AGT AT A- AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT
29931 GTGTGTGTAT
Statistics
Matches: 786, Mismatches: 167, Indels: 262
0.65 0.14 0.22
Matches are distributed among these distances:
1 67 0.09
2 643 0.82
3 74 0.09
4 2 0.00
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:30855 original size:185 final size:182
Alignment explanation
Indices: 30547--30933 Score: 602
Period size: 185 Copynumber: 2.1 Consensus size: 182
30537 TTTTCTAACT
* * *
30547 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAATATTCTAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAATTCTAATTAATTTAAATAATATATAAT
* * *
30611 TTTAAAATAAAATTTTATAATTTTTTTAAATTAATTAATATTGATTTATGTTTAAAAGTTATTGG
66 TTTAAAAAAAAATTTTATAAATTTTTTAAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGG
* * *
30676 ATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGTCCATATGTTA
131 ATCTTAAATTATTAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTA
30728 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAATTAC-AATTAATTTAAATAATATAT-
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAA-AATT-CTAATTAATTTAAATAATATATA
30791 ATTTATAAATTAAAAAATTTATATAAATTTTTT-AATTAATTAATATTGATTTAGGTTTAAAAGT
64 ATTT-TAAA--AAAAAATTT-TATAAATTTTTTAAATTAATTAATATTGATTTAGGTTTAAAAGT
30855 TATTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTA
125 TATTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTA
*
30913 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
30934 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
181 7 0.04
182 30 0.16
183 27 0.14
184 1 0.01
185 113 0.60
186 11 0.06
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (182 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAATTCTAATTAATTTAAATAATATATAAT
TTTAAAAAAAAATTTTATAAATTTTTTAAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGG
ATCTTAAATTATTAATTGGGTTTTAAATGATTTAGGTTGAGCCCATATGTTA
Found at i:31162 original size:50 final size:50
Alignment explanation
Indices: 31104--31295 Score: 199
Period size: 49 Copynumber: 3.8 Consensus size: 50
31094 TGAACACCCC
* * *
31104 TAGATCTAACCCAAAAAATCATTGTTCATCTGGAAAAAAATCTTACTTTT
1 TAGATCTAACCCAAAAAATCACTGTTCATCTAGAAAAAAATCTTATTTTT
* * * * *
31154 TAGATCTAACCCAAAAAATTATTGTTCAT-AAAAAAAAAATCTCATTTTT
1 TAGATCTAACCCAAAAAATCACTGTTCATCTAGAAAAAAATCTTATTTTT
* * * *
31203 TATATCTAACCCAGAAAATCACTGTTCATCCAG-AAAATATCTCATATTTTTT
1 TAGATCTAACCCAAAAAATCACTGTTCATCTAGAAAAAAATCT--TA-TTTTT
* * *
31255 TAGATCTAACCCATGAATAGCACTGTTCATCTAGAAAAAAA
1 TAGATCTAACCCA-AAAAATCACTGTTCATCTAGAAAAAAA
31296 ATTTGTTAGT
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 48 0.41
50 29 0.25
51 1 0.01
52 17 0.15
53 17 0.15
54 5 0.04
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (50 bp):
TAGATCTAACCCAAAAAATCACTGTTCATCTAGAAAAAAATCTTATTTTT
Found at i:31362 original size:21 final size:21
Alignment explanation
Indices: 31298--31367 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
31288 GAAAAAAAAT
* *
31298 TTGTTAGTGACTCTTTGCCTA
1 TTGTTCGTGACTCTTTACCTA
*
31319 TTGTTCTTGA--C--TA-CTA
1 TTGTTCGTGACTCTTTACCTA
* *
31335 ATCTTCGTGACTCTTTACCTA
1 TTGTTCGTGACTCTTTACCTA
31356 TTGTTCGTGACT
1 TTGTTCGTGACT
31368 ACACATTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
16 10 0.28
17 1 0.03
18 1 0.03
19 1 0.03
20 2 0.06
21 21 0.58
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (21 bp):
TTGTTCGTGACTCTTTACCTA
Found at i:31619 original size:25 final size:25
Alignment explanation
Indices: 31573--31638 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
31563 AAAATATGTG
*
31573 TTTTATAATTTTATTT-TATTTTCTT
1 TTTTATAATTTT-TTTCTTTTTTCTT
* *
31598 TTTTATATGTTTTTTTCTTTTTTGTT
1 TTTTATA-ATTTTTTTCTTTTTTCTT
31624 TTTTATAATTTTTTT
1 TTTTATAATTTTTTT
31639 ATATTATGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 17 0.49
26 18 0.51
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (25 bp):
TTTTATAATTTTTTTCTTTTTTCTT
Found at i:31648 original size:25 final size:24
Alignment explanation
Indices: 31567--31668 Score: 82
Period size: 25 Copynumber: 4.1 Consensus size: 24
31557 AGGTAAAAAA
*
31567 TATGTGTTTTATAATTTTATTTTAT
1 TATGTTTTTTATAATTTT-TTTTAT
* * * *
31592 TTTCTTTTTTATATGTTTTTTTCTTT
1 TATGTTTTTTATA-ATTTTTTT-TAT
*
31618 TTTGTTTTTTATAATTTTTTTATAT
1 TATGTTTTTTATAATTTTTTT-TAT
*
31643 TATGTTTTGTAT--TTGTTTTTTAT
1 TATGTTTTTTATAATT-TTTTTTAT
31666 TAT
1 TAT
31669 TCATATTGTG
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
23 8 0.13
24 5 0.08
25 32 0.51
26 18 0.29
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.75
Consensus pattern (24 bp):
TATGTTTTTTATAATTTTTTTTAT
Found at i:31682 original size:21 final size:20
Alignment explanation
Indices: 31652--31690 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31642 TTATGTTTTG
*
31652 TATTTGTTTTTTATTATTCA
1 TATTTGTTTTGTATTATTCA
31672 TATTGTGTTTTGTATTATT
1 TATT-TGTTTTGTATTATT
31691 TTTTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (20 bp):
TATTTGTTTTGTATTATTCA
Found at i:31774 original size:25 final size:24
Alignment explanation
Indices: 31736--31921 Score: 117
Period size: 25 Copynumber: 7.7 Consensus size: 24
31726 ATGTTTTGTT
31736 TTTTGTTATATGTTATTTATTATTTG
1 TTTTG-TATATGTT-TTTATTATTTG
31762 TTTTGTATATG---TTATTA-TT-
1 TTTTGTATATGTTTTTATTATTTG
*
31781 TTTCGT-TACCTGTTTTTA-TATTTTG
1 TTTTGTATA--TGTTTTTATTA-TTTG
*
31806 TTTTGT-TATGTTTTTATTATTTA
1 TTTTGTATATGTTTTTATTATTTG
*
31829 TATAGTGTTATATGTTATTTATTATTT-
1 T-T-TTG-TATATGTT-TTTATTATTTG
31856 TTTTGTATATGTTTTATATTATTAT-
1 TTTTGTATATGTTTT-TATTATT-TG
*
31881 TTTTCGTTATCTGTTTTTA-TATTATG
1 TTTT-G-TATATGTTTTTATTATT-TG
*
31907 TTTTGT-TTTGTTTTT
1 TTTTGTATATGTTTTT
31922 TAGTAGTATG
Statistics
Matches: 134, Mismatches: 7, Indels: 41
0.74 0.04 0.23
Matches are distributed among these distances:
18 2 0.01
19 5 0.04
20 4 0.03
21 6 0.04
22 2 0.01
23 25 0.19
24 21 0.16
25 29 0.22
26 14 0.10
27 16 0.12
28 10 0.07
ACGTcount: A:0.18, C:0.03, G:0.11, T:0.69
Consensus pattern (24 bp):
TTTTGTATATGTTTTTATTATTTG
Found at i:31895 original size:101 final size:95
Alignment explanation
Indices: 31739--31921 Score: 269
Period size: 101 Copynumber: 1.9 Consensus size: 95
31729 TTTTGTTTTT
*
31739 TGTTATATGTTATTTATTATTTGTTTTGTATATGTTATTATTTTTCGTTACCTGTTTTTATATTT
1 TGTTATATGTTATTTATTATTTGTTTTGTATATGTTATTATTTTTCGTTACCTGTTTTTATATTA
31804 TGTTTTGTTATGTTTTTATTATTTATATAG
66 TGTTTTGTTATGTTTTTATTATTTATATAG
*
31834 TGTTATATGTTATTTATTATTT-TTTTGTATATGTTTTATATTATTATTTTTCGTTATCTGTTTT
1 TGTTATATGTTATTTATTATTTGTTTTGTATATG-------TTATTATTTTTCGTTACCTGTTTT
*
31898 TATATTATGTTTTGTTTTGTTTTT
59 TATATTATGTTTTGTTATGTTTTT
31922 TAGTAGTATG
Statistics
Matches: 78, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
94 11 0.14
95 22 0.28
101 45 0.58
ACGTcount: A:0.18, C:0.03, G:0.11, T:0.68
Consensus pattern (95 bp):
TGTTATATGTTATTTATTATTTGTTTTGTATATGTTATTATTTTTCGTTACCTGTTTTTATATTA
TGTTTTGTTATGTTTTTATTATTTATATAG
Found at i:31911 original size:51 final size:48
Alignment explanation
Indices: 31773--31921 Score: 167
Period size: 51 Copynumber: 3.0 Consensus size: 48
31763 TTTGTATATG
*
31773 TTATTATTTTTCGTTACCTGTTTTTATATTTTGTTTTGTTATGTTTTTA
1 TTATTATTTTTCGTTATCTGTTTTTATA-TTTGTTTTGTTATGTTTTTA
** *
31822 TTATTTATATAGT-GTTATATGTTATTTATTATTT-TTTTGTATATGTTTTATA
1 TTA-TTAT-TTTTCGTTATCTGTT-TTTA-TATTTGTTTTGT-TATGTTTT-TA
*
31874 TTATTATTTTTCGTTATCTGTTTTTATATTATGTTTTGTTTTGTTTTT
1 TTATTATTTTTCGTTATCTGTTTTTATATT-TGTTTTGTTATGTTTTT
31922 TAGTAGTATG
Statistics
Matches: 83, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
49 8 0.10
50 32 0.39
51 36 0.43
52 7 0.08
ACGTcount: A:0.17, C:0.03, G:0.10, T:0.69
Consensus pattern (48 bp):
TTATTATTTTTCGTTATCTGTTTTTATATTTGTTTTGTTATGTTTTTA
Found at i:31922 original size:25 final size:24
Alignment explanation
Indices: 31679--31922 Score: 61
Period size: 25 Copynumber: 9.7 Consensus size: 24
31669 TCATATTGTG
* *
31679 TTTTGTATTATTTTTTTAT-TTAT
1 TTTTGTTTTGTTTTTTTATATTAT
* * *
31702 TTTCGTTATCTGTTTTTTAATAGTAT
1 TTTTGTT-T-TGTTTTTTTATATTAT
*
31728 GTTTTGTTTTTTGTTATATGTTAT-TTAT
1 -TTTTG--TTTTGTT-T-TTTTATATTAT
* * *
31756 TATTTGTTTTGTATATGT-TATTAT
1 T-TTTGTTTTGTTTTTTTATATTAT
*** * *
31780 TTTTCGTTACCTGTTTTTATATTTT
1 TTTT-GTTTTGTTTTTTTATATTAT
*
31805 GTTTTGTTATGTTTTTATTAT-TTAT
1 -TTTTGTTTTGTTTTT-TTATATTAT
** *
31830 ATAGTGTTATATG-TTATTTATTATT-T
1 -TTTTGTT-T-TGTTTTTTTA-TATTAT
* *
31856 TTTTGTATATG-TTTTATATTATTAT
1 TTTTGT-TTTGTTTTTTTA-TATTAT
* * *
31881 TTTTCGTTATCTGTTTTTATATTAT
1 TTTT-GTTTTGTTTTTTTATATTAT
31906 GTTTTGTTTTGTTTTTT
1 -TTTTGTTTTGTTTTTT
31923 AGTAGTATGT
Statistics
Matches: 158, Mismatches: 40, Indels: 44
0.65 0.17 0.18
Matches are distributed among these distances:
23 9 0.06
24 26 0.16
25 61 0.39
26 34 0.22
27 13 0.08
28 9 0.06
29 6 0.04
ACGTcount: A:0.17, C:0.03, G:0.11, T:0.69
Consensus pattern (24 bp):
TTTTGTTTTGTTTTTTTATATTAT
Found at i:31935 original size:15 final size:15
Alignment explanation
Indices: 31915--31944 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31905 TGTTTTGTTT
31915 TGTTTTTTAGTAGTA
1 TGTTTTTTAGTAGTA
*
31930 TGTTTTTTATTAGTA
1 TGTTTTTTAGTAGTA
31945 ATTCTAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (15 bp):
TGTTTTTTAGTAGTA
Found at i:32858 original size:37 final size:36
Alignment explanation
Indices: 32799--32872 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
32789 TTCAGGTTGG
* * *
32799 TATTTTATAATTTTAATTATTTTAATTTGA-TTATTT
1 TATTTTACAATTCTAACTATTTTAATTT-ATTTATTT
*
32835 TATTTTCACAATTCTAACTATTTTGATTTATTTATTT
1 TATTTT-ACAATTCTAACTATTTTAATTTATTTATTT
32872 T
1 T
32873 CAGAATTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (36 bp):
TATTTTACAATTCTAACTATTTTAATTTATTTATTT
Found at i:33307 original size:7 final size:8
Alignment explanation
Indices: 33290--33315 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
33280 ATTTAAATTG
33290 TTTATTTT
1 TTTATTTT
33298 TTTATTTT
1 TTTATTTT
33306 TTTATTTT
1 TTTATTTT
33314 TT
1 TT
33316 GCTTTTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:33537 original size:57 final size:57
Alignment explanation
Indices: 33475--33583 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
33465 AGGGTGCAAC
* *
33475 TGCTTTTACATTTACTTCTTTTTCATTAATTTTCATGAATTTCAGCAAGCATGTTAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
*
33532 TGCTTTTACATTTACTGCTTTTTTATTAATTTTCATAAATTTCAGCAAGCAT
1 TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCAT
33584 ATAAATGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (57 bp):
TGCTTTTACATTTACTGCTTTTTCATTAATTTTCATAAATTTCAGCAAGCATGTTAT
Found at i:34348 original size:25 final size:25
Alignment explanation
Indices: 34273--34340 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
34263 AACTGCGCAG
34273 AATTTGTCCTGAAAGACCACGTAGA
1 AATTTGTCCTGAAAGACCACGTAGA
34298 AATTTGTCCTGAAAGACCACGTAGA
1 AATTTGTCCTGAAAGACCACGTAGA
*
34323 AATTTGTCCTGAAGGACC
1 AATTTGTCCTGAAAGACC
34341 GCATAGAACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (25 bp):
AATTTGTCCTGAAAGACCACGTAGA
Found at i:41306 original size:24 final size:24
Alignment explanation
Indices: 41279--41355 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
41269 AGAACTGCGC
41279 AGAATTTGTCCTGAAAGACCACGT
1 AGAATTTGTCCTGAAAGACCACGT
*
41303 AGAATTTGTCCTGAAGGACCACGT
1 AGAATTTGTCCTGAAAGACCACGT
* * * *
41327 AGAAATTTTTCCCGAATGACCGCGT
1 AG-AATTTGTCCTGAAAGACCACGT
41352 AGAA
1 AGAA
41356 CCCTCGACTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 27 0.57
25 20 0.43
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (24 bp):
AGAATTTGTCCTGAAAGACCACGT
Found at i:43044 original size:28 final size:28
Alignment explanation
Indices: 43011--43075 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
43001 TTGTCTTGTA
43011 AATTGTTGTTATTGGTCTGATAGAACTC
1 AATTGTTGTTATTGGTCTGATAGAACTC
43039 AATTGTTGTTATTGGTCTGATAGAACTC
1 AATTGTTGTTATTGGTCTGATAGAACTC
43067 AATTGTTGT
1 AATTGTTGT
43076 AAATTCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.45
Consensus pattern (28 bp):
AATTGTTGTTATTGGTCTGATAGAACTC
Found at i:43833 original size:16 final size:16
Alignment explanation
Indices: 43812--43847 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43802 GGTTGAGTCA
*
43812 ATAACATATTAGGTTT
1 ATAACATATTAGGTTG
*
43828 ATAACATGTTAGGTTG
1 ATAACATATTAGGTTG
43844 ATAA
1 ATAA
43848 TAGATCGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (16 bp):
ATAACATATTAGGTTG
Found at i:44375 original size:30 final size:30
Alignment explanation
Indices: 44330--44400 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
44320 TTTGTATCTT
44330 TTATACCACTAAACTTTTAATTTT-TTTCAA
1 TTATACCACTAAAC-TTTAATTTTATTTCAA
* * *
44360 TTATAACACTGAACTTTGATTTTATTTCAA
1 TTATACCACTAAACTTTAATTTTATTTCAA
44390 TTATACCACTA
1 TTATACCACTA
44401 GGCTGTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 8 0.23
30 27 0.77
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (30 bp):
TTATACCACTAAACTTTAATTTTATTTCAA
Found at i:46449 original size:19 final size:19
Alignment explanation
Indices: 46425--46471 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
46415 AATGTTATAT
*
46425 ATGATTTTGAAAAAATTTA
1 ATGATTTTGAAAAAAATTA
46444 ATGATTTTGAAAAAAATTA
1 ATGATTTTGAAAAAAATTA
46463 ATGATTTTG
1 ATGATTTTG
46472 TGACCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.43
Consensus pattern (19 bp):
ATGATTTTGAAAAAAATTA
Found at i:48071 original size:15 final size:15
Alignment explanation
Indices: 48053--48087 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
48043 TAAAAGTATA
48053 AAATTTAAATTACTG
1 AAATTTAAATTACTG
*
48068 AAATTTAGATTACTG
1 AAATTTAAATTACTG
48083 AAATT
1 AAATT
48088 ATGACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (15 bp):
AAATTTAAATTACTG
Found at i:59437 original size:37 final size:36
Alignment explanation
Indices: 59391--59473 Score: 139
Period size: 37 Copynumber: 2.3 Consensus size: 36
59381 AGTTTGGATC
59391 AATTCAGTTCGGATCATTTTAGGTTGATTTGAAATCA
1 AATTCAGTTCGGATCATTTTAGGTTGATTTGAAA-CA
*
59428 AATTCAGTTCGGATTATTTTAGGTTGATTTGAAACA
1 AATTCAGTTCGGATCATTTTAGGTTGATTTGAAACA
*
59464 TATTCAGTTC
1 AATTCAGTTC
59474 AAGTTTGAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 11 0.25
37 33 0.75
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (36 bp):
AATTCAGTTCGGATCATTTTAGGTTGATTTGAAACA
Found at i:62081 original size:14 final size:15
Alignment explanation
Indices: 62051--62089 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
62041 AATAATAATT
*
62051 ATAATTATA-ATACA
1 ATAATAATATATACA
62065 ATAATAATATATA-A
1 ATAATAATATATACA
62079 ATAATAATATA
1 ATAATAATATA
62090 AATAATGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATAATATATACA
Found at i:62504 original size:138 final size:137
Alignment explanation
Indices: 62248--62603 Score: 534
Period size: 138 Copynumber: 2.6 Consensus size: 137
62238 CAAACTGTGT
62248 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
* * *
62313 CCTTCGTGATGAAGACATCTGGCTATTTAAGGATGACACTGCTCCTTCATGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACACTGCTCCTTCATGATGAGGAGCTCTGA
62378 TCAATGG
131 TCAATGG
* * * *
62385 ATGACATTGTTCCTTCATGATGAGGACGTCTAGCCATCTTTAAAGATATTTTGAAATAACACGGT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATA-TTTGAGATAACTCGGT
* * * *
62450 TCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGA-TGCTTCTTCGTGATGAGGAGCTCT
65 TCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGA-CACTGCTCCTTCATGATGAGGAGCTCT
**
62514 GATCGGTGG
129 GATCAATGG
* * *
62523 ATGACATTGTTCTTTTGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAATTCGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
*
62588 CCTACGTGATGAGGAC
66 CCTTCGTGATGAGGAC
62604 GTCTAACCAT
Statistics
Matches: 196, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
137 75 0.38
138 120 0.61
139 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
CCTTCGTGATGAGGACATCTGGCTATCTAAGGATGACACTGCTCCTTCATGATGAGGAGCTCTGA
TCAATGG
Found at i:62598 original size:54 final size:54
Alignment explanation
Indices: 62539--62669 Score: 199
Period size: 54 Copynumber: 2.4 Consensus size: 54
62529 TTGTTCTTTT
**
62539 GTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAATTCGGTTCCTAC
1 GTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTAC
** *
62593 GTGATGAGGACGTCTAACCATCTTTAAAGATATTTGAGATAACACGGTTCCTTC
1 GTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTAC
* *
62647 GTGATGAGGACATCTGGCTATCT
1 GTGATGAGGACGTCTGGCCATCT
62670 AAGGATTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (54 bp):
GTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGGTTCCTAC
Found at i:62733 original size:21 final size:19
Alignment explanation
Indices: 62691--62734 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
62681 TTTCCTAAAA
*
62691 TATGAATAAATGATGCATT
1 TATGAATAAATGATCCATT
*
62710 TATGAATATCATGATCCTATT
1 TATGAATA-AATGATCC-ATT
62731 TATG
1 TATG
62735 CCTAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (19 bp):
TATGAATAAATGATCCATT
Found at i:75685 original size:16 final size:16
Alignment explanation
Indices: 75646--75706 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 16
75636 TCTTTGCTAG
*
75646 TTTTTTTCTCTGTTTC
1 TTTTTTTCTCTGTTGC
75662 TTTCTTTT-TCTGTTCGC
1 TTT-TTTTCTCTGTT-GC
75679 TTTTTTTGCT-TGTTGTC
1 TTTTTTT-CTCTGTTG-C
75696 TCTTTTTTCTC
1 T-TTTTTTCTC
75707 CCCCTTTTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
16 14 0.38
17 16 0.43
18 7 0.19
ACGTcount: A:0.00, C:0.20, G:0.10, T:0.70
Consensus pattern (16 bp):
TTTTTTTCTCTGTTGC
Found at i:75894 original size:22 final size:22
Alignment explanation
Indices: 75869--75923 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
75859 CATAGCGGTG
*
75869 GAGCAGTTGGATTTAGGCGGCA
1 GAGCAGTTGGATGTAGGCGGCA
* **
75891 GAGCAGTTGGGTGTAGGCGGTG
1 GAGCAGTTGGATGTAGGCGGCA
75913 GAGCAGTTGGA
1 GAGCAGTTGGA
75924 GGCAGCACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.11, G:0.47, T:0.22
Consensus pattern (22 bp):
GAGCAGTTGGATGTAGGCGGCA
Found at i:76188 original size:3 final size:3
Alignment explanation
Indices: 76182--76229 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
76172 TATTATTTAT
* *
76182 TAA TAA TAA TTA TAA TAA TAA T-A CAA TAA TAA TATA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TAA
76228 TA
1 TA
76230 TAAATAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 32 0.84
4 4 0.11
5 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:76212 original size:14 final size:13
Alignment explanation
Indices: 76182--76237 Score: 71
Period size: 12 Copynumber: 4.3 Consensus size: 13
76172 TATTATTTAT
*
76182 TAATAATAAT-TA
1 TAATAATAATAAA
76194 TAATAATAATACAA
1 TAATAATAATA-AA
76208 TAATAATATATAAA
1 TAATAATA-ATAAA
76222 TAATAAT-ATAAA
1 TAATAATAATAAA
76234 TAAT
1 TAAT
76238 GACGGGACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
12 19 0.47
14 18 0.45
15 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:78756 original size:36 final size:37
Alignment explanation
Indices: 78709--78778 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
78699 ATTTAGGGGA
78709 GAATCGATACCCCCCCA-GGGGGAATCTGTTCCCAGG
1 GAATCGATACCCCCCCAGGGGGGAATCTGTTCCCAGG
78745 GAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
1 GAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
78779 CCTGCACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.17
Consensus pattern (37 bp):
GAATCGATACCCCCCCAGGGGGGAATCTGTTCCCAGG
Found at i:84974 original size:15 final size:15
Alignment explanation
Indices: 84954--85004 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
84944 CCGTAGGACC
84954 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
84969 ACTACGTCCCAAAAGG
1 ACTACGTCCC-GAAGG
* *
84985 ACTTCGTCTCGAAGG
1 ACTACGTCCCGAAGG
85000 ACTAC
1 ACTAC
85005 AATACCCTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:86533 original size:17 final size:17
Alignment explanation
Indices: 86491--86535 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
86481 ATTTTGACTT
*
86491 AAAATAAAAAATTAAAA
1 AAAATAATAAATTAAAA
* *
86508 AAAAGTAATATATTTAAA
1 AAAA-TAATAAATTAAAA
86526 AAAATAATAA
1 AAAATAATAA
86536 TGATCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAATAATAAATTAAAA
Found at i:90211 original size:28 final size:28
Alignment explanation
Indices: 90151--90211 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
90141 GGATTAAATT
* *
90151 ATTTTTCTAAATTTAGAGAATTATTTAT
1 ATTTTTCTAAATTTAGAAAATTATTTAA
* *
90179 TTTTTTTTAAATTTA-AAAATTATTTTAA
1 ATTTTTCTAAATTTAGAAAATTA-TTTAA
90207 ATTTT
1 ATTTT
90212 AAATATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (28 bp):
ATTTTTCTAAATTTAGAAAATTATTTAA
Found at i:90227 original size:17 final size:16
Alignment explanation
Indices: 90205--90255 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
90195 AAATTATTTT
90205 AAAT-TTTAAATATAA
1 AAATATTTAAATATAA
90220 AAATATTTAATATATTAA
1 AAATATTTAA-ATA-TAA
90238 AAA-A-TTAAATATAA
1 AAATATTTAAATATAA
90252 AAAT
1 AAAT
90256 TAAATACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 9 0.28
17 4 0.12
18 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATTTAAATATAA
Found at i:90237 original size:24 final size:25
Alignment explanation
Indices: 90185--90238 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
90175 TTATTTTTTT
* *
90185 TTAAATTTAAAAATTATTTTAAATT
1 TTAAATATAAAAATTATTTTAAATA
90210 TTAAATATAAAAA-TA-TTTAATATA
1 TTAAATATAAAAATTATTTTAA-ATA
90234 TTAAA
1 TTAAA
90239 AAATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 9 0.35
25 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAATATAAAAATTATTTTAAATA
Found at i:90255 original size:13 final size:13
Alignment explanation
Indices: 90237--90261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90227 TAATATATTA
90237 AAAAATTAAATAT
1 AAAAATTAAATAT
90250 AAAAATTAAATA
1 AAAAATTAAATA
90262 CACATATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:91387 original size:31 final size:30
Alignment explanation
Indices: 91352--91453 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 30
91342 GTTTTTACTT
91352 TGATGAGGTTT-TGTTTCCTTTGTTTTTGTTG
1 TGATGA-GTTTATGTTTCCTTTG-TTTTGTTG
** * *
91383 TGATGAGTTTCCGTTTTCC-TTGGTTTGCTG
1 TGATGAGTTTATG-TTTCCTTTGTTTTGTTG
* *
91413 TAATGAGTTTATGTTTCCTTTGCTTTTATTG
1 TGATGAGTTTATGTTTCCTTTG-TTTTGTTG
91444 TGATGAGTTT
1 TGATGAGTTT
91454 TTGGTACGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 5 0.09
30 23 0.40
31 24 0.42
32 5 0.09
ACGTcount: A:0.11, C:0.10, G:0.24, T:0.56
Consensus pattern (30 bp):
TGATGAGTTTATGTTTCCTTTGTTTTGTTG
Found at i:99478 original size:21 final size:22
Alignment explanation
Indices: 99453--99494 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
99443 TACTGCCTTA
99453 GGGGTTTCGAAACCA-CCTAAG
1 GGGGTTTCGAAACCATCCTAAG
*
99474 GGGGTTTCTAAACCATCCTAA
1 GGGGTTTCGAAACCATCCTAA
99495 AAAACTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
GGGGTTTCGAAACCATCCTAAG
Found at i:100389 original size:22 final size:22
Alignment explanation
Indices: 100341--100394 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
100331 TTCAGCTGTT
* *
100341 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
100363 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
100385 ATAACTCCTG
1 ATAACTCCTG
100395 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:100678 original size:6 final size:6
Alignment explanation
Indices: 100667--100709 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
100657 GACACGTATT
*
100667 ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
100710 GCCGAGCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:101869 original size:6 final size:6
Alignment explanation
Indices: 101858--101947 Score: 119
Period size: 6 Copynumber: 15.2 Consensus size: 6
101848 GACACGTATT
*
101858 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * * * *
101906 A-CTCG ACCTCG ACCTCG ACCTCG ACCTCG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
101948 GCCGAGCCGA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
5 5 0.06
6 76 0.94
ACGTcount: A:0.28, C:0.49, G:0.17, T:0.07
Consensus pattern (6 bp):
ACCACG
Found at i:103105 original size:6 final size:6
Alignment explanation
Indices: 103094--103184 Score: 155
Period size: 6 Copynumber: 15.2 Consensus size: 6
103084 GACACGTATT
103094 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * *
103142 ACCACG ACCTCG ACCTCG ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
103185 GCCGAGCCGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:103752 original size:23 final size:21
Alignment explanation
Indices: 103726--103779 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
103716 AAAGTTTTAG
103726 AATAAATAACATAGATTTATAT
1 AATAAATAACA-AGATTTATAT
* * *
103748 AAATAATTTAACAATATTTGTAT
1 -AATAA-ATAACAAGATTTATAT
103771 AATAAATAA
1 AATAAATAA
103780 TATTGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 13 0.50
24 5 0.19
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (21 bp):
AATAAATAACAAGATTTATAT
Done.