Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 196 of 250
Found at i:61211224 original size:58 final size:60
Alignment explanation
Indices: 61211130--61211252 Score: 146
Period size: 58 Copynumber: 2.1 Consensus size: 60
61211120 TCATTCTTTT
* *
61211130 TTTTTTCATTTTCATTTAGGAGAAAACCACATTCA-TTTCTATATGATTC-CATTTATCCA
1 TTTTTTCATTTTCATTTAGGAGAAAACCACAATCATTTTC-AAATGATTCACATTTATCCA
* * * *
61211189 TTTTTT-ATTTTCAGTTT-GGAGAAAACTATAATCATTTTCAAATGTTTCACATTTCTCCA
1 TTTTTTCATTTTCA-TTTAGGAGAAAACCACAATCATTTTCAAATGATTCACATTTATCCA
61211248 TTTTT
1 TTTTT
61211253 ACCATTTCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
58 28 0.51
59 27 0.49
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (60 bp):
TTTTTTCATTTTCATTTAGGAGAAAACCACAATCATTTTCAAATGATTCACATTTATCCA
Found at i:61213800 original size:20 final size:20
Alignment explanation
Indices: 61213756--61213794 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61213746 TATTTTTCAA
* *
61213756 AGTTTAATATTTAGGGTTCG
1 AGTTTAAGATTTAAGGTTCG
61213776 AGTTTAAGATTTAAGGTTC
1 AGTTTAAGATTTAAGGTTC
61213795 ATGTTTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (20 bp):
AGTTTAAGATTTAAGGTTCG
Found at i:61215368 original size:19 final size:18
Alignment explanation
Indices: 61215321--61215412 Score: 71
Period size: 19 Copynumber: 4.9 Consensus size: 18
61215311 TAAAAAAACG
61215321 TAAAAAATCATT-AAAATT
1 TAAAAAAT-ATTAAAAATT
61215339 TAAAAAA-ATTAAAAATT
1 TAAAAAATATTAAAAATT
*
61215356 TAAAAAATTATTAGAAATT
1 TAAAAAA-TATTAAAAATT
* * *
61215375 AATTAAAAATAATAAAATTT
1 --TAAAAAATATTAAAAATT
* *
61215395 TATAAAATTTATAAAAAT
1 TAAAAAATAT-TAAAAAT
61215413 ACTTTATTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
16 3 0.05
17 13 0.22
18 13 0.22
19 15 0.26
20 8 0.14
21 6 0.10
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAAAAATATTAAAAATT
Found at i:61215405 original size:9 final size:9
Alignment explanation
Indices: 61215332--61215410 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
61215322 AAAAAATCAT
61215332 TAAAATTTA
1 TAAAATTTA
* *
61215341 AAAAAATTA
1 TAAAATTTA
61215350 -AAAATTTA
1 TAAAATTTA
*
61215358 -AAAAATTA
1 TAAAATTTA
*
61215366 TTAGAAATTAA
1 -TA-AAATTTA
* *
61215377 TTAAAAATAA
1 -TAAAATTTA
61215387 TAAAATTTTA
1 TAAAA-TTTA
61215397 TAAAATTTA
1 TAAAATTTA
61215406 TAAAA
1 TAAAA
61215411 ATACTTTATT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
8 14 0.25
9 21 0.37
10 14 0.25
11 8 0.14
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (9 bp):
TAAAATTTA
Found at i:61215870 original size:15 final size:16
Alignment explanation
Indices: 61215850--61215884 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
61215840 TTAAAAATTA
61215850 ATTTTAAATTTTTTT-
1 ATTTTAAATTTTTTTG
*
61215865 ATTTTATATTTTTTTG
1 ATTTTAAATTTTTTTG
61215881 ATTT
1 ATTT
61215885 GTCGCCTGTT
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:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
ATTTTAAATTTTTTTG
Found at i:61216790 original size:24 final size:26
Alignment explanation
Indices: 61216750--61216801 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
61216740 AGAATTTTTA
61216750 ATAAAATTTATATATTTTTTAAAAAT
1 ATAAAATTTATATATTTTTTAAAAAT
*
61216776 ATAAAATTTA-A-ATTTTTTATAAAT
1 ATAAAATTTATATATTTTTTAAAAAT
61216800 AT
1 AT
61216802 TTTGAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.56
25 1 0.04
26 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATAAAATTTATATATTTTTTAAAAAT
Found at i:61216811 original size:19 final size:19
Alignment explanation
Indices: 61216789--61216851 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
61216779 AAATTTAAAT
61216789 TTTTTATAAA-TATTTTGAA
1 TTTTTA-AAATTATTTTGAA
*
61216808 TTTTAAAAATTATTTTGAAA
1 TTTTTAAAATTATTTTG-AA
* *
61216828 ATTTGAAAATTATTTTGAA
1 TTTTTAAAATTATTTTGAA
61216847 TTTTT
1 TTTTT
61216852 TTATAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.08
19 17 0.46
20 17 0.46
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTTAAAATTATTTTGAA
Found at i:61216811 original size:20 final size:21
Alignment explanation
Indices: 61216786--61216857 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 21
61216776 ATAAAATTTA
61216786 AATTTTTTATAAA-TATTTTG
1 AATTTTTTATAAATTATTTTG
*
61216806 AA--TTTTAAAAATTATTTTG
1 AATTTTTTATAAATTATTTTG
** *
61216825 AAAATTTGA-AAATTATTTTG
1 AATTTTTTATAAATTATTTTG
61216845 AATTTTTTTATAA
1 AA-TTTTTTATAA
61216858 TTTTTGTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 8 0.19
19 9 0.21
20 15 0.36
21 8 0.19
22 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (21 bp):
AATTTTTTATAAATTATTTTG
Found at i:61221451 original size:207 final size:206
Alignment explanation
Indices: 61220933--61221955 Score: 1244
Period size: 207 Copynumber: 5.0 Consensus size: 206
61220923 TAGTATAGCT
* * * * *
61220933 TGCGACAAATCTTCAATCATATGCCTCATCTTTGACAACTCTT-TTTCTTGGCTTTGA-TTT-TC
1 TGCGACAATTCTTCTATCATACGCCTCATCTCTGACAACT-TTATTTGTTGGCTTTGATTTTCTC
* * * ** *
61220995 -TCTTGACCTTTTATATGTCCATTCATGGCTTAAAAGTGA-TTTCTAATATAAGTTATAGGATCT
65 TTCTTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTTC-AATATAAGTCCTAAGATCT
* * * *
61221058 AATTA-AGCTCTGATACCAAAATTGATGTCGTAAATTATTAGGTTGATTGAAAAACCTAAATAGC
129 AATTAGA-CTCTGATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGGAAAATCTAAATAGC
61221122 TAAAAAAAATTAAAA
193 T-AAAAAAATTAAAA
* * *
61221137 T--GTCAATTCTTCTATCATA-GTCTCATCTCTGACAA-TTCTATTTGTTGGCTTTGATTTGCTC
1 TGCGACAATTCTTCTATCATACGCCTCATCTCTGACAACTT-TATTTGTTGGCTTTGATTTTCTC
* * * *
61221198 TTCATTGATCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTTCAATACAAGTCATAAAATCT
65 TTC-TTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTTCAATATAAGTCCTAAGATCT
* * *
61221263 AATTAGACTCTGATACCAAAATTGATGCGGTAAATTATTAGGCTGAGTGGAAATTCTAAATAGCT
129 AATTAGACTCTGATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGGAAAATCTAAATAGCT
*
61221328 AAAAATATTAAAA
194 AAAAAAATTAAAA
* * *
61221341 TGCGACAATTCTTCTATCATATGCCTCATCTCTGACAACTTTATTTCTTAGCTTTGATTTTCTCT
1 TGCGACAATTCTTCTATCATACGCCTCATCTCTGACAACTTTATTTGTTGGCTTTGATTTTCTCT
* *
61221406 TACTTTACCTCTTGTATGTCCAATCATGGCTTAAAAGTAATTTTCAATATAAGTCCTAAGATCTA
66 T-CTTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTTCAATATAAGTCCTAAGATCTA
* *
61221471 ATTATG-CTCTGATACCAAAAATGATGTGGTAAATTATTAAGTTGAGTGGAAAATCTAAATAGCT
130 ATTA-GACTCTGATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGGAAAATCTAAATAGCT
61221535 AAAAAAATTAAAA
194 AAAAAAATTAAAA
* * * * * *
61221548 TGGGACAATTCTTCTATCATGCGCCTCATCTCTAACCACTCTATTTGTTGGTTTTGATTTTCTCT
1 TGCGACAATTCTTCTATCATACGCCTCATCTCTGACAACTTTATTTGTTGGCTTTGATTTTCTCT
* * * * * *
61221613 TCCTTGACCTCTTGTATGTTCAGTCATGGCTTAAAAGCGATTTCCAATACAAGTCCTAGGATCTA
66 T-CTTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTTCAATATAAGTCCTAAGATCTA
* * * * *
61221678 ATTAGGCTTTGATATCAAAATTGATGTGGTTAATTATTAGGTTGAGTGAAAAATCTAAATAG--A
130 ATTAGACTCTGATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGGAAAATCTAAATAGCTA
61221741 AAAAAATTTTAAAA
195 AAAAAA--TTAAAA
* * * * * *
61221755 TGCGACTATTCTTCTATCATGCCCCTCATCTCTTACAACTCTATTTGTTGGCTTTGATTTTCTTT
1 TGCGACAATTCTTCTATCATACGCCTCATCTCTGACAACTTTATTTGTTGGCTTTGATTTTCTCT
* * * * *
61221820 TCCTTGACCTCTTGTATTTCCAATCATAGCTTAAAAGTGATTTCCAATATAAGTCCTAAGATTTG
66 T-CTTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTTCAATATAAGTCCTAAGATCTA
* * * * * *
61221885 ATTAGGCTTTGATACAAAAAATGATGTGGTAAATTATTAGGTTGAGTGGAAAGTCTAAATTGCTA
130 ATTAGACTCTGATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGGAAAATCTAAATAGCTA
61221950 AAAAAA
195 AAAAAA
61221956 ATAGGAGATA
Statistics
Matches: 713, Mismatches: 87, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
199 1 0.00
200 2 0.00
201 27 0.04
202 17 0.02
203 2 0.00
204 16 0.02
205 111 0.16
206 23 0.03
207 503 0.71
208 4 0.01
209 7 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (206 bp):
TGCGACAATTCTTCTATCATACGCCTCATCTCTGACAACTTTATTTGTTGGCTTTGATTTTCTCT
TCTTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTTCAATATAAGTCCTAAGATCTAA
TTAGACTCTGATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTGGAAAATCTAAATAGCTAA
AAAAATTAAAA
Found at i:61227883 original size:11 final size:11
Alignment explanation
Indices: 61227852--61227876 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61227842 CAGTTTCAAT
61227852 AGTGTTTTTTG
1 AGTGTTTTTTG
61227863 AGTGTTTTTTG
1 AGTGTTTTTTG
61227874 AGT
1 AGT
61227877 TATTTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (11 bp):
AGTGTTTTTTG
Found at i:61230439 original size:37 final size:39
Alignment explanation
Indices: 61230397--61230472 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 39
61230387 AAGGCAAAAT
* * *
61230397 TGACATTATATATTTT-TAA-TTATATTTTAAAATTTAA
1 TGACATTATATATTTTCAAAGTAATATATTAAAATTTAA
61230434 TGACATTATATATTTTCAAAGTAATATATTAAAATTTAA
1 TGACATTATATATTTTCAAAGTAATATATTAAAATTTAA
61230473 CAAATTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 16 0.47
38 2 0.06
39 16 0.47
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (39 bp):
TGACATTATATATTTTCAAAGTAATATATTAAAATTTAA
Found at i:61232590 original size:23 final size:23
Alignment explanation
Indices: 61232555--61232607 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
61232545 AAAATTATAC
* *
61232555 CATCTTGGGTCTTACCATTTTCT
1 CATCTTTGGTCTTACCATTTGCT
* *
61232578 CATCTTTGTTCTTACTATTTGCT
1 CATCTTTGGTCTTACCATTTGCT
*
61232601 TATCTTT
1 CATCTTT
61232608 ATTATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.09, T:0.55
Consensus pattern (23 bp):
CATCTTTGGTCTTACCATTTGCT
Found at i:61239511 original size:129 final size:132
Alignment explanation
Indices: 61239203--61239621 Score: 338
Period size: 131 Copynumber: 3.2 Consensus size: 132
61239193 GGCAATCGTG
* * * * ** * * * *
61239203 GAATCGTGCCCTAAT-GTGCTGGGTTGCAATTTCTCGTTTGCTTAAAATAATCAAATATCCCTCC
1 GAATCGTGCCCT-ATCGTGCTGGGTTGCGACTTCTCATTCGCCCAAAACAATCGAAGATCCCTTC
* * * * * * * * * * * * *
61239267 AAAATTTCACGCATGTCTTCTAAAAATCATTTAAAACGAAGGCAA-TATTCGGTGATTGACAATT
65 GAAGTTTCACTCACGTTTTCTAAAAACCCTTTAAAACGAAAG-AAGTGTTCGATGTTTGGCAGTT
61239331 CGG-
129 CGGA
* * * * * * * *
61239334 GAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGCTCAAAACAATCGAATATTCCTT-T
1 GAATCGTGCCCTATCGTGCTGGGTTGCGACTTCTCATTCGCCCAAAACAATCGAAGATCCCTTCG
* * *
61239398 AGGTTTTCACTCATGTTTAT-TAAAAA-CCTTTCAAAAC-AAAGGA-TGTTCGATGTTTGGC-GA
66 AAG-TTTCACTCACGTTT-TCTAAAAACCCTTT-AAAACGAAAGAAGTGTTCGATGTTTGGCAG-
*
61239458 TT-TGA
127 TTCGGA
* *
61239463 GAATCGTGCCCTATCGTGCTGGGTTGCG-CTTTTTCATTCGCCCTAAACAATCGAAGATCCCTTC
1 GAATCGTGCCCTATCGTGCTGGGTTGCGAC-TTCTCATTCGCCCAAAACAATCGAAGATCCCTTC
*
61239527 GAAGTTTCATTCACGTTTTCTAAAAACCCTTTAAAACGAAAGAAGTGTTCGATGTTTGGCAGTTC
65 GAAGTTTCACTCACGTTTTCTAAAAACCCTTTAAAACGAAAGAAGTGTTCGATGTTTGGCAGTTC
*
61239592 GGG
130 GGA
*
61239595 GAATAGTGCCCTATCGTGCTGGGTTGC
1 GAATCGTGCCCTATCGTGCTGGGTTGC
61239622 AATCTCCTGT
Statistics
Matches: 234, Mismatches: 40, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
128 3 0.01
129 89 0.38
130 22 0.09
131 91 0.39
132 29 0.12
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (132 bp):
GAATCGTGCCCTATCGTGCTGGGTTGCGACTTCTCATTCGCCCAAAACAATCGAAGATCCCTTCG
AAGTTTCACTCACGTTTTCTAAAAACCCTTTAAAACGAAAGAAGTGTTCGATGTTTGGCAGTTCG
GA
Found at i:61241567 original size:5 final size:5
Alignment explanation
Indices: 61241557--61241587 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
61241547 TATTAATATT
61241557 TTATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T
61241588 ATAACAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:61242209 original size:29 final size:30
Alignment explanation
Indices: 61242150--61242207 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
61242140 TCCGAGCCTT
**
61242150 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATAAAAAAGTTTA
* *
61242180 GGGGCAAAATTGTAATTTTAAAAAAGTT
1 GGGGCAAAAATGTAATTATAAAAAAGTT
61242208 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATAAAAAAGTTTA
Found at i:61242437 original size:13 final size:13
Alignment explanation
Indices: 61242419--61242450 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
61242409 TTTTCAGCAA
61242419 TTATGAATTTATT
1 TTATGAATTTATT
61242432 TTATGAATTTATT
1 TTATGAATTTATT
*
61242445 TGATGA
1 TTATGA
61242451 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:61242658 original size:50 final size:50
Alignment explanation
Indices: 61242545--61242786 Score: 288
Period size: 50 Copynumber: 4.7 Consensus size: 50
61242535 ATTTGGGTAA
* * * *
61242545 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAATATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
61242601 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
61242651 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
61242701 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
61242751 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
61242787 TTTGGCATGT
Statistics
Matches: 165, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.18
52 1 0.01
53 2 0.01
55 2 0.01
56 39 0.24
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:61242734 original size:100 final size:103
Alignment explanation
Indices: 61242545--61242794 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
61242535 ATTTGGGTAA
*
61242545 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAATATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
61242610 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
61242651 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
61242713 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
61242751 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
61242795 GTTATTATCA
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.39
101 38 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:61244567 original size:26 final size:26
Alignment explanation
Indices: 61244520--61244593 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
61244510 TTTCTCACCC
**
61244520 CAATTTTACCGTA-GTAAAATTTTGA
1 CAATTTTACCCCAGGTAAAATTTTGA
*
61244545 TAATTTTACCCCAGGTAAAATTTTGA
1 CAATTTTACCCCAGGTAAAATTTTGA
* * *
61244571 CGATTTTACCCCTGATAAAATTT
1 CAATTTTACCCCAGGTAAAATTT
61244594 CGAGAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 10 0.24
26 31 0.76
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (26 bp):
CAATTTTACCCCAGGTAAAATTTTGA
Found at i:61244754 original size:12 final size:12
Alignment explanation
Indices: 61244737--61244770 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
61244727 GGATTGTAAG
61244737 TTTCCATTTTCA
1 TTTCCATTTTCA
*
61244749 TTTCCATTTCCA
1 TTTCCATTTTCA
*
61244761 TTTTCATTTT
1 TTTCCATTTT
61244771 TGGAAACCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTCCATTTTCA
Found at i:61246938 original size:21 final size:20
Alignment explanation
Indices: 61246913--61246959 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
61246903 CTAAAATGTG
*
61246913 AATTTAATTGAATTGAATATA
1 AATTTAATTAAATTGAAT-TA
* *
61246934 AATTTTATTAAATTGAGTTA
1 AATTTAATTAAATTGAATTA
61246954 AATTTA
1 AATTTA
61246960 CCCGTATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (20 bp):
AATTTAATTAAATTGAATTA
Found at i:61247435 original size:26 final size:26
Alignment explanation
Indices: 61247395--61247469 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
61247385 ACAACACTTA
* * *
61247395 TGAGCGTCTCAATTAAAGGCTCTTTG
1 TGAGCGTCCCGATTAATGGCTCTTTG
*
61247421 TGAGCGTCCCGATTAATGGCTCTCTG
1 TGAGCGTCCCGATTAATGGCTCTTTG
* * *
61247447 -AAGCTTCCTGATTAATGGCTCTT
1 TGAGCGTCCCGATTAATGGCTCTT
61247470 CAGAGCTACC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 19 0.46
26 22 0.54
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (26 bp):
TGAGCGTCCCGATTAATGGCTCTTTG
Found at i:61247476 original size:25 final size:24
Alignment explanation
Indices: 61247422--61247516 Score: 86
Period size: 25 Copynumber: 3.9 Consensus size: 24
61247412 GGCTCTTTGT
* *
61247422 GAGCGTCCCGATTAATGGCTCTCT
1 GAGCTTCCCGATTAATGGCTCTCA
*
61247446 GAAGCTTCCTGATTAATGGCTCTTCA
1 G-AGCTTCCCGATTAATGGCTC-TCA
* * *
61247472 GAGCTACCCG-TTATTGGCTCACA
1 GAGCTTCCCGATTAATGGCTCTCA
*
61247495 TGAGCTTCTCGATT-ATGGCTCT
1 -GAGCTTCCCGATTAATGGCTCT
61247517 TATGAGTTTC
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
23 2 0.04
24 24 0.43
25 27 0.48
26 3 0.05
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGATTAATGGCTCTCA
Found at i:61247521 original size:24 final size:25
Alignment explanation
Indices: 61247391--61247527 Score: 93
Period size: 24 Copynumber: 5.5 Consensus size: 25
61247381 CACCACAACA
* * * *
61247391 CTTATGAGCGTCTCAATTAAAGGCT
1 CTTATGAGCTTCCCGATTAATGGCT
* *
61247416 CTTTGTGAGCGTCCCGATTAATGGCT
1 C-TTATGAGCTTCCCGATTAATGGCT
* *
61247442 C-TCTGAAGCTTCCTGATTAATGGCT
1 CTTATG-AGCTTCCCGATTAATGGCT
* *
61247467 CTTCA-GAGCTACCCG-TTATTGGCT
1 CTT-ATGAGCTTCCCGATTAATGGCT
** *
61247491 CACATGAGCTTCTCGATT-ATGGCT
1 CTTATGAGCTTCCCGATTAATGGCT
*
61247515 CTTATGAGTTTCC
1 CTTATGAGCTTCC
61247528 TGTTATACAA
Statistics
Matches: 86, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
23 1 0.01
24 34 0.40
25 28 0.33
26 23 0.27
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (25 bp):
CTTATGAGCTTCCCGATTAATGGCT
Found at i:61247577 original size:25 final size:25
Alignment explanation
Indices: 61247421--61247589 Score: 71
Period size: 25 Copynumber: 6.8 Consensus size: 25
61247411 AGGCTCTTTG
* *
61247421 TGAGCGTCCCGATTA-ATGGCTCTC-
1 TGAGCTTCCCG-TTATATGGCTCACA
* *
61247445 TGAAGCTTCCTGATTA-ATGGCTCTTCA
1 TG-AGCTTCCCG-TTATATGGCTC-ACA
*
61247472 -GAGCTACCCGTTAT-TGGCTCACA
1 TGAGCTTCCCGTTATATGGCTCACA
* * **
61247495 TGAGCTTCTCGAT-TATGGCTCTTA
1 TGAGCTTCCCGTTATATGGCTCACA
* * *** * **
61247519 TGAGTTTCCTGTTATACAACCCGGA
1 TGAGCTTCCCGTTATATGGCTCACA
*
61247544 TAAGCTTCCCGTTATATGGCTCACA
1 TGAGCTTCCCGTTATATGGCTCACA
* * *
61247569 TGAGTTTCCCATTATTTGGCT
1 TGAGCTTCCCGTTATATGGCT
61247590 AGAGAGAGGG
Statistics
Matches: 105, Mismatches: 33, Indels: 13
0.70 0.22 0.09
Matches are distributed among these distances:
23 3 0.03
24 36 0.34
25 63 0.60
26 3 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGTTATATGGCTCACA
Found at i:61248580 original size:13 final size:13
Alignment explanation
Indices: 61248562--61248594 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
61248552 ACACACGGGA
61248562 GTGTGACTTGGCC
1 GTGTGACTTGGCC
61248575 GTGTGACTTGGCC
1 GTGTGACTTGGCC
61248588 GTGTGAC
1 GTGTGAC
61248595 CTAAGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.39, T:0.30
Consensus pattern (13 bp):
GTGTGACTTGGCC
Found at i:61262827 original size:16 final size:17
Alignment explanation
Indices: 61262806--61262843 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
61262796 TATTTTATAC
61262806 TTTCCT-TTCTCTTATT
1 TTTCCTATTCTCTTATT
*
61262822 TTTCCTATTCTTTTATT
1 TTTCCTATTCTCTTATT
61262839 TTTCC
1 TTTCC
61262844 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCCTATTCTCTTATT
Found at i:61262869 original size:10 final size:9
Alignment explanation
Indices: 61262846--61262892 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 9
61262836 ATTTTTCCAT
61262846 AAATAAATA
1 AAATAAATA
61262855 GAAATAGAA-A
1 -AAATA-AATA
61262865 TAAATAATATA
1 -AAATAA-ATA
61262876 AAATAAATA
1 AAATAAATA
61262885 AAATAAAT
1 AAATAAAT
61262893 TTAAATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
9 12 0.36
10 18 0.55
11 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (9 bp):
AAATAAATA
Found at i:61263196 original size:6 final size:6
Alignment explanation
Indices: 61263185--61263218 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
61263175 ATTTATTTAC
*
61263185 AAAAAG AAAAAG AAAAAG AAAAAG AAAGAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
61263219 GAGTAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:61275369 original size:12 final size:12
Alignment explanation
Indices: 61275352--61275376 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61275342 AAATAAAAGG
61275352 ATTAAATCGCTT
1 ATTAAATCGCTT
61275364 ATTAAATCGCTT
1 ATTAAATCGCTT
61275376 A
1 A
61275377 AAAGTTTAGG
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTAAATCGCTT
Found at i:61276993 original size:41 final size:41
Alignment explanation
Indices: 61276827--61276982 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
61276817 TTTATCGTTA
* * * *
61276827 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
61276868 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
61276909 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
61276950 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
61276983 AAGAGCCGGT
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 102 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:61277253 original size:33 final size:33
Alignment explanation
Indices: 61277197--61277294 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
61277187 ATAGATATGT
*
61277197 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
61277229 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
61277262 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
61277295 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:61283980 original size:21 final size:23
Alignment explanation
Indices: 61283934--61283981 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
61283924 TGGATGAAAT
61283934 ATAATTAAAAATATGATAGTTGAA
1 ATAATTAAAAATATGA-AGTTGAA
*
61283958 ATAATTAAAAGTATG-AG-TGAA
1 ATAATTAAAAATATGAAGTTGAA
61283979 ATA
1 ATA
61283982 TATATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
24 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (23 bp):
ATAATTAAAAATATGAAGTTGAA
Found at i:61284628 original size:41 final size:41
Alignment explanation
Indices: 61284462--61284617 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
61284452 TTTATCGTTA
* * * *
61284462 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
61284503 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
61284544 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
61284585 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
61284618 AAGAGCCGGT
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 102 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:61284888 original size:33 final size:33
Alignment explanation
Indices: 61284832--61284929 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
61284822 ATAGATATGT
*
61284832 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
61284864 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
61284897 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
61284930 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:61288385 original size:9 final size:9
Alignment explanation
Indices: 61288371--61288483 Score: 100
Period size: 9 Copynumber: 11.9 Consensus size: 9
61288361 ATGTATTAGT
61288371 TAAGTTATG
1 TAAGTTATG
61288380 TAAGTTGTTATG
1 TAA---GTTATG
*
61288392 TACGTTATG
1 TAAGTTATG
*
61288401 TGAGTTATG
1 TAAGTTATG
*
61288410 TAAATTATG
1 TAAGTTATG
61288419 TAAGTTATG
1 TAAGTTATG
*
61288428 TAAATTATG
1 TAAGTTATG
61288437 TAAGTTGTTATG
1 TAA---GTTATG
* *
61288449 TAAATTACG
1 TAAGTTATG
*
61288458 TAAGTTATA
1 TAAGTTATG
*
61288467 TGAGTTATG
1 TAAGTTATG
61288476 TAAGTTAT
1 TAAGTTAT
61288484 ATAATTTATT
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
9 66 0.80
12 16 0.20
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:61288439 original size:57 final size:57
Alignment explanation
Indices: 61288375--61288492 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 57
61288365 ATTAGTTAAG
** * * * *
61288375 TTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATGTAAA
1 TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATATAAA
* * *
61288432 TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATGAGTTATGTAAGTTATATAAT
1 TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATATAAA
61288489 TTAT
1 TTAT
61288493 TGAAGTAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (57 bp):
TTATGTAAGTTGTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTTATATAAA
Found at i:61288447 original size:39 final size:39
Alignment explanation
Indices: 61288404--61288481 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
61288394 CGTTATGTGA
* *
61288404 GTTATGTAAATTATGTAAGTTATGTAAATTATGTAAGTT
1 GTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTT
* *
61288443 GTTATGTAAATTACGTAAGTTATATGAGTTATGTAAGTT
1 GTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTT
61288482 ATATAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (39 bp):
GTTATGTAAATTACGTAAGTTATATAAATTATGTAAGTT
Found at i:61292206 original size:158 final size:156
Alignment explanation
Indices: 61291922--61292263 Score: 354
Period size: 158 Copynumber: 2.2 Consensus size: 156
61291912 CACTAATGTT
*
61291922 TTTTGCGGCGTTTATT-TAAAAAACGCCGCTAATCCCTATATACTCAACTAAAACGACGACGTGT
1 TTTTGCGGCGTTT-TTAT-AAAAACGCCGCAAATCCCTATATACTCAACTAAAACGACGACGTGT
* * * **
61291986 ACTATAAACTTGAATTATTTTGCGGCGTTTTTGAAAGTGCCACTAATACCCGTATATACTAAAAC
64 ACCATAAACTTGAATTATGTTGCGGCGTTTTTAAAAACGCCACTAATACCCGTATATACTAAAAC
** *
61292051 GGTGCCGTTTTCGTTAAACTA-ATCTGTA
129 GACGCCGTTTTCGTTAAACTATA-CTATA
* * *
61292079 TTTTGTGGCGTTTTCTATAAAAACGCCGCAAATCCCCTATATATTGAACTAAAACGACGACGCT-
1 TTTTGCGGCGTTTT-TATAAAAACGCCGCAAAT-CCCTATATACTCAACTAAAACGACGACG-TG
* * * * * *
61292143 T-CCAGTACACTTTACTTCTGTTGCGGCGTTTTTAAAAACGCCACTAGTACTC-TATCA-ATCTA
63 TACCA-TAAACTTGAATTATGTTGCGGCGTTTTTAAAAACGCCACTAATACCCGTAT-ATA-CTA
* * *
61292205 AAACGACGCCGTTTTCTTTCAACTATACTATT
125 AAACGACGCCGTTTTCGTTAAACTATACTATA
*
61292237 TTTTGCGGCGTTTTTTTAAAAAACGCC
1 TTTTGCGGCGTTTTTAT-AAAAACGCC
61292264 ACTAATCTCT
Statistics
Matches: 153, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
156 1 0.01
157 35 0.23
158 115 0.75
159 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (156 bp):
TTTTGCGGCGTTTTTATAAAAACGCCGCAAATCCCTATATACTCAACTAAAACGACGACGTGTAC
CATAAACTTGAATTATGTTGCGGCGTTTTTAAAAACGCCACTAATACCCGTATATACTAAAACGA
CGCCGTTTTCGTTAAACTATACTATA
Found at i:61293260 original size:14 final size:14
Alignment explanation
Indices: 61293240--61293284 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
61293230 TCCTACACCT
61293240 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
61293254 TATACCCTAAA-TCA
1 TAAACCCTAAACT-A
61293268 TAAACCCTAAACTA
1 TAAACCCTAAACTA
61293282 TAA
1 TAA
61293285 TGATAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:61293569 original size:7 final size:7
Alignment explanation
Indices: 61293557--61293652 Score: 86
Period size: 7 Copynumber: 13.7 Consensus size: 7
61293547 AAAAATGCCA
61293557 CTAAACC
1 CTAAACC
61293564 CTAAACC
1 CTAAACC
61293571 CTAAACC
1 CTAAACC
*
61293578 CTAAACT
1 CTAAACC
61293585 CTAAACC
1 CTAAACC
*
61293592 CTTAACC
1 CTAAACC
*
61293599 CTTAACC
1 CTAAACC
*
61293606 CCAAACAC
1 CTAAAC-C
* * *
61293614 TTACACT
1 CTAAACC
* *
61293621 TTAAACT
1 CTAAACC
61293628 CT-AACC
1 CTAAACC
*
61293634 CTAACCC
1 CTAAACC
61293641 CTAAACC
1 CTAAACC
61293648 CTAAA
1 CTAAA
61293653 TCACAATCCC
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
6 5 0.07
7 64 0.88
8 4 0.05
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:61293581 original size:21 final size:21
Alignment explanation
Indices: 61293557--61293669 Score: 86
Period size: 21 Copynumber: 5.4 Consensus size: 21
61293547 AAAAATGCCA
61293557 CTAAACCCTAAACCCTAAACC
1 CTAAACCCTAAACCCTAAACC
* *
61293578 CTAAACTCTAAACCCTTAACC
1 CTAAACCCTAAACCCTAAACC
* * * * *
61293599 CTTAACCCCAAACACTTACACT
1 CTAAACCCTAAAC-CCTAAACC
* * *
61293621 TTAAACTCT-AACCCTAACCC
1 CTAAACCCTAAACCCTAAACC
* *
61293641 CTAAACCCTAAATCAC-AATCC
1 CTAAACCCTAAA-CCCTAAACC
61293662 CTAAACCC
1 CTAAACCC
61293670 ATAATTCATC
Statistics
Matches: 68, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
20 11 0.16
21 46 0.68
22 11 0.16
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (21 bp):
CTAAACCCTAAACCCTAAACC
Found at i:61293749 original size:46 final size:46
Alignment explanation
Indices: 61293696--61293831 Score: 245
Period size: 46 Copynumber: 3.0 Consensus size: 46
61293686 CTTCAAATAC
* *
61293696 TAGTTAACTCCTAAACCTTAAACCCTAAACTATATATCTTAAACTT
1 TAGTTAACTCATAAACCTTAAACCCTAAACTATATATCTTAAACTA
61293742 TAGTTAACTCATAAACCTTAAACCCTAAACTATATATCTTAAACTA
1 TAGTTAACTCATAAACCTTAAACCCTAAACTATATATCTTAAACTA
*
61293788 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
1 TAGTTAACTCATAAACCTTAAACCCTAAACTATATATCTTAAAC
61293832 CATAAACCAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACTATATATCTTAAACTA
Found at i:61293811 original size:7 final size:7
Alignment explanation
Indices: 61293797--61293845 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
61293787 ATAGTTAACT
61293797 CATAAAC
1 CATAAAC
*
61293804 CTTAAAC
1 CATAAAC
*
61293811 CCTAAAC
1 CATAAAC
* *
61293818 CATATAT
1 CATAAAC
*
61293825 CTTAAAC
1 CATAAAC
61293832 CATAAAC
1 CATAAAC
61293839 CATAAAC
1 CATAAAC
61293846 TATAGTGATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
CATAAAC
Found at i:61294068 original size:41 final size:41
Alignment explanation
Indices: 61294007--61294216 Score: 264
Period size: 41 Copynumber: 5.1 Consensus size: 41
61293997 GTTATATGAC
* *
61294007 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGAGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
61294048 TTTTAGCGGAGTTTTTCCAAAAGCGCCACTAATGCTCTGGT
1 TTTTAGCGGAGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
61294089 TTTTAGCGGGGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGAGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * * * *
61294130 TTTTAGCGGCGTTTTGCCAGAAGCACCGCTAATGCTCT-AT
1 TTTTAGCGGAGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * * *
61294170 TTTTTGCGGCATTTTTTACTAAAA-CGCCGCTATTGCTCT-GT
1 TTTTAGCGG-AGTTTTT-CCAAAAGCGCCGCTAATGCTCTGGT
61294211 TTTTAG
1 TTTTAG
61294217 TGGCATTTTT
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 9 0.06
41 134 0.91
42 4 0.03
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGAGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:61294255 original size:123 final size:123
Alignment explanation
Indices: 61294007--61294255 Score: 290
Period size: 123 Copynumber: 2.0 Consensus size: 123
61293997 GTTATATGAC
* *
61294007 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGAGTTTTTCCAAAAGC
1 TTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTCTGATTTTTAGCGGAGTTTTTCCAAAAGC
** *
61294072 GCCACTAATGCTCTGGTTTTTAGCGGGGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
66 GCCACTAATGCTCTGGTTTTTAGCGGCATTTTTCCAAAAGCGCCGCTAATGCTATGGT
* * * * *
61294130 TTTTAGCGGCGTTTTGCCAGAAGCACCGCTAATGCTCT-ATTTTTTGCGGCATTTTTTACTAAAA
1 TTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTCTGATTTTTAGCGG-AGTTTTT-CCAAAA
* * * ** *
61294194 -CGCCGCTATTGCTCT-GTTTTTAGTGGCATTTTTGGTAAAA-CGCCGCTATTGCTATGTGT
64 GCGCCACTAATGCTCTGGTTTTTAGCGGCATTTTT-CCAAAAGCGCCGCTAATGCTATG-GT
61294253 TTT
1 TTT
61294256 ACAATTTTTG
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
122 38 0.36
123 63 0.59
124 5 0.05
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (123 bp):
TTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTCTGATTTTTAGCGGAGTTTTTCCAAAAGC
GCCACTAATGCTCTGGTTTTTAGCGGCATTTTTCCAAAAGCGCCGCTAATGCTATGGT
Found at i:61294295 original size:12 final size:12
Alignment explanation
Indices: 61294280--61294305 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61294270 GTTTTTTGAT
61294280 AAAACGCCGCTA
1 AAAACGCCGCTA
61294292 AAAACGCCGCTA
1 AAAACGCCGCTA
61294304 AA
1 AA
61294306 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:61294387 original size:25 final size:25
Alignment explanation
Indices: 61294359--61294438 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
61294349 CCATAACTCA
*
61294359 TATGAGCTTCTAGATTTACAGCTCG
1 TATGAGCTTCTCGATTTACAGCTCG
* **
61294384 TATGAACTTCTCGATTTGTAGCTCG
1 TATGAGCTTCTCGATTTACAGCTCG
* * * *
61294409 TTTGAGCTTCCCGATTCACAGCTTG
1 TATGAGCTTCTCGATTTACAGCTCG
61294434 TATGA
1 TATGA
61294439 ACATACATGA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (25 bp):
TATGAGCTTCTCGATTTACAGCTCG
Found at i:61303497 original size:17 final size:18
Alignment explanation
Indices: 61303475--61303516 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
61303465 GATACGATAT
61303475 AATAAAATGAAT-AAAG-A
1 AATAAAAT-AATCAAAGAA
61303492 AATAAAA-AATCAAAGAA
1 AATAAAATAATCAAAGAA
61303509 AATAAAAT
1 AATAAAAT
61303517 TATAAGTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 4 0.18
17 15 0.68
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (18 bp):
AATAAAATAATCAAAGAA
Found at i:61304484 original size:28 final size:29
Alignment explanation
Indices: 61304429--61304484 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
61304419 TACTTCTTTC
*
61304429 ATTAAATATAATTAAACATTTTGTTCATA
1 ATTAAATATAATTAAACATTTTATTCATA
*
61304458 ATTAAATATAATT-TACATTTTATTCAT
1 ATTAAATATAATTAAACATTTTATTCAT
61304485 TTTAGTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTAAATATAATTAAACATTTTATTCATA
Found at i:61312869 original size:19 final size:18
Alignment explanation
Indices: 61312834--61312885 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
61312824 TAAATTATTA
61312834 TTTAATAATTACAATAT-TT
1 TTTAA-AATTA-AATATGTT
61312853 GTTTAAAATTAATATATGTT
1 -TTTAAAATTAA-ATATGTT
*
61312873 TTTAATATTAAAT
1 TTTAAAATTAAAT
61312886 GAAAAGTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 3 0.10
19 19 0.66
20 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
TTTAAAATTAAATATGTT
Found at i:61324433 original size:25 final size:26
Alignment explanation
Indices: 61324405--61324453 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
61324395 TTTATTTATT
61324405 AAAATAATATAA-AAAATTAATTACA
1 AAAATAATATAACAAAATTAATTACA
* *
61324430 AAAATGATATAACTAAATTAATTA
1 AAAATAATATAACAAAATTAATTA
61324454 TAAATATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATAATATAACAAAATTAATTACA
Found at i:61325490 original size:30 final size:30
Alignment explanation
Indices: 61325430--61325491 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
61325420 AGTTTATATA
* *
61325430 TTTATAATTTTTAAAAGATTAAATTAAATT
1 TTTATAATTTTTAAAAGAGTAAAGTAAATT
* *
61325460 TTTATTATTTTTAAGAG-GTAAAGTATAATT
1 TTTATAATTTTTAAAAGAGTAAAGTA-AATT
61325490 TT
1 TT
61325492 ACTTTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (30 bp):
TTTATAATTTTTAAAAGAGTAAAGTAAATT
Found at i:61326871 original size:147 final size:147
Alignment explanation
Indices: 61326604--61326901 Score: 560
Period size: 147 Copynumber: 2.0 Consensus size: 147
61326594 GGGTAAAGTA
61326604 CAAAAATGGTCACTAAAATATTCAAAATTAAACTTTTTTGTTCACCTACCATTAACACTCATTTG
1 CAAAAATGGTCACTAAAATATTCAAAATTAAACTTTTTTGTTCACCTACCATTAACACTCATTTG
*
61326669 TAAATTGACAGAAGTGTTGACGTGAAATTTTTTATTATTAATCTAATAATAAATTTAGTTTTTTT
66 TAAATTGACAGAAGTGTTGACGTGAAATTTTTTATTATTAATCTAATAATAAATTTAGTTTTTTA
61326734 AAATTTACACATTATAT
131 AAATTTACACATTATAT
61326751 CAAAAATGGTCACTAAAATATTCAAAATTAAACTTTTTTGTTCACCTACCATTAACACTCATTTG
1 CAAAAATGGTCACTAAAATATTCAAAATTAAACTTTTTTGTTCACCTACCATTAACACTCATTTG
* * *
61326816 TAATTTGACGGAAGTGTTGACGTGAAATTTTTTATTATTAGTCTAATAATAAATTTAGTTTTTTA
66 TAAATTGACAGAAGTGTTGACGTGAAATTTTTTATTATTAATCTAATAATAAATTTAGTTTTTTA
61326881 AAATTTACACATTATAT
131 AAATTTACACATTATAT
61326898 CAAA
1 CAAA
61326902 TTGATTTTAA
Statistics
Matches: 147, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (147 bp):
CAAAAATGGTCACTAAAATATTCAAAATTAAACTTTTTTGTTCACCTACCATTAACACTCATTTG
TAAATTGACAGAAGTGTTGACGTGAAATTTTTTATTATTAATCTAATAATAAATTTAGTTTTTTA
AAATTTACACATTATAT
Found at i:61331141 original size:66 final size:66
Alignment explanation
Indices: 61331035--61331167 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
61331025 GTTACATTAC
61331035 TTCTTGTTCTGTTTCTCTGTTTTCGATTCGTACTTGGGAATTTCATTATGCTCTTTTCCTATTGT
1 TTCTTGTTCTGTTTCTCTGTTTTCGATTCGTACTTGGGAATTTCATTATGCTCTTTTCCTATTGT
61331100 A
66 A
61331101 TTCTTGTTCTGTTTCTCTGTTTTCGATTCGTACTTGGGAATTTCATTATGCTCTTTTCCTATTGT
1 TTCTTGTTCTGTTTCTCTGTTTTCGATTCGTACTTGGGAATTTCATTATGCTCTTTTCCTATTGT
61331166 A
66 A
61331167 T
1 T
61331168 AGGCCTGGTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.12, C:0.18, G:0.15, T:0.55
Consensus pattern (66 bp):
TTCTTGTTCTGTTTCTCTGTTTTCGATTCGTACTTGGGAATTTCATTATGCTCTTTTCCTATTGT
A
Found at i:61331216 original size:4 final size:4
Alignment explanation
Indices: 61331202--61331234 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
61331192 TTAGTAGTAA
61331202 TATT ATATT TATT TATT TATT TATT TATT TATT
1 TATT -TATT TATT TATT TATT TATT TATT TATT
61331235 CAGGTGACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:61332998 original size:23 final size:23
Alignment explanation
Indices: 61332971--61333026 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 23
61332961 TATTTCATGC
61332971 TATTTTTTTAA-AAATATTTTAAG
1 TATTTTTTTAATAAAT-TTTTAAG
*
61332994 TATTTTTTTAATTTTAATTTTTAAG
1 TATTTTTTTAA--TAAATTTTTAAG
61333019 TATTTTTT
1 TATTTTTT
61333027 AATTTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.38
25 15 0.52
26 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (23 bp):
TATTTTTTTAATAAATTTTTAAG
Found at i:61333050 original size:25 final size:25
Alignment explanation
Indices: 61332987--61333038 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
61332977 TTTAAAAATA
61332987 TTTTAAGTATTTTTTTAATTTTAAT
1 TTTTAAGTATTTTTTTAATTTTAAT
61333012 TTTTAAGTA-TTTTTTAATTTTAAT
1 TTTTAAGTATTTTTTTAATTTTAAT
61333036 TTT
1 TTT
61333039 ACTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTAAGTATTTTTTTAATTTTAAT
Found at i:61350223 original size:11 final size:11
Alignment explanation
Indices: 61350207--61350252 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
61350197 TTCTTTATAT
61350207 ATTTTTTTGAA
1 ATTTTTTTGAA
61350218 ATTTTTTTG-A
1 ATTTTTTTGAA
61350228 ATTTTTTAT-AA
1 ATTTTTT-TGAA
*
61350239 A-TATTTTGAA
1 ATTTTTTTGAA
61350249 ATTT
1 ATTT
61350253 AAAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
9 1 0.03
10 15 0.52
11 13 0.45
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
ATTTTTTTGAA
Found at i:61350581 original size:20 final size:19
Alignment explanation
Indices: 61350539--61350581 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
61350529 TAATAGTGTT
61350539 ATAATTTTATTTATTAATTA
1 ATAATTTTATTTATTAA-TA
61350559 ATAATTTTAATATTATTAA-A
1 ATAATTTT-AT-TTATTAATA
61350579 ATA
1 ATA
61350582 TTAATCATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 12 0.57
21 2 0.10
22 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATTTTATTTATTAATA
Found at i:61351052 original size:17 final size:20
Alignment explanation
Indices: 61351032--61351076 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
61351022 ACTATTTAAT
61351032 TAAATAA-AT-TTA-TTTTA
1 TAAATAATATATTAGTTTTA
*
61351049 TAAAATAATGTATTAGTTTTA
1 T-AAATAATATATTAGTTTTA
61351070 TAAATAA
1 TAAATAA
61351077 GAATTCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 6 0.26
19 1 0.04
20 9 0.39
21 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAATAATATATTAGTTTTA
Found at i:61352754 original size:18 final size:20
Alignment explanation
Indices: 61352728--61352768 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
61352718 GAAATATTTA
*
61352728 TTTTGATGT-TTTTA-GTAT
1 TTTTGATGTATTATATGTAT
*
61352746 TTTTTATGTATTATATGTAT
1 TTTTGATGTATTATATGTAT
61352766 TTT
1 TTT
61352769 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (20 bp):
TTTTGATGTATTATATGTAT
Found at i:61352799 original size:12 final size:12
Alignment explanation
Indices: 61352769--61352801 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
61352759 TATGTATTTT
61352769 AAAATT-ATATA
1 AAAATTAATATA
61352780 AAAA-TAATATA
1 AAAATTAATATA
61352791 AAAATTAATAT
1 AAAATTAATAT
61352802 TGGTAGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:61359444 original size:18 final size:18
Alignment explanation
Indices: 61359418--61359453 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61359408 GATATTTTTA
*
61359418 TTTTCATTTAATTGAATT
1 TTTTAATTTAATTGAATT
*
61359436 TTTTAATTTAATTTAATT
1 TTTTAATTTAATTGAATT
61359454 AAAATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTAATTTAATTGAATT
Found at i:61368698 original size:6 final size:6
Alignment explanation
Indices: 61368677--61368710 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
61368667 AACCCTAATA
*
61368677 ACCTAT A-CTAT GCCTAT ACCTAT ACCTAT ACCTA
1 ACCTAT ACCTAT ACCTAT ACCTAT ACCTAT ACCTA
61368711 ACCCAGTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (6 bp):
ACCTAT
Found at i:61370912 original size:22 final size:21
Alignment explanation
Indices: 61370869--61370916 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
61370859 TAAGGGTTTT
61370869 ATAATTTTATAAAAATATTTA
1 ATAATTTTATAAAAATATTTA
* *
61370890 ACTAATTTT-TAGAATTATATTA
1 A-TAATTTTATAAAAATAT-TTA
61370912 ATAAT
1 ATAAT
61370917 AAAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAATTTTATAAAAATATTTA
Found at i:61380747 original size:34 final size:34
Alignment explanation
Indices: 61380709--61380804 Score: 83
Period size: 34 Copynumber: 2.8 Consensus size: 34
61380699 GAAGATATAC
*
61380709 ATACATAAAATAATATGAAATCAATAATACATAT
1 ATACATAAAATAATATGAAATCAATAATAAATAT
* *
61380743 ATACACATAAA-AA-ATGAAA--AATTAAAGGAAATAT
1 ATACATA-AAATAATATGAAATCAA-T-AA-TAAATAT
* *
61380777 TTACATAAAATAATAGGAAATCAATAAT
1 ATACATAAAATAATATGAAATCAATAAT
61380805 GTATACTTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
31 2 0.04
32 1 0.02
33 11 0.23
34 20 0.43
35 10 0.21
36 1 0.02
37 2 0.04
ACGTcount: A:0.60, C:0.07, G:0.06, T:0.26
Consensus pattern (34 bp):
ATACATAAAATAATATGAAATCAATAATAAATAT
Found at i:61382413 original size:127 final size:130
Alignment explanation
Indices: 61382153--61382444 Score: 385
Period size: 127 Copynumber: 2.2 Consensus size: 130
61382143 GCCACCTTCG
* * *
61382153 ATCTGCTCCATAGTCGATATAGGGAA-ATAAGATCTGTTATTTTCAGTCTGTTTCCTTGCTACCT
1 ATCTGCTCCATAGCCGATACA-TGAAGATAAGATCTGTTATTTTCAGTCTG--T-CTTGCTACCT
* * * *
61382217 CAAGAAGATAAGACTTGCATATTGAGCCTGCTCCACTACAACTTCAGAGAGATAATGCTAGTGGT
62 CAAGAAGATAAGACTTGCATATTGAACCTACTCCACTACAACTTCAGAGAGATAAGGCTAGTGGC
61382282 TAAA
127 TAAA
*
61382286 ATCTGCTCCATAGCCGATACATGAAGATAAGATCTGTTATTTTCAGTCTG-CTT-CTACCT-TAG
1 ATCTGCTCCATAGCCGATACATGAAGATAAGATCTGTTATTTTCAGTCTGTCTTGCTACCTCAAG
* * * * *
61382348 AAGATAAGATTTGTATATTGAACCTACTCCACTTCAACTTCAGGGAGATAAGGCTGGTGGCTAAA
66 AAGATAAGACTTGCATATTGAACCTACTCCACTACAACTTCAGAGAGATAAGGCTAGTGGCTAAA
* *
61382413 ATTTGCTCCATAGCCGATACATGGAGATAAGA
1 ATCTGCTCCATAGCCGATACATGAAGATAAGA
61382445 CTCGCCATTT
Statistics
Matches: 143, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
127 88 0.62
128 6 0.04
129 3 0.02
132 3 0.02
133 43 0.30
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (130 bp):
ATCTGCTCCATAGCCGATACATGAAGATAAGATCTGTTATTTTCAGTCTGTCTTGCTACCTCAAG
AAGATAAGACTTGCATATTGAACCTACTCCACTACAACTTCAGAGAGATAAGGCTAGTGGCTAAA
Found at i:61382612 original size:161 final size:163
Alignment explanation
Indices: 61382292--61382841 Score: 606
Period size: 161 Copynumber: 3.2 Consensus size: 163
61382282 TAAAATCTGC
* * * *
61382292 TCCATAGCCGATACATGAAGATAAGATCTGTTATTTTCAGTCTGCTTCTACCTTAGAAGATAAGA
1 TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCA---TGATTC-A----GGAAGATAAGA
* * * * *
61382357 TTTGTATATTGAACCTACTCCACTTCAACTTCAGGGAGATAAGGCTGGTGGCTAAAATTTGCTCC
58 CTTGTATATTGAACCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTAAAATCTGCTCC
*
61382422 ATAGCCGATACATGGAGATAAGACTCGCCATTTTTTATCTA
123 ATAGCCGATACATGGAGATAAGACTCGCCATTTTTGATCTA
*
61382463 CTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCA-G-TT-AGGAAGATAAGACTTGCAT
1 -TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCATGATTCAGGAAGATAAGACTTGTAT
* *
61382525 ATTGAGCCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTAAAATCTACTCCATAGCCG
65 ATTGAACCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCG
*
61382590 ATACATGGAGATAAGACTCGCCATTTTCGATCTGA
130 ATACATGGAGATAAGACTCGCCATTTTTGATCT-A
*
61382625 TCCATAGCCGATACATAGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGA
1 TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCA----------TG--A-TTCAGGAAGA
* * * * * *
61382690 TAAGACTTGTATCTTCAACCTGCTCTC-TTGCTACCTC-AGAGAGATAAAGCTGGTGGCTAAAAT
53 TAAGACTTGTATATTGAACCTGCTC-CACTGCAACTTCAAG-GAGATAAGGCTGGTGGCTAAAAT
* *
61382753 CTGCTCCATAGCCGATACATGGAGATAAGACTCACCATTTTTGATCTGT
116 CTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTTGATCT-A
* *
61382802 TCCATAGCCGATACATGGAGATAAGTTCTATAATTTTCAT
1 TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAT
61382842 CGATATCGCT
Statistics
Matches: 330, Mismatches: 29, Indels: 43
0.82 0.07 0.11
Matches are distributed among these distances:
161 143 0.43
162 1 0.00
165 1 0.00
167 3 0.01
168 1 0.00
172 38 0.12
176 4 0.01
177 138 0.42
178 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (163 bp):
TCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCATGATTCAGGAAGATAAGACTTGTATA
TTGAACCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGA
TACATGGAGATAAGACTCGCCATTTTTGATCTA
Found at i:61392652 original size:46 final size:46
Alignment explanation
Indices: 61392577--61392729 Score: 173
Period size: 47 Copynumber: 3.2 Consensus size: 46
61392567 TGCACATAGT
* ** *
61392577 CACATATCACATACCGATGCCATAGCCCAGCCATGGTCTTACATGGAT
1 CACATATCAC--ACCGATGCCATATCCCAGATATGGTCTTACATGGAG
* *
61392625 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACA-GTAG
1 CACATATCACACCGATGCCATATCCCAGATATGGTC-T-TACATGGAG
* * *
61392672 CACATATCACACCGATGTCATATCCCGGATATGGTCTTATATGGAAG
1 CACATATCACACCGATGCCATATCCCAGATATGGTCTTACATGG-AG
61392719 CACATATCACA
1 CACATATCACA
61392730 TTTCTCCGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
45 3 0.03
46 24 0.27
47 49 0.54
48 14 0.16
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (46 bp):
CACATATCACACCGATGCCATATCCCAGATATGGTCTTACATGGAG
Found at i:61392694 original size:47 final size:47
Alignment explanation
Indices: 61392559--61392729 Score: 168
Period size: 47 Copynumber: 3.6 Consensus size: 47
61392549 ATAGTAAAAC
** * *
61392559 TATGGTCTTGCACA-TAGTCACATATCACATACCGATGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATATCCCAGA
* * * *
61392608 CATGGTC-T-TACATGGATCACATATCACACTGATGCCATATCCCAGA
1 TATGGTCTTATACA-GTAGCACATATCACACCGATGCCATATCCCAGA
* *
61392654 TATGGTCTTATACAGTAGCACATATCACACCGATGTCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCAGA
** *
61392701 TATGGTCTTATATGGAAGCACATATCACA
1 TATGGTCTTATACAGTAGCACATATCACA
61392730 TTTCTCCGAA
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
46 22 0.22
47 58 0.57
48 15 0.15
49 7 0.07
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCAGA
Found at i:61394386 original size:12 final size:12
Alignment explanation
Indices: 61394369--61394422 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
61394359 TCTTAGCTAA
61394369 TTGCTCTTGCAT
1 TTGCTCTTGCAT
61394381 TTGCTCTTGCAT
1 TTGCTCTTGCAT
* * *
61394393 CTGTTCCTGCAT
1 TTGCTCTTGCAT
*
61394405 TT-CTTTTTGCAT
1 TTGC-TCTTGCAT
61394417 TTGCTC
1 TTGCTC
61394423 CAATTTTTCT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 31 0.97
13 1 0.03
ACGTcount: A:0.07, C:0.26, G:0.15, T:0.52
Consensus pattern (12 bp):
TTGCTCTTGCAT
Found at i:61396293 original size:22 final size:23
Alignment explanation
Indices: 61396267--61396312 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
61396257 CAACCAAACC
61396267 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
61396289 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
61396312 A
1 A
61396313 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:61396318 original size:23 final size:23
Alignment explanation
Indices: 61396274--61396318 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
61396264 ACCAATTCAA
*
61396274 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
61396297 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
61396319 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:61406894 original size:29 final size:29
Alignment explanation
Indices: 61406861--61407127 Score: 209
Period size: 29 Copynumber: 9.3 Consensus size: 29
61406851 AACCGAGCAT
* * *
61406861 TGTGTGGGTGAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
* ** *
61406890 TGTGTGTGCGAGTTCCGTAATAGA-GCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
*
61406918 TGTGTGTGCGAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
* **** *
61406947 TGTGTGTGCGAGTTCCG-TAACCAAGCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
* *
61406975 TGTGTGTTCGAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
* ** *
61407004 TGTGTGTGCGAGTTCCGTAATCGA-GCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
* *
61407032 TGTGTGTGTGAGATCAGTTGTTGAGGCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
* * **** *
61407061 TGTGTGTGTGAGTTCCG-TAACAAAGCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
* *
61407089 TGTGTGTGCAAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGATCCGTTGTTGAGGCAC
61407118 TAAGTGTGTG
1 T--GTGTGTG
61407128 AAATGAGATC
Statistics
Matches: 177, Mismatches: 55, Indels: 10
0.73 0.23 0.04
Matches are distributed among these distances:
28 84 0.47
29 86 0.49
31 7 0.04
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.31
Consensus pattern (29 bp):
TGTGTGTGCGAGATCCGTTGTTGAGGCAC
Found at i:61407128 original size:57 final size:57
Alignment explanation
Indices: 61406827--61407127 Score: 444
Period size: 57 Copynumber: 5.2 Consensus size: 57
61406817 AAGTGAACAT
* * * * *
61406827 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCATTGTGTGGGTGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACAGAGCACTGTGTGTGCGAGATCGGTTGTTG
*
61406884 AGGCACTGTGTGTGCGAGTTCCGTAATAGAGCACTGTGTGTGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACAGAGCACTGTGTGTGCGAGATCGGTTGTTG
*
61406941 AGGCACTGTGTGTGCGAGTTCCGTAACCA-AGCACTGTGTGTTCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAA-CAGAGCACTGTGTGTGCGAGATCGGTTGTTG
* *
61406998 AGGCACTGTGTGTGCGAGTTCCGTAATC-GAGCACTGTGTGTGTGAGATCAGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAA-CAGAGCACTGTGTGTGCGAGATCGGTTGTTG
* * *
61407055 AGGCACTGTGTGTGTGAGTTCCGTAACAAAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACAGAGCACTGTGTGTGCGAGATCGGTTGTTG
61407112 AGGCACTAAGTGTGTG
1 AGGCACT--GTGTGTG
61407128 AAATGAGATC
Statistics
Matches: 222, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
56 1 0.00
57 213 0.96
58 1 0.00
59 7 0.03
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (57 bp):
AGGCACTGTGTGTGCGAGTTCCGTAACAGAGCACTGTGTGTGCGAGATCGGTTGTTG
Found at i:61412038 original size:28 final size:28
Alignment explanation
Indices: 61411998--61412076 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
61411988 GCAATCAAAT
* * *
61411998 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
61412026 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
61412054 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
61412077 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:61419372 original size:24 final size:25
Alignment explanation
Indices: 61419340--61419386 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
61419330 TGGAATGGAT
61419340 TTTACTTTTTAAA-ATTATTTTACAA
1 TTTACTTTTTAAATATT-TTTTACAA
61419365 TTTA-TTTTTAAATATTTTTTAC
1 TTTACTTTTTAAATATTTTTTAC
61419387 TAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTACTTTTTAAATATTTTTTACAA
Found at i:61419508 original size:14 final size:14
Alignment explanation
Indices: 61419489--61419531 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
61419479 TCTAATTATA
61419489 CATTATATGGATTT
1 CATTATATGGATTT
*
61419503 CATTATAATAGATTT
1 CATTAT-ATGGATTT
*
61419518 CATTATCTGGATTT
1 CATTATATGGATTT
61419532 TATATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (14 bp):
CATTATATGGATTT
Found at i:61420354 original size:10 final size:10
Alignment explanation
Indices: 61420339--61420384 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
61420329 ATTTTCATTC
61420339 ATCTTTATTT
1 ATCTTTATTT
*
61420349 ATCTTTAATT
1 ATCTTTATTT
61420359 ATCTTTATTT
1 ATCTTTATTT
61420369 AT-TTGTATTT
1 ATCTT-TATTT
61420379 ATCTTT
1 ATCTTT
61420385 TAGAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.06
10 28 0.88
11 2 0.06
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (10 bp):
ATCTTTATTT
Found at i:61425386 original size:28 final size:28
Alignment explanation
Indices: 61425346--61425410 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
61425336 TGTACTTATT
*
61425346 ATACCCCTATGTATGCAAAATTACCATA
1 ATACCCCTATGTATGCAAAATGACCATA
* *
61425374 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATA
61425402 ATACCCCTA
1 ATACCCCTA
61425411 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.28, G:0.08, T:0.29
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATA
Found at i:61425574 original size:27 final size:28
Alignment explanation
Indices: 61425527--61425605 Score: 106
Period size: 27 Copynumber: 2.8 Consensus size: 28
61425517 CTAGTGGCTA
* *
61425527 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
**
61425555 TGCCAC-CTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
61425582 TGCCACAAAATATCTGTATCTGGT
1 TGCCACAAAATATCTGT-TCTGGT
61425606 AACTCTGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
27 23 0.53
28 14 0.33
29 6 0.14
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGGCAC
Found at i:61425617 original size:29 final size:28
Alignment explanation
Indices: 61425527--61425617 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 28
61425517 CTAGTGGCTA
* ** *
61425527 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTAACAC
** **
61425555 TGCCAC-CTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTAACAC
*
61425582 TGCCACAAAATATCTGTATCTGGTAACTC
1 TGCCACAAAATATCTGT-TCTGGTAACAC
*
61425611 TGTCACA
1 TGCCACA
61425618 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 23 0.45
28 14 0.27
29 14 0.27
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTAACAC
Found at i:61429526 original size:5 final size:5
Alignment explanation
Indices: 61429511--61429563 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
61429501 TAACCCAATT
61429511 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA CTATTTA --TTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -T-TTTA TTTTA TTTTA TTTTA
61429560 TTTT
1 TTTT
61429564 TTTGGATGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.07
4 4 0.09
5 31 0.72
6 1 0.02
7 4 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:61431150 original size:10 final size:10
Alignment explanation
Indices: 61431135--61431184 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
61431125 TAATCTTAGG
61431135 ATTTAT-TTT
1 ATTTATCTTT
61431144 CATTTATCTTT
1 -ATTTATCTTT
*
61431155 AATTATCTTT
1 ATTTATCTTT
61431165 ATTTAT-TTGT
1 ATTTATCTT-T
61431175 ATTTATCTTT
1 ATTTATCTTT
61431185 TAAAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:61439132 original size:45 final size:44
Alignment explanation
Indices: 61439007--61439147 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 44
61438997 CATGTAGTAT
* * *
61439007 AATTCGTATTCTATTTTGATTTTTTTTT-TTGAAATAATAGTTC
1 AATTAGTATTATATTTTGATTTTTTTTTATTGAAATAATAGTTA
*
61439050 AATTAGTATTATATTTTGA--TTCTTTTATTGAAATAATAGTTA
1 AATTAGTATTATATTTTGATTTTTTTTTATTGAAATAATAGTTA
* *
61439092 AATTAGTATTGTATTTTTATTTTTATTTTATTGAAATAATAGTTA
1 AATTAGTATTATATTTTGATTTTT-TTTTATTGAAATAATAGTTA
* *
61439137 TATAAGTATTA
1 AATTAGTATTA
61439148 AATGAAAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 6 0.07
42 31 0.37
43 17 0.20
44 2 0.02
45 28 0.33
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (44 bp):
AATTAGTATTATATTTTGATTTTTTTTTATTGAAATAATAGTTA
Found at i:61442833 original size:18 final size:18
Alignment explanation
Indices: 61442810--61442871 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
61442800 TGTATTAAAT
61442810 AAATATTATAATAAGTAA
1 AAATATTATAATAAGTAA
* *
61442828 AAATATGTAATGTATTAA-TAT
1 AAATAT-T-A--TAATAAGTAA
*
61442849 AAATATTATTATAAGTAA
1 AAATATTATAATAAGTAA
61442867 AAATA
1 AAATA
61442872 AGAGTGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 4 0.12
18 13 0.38
19 2 0.06
20 2 0.06
21 8 0.24
22 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATATTATAATAAGTAA
Found at i:61443324 original size:11 final size:11
Alignment explanation
Indices: 61443310--61443337 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
61443300 ATTTAAATTT
61443310 TATAAAAATAA
1 TATAAAAATAA
61443321 TATAAAAATAA
1 TATAAAAATAA
61443332 TATAAA
1 TATAAA
61443338 GTACTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:61453439 original size:96 final size:96
Alignment explanation
Indices: 61453275--61453464 Score: 371
Period size: 96 Copynumber: 2.0 Consensus size: 96
61453265 TCTGAAAGCA
*
61453275 TTGATCATCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
1 TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
61453340 GAATTGATCAACCTGGGATAAGATCCACCGT
66 GAATTGATCAACCTGGGATAAGATCCACCGT
61453371 TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
1 TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
61453436 GAATTGATCAACCTGGGATAAGATCCACC
66 GAATTGATCAACCTGGGATAAGATCCACC
61453465 ATAGATAGCA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (96 bp):
TTGATCACCCTATTAATTCATTTCGCCTTTGCAAAGCCATTTAGTTCGGGTGCCCTCTCTCATGA
GAATTGATCAACCTGGGATAAGATCCACCGT
Found at i:61458929 original size:41 final size:42
Alignment explanation
Indices: 61458846--61458967 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
61458836 ATTCTTGAAC
* * * *
61458846 ATTAGCTTGCTCACAAACGGGTAGCAAGGAAACATGAAAAAT
1 ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAAT
* *
61458888 ATTAGCTTGCTAAC-AACGTGCAACAAAGAAGCATGAAAAAT
1 ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAAT
* * *
61458929 ATCAGCTTACTGACAAACGTGCAGCAAGGAAGCATGAAA
1 ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAA
61458968 CAATCTGCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 33 0.49
42 35 0.51
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
ATTAGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAAT
Found at i:61458961 original size:42 final size:42
Alignment explanation
Indices: 61458849--61458967 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 42
61458839 CTTGAACATT
* * * * *
61458849 AGCTTGCTCACAAACGGGTAGCAAGGAAACATGAAAAATATT
1 AGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAATATC
* *
61458891 AGCTTGCTAAC-AACGTGCAACAAAGAAGCATGAAAAATATC
1 AGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAATATC
* *
61458932 AGCTTACTGACAAACGTGCAGCAAGGAAGCATGAAA
1 AGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAA
61458968 CAATCTGCTC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 33 0.51
42 32 0.49
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (42 bp):
AGCTTGCTAACAAACGTGCAGCAAGGAAGCATGAAAAATATC
Found at i:61461548 original size:2 final size:2
Alignment explanation
Indices: 61461541--61461567 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61461531 TTCATTTTAT
61461541 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
61461568 TATATATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:61468472 original size:26 final size:26
Alignment explanation
Indices: 61468432--61468494 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
61468422 AAGATGATAT
61468432 GAAAAAGTAAATTTTT-TATTAATTAAA
1 GAAAAA-T-AATTTTTGTATTAATTAAA
*
61468459 GAAAAATAATTTTTGTATTATTTAAA
1 GAAAAATAATTTTTGTATTAATTAAA
61468485 -ATAAAATAAT
1 GA-AAAATAAT
61468495 GATTATTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 8 0.24
26 19 0.58
27 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (26 bp):
GAAAAATAATTTTTGTATTAATTAAA
Found at i:61473996 original size:26 final size:26
Alignment explanation
Indices: 61473960--61474011 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
61473950 TACGAGGCCT
61473960 TAAACATGCATTGAGAGTGGTTCGGG
1 TAAACATGCATTGAGAGTGGTTCGGG
61473986 TAAACATGCATTGAGAGTGGTTCGGG
1 TAAACATGCATTGAGAGTGGTTCGGG
61474012 GCAAAGCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (26 bp):
TAAACATGCATTGAGAGTGGTTCGGG
Found at i:61475115 original size:53 final size:53
Alignment explanation
Indices: 61475057--61475167 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 53
61475047 AACATAGAAA
*
61475057 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCGTATAAATTATACTTAAT
1 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCATATAAATTATACTTAAT
*
61475110 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCATATGAATTATACTTAAT
1 ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCATATAAATTATACTTAAT
*
61475163 CTTAA
1 ATTAA
61475168 CATAGATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (53 bp):
ATTAAACAAAGTAAGCTATATAGCTTAGTAAGCTCATATAAATTATACTTAAT
Found at i:61476487 original size:11 final size:11
Alignment explanation
Indices: 61476471--61476496 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61476461 TAGAAGAGAC
61476471 GAAACAGGGGA
1 GAAACAGGGGA
61476482 GAAACAGGGGA
1 GAAACAGGGGA
61476493 GAAA
1 GAAA
61476497 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:61477170 original size:18 final size:18
Alignment explanation
Indices: 61477147--61477195 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
61477137 ATGTGAGGTA
*
61477147 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
61477165 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
61477183 ATTATTATTATTA
1 AGTATTATTATTA
61477196 TGAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:61477175 original size:3 final size:3
Alignment explanation
Indices: 61477149--61477196 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
61477139 GTGAGGTAAG
* * * *
61477149 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61477197 GAGTGGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:61477196 original size:12 final size:12
Alignment explanation
Indices: 61477149--61477196 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
61477139 GTGAGGTAAG
* *
61477149 TATTAATATTAG
1 TATTAGTATTAT
61477161 TATTAGTATTAT
1 TATTAGTATTAT
61477173 TATTAGTATTAT
1 TATTAGTATTAT
*
61477185 TATTATTATTAT
1 TATTAGTATTAT
61477197 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:61477391 original size:24 final size:24
Alignment explanation
Indices: 61477337--61477408 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
61477327 TGTGTGAAGT
*
61477337 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
61477360 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
61477385 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
61477409 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:61477611 original size:37 final size:39
Alignment explanation
Indices: 61477552--61477647 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
61477542 CGGATAGATT
* * * *
61477552 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
61477589 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
61477628 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
61477648 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:61513010 original size:18 final size:18
Alignment explanation
Indices: 61512970--61513012 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
61512960 CAAAATTCCT
*
61512970 TTAAAATATAAAAATTCA
1 TTAAAATATAAAAAATCA
61512988 TTAAAATATAAAAAAATCA
1 TTAAAATAT-AAAAAATCA
61513007 -TAAAAT
1 TTAAAAT
61513013 TAGTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAAAATATAAAAAATCA
Found at i:61517859 original size:2 final size:2
Alignment explanation
Indices: 61517852--61517923 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
61517842 AATACCTATG
61517852 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
61517894 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
61517924 CACTTGCTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:61521371 original size:24 final size:24
Alignment explanation
Indices: 61521343--61521394 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
61521333 TTAGCAAGTC
*
61521343 AAATAAACTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
61521367 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
61521391 AAAT
1 AAAT
61521395 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:61524202 original size:9 final size:9
Alignment explanation
Indices: 61524164--61524206 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
61524154 CATTGATTAG
61524164 ATAAAAATT
1 ATAAAAATT
* *
61524173 GTTAAAATT
1 ATAAAAATT
61524182 ATTAAAATATT
1 A-TAAAA-ATT
61524193 ATAAAAATT
1 ATAAAAATT
61524202 ATAAA
1 ATAAA
61524207 TTGTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 15 0.54
10 9 0.32
11 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (9 bp):
ATAAAAATT
Found at i:61524206 original size:19 final size:17
Alignment explanation
Indices: 61524167--61524235 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 17
61524157 TGATTAGATA
61524167 AAAATTGTT-AAAATTATT
1 AAAATT-TTAAAAATTA-T
61524185 AAAATATTATAAAAATTAT
1 AAAAT-TT-TAAAAATTAT
*
61524204 AAATTGTTTAAAACATTA-
1 AAAAT-TTTAAAA-ATTAT
61524222 AAAATTTGTAAAAA
1 AAAATTT-TAAAAA
61524236 ATAGAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
17 3 0.07
18 20 0.47
19 13 0.30
20 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (17 bp):
AAAATTTTAAAAATTAT
Found at i:61526521 original size:15 final size:15
Alignment explanation
Indices: 61526489--61526524 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
61526479 AGTACTTTAG
*
61526489 TTTTCAATACTTAAT
1 TTTTCAACACTTAAT
*
61526504 TTTTCAACACTTATT
1 TTTTCAACACTTAAT
61526519 TTTTCA
1 TTTTCA
61526525 GTTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTCAACACTTAAT
Found at i:61526730 original size:16 final size:15
Alignment explanation
Indices: 61526707--61526736 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
61526697 ATAAATTTAC
61526707 AAAAAAATGATGTTA
1 AAAAAAATGATGTTA
61526722 AAAATAAATGATGTT
1 AAAA-AAATGATGTT
61526737 TTGGTAGAAT
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:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
AAAAAAATGATGTTA
Found at i:61535441 original size:28 final size:28
Alignment explanation
Indices: 61535401--61535459 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
61535391 AAGTGAGCCT
61535401 TAAGCGTTTTACCTTTTCCTTTAAAAAC
1 TAAGCGTTTTACCTTTTCCTTTAAAAAC
61535429 TAAGCGTTTTACCTTTTCCTTTAAAAAC
1 TAAGCGTTTTACCTTTTCCTTTAAAAAC
61535457 TAA
1 TAA
61535460 CTTGATTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (28 bp):
TAAGCGTTTTACCTTTTCCTTTAAAAAC
Found at i:61543938 original size:16 final size:17
Alignment explanation
Indices: 61543902--61543938 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
61543892 AATTTTATTT
*
61543902 TAATAATAATTTTTAAA
1 TAATAATAATATTTAAA
61543919 -AATAATAA-ATTTAAA
1 TAATAATAATATTTAAA
61543934 TAATA
1 TAATA
61543939 TTCTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATAATATTTAAA
Found at i:61543963 original size:7 final size:7
Alignment explanation
Indices: 61543951--61543977 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
61543941 CTTCATTTAA
61543951 AATATTC
1 AATATTC
61543958 AATATTC
1 AATATTC
61543965 AATATTC
1 AATATTC
61543972 AATATT
1 AATATT
61543978 TTAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
AATATTC
Found at i:61548484 original size:43 final size:43
Alignment explanation
Indices: 61548423--61548643 Score: 252
Period size: 43 Copynumber: 5.2 Consensus size: 43
61548413 ATATGTAACA
*
61548423 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTGTATAAAAAACG
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
*
61548466 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTATATAAAAAACG
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
**
61548509 CTACTAAAGACCAGGACTTTTAGCGGCGCTTTTAT-AAAAACG
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
* * * * * *
61548551 CCACTATAGAACAGGACTTTTAACGGCG-TTTTTTAAAAAAGTG
1 CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAA-CG
* * * * *
61548594 CCGCTAAATGTCCTGGTC-TTTAGTGGCGCTTTT-TATAAAAGCG
1 CCGCTAAA-GACCAGGACTTTTAGCGGCGCTTTTATA-AAAAACG
61548637 CCGCTAA
1 CCGCTAA
61548644 TTTGCCCAGT
Statistics
Matches: 153, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.03
42 36 0.24
43 99 0.65
44 13 0.08
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
CCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTATAAAAAACG
Found at i:61552908 original size:10 final size:11
Alignment explanation
Indices: 61552893--61552921 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
61552883 AGGTGATCAT
61552893 GGGCCGGG-TC
1 GGGCCGGGTTC
61552903 GGGCCGGGTTC
1 GGGCCGGGTTC
61552914 GGGCCGGG
1 GGGCCGGG
61552922 CCCATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.00, C:0.28, G:0.62, T:0.10
Consensus pattern (11 bp):
GGGCCGGGTTC
Found at i:61553113 original size:26 final size:24
Alignment explanation
Indices: 61553083--61553132 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
61553073 AAATAAAAAA
*
61553083 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
61553109 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
61553133 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:61553152 original size:21 final size:21
Alignment explanation
Indices: 61553103--61553161 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
61553093 ATAATAAATC
*
61553103 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
61553123 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
61553145 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
61553162 TTCTTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:61553238 original size:15 final size:16
Alignment explanation
Indices: 61553208--61553240 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
61553198 AAATGGTTAT
61553208 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
61553225 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
61553240 A
1 A
61553241 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:61556992 original size:28 final size:28
Alignment explanation
Indices: 61556939--61557022 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
61556929 CACTTTGTGC
61556939 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
61556968 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
61556996 GATAT-TGATGTGTTTTGGAGGATTATA
1 TAT-TCTGGTGTGTTTTGGAGGATTATA
61557023 CTGGTGTGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 31 0.62
29 19 0.38
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:61557276 original size:21 final size:21
Alignment explanation
Indices: 61557226--61557308 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
61557216 GACTATACTG
* *
61557226 ATCAGGCACTTTATATGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
61557247 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTATGTGTCGT
*
61557270 ATCAGGCACCTCATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
61557291 TTCAGGCA-CTTATGTGTC
1 ATCAGGCACCTTATGTGTC
61557309 ATATACTGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 9 0.17
21 26 0.49
23 18 0.34
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:61557289 original size:44 final size:41
Alignment explanation
Indices: 61557226--61557308 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 41
61557216 GACTATACTG
* * *
61557226 ATCAGGCACTTTATATGTCGTATTTCAGGCACCTTGTGTGTCGT
1 ATCAGGCACCTCATATGTCG--TTTCAGGCA-CTTATGTGTCGT
*
61557270 ATCAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTC
1 ATCAGGCACCTCATATGTCGTTTCAGGCACTTATGTGTC
61557309 ATATACTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
42 9 0.26
44 17 0.49
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCAGGCACCTCATATGTCGTTTCAGGCACTTATGTGTCGT
Found at i:61558548 original size:46 final size:48
Alignment explanation
Indices: 61558390--61558576 Score: 154
Period size: 46 Copynumber: 3.9 Consensus size: 48
61558380 TGGTTGGACC
61558390 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
** * * * *
61558436 ATGGCATCAGAGATATGTGATTACATGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
*
61558489 ATGGCATC--AGTGTGATATGTGATTCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* * *
61558535 ATGGC-TACGGTGTGTGATATGTGACTAT-GTGCAAGACCATAG
1 ATGGCAT-CAGAGTGTGATATGTGA-T-TCGTGTAAGACCATAG
61558577 TTTTACTATG
Statistics
Matches: 112, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
45 1 0.01
46 33 0.29
47 7 0.06
48 18 0.16
49 13 0.12
50 1 0.01
51 7 0.06
52 4 0.04
53 27 0.24
54 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Done.