Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 186 of 228
Found at i:55456511 original size:26 final size:26
Alignment explanation
Indices: 55456481--55456609 Score: 102
Period size: 26 Copynumber: 5.3 Consensus size: 26
55456471 TTCATTTCTA
55456481 TTTCCATTTCATTTAAATTATCTTTT
1 TTTCCATTTCATTTAAATTATCTTTT
*
55456507 TTT-C----CATTTAAATT-TATTTT
1 TTTCCATTTCATTTAAATTATCTTTT
*
55456527 TTTCTCATTTCATTTAAATCATCTTTT
1 TTTC-CATTTCATTTAAATTATCTTTT
**
55456554 TTT-C----CATTTAAATT-TAATTT
1 TTTCCATTTCATTTAAATTATCTTTT
*
55456574 TTTCTCATTTCATTTAAATTATCTTTC
1 TTTC-CATTTCATTTAAATTATCTTTT
*
55456601 TTTCTATTT
1 TTTCCATTT
55456610 TAATTTACGT
Statistics
Matches: 79, Mismatches: 10, Indels: 28
0.68 0.09 0.24
Matches are distributed among these distances:
20 15 0.19
21 19 0.24
22 2 0.03
25 2 0.03
26 26 0.33
27 15 0.19
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTCCATTTCATTTAAATTATCTTTT
Found at i:55456514 original size:21 final size:21
Alignment explanation
Indices: 55456490--55456614 Score: 90
Period size: 21 Copynumber: 5.5 Consensus size: 21
55456480 ATTTCCATTT
55456490 CATTTAAATTATCTTTTTTTC
1 CATTTAAATTATCTTTTTTTC
55456511 CATTTAAATTTAT-TTTTTTCTC
1 CATTTAAA-TTATCTTTTTT-TC
*
55456533 ATTTCATTTAAATCATCTTTTTTTC
1 ----CATTTAAATTATCTTTTTTTC
* *
55456558 CATTTAAATTTAATTTTTTCTCATTT
1 CATTTAAA-TT-ATCTTTT-T--TTC
*
55456584 CATTTAAATTATCTTTCTTTC
1 CATTTAAATTATCTTTTTTTC
* *
55456605 TATTTTAATT
1 CATTTAAATT
55456615 TACGTTTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
21 32 0.39
22 7 0.08
23 7 0.08
24 6 0.07
25 7 0.08
26 24 0.29
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.62
Consensus pattern (21 bp):
CATTTAAATTATCTTTTTTTC
Found at i:55456536 original size:47 final size:47
Alignment explanation
Indices: 55456481--55456630 Score: 221
Period size: 47 Copynumber: 3.2 Consensus size: 47
55456471 TTCATTTCTA
55456481 TTTC-CATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTATTTT
1 TTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTATTTT
* *
55456527 TTTCTCATTTCATTTAAATCATCTTTTTTTCCATTTAAATTTAATTT
1 TTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTATTTT
* * *
55456574 TTTCTCATTTCATTTAAATTATCTTTCTTTCTATTTTAATTTACGTTTT
1 TTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTA--TTTT
*
55456623 TTTTTCAT
1 TTTCTCAT
55456631 ATTAATTTTT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
46 4 0.04
47 79 0.85
49 10 0.11
ACGTcount: A:0.23, C:0.14, G:0.01, T:0.63
Consensus pattern (47 bp):
TTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTATTTT
Found at i:55456856 original size:44 final size:44
Alignment explanation
Indices: 55456661--55456853 Score: 314
Period size: 44 Copynumber: 4.4 Consensus size: 44
55456651 AATTTATTTC
55456661 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
* *
55456705 ATTTAATGTGTTTTAAAATAAAGATGTATTTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
*
55456749 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTACA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
* * *
55456793 ATTTAATGTGCTTTAAATTAAATATGCATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
* *
55456837 ATTTAACGTTTTTTAAA
1 ATTTAATGTGTTTTAAA
55456854 TTAGGAATAA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 137 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (44 bp):
ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
Found at i:55459880 original size:159 final size:161
Alignment explanation
Indices: 55459646--55459943 Score: 528
Period size: 159 Copynumber: 1.9 Consensus size: 161
55459636 ATTCCTATTT
*
55459646 TTTTTTACTTTGAAATACACAACCTTCTTCAGTTGTATTTATTATTTCTCTATCGAAATGAACAT
1 TTTTTTACTTTGAAATACACAACCTTCTTCAGTTGTATTTATCATTTCTCTATCGAAATGAACAT
***
55459711 AAACAAACAAAATTTGGGAACTCATCTTAAAATTTTTTTGCTTCCTTCTTAACAAAGAAAAAACT
66 AAACAAACAAAATTTGGGAACTCATCTTAAAAAAATTTTGCTTCCTTCTTAACAAAGAAAAAACT
55459776 AATATTTTTGCTTCTTTCTTAACAAAGAAAA
131 AATATTTTTGCTTCTTTCTTAACAAAGAAAA
* *
55459807 TTTTTT-CTTTGAAATACACGACCTTTTTCAGTTGTATTTATCATTT-TCTATCGAAATGAACAT
1 TTTTTTACTTTGAAATACACAACCTTCTTCAGTTGTATTTATCATTTCTCTATCGAAATGAACAT
55459870 AAACAAACAAAATTTGGGAACTCATCTTAAAAAAATTTTGCTTCCTTCTTAACAAAGAAAAAACT
66 AAACAAACAAAATTTGGGAACTCATCTTAAAAAAATTTTGCTTCCTTCTTAACAAAGAAAAAACT
55459935 AATATTTTT
131 AATATTTTT
55459944 AATCTCGATT
Statistics
Matches: 131, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
159 88 0.67
160 37 0.28
161 6 0.05
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40
Consensus pattern (161 bp):
TTTTTTACTTTGAAATACACAACCTTCTTCAGTTGTATTTATCATTTCTCTATCGAAATGAACAT
AAACAAACAAAATTTGGGAACTCATCTTAAAAAAATTTTGCTTCCTTCTTAACAAAGAAAAAACT
AATATTTTTGCTTCTTTCTTAACAAAGAAAA
Found at i:55460335 original size:61 final size:61
Alignment explanation
Indices: 55460236--55460356 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 61
55460226 TTGGAGCCAG
* * *
55460236 CCATCAGTGTTCCAAAGTAAAAAAAATGGCCTTCGGACCCAAAAAATGTACTTGGTGTTGA
1 CCATCAGTGTCCCAAAGTAAAAAAAATGACCTTCGGACCCAAAAAATGTACCTGGTGTTGA
* * *
55460297 CCATCAGTGTCCCAAAGTAAAAAAAATTACCTTGGGACCCGAAAAATGTACCTGGTGTTG
1 CCATCAGTGTCCCAAAGTAAAAAAAATGACCTTCGGACCCAAAAAATGTACCTGGTGTTG
55460357 GCATCTACTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (61 bp):
CCATCAGTGTCCCAAAGTAAAAAAAATGACCTTCGGACCCAAAAAATGTACCTGGTGTTGA
Found at i:55467886 original size:25 final size:25
Alignment explanation
Indices: 55467834--55467891 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
55467824 AAAAGAAATA
* **
55467834 AATACATATATTTATTGTTATATTG
1 AATAAATATATTTATTGTTATAGGG
*
55467859 AATTAATATATTTATT-TATATAGGG
1 AATAAATATATTTATTGT-TATAGGG
55467884 AATAAATA
1 AATAAATA
55467892 AATGTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (25 bp):
AATAAATATATTTATTGTTATAGGG
Found at i:55468155 original size:29 final size:31
Alignment explanation
Indices: 55468113--55468174 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
55468103 TAGTAAAAGT
55468113 AAAATTATACTTTAACCCCTTAAAAA-TATA
1 AAAATTATACTTTAACCCCTTAAAAATTATA
* * **
55468143 AAAATTTTA-TTTAATCTTTTAAAAATTATA
1 AAAATTATACTTTAACCCCTTAAAAATTATA
55468173 AA
1 AA
55468175 GATATAGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAATTATACTTTAACCCCTTAAAAATTATA
Found at i:55469721 original size:22 final size:23
Alignment explanation
Indices: 55469678--55469723 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
55469668 AGAAAACTGA
* *
55469678 TGCTACTTTATTTTTTACTGTTT
1 TGCTACTGTATTTTTCACTGTTT
*
55469701 TGCTACTGT-TTTTTCATTGTTT
1 TGCTACTGTATTTTTCACTGTTT
55469723 T
1 T
55469724 ACTATCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.65
Consensus pattern (23 bp):
TGCTACTGTATTTTTCACTGTTT
Found at i:55471423 original size:11 final size:11
Alignment explanation
Indices: 55471407--55471443 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55471397 TAAACCAAAT
55471407 TAAAATATATA
1 TAAAATATATA
55471418 TAAAATATATA
1 TAAAATATATA
55471429 -ATAAATATA-A
1 TA-AAATATATA
55471439 TAAAA
1 TAAAA
55471444 GTCCAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAATATATA
Found at i:55471493 original size:15 final size:15
Alignment explanation
Indices: 55471475--55471512 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
55471465 CAAGTTACAG
55471475 AAACCCAACTAGCCT
1 AAACCCAACTAGCCT
*
55471490 AAACCCAATTAGCCT
1 AAACCCAACTAGCCT
*
55471505 AAGCCCAA
1 AAACCCAA
55471513 TACCCTAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.37, G:0.08, T:0.13
Consensus pattern (15 bp):
AAACCCAACTAGCCT
Found at i:55471513 original size:15 final size:15
Alignment explanation
Indices: 55471478--55471526 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
55471468 GTTACAGAAA
* *
55471478 CCCAACTAGCCTAAA
1 CCCAATTAGCCTAAG
55471493 CCCAATTAGCCTAAG
1 CCCAATTAGCCTAAG
*
55471508 CCCAA-TACCCT-AG
1 CCCAATTAGCCTAAG
55471521 CCCAAT
1 CCCAAT
55471527 CACGAAGCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 7 0.23
14 5 0.17
15 18 0.60
ACGTcount: A:0.35, C:0.41, G:0.08, T:0.16
Consensus pattern (15 bp):
CCCAATTAGCCTAAG
Found at i:55474737 original size:16 final size:17
Alignment explanation
Indices: 55474696--55474742 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
55474686 GTTCTTGTTT
55474696 TCATTTTATTGTTTTTATC
1 TCATTTTA-T-TTTTTATC
*
55474715 TCTTTTTATTTTTTATC
1 TCATTTTATTTTTTATC
55474732 T-ATTTTATTTT
1 TCATTTTATTTT
55474743 CATTTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 9 0.35
18 1 0.04
19 7 0.27
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (17 bp):
TCATTTTATTTTTTATC
Found at i:55479716 original size:17 final size:16
Alignment explanation
Indices: 55479688--55479727 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
55479678 ATACTTCATT
55479688 TGAAAAAAAAAACAAA
1 TGAAAAAAAAAACAAA
*
55479704 TGAAAAGAAAAAAGAAA
1 TGAAAA-AAAAAACAAA
*
55479721 AGAAAAA
1 TGAAAAA
55479728 TGAAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (16 bp):
TGAAAAAAAAAACAAA
Found at i:55479720 original size:12 final size:12
Alignment explanation
Indices: 55479705--55479740 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
55479695 AAAAACAAAT
55479705 GAAAAGAAAAAA
1 GAAAAGAAAAAA
*
55479717 GAAAAGAAAAAT
1 GAAAAGAAAAAA
55479729 GAAAAAGAAAAA
1 G-AAAAGAAAAA
55479741 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:55479741 original size:24 final size:22
Alignment explanation
Indices: 55479689--55479741 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
55479679 TACTTCATTT
*
55479689 GAAAAA-AAAAACAAATGAAAA
1 GAAAAAGAAAAAAAAATGAAAA
55479710 GAAAAAAGAAAAGAAAAATGAAAAA
1 G-AAAAAGAAAA-AAAAATG-AAAA
55479735 GAAAAAG
1 GAAAAAG
55479742 GAGAGGCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 5 0.19
23 4 0.15
24 12 0.44
25 5 0.19
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (22 bp):
GAAAAAGAAAAAAAAATGAAAA
Found at i:55481064 original size:50 final size:50
Alignment explanation
Indices: 55481004--55481269 Score: 191
Period size: 50 Copynumber: 5.4 Consensus size: 50
55480994 ATTAAAGCTA
*
55481004 CAACGACGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
1 CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
* * * * ** ** * **
55481054 CAATGGCGAATC-T--TTCCATGGCGA-TGCAGTAGAGCAGATTAAAGCTA
1 CAACGGCGAATCTTGCTTCCCTGAC-ATTGCAATTTAAAAGATTGAAGCCG
* * *
55481101 CAACGGTGAATCTTGCTTCCCCGACATTGTAATTTAAAAGATTGAAGCCG
1 CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
* ** * * * ** * * **
55481151 CAACGGTGAATCTTAATTCCATGGCGA-TGCAGTGGAACAGATTAAAGCTA
1 CAACGGCGAATCTTGCTTCCCTGAC-ATTGCAATTTAAAAGATTGAAGCCG
* * * *
55481201 TAACGGCGAATCTTGCTTCCCCGATATTGCAATTTAAAAGATTGAGGCCG
1 CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
*
55481251 CAACGGCGAATCTTACTTC
1 CAACGGCGAATCTTGCTTC
55481270 TTTAGTGGTG
Statistics
Matches: 152, Mismatches: 57, Indels: 14
0.68 0.26 0.06
Matches are distributed among these distances:
47 32 0.21
48 2 0.01
49 3 0.02
50 114 0.75
51 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
Found at i:55481218 original size:100 final size:99
Alignment explanation
Indices: 55480981--55481326 Score: 471
Period size: 100 Copynumber: 3.5 Consensus size: 99
55480971 TCCCTGGCAG
* * *
55480981 TGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCTGACATTGCAATTTAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
*
55481046 TGAAGCCGCAATGGCGAATC-T-TTCCATGGCGA
66 TGAAGCCGCAACGGCGAATCTTATTCCATGGCGA
* * * *
55481078 TGCAGTAGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGTAATTTAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
*
55481143 TGAAGCCGCAACGGTGAATCTTAATTCCATGGCGA
66 TGAAGCCGCAACGGCGAATCTT-ATTCCATGGCGA
* *
55481178 TGCAGTGGAACAGATTAAAGCTATAACGGCGAATCTTGCTTCCCCGATATTGCAATTTAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
* ** * * *
55481243 TGAGGCCGCAACGGCGAATCTTACTTCTTTAGTGG
66 TGAAGCCGCAACGGCGAATCTTA-TTCCATGGCGA
* * * *
55481278 TGTAATGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACA
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACA
55481327 CCGTAGTTCA
Statistics
Matches: 219, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
97 78 0.36
98 1 0.00
99 1 0.00
100 139 0.63
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (99 bp):
TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
TGAAGCCGCAACGGCGAATCTTATTCCATGGCGA
Found at i:55482236 original size:45 final size:45
Alignment explanation
Indices: 55481363--55482235 Score: 1092
Period size: 45 Copynumber: 19.4 Consensus size: 45
55481353 ACATTGCAGA
* *
55481363 TCTTGTCTTCCTGTATTGGCAGCAAAGTAGA-TCGAAGATAACAAC
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* * *
55481408 TCTTATCTTCCTGTATTGGCACCGAAGTAGACTGAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * * * * * *
55481453 TTTTGTCTTCTTGTGTTGGTAGCAAAGTAGACTAAAGATAA-TAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
**
55481497 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-TCGAAGATAGTAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
55481543 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * *
55481587 ATCTTGTCTTCTTGTATTGGCAGCGAAATAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* *
55481633 TCTTATCTTCCTGTATTGGCAGCAAAGTAGACTGAAGATAACAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
55481678 TCTTGTCTTCCTGTATTGGCAGCGAAGTATACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * *
55481722 ATCTTATCTTCCTGTATTGGCAGTGAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
*
55481768 TCTTGTCTTTCTGTATTGGCAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* *
55481812 ATCTTGTCTTCCTGTATTGGCAACGAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* * * * *
55481858 TCTTATCTTCCTGTTTTAGCAGCGAAATAGACTGAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
55481903 TCTTGTCTTCCTGTATTGACAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
55481947 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* *
55481993 TCTTGTCTTTCTGTATTGGCAACGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
55482037 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* *
55482083 TCTTGTCTTCCTGTATTAGCAGCAAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * * *
55482127 ATCTTGTCTTCCTCTATTGCCAGCAAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* *
55482173 TCTTGTCTTCCTGTATTGACAACGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* *
55482217 ATCTTGCCTTCCTATATTG
1 -TCTTGTCTTCCTGTATTG
55482236 ATGGTGAAGC
Statistics
Matches: 720, Mismatches: 80, Indels: 56
0.84 0.09 0.07
Matches are distributed among these distances:
44 22 0.03
45 677 0.94
46 21 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (45 bp):
TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
Found at i:55482416 original size:50 final size:50
Alignment explanation
Indices: 55482327--55482422 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
55482317 GCAGTGGAAC
* * *
55482327 AGATTGAAGCTACAACGGCAAATCTTGTTTCCCCGACATTGTAATTTAAA
1 AGATTGAAGCTACAACGGCAAATCTTCTTTCCCCAACATTGCAATTTAAA
* * * *
55482377 AGATTGAAGCTACGATGGCGAATCTTACTTT-CCTAACATTGCAATT
1 AGATTGAAGCTACAACGGCAAATCTT-CTTTCCCCAACATTGCAATT
55482423 AAACATACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 35 0.92
51 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCAAATCTTCTTTCCCCAACATTGCAATTTAAA
Found at i:55482587 original size:27 final size:27
Alignment explanation
Indices: 55482549--55482601 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
55482539 GCAGTAGTGG
55482549 AGCAGACAAAAGAAACCAATCCTATCA
1 AGCAGACAAAAGAAACCAATCCTATCA
55482576 AGCAGACAAAAGAAACCAATCCTATC
1 AGCAGACAAAAGAAACCAATCCTATC
55482602 TTCCTGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (27 bp):
AGCAGACAAAAGAAACCAATCCTATCA
Found at i:55482646 original size:44 final size:43
Alignment explanation
Indices: 55482598--55482797 Score: 187
Period size: 44 Copynumber: 4.6 Consensus size: 43
55482588 AAACCAATCC
* *
55482598 TATCTTCCTGAAGTTGCAGTTGAGCAGATCAAAACCACAGATCT
1 TATC-TCCTGAAGTTGCAGTGGAGCAGATCAAAATCACAGATCT
* *
55482642 TATCTCTCTGAAGTTGCAGTAGAGCAGATC-ACATC-CAG-TCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGATCAAAATCACAGATCT
* * ** *
55482683 TATCTCCCTGAAGTTTCAGTGGAGCAG-GCAAAAGAAACCA-ATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGATCAAAA-TCA-CAGATCT
*
55482727 TATCTCCTTAAAGTTGCAGTGGAGC-GAATCAAAATCACAGATCT
1 TATCTCC-TGAAGTTGCAGTGGAGCAG-ATCAAAATCACAGATCT
*
55482771 TATCTCTCTAAAGTTGCAGTGGAGCAG
1 TATCTC-CTGAAGTTGCAGTGGAGCAG
55482798 GTTGAAGATA
Statistics
Matches: 127, Mismatches: 16, Indels: 25
0.76 0.10 0.15
Matches are distributed among these distances:
40 1 0.01
41 28 0.22
42 4 0.03
43 10 0.08
44 77 0.61
45 7 0.06
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (43 bp):
TATCTCCTGAAGTTGCAGTGGAGCAGATCAAAATCACAGATCT
Found at i:55483505 original size:19 final size:17
Alignment explanation
Indices: 55483491--55483526 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
55483481 CATTTTATTA
55483491 TTTTTATCTCTTTTTAT
1 TTTTTATCTCTTTTTAT
55483508 TTTTTATCTC-TTTTAT
1 TTTTTATCTCTTTTTAT
55483524 TTT
1 TTT
55483527 CATTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATCTCTTTTTAT
Found at i:55488640 original size:20 final size:20
Alignment explanation
Indices: 55488615--55488652 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55488605 ATTCTGAGAT
55488615 ATATTATTAAAATTCTAATA
1 ATATTATTAAAATTCTAATA
*
55488635 ATATTATTATAATTCTAA
1 ATATTATTAAAATTCTAA
55488653 GATACAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATTAAAATTCTAATA
Found at i:55490587 original size:7 final size:7
Alignment explanation
Indices: 55490575--55490601 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55490565 CTCCTTTATT
55490575 TAATTTA
1 TAATTTA
55490582 TAATTTA
1 TAATTTA
55490589 TAATTTA
1 TAATTTA
55490596 TAATTT
1 TAATTT
55490602 TAAAACTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAATTTA
Found at i:55491345 original size:20 final size:21
Alignment explanation
Indices: 55491299--55491345 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
55491289 ATTTAATTTT
*
55491299 TTTTTCTTTTATATCCTTTTA
1 TTTTTCTTTTATATCCCTTTA
** *
55491320 ACTTTCTTTT-TTTCCCTTTA
1 TTTTTCTTTTATATCCCTTTA
55491340 TTTTTC
1 TTTTTC
55491346 ATTCTCTTCT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTCTTTTATATCCCTTTA
Found at i:55493674 original size:17 final size:18
Alignment explanation
Indices: 55493652--55493686 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55493642 TATATGATAG
55493652 GTTAATAAATT-TAAATT
1 GTTAATAAATTATAAATT
*
55493669 GTTAATAATTTATAAATT
1 GTTAATAAATTATAAATT
55493687 TTTATTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
GTTAATAAATTATAAATT
Found at i:55499198 original size:20 final size:19
Alignment explanation
Indices: 55499152--55499202 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
55499142 AAGTCAACTT
55499152 GTATCGATACTTGGATAAA
1 GTATCGATACTTGGATAAA
* *
55499171 GTACCGATTCTTGGACCT-AA
1 GTATCGATACTTGGA--TAAA
55499191 GTATCGATACTT
1 GTATCGATACTT
55499203 TACATTGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.50
20 12 0.46
21 1 0.04
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (19 bp):
GTATCGATACTTGGATAAA
Found at i:55500988 original size:24 final size:24
Alignment explanation
Indices: 55500958--55501035 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
55500948 TGTATAACAA
55500958 GAAGCTCATAAGAGCCATAATCAG
1 GAAGCTCATAAGAGCCATAATCAG
** *
55500982 GAAGCTCATGTGAGCCAATAA-CGG
1 GAAGCTCATAAGAGCC-ATAATCAG
* **
55501006 GTAGCTCCGAAGAGCCATTAAT-AG
1 GAAGCTCATAAGAGCCA-TAATCAG
55501030 GAAGCT
1 GAAGCT
55501036 TCAGATACCC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
23 1 0.02
24 36 0.88
25 4 0.10
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCATAATCAG
Found at i:55501107 original size:25 final size:26
Alignment explanation
Indices: 55501077--55501134 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
55501067 AGCCATATCG
*
55501077 GGAAGCTC-CGGAAAGCCATTAATCA
1 GGAAGCTCACAGAAAGCCATTAATCA
* * *
55501102 GGAAGCTCACAGAGAGCCTTTAATCG
1 GGAAGCTCACAGAAAGCCATTAATCA
55501128 GGAAGCT
1 GGAAGCT
55501135 TTGAAAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACAGAAAGCCATTAATCA
Found at i:55501124 original size:26 final size:25
Alignment explanation
Indices: 55500970--55501134 Score: 76
Period size: 24 Copynumber: 6.8 Consensus size: 25
55500960 AGCTCATAAG
**
55500970 AGCCA-TAATCAGGAAGCT-CATGTG
1 AGCCATTAATCAGGAAGCTCCA-GAA
* * *
55500994 AGCCAATAA-CGGGTAGCTCC-GAA
1 AGCCATTAATCAGGAAGCTCCAGAA
* *
55501017 GAGCCATTAAT-AGGAAGCTTCAGAT
1 -AGCCATTAATCAGGAAGCTCCAGAA
* * * * **
55501042 ACCCA-TATATCGGGAAGTTCAAGCG
1 AGCCATTA-ATCAGGAAGCTCCAGAA
* *
55501067 AGCCA-T-ATCGGGAAGCTCCGGAA
1 AGCCATTAATCAGGAAGCTCCAGAA
*
55501090 AGCCATTAATCAGGAAGCTCACAGAG
1 AGCCATTAATCAGGAAGCTC-CAGAA
* *
55501116 AGCCTTTAATCGGGAAGCT
1 AGCCATTAATCAGGAAGCT
55501135 TTGAAAGCCA
Statistics
Matches: 104, Mismatches: 27, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
23 20 0.19
24 34 0.33
25 30 0.29
26 20 0.19
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
AGCCATTAATCAGGAAGCTCCAGAA
Found at i:55503441 original size:42 final size:42
Alignment explanation
Indices: 55503395--55503494 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
55503385 CCGTGTGACC
*
55503395 AGGCCGTGTGACTCACACGGCCTAGACACACGCCTGTGTCTA
1 AGGCCGTGTGACTCACACGGCCTAGACACACGCCCGTGTCTA
* * * * *
55503437 AGGCCGTGTGACTCCCGCGGTCTAGAGACACGCCCGTTTCTA
1 AGGCCGTGTGACTCACACGGCCTAGACACACGCCCGTGTCTA
* *
55503479 AAGCCGTGTAACTCAC
1 AGGCCGTGTGACTCAC
55503495 TGACTTGCAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (42 bp):
AGGCCGTGTGACTCACACGGCCTAGACACACGCCCGTGTCTA
Found at i:55504550 original size:20 final size:22
Alignment explanation
Indices: 55504516--55504556 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
55504506 CTTTACTTTC
*
55504516 CACACTCATTCCATATGCATAA
1 CACACTCATTCCATAAGCATAA
55504538 CACAC-CATT-CATAAGCATA
1 CACACTCATTCCATAAGCATA
55504557 TCATTCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.24
Consensus pattern (22 bp):
CACACTCATTCCATAAGCATAA
Found at i:55505269 original size:25 final size:25
Alignment explanation
Indices: 55505144--55505272 Score: 79
Period size: 25 Copynumber: 5.2 Consensus size: 25
55505134 AAGCTCTTTC
*
55505144 GAGCCATATAAT-GGGAAGCTCATGA
1 GAGCCAT-TAATAGGAAAGCTCATGA
* * * *
55505169 AAGTCATATAACAGG-AAGCTCATAA
1 GAGCCAT-TAATAGGAAAGCTCATGA
* * * *
55505194 GAGCC-GTAATTGGAAAGTTCATGC
1 GAGCCATTAATAGGAAAGCTCATGA
* * * *
55505218 GAGCCAAT-ATTGGGAAGCTC-CGAA
1 GAGCCATTAATAGGAAAGCTCATG-A
55505242 GAGCCATTAATAGGAAAGCTCATGA
1 GAGCCATTAATAGGAAAGCTCATGA
55505267 GAGCCA
1 GAGCCA
55505273 ATTATCGAGA
Statistics
Matches: 77, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
23 6 0.08
24 29 0.38
25 39 0.51
26 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATAGGAAAGCTCATGA
Found at i:55505271 original size:49 final size:48
Alignment explanation
Indices: 55505182--55505274 Score: 123
Period size: 49 Copynumber: 1.9 Consensus size: 48
55505172 TCATATAACA
* * * *
55505182 GGAAGCTCATAAGAGCCGTAATTGGAAAGTTCATGCGAGCCAATATTG
1 GGAAGCTCAGAAGAGCCGTAATAGGAAAGCTCATGAGAGCCAATATTG
* *
55505230 GGAAGCTCCGAAGAGCCATTAATAGGAAAGCTCATGAGAGCCAAT
1 GGAAGCTCAGAAGAGCC-GTAATAGGAAAGCTCATGAGAGCCAAT
55505275 TATCGAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 15 0.39
49 23 0.61
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.19
Consensus pattern (48 bp):
GGAAGCTCAGAAGAGCCGTAATAGGAAAGCTCATGAGAGCCAATATTG
Found at i:55505320 original size:25 final size:24
Alignment explanation
Indices: 55505257--55505423 Score: 95
Period size: 25 Copynumber: 6.7 Consensus size: 24
55505247 ATTAATAGGA
* *
55505257 AAGCTCATGAGAGCCAATTATCGAG
1 AAGCTCAT-AGAGCCAATTAACGGG
* * *
55505282 AAACTCCAGAGAGCCAATTACCGGG
1 AAGCT-CATAGAGCCAATTAACGGG
*
55505307 AAGCTCATACGAGCC-ATAAACGGG
1 AAGCTCATA-GAGCCAATTAACGGG
* *
55505331 AAGCTCAAAAAAGCC-ATTAAATCGGG
1 AAGCTC-ATAGAGCCAATT-AA-CGGG
* * *
55505357 AAGCTCATGAGAGCTAAATAATGGG
1 AAGCTCAT-AGAGCCAATTAACGGG
* * * *
55505382 AACCTTATAAGAGCCAAGTATCGGG
1 AAGCTCAT-AGAGCCAATTAACGGG
*
55505407 AAGCTCGTGAGAGCCAA
1 AAGCTCAT-AGAGCCAA
55505424 ATATTGAGAC
Statistics
Matches: 108, Mismatches: 27, Indels: 14
0.72 0.18 0.09
Matches are distributed among these distances:
24 22 0.20
25 66 0.61
26 18 0.17
27 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (24 bp):
AAGCTCATAGAGCCAATTAACGGG
Found at i:55505332 original size:24 final size:26
Alignment explanation
Indices: 55505303--55505364 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 26
55505293 AGCCAATTAC
**
55505303 CGGGAAGCTCATACGAGCCA-TAAA-
1 CGGGAAGCTCATAAAAGCCATTAAAT
*
55505327 CGGGAAGCTCAAAAAAGCCATTAAAT
1 CGGGAAGCTCATAAAAGCCATTAAAT
55505353 CGGGAAGCTCAT
1 CGGGAAGCTCAT
55505365 GAGAGCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 17 0.53
25 4 0.12
26 11 0.34
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CGGGAAGCTCATAAAAGCCATTAAAT
Found at i:55508787 original size:17 final size:18
Alignment explanation
Indices: 55508765--55508799 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55508755 AACAAGTAAT
55508765 TTAATATT-TTTATTTTA
1 TTAATATTATTTATTTTA
55508782 TTAATATTATTTATTTTA
1 TTAATATTATTTATTTTA
55508800 AATGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTAATATTATTTATTTTA
Found at i:55516043 original size:19 final size:18
Alignment explanation
Indices: 55516003--55516046 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
55515993 TTTCTCTTTT
55516003 TTGCATTCATTGTATTCA
1 TTGCATTCATTGTATTCA
55516021 TTGCATTCA-TGTATTAACA
1 TTGCATTCATTGTATT--CA
55516040 TTGCATT
1 TTGCATT
55516047 GTATCATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 9 0.38
19 9 0.38
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (18 bp):
TTGCATTCATTGTATTCA
Found at i:55516060 original size:19 final size:18
Alignment explanation
Indices: 55516004--55516060 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
55515994 TTCTCTTTTT
55516004 TGCATTCATTGTATTCAT-
1 TGCATTCATTGTA-TCATA
55516022 TGCATTCA-TGTAT--TA
1 TGCATTCATTGTATCATA
*
55516037 -ACATTGCATTGTATCATA
1 TGCATT-CATTGTATCATA
55516055 TGCATT
1 TGCATT
55516061 AAGTCTCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 6 0.19
17 4 0.13
18 10 0.32
19 4 0.13
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (18 bp):
TGCATTCATTGTATCATA
Found at i:55518605 original size:22 final size:23
Alignment explanation
Indices: 55518563--55518606 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
55518553 ACTTCACTTT
*
55518563 AAAAAAAAATAATAAATGAAAAC
1 AAAAAAAAATAATAAAAGAAAAC
55518586 AAAAAAAGAA-AA-AAAAGAAAA
1 AAAAAAA-AATAATAAAAGAAAA
55518607 AGAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAAAAAAATAATAAAAGAAAAC
Found at i:55519322 original size:15 final size:16
Alignment explanation
Indices: 55519298--55519328 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55519288 TAAAAATGAC
55519298 AATATGCATTCATACA
1 AATATGCATTCATACA
55519314 AATAT-CATTCATACA
1 AATATGCATTCATACA
55519329 CATCTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (16 bp):
AATATGCATTCATACA
Found at i:55519675 original size:54 final size:52
Alignment explanation
Indices: 55519606--55520164 Score: 203
Period size: 54 Copynumber: 11.4 Consensus size: 52
55519596 TTCCCTGGCA
* * *
55519606 TTGCAGTGAAACAGATTAAAGCTACAAATTATGCCAAATCTTATCTTCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTAT--CGAATCTTATCTTCCTGAAG
* * *
55519660 TTGCAGTGGAGCAGATTGAAGCTAC-------C-AACCTTATC-TCTTTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTC-CTGAAG
* * * * **
55519704 TTACAGCGGAGCAGACTGAAG--AC-----ATCGAATCTTAT-TTCCCTGGCG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTT-CCTGAAG
* * *
55519749 TTGCAGTGGAACAGATTAAAGCTA-AATATTATAACGGATCTTATCTTCCTAAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAA-ATTAT--CGAATCTTATCTTCCTGAAG
* *
55519803 TTGCAGTTGAGCAGATTAAAGCTACAAGTTATTGCGAATCTTATCTTCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTA-T-CGAATCTTATCTTCCTGAAG
** * *
55519857 TTGCAGTGGAGCAGATTAAAGC--C--ACCA--GCA--TTATCTCCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTCCTGAAG
* * * * * **
55519901 TTACAGCGGAGCAGACTGAAG--AC-----AGCGAATCTTAT-TTCCCTGGCG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTT-CCTGAAG
* * *
55519946 TTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTAT--CGAATCTTATCTTCCTGAAG
* * ** * *
55520000 TTACGGTGGAGCAGATTAAAGC--C--ACCA--GCA--TTATCTCCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTCCTGAAG
* * *
55520044 TTGCAGCGGAGCAGACT---G--A-AAA-CATCGAATCTTAT-TTCCCT-AACG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTT-CCTGAA-G
* * * * *
55520089 TTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGGATTTTATCTTTCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTAT--CGAATCTTATCTTCCTGAAG
*
55520143 TTGCAGTAGAGCAGATTAAAGC
1 TTGCAGTGGAGCAGATTAAAGC
55520165 CACCAGCATT
Statistics
Matches: 374, Mismatches: 76, Indels: 110
0.67 0.14 0.20
Matches are distributed among these distances:
41 4 0.01
42 3 0.01
43 6 0.02
44 92 0.25
45 74 0.20
46 5 0.01
47 3 0.01
48 1 0.00
50 4 0.01
51 3 0.01
52 7 0.02
54 161 0.43
55 11 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (52 bp):
TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTCCTGAAG
Found at i:55519753 original size:143 final size:142
Alignment explanation
Indices: 55519489--55519827 Score: 464
Period size: 143 Copynumber: 2.4 Consensus size: 142
55519479 GATTGAAGTC
* * * * *
55519489 ATTATGACAGATCTTATCTTCTTGAAGTTGTAGTGGAGCAAAGATTGAAGCCACTAGCCTTATCT
1 ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGC--AGATTGAAGCTACCAACCTTATCT
* *
55519554 CCCTGAAGTTGCGCGGAGCAGATTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACA
64 CCCTGAAGTTACGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACA
55519619 GATTAAAGCTACAA-
129 GATTAAAGCTA-AAT
* * *
55519633 ATTATGCCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAACCTTATCTCT
1 ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAACCTTATCTCC
* * * *
55519698 TTGAAGTTACAGCGGAGCAGACTGAAGACATCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTAC-GCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACAG
55519763 ATTAAAGCTAAAT
130 ATTAAAGCTAAAT
* * * * *
55519776 ATTATAACGGATCTTATCTTCCTAAAGTTGCAGTTGAGCAGATTAAAGCTAC
1 ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
55519828 AAGTTATTGC
Statistics
Matches: 172, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
142 32 0.19
143 105 0.61
144 35 0.20
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (142 bp):
ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAACCTTATCTCC
CTGAAGTTACGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACAGA
TTAAAGCTAAAT
Found at i:55519820 original size:197 final size:197
Alignment explanation
Indices: 55519617--55520021 Score: 634
Period size: 197 Copynumber: 2.1 Consensus size: 197
55519607 TGCAGTGAAA
*
55519617 CAGATTAAAGCTACAAATTA-TGCCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAG
1 CAGATTAAAGCTACAAATTATTG-CAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * ** *
55519681 CTACCAACCTTATCTCTTTGAAGTTACAGCGGAGCAGACTGAAGACATCGAATCTTATTTCCCTG
65 CCACCAACATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTG
*
55519746 GCGTTGCAGTGGAACAGATTAAAGCTA-AATATTATAACGGATCTTATCTTCCTAAAGTTGCAGT
130 GCGTTGCAGTGGAACAGATTAAAGCTACAA-ATTATAACGGATCTTATCTTCCTAAAGTTACAGT
*
55519810 TGAG
194 GGAG
* *
55519814 CAGATTAAAGCTACAAGTTATTGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGC
1 CAGATTAAAGCTACAAATTATTGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGC
*
55519879 CACCAGCATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGG
66 CACCAACATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGG
** * * *
55519944 CGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAAGTTACGGTGG
131 CGTTGCAGTGGAACAGATTAAAGCTACAAATTATAACGGATCTTATCTTCCTAAAGTTACAGTGG
55520009 AG
196 AG
55520011 CAGATTAAAGC
1 CAGATTAAAGC
55520022 CACCAGCATT
Statistics
Matches: 190, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
197 186 0.98
198 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (197 bp):
CAGATTAAAGCTACAAATTATTGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGC
CACCAACATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGG
CGTTGCAGTGGAACAGATTAAAGCTACAAATTATAACGGATCTTATCTTCCTAAAGTTACAGTGG
AG
Found at i:55519898 original size:44 final size:45
Alignment explanation
Indices: 55519843--55520201 Score: 183
Period size: 44 Copynumber: 7.6 Consensus size: 45
55519833 ATTGCGAATC
*
55519843 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCA-
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
* * * * * * *
55519887 TTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGC-GAAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
* ** * **
55519931 CTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGAT
1 -TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--C--ACCA--GC--AT
* * * *
55519985 CTTATCTTCTTGAAGTTACGGTGGAGCAGATTAAAGCCACCAGCA-
1 -TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
* * * * *
55520030 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAA-ACATC-GAAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCCACCAGCAT
* * * **
55520074 CTTATTTCCCT-AACGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGGATT
1 -TTATCTCCCTGAA-GTTGCAGTGGAGCAGATTAAAGC--C--ACCA--GC--A-T
** *
55520129 TTATCTTTCTGAAGTTGCAGTAGAGCAGATTAAAGCCACCAGCA-
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
*
55520173 TTATCTCCCTGAAGTTGCAGCGGAGCAGA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
55520202 CTGAAGACAG
Statistics
Matches: 229, Mismatches: 59, Indels: 54
0.67 0.17 0.16
Matches are distributed among these distances:
43 4 0.02
44 91 0.40
45 53 0.23
46 2 0.01
47 2 0.01
48 4 0.02
49 3 0.01
50 4 0.02
52 4 0.02
54 59 0.26
55 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
Found at i:55520260 original size:143 final size:143
Alignment explanation
Indices: 55519802--55520246 Score: 712
Period size: 143 Copynumber: 3.1 Consensus size: 143
55519792 TCTTCCTAAA
* * * * * *
55519802 GTTGCAGTTGAGCAGATTAAAGCTACAAGTTATTGCGAATCTTATCTTCCTGAAGTTGCAGTGGA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTCTGAAGTTGCAGTGGA
*
55519867 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATC
66 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
55519932 TTATTTCCCTGGC
131 TTATTTCCCTGGC
* *
55519945 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATC-TTCTTGAAGTTACGGTGG
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTC-TGAAGTTGCAGTGG
* *
55520009 AGCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAAACATCGAAT
65 AGCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAAT
**
55520074 CTTATTTCCCTAAC
130 CTTATTTCCCTGGC
* * *
55520088 GTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGGATTTTATCTTTCTGAAGTTGCAGTAGA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTCTGAAGTTGCAGTGGA
55520153 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
66 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
55520218 TTATTTCCCTGGC
131 TTATTTCCCTGGC
* *
55520231 GTTGCAATGGAGCAGA
1 GTTGCAGTGGAACAGA
55520247 CTAGAACCAC
Statistics
Matches: 275, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
142 2 0.01
143 270 0.98
144 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (143 bp):
GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTCTGAAGTTGCAGTGGA
GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
TTATTTCCCTGGC
Found at i:55520457 original size:133 final size:133
Alignment explanation
Indices: 55520181--55520463 Score: 413
Period size: 133 Copynumber: 2.1 Consensus size: 133
55520171 CATTATCTCC
* *
55520181 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
1 CTGAAGTTGTAGCGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
* * * * *
55520246 ACTAGAACCACAAATCTCGTCCCCCTGAAGTTGCGGCAGAGTAGATTGAGGGTACAAATCGTATT
66 ACTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGATTGAGGGTACAAATCGTATC
*
55520311 TCT
131 TAT
* * * * * *
55520314 TTGAAATTGTAGCGGAGCAGACTGAATACAGCAAATCTTATTTCCTTGGCGTTGTAGTGGAGCAG
1 CTGAAGTTGTAGCGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
* *
55520379 ATTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGGTTGAGGGTACAAATCGTATC
66 ACTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGATTGAGGGTACAAATCGTATC
55520444 TAT
131 TAT
*
55520447 CTGAAGTTGTAGTGGAG
1 CTGAAGTTGTAGCGGAG
55520464 TGGATCGAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
133 131 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (133 bp):
CTGAAGTTGTAGCGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
ACTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGATTGAGGGTACAAATCGTATC
TAT
Found at i:55520495 original size:28 final size:28
Alignment explanation
Indices: 55520455--55520511 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
55520445 ATCTGAAGTT
*
55520455 GTAGTGGAGTGGATCGAAACAACAAGAC
1 GTAGTGGACTGGATCGAAACAACAAGAC
*
55520483 GTAGTGGACTGGATCGAAGCAACAAGAC
1 GTAGTGGACTGGATCGAAACAACAAGAC
55520511 G
1 G
55520512 CATAGACTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.33, T:0.14
Consensus pattern (28 bp):
GTAGTGGACTGGATCGAAACAACAAGAC
Found at i:55522101 original size:5 final size:6
Alignment explanation
Indices: 55522053--55522108 Score: 51
Period size: 6 Copynumber: 8.7 Consensus size: 6
55522043 AATTAGTTTG
*
55522053 TTTTAT TTTTATT TCTTTCAT TATTTA- TCTTAT TATTTAT TTTTAT TTTTAT
1 TTTTAT TTTTA-T T-TTT-AT T-TTTAT TTTTAT T-TTTAT TTTTAT TTTTAT
55522105 TTTT
1 TTTT
55522109 CTCTTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 3 0.07
6 22 0.52
7 8 0.19
8 8 0.19
9 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:55522114 original size:30 final size:34
Alignment explanation
Indices: 55522054--55522119 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 34
55522044 ATTAGTTTGT
55522054 TTTATTTTTATTTCTTTCATTATTTATCTTATTA
1 TTTATTTTTATTTCTTTCATTATTTATCTTATTA
*
55522088 TTTATTTTTA-TT-TTT-ATT-TTTCTCTTATTA
1 TTTATTTTTATTTCTTTCATTATTTATCTTATTA
55522118 TT
1 TT
55522120 GTCGTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 13 0.42
31 3 0.10
32 3 0.10
33 2 0.06
34 10 0.32
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (34 bp):
TTTATTTTTATTTCTTTCATTATTTATCTTATTA
Found at i:55525121 original size:4 final size:4
Alignment explanation
Indices: 55525114--55525164 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
55525104 TTTATATATA
55525114 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
55525162 TAT
1 TAT
55525165 TGCTTATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:55529454 original size:27 final size:27
Alignment explanation
Indices: 55529416--55529467 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
55529406 ATCCATGATG
*
55529416 CTTTTACTTATTAAAAATTTCAAATTT
1 CTTTTACCTATTAAAAATTTCAAATTT
55529443 CTTTTACCTATTAAAAATTTCAAAT
1 CTTTTACCTATTAAAAATTTCAAAT
55529468 ATATTTGAAA
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:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (27 bp):
CTTTTACCTATTAAAAATTTCAAATTT
Found at i:55530305 original size:16 final size:16
Alignment explanation
Indices: 55530284--55530338 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
55530274 AGAATGGAAA
55530284 GAAAATTGAAAGGATG
1 GAAAATTGAAAGGATG
**
55530300 GAAAATTGGAGGGGATG
1 GAAAATT-GAAAGGATG
*
55530317 GAAAACT-AGAAGGATG
1 GAAAATTGA-AAGGATG
55530333 GAAAAT
1 GAAAAT
55530339 ATAATTTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 17 0.55
17 13 0.42
ACGTcount: A:0.47, C:0.02, G:0.35, T:0.16
Consensus pattern (16 bp):
GAAAATTGAAAGGATG
Found at i:55531122 original size:18 final size:17
Alignment explanation
Indices: 55531083--55531124 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
55531073 TATTTCTTTT
*
55531083 TTTTTC-TTTTTCTAAA
1 TTTTTCTTTTTTCAAAA
55531099 TCTTTTCTTTTTTCAATAA
1 T-TTTTCTTTTTTCAA-AA
55531118 TTTTTCT
1 TTTTTCT
55531125 CATCTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 5 0.23
18 13 0.59
19 3 0.14
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTCTTTTTTCAAAA
Found at i:55531405 original size:11 final size:11
Alignment explanation
Indices: 55531389--55531414 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55531379 TATTTTTTAA
55531389 TTTTAAAATAT
1 TTTTAAAATAT
55531400 TTTTAAAATAT
1 TTTTAAAATAT
55531411 TTTT
1 TTTT
55531415 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:55533460 original size:297 final size:293
Alignment explanation
Indices: 55532909--55533728 Score: 821
Period size: 298 Copynumber: 2.8 Consensus size: 293
55532899 GCATATGATG
* * * * *
55532909 TTTAT-CTATACTATTATTTAAGCTCCTAACTGAGTTGGTGTCACCCTTAATTAGGTCACCAACT
1 TTTATACT-TACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACTAGATCACCAAAT
* * **
55532973 CGATTAG-GAAAATTAT-GAAAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGA-ACACA
65 TGATTAGAAAAAATTATAG-AAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGA-GTA
* * * * * *
55533035 CTTTAGTTTTTT-TTATTAAAAAGATCAATAAAAATATGCAAATGATGATATTTGAGA-TTGAAC
128 CTTTAGTTTTTTATTTTTTAAAA-AT--A-AAAAATATGCATATG-TGA-ATTT-AAACCTAAAC
* * * *
55533098 TAATTGCATTAATAAAATCTTTAATTTACCACTCAACTAAAATTTTATTTTAATATTTTATACAT
186 -AATTGCATTAGTAAATTTTTTAATTTACCACTCAACTAAAATTTTATTTTAACATTTTATACAT
55533163 TTTAA-TTTATTATGCAAACTTAATCACTTCCATCAATTGTATA
250 TTTAATTTTATTATGCAAACTTAATCACTTCCATCAATTGTATA
55533206 TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACCTA-ATCACCAAAT
1 TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAA-CTAGATCACCAAAT
* *
55533270 TGATTAGAAAAAATTATAGAAATACCCTTTTGTAATTAAAATAAGTTATATTATTTGAGGGTACT
65 TGATTAGAAAAAATTATAGAAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGAGTACT
55533335 TTAGTATTTTTATTTTTTAAAAATAAAAAATATGCATATAGTGAGATTTAAACCTAAATCAATTG
130 TTAGT-TTTTTATTTTTTAAAAATAAAAAATATGCATAT-GTGA-ATTTAAACCTAAA-CAATTG
* *
55533400 CATTAGTAAATTTTTTAATTTGCCACTCAACTAAAATTTTATTTTGACATTTTCATACATTTTAA
191 CATTAGTAAATTTTTTAATTTACCACTCAACTAAAATTTTATTTTAACATTTT-ATACATTTTAA
* * * * *
55533465 TTTTATTATGCATACTTTATTACTTCCATCAATTTTATT
255 TTTTATTATGCAAACTTAATCACTTCCATCAATTGTATA
*** * * * *
55533504 TTTATACTTACTATTA-TT--GCTCTTGTTTGAGTTGATGTTACCCTCAA-TCAGATTACC-AAC
1 TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACT-AGATCACCAAAT
* * * * * *
55533564 TCATTA-AAGAATTTACGAAATACCATTACCCTTTTGTAATTAAAATAAATTATATTATTCGAGA
65 TGATTAGAAAAAATTA-TAGA-A--A-TACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGA
* * * *
55533628 GTACTTTAGTCTTTTTATTTTTTTTAAAAAT-AAAATTAAGCATATGGTGTAATTTGAACCCAAA
125 GTACTTTAGT-TTTTTA--TTTTTTAAAAATAAAAAATATGCATAT-GTG-AATTTAAACCTAAA
**
55533692 CCAATTATATTAGTAAAATTTTTT-A-TTACCAC-CAACT
185 -CAATTGCATTAGT-AAATTTTTTAATTTACCACTCAACT
55533729 CGGTTAGAAA
Statistics
Matches: 446, Mismatches: 54, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
293 8 0.02
294 10 0.02
295 32 0.07
296 75 0.17
297 81 0.18
298 164 0.37
299 46 0.10
300 30 0.07
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (293 bp):
TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACTAGATCACCAAATT
GATTAGAAAAAATTATAGAAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGAGTACTT
TAGTTTTTTATTTTTTAAAAATAAAAAATATGCATATGTGAATTTAAACCTAAACAATTGCATTA
GTAAATTTTTTAATTTACCACTCAACTAAAATTTTATTTTAACATTTTATACATTTTAATTTTAT
TATGCAAACTTAATCACTTCCATCAATTGTATA
Found at i:55538078 original size:29 final size:29
Alignment explanation
Indices: 55538033--55538106 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
55538023 ACGACGCAGA
55538033 CCCATCAACAGCACCCAGACAATCACCGG
1 CCCATCAACAGCACCCAGACAATCACCGG
* * * *
55538062 CCCATCATCAGCGCCCATACAATCACCAAG
1 CCCATCAACAGCACCCAGACAATCACC-GG
*
55538092 CCCAACAACAGCACC
1 CCCATCAACAGCACC
55538107 GACACAGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.35, C:0.46, G:0.11, T:0.08
Consensus pattern (29 bp):
CCCATCAACAGCACCCAGACAATCACCGG
Found at i:55538202 original size:18 final size:18
Alignment explanation
Indices: 55538179--55538216 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55538169 TGCCAGGTGC
* *
55538179 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
55538197 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
55538215 GT
1 GT
55538217 TTCCGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:55542084 original size:125 final size:126
Alignment explanation
Indices: 55541859--55542400 Score: 696
Period size: 125 Copynumber: 4.3 Consensus size: 126
55541849 TCAGGCCAAA
* * * *
55541859 CAGGAGCTACTGTAGCAAAAGCGTGTCCATGTAGGAGCTTCTTTCAGTACTTTTGCTGTCAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
*
55541924 ATCCTGCTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTACTCGAAATTA-TTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* * * * *
55541984 CAGGAGTTACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTTAGTATTTTTGTTGGCAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
* ** *
55542049 ATCCTACTTAAAATGTTTTTGACACTATTTGCTCAGAAATGTCTACTCGAAATTA-TTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* * * * * * *
55542109 CAAGAGCTACTATAGCAAAAGTGCGTCAATGGGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
* * * ** *
55542174 ATCTTGCTTAAAGCATTTTTGACACTATTTGCTTAGAAATATCTACTTGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* ** * *
55542235 CAGGAGCTACTGTAGCAAAAGCGCGTCCACATGAAAGCTTCTTTCAGTACTTTTACT-GAAAATG
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAA-G
** *
55542299 CATCCTGCTTAAAGCGTTTTT-ACACTATTTGCTCAGAAACGTCTTTTCAAAATTATTTTTTT
65 CATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTA-TTTTTT
* * *
55542361 CAGAAGCTACTGTAACAAAAGAGCGTCCACGTGGGAGCTT
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
55542401 TTTTAAATTA
Statistics
Matches: 355, Mismatches: 59, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
125 243 0.68
126 112 0.32
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
Found at i:55542637 original size:95 final size:95
Alignment explanation
Indices: 55542437--55542735 Score: 397
Period size: 95 Copynumber: 3.1 Consensus size: 95
55542427 AGTAACCATA
* * *
55542437 AACCCCAAACCCTAATTTATTTGAGTTTTTCCTTTAAAACCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTC-TTAAAAACCTAAACACTAAACCCTAATCTAAT
*
55542502 TTTTTAAAAATTTATAATTAATTTACTCAAGT
64 TTTTTAAAAATTTATAATTAATTTACTTAAGT
*
55542534 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACTCTTAACACTAAACCCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAAC-CTAAACACTAAACCCTAATCTAATT
*
55542599 TTTTAAAAATTT-TAATTAAATTACTTAAGT
65 TTTTAAAAATTTATAATTAATTTACTTAAGT
* * *
55542629 AACCCTAAACCCTAATTTAATTGATTTTTTCTTTAAAAACCATAAACAC-AAAACCTAATCCAA-
1 AACCCTAAACCCTAATTTATTTGATTTTTTC-TTAAAAACC-TAAACACTAAACCCTAATCTAAT
* * * * *
55542692 TTTTGAAAATTTTATAATTAATTTAATTGAGA
64 TTTTTAAAAATTTATAATTAATTTACTTAAGT
*
55542724 AATCCTAAACCC
1 AACCCTAAACCC
55542736 CAATCCCTTA
Statistics
Matches: 181, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
94 11 0.06
95 91 0.50
96 56 0.31
97 23 0.13
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCTAAACACTAAACCCTAATCTAATTT
TTTAAAAATTTATAATTAATTTACTTAAGT
Found at i:55549072 original size:24 final size:24
Alignment explanation
Indices: 55549038--55549088 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
55549028 TTTCTAGAAG
* *
55549038 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
55549062 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
55549086 ATT
1 ATT
55549089 CGACTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:55552804 original size:22 final size:22
Alignment explanation
Indices: 55552758--55552833 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 22
55552748 TGTCAATGAA
55552758 TTTCCAGAGAAAAAGA-AAAGG-T
1 TTTCCAG-GAAAAA-ACAAAGGAT
*
55552780 TTTCCAGGAAAAAACATAGGAT
1 TTTCCAGGAAAAAACAAAGGAT
* **
55552802 TTTCCGAGAAAGAAAACCGAGGAT
1 TTTCC-AGGAA-AAAACAAAGGAT
55552826 TTTCCAGG
1 TTTCCAGG
55552834 GTCTAAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 10 0.22
22 13 0.29
23 6 0.13
24 15 0.33
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.21
Consensus pattern (22 bp):
TTTCCAGGAAAAAACAAAGGAT
Found at i:55556268 original size:17 final size:16
Alignment explanation
Indices: 55556241--55556275 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
55556231 ATTTTCTCAA
55556241 AAATAAATAAAAAAAG
1 AAATAAATAAAAAAAG
*
55556257 AAATACAATAAAAATAG
1 AAATA-AATAAAAAAAG
55556274 AA
1 AA
55556276 TTTTGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAATAAAAAAAG
Found at i:55557463 original size:4 final size:4
Alignment explanation
Indices: 55557448--55557488 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
55557438 TATTTTATCT
55557448 TTTA TCTTA TTTA TTTA TTTA TTT- TTTCA TTTA TTTA TTTA
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
55557489 CCTATCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 24 0.71
5 7 0.21
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:55564576 original size:13 final size:13
Alignment explanation
Indices: 55564551--55564588 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
55564541 ATTAAAAATC
55564551 TAAATTATT-ATT
1 TAAATTATTAATT
55564563 T-AATATATTAATT
1 TAAAT-TATTAATT
55564576 TAAATTATTAATT
1 TAAATTATTAATT
55564589 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.13
12 5 0.22
13 12 0.52
14 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAAATTATTAATT
Found at i:55564720 original size:105 final size:103
Alignment explanation
Indices: 55564569--55564866 Score: 304
Period size: 105 Copynumber: 2.9 Consensus size: 103
55564559 TATTTAATAT
* * *** **
55564569 ATTAATTTAAATTATTAATTATTTTAAATAAATTAGGTTTAGAATTATCCTAATTTAATTTAAAC
1 ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
55564634 TCATAATTATCTTAATTGAAATCCAAATTAATATCTAAACA
66 TCATAATTATCTTAATT-AAAT--AAATTAATATCTAAACA
* ** *
55564675 ATTAA-TTAAATTCCTAATTATCTTATCTAAATTAGAACTCTAATTATCCTAATTTAATTCAAAC
1 ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
* * * * * *
55564739 TCTTAA-T-TC--AA--ATATAAAATATTATCTAACCT
66 TCATAATTATCTTAATTAAATAAATTAATATCTAAACA
* * *
55564771 ATTAATTTAAATTATTAATTATCTTAAATAAATTAGAACTCTAGTTATCCTTATTTAATTTAAAC
1 ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
* *
55564836 TCCTAATTATCTTATTTAAATTAAAATTAAT
66 TCATAATTATCTTAATTAAA-T-AAATTAAT
55564867 TTAATTTAAA
Statistics
Matches: 154, Mismatches: 29, Indels: 19
0.76 0.14 0.09
Matches are distributed among these distances:
96 18 0.12
97 57 0.37
98 4 0.03
99 2 0.01
101 3 0.02
103 4 0.03
104 2 0.01
105 59 0.38
106 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (103 bp):
ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
TCATAATTATCTTAATTAAATAAATTAATATCTAAACA
Found at i:55564808 original size:97 final size:96
Alignment explanation
Indices: 55564665--55564843 Score: 259
Period size: 97 Copynumber: 1.9 Consensus size: 96
55564655 TCCAAATTAA
* **
55564665 TATCTAAACAATTAATTAAATTCCTAATTATCTTATCTAAATTAGAACTCTAATTATCCTAATTT
1 TATCTAAACAATTAATTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTT
*
55564730 AATTCAAACTCTTAATTCAAATATAAAATAT
66 AATTCAAACTCCTAATTCAAATATAAAATAT
* * * * *
55564761 TATCTAACCTATTAATTTAAATTATTAATTATCTTAAATAAATTAGAACTCTAGTTATCCTTATT
1 TATCTAAACAATTAA-TTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATT
*
55564826 TAATTTAAACTCCTAATT
65 TAATTCAAACTCCTAATT
55564844 ATCTTATTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 13 0.18
97 59 0.82
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (96 bp):
TATCTAAACAATTAATTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTT
AATTCAAACTCCTAATTCAAATATAAAATAT
Found at i:55564830 original size:26 final size:26
Alignment explanation
Indices: 55564772--55564860 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
55564762 ATCTAACCTA
* ** *
55564772 TTAATTTAAATTATTAATTATCTTAA
1 TTAATTTAAACTCCTAATTATCTTAT
* * *
55564798 ATAAATTAGAACT-CTAGTTATCCTTAT
1 TTAATTTA-AACTCCTAATTAT-CTTAT
55564825 TTAATTTAAACTCCTAATTATCTTAT
1 TTAATTTAAACTCCTAATTATCTTAT
*
55564851 TTAAATTAAA
1 TTAATTTAAA
55564861 ATTAATTTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
26 30 0.60
27 20 0.40
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAATTTAAACTCCTAATTATCTTAT
Found at i:55564845 original size:21 final size:21
Alignment explanation
Indices: 55564821--55564879 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
55564811 CTAGTTATCC
**
55564821 TTATTTAATTTAAACTCCTAA
1 TTATTTAATTTAAACTCAAAA
*
55564842 TTATCTT-ATTTAAA-TTAAAA
1 TTAT-TTAATTTAAACTCAAAA
55564862 TTAATTTAATTTAAACTC
1 TT-ATTTAATTTAAACTC
55564880 TTAGTTGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 7 0.23
21 20 0.67
22 3 0.10
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTTAATTTAAACTCAAAA
Found at i:55564845 original size:27 final size:25
Alignment explanation
Indices: 55564786--55564860 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
55564776 TTTAAATTAT
**
55564786 TAATTATCTTAAATAAATTAGAACTC
1 TAATTATCTTATTTAAATTA-AACTC
* *
55564812 TAGTTATCCTTATTTAATTTAAACTCC
1 TAATTAT-CTTATTTAAATTAAACT-C
55564839 TAATTATCTTATTTAAATTAAA
1 TAATTATCTTATTTAAATTAAA
55564861 ATTAATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 24 0.59
27 17 0.41
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (25 bp):
TAATTATCTTATTTAAATTAAACTC
Found at i:55568967 original size:14 final size:14
Alignment explanation
Indices: 55568948--55568976 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55568938 CCATACTTCC
55568948 GTGAAACCCATATG
1 GTGAAACCCATATG
55568962 GTGAAACCCATATG
1 GTGAAACCCATATG
55568976 G
1 G
55568977 ACAAGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (14 bp):
GTGAAACCCATATG
Found at i:55573888 original size:6 final size:6
Alignment explanation
Indices: 55573871--55573917 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
55573861 AAAATGAGAC
*
55573871 TATAAA TGTAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAA
55573918 TTTGACTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:55577795 original size:14 final size:14
Alignment explanation
Indices: 55577772--55577802 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55577762 TGTCGTGTTT
*
55577772 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
55577786 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
55577800 TTA
1 TTA
55577803 AAACAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:55578358 original size:103 final size:103
Alignment explanation
Indices: 55578179--55578383 Score: 365
Period size: 103 Copynumber: 2.0 Consensus size: 103
55578169 GTACAGCTCG
* *
55578179 CAGAAACCGTAGAGAAGCAAGGCATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
1 CAGAAACCGTAAAGAAGCAAGACATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
55578244 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCAC
66 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCAC
* * *
55578282 CAGAAACCGTAAAGAAGCACGACATAGTTGACAGTATATAGTGGAAGAGTAATAGGACGTTATTA
1 CAGAAACCGTAAAGAAGCAAGACATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
55578347 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCA
66 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCA
55578384 GCTACCTCTT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (103 bp):
CAGAAACCGTAAAGAAGCAAGACATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
TTATCACTGAAGAGATGGGTGATAATCAGAATAATCAC
Found at i:55595090 original size:12 final size:12
Alignment explanation
Indices: 55595073--55595098 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55595063 ACCGTCCACC
55595073 CATTACTAAGCA
1 CATTACTAAGCA
55595085 CATTACTAAGCA
1 CATTACTAAGCA
55595097 CA
1 CA
55595099 ATGCTGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (12 bp):
CATTACTAAGCA
Found at i:55598820 original size:19 final size:19
Alignment explanation
Indices: 55598798--55598834 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
55598788 TTTTTATTTT
55598798 TTTA-TTTAATTATAAAGTA
1 TTTAGTTTAATT-TAAAGTA
55598817 TTTAGTTTAATTTAAAGT
1 TTTAGTTTAATTTAAAGT
55598835 TTTTCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTAGTTTAATTTAAAGTA
Found at i:55615315 original size:19 final size:18
Alignment explanation
Indices: 55615280--55615315 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55615270 GAAGCAAGCA
*
55615280 ATGATTGAAGAAATCAGG
1 ATGATTGAAAAAATCAGG
55615298 ATGATTGAAAAGAATCAG
1 ATGATTGAAAA-AATCAG
55615316 ACCTGGAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (18 bp):
ATGATTGAAAAAATCAGG
Found at i:55617476 original size:20 final size:19
Alignment explanation
Indices: 55617451--55617494 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
55617441 TAGTGAAATT
55617451 GGAGAAATAAAGAATAAAG-A
1 GGAGAAA-AAAGAA-AAAGAA
55617471 GGAG-AAAAAGAAAAAGAA
1 GGAGAAAAAAGAAAAAGAA
55617489 GGAGAA
1 GGAGAA
55617495 GATACATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 3 0.14
20 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.05
Consensus pattern (19 bp):
GGAGAAAAAAGAAAAAGAA
Found at i:55617660 original size:66 final size:68
Alignment explanation
Indices: 55617560--55617696 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 68
55617550 CAAGGAGGCA
* * * * *
55617560 AAGATGAAGAAAGAAGGAAAACACGAGGATAAAGAGG-T-GGTAAAAGAAGATGAAGAGAAAGAA
1 AAGAAGAAGAAAGAAGAAAAACACAAGGAAAAAGAGGTTAGGGAAAAGAAGATGAAGAGAAAGAA
55617623 GAG
66 GAG
*
55617626 AAGAAGAAGAAAGAA-AAAAAGCACAAGGAAAAAGAGGTTGAGGGAGAAGAAGATGAAGAGAAAG
1 AAGAAGAAGAAAGAAGAAAAA-CACAAGGAAAAAGAGGTT-AGGGAAAAGAAGATGAAGAGAAAG
*
55617690 ATGAG
64 AAGAG
55617695 AA
1 AA
55617697 AAAATAGAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
65 4 0.07
66 28 0.47
67 1 0.02
69 27 0.45
ACGTcount: A:0.58, C:0.03, G:0.33, T:0.07
Consensus pattern (68 bp):
AAGAAGAAGAAAGAAGAAAAACACAAGGAAAAAGAGGTTAGGGAAAAGAAGATGAAGAGAAAGAA
GAG
Found at i:55624498 original size:18 final size:16
Alignment explanation
Indices: 55624464--55624499 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
55624454 CAATGTATAA
55624464 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
55624480 TATTTTATAATATACTTT
1 TATTTT-TAATA-ACTTT
55624498 TA
1 TA
55624500 AAAACCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:55629302 original size:22 final size:21
Alignment explanation
Indices: 55629263--55629327 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
55629253 ATAATCAAAC
* *
55629263 AATAACAAAAAAGTAGCAACAA
1 AATAATAAAAAA-CAGCAACAA
* *
55629285 AATAGTAAGAAAACAGCAGCAA
1 AATAATAA-AAAACAGCAACAA
* *
55629307 AATAATAAAAAATAACAACAA
1 AATAATAAAAAACAGCAACAA
55629328 TAAAACAAGC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 10 0.29
22 20 0.59
23 4 0.12
ACGTcount: A:0.68, C:0.12, G:0.09, T:0.11
Consensus pattern (21 bp):
AATAATAAAAAACAGCAACAA
Found at i:55633431 original size:17 final size:17
Alignment explanation
Indices: 55633409--55633443 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55633399 ATGATAGTTC
55633409 AAAAAT-AAATAGATTTT
1 AAAAATAAAATA-ATTTT
55633426 AAAAATAAAATAATTTT
1 AAAAATAAAATAATTTT
55633443 A
1 A
55633444 CATCATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATAAAATAATTTT
Found at i:55635326 original size:34 final size:37
Alignment explanation
Indices: 55635276--55635347 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
55635266 GGCCCGGGAA
*
55635276 TAAATATATTTTTTATTTTTTA-TTTTAAAATACTTT
1 TAAATATATTTTTTATTTTTTATTTTTAAAATAATTT
55635312 TAAA-ATA-TTTTTATTTTTTATTTTTAAAATAATTT
1 TAAATATATTTTTTATTTTTTATTTTTAAAATAATTT
55635347 T
1 T
55635348 TTAATGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 13 0.38
35 17 0.50
36 4 0.12
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (37 bp):
TAAATATATTTTTTATTTTTTATTTTTAAAATAATTT
Found at i:55635357 original size:26 final size:24
Alignment explanation
Indices: 55635309--55635359 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
55635299 TTTAAAATAC
* *
55635309 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
55635333 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
55635359 T
1 T
55635360 AAAAAATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:55635647 original size:17 final size:18
Alignment explanation
Indices: 55635625--55635659 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
55635615 TTTTATTAAT
55635625 TAAAAAAATT-CAAAAAG
1 TAAAAAAATTACAAAAAG
55635642 TAAAAAAATTACAAAAAG
1 TAAAAAAATTACAAAAAG
55635660 ACCCCTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
TAAAAAAATTACAAAAAG
Found at i:55637058 original size:12 final size:13
Alignment explanation
Indices: 55637041--55637069 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55637031 AGGTTTCCAA
55637041 AAATGGAAA-TGG
1 AAATGGAAATTGG
55637053 AAATGGAAATTGG
1 AAATGGAAATTGG
55637066 AAAT
1 AAAT
55637070 TTGTAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (13 bp):
AAATGGAAATTGG
Found at i:55637291 original size:26 final size:27
Alignment explanation
Indices: 55637221--55637310 Score: 112
Period size: 26 Copynumber: 3.3 Consensus size: 27
55637211 AATTTATCAG
55637221 GGGTAAAATCGTCAAAATTTTGACATCCAT
1 GGGTAAAATCGTCAAAATTTTGACA---AT
*
55637251 GAGTAAAATCGTCAAAATTTT-ACAAT
1 GGGTAAAATCGTCAAAATTTTGACAAT
* *
55637277 GGGTAAAATCATCAAAATTTTGA-TAT
1 GGGTAAAATCGTCAAAATTTTGACAAT
55637303 GGGTAAAA
1 GGGTAAAA
55637311 CATGGATAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
26 31 0.56
27 1 0.02
29 3 0.05
30 20 0.36
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (27 bp):
GGGTAAAATCGTCAAAATTTTGACAAT
Found at i:55645325 original size:345 final size:345
Alignment explanation
Indices: 55644693--55645384 Score: 1233
Period size: 345 Copynumber: 2.0 Consensus size: 345
55644683 TAGATAAATT
*
55644693 GTGAAAATGTTAATATGAGATCATATGCATCAAGTTAAATGTTATAAGGCAATTAGGACTGATAA
1 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
* * *
55644758 TTGAAATAAATTCATGTATAAATCAAAAACTGATAGATAATAGTGGAAAAAGGAAATTTTCAAAT
66 TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
* * *
55644823 TAGTCTCTGATACTTCTATCCTTGTTGTTTGTTCTTGGTAAGTTCGTACAAGACTTACTTTATTA
131 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
*
55644888 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATATATGCTTTTG
196 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATAAATGCTTTTG
55644953 GCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTAG
261 GCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTAG
55645018 TAATTGATTAATGGTATAAA
326 TAATTGATTAATGGTATAAA
* *
55645038 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATTTTATAAGGCAATTGGGACTGATAA
1 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
*
55645103 TTGAAATAAATTCATGTATAAATCAAGAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
66 TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
*
55645168 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATGCAAGACTTACTTTATTA
131 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
* * *
55645233 ATTGATGATATATTTGTGCTATGTTGTTTTGTTTTATGGTTGAATTGTTATTATACAATGTTTTT
196 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATA-AATGCTTTT
55645298 GGCATCAAAAGGATTAAATCG-AAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
260 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
55645362 GTAATTGATTAATGGTATAAA
325 GTAATTGATTAATGGTATAAA
55645383 GT
1 GT
55645385 AAATACTATA
Statistics
Matches: 331, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
345 303 0.92
346 28 0.08
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (345 bp):
GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATAAATGCTTTTG
GCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTAG
TAATTGATTAATGGTATAAA
Found at i:55647938 original size:17 final size:17
Alignment explanation
Indices: 55647916--55647951 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55647906 TTTATATAAA
55647916 AGTAAAATTATCCTTTG
1 AGTAAAATTATCCTTTG
*
55647933 AGTAAAATTATCTTTTG
1 AGTAAAATTATCCTTTG
55647950 AG
1 AG
55647952 AAACTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (17 bp):
AGTAAAATTATCCTTTG
Found at i:55663115 original size:146 final size:144
Alignment explanation
Indices: 55662785--55663512 Score: 1187
Period size: 146 Copynumber: 5.2 Consensus size: 144
55662775 CGTTTTTATA
55662785 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
1 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
55662850 CGACGCCGTTTTGCTATTCT-AAA----TTTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTT
66 CGACGCCGTTTTGCTATTCTAAAATTTTTTTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTT
*
55662910 ATATAGGAAACGCC
131 TTATAGGAAACGCC
*
55662924 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAA
1 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
*
55662989 CGACGCCGTTTTGCTATTCTAACAATTTTTTATTTTTTTATAAGTTGATTTATTTTTTGCGGCGT
66 CGACGCCGTTTTGCTATTCTAA-AATTTTTT-TTTTTTTATAAATTGATTTATTTTTTGCGGCGT
*
55663054 TTTTATAGAAAACGCC
129 TTTTATAGGAAACGCC
55663070 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
1 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
55663135 CGACGCCGTTTTGCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGT
66 CGACGCCGTTTTGCTATTCTAAAA-TTTTTT-TTTTTTTATAAATTGATTTATTTTTTGCGGCGT
55663200 TTTTATAGGAAACGCC
129 TTTTATAGGAAACGCC
55663216 GCTATTGCTTACCTTTA-----G---------AAGCGCCGCAAAA-TTTTT-ATTTTGAACAAAA
1 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
55663265 CGACGCC-TTTTGCTATTCT-AAATTTTTTTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTT
66 CGACGCCGTTTTGCTATTCTAAAATTTTTTTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTT
55663328 TTATAGGAAACGCC
131 TTATAGGAAACGCC
*
55663342 GCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
1 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
*
55663407 CGACGCCGCTTTGCTATTCTAAAATTTTTTTATTTTTTATAAATTGATTTATTTTTTGCGGCGTT
66 CGACGCCGTTTTGCTATTCTAAAATTTTTTT-TTTTTTATAAATTGATTTATTTTTTGCGGCGTT
55663472 TTTATAGGAAACGCC
130 TTTATAGGAAACGCC
*
55663487 GCTATTGCTTACCTTTAGCGACGCTT
1 GCTATTGCTTACCTTTAGCGGCGCTT
55663513 TACGAAAAAC
Statistics
Matches: 553, Mismatches: 9, Indels: 48
0.91 0.01 0.08
Matches are distributed among these distances:
126 66 0.12
127 6 0.01
128 3 0.01
129 12 0.02
130 20 0.04
131 6 0.01
132 13 0.02
139 84 0.15
140 14 0.03
141 8 0.01
142 20 0.04
143 11 0.02
144 10 0.02
145 77 0.14
146 203 0.37
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (144 bp):
GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
CGACGCCGTTTTGCTATTCTAAAATTTTTTTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTT
TTATAGGAAACGCC
Found at i:55663331 original size:272 final size:277
Alignment explanation
Indices: 55662956--55663504 Score: 1002
Period size: 272 Copynumber: 2.0 Consensus size: 277
55662946 GCTTCTTATA
55662956 AAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCGTTTTGCTATTCTAACAATTTTTTA
1 AAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCGTTTTGCTATTCTAACAATTTTTTA
*
55663021 TTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTT
66 TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTT
* *
55663086 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
131 AGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCTA
55663151 TTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCC
196 TTCTAAAATTTTTTTA-TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCC
55663216 GCTATTGCTTACCTTTAG
260 GCTATTGCTTACCTTTAG
*
55663234 AAGCGCCGCAAAA-TTTTT-ATTTTGAACAAAACGACGCC-TTTTGCTATTCT-A-AATTTTTT-
1 AAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCGTTTTGCTATTCTAACAATTTTTTA
*
55663293 TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTT
66 TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTT
55663358 AGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCTA
131 AGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCTA
55663423 TTCTAAAATTTTTTTATTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCG
196 TTCTAAAATTTTTTTATTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCG
55663488 CTATTGCTTACCTTTAG
261 CTATTGCTTACCTTTAG
55663505 CGACGCTTTA
Statistics
Matches: 266, Mismatches: 5, Indels: 7
0.96 0.02 0.03
Matches are distributed among these distances:
271 66 0.25
272 142 0.53
273 8 0.03
274 1 0.00
275 12 0.05
276 19 0.07
277 5 0.02
278 13 0.05
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (277 bp):
AAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCGTTTTGCTATTCTAACAATTTTTTA
TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTT
AGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCTA
TTCTAAAATTTTTTTATTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCG
CTATTGCTTACCTTTAG
Found at i:55663411 original size:142 final size:143
Alignment explanation
Indices: 55663234--55663512 Score: 501
Period size: 145 Copynumber: 2.0 Consensus size: 143
55663224 TTACCTTTAG
*
55663234 AAGCGCCGCAAAATTTTTATTTTGAACAAAACGACGCC-TTTTGCTATTCT-AAATTTTTTT-TT
1 AAGCGCCGCAAAATTTTTATTTTGAACAAAACGACGCCGCTTTGCTATTCTAAAATTTTTTTATT
55663296 TTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGC
66 TTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGC
*
55663361 GGCGCTTCATATA
131 GACGCTTCATATA
55663374 AAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCTATTCTAAAATTTTTTTA
1 AAGCGCCGCAAAA-TTTTT-ATTTTGAACAAAACGACGCCGCTTTGCTATTCTAAAATTTTTTTA
55663439 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
64 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTA
55663504 GCGACGCTT
129 GCGACGCTT
55663513 TACGAAAAAC
Statistics
Matches: 132, Mismatches: 2, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
140 13 0.10
141 5 0.04
142 20 0.15
143 11 0.08
144 10 0.08
145 73 0.55
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (143 bp):
AAGCGCCGCAAAATTTTTATTTTGAACAAAACGACGCCGCTTTGCTATTCTAAAATTTTTTTATT
TTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTTTAGC
GACGCTTCATATA
Found at i:55663640 original size:63 final size:66
Alignment explanation
Indices: 55663538--55663663 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 66
55663528 TAAATCTCTG
* * *
55663538 AAAGTTCAGAAAACGGCATCGTTGGGCTTGGGTTTTTTGCGGCGCTTTAC-C-AAAACGCTAAAT
1 AAAGCTCAGAAAACGG-A-CGTTGGGCTTAGGTTATTTGCGGCGCTTTACTCAAAAACGCTAAAT
55663601 CCC
64 CCC
*
55663604 AAAGCTCAGAAAACGG-CGTTGGGCTTAGGTTATTTGCGGCGCTTTGCTCAAAAACGCTAA
1 AAAGCTCAGAAAACGGACGTTGGGCTTAGGTTATTTGCGGCGCTTTACTCAAAAACGCTAA
55663664 TGCTTTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
63 28 0.52
64 1 0.02
65 10 0.19
66 15 0.28
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (66 bp):
AAAGCTCAGAAAACGGACGTTGGGCTTAGGTTATTTGCGGCGCTTTACTCAAAAACGCTAAATCC
C
Found at i:55663742 original size:12 final size:12
Alignment explanation
Indices: 55663725--55663750 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55663715 TTTTTTATCC
55663725 AAACGCCGCTAA
1 AAACGCCGCTAA
55663737 AAACGCCGCTAA
1 AAACGCCGCTAA
55663749 AA
1 AA
55663751 GCCTGTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:55664515 original size:25 final size:25
Alignment explanation
Indices: 55664486--55664567 Score: 71
Period size: 30 Copynumber: 3.1 Consensus size: 25
55664476 TAAGGTAGAT
55664486 ATAAAAATTTTAAATAAATAAAAAA
1 ATAAAAATTTTAAATAAATAAAAAA
*
55664511 AT-AAAATTATTAAAT-ATTAAAATAA
1 ATAAAAATT-TTAAATAAATAAAA-AA
55664536 TATAATATTAATATTTAAA-AAATAAAAAA
1 -ATAA-A--AAT-TTTAAATAAATAAAAAA
55664565 ATA
1 ATA
55664568 TAGACGTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
24 12 0.26
25 10 0.22
26 2 0.04
27 1 0.02
28 4 0.09
29 2 0.04
30 14 0.30
31 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAAAAATTTTAAATAAATAAAAAA
Found at i:55665022 original size:16 final size:16
Alignment explanation
Indices: 55664973--55665029 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
55664963 TATATTTATA
*
55664973 TTTATTTTAATATAAT
1 TTTATTTTAATATAGT
55664989 ATTTAATAATTTAATATAGT
1 -TTT-AT--TTTAATATAGT
*
55665009 TTTATTTTATTATAGT
1 TTTATTTTAATATAGT
55665025 TTTAT
1 TTTAT
55665030 ATATAGTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 15 0.43
17 3 0.09
18 4 0.11
19 3 0.09
20 10 0.29
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (16 bp):
TTTATTTTAATATAGT
Found at i:55666445 original size:36 final size:36
Alignment explanation
Indices: 55666403--55666491 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
55666393 ACTTACATTC
*
55666403 ATTATGT-GTTAATTTCAAGA-ATATATAATGTTTTTA
1 ATTATGTAG-TAA-TTCAAGACATATATAATATTTTTA
* * *
55666439 ATTATGTAGTGATTCAAGACTTATGTAATATTTTTA
1 ATTATGTAGTAATTCAAGACATATATAATATTTTTA
*
55666475 ATTATGTAGTGATTCAA
1 ATTATGTAGTAATTCAA
55666492 TTCGGTTGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 7 0.15
36 39 0.83
37 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.47
Consensus pattern (36 bp):
ATTATGTAGTAATTCAAGACATATATAATATTTTTA
Found at i:55671799 original size:17 final size:17
Alignment explanation
Indices: 55671777--55671812 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55671767 AAAAGAGTTT
55671777 CTCAAAAGATAATTTTA
1 CTCAAAAGATAATTTTA
*
55671794 CTCAAAGGATAATTTTA
1 CTCAAAAGATAATTTTA
55671811 CT
1 CT
55671813 TTTATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (17 bp):
CTCAAAAGATAATTTTA
Found at i:55681996 original size:30 final size:27
Alignment explanation
Indices: 55681921--55682010 Score: 112
Period size: 26 Copynumber: 3.3 Consensus size: 27
55681911 CTTATCCATG
* *
55681921 TTTTACCCA-TATCAAAATTTTGATGA
1 TTTTACCCATTGTCAAAATTTTGACGA
55681947 TTTTACCCATTGT-AAAATTTTGACGA
1 TTTTACCCATTGTCAAAATTTTGACGA
*
55681973 TTTTACTCATGGATGTCAAAATTTTGACGA
1 TTTTACCCAT---TGTCAAAATTTTGACGA
55682003 TTTTACCC
1 TTTTACCC
55682011 CTGATAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
26 30 0.55
27 2 0.04
29 3 0.05
30 20 0.36
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (27 bp):
TTTTACCCATTGTCAAAATTTTGACGA
Found at i:55682184 original size:12 final size:13
Alignment explanation
Indices: 55682160--55682188 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55682150 TGGATTACAA
55682160 ATTTCCAATTTCC
1 ATTTCCAATTTCC
55682173 ATTTCC-ATTTCC
1 ATTTCCAATTTCC
55682185 ATTT
1 ATTT
55682189 TTGGAAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTCCAATTTCC
Found at i:55683592 original size:17 final size:18
Alignment explanation
Indices: 55683564--55683598 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
55683554 GCTTAAGGGT
55683564 CTTTTTGTAATTTTTTTA
1 CTTTTTGTAATTTTTTTA
55683582 CTTTTTG-AATTTTTTTA
1 CTTTTTGTAATTTTTTTA
55683599 ATTAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
CTTTTTGTAATTTTTTTA
Found at i:55683919 original size:34 final size:36
Alignment explanation
Indices: 55683875--55683945 Score: 119
Period size: 34 Copynumber: 2.0 Consensus size: 36
55683865 TAAACATTAA
*
55683875 AAAATTATTTTAAAATAAAAAAT-AAAAATAT-TTT
1 AAAAGTATTTTAAAATAAAAAATAAAAAATATATTT
55683909 AAAAGTATTTTAAAATAAAAAATAAAAAATATATTT
1 AAAAGTATTTTAAAATAAAAAATAAAAAATATATTT
55683945 A
1 A
55683946 TTCCCGGGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 22 0.65
35 8 0.24
36 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (36 bp):
AAAAGTATTTTAAAATAAAAAATAAAAAATATATTT
Found at i:55685809 original size:18 final size:17
Alignment explanation
Indices: 55685775--55685809 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55685765 CGAAATGATG
55685775 TAAAATTATTTTATTTT
1 TAAAATTATTTTATTTT
55685792 TAAAATCTA-TTTATTTT
1 TAAAAT-TATTTTATTTT
55685809 T
1 T
55685810 GAACTATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TAAAATTATTTTATTTT
Found at i:55689513 original size:9 final size:9
Alignment explanation
Indices: 55689496--55689534 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
55689486 ATTTTAAATT
*
55689496 AATAATTAA
1 AATATTTAA
55689505 AATATTTAA
1 AATATTTAA
55689514 AA-ATTTAA
1 AATATTTAA
55689522 AATAATTTAA
1 AAT-ATTTAA
55689532 AAT
1 AAT
55689535 GAACATCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.30
9 10 0.37
10 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATTTAA
Found at i:55689528 original size:10 final size:10
Alignment explanation
Indices: 55689496--55689534 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
55689486 ATTTTAAATT
55689496 AATAA-TTAA
1 AATAATTTAA
55689505 AAT-ATTT-A
1 AATAATTTAA
55689513 AA-AATTTAA
1 AATAATTTAA
55689522 AATAATTTAA
1 AATAATTTAA
55689532 AAT
1 AAT
55689535 GAACATCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.31
9 8 0.31
10 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATAATTTAA
Found at i:55689923 original size:22 final size:21
Alignment explanation
Indices: 55689887--55689928 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
55689877 ATTGTTGTTA
*
55689887 TTTTTTATTATTTTGCTGCTG
1 TTTTTTACTATTTTGCTGCTG
*
55689908 TTTTCTTACTATTTTGTTGCT
1 TTTT-TTACTATTTTGCTGCT
55689929 ACTTTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.67
Consensus pattern (21 bp):
TTTTTTACTATTTTGCTGCTG
Found at i:55694733 original size:18 final size:16
Alignment explanation
Indices: 55694710--55694745 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
55694700 AAAGGGTTTT
55694710 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
55694728 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
55694744 TA
1 TA
55694746 TTATACATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:55714637 original size:18 final size:16
Alignment explanation
Indices: 55714603--55714638 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
55714593 CCATGTATAA
55714603 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
55714619 TATTTTATAATATACTTT
1 TATTTT-TAATA-ACTTT
55714637 TA
1 TA
55714639 AAAACCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:55718073 original size:16 final size:17
Alignment explanation
Indices: 55718045--55718076 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55718035 ATATAGTGGT
55718045 CTTAATGTTATGCTTTG
1 CTTAATGTTATGCTTTG
55718062 CTTAAT-TTATGCTTT
1 CTTAATGTTATGCTTT
55718077 TTTTTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (17 bp):
CTTAATGTTATGCTTTG
Found at i:55719397 original size:22 final size:21
Alignment explanation
Indices: 55719367--55719417 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
55719357 CAAAAAAAGT
*
55719367 AGCAACAAAATAGTAAGAAAAC
1 AGCAACAAAATAATAA-AAAAC
* *
55719389 AGCAGCAAAATAATAAAAAAT
1 AGCAACAAAATAATAAAAAAC
*
55719410 AACAACAA
1 AGCAACAA
55719418 TAAAACAAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.67, C:0.14, G:0.10, T:0.10
Consensus pattern (21 bp):
AGCAACAAAATAATAAAAAAC
Found at i:55719789 original size:16 final size:16
Alignment explanation
Indices: 55719759--55719796 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
55719749 TATGATGTTC
55719759 ATTTTAAATTATTTTAA
1 ATTTTAAATTATTTT-A
55719776 ATTTTAAA-TATTTTA
1 ATTTTAAATTATTTTA
55719791 ATTTTA
1 ATTTTA
55719797 TTTAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTAAATTATTTTA
Found at i:55727123 original size:12 final size:13
Alignment explanation
Indices: 55727106--55727134 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55727096 AGGTTTCCAA
55727106 AAATGGAAA-TGG
1 AAATGGAAATTGG
55727118 AAATGGAAATTGG
1 AAATGGAAATTGG
55727131 AAAT
1 AAAT
55727135 TTGTAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (13 bp):
AAATGGAAATTGG
Found at i:55727356 original size:26 final size:27
Alignment explanation
Indices: 55727286--55727375 Score: 112
Period size: 26 Copynumber: 3.3 Consensus size: 27
55727276 AATTTATCAG
55727286 GGGTAAAATCGTCAAAATTTTGACATCCAT
1 GGGTAAAATCGTCAAAATTTTGACA---AT
*
55727316 GAGTAAAATCGTCAAAATTTT-ACAAT
1 GGGTAAAATCGTCAAAATTTTGACAAT
* *
55727342 GGGTAAAATCATCAAAATTTTGA-TAT
1 GGGTAAAATCGTCAAAATTTTGACAAT
55727368 GGGTAAAA
1 GGGTAAAA
55727376 CATGGATAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
26 31 0.56
27 1 0.02
29 3 0.05
30 20 0.36
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (27 bp):
GGGTAAAATCGTCAAAATTTTGACAAT
Found at i:55735415 original size:346 final size:346
Alignment explanation
Indices: 55734782--55735475 Score: 1253
Period size: 346 Copynumber: 2.0 Consensus size: 346
55734772 TAGATAAATT
*
55734782 GTGAAAATGTTAATATGAGATCATATGCATCAAGTTAAATGTTATAAGGCAATTAGGACTGATAA
1 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
* * *
55734847 TTGAAATAAATTCATGTATAAATCAAAAACTGATAGATAATAGTGGAAAAAGGAAATTTTCAAAT
66 TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
* * *
55734912 TAGTCTCTGATACTTCTATCCTTGTTGTTTGTTCTTGGTAAGTTCGTACAAGACTTACTTTATTA
131 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
*
55734977 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATATAATGCTTTT
196 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATACAATGCTTTT
55735042 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
261 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
55735107 GTAATTGATTAATGGTATAAA
326 GTAATTGATTAATGGTATAAA
* *
55735128 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATTTTATAAGGCAATTGGGACTGATAA
1 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
*
55735193 TTGAAATAAATTCATGTATAAATCAAGAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
66 TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
*
55735258 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATGCAAGACTTACTTTATTA
131 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
* * *
55735323 ATTGATGATATATTTGTGCTATGTTGTTTTGTTTTATGGTTGAATTGTTATTATACAATGTTTTT
196 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATACAATGCTTTT
55735388 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
261 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
55735453 GTAATTGATTAATGGTATAAA
326 GTAATTGATTAATGGTATAAA
55735474 GT
1 GT
55735476 AAATACTATA
Statistics
Matches: 333, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
346 333 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (346 bp):
GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATACAATGCTTTT
GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
GTAATTGATTAATGGTATAAA
Found at i:55738034 original size:17 final size:17
Alignment explanation
Indices: 55738012--55738047 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55738002 TTTATATAAA
55738012 AGTAAAATTATCCTTTG
1 AGTAAAATTATCCTTTG
*
55738029 AGTAAAATTATCTTTTG
1 AGTAAAATTATCCTTTG
55738046 AG
1 AG
55738048 AAACTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (17 bp):
AGTAAAATTATCCTTTG
Found at i:55743550 original size:9 final size:9
Alignment explanation
Indices: 55743536--55743566 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55743526 TTTGGTTAAA
55743536 AATTAACCG
1 AATTAACCG
55743545 AATTAACCG
1 AATTAACCG
*
55743554 AATTACCCG
1 AATTAACCG
55743563 AATT
1 AATT
55743567 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:55743612 original size:37 final size:37
Alignment explanation
Indices: 55743565--55743639 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
55743555 ATTACCCGAA
*
55743565 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
* *
55743602 TTGAATCACTACATAATTAAAAACATTATATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
55743639 T
1 T
55743640 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:55743653 original size:37 final size:37
Alignment explanation
Indices: 55743565--55743656 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
55743555 ATTACCCGAA
* *
55743565 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
* * *
55743602 TTGAATCACTACATAATTAAAAACATTATATAATTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
55743638 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
55743657 GAAATGTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 3 0.06
37 43 0.88
38 3 0.06
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:55743824 original size:38 final size:39
Alignment explanation
Indices: 55743773--55743850 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
55743763 ACTTAAGAGT
*
55743773 TAGACTTTAGTTTTATTTTTATTGAGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGG
*
55743811 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGG
55743850 T
1 T
55743851 TGGGTTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 26 0.70
39 11 0.30
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGG
Done.