Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 47 of 211
Found at i:12530795 original size:14 final size:15
Alignment explanation
Indices: 12530776--12530806 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12530766 ATACCTACCC
12530776 AAAATCAAAAA-TAA
1 AAAATCAAAAATTAA
12530790 AAAATCAAAAATTAA
1 AAAATCAAAAATTAA
12530805 AA
1 AA
12530807 CCCAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATCAAAAATTAA
Found at i:12538230 original size:17 final size:17
Alignment explanation
Indices: 12538201--12538360 Score: 87
Period size: 17 Copynumber: 9.4 Consensus size: 17
12538191 CGCCTAACAT
*
12538201 AGCTCGCACCTTTGGTG
1 AGCTCGCAGCTTTGGTG
*
12538218 A-CTTCGCAGCTTTGATG
1 AGC-TCGCAGCTTTGGTG
*
12538235 AGCTCGCAGCCTTGGTG
1 AGCTCGCAGCTTTGGTG
* * *
12538252 AGCTCACA-ATATTGATG
1 AGCTCGCAGCT-TTGGTG
*
12538269 AGATCGCAG-TCTTGGTG
1 AGCTCGCAGCT-TTGGTG
*
12538286 AGCTCGTA-CATTTGAG-G
1 AGCTCGCAGC-TTTG-GTG
* **
12538303 AGCTCACAATTTTGGTG
1 AGCTCGCAGCTTTGGTG
*
12538320 AGCTCGCAACTTTAGGTG
1 AGCTCGCAGCTTT-GGTG
** * *
12538338 AGCTTACATCTTTGGTA
1 AGCTCGCAGCTTTGGTG
12538355 AGCTCG
1 AGCTCG
12538361 TACCTTTGGG
Statistics
Matches: 108, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
16 2 0.02
17 89 0.82
18 17 0.16
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.31
Consensus pattern (17 bp):
AGCTCGCAGCTTTGGTG
Found at i:12538339 original size:18 final size:17
Alignment explanation
Indices: 12538302--12538341 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
12538292 TACATTTGAG
*
12538302 GAGCTCACAATTTTGGT
1 GAGCTCACAATTTAGGT
*
12538319 GAGCTCGCAACTTTAGGT
1 GAGCTCACAA-TTTAGGT
12538337 GAGCT
1 GAGCT
12538342 TACATCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (17 bp):
GAGCTCACAATTTAGGT
Found at i:12541901 original size:51 final size:51
Alignment explanation
Indices: 12541816--12541920 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
12541806 TAAAGTTAGT
* * *
12541816 TGATGAGGTTTAAAATAAGTTACTTGTGTAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
12541867 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
12541918 TGA
1 TGA
12541921 ATTTGAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (51 bp):
TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
Found at i:12541906 original size:26 final size:26
Alignment explanation
Indices: 12541826--12541907 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
12541816 TGATGAGGTT
*
12541826 TAAAATAAGTTACTTGTGTAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
* * * **
12541852 TAAAA-ATGTTAACCATG-ATA-AGGCT
1 TAAAATAAGTT-A-CTTGTATAGTGGAA
12541877 TAAAATAAGTTACTTGTATAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
12541903 TAAAA
1 TAAAA
12541908 ATGTTAACCA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (26 bp):
TAAAATAAGTTACTTGTATAGTGGAA
Found at i:12549325 original size:14 final size:14
Alignment explanation
Indices: 12549306--12549336 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12549296 GGAATGAAAA
*
12549306 TATTTTTTTCTCTT
1 TATTTTTTTCTATT
12549320 TATTTTTTTCTATT
1 TATTTTTTTCTATT
12549334 TAT
1 TAT
12549337 ACAGGCTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTTTTCTATT
Found at i:12549997 original size:16 final size:15
Alignment explanation
Indices: 12549976--12550005 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12549966 AAGTTTATTC
12549976 ATATATATATATTTAG
1 ATATATAT-TATTTAG
12549992 ATATATATTATTTA
1 ATATATATTATTTA
12550006 TACTTTAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATATATTATTTAG
Found at i:12562907 original size:17 final size:19
Alignment explanation
Indices: 12562872--12562909 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
12562862 TTAACTTTTC
12562872 TTATTTTTATCAGATTATT
1 TTATTTTTATCAGATTATT
12562891 TTATTTTT-TCA-ATTATT
1 TTATTTTTATCAGATTATT
12562908 TT
1 TT
12562910 TTTCAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTTTTATCAGATTATT
Found at i:12562911 original size:19 final size:21
Alignment explanation
Indices: 12562867--12562911 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
12562857 ATTAATTAAC
12562867 TTTTCTTATTTTTATCAGATTA
1 TTTT-TTATTTTTATCAGATTA
12562889 --TTTTATTTTT-TCA-ATTA
1 TTTTTTATTTTTATCAGATTA
12562906 TTTTTT
1 TTTTTT
12562912 TCAACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
17 4 0.19
18 3 0.14
19 12 0.57
20 2 0.10
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTATTTTTATCAGATTA
Found at i:12569468 original size:14 final size:14
Alignment explanation
Indices: 12569448--12569481 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12569438 AACCACGTCT
*
12569448 TTTTTTTTCTTTTTC
1 TTTTTTTT-TTTGTC
12569463 TTTTTTTTTTTGTC
1 TTTTTTTTTTTGTC
12569477 TTTTT
1 TTTTT
12569482 GCATGCATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTGTC
Found at i:12570499 original size:17 final size:17
Alignment explanation
Indices: 12570448--12570499 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
12570438 ATGGAAACAT
* * *
12570448 AATCTTCAAGGATATGT
1 AATCTTAAAAGATATGC
*
12570465 AATCTTAGATATGATATGC
1 AATCTTA-A-AAGATATGC
12570484 AATCTTAAAAGATATG
1 AATCTTAAAAGATATG
12570500 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (17 bp):
AATCTTAAAAGATATGC
Found at i:12583230 original size:44 final size:44
Alignment explanation
Indices: 12583162--12583361 Score: 189
Period size: 44 Copynumber: 4.6 Consensus size: 44
12583152 AACCGTTACA
*
12583162 CGGTGGAATCAGCACTTAGTAACCACCTCACGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* * *
12583206 TGGTGGAATTAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* * * *** * *
12583250 CGATGGAATCAGTACTTAGCAACCACCTTATAATC-AATGAT-G
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* * *
12583292 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAATT--AAGGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACC--TCAC-GTTCAAAGGATCC
12583334 CGGTGGAATCAGCACTTAGCAACCACCT
1 CGGTGGAATCAGCACTTAGCAACCACCT
12583362 TTATTGTTAG
Statistics
Matches: 129, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
40 2 0.02
41 18 0.14
42 13 0.10
43 26 0.20
44 70 0.54
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (44 bp):
CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
Found at i:12588244 original size:40 final size:41
Alignment explanation
Indices: 12588170--12588246 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
12588160 CACATTTATA
* * *
12588170 ATCAATAATTCGGGGAATCTGCACTTAGTAACCCTTTTTTG
1 ATCAATAATTCAGGGAACCTGCACTTAGCAACCCTTTTTTG
*
12588211 ATCAATGATTCAGGGAACCTGC-CTTAGCAACCCTTT
1 ATCAATAATTCAGGGAACCTGCACTTAGCAACCCTTT
12588247 ACATTCAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 13 0.41
41 19 0.59
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (41 bp):
ATCAATAATTCAGGGAACCTGCACTTAGCAACCCTTTTTTG
Found at i:12606822 original size:42 final size:43
Alignment explanation
Indices: 12606723--12606834 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 43
12606713 CAACCATAAG
* * * *
12606723 GAGCTGAACAGAAACCCATAAGGGTTAATCTGAGGCTTAGAAA
1 GAGCTGAACTGAAACCCATAAGGGTTAAACTGAAGCTCAGAAA
* * * *
12606766 -AGATAAACTAAAACCCATTAGGGTTAAACTGAAGCTCA-AAA
1 GAGCTGAACTGAAACCCATAAGGGTTAAACTGAAGCTCAGAAA
*
12606807 GAGCTGAATTGAAACCCATAAGGGTTAA
1 GAGCTGAACTGAAACCCATAAGGGTTAA
12606835 TCTAAAACTC
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
41 3 0.05
42 52 0.95
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (43 bp):
GAGCTGAACTGAAACCCATAAGGGTTAAACTGAAGCTCAGAAA
Found at i:12606847 original size:21 final size:20
Alignment explanation
Indices: 12606818--12606871 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
12606808 AGCTGAATTG
* *
12606818 AAACCCATAAGGGTTAATCTA
1 AAACTCATAAGAGTTAA-CTA
*
12606839 AAACTCATATGAGTTAACTA
1 AAACTCATAAGAGTTAACTA
* *
12606859 AAGCTCATGAGAG
1 AAACTCATAAGAG
12606872 CTAAACTGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (20 bp):
AAACTCATAAGAGTTAACTA
Found at i:12611949 original size:15 final size:16
Alignment explanation
Indices: 12611909--12611960 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
12611899 GTCCTGTTTG
** *
12611909 TTATTTTTGCTATTAA
1 TTATTTTTATTATTTA
*
12611925 TTAATTTTATTATTT-
1 TTATTTTTATTATTTA
12611940 TTATTTTTATTATTTA
1 TTATTTTTATTATTTA
12611956 TTATT
1 TTATT
12611961 ATTACTCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTTTATTATTTA
Found at i:12611952 original size:3 final size:3
Alignment explanation
Indices: 12611931--12611992 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
12611921 TTAATTAATT
* * * *
12611931 TTA TTA TTT TTA TTT TTA TTA TTTA TTA TTA TTA CTC TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
12611977 TTGA -TA TTA TTA TTA T
1 TT-A TTA TTA TTA TTA T
12611993 GTTTGGTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 1 0.02
3 43 0.90
4 4 0.08
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12611955 original size:22 final size:22
Alignment explanation
Indices: 12611930--12611975 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
12611920 ATTAATTAAT
* * *
12611930 TTTATTATTTTTATTTTTATTA
1 TTTATTATTATTACTCTTATTA
12611952 TTTATTATTATTACTCTTATTA
1 TTTATTATTATTACTCTTATTA
12611974 TT
1 TT
12611976 ATTGATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTATTATTATTACTCTTATTA
Found at i:12611971 original size:15 final size:13
Alignment explanation
Indices: 12611931--12611992 Score: 72
Period size: 15 Copynumber: 4.5 Consensus size: 13
12611921 TTAATTAATT
12611931 TTATTATT-TTTA
1 TTATTATTATTTA
*
12611943 TTTTTATTATTTA
1 TTATTATTATTTA
12611956 TTATTATTACTCTTA
1 TTATTATTA-T-TTA
12611971 TTATTATTGATATTA
1 TTATTATT-AT-TTA
12611986 TTATTAT
1 TTATTAT
12611993 GTTTGGTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.16
13 12 0.28
14 1 0.02
15 22 0.51
16 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:12612831 original size:10 final size:10
Alignment explanation
Indices: 12612816--12612846 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
12612806 TATTAATTAA
12612816 TTTTATTATT
1 TTTTATTATT
12612826 TTTTATTATT
1 TTTTATTATT
12612836 TATTTATTATT
1 T-TTTATTATT
12612847 ACTCTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTATTATT
Found at i:12614142 original size:14 final size:14
Alignment explanation
Indices: 12614123--12614149 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12614113 GATATTGTAC
12614123 AAATCCAGTCCCTT
1 AAATCCAGTCCCTT
12614137 AAATCCAGTCCCT
1 AAATCCAGTCCCT
12614150 GAGGATTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (14 bp):
AAATCCAGTCCCTT
Found at i:12614639 original size:16 final size:16
Alignment explanation
Indices: 12614615--12614667 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
12614605 TTATTTCAAC
*
12614615 ATTTATATATATTATT
1 ATTTATATAAATTATT
*
12614631 ATTTGTATAAATTATT
1 ATTTATATAAATTATT
* * *
12614647 GTCTATATTAAATTTTT
1 ATTTATA-TAAATTATT
12614664 ATTT
1 ATTT
12614668 TTACTACTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTTATATAAATTATT
Found at i:12621843 original size:34 final size:35
Alignment explanation
Indices: 12621788--12621854 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12621778 CAAACACCAG
*
12621788 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
12621823 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12621855 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12625255 original size:22 final size:23
Alignment explanation
Indices: 12625227--12625287 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
12625217 AAAAAGCTTT
12625227 TATTTTTATAATTTTTTA-AAAA
1 TATTTTTATAATTTTTTATAAAA
*
12625249 TATTTTTATACTTTTTTATAAAA
1 TATTTTTATAATTTTTTATAAAA
*
12625272 AATATTTTAT-ATTTTT
1 TAT-TTTTATAATTTTT
12625288 AACTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.50
23 11 0.32
24 6 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTTATAATTTTTTATAAAA
Found at i:12636450 original size:22 final size:23
Alignment explanation
Indices: 12636406--12636456 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
12636396 ATGAATGTTG
*
12636406 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT-ACATATAATTAT
12636430 TTTAAATTTAT-CATATAATTAT
1 TTTAAATTTATACATATAATTAT
12636452 TTTAA
1 TTTAA
12636457 GTTTCATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 15 0.58
24 11 0.42
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAATTTATACATATAATTAT
Found at i:12641723 original size:21 final size:21
Alignment explanation
Indices: 12641689--12641728 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12641679 GTTTAGATTC
**
12641689 AAAAAAAATCAAAAACAAAAG
1 AAAAAAAAGAAAAAACAAAAG
*
12641710 AAAAAAAAGAAAAATCAAA
1 AAAAAAAAGAAAAAACAAA
12641729 GTCAAAAGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.07, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGAAAAAACAAAAG
Found at i:12641724 original size:27 final size:26
Alignment explanation
Indices: 12641689--12641749 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
12641679 GTTTAGATTC
12641689 AAAAAAAATCAAAAACAAAAGAAAAA
1 AAAAAAAATCAAAAACAAAAGAAAAA
** *
12641715 AAAGAAAAATCAAAGTCAAAAGCAAAA
1 AAA-AAAAATCAAAAACAAAAGAAAAA
12641742 AAAAAAAA
1 AAAAAAAA
12641750 GAAATCAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.80, C:0.08, G:0.07, T:0.05
Consensus pattern (26 bp):
AAAAAAAATCAAAAACAAAAGAAAAA
Found at i:12641760 original size:34 final size:33
Alignment explanation
Indices: 12641697--12641769 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 33
12641687 TCAAAAAAAA
12641697 TCAAAAACAAAAGAAAAAAAAGAAAAATCAAAG
1 TCAAAAACAAAAGAAAAAAAAGAAAAATCAAAG
*
12641730 TCAAAAGCAAAA-AAAAAAAAGAAATCAATCAAAG
1 TCAAAAACAAAAGAAAAAAAAGAAA--AATCAAAG
12641764 TCAAAA
1 TCAAAA
12641770 TAAAAATATG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
32 12 0.32
33 11 0.30
34 14 0.38
ACGTcount: A:0.73, C:0.11, G:0.08, T:0.08
Consensus pattern (33 bp):
TCAAAAACAAAAGAAAAAAAAGAAAAATCAAAG
Found at i:12641763 original size:27 final size:27
Alignment explanation
Indices: 12641689--12641775 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 27
12641679 GTTTAGATTC
12641689 AAAAA-AAATCAA--AAA-CAAAAGAAA
1 AAAAAGAAATCAATCAAAGCAAAA-AAA
12641713 AAAAAGAAAAATCAAAGTCAAAAGCAAAAAAA
1 AAAAAG--AAATC-AA-TC-AAAGCAAAAAAA
*
12641745 AAAAAGAAATCAATCAAAGTCAAAATAA
1 AAAAAGAAATCAATCAAAG-CAAAAAAA
12641773 AAA
1 AAA
12641776 TATGAAAATG
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
24 5 0.10
27 9 0.17
28 14 0.27
29 2 0.04
30 5 0.10
32 12 0.23
33 5 0.10
ACGTcount: A:0.76, C:0.09, G:0.07, T:0.08
Consensus pattern (27 bp):
AAAAAGAAATCAATCAAAGCAAAAAAA
Found at i:12644177 original size:88 final size:87
Alignment explanation
Indices: 12643963--12644187 Score: 263
Period size: 87 Copynumber: 2.6 Consensus size: 87
12643953 AGATCAGTGA
* * *
12643963 AGATCGAAAACA-AAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTTG
1 AGATCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
* * *
12644027 CCTCCCTAAGAAATAGTGGAGC
66 CCTCCCTAAGAAACAGCGAAGC
* * *
12644049 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
* ** ** *
12644114 CCTTCCTGCGTCGACGGCGAAGC
66 CCTCCCTAAG-AAACAGCGAAGC
* * * *
12644137 AGATGGAAGGCACAAGCCTTGCCTCCCTCAGTTGTAGTGGAGCAGGTTGAA
1 AGATCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAA
12644188 TATTGGAAAT
Statistics
Matches: 115, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
86 10 0.09
87 55 0.48
88 50 0.43
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (87 bp):
AGATCGAAGACACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
CCTCCCTAAGAAACAGCGAAGC
Found at i:12644356 original size:131 final size:131
Alignment explanation
Indices: 12644190--12644900 Score: 762
Period size: 131 Copynumber: 5.4 Consensus size: 131
12644180 AGGTTGAATA
* * *
12644190 TTGGAAATTACAGATCTTATCTCCTTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATC
1 TTGGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATC
** *
12644255 TTCCCCAGGAGTAGGGAAATAGATTTAAGCCACAAGTCCTATTTCTCTGAGCAACAGTGGAATAT
66 TTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAACAGTGGAATAT
12644320 G
131 G
* * *
12644321 TTGTAAACTACAAATCTTATCTCCCTAAGAAATAGTGGAGCAGATCGAAGACAGCGAATCTTATC
1 TTGGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATC
* *
12644386 TTCCCCATGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTG-GCCAACA-TGGAATA
66 TTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATTTCCCTGAG-CAACAGTGGAATA
12644449 TG
130 TG
* * * * * ***
12644451 TT-GAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGC-AGATCTCGC
1 TTGGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGA-ATCTTAT
* ** * * * ****
12644514 CTTCCTGC-GTCG-ACGGCGAAGCAGATCTAAGGCACAAG-CCT-TGCCTCCCTCG-GTTGTAGT
65 CTTCC-CCAGGAGTA-GG-GAAGCAGATTTAAGCCACAAGTCCTAT--TTCCCT-GAGCAACAGT
*
12644574 GGAGCAGGTTGAAG
124 GGA--A---T-ATG
* * *
12644588 ATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGTGAATCTTAT
1 -TTGGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTAT
* * *
12644653 CTTCCCCAGGAGTAGGGAAACAGATTTAAGCTACAAGTCCTATTTCCCTGAGCAGCAGTGGAATA
65 CTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAACAGTGGAATA
*
12644718 GG
130 TG
*
12644720 TTGGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATAGCGAATCTTATC
1 TTGGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATC
* * * *
12644785 TTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCT-AGTCAGCAGAGAAATA
66 TTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATTTCCCTGAG-CAACAGTGGAATA
*
12644849 GG
130 TG
* * * *
12644851 TTAGG--ATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA
1 TT-GGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGA
12644901 TGACGGGTTT
Statistics
Matches: 488, Mismatches: 67, Indels: 51
0.81 0.11 0.08
Matches are distributed among these distances:
128 3 0.01
129 59 0.12
130 82 0.17
131 235 0.48
132 4 0.01
133 2 0.00
136 2 0.00
137 3 0.01
138 33 0.07
139 62 0.13
140 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (131 bp):
TTGGAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATC
TTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAACAGTGGAATAT
G
Found at i:12644706 original size:399 final size:400
Alignment explanation
Indices: 12644097--12644901 Score: 1373
Period size: 399 Copynumber: 2.0 Consensus size: 400
12644087 GGAGTAGGTT
* *
12644097 GAAGATAGCAGATCTTGCCTTCCTGCGTCGACGGCGAAGCAGATGGAAGGCACAAGCCTTGCCTC
1 GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
* *
12644162 CCTCAGTTGTAGTGGAGCAGGTTGAATATTGGAAATTACAGATCTTATCTCCTTAAGCAATAGTG
66 CCTCAGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
*
12644227 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAATAGATTTAAGCCACAAGT
131 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGT
* * *
12644292 CCTATTTCTCTGAGCAACAGTGGAATATGTTGTAAACTACAAATCTTATCTCCCTAAGAAATAGT
196 CCTATTTCCCTGAGCAACAGTGGAATAGGTTGGAAACTACAAATCTTATCTCCCTAAGAAATAGT
*
12644357 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCATGAGTAGGGAAGCAGATTTAAGCCACAAG
261 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
* *
12644422 TCCTATCTCCCTGGCCAACATG-G-AATATGTT-GAGATTTCAGATCTTATCTCCCTAAGCAGTA
326 TCCTATCTCCCTAGCCAACA-GAGAAATAGGTTAG-GATTTCAGATCTTATCTCCCTAAGCAGTA
12644484 GTGGAGCAGATC
389 GTGGAGCAGATC
*
12644496 GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCTAAGGCACAAGCCTTGCCTC
1 GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
*
12644561 CCTCGGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
66 CCTCAGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
* *
12644626 GAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCTACAAGT
131 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGT
* * *
12644691 CCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACTACAGATCTTATCTCCCTAAGCAATAGT
196 CCTATTTCCCTGAGCAACAGTGGAATAGGTTGGAAACTACAAATCTTATCTCCCTAAGAAATAGT
*
12644756 GGAGCAGATCGAAGATAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
261 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
* *
12644821 TCCTATCTCCCTAGTCAGCAGAGAAATAGGTTAGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
326 TCCTATCTCCCTAGCCAACAGAGAAATAGGTTAGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
12644886 GGAGTAGATC
391 GGAGCAGATC
12644896 GAAGAT
1 GAAGAT
12644902 GACGGGTTTT
Statistics
Matches: 381, Mismatches: 22, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
398 1 0.00
399 326 0.86
400 53 0.14
401 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (400 bp):
GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
CCTCAGTTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
GAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGT
CCTATTTCCCTGAGCAACAGTGGAATAGGTTGGAAACTACAAATCTTATCTCCCTAAGAAATAGT
GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
TCCTATCTCCCTAGCCAACAGAGAAATAGGTTAGGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATC
Found at i:12645013 original size:132 final size:132
Alignment explanation
Indices: 12644690--12645096 Score: 391
Period size: 132 Copynumber: 3.1 Consensus size: 132
12644680 AAGCTACAAG
* * * * *
12644690 TCCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAA-ACTACAGATCTTATCTCCCTAAGCAATA
1 TCCTATATCCCTGGGCAGCAGTGGAATAGATT-GAAGATTACAGATCTTATCTCCCTAAGCAGTA
* * * * * * **
12644754 GTGGAGCAGATCGAAGAT-AGC-GAATCTTATCTTCCC-CAGG--AGTAG-GGAAGCAGATTTAA
65 GTGGAGCAGATCGAAGATGA-CAG-ATTTTA-CCTCCCTGAGGTTA-CAGTGG-AGTACATAGAA
12644813 GCCAC-AA
125 GCCACTAA
* * * * * * * *
12644820 GTCCTATCTCCCTAGTCAGCAGAGAAATAGGTT-AGGATTTCAGATCTTATCTCCCTAAGCAGTA
1 -TCCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTA
* * * * *
12644884 GTGGAGTAGATCGAAGATGACGGGTTTTACCTCCCTGTGGTTACAGTGGAGTACATAGAAGCCAG
65 GTGGAGCAGATCGAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATAGAAGCCAC
12644949 TAA
130 TAA
*
12644952 TTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
1 TCCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
* * * * *
12645017 TGGAGCAGATCGAGGATGGCAGATTTTACCTTCCTGAGGTTACAGTGGAGTATATTGAAGCCACT
66 TGGAGCAGATCGAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATAGAAGCCACT
12645082 AA
131 AA
*
12645084 TCCTATCTCCCTG
1 TCCTATATCCCTG
12645097 AAATTACAGT
Statistics
Matches: 224, Mismatches: 43, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
129 6 0.03
130 49 0.22
131 66 0.29
132 103 0.46
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (132 bp):
TCCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATAGAAGCCACT
AA
Found at i:12645342 original size:50 final size:49
Alignment explanation
Indices: 12645288--12645546 Score: 209
Period size: 50 Copynumber: 5.2 Consensus size: 49
12645278 GCAATGGAAC
* *
12645288 AGATTAATGCCACAATGACGAATCTTGCTTCCCAGACATTGCAGTTAAAA
1 AGATTAAAGCCACAA-GACGAATCTTACTTCCCAGACATTGCAGTTAAAA
* * ** * * *
12645338 AGATTAAAGCTACAACAGCGAATCTTACTTCTTA-AGCAGTGCAGTGAAAT
1 AGATTAAAGCCACAAGA-CGAATCTTACTTCCCAGA-CATTGCAGTTAAAA
* * * * *
12645388 AGATTAAAGCCACAACGATGAATCTTGCTTCCCCGACATCGCATTTAAAA
1 AGATTAAAGCCACAA-GACGAATCTTACTTCCCAGACATTGCAGTTAAAA
* * ** ** *
12645438 AGATTAAAGCCACAACA-GCAAGTCTTACTTCTCA-AGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAAGACG-AA-TCTTACTTCCCAGA-CATTGCAGTTAAAA
* * *
12645488 AGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAAC
1 AGATTAAAGCCACAA-GACGAATCTTACTTCCCAGACATTGCAGTTAAAA
12645538 AGATTAAAG
1 AGATTAAAG
12645547 TTACGAGTTA
Statistics
Matches: 159, Mismatches: 40, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
48 1 0.01
49 6 0.04
50 146 0.92
51 5 0.03
52 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (49 bp):
AGATTAAAGCCACAAGACGAATCTTACTTCCCAGACATTGCAGTTAAAA
Found at i:12645436 original size:100 final size:100
Alignment explanation
Indices: 12645276--12645546 Score: 382
Period size: 100 Copynumber: 2.7 Consensus size: 100
12645266 TTCCCTAGCG
* * * * *
12645276 GTGCAATGGAACAGATTAATGCCACAATGACGAATCTTGCTTCCCAGACATTGCAGTTAAAAAGA
1 GTGCAGTGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* *
12645341 TTAAAGCTACAACAGCGAA-TCTTACTTCTTAAGCA
66 TTAAAGCCACAACAGC-AAGTCTTACTTCTCAAGCA
* * * *
12645376 GTGCAGTGAAATAGATTAAAGCCACAACGATGAATCTTGCTTCCCCGACATCGCATTTAAAAAGA
1 GTGCAGTGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
*
12645441 TTAAAGCCACAACAGCAAGTCTTACTTCTCAAGCG
66 TTAAAGCCACAACAGCAAGTCTTACTTCTCAAGCA
* * * *
12645476 GTGCAGTGGAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAACAGA
1 GTGCAGTGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
12645541 TTAAAG
66 TTAAAG
12645547 TTACGAGTTA
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 2 0.01
100 148 0.99
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (100 bp):
GTGCAGTGAAACAGATTAAAGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
TTAAAGCCACAACAGCAAGTCTTACTTCTCAAGCA
Found at i:12647103 original size:22 final size:22
Alignment explanation
Indices: 12647059--12647117 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
12647049 ATGAATGTTG
*
12647059 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
12647083 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
12647105 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
12647118 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:12649978 original size:43 final size:43
Alignment explanation
Indices: 12649940--12650168 Score: 262
Period size: 43 Copynumber: 5.3 Consensus size: 43
12649930 ATGCACTTCA
* *
12649940 TGTGCCAGTATATTTACTTTGGTTCGTCCGATGATGCACTGTG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * * * *
12649983 TGTGCCAGCATATTTGTTTTGGTTCGTTCGATAATGCACTGTG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * *
12650026 TGTGCCAATATATTTGCTTCGGTTCATCCGGTGATGCACTGTG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * ** * * *
12650069 TCTGTCAGTATATTTGCTTCAATTCGTCTGATAATGCACTATG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* *
12650112 TGTGCCAGTATATTTGCTTCAGTTCGTCCGATGATGCGA-TATG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGC-ACTGTG
*
12650155 TGTGCCAATATATT
1 TGTGCCAGTATATT
12650169 CACTTTGATT
Statistics
Matches: 156, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
43 155 0.99
44 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (43 bp):
TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
Found at i:12650188 original size:86 final size:86
Alignment explanation
Indices: 12649940--12650192 Score: 292
Period size: 86 Copynumber: 2.9 Consensus size: 86
12649930 ATGCACTTCA
* * * * *
12649940 TGTGCCAGTATATTTACTTTGGTTCGTCCGATGATGCACTGTGTGTGCCAGCATATTTGTTTTGG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTTGA
* *
12650005 TTCGTTCGATAATGCACTGTG
66 TTCGTCCGATAATGCACTATG
* * * * * **
12650026 TGTGCCAATATATTTGCTTCGGTTCATCCGGTGATGCACTGTGTCTGTCAGTATATTTGCTTCAA
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTTGA
*
12650091 TTCGTCTGATAATGCACTATG
66 TTCGTCCGATAATGCACTATG
* * * **
12650112 TGTGCCAGTATATTTGCTTCAGTTCGTCCGATGATGCGA-TATGTGTGCCAATATATTCACTTTG
1 TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGC-ACTGTGTGTGCCAGTATATTTGCTTTG
**
12650176 ATTTATCCGATAATGCA
65 ATTCGTCCGATAATGCA
12650193 TTGAGGTGTC
Statistics
Matches: 136, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
86 135 0.99
87 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (86 bp):
TGTGCCAGTATATTTGCTTCGGTTCGTCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTTGA
TTCGTCCGATAATGCACTATG
Found at i:12657576 original size:28 final size:27
Alignment explanation
Indices: 12657543--12657641 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
12657533 TAATGAGATT
12657543 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* **
12657570 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
12657599 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
12657627 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
12657642 TACTTATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 56 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:12658548 original size:25 final size:24
Alignment explanation
Indices: 12658516--12658788 Score: 193
Period size: 25 Copynumber: 11.5 Consensus size: 24
12658506 ATTTAATGTA
12658516 TAATGCTGTCCAATTTTGAGCATAT
1 TAATGCTGTCCAATTTTGAG-ATAT
*
12658541 TATTGCTGTCCAATTTTGAGTATAT
1 TAATGCTGTCCAATTTTGAG-ATAT
* *
12658566 TGATGCTGTCC-ATTTT-A-ATGT
1 TAATGCTGTCCAATTTTGAGATAT
12658587 ATAATGCTGTCCAATTTTGAGTATAT
1 -TAATGCTGTCCAATTTTGAG-ATAT
* *
12658613 TGATGCTGTCC-ATTTT-A-ATGT
1 TAATGCTGTCCAATTTTGAGATAT
*
12658634 ATAATGCTGTCCAATTTTAAGTATAT
1 -TAATGCTGTCCAATTTTGAG-ATAT
* *
12658660 TGATGCTGTCC-ATTTT-A-ATGT
1 TAATGCTGTCCAATTTTGAGATAT
* *
12658681 ATAATGCTATCAAATTTTGAGTATATT
1 -TAATGCTGTCCAATTTTGAG-ATA-T
*
12658708 TAA-GCTGTCTAA-TTTGATG-TA-
1 TAATGCTGTCCAATTTTGA-GATAT
*
12658729 TAATGCTATCC-ATTTTGAGCATAT
1 TAATGCTGTCCAATTTTGAG-ATAT
*
12658753 TATTGCTGTCCAA-TTTGATGA-A-
1 TAATGCTGTCCAATTTTGA-GATAT
12658775 TAATTGCTGTCCAA
1 TAA-TGCTGTCCAA
12658789 AACAGGGTTG
Statistics
Matches: 199, Mismatches: 24, Indels: 52
0.72 0.09 0.19
Matches are distributed among these distances:
21 14 0.07
22 40 0.20
23 33 0.17
24 38 0.19
25 62 0.31
26 11 0.06
27 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (24 bp):
TAATGCTGTCCAATTTTGAGATAT
Found at i:12658595 original size:47 final size:47
Alignment explanation
Indices: 12658544--12658788 Score: 341
Period size: 47 Copynumber: 5.2 Consensus size: 47
12658534 AGCATATTAT
12658544 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
12658591 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
*
12658638 TGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
* * * * * * *
12658685 TGCTATCAAATTTTGAGTATATTTAAGCTGTCTAATTTGATGTATAA
1 TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
* * * * *
12658732 TGCTATCC-ATTTTGAGCATATT-ATTGCTGTCCAATTTGATGAATAA
1 TGCTGTCCAATTTTGAGTATATTGA-TGCTGTCCATTTTAATGTATAA
12658778 TTGCTGTCCAA
1 -TGCTGTCCAA
12658789 AACAGGGTTG
Statistics
Matches: 180, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 32 0.18
47 146 0.81
48 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (47 bp):
TGCTGTCCAATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAA
Found at i:12658624 original size:72 final size:70
Alignment explanation
Indices: 12658507--12658768 Score: 270
Period size: 72 Copynumber: 3.7 Consensus size: 70
12658497 TTTGTTATAA
12658507 TTTAATGTATAATGCTGTCCAATTTTGAGCATATTATTGCTGTCCAATTTTGAGTATATTGATGC
1 TTTAATGTATAATGCTGTCC-ATTTTGAGCATATTATTGCTGTCCAATTTTGAGTATATT-ATGC
12658572 TGTCCAT
64 TGTCCAT
* *
12658579 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGA-TGCTGTCC-ATTTTAATGTATA--ATG
1 TTTAATGTATAATGCTGTCC-ATTTTGAGCATATT-ATTGCTGTCCAATTTTGA-GTATATTATG
12658640 CTGTCCAAT
63 CTGTCC-AT
* * * *
12658649 TTTAA-GTATATTGATGCTGTCCATTTT-A--ATGTATAATGCTATCAAATTTTGAGTATATTTA
1 TTTAATGTATA---ATGCTGTCCATTTTGAGCATAT-TATTGCTGTCCAATTTTGAGTATA-TTA
* * *
12658710 AGCTGTCTAA
61 TGCTGTCCAT
* *
12658720 TTTGATGTATAATGCTATCCATTTTGAGCATATTATTGCTGTCCAATTT
1 TTTAATGTATAATGCTGTCCATTTTGAGCATATTATTGCTGTCCAATTT
12658769 GATGAATAAT
Statistics
Matches: 159, Mismatches: 15, Indels: 33
0.77 0.07 0.16
Matches are distributed among these distances:
68 4 0.03
69 39 0.25
70 15 0.09
71 29 0.18
72 71 0.45
73 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (70 bp):
TTTAATGTATAATGCTGTCCATTTTGAGCATATTATTGCTGTCCAATTTTGAGTATATTATGCTG
TCCAT
Found at i:12679975 original size:15 final size:15
Alignment explanation
Indices: 12679955--12680005 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12679945 AAATTTTTTA
12679955 AAATTATAAAAATAT
1 AAATTATAAAAATAT
* *
12679970 AAATTATTAAAGTAAT
1 AAATTATAAAAAT-AT
* *
12679986 AACTTATAAAAACAT
1 AAATTATAAAAATAT
12680001 AAATT
1 AAATT
12680006 TAATTTCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (15 bp):
AAATTATAAAAATAT
Found at i:12684296 original size:44 final size:43
Alignment explanation
Indices: 12684248--12684403 Score: 109
Period size: 44 Copynumber: 3.4 Consensus size: 43
12684238 TCATTCCAAC
12684248 CCACTGCAACTTCAGAGGTATAGGATTTGTAGCTTCATCTTGCT
1 CCACTGCAACTTCAGAGG-ATAGGATTTGTAGCTTCATCTTGCT
* * * * ***
12684292 CCACTGTAACTTTAGGAAGATAAGATTTTCTATGGTAGCTTCACTCCAAC-
1 CCACTGCAACTTCA-GAGGATAGGA---T-T-T-GTAGCTTCA-TCTTGCT
* *
12684342 CCACTGCCACTTCAGGGGCATAGGATTTGTAGCTTCATCTTGCT
1 CCACTGCAACTTCAGAGG-ATAGGATTTGTAGCTTCATCTTGCT
* *
12684386 CCATTGTAACTTCA-AGGA
1 CCACTGCAACTTCAGAGGA
12684404 GATAAGATTC
Statistics
Matches: 82, Mismatches: 20, Indels: 22
0.66 0.16 0.18
Matches are distributed among these distances:
42 1 0.01
43 5 0.06
44 37 0.45
45 4 0.05
46 1 0.01
47 2 0.02
48 1 0.01
49 3 0.04
50 25 0.30
51 3 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (43 bp):
CCACTGCAACTTCAGAGGATAGGATTTGTAGCTTCATCTTGCT
Found at i:12684451 original size:94 final size:94
Alignment explanation
Indices: 12684187--12684453 Score: 347
Period size: 94 Copynumber: 2.8 Consensus size: 94
12684177 GTGTCACAGT
* ** * ** * *
12684187 TTCATATTGCTCCATTACAGCTTCAAGGAGATAAGATTTGTTGTTGTAGTTTCATTCCAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
* *
12684252 TGCAACTTCAGAGGTATAGGATTTGTAGC
66 TGCAACTTCAGGGGCATAGGATTTGTAGC
* * * * *
12684281 TTCATCTTGCTCCACTGTAACTT-TAGGAAGATAAGATTTTCTATGGTAGCTTCACTCCAACCCA
1 TTCATCTTGCTCCATTGTAACTTCAAGG-AGATAAGATTTACTATTGTAGCTTCATTCCAACCCA
*
12684345 CTGCCACTTCAGGGGCATAGGATTTGTAGC
65 CTGCAACTTCAGGGGCATAGGATTTGTAGC
* *
12684375 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTCACTATTGTAGCTTCATTCAAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
*
12684440 TACAACTTCAGGGG
66 TGCAACTTCAGGGG
12684454 GACTGGAGTT
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
93 3 0.02
94 141 0.96
95 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (94 bp):
TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
TGCAACTTCAGGGGCATAGGATTTGTAGC
Found at i:12691313 original size:20 final size:20
Alignment explanation
Indices: 12691284--12691321 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12691274 AATTTTCTCC
12691284 TCTTCCAACTTCTCTATCCT
1 TCTTCCAACTTCTCTATCCT
*
12691304 TCTTCTAACTTCTCTATC
1 TCTTCCAACTTCTCTATC
12691322 TTTTTTCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (20 bp):
TCTTCCAACTTCTCTATCCT
Found at i:12694106 original size:13 final size:13
Alignment explanation
Indices: 12694090--12694116 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12694080 ATTAGTACTT
12694090 ATAATAATTAATG
1 ATAATAATTAATG
12694103 ATAATAATTAATG
1 ATAATAATTAATG
12694116 A
1 A
12694117 CCAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATAATAATTAATG
Found at i:12695374 original size:15 final size:15
Alignment explanation
Indices: 12695354--12695383 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12695344 AATTTTAAGT
12695354 TTTGGGCTATTGGGC
1 TTTGGGCTATTGGGC
*
12695369 TTTGGGCTGTTGGGC
1 TTTGGGCTATTGGGC
12695384 CTTTTGGGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.43, T:0.40
Consensus pattern (15 bp):
TTTGGGCTATTGGGC
Found at i:12695614 original size:19 final size:20
Alignment explanation
Indices: 12695577--12695614 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12695567 ATATATAAGA
* *
12695577 TAAATAAAACTAGTCTAAAC
1 TAAATAAAACTAATATAAAC
12695597 TAAA-AAAACTAATATAAA
1 TAAATAAAACTAATATAAA
12695615 TAAGAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.24
Consensus pattern (20 bp):
TAAATAAAACTAATATAAAC
Found at i:12697182 original size:30 final size:31
Alignment explanation
Indices: 12697148--12697207 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
12697138 AAACCTTTTA
*
12697148 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
12697178 TTTTCCTCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
12697208 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:12713823 original size:132 final size:132
Alignment explanation
Indices: 12713627--12714069 Score: 531
Period size: 132 Copynumber: 3.4 Consensus size: 132
12713617 GAACAGATCA
* * * * *
12713627 TTGAAGATAACAGATCTTATCTCCCTAAGCACTCGTGGAGCAGATCAAAGACGAAAAAACTTATC
1 TTGAAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATC
* *
12713692 TTTCCAAGATAGTGGGAAGCATATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTA
66 TTTCCAAGATAGTGGGAAGCAAATTTAAGCCACCAAGCCTTGTCTCCCTGAACAGCAGTGGAGTA
12713757 GG
131 GG
* * *
12713759 TTGAAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGAAGATCGAAGATGACAAATTTTATC
1 TTGAAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATC
* * * * * *
12713824 TTTCCAAGATAGTGGAAAGCAGATTTAAGCCACCAGGCCTCGTCTCCCTGAACAGTAGTGGAGGA
66 TTTCCAAGATAGTGGGAAGCAAATTTAAGCCACCAAGCCTTGTCTCCCTGAACAGCAGTGGAGTA
12713889 GG
131 GG
* * * *
12713891 TTGAAGATAGCAGATATTA-CTCCCTAAGCACTAGTGGAGCAGATCGAAAACGACGAATCATATC
1 TTGAAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATC
* * * * *
12713955 TTCCCCAG-GAGTAGGGAAACAAATTTAAGCCA-CAAGTCCTATG--TCCCTGACCAGCAGTGGA
66 TTTCCAAGATAGT-GGGAAGCAAATTTAAGCCACCAAG-CCT-TGTCTCCCTGAACAGCAGTGGA
*
12714016 ATAGG
128 GTAGG
* * *
12714021 TTGGAA-ATTA-CAGATCTTATCTCCCTAAGCATTAGCGGAGCGGATCGAA
1 TT-GAAGA-TAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAA
12714070 TACGGTGAAT
Statistics
Matches: 267, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
130 36 0.13
131 95 0.36
132 136 0.51
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (132 bp):
TTGAAGATAGCAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGAAGACGACAAATCTTATC
TTTCCAAGATAGTGGGAAGCAAATTTAAGCCACCAAGCCTTGTCTCCCTGAACAGCAGTGGAGTA
GG
Found at i:12716817 original size:216 final size:215
Alignment explanation
Indices: 12716444--12716876 Score: 857
Period size: 216 Copynumber: 2.0 Consensus size: 215
12716434 TCGATTTCAA
12716444 AATAAAGGCAATATTTGATGTTTAAGAATTTCGAGAAATTGAACCCTAACTTACTAGGTTCGGGT
1 AATAAAGGCAATATTTGATGTTTAAGAATTTCGAGAAATTGAACCCTAACTTACTAGGTTCGGGT
12716509 TTCTCAATTGACTTGAATAATCAAATATCCTTCTTAAAACACATGATTTTCTTAAAAAGAGAAAA
66 TTCTCAATTGACTTGAATAATCAAATATCCTTCTTAAAACACATGATTTTCTTAAAAAGAGAAAA
12716574 CCTAATTTCGAAGATTGAAACTGTCGCACTCTAACTTACTGAGCGTGGCAATTTATCTCTTTGAA
131 CCTAATTTCGAAGATTGAAACTGTCGCACTCTAACTTACTGAGCGTGGCAATTTATCTCTTTGAA
12716639 ATAAGTGAGTCTTATCACCC
196 ATAAGTGAGTCTTATCACCC
12716659 AATAAAGGCAATATTTGATGTTTAAGAACTTTCGAGAAATTGAACCCTAACTTACTAGGTTCGGG
1 AATAAAGGCAATATTTGATGTTTAAGAA-TTTCGAGAAATTGAACCCTAACTTACTAGGTTCGGG
12716724 TTTCTCAATTGACTTGAATAATCAAATATCCTTCTTAAAACACATGATTTTCTTAAAAAGAGAAA
65 TTTCTCAATTGACTTGAATAATCAAATATCCTTCTTAAAACACATGATTTTCTTAAAAAGAGAAA
12716789 ACCTAATTTCGAAGATTGAAACTGTCGCACTCTAACTTACTGAGCGTGGCAATTTATCTCTTTGA
130 ACCTAATTTCGAAGATTGAAACTGTCGCACTCTAACTTACTGAGCGTGGCAATTTATCTCTTTGA
12716854 AATAAGTGAGTCTTATCACCC
195 AATAAGTGAGTCTTATCACCC
12716875 AA
1 AA
12716877 ATTTTAAAAT
Statistics
Matches: 217, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
215 28 0.13
216 189 0.87
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (215 bp):
AATAAAGGCAATATTTGATGTTTAAGAATTTCGAGAAATTGAACCCTAACTTACTAGGTTCGGGT
TTCTCAATTGACTTGAATAATCAAATATCCTTCTTAAAACACATGATTTTCTTAAAAAGAGAAAA
CCTAATTTCGAAGATTGAAACTGTCGCACTCTAACTTACTGAGCGTGGCAATTTATCTCTTTGAA
ATAAGTGAGTCTTATCACCC
Found at i:12717532 original size:43 final size:43
Alignment explanation
Indices: 12717498--12717841 Score: 310
Period size: 43 Copynumber: 8.0 Consensus size: 43
12717488 ACGCTGCAAT
*
12717498 AGACCCTGATCTATAGCGGCG-TTTCTACCACAAACGCCACTAA
1 AGACCCTGATCTTTAGCGGCGCTTTC-ACCACAAACGCCACTAA
* * *
12717541 AGAACCT-ATTCTTTAGCGGCGCTTTC-CCTCAAACGCCGC-AA
1 AGACCCTGA-TCTTTAGCGGCGCTTTCACCACAAACGCCACTAA
* *
12717582 TTGACCCTGATCTATAGCGGCGC-TTCGACCACAAACGCCACTAA
1 -AGACCCTGATCTTTAGCGGCGCTTTC-ACCACAAACGCCACTAA
* * * * **
12717626 AGAACCT-ATTCTTTAGCGGTGCTTTCCCCTCAAACATCAC-AA
1 AGACCCTGA-TCTTTAGCGGCGCTTTCACCACAAACGCCACTAA
* *
12717668 TAGACCCTGATCTATAGCGGCGC-TTCGACCACAAATGCCACTAA
1 -AGACCCTGATCTTTAGCGGCGCTTTC-ACCACAAACGCCACTAA
* * **
12717712 AGAACCTAATCTTTAGCGGCGCTTTC-CCACAAACGCTGCTAA
1 AGACCCTGATCTTTAGCGGCGCTTTCACCACAAACGCCACTAA
* * ** *
12717754 AGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAA
1 AGACCCTGATCTTTAGCGGCGCTTTCACCACAAACGCCACTAA
* * * * *
12717797 AGACCCTTATCTTTAGCGGTGCTTTGACCAAAAACACCACTAA
1 AGACCCTGATCTTTAGCGGCGCTTTCACCACAAACGCCACTAA
12717840 AG
1 AG
12717842 GCCAACACCT
Statistics
Matches: 240, Mismatches: 46, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
41 5 0.02
42 69 0.29
43 151 0.63
44 15 0.06
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (43 bp):
AGACCCTGATCTTTAGCGGCGCTTTCACCACAAACGCCACTAA
Found at i:12717671 original size:171 final size:171
Alignment explanation
Indices: 12717494--12717821 Score: 489
Period size: 171 Copynumber: 1.9 Consensus size: 171
12717484 TCAAACGCTG
* * *
12717494 CAATAGACCCTGATCTATAGCGGCGTTTCTACCACAAACGCCACTAAAGAACCTATTCTTTAGCG
1 CAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGCG
* * *
12717559 GCGCTTTCCCTCAAACGCCGC-AATTGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCAC
66 GCGCTTTCCCACAAACGCCGCTAA-AGACCATGATCTATAGCGGCGCTTCGACCACAAACGCCAC
12717623 TAAAGAACC-TATTCTTTAGCGGTGCTTTCCCCTCAAACATCA
130 TAAAGAACCTTA-TCTTTAGCGGTGCTTTCCCCTCAAACATCA
*
12717665 CAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAATGCCACTAAAGAACCTAATCTTTAGCG
1 CAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGCG
* * * *** *
12717730 GCGCTTTCCCACAAACGCTGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCT
66 GCGCTTTCCCACAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTCGACCACAAACGCCACT
*
12717795 AAAGACCCTTATCTTTAGCGGTGCTTT
131 AAAGAACCTTATCTTTAGCGGTGCTTT
12717822 GACCAAAAAC
Statistics
Matches: 140, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
171 136 0.97
172 4 0.03
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (171 bp):
CAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAATCTTTAGCG
GCGCTTTCCCACAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTCGACCACAAACGCCACT
AAAGAACCTTATCTTTAGCGGTGCTTTCCCCTCAAACATCA
Found at i:12717788 original size:128 final size:128
Alignment explanation
Indices: 12717591--12717841 Score: 267
Period size: 128 Copynumber: 2.0 Consensus size: 128
12717581 ATTGACCCTG
* *
12717591 ATCTATAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTATTCTTTAGCGGTGCTTTCCCCT
1 ATCTATAGCGGCGCTTC-ACCACAAACGCCACTAAAGAACCTATTCTTTAGCGGCGCTTTCCCCA
* * **
12717656 CAAACATCAC-AATAGACCCTGATCTATAGCGGCGCTTCGACCACAAATGCCACTAAAGAACCTA
65 CAAACACCACTAA-AGACCCTGATCTATAGCGGCGCTTCGACCAAAAACACCACTAAAGAACCTA
* ** * **
12717720 ATCTTTAGCGGCGCTTTC-CCACAAACGCTGCTAAAG-ACC-ATGATCTTTAGTGGCGCTTTTTC
1 ATCTATAGCGGCGC-TTCACCACAAACGCCACTAAAGAACCTAT--TCTTTAGCGGCGCTTTCCC
* * * * * *
12717782 CACAAACGCCGCTAAAGACCCTTATCTTTAGCGGTGCTTTGACCAAAAACACCACTAAAG
63 CACAAACACCACTAAAGACCCTGATCTATAGCGGCGCTTCGACCAAAAACACCACTAAAG
12717842 GCCAACACCT
Statistics
Matches: 100, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
126 2 0.02
127 3 0.03
128 77 0.77
129 15 0.15
130 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (128 bp):
ATCTATAGCGGCGCTTCACCACAAACGCCACTAAAGAACCTATTCTTTAGCGGCGCTTTCCCCAC
AAACACCACTAAAGACCCTGATCTATAGCGGCGCTTCGACCAAAAACACCACTAAAGAACCTA
Found at i:12717809 original size:85 final size:85
Alignment explanation
Indices: 12717464--12717821 Score: 452
Period size: 85 Copynumber: 4.2 Consensus size: 85
12717454 AAGATCAGAG
** * * *
12717464 TCTTTAGCGGCATTTTTCTCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGTTTCTACCAC
1 TCTTTAGCGGC-GCTTTCCCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
12717529 AAACGCCACTAAAGAACCTAT
65 AAACGCCACTAAAGAACCTAT
* *
12717550 TCTTTAGCGGCGCTTTCCCTCAAACGCCGCAATTGACCCTGATCTATAGCGGCGCTTCGACCACA
1 TCTTTAGCGGCGCTTTCCCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGCTTCGACCACA
12717615 AACGCCACTAAAGAACCTAT
66 AACGCCACTAAAGAACCTAT
* * *
12717635 TCTTTAGCGGTGCTTTCCCCTCAAAC-ATCACAATAGACCCTGATCTATAGCGGCGCTTCGACCA
1 TCTTTAGCGGCGCTTT-CCCTCAAACGCT-GCAATAGACCCTGATCTATAGCGGCGCTTCGACCA
* *
12717699 CAAATGCCACTAAAGAACCTAA
64 CAAACGCCACTAAAGAACCTAT
* * * * ***
12717721 TCTTTAGCGGCGCTTTCCCACAAACGCTGCTAA-AGACCATGATCTTTAGTGGCGCTTTTTCCAC
1 TCTTTAGCGGCGCTTTCCCTCAAACGCTGC-AATAGACCCTGATCTATAGCGGCGCTTCGACCAC
* *
12717785 AAACGCCGCTAAAGACCCT-T
65 AAACGCCACTAAAGAACCTAT
*
12717805 ATCTTTAGCGGTGCTTT
1 -TCTTTAGCGGCGCTTT
12717822 GACCAAAAAC
Statistics
Matches: 238, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
85 147 0.62
86 91 0.38
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (85 bp):
TCTTTAGCGGCGCTTTCCCTCAAACGCTGCAATAGACCCTGATCTATAGCGGCGCTTCGACCACA
AACGCCACTAAAGAACCTAT
Found at i:12717865 original size:85 final size:85
Alignment explanation
Indices: 12717696--12717865 Score: 180
Period size: 85 Copynumber: 2.0 Consensus size: 85
12717686 GGCGCTTCGA
* * * * ** *
12717696 CCACAAATGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCACAAACGCTGCTAAAGACCAT
1 CCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTACCAAAAACACCACTAAAGACCAA
* * * *
12717761 GATCTTTAGTGGCGCTTTTT
66 CACCTTTAGTGACGATTTTT
* * * * *
12717781 CCACAAACGCCGCTAAAGACCCTTATCTTTAGCGGTGCTTTGACCAAAAACACCACTAAAGGCCA
1 CCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTT-ACCAAAAACACCACTAAAGACCA
12717846 ACACCTTTAGTGAC-ATTTTT
65 ACACCTTTAGTGACGATTTTT
12717866 TTTTAAAAAT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
85 41 0.60
86 27 0.40
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (85 bp):
CCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTACCAAAAACACCACTAAAGACCAA
CACCTTTAGTGACGATTTTT
Found at i:12718276 original size:21 final size:21
Alignment explanation
Indices: 12718207--12718276 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
12718197 CGCTTTAGCC
* *
12718207 TCTGCTTCCCTCGCTGCAGCA
1 TCTGCTTCTCTCGCTGCCGCA
* * * *
12718228 TGTACTTCTCTCGCTGCCACC
1 TCTGCTTCTCTCGCTGCCGCA
* *
12718249 TCAGCTTCTCTTGCTGCCGCA
1 TCTGCTTCTCTCGCTGCCGCA
12718270 TCTGCTT
1 TCTGCTT
12718277 TAAGCTGTTG
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.09, C:0.40, G:0.17, T:0.34
Consensus pattern (21 bp):
TCTGCTTCTCTCGCTGCCGCA
Found at i:12718330 original size:65 final size:67
Alignment explanation
Indices: 12718246--12718388 Score: 195
Period size: 65 Copynumber: 2.2 Consensus size: 67
12718236 TCTCGCTGCC
* *
12718246 ACCTCAGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGTTGCTGGAGTTCTTCATA-CTTTCGTT
1 ACCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTCGTT
12718310 GA
66 GA
* * *
12718312 ACCTCAGC-TCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT--TT
1 ACCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTCGTT
12718374 GA
66 GA
* *
12718376 ACATCATCTTCTC
1 ACCTCAGCTTCTC
12718389 GATTTGCTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 10 0.15
65 46 0.68
66 12 0.18
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (67 bp):
ACCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTCGTT
GA
Found at i:12723784 original size:16 final size:16
Alignment explanation
Indices: 12723763--12723854 Score: 64
Period size: 16 Copynumber: 5.8 Consensus size: 16
12723753 ATTAAGCTAC
12723763 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
12723779 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
* * *
12723795 GAAAATTATGTAAGTTGT
1 GTAAGTTATGT-A-TTAT
* * *
12723813 GT-A-TTGTGAAATAT
1 GTAAGTTATGTATTAT
*
12723827 GTAAGTTATGTAAGT-T
1 GTAAGTTATGT-ATTAT
12723843 GTAAGTTATGTA
1 GTAAGTTATGTA
12723855 AGTTGTAAGT
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 43 0.74
17 4 0.07
18 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.46
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:12723802 original size:25 final size:24
Alignment explanation
Indices: 12723774--12723838 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 24
12723764 TAAGTTATGT
*
12723774 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATG-AA
* *
12723799 ATTATGTAAGTTGTGTATTGTGAA
1 ATTATGTAAGTTATGTATTATGAA
12723823 A-TATGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
12723839 AGTTGTAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 14 0.39
24 3 0.08
25 19 0.53
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.46
Consensus pattern (24 bp):
ATTATGTAAGTTATGTATTATGAA
Found at i:12723838 original size:9 final size:9
Alignment explanation
Indices: 12723763--12724299 Score: 110
Period size: 9 Copynumber: 62.3 Consensus size: 9
12723753 ATTAAGCTAC
12723763 GTAAGTTAT
1 GTAAGTTAT
12723772 GT-A-TTAT
1 GTAAGTTAT
12723779 GTAAGTTAT
1 GTAAGTTAT
*
12723788 -TTA-TTAT
1 GTAAGTTAT
* *
12723795 GAAAATTAT
1 GTAAGTTAT
*
12723804 GTAAGTTGT
1 GTAAGTTAT
*
12723813 GT-A-TTGT
1 GTAAGTTAT
*
12723820 G-AA-ATAT
1 GTAAGTTAT
12723827 GTAAGTTAT
1 GTAAGTTAT
12723836 GTAAG-T-T
1 GTAAGTTAT
12723843 GTAAGTTAT
1 GTAAGTTAT
12723852 GTAAG-T-T
1 GTAAGTTAT
*
12723859 GTAAGTTAA
1 GTAAGTTAT
*
12723868 CTAAGTTAT
1 GTAAGTTAT
*
12723877 GTAATTTAT
1 GTAAGTTAT
12723886 GT-A--TAT
1 GTAAGTTAT
* *
12723892 -TAACTAAT
1 GTAAGTTAT
12723900 -TAAGTTAT
1 GTAAGTTAT
*
12723908 GTAATTTAT
1 GTAAGTTAT
*
12723917 GTATAATATTAAT
1 G--TAA-GTT-AT
12723930 GTAAGTTAT
1 GTAAGTTAT
*
12723939 GTATA-ATAT
1 GTA-AGTTAT
*
12723948 -TAA-TTAA
1 GTAAGTTAT
*
12723955 CTAAGTTAT
1 GTAAGTTAT
*
12723964 GTAATTTAT
1 GTAAGTTAT
*
12723973 GTATAATATTAAT
1 G--TAA-GTT-AT
12723986 GTAAGTTAT
1 GTAAGTTAT
*
12723995 GTAATTTAT
1 GTAAGTTAT
12724004 GT-A--TAT
1 GTAAGTTAT
* *
12724010 -TAACTAAT
1 GTAAGTTAT
12724018 -TAAGTTAT
1 GTAAGTTAT
*
12724026 GTAATTTAT
1 GTAAGTTAT
*
12724035 G-AA-TAAT
1 GTAAGTTAT
***
12724042 -TAAAAAAAT
1 GT-AAGTTAT
12724051 GTAAGTTAT
1 GTAAGTTAT
12724060 GTAAG-T-T
1 GTAAGTTAT
12724067 GTAAG-T-T
1 GTAAGTTAT
12724074 GTAAGTTAT
1 GTAAGTTAT
*
12724083 GTATA-ATAT
1 GTA-AGTTAT
*
12724092 -TAA-TTAA
1 GTAAGTTAT
*
12724099 CTAAGTTAT
1 GTAAGTTAT
*
12724108 GTAATTTAT
1 GTAAGTTAT
*
12724117 GTATAATATTAAT
1 G--TAA-GTT-AT
*
12724130 GTATGTTAT
1 GTAAGTTAT
*
12724139 GTAATTTAT
1 GTAAGTTAT
12724148 GT-A--TAT
1 GTAAGTTAT
* *
12724154 -TAACTAAT
1 GTAAGTTAT
12724162 -TAAGTTAT
1 GTAAGTTAT
*
12724170 GTAATTTAT
1 GTAAGTTAT
*
12724179 GTATAATATTAAT
1 G--TAA-GTT-AT
12724192 GTAAGTTAT
1 GTAAGTTAT
*
12724201 GTATA-ATAT
1 GTA-AGTTAT
*
12724210 -TAA-TTAA
1 GTAAGTTAT
*
12724217 CTAAGTTAT
1 GTAAGTTAT
*
12724226 GTAATTTAT
1 GTAAGTTAT
*
12724235 GTATAATATTAAT
1 G--TAA-GTT-AT
12724248 GTAAGTTAT
1 GTAAGTTAT
*
12724257 GTAATTTAT
1 GTAAGTTAT
12724266 GT-A--TAT
1 GTAAGTTAT
12724272 -TAA-TTAAT
1 GTAAGTT-AT
12724280 -TAAGTTAT
1 GTAAGTTAT
*
12724288 GTAATTTAT
1 GTAAGTTAT
12724297 GTA
1 GTA
12724300 TAATATTAAT
Statistics
Matches: 400, Mismatches: 65, Indels: 126
0.68 0.11 0.21
Matches are distributed among these distances:
5 4 0.01
6 16 0.04
7 57 0.14
8 68 0.17
9 187 0.47
10 14 0.04
11 29 0.07
12 10 0.03
13 15 0.04
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:12723844 original size:25 final size:24
Alignment explanation
Indices: 12723776--12723858 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 24
12723766 AGTTATGTAT
* *
12723776 TATGTAAGTTAT-TTATTATGAAAA
1 TATGTAAGTTATGTAATTGTG-AAA
*
12723800 TTATGTAAGTTGTGT-ATTGTGAAA
1 -TATGTAAGTTATGTAATTGTGAAA
*
12723824 TATGTAAGTTATGTAAGTTGT-AAGT
1 TATGTAAGTTATGTAA-TTGTGAA-A
12723849 TATGTAAGTT
1 TATGTAAGTT
12723859 GTAAGTTAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
23 13 0.26
24 6 0.12
25 30 0.60
26 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (24 bp):
TATGTAAGTTATGTAATTGTGAAA
Found at i:12723874 original size:16 final size:16
Alignment explanation
Indices: 12723826--12723866 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
12723816 TTGTGAAATA
12723826 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
12723842 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
12723858 TGTAAGTTA
1 TGTAAGTTA
12723867 ACTAAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:12723907 original size:31 final size:31
Alignment explanation
Indices: 12723864--12724344 Score: 406
Period size: 31 Copynumber: 15.3 Consensus size: 31
12723854 AAGTTGTAAG
*
12723864 TTAACTAAGTTATGTAATTTATGTATATTAA
1 TTAATTAAGTTATGTAATTTATGTATATTAA
* *
12723895 CTAATTAAGTTATGTAATTTATGTATAAT-A
1 TTAATTAAGTTATGTAATTTATGTATATTAA
12723925 TTAATGTAAGTTATGT-A--TA---ATATTAA
1 TTAAT-TAAGTTATGTAATTTATGTATATTAA
* *
12723951 TTAACTAAGTTATGTAATTTATGTATAAT-A
1 TTAATTAAGTTATGTAATTTATGTATATTAA
12723981 TTAATGTAAGTTATGTAATTTATGTATATTAA
1 TTAAT-TAAGTTATGTAATTTATGTATATTAA
* *
12724013 CTAATTAAGTTATGTAATTTATGAATAATTAAA
1 TTAATTAAGTTATGTAATTTATGTAT-ATT-AA
**
12724046 AAAATGTAAGTTATGTAAGTTGTAAGTTGTA-AGTTATGTA
1 TTAAT-TAAGTTATGTAA-TT-T-A--TGTATA-TTA---A
* ** *
12724086 TAATATTAA-TTAACTAAGTTATGTAATTTATGTATAATA
1 TTA-ATTAAGTTATGTAATTTATGT-A--TA--T-T-A-A
*
12724125 TTAATGTATGTTATGTAATTTATGTATATTAA
1 TTAAT-TAAGTTATGTAATTTATGTATATTAA
* *
12724157 CTAATTAAGTTATGTAATTTATGTATAAT-A
1 TTAATTAAGTTATGTAATTTATGTATATTAA
12724187 TTAATGTAAGTTATGT-A--TA---ATATTAA
1 TTAAT-TAAGTTATGTAATTTATGTATATTAA
* *
12724213 TTAACTAAGTTATGTAATTTATGTATAAT-A
1 TTAATTAAGTTATGTAATTTATGTATATTAA
12724243 TTAATGTAAGTTATGTAATTTATGTATATTAA
1 TTAAT-TAAGTTATGTAATTTATGTATATTAA
*
12724275 TTAATTAAGTTATGTAATTTATGTATAAT-A
1 TTAATTAAGTTATGTAATTTATGTATATTAA
*
12724305 TTAATGTAAGTTATGTATTTTATGTATATTAA
1 TTAAT-TAAGTTATGTAATTTATGTATATTAA
12724337 TTAATTAA
1 TTAATTAA
12724345 ATGATATGTA
Statistics
Matches: 371, Mismatches: 35, Indels: 88
0.75 0.07 0.18
Matches are distributed among these distances:
25 28 0.08
26 12 0.03
28 8 0.02
30 28 0.08
31 190 0.51
32 25 0.07
33 6 0.02
34 16 0.04
35 4 0.01
36 2 0.01
37 6 0.02
38 6 0.02
39 18 0.05
40 19 0.05
41 3 0.01
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.47
Consensus pattern (31 bp):
TTAATTAAGTTATGTAATTTATGTATATTAA
Found at i:12723931 original size:22 final size:22
Alignment explanation
Indices: 12723906--12723951 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12723896 TAATTAAGTT
*
12723906 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
12723928 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
12723950 AT
1 AT
12723952 TAACTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:12723965 original size:25 final size:22
Alignment explanation
Indices: 12723913--12723966 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
12723903 GTTATGTAAT
*
12723913 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATCTAAG
12723935 TTATGTATAATATTAATTAACTAAG
1 TTATGTATAATATTAA-T--CTAAG
12723960 TTATGTA
1 TTATGTA
12723967 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.57
23 1 0.04
25 11 0.39
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
TTATGTATAATATTAATCTAAG
Found at i:12724138 original size:22 final size:22
Alignment explanation
Indices: 12724113--12724213 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
12724103 GTTATGTAAT
12724113 TTATGTATAATATTAATGTATG
1 TTATGTATAATATTAATGTATG
*
12724135 TTATG--TAAT-TT-ATGTATA
1 TTATGTATAATATTAATGTATG
** *
12724153 TTAACTAATTAA-GTT-ATGTAAT-
1 TTATGT-A-TAATATTAATGT-ATG
*
12724175 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATGTATG
12724197 TTATGTATAATATTAAT
1 TTATGTATAATATTAAT
12724214 TAACTAAGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
18 9 0.14
19 2 0.03
20 7 0.11
21 4 0.06
22 39 0.62
23 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.50
Consensus pattern (22 bp):
TTATGTATAATATTAATGTATG
Found at i:12724227 original size:25 final size:22
Alignment explanation
Indices: 12724175--12724228 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
12724165 GTTATGTAAT
*
12724175 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATCTAAG
12724197 TTATGTATAATATTAATTAACTAAG
1 TTATGTATAATATTAA-T--CTAAG
12724222 TTATGTA
1 TTATGTA
12724229 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.57
23 1 0.04
25 11 0.39
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
TTATGTATAATATTAATCTAAG
Found at i:12724256 original size:22 final size:21
Alignment explanation
Indices: 12724222--12724322 Score: 79
Period size: 22 Copynumber: 4.8 Consensus size: 21
12724212 ATTAACTAAG
*
12724222 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
12724243 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAAGTTATGTATAATA
*
12724262 TTATGTATA-TTAAT-TAATTAA-G
1 TTATGTA-AGTT-ATGT-A-TAATA
*
12724284 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
12724305 TTAATGTAAGTTATGTAT
1 TT-ATGTAAGTTATGTAT
12724323 TTTATGTATA
Statistics
Matches: 65, Mismatches: 3, Indels: 23
0.71 0.03 0.25
Matches are distributed among these distances:
18 7 0.11
19 5 0.08
20 7 0.11
21 8 0.12
22 38 0.58
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
TTATGTAAGTTATGTATAATA
Found at i:12724291 original size:118 final size:118
Alignment explanation
Indices: 12723842--12724322 Score: 568
Period size: 118 Copynumber: 4.1 Consensus size: 118
12723832 TTATGTAAGT
* *
12723842 TGTAAGTTATGTA-AGT-TGTAAGTTAACTAAGTTATGTAATTTATGTATATTAACTAATTAAGT
1 TGTAAGTTATGTATAATAT-TAA-TTAACTAAGTTATGTAATTTATGTATAATAACTAATTAAGT
* *
12723905 TATGTAATTTATGTATAAT-ATTAATGTAAGTTATGTATAATATTAAT-TAACTAA-GTT-A
64 TATGTAATTTATGTATATTAATTAAT-TAAGTTATG--TAAT-TT-ATGT-A-TAATATTAA
* * *
12723963 TGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTATATTAACTAATTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAACTAATTAAGTTA
** * *
12724025 TGTAATTTATG-A-A-TAATTAA--AA-AAATGTAAGTTATGTA-AGT-TGTAA
66 TGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATAT-TAA
* *
12724071 GTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAAT-ATTAATGTATG
1 --TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAACTAAT-TAAG
*
12724135 TTATGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGTATAATATTAA
63 TTATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
12724191 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAAT-ATTAATGTAAGTT
1 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAACTAAT-TAAGTT
12724255 ATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
65 ATGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
12724309 TGTAAGTTATGTAT
1 TGTAAGTTATGTAT
12724323 TTTATGTATA
Statistics
Matches: 320, Mismatches: 19, Indels: 45
0.83 0.05 0.12
Matches are distributed among these distances:
106 2 0.01
107 1 0.00
108 4 0.01
109 3 0.01
110 24 0.08
111 1 0.00
112 8 0.03
113 42 0.13
114 1 0.00
115 2 0.01
116 12 0.04
117 1 0.00
118 181 0.57
119 13 0.04
120 6 0.02
121 13 0.04
122 5 0.02
123 1 0.00
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (118 bp):
TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATAACTAATTAAGTTA
TGTAATTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
Found at i:12729479 original size:15 final size:15
Alignment explanation
Indices: 12729459--12729496 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12729449 TTGAAATTAA
12729459 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
12729474 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
12729489 CCCTAAAT
1 CCCTAAAT
12729497 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:12730031 original size:41 final size:40
Alignment explanation
Indices: 12729963--12730316 Score: 186
Period size: 41 Copynumber: 8.8 Consensus size: 40
12729953 TTTTGTTACT
* ** * *
12729963 ATTAGCGGCGCTTCGGCAAAAATGCCGCTAAAGGTAAATAC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGATAAA-AC
* * *
12730004 ATTAGCGGCGCTTAGATACAAACGCCGCTGAAGACAAGAGA-
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGATAA-A-AC
* * * * *
12730045 ATTAGTGGCGCTCAGTTAAAAACGCCGCTAAAGATTCAAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGA-TAAAAC
* *** *
12730086 ATTAGCGACGCTT-GTATAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTAG-ATAAAAACGCCGCTAAAGA-TAAAAC
* * * ** *
12730127 ATTAGTGGCGCATAGACAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGAT-AAAAC
* * * ** *
12730168 ATTAGCGGCACATAGACAAAAACGCCGCTAAAGATCTGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGAT-AAAAC
* * ** *
12730209 ATTAGCGGCG-TT---T--AGAGGCCGCTAAAGACTCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGA-TAAAAC
* ** *
12730244 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCGGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGAT-AAAAC
* *
12730285 ATTAGC-GCGCTTACACAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAG
12730317 GTTTAAAAAA
Statistics
Matches: 256, Mismatches: 43, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
35 27 0.11
36 3 0.01
40 28 0.11
41 194 0.76
42 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGATAAAAC
Found at i:12730244 original size:35 final size:35
Alignment explanation
Indices: 12730191--12730259 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
12730181 AGACAAAAAC
*
12730191 GCCGCTAAAGATCTGAGCATTAGCGGCGTTTAGAG
1 GCCGCTAAAGATCTGAGCATTAGCGGCGCTTAGAG
12730226 GCCGCTAAAGA-CTCGAGCATTAGCGGCGCTTAGA
1 GCCGCTAAAGATCT-GAGCATTAGCGGCGCTTAGA
12730260 CAAAAACGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 30 0.94
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (35 bp):
GCCGCTAAAGATCTGAGCATTAGCGGCGCTTAGAG
Found at i:12730260 original size:76 final size:76
Alignment explanation
Indices: 12730003--12730291 Score: 251
Period size: 82 Copynumber: 3.6 Consensus size: 76
12729993 AAGGTAAATA
* * * * * * *
12730003 CATTAGCGGCGCTTAGATACAAACGCCGCTGAAGA-CAAGAGAATTAGTGGCGCTCAGTTAAAAA
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATC-CGAGCATTAGCGGCG--CA--T-AGAA
*
12730067 CGCCGCTAAAGATTCAAG
60 CGCCGCTAAAGA-TCGAG
* * * *
12730085 CATTAGCGACGCTT-GTATAAAAACGCCGCTAAAGACCCGAGCATTAGTGGCGCATAGACAAAAA
1 CATTAGCGGCGCTTAG-ACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAG-----AA
12730149 CGCCGCTAAAGATCCGAG
60 CGCCGCTAAAGAT-CGAG
* * * ** *
12730167 CATTAGCGGCACATAGACAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGTTTAG-AGGCCGC
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAGAACGCCGC
12730231 TAAAGACTCGAG
66 TAAAGA-TCGAG
*
12730243 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCGGAGCATTAGCG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCG
12730292 CGCTTACACA
Statistics
Matches: 177, Mismatches: 20, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
76 62 0.35
77 2 0.01
78 1 0.01
80 2 0.01
81 2 0.01
82 106 0.60
83 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (76 bp):
CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAGAACGCCGC
TAAAGATCGAG
Found at i:12730459 original size:40 final size:40
Alignment explanation
Indices: 12730379--12730471 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
12730369 TTATATAAAA
* **
12730379 CGCCGCTAATTC-CTATTTTTAGCGGCGCTTCCGGATAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGGATAAT
* * * *
12730418 CGCCTCTGATGCTCTACCTTTAGCGGCGCTT-TGGCTAAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGGAT-AAT
12730458 CGCCGCTAATGCTC
1 CGCCGCTAATGCTC
12730472 GATTTTTTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
39 12 0.28
40 31 0.72
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (40 bp):
CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGGATAAT
Found at i:12730852 original size:20 final size:21
Alignment explanation
Indices: 12730819--12730857 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
12730809 GTACATGCAT
12730819 ACATATATTTTTATAATATTG
1 ACATATATTTTTATAATATTG
12730840 ACATATA-TTTTATAATAT
1 ACATATATTTTTATAATAT
12730858 ATACGCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (21 bp):
ACATATATTTTTATAATATTG
Found at i:12731360 original size:108 final size:108
Alignment explanation
Indices: 12731162--12731362 Score: 339
Period size: 108 Copynumber: 1.9 Consensus size: 108
12731152 AGAAATTTTT
* * * * * *
12731162 TTTCTAAATAAGGCAATGTTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAACAAGGCAATATTTTACATTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
12731227 CGATTTCTCGTTCGACCAAATAGCCAAAAAATCCTTTTTAAAC
66 CGATTTCTCGTTCGACCAAATAGCCAAAAAATCCTTTTTAAAC
12731270 TTTCAAAACAAGGCAATATTTTACATTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAACAAGGCAATATTTTACATTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
*
12731335 CGATTTCTCGTTCGACTAAATAGCCAAA
66 CGATTTCTCGTTCGACCAAATAGCCAAA
12731363 TATCCTCTTA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 86 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (108 bp):
TTTCAAAACAAGGCAATATTTTACATTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTCGACCAAATAGCCAAAAAATCCTTTTTAAAC
Found at i:12732373 original size:9 final size:9
Alignment explanation
Indices: 12732356--12732392 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12732346 TGAGTTTTCG
12732356 AATTCGAAT
1 AATTCGAAT
*
12732365 AACTCGAAT
1 AATTCGAAT
12732374 AATTCGAAT
1 AATTCGAAT
12732383 AATTCGAAT
1 AATTCGAAT
12732392 A
1 A
12732393 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12732660 original size:30 final size:32
Alignment explanation
Indices: 12732606--12732666 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
12732596 AAACCTTTTA
*
12732606 TTTCCCCACAAAATTTTTACTCCC-TCCCATT
1 TTTCCCCACAAAACTTTTACTCCCTTCCCATT
* *
12732637 TTTCCCC-TAAAACTTTTATTCCCTTCCCAT
1 TTTCCCCACAAAACTTTTACTCCCTTCCCAT
12732667 CTCACCTCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTCCCCACAAAACTTTTACTCCCTTCCCATT
Found at i:12737581 original size:20 final size:21
Alignment explanation
Indices: 12737556--12737598 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
12737546 GGTTTTTTAC
12737556 AAAAATATTATAAA-AA-ATAA
1 AAAAATATTA-AAATAATATAA
12737576 AAAAATATTAAAATAATATAA
1 AAAAATATTAAAATAATATAA
12737597 AA
1 AA
12737599 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.57
21 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATATTAAAATAATATAA
Found at i:12737659 original size:50 final size:50
Alignment explanation
Indices: 12737572--12737680 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
12737562 ATTATAAAAA
* **** ** *
12737572 ATAAAAAAATATTAAAATAATATAAAATTTTTATTATTTATGAAAATATT
1 ATAAAAAAATATCAAAATAATATAAAAAAAGTATTATTTACCAAAATAAT
12737622 ATAAAAAAATATCAAAATAATATAAAAAAAAGT-TTATTTACCAAAATAAT
1 ATAAAAAAATATCAAAATAATAT-AAAAAAAGTATTATTTACCAAAATAAT
*
12737672 ACAAAAAAA
1 ATAAAAAAA
12737681 AAACGGCTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 44 0.90
51 5 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (50 bp):
ATAAAAAAATATCAAAATAATATAAAAAAAGTATTATTTACCAAAATAAT
Found at i:12738306 original size:144 final size:141
Alignment explanation
Indices: 12738147--12738424 Score: 468
Period size: 144 Copynumber: 2.0 Consensus size: 141
12738137 AATACATTTA
*
12738147 AAAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
1 AAAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACACTATGTTTGAAATGTAT
* * *
12738212 TCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAACTCTTATTTCAG-TCCTTTGTTCGTATT
66 TCATTTAGTGTGTTTTTTAAATAAA--TT-AAAAAAACCCTTATTTCGGCT-CTTTGTTCGTACT
12738276 TTTTTCCCTTTCAAT
127 TTTTTCCCTTTCAAT
*
12738291 AAAAATATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACACTATGTTTGAAATGTAT
1 AAAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACACTATGTTTGAAATGTAT
12738356 TCATTTAGTGTGTTTTTTAAATAAATTAAAAAAACCCTTATTTCGGCTCTTTGTTCGTACTTTTT
66 TCATTTAGTGTGTTTTTTAAATAAATTAAAAAAACCCTTATTTCGGCTCTTTGTTCGTACTTTTT
12738421 TCCC
131 TCCC
12738425 CGGATTTTAT
Statistics
Matches: 128, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
141 37 0.29
142 3 0.02
144 88 0.69
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (141 bp):
AAAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACACTATGTTTGAAATGTAT
TCATTTAGTGTGTTTTTTAAATAAATTAAAAAAACCCTTATTTCGGCTCTTTGTTCGTACTTTTT
TCCCTTTCAAT
Found at i:12745591 original size:20 final size:20
Alignment explanation
Indices: 12745566--12745603 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12745556 GGACCATGCA
*
12745566 AAACAATGTTGTTTTACCCT
1 AAACAATGCTGTTTTACCCT
12745586 AAACAATGCTGTTTTACC
1 AAACAATGCTGTTTTACC
12745604 TTGATCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
AAACAATGCTGTTTTACCCT
Found at i:12748186 original size:20 final size:20
Alignment explanation
Indices: 12748161--12748203 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12748151 CACTTAAATC
12748161 TGTTCATTGATGAACTGTTT
1 TGTTCATTGATGAACTGTTT
12748181 TGTTCATTGATGAACTGTTT
1 TGTTCATTGATGAACTGTTT
12748201 TGT
1 TGT
12748204 GAGTGAGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51
Consensus pattern (20 bp):
TGTTCATTGATGAACTGTTT
Found at i:12751694 original size:3 final size:3
Alignment explanation
Indices: 12751686--12751719 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12751676 CCAATACACT
12751686 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
12751720 TCCTTAACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12753208 original size:9 final size:9
Alignment explanation
Indices: 12753192--12753298 Score: 151
Period size: 9 Copynumber: 11.4 Consensus size: 9
12753182 TTTTGGTTAA
12753192 AATTACCCG
1 AATTACCCG
*
12753201 ACTTACCCG
1 AATTACCCG
12753210 AATTACCCG
1 AATTACCCG
*
12753219 ACTTACCCG
1 AATTACCCG
12753228 AATTACCCG
1 AATTACCCG
12753237 AAAATTACCCG
1 --AATTACCCG
12753248 AATTACCCG
1 AATTACCCG
12753257 AATTACCCG
1 AATTACCCG
*
12753266 AAAATTACCCA
1 --AATTACCCG
12753277 AATTACCCG
1 AATTACCCG
12753286 AATTACCCG
1 AATTACCCG
12753295 AATT
1 AATT
12753299 GAATCACTAC
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
9 71 0.81
11 17 0.19
ACGTcount: A:0.36, C:0.33, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:12753250 original size:38 final size:37
Alignment explanation
Indices: 12753191--12753298 Score: 155
Period size: 38 Copynumber: 2.9 Consensus size: 37
12753181 TTTTTGGTTA
* * *
12753191 AAATTACCCGACTTACCCGAATTACCCGACTTACCCG
1 AAATTACCCAAATTACCCGAATTACCCGAATTACCCG
12753228 -AATTACCCGAAAATTACCCGAATTACCCGAATTACCCG
1 AAATTACCC--AAATTACCCGAATTACCCGAATTACCCG
12753266 AAAATTACCCAAATTACCCGAATTACCCGAATT
1 -AAATTACCCAAATTACCCGAATTACCCGAATT
12753299 GAATCACTAC
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
36 8 0.12
38 48 0.75
40 8 0.12
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.22
Consensus pattern (37 bp):
AAATTACCCAAATTACCCGAATTACCCGAATTACCCG
Found at i:12753253 original size:29 final size:28
Alignment explanation
Indices: 12753193--12753296 Score: 156
Period size: 29 Copynumber: 3.7 Consensus size: 28
12753183 TTTGGTTAAA
*
12753193 ATTACCCGACTTACCCG-AATTACCCGA
1 ATTACCCGAATTACCCGAAATTACCCGA
*
12753220 CTTACCCGAATTACCCGAAAATTACCCGA
1 ATTACCCGAATTACCCG-AAATTACCCGA
*
12753249 ATTACCCGAATTACCCGAAAATTACCCAA
1 ATTACCCGAATTACCCG-AAATTACCCGA
12753278 ATTACCCGAATTACCCGAA
1 ATTACCCGAATTACCCGAA
12753297 TTGAATCACT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
27 15 0.21
28 2 0.03
29 54 0.76
ACGTcount: A:0.36, C:0.34, G:0.10, T:0.21
Consensus pattern (28 bp):
ATTACCCGAATTACCCGAAATTACCCGA
Found at i:12753328 original size:17 final size:17
Alignment explanation
Indices: 12753306--12753403 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
12753296 ATTGAATCAC
12753306 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
12753323 TACATAAATATTTGAATCAC
1 TACAT--A-ATTAAAAACAT
*
12753343 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
12753360 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
12753380 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
12753397 TACATAA
1 TACATAA
12753404 GTCTTGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 30 0.54
18 1 0.02
19 1 0.02
20 24 0.43
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:12753404 original size:37 final size:37
Alignment explanation
Indices: 12753297--12753412 Score: 198
Period size: 37 Copynumber: 3.2 Consensus size: 37
12753287 ATTACCCGAA
* * *
12753297 TTGAATCACTACATAATTAAAAACATTACATAAATAT
1 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
12753334 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
12753371 TTGAATCACTACATAATTAAAAATATTACATAAGTC-
1 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
12753407 TTGAAT
1 TTGAAT
12753413 TAACACATAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 70 0.92
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAATATTACATAAGTCT
Found at i:12753480 original size:24 final size:24
Alignment explanation
Indices: 12753453--12753511 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
12753443 ATTCTCCATT
* *
12753453 TATATCCATTTCATCTTTCTAAAA
1 TATATCCATTTCATCTCTCCAAAA
12753477 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
12753501 TATCTCCATTT
1 TATATCCATTT
12753512 GCATTAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:12757814 original size:17 final size:19
Alignment explanation
Indices: 12757782--12757828 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
12757772 CTTAAATGTC
* *
12757782 TTTATTCTTGTTTGTTTA-T
1 TTTATTATT-TTTGTTAACT
12757801 TTT-TTATTTTTGTTAACT
1 TTTATTATTTTTGTTAACT
12757819 TTTATTATTT
1 TTTATTATTT
12757829 ACCATGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (19 bp):
TTTATTATTTTTGTTAACT
Found at i:12769954 original size:87 final size:87
Alignment explanation
Indices: 12769845--12770140 Score: 305
Period size: 87 Copynumber: 3.4 Consensus size: 87
12769835 TGAAGCCAGA
*
12769845 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTAC
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTAC
12769910 AGTGGAGCGGATTAAAATAAAT
66 AGTGGAGCGGATTAAAATAAAT
* * * * * ** * *
12769932 GATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACA-TCA-GGTCTTATTTCCCTG-AGATT
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGCAGATCAAAGACACTATCCTATCTCCCTGAAG-TT
* ** **
12769993 ACAGTGGAGCAGACCAAAGA-ATTT
64 ACAGTGGAGCGGATTAAA-ATAAAT
* *
12770017 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTT
1 --GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTT
* *
12770082 ACAATGGAGCGGATTAAAATAAAG
64 ACAGTGGAGCGGATTAAAATAAAT
* * * *
12770106 GATTTTATCTCTCTGAGGTTACAGCAGAGTAGATC
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATC
12770141 GCATCAAGTC
Statistics
Matches: 161, Mismatches: 38, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
84 2 0.01
85 30 0.19
86 4 0.02
87 91 0.57
88 4 0.02
89 28 0.17
90 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (87 bp):
GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTAC
AGTGGAGCGGATTAAAATAAAT
Found at i:12770092 original size:174 final size:174
Alignment explanation
Indices: 12769844--12770180 Score: 559
Period size: 174 Copynumber: 1.9 Consensus size: 174
12769834 TTGAAGCCAG
12769844 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTA
* * * *
12769909 CAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAG
66 CAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAA
*
12769974 GTCTTATTTCCCTG-AGATTACAGTGGAGCAGACCAAAGAATTTC
131 GTCTTATTTCCCTGAAGA-TACAGTGGAACAGACCAAAGAATTTC
*
12770018 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTA
* * * *
12770083 CAATGGAGCGGATTAAAATAAAGGATTTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAA
66 CAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAA
*
12770148 GTCTTATTTCCCTGAAGATGCAGTGGAACAGAC
131 GTCTTATTTCCCTGAAGATACAGTGGAACAGAC
12770181 TGAAAACAAG
Statistics
Matches: 151, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
174 148 0.98
175 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (174 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTA
CAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAA
GTCTTATTTCCCTGAAGATACAGTGGAACAGACCAAAGAATTTC
Found at i:12770141 original size:87 final size:86
Alignment explanation
Indices: 12769806--12770141 Score: 304
Period size: 87 Copynumber: 3.9 Consensus size: 86
12769796 ATACAGGTCT
* * * *** * *
12769806 TATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCGGATT-AAAATAAAGATCTTATCTCCCTGAGATTACAGCA
*
12769871 GAGCAGATCAAAGACACTATCC
65 GAGCAGATCGAAGACACTATCC
* *
12769893 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAATGATCTTATCTCTCTGA-AGTTACAGT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCCCTGAGA-TTACAGC
* * ** *
12769957 AGAGAAGATC-ACA-TCA-GGTCT
64 AGAGCAGATCGA-AGACACTATCC
* * ** **
12769978 TATTTCCCTG-AGATTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTACA
1 TATCTCCCTGAAG-TTACAGTGGAGCGGA-TTAA-AA-TAAAGATCTTATCTCCCTGAGATTACA
*
12770042 GCGGAGCAGATCGAAGACACTATCC
62 GCAGAGCAGATCGAAGACACTATCC
* * * *
12770067 TATCTCCCTGAAGTTACAATGGAGCGGATTAAAATAAAGGATTTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAA-GATCTTATCTCCCTGAGATTACAGCA
*
12770132 GAGTAGATCG
65 GAGCAGATCG
12770142 CATCAAGTCT
Statistics
Matches: 195, Mismatches: 41, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
84 2 0.01
85 25 0.13
86 12 0.06
87 122 0.63
88 8 0.04
89 24 0.12
90 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (86 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGATCTTATCTCCCTGAGATTACAGCAG
AGCAGATCGAAGACACTATCC
Found at i:12772269 original size:17 final size:19
Alignment explanation
Indices: 12772237--12772283 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
12772227 CTTAAATGTC
* *
12772237 TTTATTCTTGTTTGTTTA-T
1 TTTATTATT-TTTGTTAACT
12772256 TTT-TTATTTTTGTTAACT
1 TTTATTATTTTTGTTAACT
12772274 TTTATTATTT
1 TTTATTATTT
12772284 ACCATGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (19 bp):
TTTATTATTTTTGTTAACT
Found at i:12773225 original size:8 final size:8
Alignment explanation
Indices: 12773212--12773237 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12773202 CAAATGTTCG
12773212 TATTTAAT
1 TATTTAAT
12773220 TATTTAAT
1 TATTTAAT
12773228 TATTTAAT
1 TATTTAAT
12773236 TA
1 TA
12773238 ACAATATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTAAT
Found at i:12773372 original size:27 final size:27
Alignment explanation
Indices: 12773342--12773394 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
12773332 AAAGATGAAA
12773342 GAAAAAATTAAGACAATAGTATACAAT
1 GAAAAAATTAAGACAATAGTATACAAT
12773369 GAAAAAATTAAGACAATAGTATACAA
1 GAAAAAATTAAGACAATAGTATACAA
12773395 CGACATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (27 bp):
GAAAAAATTAAGACAATAGTATACAAT
Found at i:12780616 original size:23 final size:23
Alignment explanation
Indices: 12780570--12780619 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
12780560 GTTTTAAGTT
*
12780570 TTTATATGTATTATTATTTGAAA
1 TTTATATGTATCATTATTTGAAA
12780593 TTTACTATGTATCATTATTT-AAA
1 TTTA-TATGTATCATTATTTGAAA
12780616 TTTA
1 TTTA
12780620 ACATATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTATATGTATCATTATTTGAAA
Found at i:12784585 original size:15 final size:15
Alignment explanation
Indices: 12784555--12784584 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12784545 ATTATTTCAT
12784555 TTTATAAATAAAAAA
1 TTTATAAATAAAAAA
12784570 TTTATTAAATAAAAA
1 TTTA-TAAATAAAAA
12784585 TAAAAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTATAAATAAAAAA
Found at i:12784626 original size:13 final size:13
Alignment explanation
Indices: 12784610--12784634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12784600 TAATATATTT
12784610 ATTAATTATAAAC
1 ATTAATTATAAAC
12784623 ATTAATTATAAA
1 ATTAATTATAAA
12784635 TAAAAAAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAATTATAAAC
Found at i:12785544 original size:18 final size:18
Alignment explanation
Indices: 12785521--12785556 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12785511 GTAATATGTT
*
12785521 ATATTATGTTATTTATAA
1 ATATTATGTAATTTATAA
12785539 ATATTATGTAATTTATAA
1 ATATTATGTAATTTATAA
12785557 TACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATTATGTAATTTATAA
Found at i:12790332 original size:20 final size:20
Alignment explanation
Indices: 12790309--12790346 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12790299 ATAGTATTAA
*
12790309 TAATATTAAAATAATTAATT
1 TAATAATAAAATAATTAATT
12790329 TAATAATAAAATAATTAA
1 TAATAATAAAATAATTAA
12790347 AATAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATAATAAAATAATTAATT
Found at i:12791058 original size:15 final size:16
Alignment explanation
Indices: 12791034--12791068 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
12791024 AAAGAAAAAA
12791034 AAAAGAAAAATAAAT-
1 AAAAGAAAAATAAATG
*
12791049 AAAAGTAAAATAAATG
1 AAAAGAAAAATAAATG
12791065 AAAA
1 AAAA
12791069 ACTCAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAAGAAAAATAAATG
Found at i:12794712 original size:27 final size:27
Alignment explanation
Indices: 12794676--12794730 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12794666 CCACATGGAG
12794676 AAAGGACATGGAGAAGTCATAACGTGA
1 AAAGGACATGGAGAAGTCATAACGTGA
*
12794703 AAAGGCCATGGAGAAGTCATAACGTGA
1 AAAGGACATGGAGAAGTCATAACGTGA
12794730 A
1 A
12794731 GAGGTGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.29, T:0.15
Consensus pattern (27 bp):
AAAGGACATGGAGAAGTCATAACGTGA
Found at i:12801418 original size:91 final size:91
Alignment explanation
Indices: 12801261--12801522 Score: 305
Period size: 91 Copynumber: 2.9 Consensus size: 91
12801251 GACACACTAG
* * * * * *
12801261 ATGCACATAGAGTAAA-CCTGTAGGCTAAATGTT-TTCCCCGATAACATGCCATATTGCTCATAA
1 ATGCACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAA
*
12801324 GAGCTTTTCCACCGATATAATGCTAA
66 GAGCTTTTCCACCGATATAATGCCAA
* *
12801350 ATGCACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGTTAGATTGCTCATTA
1 ATGCACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAA
* * *
12801415 GAGC-TTTCTCGCTGATATCATGCCAA
66 GAGCTTTTC-CACCGATATAATGCCAA
* * * * * * *
12801441 GTGTACATATTGCAAAGCCCGTAGGCTAAATATTCTCCCCCAATAACACGGTAGATTGCTCATAA
1 ATGCACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAA
* *
12801506 GAGCTTTCCCATCGATA
66 GAGCTTTTCCACCGATA
12801523 ACACACTAGA
Statistics
Matches: 145, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
89 14 0.10
90 20 0.14
91 108 0.74
92 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (91 bp):
ATGCACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAA
GAGCTTTTCCACCGATATAATGCCAA
Found at i:12813814 original size:5 final size:5
Alignment explanation
Indices: 12813804--12813828 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12813794 ACCAAAAAAT
12813804 CCCAA CCCAA CCCAA CCCAA CCCAA
1 CCCAA CCCAA CCCAA CCCAA CCCAA
12813829 TGCATATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCAA
Found at i:12815083 original size:6 final size:6
Alignment explanation
Indices: 12815072--12815098 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12815062 ATCTTGTGGA
12815072 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
12815099 GAGATGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:12818115 original size:30 final size:30
Alignment explanation
Indices: 12818079--12818136 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12818069 TTGGGCATTC
* * *
12818079 CCACACGGGTTGGCCATATTCCCGTGTGAG
1 CCACACGGGCTGGCCATATGCCCATGTGAG
12818109 CCACACGGGCTGGCCATATGCCCATGTG
1 CCACACGGGCTGGCCATATGCCCATGTG
12818137 CTAGCCTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (30 bp):
CCACACGGGCTGGCCATATGCCCATGTGAG
Found at i:12821947 original size:12 final size:12
Alignment explanation
Indices: 12821930--12821957 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12821920 AATACATAAA
12821930 TCTTTTTTTTCT
1 TCTTTTTTTTCT
12821942 TCTTTTTTTTCT
1 TCTTTTTTTTCT
12821954 TCTT
1 TCTT
12821958 CCCCAACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTTTTTTTCT
Found at i:12822260 original size:5 final size:5
Alignment explanation
Indices: 12822250--12822332 Score: 107
Period size: 5 Copynumber: 16.2 Consensus size: 5
12822240 CCGCTTAGTC
12822250 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
*
12822300 TATT-T ATTTAT TTT-T TATTAG TTTAT TATTAT T
1 T-TTAT -TTTAT TTTAT T-TTAT TTTAT T-TTAT T
12822333 ATTCTTAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
4 2 0.03
5 58 0.83
6 10 0.14
ACGTcount: A:0.22, C:0.00, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:12824366 original size:7 final size:6
Alignment explanation
Indices: 12824345--12824389 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
12824335 AGTCTATTTG
* *
12824345 TTTTAT TTTTAT TTTTATT TTTTAT TTTTAT GTTTAT TGTTAT TT
1 TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TT
12824390 GCTTAAGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:12824369 original size:19 final size:19
Alignment explanation
Indices: 12824345--12824382 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12824335 AGTCTATTTG
*
12824345 TTTTATTTTTATTTTTATT
1 TTTTATTTTTATGTTTATT
12824364 TTTTATTTTTATGTTTATT
1 TTTTATTTTTATGTTTATT
12824383 GTTATTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTATTTTTATGTTTATT
Found at i:12832831 original size:20 final size:20
Alignment explanation
Indices: 12832806--12832844 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12832796 CATTTCGGTT
12832806 CTGATGCAACATGTTTCGAC
1 CTGATGCAACATGTTTCGAC
*
12832826 CTGATGCAAGATGTTTCGA
1 CTGATGCAACATGTTTCGA
12832845 AATCTCAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (20 bp):
CTGATGCAACATGTTTCGAC
Found at i:12834460 original size:59 final size:61
Alignment explanation
Indices: 12834384--12834571 Score: 215
Period size: 61 Copynumber: 3.1 Consensus size: 61
12834374 TTTAAGAATA
*
12834384 TTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT
1 TTTAA-ATTAATAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT
* * * ** * * *
12834446 TTTAAATT-AT-ATTTTA-TAGTATTATATATTATGATTTTATTAAATTCATATAAGAA-TA-
1 TTTAAATTAATAATTTTATTA-AATTATATATTTTTATTAAATTATATTTA-ATAATAATTAT
12834504 TTTAATATTAATAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT
1 TTTAA-ATTAATAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT
*
12834566 GTTAAA
1 TTTAAA
12834572 ATATGATTAA
Statistics
Matches: 100, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
58 7 0.07
59 33 0.33
60 15 0.15
61 34 0.34
62 11 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (61 bp):
TTTAAATTAATAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT
Found at i:12834524 original size:19 final size:19
Alignment explanation
Indices: 12834479--12834551 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
12834469 ATATATTATG
12834479 ATTTTA-TTAAATTCATATA
1 ATTTTATTTAAATT-ATATA
***
12834498 AGAATATTTAATATTA-ATA
1 ATTTTATTTAA-ATTATATA
12834517 ATTTTA-TTAAATTATATA
1 ATTTTATTTAAATTATATA
*
12834535 TTTTTA-TTAAATTATAT
1 ATTTTATTTAAATTATAT
12834552 TTAATAATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.09
18 23 0.52
19 9 0.20
20 5 0.11
21 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (19 bp):
ATTTTATTTAAATTATATA
Found at i:12834806 original size:16 final size:16
Alignment explanation
Indices: 12834785--12834838 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
12834775 TTGATTTGCT
*
12834785 ATTACACATTTATTCC
1 ATTACACATCTATTCC
*
12834801 ATTACACCTCTATTCC
1 ATTACACATCTATTCC
* * *
12834817 AATACACCTCTAATCC
1 ATTACACATCTATTCC
*
12834833 AATACA
1 ATTACA
12834839 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACATCTATTCC
Found at i:12838661 original size:41 final size:41
Alignment explanation
Indices: 12838515--12838701 Score: 216
Period size: 41 Copynumber: 4.6 Consensus size: 41
12838505 GACTACACGT
* *
12838515 CTAGCAGGCTAAGTGCCGGTGAATTGAATCAGACTATACGTC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAG-C
** * *
12838557 C-AGCAGGCTAAGTGCCGGTGAGTTGAATCAGGCTACAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
* * *
12838597 CTAGCAAGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
* * *
12838638 CTAGCAGGCTAAGTGCCGGTGAACGGAATTAAACTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
* *
12838679 CTATCAGG-TGAAGTGCCAGTGAA
1 CTAGCAGGCT-AAGTGCCGGTGAA
12838702 TCTGTTTAAA
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
40 3 0.02
41 122 0.97
42 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGACTATAAGC
Found at i:12845310 original size:12 final size:12
Alignment explanation
Indices: 12845293--12845317 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12845283 TACAGAAAAC
12845293 AGACTCATTAAT
1 AGACTCATTAAT
12845305 AGACTCATTAAT
1 AGACTCATTAAT
12845317 A
1 A
12845318 ATTTAAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
AGACTCATTAAT
Done.