Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 133 of 218
Found at i:40632083 original size:19 final size:18
Alignment explanation
Indices: 40632052--40632097 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40632042 TAATCTAATT
*
40632052 AATTAATAAATAAGATTAA
1 AATTAA-AAATAAAATTAA
*
40632071 AATATAAAAATAAAATTGA
1 AAT-TAAAAATAAAATTAA
40632090 AATTAAAA
1 AATTAAAA
40632098 CACTAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
AATTAAAAATAAAATTAA
Found at i:40632272 original size:28 final size:28
Alignment explanation
Indices: 40632241--40632296 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
40632231 ATAAAAAAAT
40632241 AAAAAAGAAATAAAAACACTAAAATTTA
1 AAAAAAGAAATAAAAACACTAAAATTTA
* ** * *
40632269 AAAATATTAGTGAAAACACTAAAATTTA
1 AAAAAAGAAATAAAAACACTAAAATTTA
40632297 TAATTATTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.23
Consensus pattern (28 bp):
AAAAAAGAAATAAAAACACTAAAATTTA
Found at i:40632304 original size:28 final size:28
Alignment explanation
Indices: 40632253--40632307 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
40632243 AAAAGAAATA
40632253 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
* *
40632281 AAAACACTAAAATTTATAATTATTAGT
1 AAAACACTAAAATTTAAAAATATTAGT
40632308 ACTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAACACTAAAATTTAAAAATATTAGTG
Found at i:40634161 original size:42 final size:42
Alignment explanation
Indices: 40634113--40634328 Score: 310
Period size: 42 Copynumber: 5.1 Consensus size: 42
40634103 CGTTTTTGTA
*
40634113 TAGCGGCGCTTAGAAAAAAAAGCCGTTAAAGACCATGTTCTT
1 TAGCGGCGCTTAGAAAAAAAAGCCGCTAAAGACCATGTTCTT
*
40634155 TAGCGGCGCTTAGAAAGAAACA-CCGCTAAAGACCATGTTCTT
1 TAGCGGCGCTTAGAAA-AAAAAGCCGCTAAAGACCATGTTCTT
*
40634197 TAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTT
1 TAGCGGCGCTTAGAAAAAAAAGCCGCTAAAGACCATGTTCTT
* * *
40634239 CAGAGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTT
1 TAGCGGCGCTTAGAAAAAAAAGCCGCTAAAGACCATGTTCTT
* * * *
40634281 TAACGGCGCTTA-AGAGAAAAAGCCGCTAAAGAACATGATCTT
1 TAGCGGCGCTTAGA-AAAAAAAGCCGCTAAAGACCATGTTCTT
40634323 TAGCGG
1 TAGCGG
40634329 TGTTTTTCTC
Statistics
Matches: 157, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 4 0.03
42 149 0.95
43 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (42 bp):
TAGCGGCGCTTAGAAAAAAAAGCCGCTAAAGACCATGTTCTT
Found at i:40634352 original size:42 final size:42
Alignment explanation
Indices: 40634302--40634419 Score: 191
Period size: 42 Copynumber: 2.8 Consensus size: 42
40634292 AAGAGAAAAA
* *
40634302 GCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTCTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAGC
* *
40634344 GCCTCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAGC
*
40634386 GCCGCTGAAGAACATGGTCTTTAGCGGCGTTTTT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
40634420 GTTTGTAAAC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (42 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAGC
Found at i:40638745 original size:185 final size:185
Alignment explanation
Indices: 40638433--40638807 Score: 687
Period size: 185 Copynumber: 2.0 Consensus size: 185
40638423 TTTTAATGAG
* *
40638433 GAAAAAATAACAGCAATATGGTGGAGAATATGTTAACAAATCTTGTGGCAAAAAGAAAAAGAAGA
1 GAAAAAATAACAGCAATATGATGGAAAATATGTTAACAAATCTTGTGGCAAAAAGAAAAAGAAGA
*
40638498 AAGAGATGGTAAAACTAGGAGTAGGTGACGACAATAATGGGAGAAAGAAAGAAAATTGAAGAGAA
66 AAGAGATGGTAAAACTAGGAGTAGGTGACGACAACAATGGGAGAAAGAAAGAAAATTGAAGAGAA
* *
40638563 AAGAGGAGAGGAAGAGGGTGAACGGCTTGGGTAGGTAAAATTTGAATTAAATGCT
131 AAGAGGAGAGGAAGAGGGTGAACGGCTTGGGTAGGTAAAAGTTGAATTAAAGGCT
40638618 GAAAAAATAACAGCAATATGATGGAAAATATGTTAACAAATCTTGTGGCAAAAAGAAAAAGAAGA
1 GAAAAAATAACAGCAATATGATGGAAAATATGTTAACAAATCTTGTGGCAAAAAGAAAAAGAAGA
*
40638683 AAGAGATGGTAAAACTAGGTGTAGGTGACGACAACAATGGGAGAAAGAAAGAAAATTGAAGAGAA
66 AAGAGATGGTAAAACTAGGAGTAGGTGACGACAACAATGGGAGAAAGAAAGAAAATTGAAGAGAA
*
40638748 AAGAGGAGAGGAAGAGGGTGAATGGCTTGGGTAGGTAAAAGTTGAATTAAAGGCT
131 AAGAGGAGAGGAAGAGGGTGAACGGCTTGGGTAGGTAAAAGTTGAATTAAAGGCT
40638803 GAAAA
1 GAAAA
40638808 TACAATAAAA
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
185 183 1.00
ACGTcount: A:0.48, C:0.06, G:0.29, T:0.17
Consensus pattern (185 bp):
GAAAAAATAACAGCAATATGATGGAAAATATGTTAACAAATCTTGTGGCAAAAAGAAAAAGAAGA
AAGAGATGGTAAAACTAGGAGTAGGTGACGACAACAATGGGAGAAAGAAAGAAAATTGAAGAGAA
AAGAGGAGAGGAAGAGGGTGAACGGCTTGGGTAGGTAAAAGTTGAATTAAAGGCT
Found at i:40639245 original size:40 final size:38
Alignment explanation
Indices: 40639201--40639325 Score: 106
Period size: 40 Copynumber: 3.2 Consensus size: 38
40639191 ATTAGCAACG
40639201 CTTTTTAACAAACGCCACAATAGATTGAGCATTAGCGGCA
1 CTTTTTAA-AAACGCCACAATAGATT-AGCATTAGCGGCA
* * * * *
40639241 CTTTTTGAGAATGCCGCAATAAATCTAGCATTAGCGGCA
1 CTTTTTAAAAACGCCACAATAGAT-TAGCATTAGCGGCA
* * * * * *
40639280 CTTCTTGAAAAACGTCACTATAGATCAAGAATTAGCAGCA
1 CTT-TTTAAAAACGCCACAATAGAT-TAGCATTAGCGGCA
40639320 CTTTTT
1 CTTTTT
40639326 CAACAGACGC
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
39 30 0.45
40 36 0.55
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (38 bp):
CTTTTTAAAAACGCCACAATAGATTAGCATTAGCGGCA
Found at i:40639631 original size:14 final size:14
Alignment explanation
Indices: 40639614--40639659 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
40639604 TATTTTGGGA
40639614 TTAGAGTTT-TGAGT
1 TTAGAGTTTATG-GT
*
40639628 TTAGGGTTTATGGT
1 TTAGAGTTTATGGT
*
40639642 TTAGAGTTTAGGGT
1 TTAGAGTTTATGGT
40639656 TTAG
1 TTAG
40639660 GATTTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 26 0.93
15 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (14 bp):
TTAGAGTTTATGGT
Found at i:40639636 original size:7 final size:7
Alignment explanation
Indices: 40639626--40639665 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
40639616 AGAGTTTTGA
40639626 GTTTAGG
1 GTTTAGG
*
40639633 GTTTATG
1 GTTTAGG
*
40639640 GTTTAGA
1 GTTTAGG
40639647 GTTTAGG
1 GTTTAGG
40639654 GTTTAGG
1 GTTTAGG
*
40639661 ATTTA
1 GTTTA
40639666 TTATTAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:40639665 original size:21 final size:21
Alignment explanation
Indices: 40639619--40639658 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40639609 TGGGATTAGA
*
40639619 GTTTTGAGTTTAGGGTTTATG
1 GTTTAGAGTTTAGGGTTTATG
40639640 GTTTAGAGTTTAGGGTTTA
1 GTTTAGAGTTTAGGGTTTA
40639659 GGATTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (21 bp):
GTTTAGAGTTTAGGGTTTATG
Found at i:40641834 original size:11 final size:11
Alignment explanation
Indices: 40641820--40641880 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
40641810 ATTGTTTTAT
40641820 TTTTATAGAAA
1 TTTTATAGAAA
40641831 TTTTATAGAAA
1 TTTTATAGAAA
*
40641842 TTGATTGATTG--A
1 TT--TT-ATAGAAA
*
40641854 TTTTACAGAAA
1 TTTTATAGAAA
40641865 TTTTATAGAAA
1 TTTTATAGAAA
40641876 TTTTA
1 TTTTA
40641881 ATACCAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 2 0.05
10 2 0.05
11 29 0.71
12 3 0.07
13 2 0.05
14 3 0.07
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (11 bp):
TTTTATAGAAA
Found at i:40644073 original size:39 final size:33
Alignment explanation
Indices: 40644000--40644063 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
40643990 TGAGAAAAAC
40644000 AATCTTAGAATCCTATCTTGATTTTGATACAAA
1 AATCTTAGAATCCTATCTTGATTTTGATACAAA
40644033 AATCTTAGAATCCTATCTTGATTTTGATACA
1 AATCTTAGAATCCTATCTTGATTTTGATACA
40644064 CATGTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (33 bp):
AATCTTAGAATCCTATCTTGATTTTGATACAAA
Found at i:40644541 original size:41 final size:41
Alignment explanation
Indices: 40644496--40644710 Score: 156
Period size: 41 Copynumber: 5.2 Consensus size: 41
40644486 TTTACATAAT
* * * *
40644496 CGCCGCTAATGGTGC-GGTCTTTCGCGGCGTTTTCTAATATG
1 CGCCGCTAATGCT-CAGGTCTTTAGCGGCGTTTTCTAAAAAG
**
40644537 CGCCGCTAATGCTCAGGTCTTTAGCGGCGATTTT-TACGAAG
1 CGCCGCTAATGCTCAGGTCTTTAGCGGCG-TTTTCTAAAAAG
*
40644578 AGCCGCTAATGCTCAGGTCTTTAGCGGCG-TTTCTTAAAAAG
1 CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTC-TAAAAAG
** * * * *
40644619 CGCCGCTAAAAACCGCA-G-CATTAGCGGCGCATAT-TAGAAAA-
1 CGCCGCT--AATGCTCAGGTCTTTAGCGGCG-TTTTCTA-AAAAG
* * ***
40644660 CGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTTGTAGCTAG
1 CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTCTAAAAAG
40644701 CGCCGCTAAT
1 CGCCGCTAAT
40644711 AATAAAATCT
Statistics
Matches: 137, Mismatches: 24, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
39 7 0.05
40 5 0.04
41 109 0.80
42 9 0.07
43 7 0.05
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (41 bp):
CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTCTAAAAAG
Found at i:40644622 original size:82 final size:80
Alignment explanation
Indices: 40644496--40644692 Score: 195
Period size: 82 Copynumber: 2.4 Consensus size: 80
40644486 TTTACATAAT
* * * * ** * *
40644496 CGCCGCTAATGGTGCGGTCTTTCGCGGCGTTTTCTAATATGCGCCGCT-AATGCTCAGGTCTTTA
1 CGCCGCTAATGCT-CGGTCTTTAGCGGCGTTTTCTAAAAAGCGCCGCTAAAACCGCA-G-CATTA
* *
40644560 GCGGCG-ATTTTTACGAAGA
63 GCGGCGCA-TATTA-GAAAA
40644579 -GCCGCTAATGCTCAGGTCTTTAGCGGCG-TTTCTTAAAAAGCGCCGCTAAAAACCGCAGCATTA
1 CGCCGCTAATGCTC-GGTCTTTAGCGGCGTTTTC-TAAAAAGCGCCGCT-AAAACCGCAGCATTA
40644642 GCGGCGCATATTAGAAAA
63 GCGGCGCATATTAGAAAA
40644660 CGCCGCTAATGCTCCGGTCTTTAGCGGCGTTTT
1 CGCCGCTAATGCT-CGGTCTTTAGCGGCGTTTT
40644693 GTAGCTAGCG
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
81 9 0.09
82 76 0.79
83 6 0.06
84 5 0.05
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (80 bp):
CGCCGCTAATGCTCGGTCTTTAGCGGCGTTTTCTAAAAAGCGCCGCTAAAACCGCAGCATTAGCG
GCGCATATTAGAAAA
Found at i:40645885 original size:73 final size:74
Alignment explanation
Indices: 40645766--40645936 Score: 272
Period size: 73 Copynumber: 2.3 Consensus size: 74
40645756 GCATGAATTT
* * * *
40645766 GCGGCGTTTATTGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCG-TTTTTATACTGTTTA
1 GCGGCGTTTCTGGTACAAATGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTA
40645830 TTGGTATTA
66 TTGGTATTA
*
40645839 GCGGCGTTTCTGGTACAAATGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATTCTGTTTA
1 GCGGCGTTTCTGGTACAAATGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTA
40645904 TTGGTATTA
66 TTGGTATTA
* *
40645913 GTGCCGTTTCTGGTACAAATGCCG
1 GCGGCGTTTCTGGTACAAATGCCG
40645937 TAAATGATAG
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 45 0.50
74 45 0.50
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (74 bp):
GCGGCGTTTCTGGTACAAATGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTA
TTGGTATTA
Found at i:40645926 original size:74 final size:73
Alignment explanation
Indices: 40645786--40645936 Score: 266
Period size: 74 Copynumber: 2.1 Consensus size: 73
40645776 TTGTAAAAAC
*
40645786 GCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCGTTTCTG
1 GCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGCCGTTTCTG
40645851 GTACAAAT
66 GTACAAAT
* *
40645859 GCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATTCTGTTTATTGGTATTAGTGCCGTTTCT
1 GCCGCAAAAGTTTAACCAAAACGACTTCG-TTTTTATACTGTTTATTGGTATTAGCGCCGTTTCT
40645924 GGTACAAAT
65 GGTACAAAT
40645933 GCCG
1 GCCG
40645937 TAAATGATAG
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 29 0.39
74 45 0.61
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (73 bp):
GCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGCCGTTTCTG
GTACAAAT
Found at i:40648820 original size:15 final size:15
Alignment explanation
Indices: 40648800--40648835 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
40648790 ACCACCAATT
*
40648800 TGTTTTCATTTGTAC
1 TGTTTTCATTTCTAC
40648815 TGTTTTCATTTCTAC
1 TGTTTTCATTTCTAC
40648830 T-TTTTC
1 TGTTTTC
40648836 CTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (15 bp):
TGTTTTCATTTCTAC
Found at i:40649523 original size:16 final size:15
Alignment explanation
Indices: 40649491--40649867 Score: 189
Period size: 16 Copynumber: 24.1 Consensus size: 15
40649481 ATACATAACT
40649491 TACATAACTTATTAA
1 TACATAACTTATTAA
*
40649506 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
40649522 TACATAACTTATATAA
1 TACATAACTTAT-TAA
40649538 TACGACATAACTTATTAA
1 T---ACATAACTTATTAA
*
40649556 TATATATA-TT-TTAA
1 TACATA-ACTTATTAA
*
40649570 -A-ATGATACATATCT--
1 TACAT-A-ACTTAT-TAA
40649584 TACATAACTTATTAA
1 TACATAACTTATTAA
40649599 TACATAACTTATATAA
1 TACATAACTTAT-TAA
*
40649615 TACATAACTTACATAA
1 TACATAACTTA-TTAA
40649631 TACGACATAACTTATTAA
1 T---ACATAACTTATTAA
*
40649649 TATATATA-TT-TTAA
1 TACATA-ACTTATTAA
40649663 -A-ATGATAC--A-TAA
1 TACAT-A-ACTTATTAA
*
40649675 CTTACACAACTTATTAA
1 --TACATAACTTATTAA
*
40649692 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
40649708 TACATAACTTATTAA
1 TACATAACTTATTAA
*
40649723 TACATGACTTATATAA
1 TACATAACTTAT-TAA
* *
40649739 TACATAAGTTACATAA
1 TACATAACTTA-TTAA
40649755 TACGACATAACTTATTAA
1 T---ACATAACTTATTAA
*
40649773 TATATATA-TT-TTAA
1 TACATA-ACTTATTAA
*
40649787 -A-ATGATACATATCT--
1 TACAT-A-ACTTAT-TAA
40649801 TACATAACTTATTAA
1 TACATAACTTATTAA
40649816 TACATAACTTATATAA
1 TACATAACTTAT-TAA
* *
40649832 TGCATAACTTACATAA
1 TACATAACTTA-TTAA
40649848 TACGACATAACTTATTAA
1 T---ACATAACTTATTAA
40649866 TA
1 TA
40649868 TATATATTTT
Statistics
Matches: 287, Mismatches: 25, Indels: 100
0.70 0.06 0.24
Matches are distributed among these distances:
12 9 0.03
13 14 0.05
14 26 0.09
15 86 0.30
16 94 0.33
17 3 0.01
18 16 0.06
19 39 0.14
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:40649529 original size:31 final size:30
Alignment explanation
Indices: 40649491--40649745 Score: 127
Period size: 31 Copynumber: 8.2 Consensus size: 30
40649481 ATACATAACT
40649491 TACATAACTTATTAATACATAACATTTTTAA
1 TACATAACTTATTAATACATAAC-TTTTTAA
*
40649522 TACATAACTTATATAATACGACATAACTTATTAA
1 TACATAACTTAT-TAAT---ACATAACTTTTTAA
* * *
40649556 TATATATA-TT-TTAA-A-ATGATACATATCT--
1 TACATA-ACTTATTAATACAT-A-AC-TTTTTAA
*
40649584 TACATAACTTATTAATACATAACTTATATAA
1 TACATAACTTATTAATACATAACTT-TTTAA
* *
40649615 TACATAACTTACATAATACGACATAACTTATTAA
1 TACATAACTTA-TTAAT---ACATAACTTTTTAA
* * ***
40649649 TATATATA-TT-TTAA-A-ATGA-TACATAA
1 TACATA-ACTTATTAATACATAACTTTTTAA
*
40649675 CTTACACAACTTATTAATACATAACATTTTTAA
1 --TACATAACTTATTAATACATAAC-TTTTTAA
* *
40649708 TACATAACTTATTAATACATGACTTATATAA
1 TACATAACTTATTAATACATAACTT-TTTAA
40649739 TACATAA
1 TACATAA
40649746 GTTACATAAT
Statistics
Matches: 169, Mismatches: 26, Indels: 58
0.67 0.10 0.23
Matches are distributed among these distances:
26 4 0.02
27 7 0.04
28 17 0.10
29 14 0.08
30 7 0.04
31 60 0.36
32 14 0.08
33 5 0.03
34 23 0.14
35 18 0.11
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (30 bp):
TACATAACTTATTAATACATAACTTTTTAA
Found at i:40649553 original size:93 final size:93
Alignment explanation
Indices: 40649449--40649725 Score: 495
Period size: 93 Copynumber: 3.0 Consensus size: 93
40649439 TACATACATT
40649449 ACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATAAC
1 ACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATAAC
40649514 ATTTTTAATACATAACTTATATAATACG
66 ATTTTTAATACATAACTTATATAATACG
*
40649542 ACATAACTTATTAATATATATATTTTAAAATGATACATATCTTACATAACTTATTAATACATAAC
1 ACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATAAC
* *
40649607 -TTATATAATACATAACTTACATAATACG
66 ATT-TTTAATACATAACTTATATAATACG
*
40649635 ACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACACAACTTATTAATACATAAC
1 ACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATAAC
40649700 ATTTTTAATACATAACTTAT-TAATAC
66 ATTTTTAATACATAACTTATATAATAC
40649726 ATGACTTATA
Statistics
Matches: 175, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
92 8 0.05
93 165 0.94
94 2 0.01
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (93 bp):
ACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATAAC
ATTTTTAATACATAACTTATATAATACG
Found at i:40649589 original size:9 final size:9
Alignment explanation
Indices: 40649575--40649630 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
40649565 TTTAAAATGA
*
40649575 TACATATCT
1 TACATAACT
40649584 TACATAACT
1 TACATAACT
*
40649593 TA-TTAA--
1 TACATAACT
40649599 TACATAACT
1 TACATAACT
*
40649608 TATATAA--
1 TACATAACT
40649615 TACATAACT
1 TACATAACT
40649624 TACATAA
1 TACATAA
40649631 TACGACATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
6 2 0.05
7 9 0.24
8 3 0.08
9 23 0.62
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:40649715 original size:124 final size:124
Alignment explanation
Indices: 40649584--40649842 Score: 448
Period size: 124 Copynumber: 2.1 Consensus size: 124
40649574 ATACATATCT
40649584 TACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAA
1 TACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAA
*
40649649 TATATATATTTTAAAATGATACATAACTTACACAACTTATTAATACATAACATT-TTTAA
66 TATATATATTTTAAAATGATACATAACTTACACAACTTATTAATACATAAC-TTATATAA
* *
40649708 TACATAACTTATTAATACATGACTTATATAATACATAAGTTACATAATACGACATAACTTATTAA
1 TACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAA
* *
40649773 TATATATATTTTAAAATGATACATATCTTACATAACTTATTAATACATAACTTATATAA
66 TATATATATTTTAAAATGATACATAACTTACACAACTTATTAATACATAACTTATATAA
*
40649832 TGCATAACTTA
1 TACATAACTTA
40649843 CATAATACGA
Statistics
Matches: 128, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
123 2 0.02
124 126 0.98
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (124 bp):
TACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAA
TATATATATTTTAAAATGATACATAACTTACACAACTTATTAATACATAACTTATATAA
Found at i:40649774 original size:50 final size:49
Alignment explanation
Indices: 40649709--40649867 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 49
40649699 CATTTTTAAT
40649709 ACATAACTTATTAATACATGACTTATATAATACATAAGTTACATAATACG
1 ACATAACTTATTAATACAT-ACTTATATAATACATAAGTTACATAATACG
** * *
40649759 ACATAACTTATTAAT--ATA--TATATTTTA-A-AATGATACAT-AT-CTT
1 ACATAACTTATTAATACATACTTATATAATACATAA-GTTACATAATAC-G
* *
40649802 ACATAACTTATTAATACATAACTTATATAATGCATAACTTACATAATACG
1 ACATAACTTATTAATACAT-ACTTATATAATACATAAGTTACATAATACG
40649852 ACATAACTTATTAATA
1 ACATAACTTATTAATA
40649868 TATATATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
42 1 0.01
43 19 0.22
44 7 0.08
45 9 0.10
46 1 0.01
47 1 0.01
48 8 0.09
49 6 0.07
50 35 0.40
51 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (49 bp):
ACATAACTTATTAATACATACTTATATAATACATAAGTTACATAATACG
Found at i:40649805 original size:93 final size:93
Alignment explanation
Indices: 40649708--40649925 Score: 368
Period size: 93 Copynumber: 2.4 Consensus size: 93
40649698 ACATTTTTAA
* *
40649708 TACATAACTTATTAATACATGACTTATATAATACATAAGTTACATAATACGACATAACTTATTAA
1 TACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAA
40649773 TATATATATTTTAAAATGATACATATCT
66 TATATATATTTTAAAATGATACATATCT
*
40649801 TACATAACTTATTAATACATAACTTATATAATGCATAACTTACATAATACGACATAACTTATTAA
1 TACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAA
40649866 TATATATATTTTAAAATGATACATATCT
66 TATATATATTTTAAAATGATACATATCT
* **
40649894 TTC--CCCTTATTAATACATAACTTATATAATAC
1 TACATAACTTATTAATACATAACTTATATAATAC
40649926 GACATAACTT
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
91 26 0.22
93 92 0.78
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (93 bp):
TACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACGACATAACTTATTAA
TATATATATTTTAAAATGATACATATCT
Found at i:40649807 original size:62 final size:62
Alignment explanation
Indices: 40649615--40649811 Score: 217
Period size: 62 Copynumber: 3.2 Consensus size: 62
40649605 ACTTATATAA
*
40649615 TACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATAACT
1 TACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATATCT
* * * * *
40649677 TACACAACTTA-TTAAT---ACATAACATTTTTAATACATA-ACTTATTAATACATGACT-TATA
1 TACATAACTTACATAATACGACATAAC-TTATTAATATATATA-TT-TTAA-A-ATGA-TACATA
**
40649736 TAA
60 TCT
*
40649739 TACATAAGTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATATCT
1 TACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATATCT
40649801 TACATAACTTA
1 TACATAACTTA
40649812 TTAATACATA
Statistics
Matches: 106, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
58 8 0.08
59 13 0.12
60 4 0.04
61 6 0.06
62 44 0.42
63 6 0.06
64 4 0.04
65 13 0.12
66 8 0.08
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (62 bp):
TACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATATCT
Found at i:40649865 original size:217 final size:215
Alignment explanation
Indices: 40649491--40649942 Score: 746
Period size: 217 Copynumber: 2.1 Consensus size: 215
40649481 ATACATAACT
* *
40649491 TACATAACTTATTAATACATAACATTTTTAATACATAACTTATATAATACGACATAACTTATTAA
1 TACATAACTTATTAATACATAACATTTATAATACATAACTTACATAATACGACATAACTTATTAA
40649556 TATATATATTTTAAAATGATACATATCTTACATAACTTATTAATACATAACTTATATAATACATA
66 TATATATATTTTAAAATGATACATATCTTACATAACTTATTAATACATAACTTATATAATACATA
40649621 ACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACACAACT
131 ACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATAACTTAC-C-ACT
*
40649686 TATTAATACATAACATT-TTTAA
194 TATTAATACATAAC-TTATATAA
* *
40649708 TACATAACTTATTAATACATGAC-TTATATAATACATAAGTTACATAATACGACATAACTTATTA
1 TACATAACTTATTAATACATAACATT-TATAATACATAACTTACATAATACGACATAACTTATTA
*
40649772 ATATATATATTTTAAAATGATACATATCTTACATAACTTATTAATACATAACTTATATAATGCAT
65 ATATATATATTTTAAAATGATACATATCTTACATAACTTATTAATACATAACTTATATAATACAT
* * *
40649837 AACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATATCTTTCCCCTT
130 AACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACCACTT
40649902 ATTAATACATAACTTATATAA
195 ATTAATACATAACTTATATAA
40649923 TACGACATAACTTATTAATA
1 T---ACATAACTTATTAATA
40649943 TATATTTTAA
Statistics
Matches: 221, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
214 2 0.01
215 21 0.10
216 3 0.01
217 179 0.81
218 16 0.07
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (215 bp):
TACATAACTTATTAATACATAACATTTATAATACATAACTTACATAATACGACATAACTTATTAA
TATATATATTTTAAAATGATACATATCTTACATAACTTATTAATACATAACTTATATAATACATA
ACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACATAACTTACCACTTA
TTAATACATAACTTATATAA
Found at i:40650000 original size:75 final size:77
Alignment explanation
Indices: 40649506--40649989 Score: 273
Period size: 75 Copynumber: 6.3 Consensus size: 77
40649496 AACTTATTAA
*
40649506 TACATAACATTTTTAATACATAACTTATATAATACGACATAACTTATTAATATATATATTTTAAA
1 TACATAAC-TTATTAATACATAACTTATATAATACGACATAACTTATTAATATATATATTTTAAA
*
40649571 ATGATACATATCT
65 ATGATACATAACT
* * * **
40649584 TACATAACTTATTAATACATAACTTATATAAT---ACATAACTTACATAATACGACATAACTTAT
1 TACATAACTTATTAATACATAACTTATATAATACGACATAACTTA-TTAATA-TATATATTTTA-
* * **
40649646 TAAT-ATATATATTT
63 AAATGATACATAACT
* * * *
40649660 TA-A-AA-TGATACATAACTTACACAACTTAT-TAAT---ACATAACATTTTTAATACATA-ACT
1 TACATAACT--TA-TTAA--TACATAACTTATATAATACGACATAAC-TTATTAATATATATA-T
*
40649717 TATTAATACATGACTTATATAA--
59 T-TTAA-A-ATGA--TACATAACT
* * * * ** * * *
40649739 TACATAAGTTACATAATACGACATAACTTAT-TAATA-TATATATTTTA-AAATGATACATATCT
1 TACATAACTTA-TTAAT---ACATAACTTATATAATACGACATAACTTATTAAT-ATATATATTT
*
40649801 TACATAACT--TA-TTAA--
61 TA-A-AA-TGATACATAACT
* *
40649816 TACATAACTTATATAATGCATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAA
1 TACATAACTTAT-TAATACATAACTTATATAATACGACATAACTTATTAATATATATATTTTAAA
*
40649881 ATGATACATATCT
65 ATGATACATAACT
* **
40649894 TTC--CCCTTATTAATACATAACTTATATAATACGACATAACTTATT-A-ATATATATTTTAAAA
1 TACATAACTTATTAATACATAACTTATATAATACGACATAACTTATTAATATATATATTTTAAAA
40649955 TGATACATAACT
66 TGATACATAACT
40649967 TACATAACTTATTAATACATAAC
1 TACATAACTTATTAATACATAAC
40649990 ATTTTTAATA
Statistics
Matches: 316, Mismatches: 51, Indels: 81
0.71 0.11 0.18
Matches are distributed among these distances:
73 30 0.09
74 24 0.08
75 66 0.21
76 46 0.15
77 66 0.21
78 28 0.09
79 3 0.01
80 8 0.03
81 29 0.09
82 11 0.03
83 5 0.02
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (77 bp):
TACATAACTTATTAATACATAACTTATATAATACGACATAACTTATTAATATATATATTTTAAAA
TGATACATAACT
Found at i:40650016 original size:16 final size:15
Alignment explanation
Indices: 40649967--40650008 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
40649957 ATACATAACT
40649967 TACATAACTTATTAA
1 TACATAACTTATTAA
*
40649982 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
40649998 TACATAACTTA
1 TACATAACTTA
40650009 CATAATACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:40655704 original size:21 final size:21
Alignment explanation
Indices: 40655680--40655738 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
40655670 AGCAGATGTG
* *
40655680 GCAGCGAGAGAAACAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
*
40655701 GCAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
*
40655722 ACAGCGAGGGAAGCAGA
1 GCAGCGAGGGAAGCAGA
40655739 ACAGCTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.17, G:0.42, T:0.05
Consensus pattern (21 bp):
GCAGCGAGGGAAGCAGAGGCT
Found at i:40655705 original size:87 final size:87
Alignment explanation
Indices: 40655533--40655698 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 87
40655523 GGCAACATCG
*
40655533 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCAGT
1 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCAGC
*
40655598 GAGAGAAGCAGAGGTAGCAGCA
66 GAGAGAAACAGAGGTAGCAGCA
* * *
40655620 AGAGAAGCTGAGGTTCAACAAAA-TTATGAAGAACTCCAGC-AGCAGCTTAAAGCAGATGTGGCA
1 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTTAAAGCAGATGCGGCA
40655683 GCGAGAGAAACAGAGG
64 GCGAGAGAAACAGAGG
40655699 CTGCAGCGAG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
86 1 0.01
87 67 0.93
88 4 0.06
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (87 bp):
AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCAGC
GAGAGAAACAGAGGTAGCAGCA
Found at i:40656109 original size:43 final size:43
Alignment explanation
Indices: 40656048--40656387 Score: 527
Period size: 43 Copynumber: 7.9 Consensus size: 43
40656038 ATTAGCGGCA
*
40656048 TTTTTTGGGTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
**
40656091 TTTTTTTCCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * ** *
40656134 TTTTTTGCCTAAGTGCCGCTAAAGAGAATGGTCTATAGTGGCA
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
*
40656177 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTCTAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
40656220 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
*
40656263 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGCGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * * *
40656306 TTTTTTGCCTAAGCGCCACTAAAGACCATGGTTTATAGCGGCG
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * *
40656349 TTTGTTGGGTAAGCACCGCTAAAGACCATGGTCTATAGT
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
40656388 AGCATTGTAA
Statistics
Matches: 271, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 271 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (43 bp):
TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
Found at i:40656449 original size:129 final size:129
Alignment explanation
Indices: 40656040--40656458 Score: 340
Period size: 129 Copynumber: 3.2 Consensus size: 129
40656030 CTGCCAAAAT
* *** * * **
40656040 TAGCGGCATTTTTTGGGTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTTCCTAAGC
1 TAGCGGCGTTTTTTGAAAAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGCTAAGC
* * * *** * ** ** *
40656105 GCCGCTAAAGACCATGGTCTATAGTGGCGTT-TTTTGCCTAAGTGCCGCTAAAGAGAATGGTCTA
66 ACCGCTAAAGACCATGGTCTATAGTAGCATTGTAAAG-CAAAACGCCGCTAAAGACCATGATCTA
* * *** * * *
40656169 TAGTGGCATTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTCTAGTGGCGTTTTTTGGCTAAGC
1 TAGCGGCGTTTTTTGAAAAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGCTAAGC
* * * * *** * * *
40656234 GCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTA
66 ACCGCTAAAGACCATGGTCTATAGTAGCATTGTAAAGCAAAACGCCGCTAAAGACCATGATCTA
*** * * *
40656298 TAGCGGCGTTTTTTGCCTAAGCGCCACTAAAGACCATGGTTTATAGCGGCGTTTGTTGGGTAAGC
1 TAGCGGCGTTTTTTGAAAAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGCTAAGC
* * ** * *
40656363 ACCGCTAAAGACCATGGTCTATAGTAGCATTGTAAAG-AAAACGCTGCTATAGGTCTTGATCTT
66 ACCGCTAAAGACCATGGTCTATAGTAGCATTGTAAAGCAAAACGCCGCTAAAGACCATGATCTA
40656426 TAGCGGCGTTTATTAT-AAAAAGCGCCGCTAAAG
1 TAGCGGCGTTT-TT-TGAAAAAGCGCCGCTAAAG
40656459 TTACCGACGC
Statistics
Matches: 249, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
128 28 0.11
129 216 0.87
130 5 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (129 bp):
TAGCGGCGTTTTTTGAAAAAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGCTAAGC
ACCGCTAAAGACCATGGTCTATAGTAGCATTGTAAAGCAAAACGCCGCTAAAGACCATGATCTA
Found at i:40656571 original size:23 final size:21
Alignment explanation
Indices: 40656529--40656572 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40656519 TTTGCGGCAC
*
40656529 TAAAAAATGCCACTGTAGCCT
1 TAAAAAATGCCACTGAAGCCT
*
40656550 TAAAAAAGTGCCGCTAGAAGCCT
1 TAAAAAA-TGCCACT-GAAGCCT
40656573 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (21 bp):
TAAAAAATGCCACTGAAGCCT
Found at i:40657134 original size:21 final size:21
Alignment explanation
Indices: 40657090--40657134 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40657080 GATCTTAACT
* *
40657090 TAATAACTTATATATATCATA
1 TAATAACTTACATATATCACA
40657111 TAATAACTTACATA-ACTCACA
1 TAATAACTTACATATA-TCACA
40657132 TAA
1 TAA
40657135 CCGGGTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATAACTTACATATATCACA
Found at i:40658073 original size:21 final size:21
Alignment explanation
Indices: 40658048--40658091 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40658038 ATTTTCAAGG
40658048 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
40658069 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
40658090 AT
1 AT
40658092 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:40658097 original size:19 final size:19
Alignment explanation
Indices: 40658047--40658102 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
40658037 AATTTTCAAG
40658047 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40658066 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
40658087 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
40658103 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40658109 original size:22 final size:23
Alignment explanation
Indices: 40658060--40658125 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
40658050 ATGCAATCTT
*
40658060 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
40658081 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
40658103 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
40658126 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:40658135 original size:22 final size:23
Alignment explanation
Indices: 40658091--40658135 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40658081 AGATATGATA
*
40658091 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
40658114 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
40658136 GTAGATATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:40658369 original size:23 final size:23
Alignment explanation
Indices: 40658325--40658369 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40658315 TCTTATTTTT
* *
40658325 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
40658348 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
40658370 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:40658566 original size:23 final size:22
Alignment explanation
Indices: 40658519--40658567 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
40658509 CTTCTATTTG
* *
40658519 TTATTTTTTATTATTAAATTAA
1 TTATTTTATATTATTAAACTAA
40658541 TTATTTTAATATTATTAATACT-A
1 TTATTTT-ATATTATTAA-ACTAA
40658564 TTAT
1 TTAT
40658568 GTGGCATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 14 0.61
24 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTTTATATTATTAAACTAA
Found at i:40658842 original size:25 final size:23
Alignment explanation
Indices: 40658814--40658866 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
40658804 ATATTTTTAT
40658814 TTTTTATAATTCACATACATATATA
1 TTTTTATAA-T-ACATACATATATA
* * *
40658839 TTTTTCTTATACGTACATATATA
1 TTTTTATAATACATACATATATA
40658862 TTTTT
1 TTTTT
40658867 TATATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.68
24 1 0.04
25 7 0.28
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTTATAATACATACATATATA
Found at i:40659054 original size:3 final size:3
Alignment explanation
Indices: 40659048--40659107 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
40659038 TTATCTTTTC
*
40659048 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
40659096 TTT ATT ATT ATT
1 ATT ATT ATT ATT
40659108 TTTTGTTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40665623 original size:44 final size:43
Alignment explanation
Indices: 40665574--40666066 Score: 691
Period size: 44 Copynumber: 11.4 Consensus size: 43
40665564 CTCCTTGGAA
40665574 AGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGTAA-TCCTATCTCCCTGGTC
40665618 AGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTGGTC
40665662 AGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTGGTC
*
40665706 AGCAGTGGAATAGGTTGAAGATTGTGATTCCTATCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTGGTC
* *
40665750 AGTAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCTTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTGGTC
* * * *
40665794 AACAGTGAAATAGGTTGAAGATTGTGAGTCATATCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTGGTC
* *
40665838 AGCAGTGGAATAGGTTGAAGATTGTGAATCTTATCTCCCTGGTT
1 AGCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTGGTC
*
40665882 AGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGTAA-TCCTATCTCCCTGGTC
* *
40665926 AGTAGTGGAATAGGTTGAAGATTGTAAGTCCTAGCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGTAA-TCCTATCTCCCTGGTC
*
40665970 AGTAGTGGAATA----G--G--TG-AATCCTATCTCCCTGGTC
1 AGCAGTGGAATAGGTTGAAGATTGTAATCCTATCTCCCTGGTC
40666004 AGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGAGT-
1 AGCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTG-GTC
*
40666048 AGCAGTGGAGTAGGTTGAA
1 AGCAGTGGAATAGGTTGAA
40666067 AATTCCATAT
Statistics
Matches: 414, Mismatches: 22, Indels: 26
0.90 0.05 0.06
Matches are distributed among these distances:
34 26 0.06
35 2 0.00
36 2 0.00
38 2 0.00
40 2 0.00
42 2 0.00
43 2 0.00
44 372 0.90
45 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (43 bp):
AGCAGTGGAATAGGTTGAAGATTGTAATCCTATCTCCCTGGTC
Found at i:40665998 original size:34 final size:34
Alignment explanation
Indices: 40665954--40666018 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
40665944 AGATTGTAAG
*
40665954 TCCTAGCTCCCTGGTCAGTAGTGGAATAGGTGAA
1 TCCTAGCTCCCTGGTCAGCAGTGGAATAGGTGAA
*
40665988 TCCTATCTCCCTGGTCAGCAGTGGAATAGGT
1 TCCTAGCTCCCTGGTCAGCAGTGGAATAGGT
40666019 TGAAGATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (34 bp):
TCCTAGCTCCCTGGTCAGCAGTGGAATAGGTGAA
Found at i:40666042 original size:78 final size:78
Alignment explanation
Indices: 40665910--40666062 Score: 238
Period size: 78 Copynumber: 2.0 Consensus size: 78
40665900 AGATTGTAAG
* *
40665910 TCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTAGCTCCCTG-GTCAGTA
1 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAGCTCCCTGAGT-AGCA
40665974 GTGGAATAGGTGAA
65 GTGGAATAGGTGAA
*
40665988 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGAGTAGCA
1 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCTAGCTCCCTGAGTAGCA
*
40666052 GTGGAGTAGGT
65 GTGGAATAGGT
40666063 TGAAAATTCC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
78 65 0.94
79 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (78 bp):
TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTAGCTCCCTGAGTAGCAG
TGGAATAGGTGAA
Found at i:40666083 original size:44 final size:44
Alignment explanation
Indices: 40665986--40666101 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
40665976 GGAATAGGTG
* * **
40665986 AATCCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGTG
1 AATCCTATCTCCCTGAGT-AGCAGTGGAGTAGGTTGAAAATTGCC
40666030 AATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATT-CC
1 AATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATTGCC
* * * *
40666073 ATATCTTATCTCCCTAAGCAGTAGTGGAG
1 A-ATCCTATCTCCCTGAGTAGCAGTGGAG
40666102 CAGATCGAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.02
44 59 0.95
45 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (44 bp):
AATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATTGCC
Found at i:40666086 original size:122 final size:122
Alignment explanation
Indices: 40665861--40666100 Score: 317
Period size: 122 Copynumber: 2.0 Consensus size: 122
40665851 GTTGAAGATT
* * *
40665861 GTGAATCTTATCTCCCTGGTTAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTC
1 GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTC
* * ** *
40665926 AGTAGTGGAATAGGTTGAAGATTGTAAGTCCTAGCTCCCT-GGTCAGTAGTGGAATAG
66 AGCAGTGGAATAGGTTGAAAATTCCAAGTCCTAGCTCCCTAAG-CAGTAGTGGAATAG
40665983 GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGAG
1 GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCTATCTCCCTG-G
* * *
40666047 T-AGCAGTGGAGTAGGTTGAAAATTCCATA-TCTTATCTCCCTAAGCAGTAGTGGA
64 TCAGCAGTGGAATAGGTTGAAAATTCCA-AGTCCTAGCTCCCTAAGCAGTAGTGGA
40666101 GCAGATCGAA
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
122 97 0.94
123 6 0.06
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (122 bp):
GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTC
AGCAGTGGAATAGGTTGAAAATTCCAAGTCCTAGCTCCCTAAGCAGTAGTGGAATAG
Found at i:40666169 original size:88 final size:87
Alignment explanation
Indices: 40666077--40666361 Score: 246
Period size: 88 Copynumber: 3.3 Consensus size: 87
40666067 AATTCCATAT
*
40666077 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
40666142 GGAAGTAGATTTAAGCCACTGGC
66 GGAAGTAGATTTAAGCCACT-GC
** * * * * * *** ** * *
40666165 CTTATCTCTATGAGTAGCAGTGGAGTAGGTTGAAGATTAT-AGGCCTTATC-TCCC-TGAGCAGT
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGGTGA-ATCTTATCTTCCCAAG-GTAGT
*
40666227 AGTGG-AGTAGGAAATTACAG--A-T--
64 AG-GGAAGTA-G-ATTTA-AGCCACTGC
* * *
40666249 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAATGTAGTAG
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
*
40666314 GGAAGCAGATTTAAGCCACTAGC
66 GGAAGTAGATTTAAGCCACT-GC
*
40666337 CTTATCTCCCTGAGCAGCAGTGGAG
1 CTTATCTCCCTAAGCAGCAGTGGAG
40666362 TAGGTTAAAA
Statistics
Matches: 144, Mismatches: 37, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
82 2 0.01
83 4 0.03
84 38 0.26
85 15 0.10
86 1 0.01
87 16 0.11
88 62 0.43
89 4 0.03
90 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (87 bp):
CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAG
GGAAGTAGATTTAAGCCACTGC
Found at i:40666295 original size:172 final size:175
Alignment explanation
Indices: 40666003--40666367 Score: 549
Period size: 172 Copynumber: 2.1 Consensus size: 175
40665993 TCTCCCTGGT
* * * *
40666003 CAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAA
1 CAGCAGTGGAGTAGGTTGAAGATTATGAAGCCTATCTCCCTGAGCAGCAGTGGAGTAGG-TGAAA
* * *
40666068 ATTCCATATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCA
65 ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCA
* * *
40666133 AGGTAGTAGGGAAGTAGATTTAAGCCACTGGCCTTATCTCTATGAG
130 AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCATGAG
* * *
40666179 TAGCAGTGGAGTAGGTTGAAGATTAT-AGGCCTTATCTCCCTGAGCAGTAGTGGAGTA-G-G-AA
1 CAGCAGTGGAGTAGGTTGAAGATTATGAAGCC-TATCTCCCTGAGCAGCAGTGGAGTAGGTGAAA
40666240 ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCA
65 ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCA
* *
40666305 ATGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCCTGAG
130 AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCATGAG
40666351 CAGCAGTGGAGTAGGTT
1 CAGCAGTGGAGTAGGTT
40666368 AAAAATTACA
Statistics
Matches: 172, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
172 121 0.70
173 1 0.01
175 4 0.02
176 46 0.27
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (175 bp):
CAGCAGTGGAGTAGGTTGAAGATTATGAAGCCTATCTCCCTGAGCAGCAGTGGAGTAGGTGAAAA
TTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAA
GGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCCATGAG
Found at i:40666405 original size:172 final size:175
Alignment explanation
Indices: 40666035--40666405 Score: 534
Period size: 172 Copynumber: 2.1 Consensus size: 175
40666025 TTGTGAATCC
* *
40666035 TATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATTCCATATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGTAGCAGTGGAGTAGG-TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
40666100 AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCACTGGC
65 AGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
* * * * * *
40666165 CTTATCTCTATGAGTAGCAGTGGAGTAGGTTGAAGATTATAGGCCT
130 CTTATCTCCATGAGCAGCAGTGGAGTAGGTTAAAAATTACAGACCT
* *
40666211 TATCTCCCTGAGCAGTAGTGGAGTA-G-G-AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
1 TATCTCCCTGAGTAGCAGTGGAGTAGGTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
*
40666273 GCAGATCGAAGACGGCGAATCTTATCTTCCCAATGTAGTAGGGAAGCAGATTTAAGCCACTAGCC
66 GCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCC
* **
40666338 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATTACAGATTT
131 TTATCTCCATGAGCAGCAGTGGAGTAGGTTAAAAATTACAGACCT
*
40666383 TATCTCCC-GAAGTTGCAGTGGAG
1 TATCTCCCTG-AGTAGCAGTGGAG
40666406 CAGATTGAAG
Statistics
Matches: 174, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
171 1 0.01
172 148 0.85
173 1 0.01
175 1 0.01
176 23 0.13
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (175 bp):
TATCTCCCTGAGTAGCAGTGGAGTAGGTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCC
TTATCTCCATGAGCAGCAGTGGAGTAGGTTAAAAATTACAGACCT
Found at i:40666474 original size:44 final size:44
Alignment explanation
Indices: 40666383--40666498 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 44
40666373 TTACAGATTT
* **
40666383 TATCTC-CCGAAGTTGCAGTGGAGCAGATTGAAGCCAATAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAACAATAATCC
* * *
40666426 TATCTCTTTGAAGTTGCAGTGGAGCAGATT-AAAATAATAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAACAATA-ATCC
* * *
40666470 TATCTCTCTGAATTTGCAGTAGAGTAGAT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGAT
40666499 CGTATTAGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 12 0.20
44 49 0.80
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAACAATAATCC
Found at i:40667036 original size:19 final size:19
Alignment explanation
Indices: 40667012--40667065 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
40667002 AATTTTCAGG
40667012 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40667031 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40667050 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40667066 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40667087 original size:23 final size:22
Alignment explanation
Indices: 40667012--40667089 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 22
40667002 AATTTTCAGG
40667012 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
40667031 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
40667050 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
40667072 GATTTTGTAATCTTAGAA
1 GA-TATGCAATCTTAGAA
40667090 ATTTAATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 32 0.60
22 8 0.15
23 13 0.25
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:40667332 original size:23 final size:23
Alignment explanation
Indices: 40667288--40667332 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40667278 TCTTATTTTG
* *
40667288 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
40667311 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
40667333 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:40667525 original size:23 final size:22
Alignment explanation
Indices: 40667478--40667526 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
40667468 CCTCTATTTG
* *
40667478 TTATTTTTTATTATTAAATTAA
1 TTATTTTATATTATTAAACTAA
40667500 TTATTTTAATATTATTAATACT-A
1 TTATTTT-ATATTATTAA-ACTAA
40667523 TTAT
1 TTAT
40667527 GTGGCATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 14 0.61
24 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTTTATATTATTAAACTAA
Found at i:40668963 original size:27 final size:27
Alignment explanation
Indices: 40668944--40669195 Score: 317
Period size: 27 Copynumber: 9.4 Consensus size: 27
40668934 GGGTATAACA
40668944 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
40668971 GTCAATTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
40668998 ATCATTTTACCTTATGAGGGTA-TTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
40669024 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
40669051 GTCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * * *
40669078 ATCATTCTACCTTATGGGGGCATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
40669105 GTCATTCTACCATATGAGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
40669132 GTTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
40669159 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
40669186 GTCATTTTAC
1 GTCATTTTAC
40669196 TTTATAGGGG
Statistics
Matches: 191, Mismatches: 33, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
26 23 0.12
27 168 0.88
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:40669008 original size:54 final size:54
Alignment explanation
Indices: 40668944--40669219 Score: 365
Period size: 54 Copynumber: 5.1 Consensus size: 54
40668934 GGGTATAACA
* * *
40668944 GTCATTTTACCCTATGAGGGTATTTCGGTCAATTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
* * * *
40668998 ATCATTTTACCTTATGAGGGTA-TTCGGTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
* * * *
40669051 GTCATTTTACCCTATGAGGGTATTTCAATCATTCTACCTTATGGGGGCATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
* * *
40669105 GTCATTCTACCATATGAGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
* ** * **
40669159 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACTTTATAGGGGTATTTTA
1 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
40669213 GTCATTT
1 GTCATTT
40669220 ATTGACCTGT
Statistics
Matches: 192, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 48 0.25
54 144 0.75
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
Found at i:40669146 original size:81 final size:81
Alignment explanation
Indices: 40668944--40669195 Score: 353
Period size: 81 Copynumber: 3.1 Consensus size: 81
40668934 GGGTATAACA
* *
40668944 GTCATTTTACCCTATGAGGGTATTTCGGTCAATTTATCCTATGGGGGTATTTCGATCATTTTACC
1 GTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACC
*
40669009 TTATGAGGGTA-TTCG
66 TTATGGGGGTATTTCG
* * * * *
40669024 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCAATCATTCTACC
1 GTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACC
*
40669089 TTATGGGGGCATTTCG
66 TTATGGGGGTATTTCG
* * * * *
40669105 GTCATTCTACCATATGAGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACC
* *
40669170 CTATGGGGGTATTTCA
66 TTATGGGGGTATTTCG
40669186 GTCATTTTAC
1 GTCATTTTAC
40669196 TTTATAGGGG
Statistics
Matches: 148, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 67 0.45
81 81 0.55
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.41
Consensus pattern (81 bp):
GTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACC
TTATGGGGGTATTTCG
Found at i:40672796 original size:32 final size:33
Alignment explanation
Indices: 40672755--40672818 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
40672745 TTTACAATGT
40672755 CGAAGAAAGAGAAAGAAGTGTTCT-CATGGTGA
1 CGAAGAAAGAGAAAGAAGTGTTCTGCATGGTGA
*
40672787 CGAAGAAAGAGAAAGAAGTGTTTTGCATGGTG
1 CGAAGAAAGAGAAAGAAGTGTTCTGCATGGTG
40672819 TTGAAGGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (33 bp):
CGAAGAAAGAGAAAGAAGTGTTCTGCATGGTGA
Found at i:40676346 original size:15 final size:14
Alignment explanation
Indices: 40676322--40676352 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
40676312 TATTGTAAGA
40676322 ATATTTTTAACATT
1 ATATTTTTAACATT
40676336 ATATCTTTTAACATT
1 ATAT-TTTTAACATT
40676351 AT
1 AT
40676353 TGTAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTTTAACATT
Found at i:40676605 original size:43 final size:43
Alignment explanation
Indices: 40676510--40676608 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
40676500 ATTTGCCAAA
* * *
40676510 GTTAGCGGCATTTGTGAAAAAATCGCCGCCAAAAGTCATGTTC
1 GTTAGCGGCGTTTGCGAAAAAAGCGCCGCCAAAAGTCATGTTC
* * * * *
40676553 GTTAACGGCGTTTGCGATAAAAGCGTCGCTAAAGGTCATGTTC
1 GTTAGCGGCGTTTGCGAAAAAAGCGCCGCCAAAAGTCATGTTC
40676596 -TATAGCGGCGTTT
1 GT-TAGCGGCGTTT
40676609 ATGTGACAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
GTTAGCGGCGTTTGCGAAAAAAGCGCCGCCAAAAGTCATGTTC
Found at i:40678071 original size:32 final size:31
Alignment explanation
Indices: 40678012--40678073 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
40678002 AATAATAATT
40678012 ATTTTTAAAATATTTTAAATATACAACTTTA
1 ATTTTTAAAATATTTTAAATATACAACTTTA
* *
40678043 ATTTTATAAAGTATTTTGAAA-ATGCAACTTT
1 ATTTT-TAAAATATTTT-AAATATACAACTTT
40678074 TATAAAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 19 0.70
33 3 0.11
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTTTTAAAATATTTTAAATATACAACTTTA
Found at i:40682613 original size:30 final size:31
Alignment explanation
Indices: 40682545--40682613 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
40682535 CTCCACGTCC
* *
40682545 CTATTTTTTATATATTCGAAATTTATTCTGT
1 CTATTTTTTATATATTAGAAATTTATTCTCT
* *
40682576 TTATTTTTTAT-TTTTAGAAATTTATTC-CT
1 CTATTTTTTATATATTAGAAATTTATTCTCT
*
40682605 CTACTTTTT
1 CTATTTTTT
40682614 GGATTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 8 0.25
30 14 0.44
31 10 0.31
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.62
Consensus pattern (31 bp):
CTATTTTTTATATATTAGAAATTTATTCTCT
Found at i:40682977 original size:9 final size:11
Alignment explanation
Indices: 40682948--40682972 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40682938 ATCACAATAC
40682948 ATATCTATAAT
1 ATATCTATAAT
40682959 ATATCTATAAT
1 ATATCTATAAT
40682970 ATA
1 ATA
40682973 CATAAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATCTATAAT
Found at i:40683535 original size:31 final size:31
Alignment explanation
Indices: 40683491--40683561 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
40683481 TTAATTCTAT
*
40683491 AAATAGCACCCAACGTTTAAGCATTTTTAATA
1 AAATAG-AACCAACGTTTAAGCATTTTTAATA
40683523 AAATAGAACCAACGTTTAAGCATTTTTAATA
1 AAATAGAACCAACGTTTAAGCATTTTTAATA
*
40683554 AGATAGAA
1 AAATAGAA
40683562 TCTAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
31 31 0.84
32 6 0.16
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (31 bp):
AAATAGAACCAACGTTTAAGCATTTTTAATA
Found at i:40690922 original size:3 final size:3
Alignment explanation
Indices: 40690916--40690995 Score: 61
Period size: 3 Copynumber: 26.7 Consensus size: 3
40690906 AAAATAATAA
* * * * * * * *
40690916 ATT ATT ATT ATT ATT ATT AGT AGT AGT AGT AGT AGT AGT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
40690964 ATT AAT ATT ATT ATT AAT ATT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40690996 CATCATATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:40691293 original size:18 final size:18
Alignment explanation
Indices: 40691267--40691333 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
40691257 AAGTTATTTA
*
40691267 TATAAATATATACATACT
1 TATATATATATACATACT
** *
40691285 TATATATATAT-TTTAAT
1 TATATATATATACATACT
* *
40691302 T-T-T-CATATACATATT
1 TATATATATATACATACT
40691317 TATATATATATACATAC
1 TATATATATATACATAC
40691334 ATACACATCT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
14 4 0.11
15 5 0.14
16 2 0.06
17 5 0.14
18 19 0.54
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATATATATACATACT
Found at i:40694822 original size:6 final size:6
Alignment explanation
Indices: 40694811--40694857 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
40694801 TCAATAATAT
*
40694811 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAT ATTATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG A-TATAG ATAT
40694858 GTATAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (6 bp):
ATATAG
Found at i:40695107 original size:113 final size:115
Alignment explanation
Indices: 40694906--40695129 Score: 398
Period size: 113 Copynumber: 2.0 Consensus size: 115
40694896 TAAGCGAGAA
* *
40694906 TCATAAAGTTTTTAAGGTGTGTGTATTATGAATGTGAACTATGGTATTCATAAGACTTCAACTGG
1 TCATAAAGTTTTTAAGGTGTGTGTATTATGAATGTGAACTATGGTATCCATAAGACTTCAACTGA
* *
40694971 CTAAAAATAGCAAAGGTATATTGCATAAAAAGTGGATTTGACTTTGGTAT
66 CTAAAAATAACAAAGGTAAATTGCATAAAAAGTGGATTTGACTTTGGTAT
40695021 TCATAAAGTTTTTAA-G-GTGTGTATTATGAATGTGAACTATGGTATCCATAAGACTTCAACTGA
1 TCATAAAGTTTTTAAGGTGTGTGTATTATGAATGTGAACTATGGTATCCATAAGACTTCAACTGA
40695084 CTAAAAATAACAAAGGTAAATTGCATAAAAAGTGGATTTGACTTTG
66 CTAAAAATAACAAAGGTAAATTGCATAAAAAGTGGATTTGACTTTG
40695130 CCAATAATAA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
113 89 0.85
114 1 0.01
115 15 0.14
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (115 bp):
TCATAAAGTTTTTAAGGTGTGTGTATTATGAATGTGAACTATGGTATCCATAAGACTTCAACTGA
CTAAAAATAACAAAGGTAAATTGCATAAAAAGTGGATTTGACTTTGGTAT
Found at i:40698313 original size:3 final size:3
Alignment explanation
Indices: 40698295--40698403 Score: 73
Period size: 3 Copynumber: 36.3 Consensus size: 3
40698285 AGCATTAGGA
40698295 AAG AAG AATG AGAG AAG AAG AA- AAG AAG AAG -AG AAG -AG AAG AAG
1 AAG AAG AA-G A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
** * * * * * *
40698339 AAG AAG GGG AAG GAG ACG CAG AAAG AAG AAA AAGG AAA AAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AA-G AAG AAG AAG AAG
*
40698386 -AG AAG GAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG A
40698404 GGGAGGGAAG
Statistics
Matches: 80, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
2 8 0.10
3 63 0.79
4 8 0.10
5 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.35, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:40698321 original size:11 final size:11
Alignment explanation
Indices: 40698294--40698344 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
40698284 AAGCATTAGG
40698294 AAAGAAGAATG-
1 AAAGAAGAA-GA
*
40698305 AGAGAAGAAGA
1 AAAGAAGAAGA
40698316 AAAGAAGAAGA
1 AAAGAAGAAGA
*
40698327 GAAG-AGAAGA
1 AAAGAAGAAGA
40698337 AGAAGAAG
1 A-AAGAAG
40698345 GGGAAGGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 7 0.21
11 24 0.73
12 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (11 bp):
AAAGAAGAAGA
Found at i:40698331 original size:16 final size:16
Alignment explanation
Indices: 40698310--40698342 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40698300 GAATGAGAGA
40698310 AGAAGAAAAGAAGAAG
1 AGAAGAAAAGAAGAAG
*
40698326 AGAAGAGAAGAAGAAG
1 AGAAGAAAAGAAGAAG
40698342 A
1 A
40698343 AGGGGAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AGAAGAAAAGAAGAAG
Found at i:40698440 original size:61 final size:60
Alignment explanation
Indices: 40698309--40698424 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 60
40698299 AGAATGAGAG
* **
40698309 AAGAAGAAAAGAAGAAGAGAAGAGAAGAAGAAGAAGGGGAAGGAGACGCAGAAAGAAGAAA
1 AAGAA-AAAAGAAAAAGAGAAGAGAAGAAGAAGAAGGGGAAGGAGACAAAGAAAGAAGAAA
* *
40698370 AAGGAAAAAGAAAAAGAGAAGGAGAAGAAGAAGAGGGAGGGAAGGA-A-AAAGAAAG
1 AAGAAAAAAGAAAAAGAGAA-GAGAAGAAGAAGA-AG-GGGAAGGAGACAAAGAAAG
40698425 GCAAAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
60 14 0.30
61 23 0.49
62 2 0.04
63 8 0.17
ACGTcount: A:0.61, C:0.02, G:0.37, T:0.00
Consensus pattern (60 bp):
AAGAAAAAAGAAAAAGAGAAGAGAAGAAGAAGAAGGGGAAGGAGACAAAGAAAGAAGAAA
Found at i:40698686 original size:30 final size:30
Alignment explanation
Indices: 40698650--40698712 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
40698640 AATTTTAATT
*
40698650 TTTATGTTATGTACATTCTATGTCTTATTA
1 TTTATGTTATGTACATACTATGTCTTATTA
40698680 TTTATGTTATGTACATACTATGTCTTATTA
1 TTTATGTTATGTACATACTATGTCTTATTA
40698710 TTT
1 TTT
40698713 TATTATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (30 bp):
TTTATGTTATGTACATACTATGTCTTATTA
Found at i:40698723 original size:22 final size:21
Alignment explanation
Indices: 40698698--40698766 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
40698688 ATGTACATAC
*
40698698 TATGTCTTATTATTTTATTATT
1 TATGT-TTATTATTTTATTATG
40698720 TATG-TTATTATTTGTTATTATG
1 TATGTTTATTA-TT-TTATTATG
*
40698742 TATGTTTTATTATTTATGTTATG
1 TATG-TTTATTATTT-TATTATG
40698765 TA
1 TA
40698767 CATTCTATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 6 0.15
21 2 0.05
22 16 0.40
23 10 0.25
24 6 0.15
ACGTcount: A:0.23, C:0.01, G:0.10, T:0.65
Consensus pattern (21 bp):
TATGTTTATTATTTTATTATG
Found at i:40698727 original size:12 final size:12
Alignment explanation
Indices: 40698707--40698763 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
40698697 CTATGTCTTA
*
40698707 TTATTTTATTAT
1 TTATGTTATTAT
40698719 TTATGTTATTA-
1 TTATGTTATTAT
40698730 TT-TGTTATTAT
1 TTATGTTATTAT
*
40698741 GTATGTTTTATTAT
1 TTATG--TTATTAT
40698755 TTATGTTAT
1 TTATGTTAT
40698764 GTACATTCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 8 0.21
11 3 0.08
12 16 0.42
14 11 0.29
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (12 bp):
TTATGTTATTAT
Found at i:40699243 original size:158 final size:159
Alignment explanation
Indices: 40698950--40699801 Score: 1354
Period size: 158 Copynumber: 5.3 Consensus size: 159
40698940 ACTAAAAAAT
** * *
40698950 GAAAATAGTATATTTAATGAAAGTAATAAAATCAGAAAAAAAAAAGAAAAATACGAACAAAGGGC
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCG---AAAATAAGAAAAATACGAACAAAGGGC
* *
40699015 AAAAATAAGGGTTTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTCAAACAT
63 CAAAATAAGGG-TTTTTTTACTAAATTTATATAAAAAAAACACTAAAATAATACATTTCAAACAT
40699080 TATGTACTAAAATAATATAAAATAATAAAATAC
127 TATGTACTAAAATAATATAAAATAATAAAATAC
* *
40699113 GAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAAT-CTGAACAAAGGGCCA
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC-GAACAAAGGGCCA
* * *
40699177 AAATAAGGG-TTTTTTACTAAATTTATATAAAAAAAACACTAAATTAATATATTTCAAATATTAT
65 AAATAAGGGTTTTTTTACTAAATTTATATAAAAAAAACACTAAAATAATACATTTCAAACATTAT
*
40699241 GTACTAAAATAATATAATATAATAAAATAC
130 GTACTAAAATAATATAAAATAATAAAATAC
*
40699271 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACAAACAAAGGGCCAA
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAA
40699336 AATAAGGGTTTTTTTTACTAAATTTATATAAAAAAACACACACTAAAATAATACATTTCAAACAT
66 AATAAGGG-TTTTTTTACTAAATTTATAT-AAAAAA-A-ACACTAAAATAATACATTTCAAACAT
40699401 TATGTACTAAAATAATATAAAATAATAAAATAC
127 TATGTACTAAAATAATATAAAATAATAAAATAC
* * *
40699434 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCAAAAATAAGAAAAATACGAACAAATGACCAA
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAA
40699499 AATAAGGG-TTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATACATTTCAAACATTAT
66 AATAAGGGTTTTTTTACTAAATTTATATAAAAAAA-ACACTAAAATAATACATTTCAAACATTAT
40699563 GTAC-AAAATAATATAAAATAATAAAATAC
130 GTACTAAAATAATATAAAATAATAAAATAC
* ** *
40699592 GAAAATAGTATATTTTTTTAAAGTAATAAAATTTGAAAATAAGAAAAATACGAACAAATGGCCAA
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAA
* * *
40699657 AATAAGGGTTTTTTTACTAAATTTATATAAAAAACAA-ACTAAATTAATACATTTCGAACTTTAT
66 AATAAGGGTTTTTTTACTAAATTTATATAAAAAA-AACACTAAAATAATACATTTCAAACATTAT
40699721 GTACTAAAATAATATAAAATAATAAAATAC
130 GTACTAAAATAATATAAAATAATAAAATAC
*
40699751 GAAAATAATATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
40699802 ATTGAAATTA
Statistics
Matches: 645, Mismatches: 34, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
158 269 0.42
159 135 0.21
160 60 0.09
161 25 0.04
162 1 0.00
163 155 0.24
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (159 bp):
GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAA
AATAAGGGTTTTTTTACTAAATTTATATAAAAAAAACACTAAAATAATACATTTCAAACATTATG
TACTAAAATAATATAAAATAATAAAATAC
Found at i:40699448 original size:321 final size:320
Alignment explanation
Indices: 40698950--40699801 Score: 1403
Period size: 321 Copynumber: 2.7 Consensus size: 320
40698940 ACTAAAAAAT
** *
40698950 GAAAATAGTATATTTAATGAAAGTAATAAAATCAGAAAAAAAAAAGAAAAATACGAACAAAGGGC
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCAG---AAAATAAGAAAAATACGAACAAAGGGC
*
40699015 AAAAATAAGGGTTTTTTTTACTAAATTTATAT-AAAAA-ACACACTAAAATAATACATTTCAAAC
63 CAAAATAAGGGTTTTTTTTACTAAATTTATATAAAAAACACACACTAAAATAATACATTTCAAAC
40699078 ATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAA
128 ATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAA
* *
40699143 ATCTGAAAATAAGAAAAAT-CTGAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAA
193 ATCCGAAAATAAGAAAAATAC-GAACAAAGGACCAAAATAAGGGTTTTTTACTAAATTTATATAA
* * * *
40699207 AAAAA-ACACTAAATTAATATATTTCAAATATTATGTACTAAAATAATATAATATAATAAAATAC
257 AAAAACACACTAAAATAATACATTTCAAACATTATGTAC-AAAATAATATAAAATAATAAAATAC
* *
40699271 GAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACAAACAAAGGGCCAA
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCAGAAAATAAGAAAAATACGAACAAAGGGCCAA
40699336 AATAAGGGTTTTTTTTACTAAATTTATATAAAAAAACACACACTAAAATAATACATTTCAAACAT
66 AATAAGGGTTTTTTTTACTAAATTTATAT-AAAAAACACACACTAAAATAATACATTTCAAACAT
*
40699401 TATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAAT
130 TATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAAT
* *
40699466 CCAAAAATAAGAAAAATACGAACAAATGACCAAAATAAGGGTTTTTTACTAAATTTATATAAAAA
195 CCGAAAATAAGAAAAATACGAACAAAGGACCAAAATAAGGGTTTTTTACTAAATTTATATAAAAA
40699531 AACACACTAAAATAATACATTTCAAACATTATGTACAAAATAATATAAAATAATAAAATAC
260 AACACACTAAAATAATACATTTCAAACATTATGTACAAAATAATATAAAATAATAAAATAC
* ** *
40699592 GAAAATAGTATATTTTTTTAAAGTAATAAAATTTGAAAATAAGAAAAATACGAACAAATGGCCAA
1 GAAAATAGTATATTTTTTGAAAGTAATAAAATCAGAAAATAAGAAAAATACGAACAAAGGGCCAA
* * *
40699657 AATAAGGG-TTTTTTTACTAAATTTATATAAAAAACA-A-ACTAAATTAATACATTTCGAACTTT
66 AATAAGGGTTTTTTTTACTAAATTTATATAAAAAACACACACTAAAATAATACATTTCAAACATT
40699719 ATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATC
131 ATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATC
40699784 CGAAAATAAGAAAAATAC
196 CGAAAATAAGAAAAATAC
40699802 ATTGAAATTA
Statistics
Matches: 501, Mismatches: 25, Indels: 14
0.93 0.05 0.03
Matches are distributed among these distances:
317 103 0.21
318 57 0.11
319 8 0.02
320 25 0.05
321 277 0.55
322 31 0.06
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (320 bp):
GAAAATAGTATATTTTTTGAAAGTAATAAAATCAGAAAATAAGAAAAATACGAACAAAGGGCCAA
AATAAGGGTTTTTTTTACTAAATTTATATAAAAAACACACACTAAAATAATACATTTCAAACATT
ATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATC
CGAAAATAAGAAAAATACGAACAAAGGACCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAA
ACACACTAAAATAATACATTTCAAACATTATGTACAAAATAATATAAAATAATAAAATAC
Found at i:40701489 original size:26 final size:25
Alignment explanation
Indices: 40701460--40701515 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
40701450 TTTCTTGCGG
** *
40701460 TTTTGATATTACTCTAGTTTGTATTT
1 TTTTGATATTAC-AAAGTTTGTACTT
*
40701486 TTTTTATATTACAAAGTTTGTACTT
1 TTTTGATATTACAAAGTTTGTACTT
40701511 TTTTG
1 TTTTG
40701516 TATAAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.21, C:0.07, G:0.11, T:0.61
Consensus pattern (25 bp):
TTTTGATATTACAAAGTTTGTACTT
Found at i:40705254 original size:37 final size:37
Alignment explanation
Indices: 40705160--40705333 Score: 131
Period size: 40 Copynumber: 4.5 Consensus size: 37
40705150 CCACTAATCC
**
40705160 TAATAACTAACACAATAATAA-TAGTTTTTTACTAAAAA
1 TAATAACT-A-ACAATAATAATTAGGGTTTTACTAAAAA
40705198 TAATACTAACTAACAATAATAATTAGGGTTTTACTAAAAA
1 T-A-A-TAACTAACAATAATAATTAGGGTTTTACTAAAAA
* ***
40705238 TAATAACTAACAATAAT-A-TAGTGTAAAAACTAACAATCA
1 TAATAACTAACAATAATAATTAGGGT-TTTACTAA-AA--A
* ***
40705277 TACTAACTAA-AATAATAATTAGGGTTTTTACTAATCC
1 TAATAACTAACAATAATAATTAGGG-TTTTACTAAAAA
*
40705314 TAATAACTAACCATAATAAT
1 TAATAACTAACAATAATAAT
40705334 AATATTAGTT
Statistics
Matches: 108, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
35 5 0.05
36 6 0.06
37 25 0.23
38 16 0.15
39 23 0.21
40 27 0.25
41 6 0.06
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (37 bp):
TAATAACTAACAATAATAATTAGGGTTTTACTAAAAA
Found at i:40705280 original size:76 final size:76
Alignment explanation
Indices: 40705190--40705331 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 76
40705180 ATAGTTTTTT
40705190 ACTAAAAATAATACTAACTAACAATAATAATTAGGG-TTTTACTAAAAATAATAACTAACAATAA
1 ACTAAAAATAATACTAACTAA-AATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAA
40705254 TATAGTGTAAAA
65 TATAGTGTAAAA
* * *** *
40705266 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTTACTAATCCTAATAACTAACCATAAT
1 ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
40705331 A
66 A
40705332 ATAATATTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 14 0.24
76 45 0.76
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
ATAGTGTAAAA
Found at i:40705564 original size:6 final size:6
Alignment explanation
Indices: 40705538--40705607 Score: 52
Period size: 6 Copynumber: 11.0 Consensus size: 6
40705528 AAATCTTATT
* * *
40705538 TTTTTC TATTTT- TTCTTC TTTTTC TTTCTTC TTTCTC TATTCTC TTTCTCTC
1 TTTTTC T-TTTTC TTTTTC TTTTTC TTT-TTC TTTTTC T-TTTTC TTT-T-TC
*
40705590 TTTTTC TTTTCC TTTTTC
1 TTTTTC TTTTTC TTTTTC
40705608 GGCATCGCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 3 0.06
6 27 0.52
7 17 0.33
8 5 0.10
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:40705567 original size:13 final size:13
Alignment explanation
Indices: 40705549--40705604 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
40705539 TTTTCTATTT
40705549 TTTCTTCTTTTTC
1 TTTCTTCTTTTTC
*
40705562 TTTCTTCTTTCTC
1 TTTCTTCTTTTTC
40705575 TATTC-TCTTTCTCTC
1 T-TTCTTCTTT-T-TC
*
40705590 TTT-TTCTTTTCC
1 TTTCTTCTTTTTC
40705602 TTT
1 TTT
40705605 TTCGGCATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.11
13 19 0.53
14 10 0.28
15 3 0.08
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTCTTTTTC
Found at i:40705572 original size:20 final size:21
Alignment explanation
Indices: 40705549--40705604 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
40705539 TTTTCTATTT
40705549 TTTCTTCTTTTTCTTTCT-TC
1 TTTCTTCTTTTTCTTTCTCTC
*
40705569 TTTC-TCTATTCTCTTTCTCTC
1 TTTCTTCT-TTTTCTTTCTCTC
*
40705590 TTT-TTCTTTTCCTTT
1 TTTCTTCTTTTTCTTT
40705605 TTCGGCATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 3 0.10
20 19 0.63
21 8 0.27
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTCTTCTTTTTCTTTCTCTC
Found at i:40719893 original size:21 final size:21
Alignment explanation
Indices: 40719867--40719909 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40719857 TCTGCAGATA
40719867 AGTTTCCACCGATTACTGAAG
1 AGTTTCCACCGATTACTGAAG
* * *
40719888 AGTTTCCATCGGTTATTGAAG
1 AGTTTCCACCGATTACTGAAG
40719909 A
1 A
40719910 AACCTTGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (21 bp):
AGTTTCCACCGATTACTGAAG
Found at i:40720718 original size:12 final size:13
Alignment explanation
Indices: 40720701--40720747 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 13
40720691 CATGTTACGA
40720701 TATATTA-GTATG
1 TATATTATGTATG
40720713 TATATTATGTATG
1 TATATTATGTATG
40720726 T-TATCTATGTTATG
1 TATAT-TATG-TATG
40720740 ATATATTA
1 -TATATTA
40720748 GTAATTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.33
13 10 0.33
14 4 0.13
15 3 0.10
16 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (13 bp):
TATATTATGTATG
Found at i:40724244 original size:16 final size:16
Alignment explanation
Indices: 40724220--40724250 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40724210 TGAATAGATG
40724220 GGAAAAGGTAGAAAAT
1 GGAAAAGGTAGAAAAT
*
40724236 GGAAGAGGTAGAAAA
1 GGAAAAGGTAGAAAA
40724251 CGATGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.35, T:0.10
Consensus pattern (16 bp):
GGAAAAGGTAGAAAAT
Found at i:40725281 original size:14 final size:16
Alignment explanation
Indices: 40725262--40725294 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40725252 ACTAAAACTT
40725262 ATAAA-TTTTAAAA-A
1 ATAAATTTTTAAAACA
40725276 ATAAATTTTTAAAACA
1 ATAAATTTTTAAAACA
40725292 ATA
1 ATA
40725295 GTTGATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAATTTTTAAAACA
Found at i:40733010 original size:16 final size:18
Alignment explanation
Indices: 40732986--40733028 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
40732976 GCATTGACCC
*
40732986 AATTCTTATAAA-TTT-T
1 AATTTTTATAAATTTTGT
40733002 AATTTTTATAAATTTTGT
1 AATTTTTATAAATTTTGT
40733020 AATTTTTAT
1 AATTTTTAT
40733029 TTCTCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 11 0.46
17 3 0.12
18 10 0.42
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTTTATAAATTTTGT
Found at i:40734121 original size:59 final size:58
Alignment explanation
Indices: 40734050--40734165 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 58
40734040 ATTCATGAGA
* *
40734050 ACTTATAGTTTAAAATTATTTTTATATAATATAATATTTTATTATATGAAAGAGAGAAG
1 ACTTATAGTTTAAAATTATTTATATATAATATAATA-TATATTATATGAAAGAGAGAAG
* *
40734109 ACTTATAGTTTAAAGTTATTTATATATAATATGATATATATTATATGAAAGAGAGAA
1 ACTTATAGTTTAAAATTATTTATATATAATATAATATATATTATATGAAAGAGAGAA
40734166 ACAATAATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 20 0.38
59 33 0.62
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (58 bp):
ACTTATAGTTTAAAATTATTTATATATAATATAATATATATTATATGAAAGAGAGAAG
Found at i:40734179 original size:58 final size:59
Alignment explanation
Indices: 40734054--40734181 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 59
40734044 ATGAGAACTT
* * * *
40734054 ATAGTTTAAAATTATTTTTATATAATATAATATTTTATTATATGAAAGAGAGAAGACTT
1 ATAGTTTAAAGTTATTTATATATAATATAATATTATATTATATGAAAGAGAGAAGACTA
*
40734113 ATAGTTTAAAGTTATTTATATATAATATGATA-TATATTATATGAAAGAGAGAA-AC-A
1 ATAGTTTAAAGTTATTTATATATAATATAATATTATATTATATGAAAGAGAGAAGACTA
40734169 ATAATGTTTAAAG
1 AT-A-GTTTAAAG
40734182 AAGGAAATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
56 2 0.03
57 3 0.05
58 28 0.45
59 29 0.47
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.41
Consensus pattern (59 bp):
ATAGTTTAAAGTTATTTATATATAATATAATATTATATTATATGAAAGAGAGAAGACTA
Found at i:40744308 original size:31 final size:31
Alignment explanation
Indices: 40744250--40744311 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
40744240 ATGCACGAAG
*
40744250 ACTTATCACAGAGAGCTCGCACGGGGAGCTT
1 ACTTATCACAGAGAGCTCGCACAGGGAGCTT
**
40744281 ACTTATCACAGAGAGCTCGCTTAGGGAGCTT
1 ACTTATCACAGAGAGCTCGCACAGGGAGCTT
40744312 GCTTGAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (31 bp):
ACTTATCACAGAGAGCTCGCACAGGGAGCTT
Found at i:40753349 original size:23 final size:23
Alignment explanation
Indices: 40753319--40753368 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
40753309 GTTATTGATT
* *
40753319 AGTGGTAGCTACGGCTACTTATC
1 AGTGGTAGCTACAGCTACATATC
*
40753342 AGTGGTAGCTTCAGCTACATATC
1 AGTGGTAGCTACAGCTACATATC
40753365 AGTG
1 AGTG
40753369 TGGCACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
AGTGGTAGCTACAGCTACATATC
Found at i:40762886 original size:30 final size:29
Alignment explanation
Indices: 40762830--40763221 Score: 94
Period size: 29 Copynumber: 13.5 Consensus size: 29
40762820 CGATAGACGT
* * *
40762830 AACCGTCCCTTTTAAT-ATTCGATGGTCGA
1 AACCATCCCTTTTCATAATT-GATGGTCCA
*
40762859 AACCATCCCTTTTCATTAATTGATGGTCCC
1 AACCATCCCTTTTCA-TAATTGATGGTCCA
* *
40762889 CACCATCCCTTTTCATAGTTGATGGT-C-
1 AACCATCCCTTTTCATAATTGATGGTCCA
* *** * *
40762916 -ATCATATTTTGTTTCATAATCGATAG-CCGA
1 AACCAT-CCCT-TTTCATAATTGATGGTCC-A
* * * **
40762946 AGCTATCCCTTTTCAT-GTTCGATGGTCGT
1 AACCATCCCTTTTCATAATT-GATGGTCCA
* * *
40762975 CACCATCCCTTTTCATAATCGATAG-CCGA
1 AACCATCCCTTTTCATAATTGATGGTCC-A
* * * * *
40763004 AGCTATCCCTTTTCGTAATCGATAG-CCGA
1 AACCATCCCTTTTCATAATTGATGGTCC-A
* * * * **
40763033 AGCTATCCCTTTTCAT-GTTCGATAGTCGT
1 AACCATCCCTTTTCATAATT-GATGGTCCA
* * * * *
40763062 CACTATCCCTTTTCATAGTTTATGG-CCGT
1 AACCATCCCTTTTCATAATTGATGGTCC-A
* * *
40763091 CACCATCCCTTTTCATAGTTGATGGCTGTC-
1 AACCATCCCTTTTCATAATTGATGG-T-CCA
* *
40763121 -ACCATCCCTTTTCATAATCGATAG-CCGA
1 AACCATCCCTTTTCATAATTGATGGTCC-A
* * *
40763149 AGCTATCCCTTTTCATAATTGATAG-CCGA
1 AACCATCCCTTTTCATAATTGATGGTCC-A
* * * * *
40763178 AGCTACCCCTTTTCATAATCGATAG-CCAA
1 AACCATCCCTTTTCATAATTGATGGTCC-A
*
40763207 AACTATCCCTTTTCA
1 AACCATCCCTTTTCA
40763222 CTTGTCGATG
Statistics
Matches: 280, Mismatches: 61, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
26 5 0.02
27 1 0.00
28 18 0.06
29 221 0.79
30 29 0.10
31 5 0.02
32 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (29 bp):
AACCATCCCTTTTCATAATTGATGGTCCA
Found at i:40762960 original size:57 final size:58
Alignment explanation
Indices: 40762835--40763193 Score: 184
Period size: 58 Copynumber: 6.2 Consensus size: 58
40762825 GACGTAACCG
* * * * * ** *
40762835 TCCCTTTTAATATTCGATGGTCGA-AACCATCCCTTTTCATTAATTGATGGTCCCCA-CCA
1 TCCCTTTTCATGTTCGATGGTC-ATCACCATCCCTTTTCA-TAATCGATAG-CCGAAGCTA
* **
40762894 TCCCTTTTCATAGTT-GATGGTCATCA-TAT-TTTGTTTCATAATCGATAGCCGAAGCTA
1 TCCCTTTTCAT-GTTCGATGGTCATCACCATCCCT-TTTCATAATCGATAGCCGAAGCTA
*
40762951 TCCCTTTTCATGTTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
1 TCCCTTTTCATGTTCGATGGTCATCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
* ** * * * ** * *
40763009 TCCCTTTTCGTAATCGATAGCCGA--AGCTATCCCTTTTCATGTTCGATAGTCGTCA-CTA
1 TCCCTTTTCATGTTCGATGGTC-ATCA-CCATCCCTTTTCATAATCGATAGCCG-AAGCTA
* * * * * * * * *
40763067 TCCCTTTTCATAGTT-TATGGCCGTCACCATCCCTTTTCATAGTTGATGGCTGTCA-CCA
1 TCCCTTTTCAT-GTTCGATGGTCATCACCATCCCTTTTCATAATCGATAGCCG-AAGCTA
** * * * *
40763125 TCCCTTTTCATAATCGATAGCCGA--AGCTATCCCTTTTCATAATTGATAGCCGAAGCTA
1 TCCCTTTTCATGTTCGATGGTC-ATCA-CCATCCCTTTTCATAATCGATAGCCGAAGCTA
*
40763183 CCCCTTTTCAT
1 TCCCTTTTCAT
40763194 AATCGATAGC
Statistics
Matches: 231, Mismatches: 52, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
56 6 0.03
57 36 0.16
58 165 0.71
59 22 0.10
60 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.36
Consensus pattern (58 bp):
TCCCTTTTCATGTTCGATGGTCATCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
Found at i:40763025 original size:87 final size:87
Alignment explanation
Indices: 40762927--40763221 Score: 344
Period size: 87 Copynumber: 3.4 Consensus size: 87
40762917 TCATATTTTG
* *
40762927 TTTCATAATCGATAGCCGAAGCTATCCCTTTTCATGTTCGATGGTCGTCACCATCCCTTTTCATA
1 TTTCATAATCGATAGCCGAAGCTATCCCTTTTCATGTTCGATAGTCGTCACTATCCCTTTTCATA
*
40762992 ATCGATAGCCGAAGCTATCCCT
66 ATTGATAGCCGAAGCTATCCCT
*
40763014 TTTCGTAATCGATAGCCGAAGCTATCCCTTTTCATGTTCGATAGTCGTCACTATCCCTTTTCATA
1 TTTCATAATCGATAGCCGAAGCTATCCCTTTTCATGTTCGATAGTCGTCACTATCCCTTTTCATA
* * * * *
40763079 GTTTATGGCCGTCA-CCATCCCT
66 ATTGATAGCCG-AAGCTATCCCT
* * * * * * ** * *
40763101 TTTCATAGTTGATGGCTGTCA-CCATCCCTTTTCATAATCGATAGCCG-AAGCTATCCCTTTTCA
1 TTTCATAATCGATAGCCG-AAGCTATCCCTTTTCATGTTCGATAGTCGTCA-CTATCCCTTTTCA
*
40763164 TAATTGATAGCCGAAGCTACCCCT
64 TAATTGATAGCCGAAGCTATCCCT
* *
40763188 TTTCATAATCGATAGCCAAAACTATCCCTTTTCA
1 TTTCATAATCGATAGCCGAAGCTATCCCTTTTCA
40763222 CTTGTCGATG
Statistics
Matches: 170, Mismatches: 33, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
86 3 0.02
87 165 0.97
88 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (87 bp):
TTTCATAATCGATAGCCGAAGCTATCCCTTTTCATGTTCGATAGTCGTCACTATCCCTTTTCATA
ATTGATAGCCGAAGCTATCCCT
Found at i:40763166 original size:29 final size:29
Alignment explanation
Indices: 40762927--40763221 Score: 283
Period size: 29 Copynumber: 10.2 Consensus size: 29
40762917 TCATATTTTG
40762927 TTTCATAATCGATAGCCGAAGCTATCCCT
1 TTTCATAATCGATAGCCGAAGCTATCCCT
** * * * *
40762956 TTTCATGTTCGATGGTCGTCA-CCATCCCT
1 TTTCATAATCGATAGCCG-AAGCTATCCCT
40762985 TTTCATAATCGATAGCCGAAGCTATCCCT
1 TTTCATAATCGATAGCCGAAGCTATCCCT
*
40763014 TTTCGTAATCGATAGCCGAAGCTATCCCT
1 TTTCATAATCGATAGCCGAAGCTATCCCT
** * *
40763043 TTTCATGTTCGATAGTCGTCA-CTATCCCT
1 TTTCATAATCGATAGCCG-AAGCTATCCCT
* ** * * *
40763072 TTTCATAGTTTATGGCCGTCA-CCATCCCT
1 TTTCATAATCGATAGCCG-AAGCTATCCCT
* * * * * *
40763101 TTTCATAGTTGATGGCTGTCA-CCATCCCT
1 TTTCATAATCGATAGCCG-AAGCTATCCCT
40763130 TTTCATAATCGATAGCCGAAGCTATCCCT
1 TTTCATAATCGATAGCCGAAGCTATCCCT
* *
40763159 TTTCATAATTGATAGCCGAAGCTACCCCT
1 TTTCATAATCGATAGCCGAAGCTATCCCT
* *
40763188 TTTCATAATCGATAGCCAAAACTATCCCT
1 TTTCATAATCGATAGCCGAAGCTATCCCT
40763217 TTTCA
1 TTTCA
40763222 CTTGTCGATG
Statistics
Matches: 223, Mismatches: 39, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.01
29 219 0.98
30 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (29 bp):
TTTCATAATCGATAGCCGAAGCTATCCCT
Found at i:40765148 original size:45 final size:45
Alignment explanation
Indices: 40765062--40765150 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
40765052 TGTGAATCGA
* * *
40765062 ACATCATTAATTAGTAAGGTGGTTGTTATGTACTGATTCCACCGG
1 ACATCATTAATTAATAAGCTGGTTGTTATGTACTGAATCCACCGG
* **
40765107 ACATCATTGATTAATAAGCTGGTT-TCTATGTGTTGAATCCACCG
1 ACATCATTAATTAATAAGCTGGTTGT-TATGTACTGAATCCACCG
40765151 AGTATCTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (45 bp):
ACATCATTAATTAATAAGCTGGTTGTTATGTACTGAATCCACCGG
Found at i:40767847 original size:23 final size:23
Alignment explanation
Indices: 40767821--40767871 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
40767811 CTTGCCTTCA
40767821 TGTAATATCCC-AAAAATTACTAC
1 TGTAATA-CCCTAAAAATTACTAC
*
40767844 TGTAATACCCTGAAAATTACTAC
1 TGTAATACCCTAAAAATTACTAC
*
40767867 AGTAA
1 TGTAA
40767872 GAAAATAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (23 bp):
TGTAATACCCTAAAAATTACTAC
Found at i:40768347 original size:13 final size:13
Alignment explanation
Indices: 40768322--40768355 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
40768312 ATTAGTTTAT
40768322 TAATATTTTAATA
1 TAATATTTTAATA
40768335 TAAT-TTTTAA-A
1 TAATATTTTAATA
40768346 TAATATTTTA
1 TAATATTTTA
40768356 TTATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 11 0.55
13 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATTTTAATA
Found at i:40768378 original size:11 final size:11
Alignment explanation
Indices: 40768353--40768379 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40768343 AAATAATATT
40768353 TTATTATTTTA
1 TTATTATTTTA
40768364 TTATTATTTTA
1 TTATTATTTTA
40768375 TTATT
1 TTATT
40768380 TTATTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:40775926 original size:22 final size:22
Alignment explanation
Indices: 40775898--40775945 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
40775888 GATTACGTCA
40775898 TATGAGTTTGTTTTATTAAACT
1 TATGAGTTTGTTTTATTAAACT
40775920 TATGAGTTTGTTTTATTAAACT
1 TATGAGTTTGTTTTATTAAACT
40775942 TATG
1 TATG
40775946 TACTGTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (22 bp):
TATGAGTTTGTTTTATTAAACT
Found at i:40778407 original size:14 final size:17
Alignment explanation
Indices: 40778382--40778418 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
40778372 AAATAATATG
40778382 ATTACTACTTT-ATT-A
1 ATTACTACTTTAATTCA
40778397 ATTAC-ACTTTAATTCA
1 ATTACTACTTTAATTCA
40778413 ATTACT
1 ATTACT
40778419 CATTTCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.26
15 8 0.42
16 6 0.32
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTACTACTTTAATTCA
Found at i:40779489 original size:134 final size:134
Alignment explanation
Indices: 40779146--40779501 Score: 373
Period size: 133 Copynumber: 2.7 Consensus size: 134
40779136 AAAACGCCAC
* * * * * *
40779146 AAAAAATTGGAATATAGCGGCGTTTTCTGAGAAACGCCGGTAACGATAACGAATTTGAGGAAAAA
1 AAAAGATTGGAATATAGTGGCGTTTTCGGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAA
* * * * *
40779211 ATCTGAGCAAAACAGTACCGTTTTGTTGTTTCAGTTTATTTCTTTACTAGCGCATTTTAAAAAAC
66 ATTTGAGCAAAAC-GTACCGTTTTATTGCTTCAGTTTATTTCCTTACTAGCGCATTGTAAAAAAC
40779276 ACCGG
130 ACCGG
* * **
40779281 AAAAGAAT-GCAT-TAGTGGCGTTTTCAGG-GAAACGCCACTAAAGATATCTAATTTGAGGAAAA
1 AAAAGATTGGAATATAGTGGCGTTTTC-GGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAA
* * * *
40779343 AATTTG-GACAAAACGCTACTGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCATTGTAAAAA
65 AATTTGAG-CAAAACG-TACCGTTTTATTGCTTCAGTTTATTTCCTTACTAGCGCATTGTAAAAA
** *
40779407 A-TGCTG
128 ACACCGG
* * * *
40779413 CAAATATTGGGATATAGTGGCGTTATT-GGAGAAATGCCGGTAAAGATATCTAATTTGAGGAAAA
1 AAAAGATTGGAATATAGTGGCGTT-TTCGGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAA
*
40779477 ATTTTGAGCAAAACGGTACCGTTTT
65 AATTTGAGCAAAAC-GTACCGTTTT
40779502 GTTGTTTCCT
Statistics
Matches: 181, Mismatches: 31, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
132 9 0.05
133 98 0.54
134 64 0.35
135 10 0.06
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (134 bp):
AAAAGATTGGAATATAGTGGCGTTTTCGGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAA
ATTTGAGCAAAACGTACCGTTTTATTGCTTCAGTTTATTTCCTTACTAGCGCATTGTAAAAAACA
CCGG
Found at i:40779525 original size:134 final size:134
Alignment explanation
Indices: 40779146--40779551 Score: 369
Period size: 133 Copynumber: 3.0 Consensus size: 134
40779136 AAAACGCCAC
* * * * * *
40779146 AAAAAATTGGAATATAGCGGCGTTTTCTGAGAAACGCCGGTAACGATAACGAATTTGAGGAAAAA
1 AAAAGATTGGAATATAGTGGCGTTTTCGGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAA
* * * * *
40779211 ATCTGAGCAAAACAGTACCGTTTTGTTGTTTCAGTTTATT-TCTTTACTAGCGCATTTTAAAAAA
66 ATTTGAGCAAAACGGTACCGTTTTGTTGTTTC-CTTT-TTATCTTTAGTAGCGCATTGTAAAAAA
40779275 CACCGG
129 CACCGG
* * **
40779281 AAAAGAAT-GCAT-TAGTGGCGTTTTCAGG-GAAACGCCACTAAAGATATCTAATTTGAGGAAAA
1 AAAAGATTGGAATATAGTGGCGTTTTC-GGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAA
* * * * * * * *
40779343 AATTTG-GACAAAACGCTACTGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCATTGTAAAAA
65 AATTTGAG-CAAAACGGTACCGTTTTGTTGTTTCCTTTT-TATCTTTAGTAGCGCATTGTAAAAA
** *
40779407 A-TGCTG
128 ACACCGG
* * * *
40779413 CAAATATTGGGATATAGTGGCGTTATT-GGAGAAATGCCGGTAAAGATATCTAATTTGAGGAAAA
1 AAAAGATTGGAATATAGTGGCGTT-TTCGGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAA
* * * *
40779477 ATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTTTATGCTTTAGTTGCGAAATGTTAAAAA
65 AATTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTTTAT-CTTTAGTAGCGCATTG-TAAAAA
*
40779542 ACGCC-G
128 ACACCGG
40779548 AAAA
1 AAAA
40779552 CGGTTCGGAT
Statistics
Matches: 214, Mismatches: 45, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
131 1 0.00
132 12 0.06
133 93 0.43
134 87 0.41
135 20 0.09
136 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (134 bp):
AAAAGATTGGAATATAGTGGCGTTTTCGGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAA
ATTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTTTATCTTTAGTAGCGCATTGTAAAAAACA
CCGG
Found at i:40782586 original size:27 final size:27
Alignment explanation
Indices: 40782530--40782587 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
40782520 TTTCTTATTG
* **
40782530 GTTTAGGGTTTTCGGTGTGTTCTCCGT
1 GTTTAGGGTTTTCGGTGTCTTCGACGT
40782557 GTTTAGGGTTTTTCGGTGTCTTCGAC-T
1 GTTTAGGG-TTTTCGGTGTCTTCGACGT
40782584 GTTT
1 GTTT
40782588 TGTTCATCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.05, C:0.14, G:0.31, T:0.50
Consensus pattern (27 bp):
GTTTAGGGTTTTCGGTGTCTTCGACGT
Found at i:40784419 original size:15 final size:15
Alignment explanation
Indices: 40784384--40784422 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
40784374 ATAAGTTTTC
*
40784384 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
40784399 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
40784415 TAAATTTA
1 TAAATTTA
40784423 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:40784598 original size:9 final size:9
Alignment explanation
Indices: 40784494--40784606 Score: 81
Period size: 9 Copynumber: 12.7 Consensus size: 9
40784484 ATAAGTTTTC
*
40784494 TACATAAGT
1 TACATAACT
40784503 TACATAA--
1 TACATAACT
**
40784510 TACACCACT
1 TACATAACT
*
40784519 TACATATCT
1 TACATAACT
*
40784528 TACAAAACT
1 TACATAACT
*
40784537 TATATAA--
1 TACATAACT
40784544 TACATAACT
1 TACATAACT
*
40784553 TATATTTAAGCT
1 TACA--TAA-CT
*
40784565 TGCATAACT
1 TACATAACT
*
40784574 TACATAAAT
1 TACATAACT
*
40784583 TAAATAACT
1 TACATAACT
40784592 TACATAACT
1 TACATAACT
40784601 TACATA
1 TACATA
40784607 TAATAACATA
Statistics
Matches: 79, Mismatches: 18, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
7 11 0.14
9 58 0.73
10 3 0.04
11 3 0.04
12 4 0.05
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.35
Consensus pattern (9 bp):
TACATAACT
Found at i:40784625 original size:22 final size:23
Alignment explanation
Indices: 40784585--40784628 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40784575 ACATAAATTA
* *
40784585 AATAACTTACATAACTTACATAT
1 AATAACATACATAAATTACATAT
40784608 AATAACATA-ATAAATTACATA
1 AATAACATACATAAATTACATA
40784629 ATACTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAACATACATAAATTACATAT
Found at i:40786347 original size:66 final size:66
Alignment explanation
Indices: 40786241--40786370 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
40786231 AACCACAGCT
* *
40786241 GAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGACGCGGCAGCGAGGGAAGT
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGACGCGGCAGCGAGAGAAGT
40786306 A
66 A
* * * *
40786307 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACGACTTAAAGCTGATGCGGCATCGAGAGAAG
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGACGCGGCAGCGAGAGAAG
40786371 CAGAAAGTAC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15
Consensus pattern (66 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGACGCGGCAGCGAGAGAAGT
A
Found at i:40786827 original size:42 final size:42
Alignment explanation
Indices: 40786689--40787010 Score: 306
Period size: 42 Copynumber: 7.7 Consensus size: 42
40786679 TACAAAAGCT
* * * * *
40786689 CCGCTAAAAAACATGTTCTGTAGCGGCGTTTGTAAAAAAAGCG
1 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATAAAAA-CG
* ** * * * * *
40786732 CCGTTAAAGATTATGATCTCTAGCGGCGTTTTTATACAAAGCG
1 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATA-AAAACG
** *
40786775 CCATTAAAGAACATGTTCTTTAGCGACGCTTATATAAAAACG
1 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATAAAAACG
* * *
40786817 CCGCTAAAGAACATGTTCTTTAGTGGCGCTTATAGAAAAACA
1 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATAAAAACG
* * *
40786859 CCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAACG
1 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATAAAAACG
* *
40786901 CCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATAAAAACG
1 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATAAAAACG
* * * * * * ** *
40786943 CCGTTAAAGACCATGTTCTTCA--GGCGTTTTTCTCTAAGCG
1 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATAAAAACG
*
40786983 CCGCTAAAGAACATGATCTTTAGCGGCG
1 CCGCTAAAGAACATGTTCTTTAGCGGCG
40787011 TTTTTGGTTG
Statistics
Matches: 231, Mismatches: 45, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
40 29 0.13
42 141 0.61
43 58 0.25
44 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
CCGCTAAAGAACATGTTCTTTAGCGGCGCTTATATAAAAACG
Found at i:40787482 original size:17 final size:18
Alignment explanation
Indices: 40787454--40787493 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
40787444 TTTTAATAAA
40787454 ATAAATTATTAAAAATTT
1 ATAAATTATTAAAAATTT
40787472 ATAAA-TATTAAAAATTT
1 ATAAATTATTAAAAATTT
40787489 ATAAA
1 ATAAA
40787494 ATCAAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATTATTAAAAATTT
Found at i:40796822 original size:19 final size:20
Alignment explanation
Indices: 40796784--40796822 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40796774 ATTCACCCCA
*
40796784 CTTTTTTCCTTCTTCGATTCG
1 CTTTATTCCTTC-TCGATTCG
40796805 CTTTATTCCTTC-CGATTC
1 CTTTATTCCTTCTCGATTC
40796823 TATATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.08, C:0.31, G:0.08, T:0.54
Consensus pattern (20 bp):
CTTTATTCCTTCTCGATTCG
Found at i:40796903 original size:14 final size:14
Alignment explanation
Indices: 40796884--40796938 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
40796874 TTCTTCACAA
40796884 TTCCTTTTCTTTTT
1 TTCCTTTTCTTTTT
40796898 TTCCTTTTCCATTTTT
1 TTCCTTTT-C-TTTTT
*
40796914 TATCCATGTTTCATTTT
1 T-TCC-T-TTTCTTTTT
40796931 TTCCTTTT
1 TTCCTTTT
40796939 GAGGTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 11 0.31
15 2 0.06
16 9 0.26
17 8 0.23
18 2 0.06
19 3 0.09
ACGTcount: A:0.07, C:0.22, G:0.02, T:0.69
Consensus pattern (14 bp):
TTCCTTTTCTTTTT
Found at i:40798848 original size:17 final size:17
Alignment explanation
Indices: 40798815--40798849 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40798805 ATTTTGTACA
*
40798815 TTTAAAATTTAGTTTTT
1 TTTAAAATATAGTTTTT
40798832 TTTAAGAATATAGTTTTT
1 TTTAA-AATATAGTTTTT
40798850 AGATTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (17 bp):
TTTAAAATATAGTTTTT
Found at i:40801622 original size:4 final size:4
Alignment explanation
Indices: 40801613--40801646 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
40801603 CATGAAAGCT
40801613 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
40801647 CATTGATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:40801663 original size:8 final size:8
Alignment explanation
Indices: 40801616--40801663 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
40801606 GAAAGCTTTT
*
40801616 ATTTATTT
1 ATTTATTC
*
40801624 ATTTATTT
1 ATTTATTC
*
40801632 ATTTATTT
1 ATTTATTC
40801640 ATTTATTC
1 ATTTATTC
*
40801648 ATTGATTC
1 ATTTATTC
*
40801656 CTTTATTC
1 ATTTATTC
40801664 TTTTTGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (8 bp):
ATTTATTC
Found at i:40801754 original size:15 final size:15
Alignment explanation
Indices: 40801713--40801756 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
40801703 TTTGCACATT
40801713 TTGTTCTTATTATTA
1 TTGTTCTTATTATTA
* *
40801728 TTATTCTCATTATTA
1 TTGTTCTTATTATTA
*
40801743 TTGTTGTTATTATT
1 TTGTTCTTATTATT
40801757 TAGTTTTCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
TTGTTCTTATTATTA
Found at i:40808711 original size:89 final size:90
Alignment explanation
Indices: 40808600--40808820 Score: 259
Period size: 89 Copynumber: 2.5 Consensus size: 90
40808590 GCTACAAATC
* * * * *
40808600 ACAAATCTTATCTCCCTGAAGTTGAAGTGGAGTAGATTGAAGTTATAGA-TCTTATCTCAC-TGA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATAAACT-TTAACTC-CTTGA
* * *
40808663 AGTTGCAGTGGAGTAGATCAGAGAT-A
64 AGTTGCAGTAGAGTAGATCAAAAATAA
* * *
40808689 ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACTTTAACTCCTTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATAAACTTTAACTCCTTGAAG
* * *
40808754 TTGTAGTAGAGTAGGTTAAAAATAA
66 TTGCAGTAGAGTAGATCAAAAATAA
* *
40808779 ACAAATCTTATCTCCCTAAAATTGCAGTGGAGTAGATTAAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAG
40808821 ACAGACTACA
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
88 1 0.01
89 70 0.64
90 39 0.35
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (90 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATAAACTTTAACTCCTTGAAG
TTGCAGTAGAGTAGATCAAAAATAA
Found at i:40808754 original size:44 final size:46
Alignment explanation
Indices: 40808511--40809430 Score: 374
Period size: 44 Copynumber: 19.8 Consensus size: 46
40808501 ATGGCGAATT
* * * * * *
40808511 TTATCTCCCTAAAGTTGCAATGGAGTAGATT-TAG-GATAGCAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATA-CAAATC
*
40808556 TTATCT-CTATGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCACAAATC
1 TTATCTCCT-TGAAGTTGCAGTGGAGCAGATTAAAGCT----AT-ACAAATC
* * * * * *
40808607 TTATCTCCCTGAAGTTGAAGTGGAGTAGATTGAAG-T-TATAGATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* * * *
40808651 TTATCTCAC-TGAAGTTGCAGTGGAGTAGATCAGAGATA-ACAAATC
1 TTATCTC-CTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* *
40808696 TTATCT-CTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA-AACT-
1 TTATCTCCT-TGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* * * * * ** *
40808740 TTAACTCCTTGAAGTTGTAGTAGAGTAGGTTAAAAATAAACAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* * * * *
40808786 TTATCTCCCTAAAATTGCAGTGGAGTAGATTAAAGACAGACTACAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAG-C-TA-TACAAATC
* *
40808835 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGC--CACAAACC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* * *
40808879 TTATCTCCTTAAAATTGCAGTGGAGCA-AGTTAAA--AATAGCAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGA-TTAAAGCTATA-CAAATC
** * * *
40808924 TTATCTTTTTAAAGTTTACAGTGGAGCAGATTGAAA--TGAT--AAGTC
1 TTATCTCCTTGAAG-TTGCAGTGGAGCAGATT-AAAGCT-ATACAAATC
* * * * * **
40808969 CTAT-ACCTCTGAAGTTGTAGTAGG-TCAGATTAAATCTACTATAGCAAGGC
1 TTATCTCCT-TGAAGTTGCAGT-GGAGCAGATTAAA---GCTATA-CAAATC
* * * ** * *
40809019 TTATATCCCTAAAGTTGCAGTGGAATAGACTAAAGCTACAAGCTTCAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCT---A--TACAAATC
* * *
40809070 TTATATCCTTGAAGTTGCAGTAGAGCAGATTGAAG--ATAGCAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATA-CAAATC
** ** *
40809115 TTATCT-CTCTGAAGTTATAGTGGATTAGATTGAAG-T-TACAAATC
1 TTATCTCCT-TGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* * * * * *
40809159 TTATCTCCCTGAAGTTGCAATGGAGTAGATTGAAG--ATACGAGTC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
** * * * * *
40809203 TCGTCGCCCTGAAGTTGCAATGGAGCAGATTGAAGATA-ACAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* * * * *
40809248 TTATTTCCCTGAAGTTGCAATGGAAG-AAATTAAAGCTACAAATTACGAATC
1 TTATCTCCTTGAAGTTGCAGTGG-AGCAGATTAAAGCT----A-TACAAATC
* * * *
40809299 TTATCTCCTTGAAGTTTCAATTGAGCAAATTAAAGC--TACAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
* ** * *
40809343 TTATTTCCCTAAAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACAAATC
1 TTATCT-CCTTGAAGTTGCAGTGGAGCAGATTAAAGCT---A--TACAAATC
* * * * *
40809395 TTATCTCCCTAAAGTTACAGTAGAGCAGATTGAAGC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGC
40809431 AACAAGTCCT
Statistics
Matches: 669, Mismatches: 137, Indels: 132
0.71 0.15 0.14
Matches are distributed among these distances:
43 5 0.01
44 200 0.30
45 190 0.28
46 48 0.07
47 8 0.01
48 5 0.01
49 41 0.06
50 28 0.04
51 128 0.19
52 16 0.02
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (46 bp):
TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTATACAAATC
Done.