Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 82 of 235
Found at i:28476413 original size:39 final size:38
Alignment explanation
Indices: 28476356--28476431 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 38
28476346 ATGGGCTTGC
*
28476356 ATATGTTATTGATGTTGCATGTATTTCCAAATGGGCCA
1 ATATGTTACTGATGTTGCATGTATTTCCAAATGGGCCA
**
28476394 ATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCC
1 ATATG-TTACTGATGTTGCATGTATTTCCAAATGGGCC
28476432 TATGGGCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (38 bp):
ATATGTTACTGATGTTGCATGTATTTCCAAATGGGCCA
Found at i:28479327 original size:12 final size:12
Alignment explanation
Indices: 28479310--28479334 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28479300 CACAACGTGC
28479310 ATGGTATTAAAA
1 ATGGTATTAAAA
28479322 ATGGTATTAAAA
1 ATGGTATTAAAA
28479334 A
1 A
28479335 ACATGATGCA
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGGTATTAAAA
Found at i:28479601 original size:12 final size:12
Alignment explanation
Indices: 28479584--28479611 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28479574 TATATGAAAT
28479584 TAATTAGTTTAA
1 TAATTAGTTTAA
28479596 TAATTAGTTTAA
1 TAATTAGTTTAA
28479608 TAAT
1 TAAT
28479612 AAGATGAAAA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
TAATTAGTTTAA
Found at i:28487648 original size:17 final size:18
Alignment explanation
Indices: 28487609--28487647 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28487599 TCCATTCTCT
28487609 ATTTTGCTTCTCTTTTTC
1 ATTTTGCTTCTCTTTTTC
*
28487627 ATTTTGCTTGT-TTTTTC
1 ATTTTGCTTCTCTTTTTC
28487644 -TTTT
1 ATTTT
28487648 TAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 6 0.30
18 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.08, T:0.72
Consensus pattern (18 bp):
ATTTTGCTTCTCTTTTTC
Found at i:28492986 original size:144 final size:144
Alignment explanation
Indices: 28492758--28493043 Score: 466
Period size: 144 Copynumber: 2.0 Consensus size: 144
28492748 CCTGAAAGCC
28492758 TATTGGAGGATAGATCCAACTTAACCAAATTCGTTAATCTCCCAATATCTTCTGGAATGGATCCA
1 TATTGGAGGATAGATCCAACTTAACCAAATTCGTTAATCTCCCAATATCTTCTGGAATGGATCCA
* * *
28492823 TTAAGTTGGTTGAGTTGAAGGAACAACGAGGTAAGATTAGTTAAGTTGCTGACAGAAGATGGTAT
66 TCAAGTTGGTTGAGTTGAAGGAACAACGAGGCAAGATTAGTTAAGTTGCTGACAGAAGATGGGAT
28492888 TGGACCAACAAGAT
131 TGGACCAACAAGAT
* *
28492902 TATTGGAGGATAGATCCAA-TTCAACCAAATTCGTTAGTCTCCCATTATCTTCTGGAATGGATCC
1 TATTGGAGGATAGATCCAACTT-AACCAAATTCGTTAATCTCCCAATATCTTCTGGAATGGATCC
* ** * *
28492966 ATCAAGTTTGTTGCTTTGAAGGTACAACGAGGCAAGATTGGTTAAGTTGCTGACAGAAGATGGGA
65 ATCAAGTTGGTTGAGTTGAAGGAACAACGAGGCAAGATTAGTTAAGTTGCTGACAGAAGATGGGA
28493031 TTGGACCAACAAG
130 TTGGACCAACAAG
28493044 CCAGTTGTTT
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
143 2 0.02
144 129 0.98
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (144 bp):
TATTGGAGGATAGATCCAACTTAACCAAATTCGTTAATCTCCCAATATCTTCTGGAATGGATCCA
TCAAGTTGGTTGAGTTGAAGGAACAACGAGGCAAGATTAGTTAAGTTGCTGACAGAAGATGGGAT
TGGACCAACAAGAT
Found at i:28494570 original size:16 final size:18
Alignment explanation
Indices: 28494549--28494581 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
28494539 CACTTCTATA
28494549 TAATTTT-TAA-TTTTTT
1 TAATTTTCTAAGTTTTTT
28494565 TAATTTTCTAAGTTTTT
1 TAATTTTCTAAGTTTTT
28494582 AAAAAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
TAATTTTCTAAGTTTTTT
Found at i:28495810 original size:8 final size:8
Alignment explanation
Indices: 28495793--28495837 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
28495783 GACTTTTTTG
*
28495793 AAAAATAT
1 AAAAAAAT
28495801 AAAAAAAT
1 AAAAAAAT
28495809 AAAAAAAT
1 AAAAAAAT
28495817 -AAAAAAT
1 AAAAAAAT
28495824 -AAAAAAT
1 AAAAAAAT
28495831 AAAAAAA
1 AAAAAAA
28495838 CAGAAATTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 14 0.40
8 21 0.60
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:28495812 original size:7 final size:7
Alignment explanation
Indices: 28495802--28495836 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
28495792 GAAAAATATA
28495802 AAAAAAT
1 AAAAAAT
28495809 AAAAAAAT
1 -AAAAAAT
28495817 AAAAAAT
1 AAAAAAT
28495824 AAAAAAT
1 AAAAAAT
28495831 AAAAAA
1 AAAAAA
28495837 ACAGAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:28495820 original size:15 final size:15
Alignment explanation
Indices: 28495793--28495837 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
28495783 GACTTTTTTG
28495793 AAAAATATAAAAAAAT
1 AAAAA-ATAAAAAAAT
28495809 AAAAAA-ATAAAAAAT
1 AAAAAATA-AAAAAAT
28495824 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
28495838 CAGAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.04
15 20 0.74
16 6 0.22
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:28495965 original size:73 final size:72
Alignment explanation
Indices: 28495835--28496046 Score: 246
Period size: 73 Copynumber: 2.9 Consensus size: 72
28495825 AAAAATAAAA
*
28495835 AAACAGAAATTGAAAATACCTCAGCATGCCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTT
1 AAACAGAAATTGAAAATACCTCAGCATGCCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
28495900 ATTTTTGAC
66 A--TTTAAC
* * ** *
28495909 AAACAGGAATTGAAAATAACTCAGTGTG-CCCCGAGGCTTAACTCACCTCTCGCAATATGAGTTG
1 AAACAGAAATTGAAAATACCTCAGCATGCCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
28495973 ATTTAAC
66 ATTTAAC
* * *** ** * *
28495980 AAACAGAAACTGAAAATACCTCAACATGTGAGCCGAGGCTCAACTCATTTCTCGCAACATGAATT
1 AAACAGAAATTGAAAATACCTCAGCATG-CCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
28496045 GA
65 GA
28496047 ATTTTTAAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
71 27 0.23
73 65 0.56
74 24 0.21
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (72 bp):
AAACAGAAATTGAAAATACCTCAGCATGCCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTAAC
Found at i:28496250 original size:251 final size:247
Alignment explanation
Indices: 28495933--28496988 Score: 762
Period size: 251 Copynumber: 4.2 Consensus size: 247
28495923 AATAACTCAG
* * * *** * * **
28495933 TGTGCCCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTAACAAACAGAAACTGAAAATA
1 TGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAATTTGAAAATA
* *
28495998 CCTCAACATGTGAGCC-GAGGCTCAACTCATTTCTCGCAACATGAATTGAATTTTTAAATAACAT
66 CCTCAACATGTGA-CCTGAGGCTCAACTCACTTCTCGCAACATGAATTG-ATTTTTAAA-AACAG
* ** * * * *
28496062 AAACTAAAAATAGAAATTG-GTATAGCTCAGTGCGTGAGCC-AATGCTCAACTCACCTCTCGCAA
128 AAACTAAAAACAGAAATTGAAAATACCTC-G-GCATG-CCCTAAGGCTCAACTCACCTCTCGCAA
* * *
28496125 TATGAGTTGATTTTTTTG-AAACT-TAATTTGAAAAGTAGATTTTGAAAATACCTCGACA
190 TATGAGTTGA-TTTTTTGAAAAATAGAATTTGAAAA-CAGATTTTGAAAATACCTCGACA
28496183 TGTGAACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAATTTGAAAAT
1 TGTG-ACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAATTTGAAAAT
*** * * *
28496248 ACCTCAGTGTGTGACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAA
65 ACCTCAACATGTGACCTGAGGCTCAACTCACTTCTCGCAACATGAATTGATTTTTAAAAACAGAA
* * * * *
28496313 ATTAAAAACAGAATTTGAAAATACCTCGGCATGCCCTGAGGCTCAACTTACTTCTCGCAATATGA
130 ACTAAAAACAGAAATTGAAAATACCTCGGCATGCCCTAAGGCTCAACTCACCTCTCGCAATATGA
* *
28496378 GTTGATTTTTTGAAAAATAGAATTTGAAAACAGATTTTGAACATACCTCGGCA
195 GTTGATTTTTTGAAAAATAGAATTTGAAAACAGATTTTGAAAATACCTCGACA
* *
28496431 TGTGGCCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAA
1 TGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAT--AATTTGAAA
* ** * *
28496496 A-ACAGATTCTGAACATACCTCGGCATGTGGCCCAAGGCTCAACTCACTTCTCGCAATATGAGTT
63 ATAC-----CT---CA-A------CATGTGACCTGAGGCTCAACTCACTTCTCGCAACATGAATT
* ** * * ** *
28496560 GACTTTTTGAAAAATAGAATTTGAAAAACAG-ATTCTGAACATACCTCGGCATGTGGCTCGAGGC
113 GA-TTTTT-AAAAACAGAAACT-AAAAACAGAAAT-TGAAAATACCTCGGCATG-CCCT-AAGGC
* * *
28496624 TCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAATAGATTTTGAA
172 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAATTTG-AAAACAGATTTTGAA
* *
28496689 CATACCTCGGCA
236 AATACCTCGACA
* * * **
28496701 TGTTG-CCCGAGGCTCAACTCACTTCTCTCGCAATATGATTTGATTTTTTTTAAAACAGGATTTG
1 TG-TGACCCAAGGCTCAACTCAC--CTCTCGCAATATGAGTTGA--TTTTTGAAAA-ATAATTTG
* * * * * * *
28496765 AAAATACCTC-GCA--TGCCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTT-----
60 AAAATACCTCAACATGTGACCTGAGGCTCAACTCACTTCTCGCAACATGAATTGATTTTTAAAAA
* * * * * ** *
28496822 --GAAAGT------AGAAATTTAAAATACCTCAGCGTGTCC-AGAGGCTCAACTCATTTCTTGCA
125 CAGAAACTAAAAACAGAAATTGAAAATACCTCGGCATGCCCTA-AGGCTCAACTCACCTCTCGCA
* ** * * *
28496878 ATATGAGTTGA-TTTTTGAAAAATATAAATTAAAAAAATAGATATTAAAAATACCTC-AGCA
189 ATATGAGTTGATTTTTTGAAAAATA-GAATT-TGAAAACAGATTTTGAAAATACCTCGA-CA
* * * *
28496938 TGTGAGCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGAATTTTGAAAA
1 TGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
28496989 TAAACATCAA
Statistics
Matches: 675, Mismatches: 88, Indels: 103
0.78 0.10 0.12
Matches are distributed among these distances:
233 8 0.01
235 17 0.03
236 15 0.02
237 74 0.11
238 1 0.00
239 16 0.02
240 2 0.00
246 4 0.01
247 44 0.07
248 73 0.11
249 33 0.05
250 30 0.04
251 90 0.13
254 7 0.01
255 35 0.05
257 4 0.01
264 38 0.06
265 6 0.01
266 13 0.02
267 25 0.04
268 4 0.01
269 52 0.08
270 44 0.07
271 2 0.00
272 26 0.04
273 11 0.02
274 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (247 bp):
TGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAATTTGAAAATA
CCTCAACATGTGACCTGAGGCTCAACTCACTTCTCGCAACATGAATTGATTTTTAAAAACAGAAA
CTAAAAACAGAAATTGAAAATACCTCGGCATGCCCTAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAAAATAGAATTTGAAAACAGATTTTGAAAATACCTCGACA
Found at i:28496333 original size:13 final size:13
Alignment explanation
Indices: 28496300--28496333 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28496290 TGAGTTGATT
28496300 TTTGAAAACAGAA
1 TTTGAAAACAGAA
* *
28496313 ATTAAAAACAGAA
1 TTTGAAAACAGAA
28496326 TTTGAAAA
1 TTTGAAAA
28496334 TACCTCGGCA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (13 bp):
TTTGAAAACAGAA
Found at i:28496467 original size:89 final size:90
Alignment explanation
Indices: 28496265--28496768 Score: 761
Period size: 90 Copynumber: 5.6 Consensus size: 90
28496255 TGTGTGACCT
* * *
28496265 GAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTG-AAAACAGAAATT-AAAAACAGAAT
1 GAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGATT
*
28496327 TTGAAAATACCTCGGCA--T-GCCC
66 TTGAACATACCTCGGCATGTGGCCC
* *
28496349 TGAGGCTCAACTTACTTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAATTTG-AAAACAGAT
1 -GAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGAT
28496413 TTTGAACATACCTCGGCATGTGGCCC
65 TTTGAACATACCTCGGCATGTGGCCC
*
28496439 AAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGATT
1 GAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGATT
*
28496504 CTGAACATACCTCGGCATGTGGCCC
66 TTGAACATACCTCGGCATGTGGCCC
*
28496529 AAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGATT
1 GAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGATT
* *
28496594 CTGAACATACCTCGGCATGTGGCTC
66 TTGAACATACCTCGGCATGTGGCCC
*
28496619 GAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAATAGATT
1 GAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGATT
*
28496684 TTGAACATACCTCGGCATGTTGCCC
66 TTGAACATACCTCGGCATGTGGCCC
* * ** * *
28496709 GAGGCTCAACTCACTTCTCTCGCAATATGATTTGATTTTTTTTAAAACAGGATTTGAAAA
1 GAGGCTCAACTCAC-T-TCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAA
28496769 TACCTCGCAT
Statistics
Matches: 389, Mismatches: 21, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
85 32 0.08
86 6 0.02
87 35 0.09
89 52 0.13
90 226 0.58
91 1 0.00
92 37 0.10
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (90 bp):
GAGGCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAATTTGAAAAACAGATT
TTGAACATACCTCGGCATGTGGCCC
Found at i:28496684 original size:13 final size:14
Alignment explanation
Indices: 28496655--28496688 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
28496645 GAGTTGACTT
28496655 TTTGAAAAATAGAA
1 TTTGAAAAATAGAA
*
28496669 TTTGAAAAATAGAT
1 TTTGAAAAATAGAA
28496683 TTTGAA
1 TTTGAA
28496689 CATACCTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (14 bp):
TTTGAAAAATAGAA
Found at i:28496818 original size:73 final size:75
Alignment explanation
Indices: 28496683--28496893 Score: 216
Period size: 72 Copynumber: 2.8 Consensus size: 75
28496673 AAAAATAGAT
* * * *
28496683 TTTGAACATACCTCGGCATGTTGCCCGAGGCTCAACTCACTTCTCTCGCAATATGATTTGATTTT
1 TTTGAAAATACCTCAGCATG--CCCCGAGGCTCAACTCAC--CTCTCGCAATATGAGTTGATTTT
* *
28496748 TTTTAAAACAG-GA
62 TTTGAAAACAGAAA
*
28496761 TTTGAAAATACCTC-GCATGCCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGA--TTTTTG
1 TTTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
**
28496823 AAAGTAGAAA
66 AAAACAGAAA
* * * ** *
28496833 TTT-AAAATACCTCAGCGTGTCCAGAGGCTCAACTCATTTCTTGCAATATGAGTTGATTTTT
1 TTTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
28496894 GAAAAATATA
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
71 20 0.18
72 39 0.34
73 17 0.15
74 3 0.03
75 17 0.15
77 5 0.04
78 13 0.11
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (75 bp):
TTTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
AAAACAGAAA
Found at i:28497865 original size:40 final size:41
Alignment explanation
Indices: 28497804--28497882 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 41
28497794 CGTGTTAATC
*
28497804 AAGACGCCCTTTTCGGGTTTTCACCTTGA-TCCTTTTTTTT
1 AAGACGCCATTTTCGGGTTTTCACCTTGATTCCTTTTTTTT
* *
28497844 AAGATGCCATTTTCGGGTTTTCATCTTGATTTCCTTTTT
1 AAGACGCCATTTTCGGGTTTTCACCTTGA-TTCCTTTTT
28497883 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 26 0.76
42 8 0.24
ACGTcount: A:0.14, C:0.22, G:0.15, T:0.49
Consensus pattern (41 bp):
AAGACGCCATTTTCGGGTTTTCACCTTGATTCCTTTTTTTT
Found at i:28503447 original size:78 final size:78
Alignment explanation
Indices: 28503318--28503476 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 78
28503308 TCCATCCGGT
28503318 CTTGAAGCAACCTTTTAAATTCCTCACACGATTGAATGTCGTGTCCTACAATTCCATGGAAATCG
1 CTTGAAGCAACCTTTTAAATTCCTCACACGATTGAATGTCGTGTCCTACAATTCCATGGAAATCG
28503383 CAAAAACTTTGAC
66 CAAAAACTTTGAC
*
28503396 CTTGAAGCAACCTTTTAAATTCCTCACACGATTGAATGTCGTGTCCTACAATTTCATGGAAATCG
1 CTTGAAGCAACCTTTTAAATTCCTCACACGATTGAATGTCGTGTCCTACAATTCCATGGAAATCG
28503461 CAAAAACTTTGAC
66 CAAAAACTTTGAC
28503474 CTT
1 CTT
28503477 CTTCTCTGAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (78 bp):
CTTGAAGCAACCTTTTAAATTCCTCACACGATTGAATGTCGTGTCCTACAATTCCATGGAAATCG
CAAAAACTTTGAC
Found at i:28509644 original size:24 final size:25
Alignment explanation
Indices: 28509565--28509658 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 25
28509555 AATAATAAGG
* * *
28509565 ATAATATAAAAAAATACATACATGAA
1 ATAATAT-AAAATATATATATATGAA
*
28509591 ATAGTATAAAATATATATATAT-AA
1 ATAATATAAAATATATATATATGAA
* *
28509615 CTAATAATATACATATATATATATGAA
1 ATAAT-ATA-AAATATATATATATGAA
*
28509642 ATAACAATAAAATATAT
1 ATAA-TATAAAATATAT
28509659 GAATAGTATG
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
24 5 0.09
25 15 0.28
26 26 0.48
27 8 0.15
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAATATAAAATATATATATATGAA
Found at i:28509744 original size:18 final size:17
Alignment explanation
Indices: 28509711--28509748 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28509701 TAAAATATAT
28509711 ATATACAATACAATAAA
1 ATATACAATACAATAAA
* *
28509728 ATATACAA-ATAATATA
1 ATATACAATACAATAAA
28509744 ATATA
1 ATATA
28509749 TAAAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATACAATACAATAAA
Found at i:28509749 original size:18 final size:17
Alignment explanation
Indices: 28509678--28509750 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 17
28509668 GATACTTACA
28509678 AATATATAC-ATAATAT
1 AATATATACAATAATAT
**
28509694 AAT-TATTTAA-AATAT
1 AATATATACAATAATAT
28509709 -ATATATACAATACA-AT
1 AATATATACAATA-ATAT
*
28509725 AAAATATACAAATAATAT
1 AATATATAC-AATAATAT
28509743 AATATATA
1 AATATATA
28509751 AAGAAAAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.05
15 13 0.30
16 7 0.16
17 9 0.20
18 13 0.30
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATATACAATAATAT
Found at i:28509969 original size:33 final size:33
Alignment explanation
Indices: 28509932--28509996 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
28509922 GCATATATGT
28509932 ATAATAATGATAAATAAATAA-ATAAAAATAAAA
1 ATAATAATGA-AAATAAATAATATAAAAATAAAA
** * *
28509965 ATAATTGTGAAAGTAAATAATATAATAATAAA
1 ATAATAATGAAAATAAATAATATAAAAATAAA
28509997 TACATATGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (33 bp):
ATAATAATGAAAATAAATAATATAAAAATAAAA
Found at i:28510074 original size:14 final size:14
Alignment explanation
Indices: 28510057--28510084 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28510047 ATATCTAAGT
28510057 ATAATATAATAATA
1 ATAATATAATAATA
28510071 ATAATATAATAATA
1 ATAATATAATAATA
28510085 TTATTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATATAATAATA
Found at i:28510537 original size:9 final size:8
Alignment explanation
Indices: 28510523--28510561 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
28510513 AAAAGGTAAT
28510523 TTTTTTTA
1 TTTTTTTA
28510531 CTTTTTTTA
1 -TTTTTTTA
*
28510540 TATTTTTA
1 TTTTTTTA
28510548 TATTTTTTA
1 T-TTTTTTA
28510557 TTTTT
1 TTTTT
28510562 GCAATGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:28510547 original size:17 final size:16
Alignment explanation
Indices: 28510524--28510561 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
28510514 AAAGGTAATT
28510524 TTTTTTACT-TTTTTTA
1 TTTTTTA-TATTTTTTA
28510540 TATTTTTATATTTTTTA
1 T-TTTTTATATTTTTTA
28510557 TTTTT
1 TTTTT
28510562 GCAATGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTATATTTTTTA
Found at i:28510622 original size:3 final size:3
Alignment explanation
Indices: 28510614--28510642 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28510604 AATAGATGAA
28510614 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28510643 AGTCACCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28513751 original size:26 final size:26
Alignment explanation
Indices: 28513715--28514526 Score: 1606
Period size: 26 Copynumber: 31.2 Consensus size: 26
28513705 CATGAAATTC
28513715 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513741 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513767 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513793 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513819 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513845 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513871 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513897 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513923 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513949 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28513975 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514001 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514027 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514053 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514079 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514105 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514131 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514157 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514183 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514209 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514235 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514261 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514287 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514313 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514339 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514365 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514391 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514417 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514443 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28514469 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28514495 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28514521 TTATCA
1 TTATCA
28514527 ATTTGTATCA
Statistics
Matches: 784, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 784 1.00
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28519067 original size:9 final size:11
Alignment explanation
Indices: 28519040--28519076 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
28519030 TAATTTTAGG
28519040 ATATATATTTT
1 ATATATATTTT
28519051 ATATATATTTT
1 ATATATATTTT
*
28519062 AAATATAATTTT
1 ATATAT-ATTTT
28519074 ATA
1 ATA
28519077 AAAATTGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATATATTTT
Found at i:28520143 original size:50 final size:51
Alignment explanation
Indices: 28520058--28520156 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 51
28520048 ATCGATTTTA
28520058 GTCTACGTAGATTTTAAAAAAAAAAGAGTTCGGGAGCCGGTTACGTATGAG
1 GTCTACGTAGATTTTAAAAAAAAAAGAGTTCGGGAGCCGGTTACGTATGAG
*
28520109 GTCTACGTAGA-TTTAAAAAAAAAAGGGTTCGGGAGCCGGTTACGTATG
1 GTCTACGTAGATTTTAAAAAAAAAAGAGTTCGGGAGCCGGTTACGTATG
28520157 GTACCAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 36 0.77
51 11 0.23
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (51 bp):
GTCTACGTAGATTTTAAAAAAAAAAGAGTTCGGGAGCCGGTTACGTATGAG
Found at i:28520958 original size:17 final size:18
Alignment explanation
Indices: 28520936--28520975 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28520926 ACTTATGTGC
28520936 ATATAAA-AATTAATAAA
1 ATATAAATAATTAATAAA
* *
28520953 ATATAAATGATTATTAAA
1 ATATAAATAATTAATAAA
28520971 ATATA
1 ATATA
28520976 TATTATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATATAAATAATTAATAAA
Found at i:28522069 original size:9 final size:9
Alignment explanation
Indices: 28522047--28522081 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
28522037 ATGGACTTTT
*
28522047 ATTTATTGG
1 ATTTATTTG
*
28522056 TTTTATTTG
1 ATTTATTTG
28522065 ATTTATTTG
1 ATTTATTTG
28522074 ATTTATTT
1 ATTTATTT
28522082 TTGGATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (9 bp):
ATTTATTTG
Found at i:28525115 original size:16 final size:17
Alignment explanation
Indices: 28525094--28525132 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
28525084 TTTTTAAATT
28525094 AAAAATAATAT-TTTTA
1 AAAAATAATATATTTTA
28525110 AAAAATAATATATTTTA
1 AAAAATAATATATTTTA
*
28525127 TAAAAT
1 AAAAAT
28525133 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAATAATATATTTTA
Found at i:28525119 original size:19 final size:17
Alignment explanation
Indices: 28525084--28525131 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 17
28525074 AGCTTAATTT
28525084 TTTTTAAATTAAAAATAATA
1 TTTTTAAA--AAAAAT-ATA
28525104 TTTTTAAAAAATAATATA
1 TTTTTAAAAAA-AATATA
28525122 TTTTATAAAA
1 TTTT-TAAAA
28525132 TTTTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.38
19 8 0.31
20 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTTAAAAAAAATATA
Found at i:28525147 original size:17 final size:18
Alignment explanation
Indices: 28525127--28525173 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
28525117 ATATATTTTA
*
28525127 TAAAATTTTA-TAAAATT
1 TAAAATATTATTAAAATT
28525144 TAAAATATTATTAAAATAT
1 TAAAATATTATTAAAAT-T
28525163 ATAAAATATTA
1 -TAAAATATTA
28525174 AATAAAGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 6 0.23
19 1 0.04
20 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATATTATTAAAATT
Found at i:28526643 original size:19 final size:19
Alignment explanation
Indices: 28526619--28526712 Score: 110
Period size: 19 Copynumber: 5.2 Consensus size: 19
28526609 ATTCTTTAAG
28526619 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28526638 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28526657 GATAT--AATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
28526674 GATATG--AT-AT-GATAT
1 GATATGCAATCTTAGATAT
*
28526689 GATAAGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
28526710 GAT
1 GAT
28526713 TTTGTAATCT
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.15
16 1 0.02
17 21 0.32
18 1 0.02
19 24 0.37
21 8 0.12
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28531943 original size:6 final size:6
Alignment explanation
Indices: 28531928--28531962 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
28531918 CATCCATTTC
*
28531928 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AGAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
28531963 TTATATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:28533468 original size:15 final size:16
Alignment explanation
Indices: 28533447--28533494 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
28533437 TTCTATTTCA
*
28533447 AAAAAAAAAGAAAAAG
1 AAAAAAAAATAAAAAG
28533463 AAAAAAAATAATAAAAAG
1 -AAAAAAA-AATAAAAAG
28533481 -AAAAAAAATAAAAA
1 AAAAAAAAATAAAAA
28533495 ATGGAGAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.28
16 6 0.21
17 7 0.24
18 8 0.28
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAAAAATAAAAAG
Found at i:28533489 original size:18 final size:17
Alignment explanation
Indices: 28533446--28533495 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 17
28533436 CTTCTATTTC
28533446 AAAAAAAA-AAGAAAAAG
1 AAAAAAAATAA-AAAAAG
28533463 AAAAAAAATAATAAAAAG
1 AAAAAAAATAA-AAAAAG
28533481 AAAAAAAATAAAAAA
1 AAAAAAAATAAAAAA
28533496 TGGAGAAGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAG
Found at i:28534891 original size:205 final size:204
Alignment explanation
Indices: 28534538--28535346 Score: 1315
Period size: 205 Copynumber: 4.0 Consensus size: 204
28534528 ATAACAGATT
*
28534538 TGGCATCTCCATTTCGACGGAGAGTAGATACATAGCAGATCTAACCTTCAGATGATTTTACTGAA
1 TGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATG-TTTTACTGAA
* * *
28534603 GCTGATCCAAGATGATTTGGCATCCTTGTG-TTCACAAGGAACAAATTGAAGACATAGCTGATTT
65 GCAGATCCAAGATGGTTTGGCATCCTTGTGCTT-ACAAGGAACAAATCGAAGACATAGCTGATTT
*
28534667 GGCTTTCACGTGCTTACGATGAAGAAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAAC
129 GGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAAC
*
28534732 AAATAGAAGTC
194 AAATCGAAGTC
* * *
28534743 TGGCATCTCCATTTCGATGGAGAGTAGATACATAGCAGATCTAACCATCAGATGTTTATACTGAA
1 TGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGTTT-TACTGAA
28534808 GCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAATTT
65 GCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG-ATTT
* *
28534873 -GCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATATCTGTATTGTCAGAGAAC
129 GGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAAC
28534937 AAATCGAAGTC
194 AAATCGAAGTC
* *
28534948 TGGCATCTCCATTTCGACAGAGACCAGATACATAGCAGATCTAACCTTCAGATGTTTATACTGAA
1 TGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGTTT-TACTGAA
* * *
28535013 GCAGATCCAAGATGGTTTGGCGTCCTTGTGCTTACAAGGGACAAATAGAAGACATAGCTGATTTG
65 GCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTG
28535078 GCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACA
130 GCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACA
28535143 AATCGAAGTC
195 AATCGAAGTC
*
28535153 TGGCATCTCCATTTCGACGGAGAACAGATACATAGCAGATCTAACCTTCAGATG----ACTGAAG
1 TGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGTTTTACTGAAG
*
28535214 CAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGTTGATTTGG
66 CAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGG
* * * * * *
28535279 TTTTCGCGTGCTTATGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTTAGAGAGCAA
131 CTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
28535344 ATC
196 ATC
28535347 AAAGAAACAG
Statistics
Matches: 569, Mismatches: 31, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
200 130 0.23
204 7 0.01
205 426 0.75
206 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (204 bp):
TGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGTTTTACTGAAG
CAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGG
CTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
ATCGAAGTC
Found at i:28535693 original size:261 final size:256
Alignment explanation
Indices: 28535182--28535696 Score: 710
Period size: 261 Copynumber: 2.0 Consensus size: 256
28535172 GAGAACAGAT
* *
28535182 ACATAGCAGATCTAACCTTCAGATGACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
1 ACATAGCAGATCTAACCTTCAGATGACTAAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTA
* *** * * *
28535247 CAAGGAACAAATCGAAGACATAGTTGATTTGGTTTTCGCGTGCTTATGCTGAAGCAAATCTAAGA
66 CAAGGAACAAATCGAAGACACAACAGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGA
* * *
28535312 TGATTTGGCATCTCTGTATTGTTAGAGAGCAAATCAAAGAAACAGATTTGGCGTCTCTGTATTCG
131 TGATTTGGCATCTCTGTATTGTCAGAAAACAAATCAAAGAAACAGATTTGGCGTCTCTGTATTCG
* *
28535377 GCGGAGAGTAGATCGAAGATATCAACAGGACAGTCATAAGTTTACAAGAAGCAGATTAAAG
196 ACGGAGAGCAGATCGAAGATATCAACAGGACAGTCATAAGTTTACAAGAAGCAGATTAAAG
*
28535438 ACATAGCAGATCTGACCTTCAGATGATTTTACTAAAGCAGATCCAAGATGATTTGGCATCCTTGT
1 ACATAGCAGATCTAACCTTCAGATG-----ACTAAAGCAGATCCAAGATGATTTGGCATCCTTGT
* * *
28535503 G-TTCACAAGGAGCAAATTGAAGACACAACAGATTTGGCTTTCACGTGCTTACGCTGAAGCAGAT
61 GCTT-ACAAGGAACAAATCGAAGACACAACAGATTTGGCTTTCACGTGCTTACGCTGAAGCAAAT
** *
28535567 CTAAGATGATTTGGCATCTCTGTATTGTCAGAAAACAAATTGAAGAAGCAGATTTGGCGTCTCTG
125 CTAAGATGATTTGGCATCTCTGTATTGTCAGAAAACAAATCAAAGAAACAGATTTGGCGTCTCTG
* * * * * *
28535632 TGTTCGACGGAGTGCAGATCGAAGATATCAACATGACAGTCTTGAGTTTGCAATG-AGCAGATTA
190 TATTCGACGGAGAGCAGATCGAAGATATCAACAGGACAGTCATAAGTTTACAA-GAAGCAGATTA
28535696 A
254 A
28535697 GGACCATGAT
Statistics
Matches: 225, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
256 24 0.11
260 2 0.01
261 198 0.88
262 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (256 bp):
ACATAGCAGATCTAACCTTCAGATGACTAAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTA
CAAGGAACAAATCGAAGACACAACAGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGA
TGATTTGGCATCTCTGTATTGTCAGAAAACAAATCAAAGAAACAGATTTGGCGTCTCTGTATTCG
ACGGAGAGCAGATCGAAGATATCAACAGGACAGTCATAAGTTTACAAGAAGCAGATTAAAG
Found at i:28536006 original size:17 final size:17
Alignment explanation
Indices: 28535986--28536019 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28535976 AAGGATATGC
28535986 AATCTTAGATATGATAT
1 AATCTTAGATATGATAT
28536003 AATCTTAGATATGATAT
1 AATCTTAGATATGATAT
28536020 GATATGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
AATCTTAGATATGATAT
Found at i:28536018 original size:5 final size:5
Alignment explanation
Indices: 28536010--28536035 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28536000 TATAATCTTA
28536010 GATAT GATAT GATAT GATAT GATAT G
1 GATAT GATAT GATAT GATAT GATAT G
28536036 CAATCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
GATAT
Found at i:28548477 original size:206 final size:207
Alignment explanation
Indices: 28548123--28548675 Score: 885
Period size: 206 Copynumber: 2.7 Consensus size: 207
28548113 GATCTAGCTG
28548123 AAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAT
1 AAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAT
* *
28548188 TTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTCAGAGA
66 TTGGCTTTCACGTGCTTACAATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
* * **
28548253 GCAAATCGAAGTTTGGCGTCTCCATATT-GACGGAGAGCAGACATATAGCAGATCTGGCCTTCAG
131 ACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAG
* *
28548317 ATGTTTATACTA
196 ATGATTAGACTA
*
28548329 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAT
1 AAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAT
* *
28548394 TTAGCTTTCACGTGTTTACAATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
66 TTGGCTTTCACGTGCTTACAATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
*
28548459 ACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTCAG
131 ACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAG
*
28548524 ATGATTAGACTG
196 ATGATTAGACTA
* * * * *
28548536 AAGC-AGATCCAAAATGGTTTGGTATCCTTATGCTTACAAGGAGCAAATCGAAAACATAGCTGAT
1 AAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAT
* * * * *
28548600 TTGGTTTTCACATGCTTACACTGAAACAAATCTAAGATGATTTGGCATCTCTGTATTGACAGAGA
66 TTGGCTTTCACGTGCTTACAATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
28548665 ACAAATCGAAG
131 ACAAATCGAAG
28548676 AAGCAGATTT
Statistics
Matches: 320, Mismatches: 26, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
206 275 0.86
207 45 0.14
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (207 bp):
AAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGAT
TTGGCTTTCACGTGCTTACAATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
ACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAG
ATGATTAGACTA
Found at i:28548688 original size:43 final size:44
Alignment explanation
Indices: 28548638--28548720 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
28548628 AATCTAAGAT
*
28548638 GATTTGGCATCTCTGTATTGA-CAGAGAACAAATCGAAGAAGCA
1 GATTTGGCATCTCTGTATTCAGCAGAGAACAAATCGAAGAAGCA
* * * *
28548681 GATTTGGCGTCTCTGTGTTCAGCGGAGAGCAAATCGAAGA
1 GATTTGGCATCTCTGTATTCAGCAGAGAACAAATCGAAGA
28548721 TATCAACATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 18 0.53
44 16 0.47
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTCAGCAGAGAACAAATCGAAGAAGCA
Found at i:28552568 original size:16 final size:15
Alignment explanation
Indices: 28552542--28552571 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28552532 AGAAGAAAAA
28552542 TTATATTTTCTCTCC
1 TTATATTTTCTCTCC
28552557 TTATACTTTTCTCTC
1 TTATA-TTTTCTCTC
28552572 TAGTTTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTTTCTCTCC
Found at i:28553363 original size:30 final size:30
Alignment explanation
Indices: 28553327--28553388 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
28553317 CAACTTAACA
*
28553327 AACAAATACCTCTAAAATAATAATAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
* *
28553357 AACAAATGCCTTTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
28553387 AA
1 AA
28553389 TAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:28555390 original size:6 final size:6
Alignment explanation
Indices: 28555379--28555433 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
28555369 GAAGTCTAAG
* *
28555379 AAAATA AAAATA AATATA AAAATA GAAATA AAAATA AAAATA AAAAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
28555426 AAAATA AA
1 AAAATA AA
28555434 TAAACTCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:28567117 original size:86 final size:86
Alignment explanation
Indices: 28566948--28567119 Score: 251
Period size: 86 Copynumber: 2.0 Consensus size: 86
28566938 AGAAAATATT
** * *
28566948 TTTTCTTTTGATTTTTTCATCTTTCCTACTAAGCACACATATGGAAAGAAATTTATATTTTCCAT
1 TTTTCTTTCAATTTTTCCATCTTTCCTACCAAGCACACATATGGAAAGAAATTTATATTTTCCAT
28567013 CTTCATATTTTTCTCCCTTTC
66 CTTCATATTTTTCTCCCTTTC
*
28567034 TTTTCTTTCAATTTTTCCGTCTTTCCTACCAAGCACACATATGGAAAGAAAATTTATATTTT-C-
1 TTTTCTTTCAATTTTTCCATCTTTCCTACCAAGCACACATATGGAAAG-AAATTTATATTTTCCA
28567097 TCTTTC-TATTTTTCTACCCTTTC
65 TC-TTCATATTTTTCT-CCCTTTC
28567120 AAATNNNNNN
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
85 11 0.14
86 54 0.69
87 13 0.17
ACGTcount: A:0.23, C:0.22, G:0.06, T:0.49
Consensus pattern (86 bp):
TTTTCTTTCAATTTTTCCATCTTTCCTACCAAGCACACATATGGAAAGAAATTTATATTTTCCAT
CTTCATATTTTTCTCCCTTTC
Found at i:28567751 original size:3 final size:3
Alignment explanation
Indices: 28567745--28567865 Score: 242
Period size: 3 Copynumber: 40.3 Consensus size: 3
28567735 NNNCTACTAC
28567745 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28567793 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28567841 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
28567866 TTAAAAAAAC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28570350 original size:72 final size:70
Alignment explanation
Indices: 28570274--28570502 Score: 209
Period size: 72 Copynumber: 3.2 Consensus size: 70
28570264 ACAAATTGGA
*
28570274 TAAATTGCCAATACAAGATGGGATTGAACCACTCAATTTGTTTTGGGAGAGGCTTAATGAAGTTA
1 TAAATTCCCAAT-CAA-ATGGGATTGAACCACTCAATTTGTTTTGGGAGAGGCTTAATGAAGTTA
28570339 AATTTGC
64 AATTTGC
* * * * * * * *
28570346 TAAATTCTCAATCTCAATGGGAATGGAACCAATCAGTCTGTTCTT-AGTGAGG-TCTAA-GAAAC
1 TAAATTCCCAATC-AAATGGG-ATTGAACCACTCAATTTGTT-TTGGGAGAGGCT-TAATG-AA-
28570408 G-T-AATGCTT-C
60 GTTAAAT--TTGC
* *
28570418 TAAATTCCCAATCAGAAAGGGGATTGAACCACTCAATTTGTTTTGGGAGAGTCTTAATGAAGTTA
1 TAAATTCCCAATC--AAATGGGATTGAACCACTCAATTTGTTTTGGGAGAGGCTTAATGAAGTTA
28570483 AATTTGC
64 AATTTGC
28570490 TAAATTCCCAATC
1 TAAATTCCCAATC
28570503 TCTTTGGGAA
Statistics
Matches: 122, Mismatches: 20, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
71 16 0.13
72 91 0.75
73 15 0.12
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (70 bp):
TAAATTCCCAATCAAATGGGATTGAACCACTCAATTTGTTTTGGGAGAGGCTTAATGAAGTTAAA
TTTGC
Found at i:28576544 original size:31 final size:31
Alignment explanation
Indices: 28576506--28576597 Score: 116
Period size: 32 Copynumber: 2.9 Consensus size: 31
28576496 GATCGTAACT
28576506 TTAAAAGAAGATATATATATATAGAAAAACC
1 TTAAAAGAAGATATATATATATAGAAAAACC
* * *
28576537 TTAAAAGAA-ATATATTATACGCATA-AATAACT
1 TTAAAAGAAGATATA-TATA--TATAGAAAAACC
28576569 TTAAAAGAAGATATATATATATAGAAAAA
1 TTAAAAGAAGATATATATATATAGAAAAA
28576598 TATTTACATA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
30 8 0.16
31 17 0.33
32 18 0.35
33 8 0.16
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (31 bp):
TTAAAAGAAGATATATATATATAGAAAAACC
Found at i:28578973 original size:53 final size:50
Alignment explanation
Indices: 28578916--28579061 Score: 150
Period size: 53 Copynumber: 2.8 Consensus size: 50
28578906 TTCTTTTTTA
28578916 TTATTGAGTCCCAAAGCGCCCTTTGCGGGTTTTCACTTTGGCCCTTTCCATTT
1 TTATTGAGTCCCAAAGCGCCCTTTGCGGGTTTTCACTTTGGCCC---CCATTT
** * * *
28578969 TTATTTG-GTCTTAAAGTGCCCTTTGCGGGTTTTCACTTTAGCCCCCTTTT
1 TTA-TTGAGTCCCAAAGCGCCCTTTGCGGGTTTTCACTTTGGCCCCCATTT
* * * * *
28579019 TTTTTAAAGTCCCAAAACGCCTTTTGCGGGTTTTCACTCTGGC
1 TTATT-GAGTCCCAAAGCGCCCTTTGCGGGTTTTCACTTTGGC
28579062 TTCCCTCTCT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
49 2 0.03
50 7 0.09
51 28 0.37
53 36 0.47
54 3 0.04
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.41
Consensus pattern (50 bp):
TTATTGAGTCCCAAAGCGCCCTTTGCGGGTTTTCACTTTGGCCCCCATTT
Found at i:28583744 original size:24 final size:24
Alignment explanation
Indices: 28583717--28583776 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28583707 TTGTGTTTAC
28583717 GTTTTGAGGGTTCTTTGTTTTCG-G
1 GTTTTG-GGGTTCTTTGTTTTCGAG
*
28583741 GTTTTCGGGGTTTTTTGTTTTCGAG
1 GTTTT-GGGGTTCTTTGTTTTCGAG
*
28583766 CTTTTGGGGTT
1 GTTTTGGGGTT
28583777 TACTCTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.03, C:0.08, G:0.33, T:0.55
Consensus pattern (24 bp):
GTTTTGGGGTTCTTTGTTTTCGAG
Found at i:28585465 original size:131 final size:131
Alignment explanation
Indices: 28585325--28585794 Score: 454
Period size: 131 Copynumber: 3.6 Consensus size: 131
28585315 GTAAAACCGA
* * * * *
28585325 AACCCAGCAC-AGTAGGGCACGATTCCTCGAATTTCTAGACATCGAGCATTGCC-TTATTTT-TA
1 AACCCAGCACGA-TAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTTATTTTATA
* *
28585387 GAATTTTTAAGAAACATAAGTGAAATTCTAAAGGGGATATTTGATTATTTTGAACCAACAGGAAA
65 GAATTTTTAAGAAACATAAGTGAAATTCTAAA-GGGATATTCGATTATTTTGAACAAAC-GGAAA
28585452 TCGC
128 TCGC
* * *
28585456 AACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACGTTACCTTTGTTTTATAG
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTTATTTTATAG
* * ** * * ** *
28585521 AATCTTTAA-AGACATGGGTAAAATT-TCAAAGGAATATTCGATGGTTTTGAACGAACGGGAAAT
66 AATTTTTAAGAAACATAAGTGAAATTCT-AAAGGGATATTCGATTATTTTGAACAAAC-GGAAAT
28585584 CGC
129 CGC
** * *
28585587 AACCCAGCACGATAGGGCACGATT-CTCGAATTGCCAAACATAAAATATTACCTTTATTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTTATTTTATAG
* * * *
28585651 AGTTTTT-AGAAAACATGAA-TGAAATTCTAAAGAGACATTCGATTATTTTGAGCAAACGAGAAA
66 AATTTTTAAG-AAACAT-AAGTGAAATTCTAAAGGGATATTCGATTATTTTGAACAAACG-GAAA
*
28585714 TTGC
128 TCGC
* * * * * * ** * *
28585718 AACCCAACACGTTAGGGCACGATTCCGCGAATTTCCAAATATCGTACATCGCCTTCATTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTTATTTTATAG
*
28585783 GATTTTT-AGAAA
66 AATTTTTAAGAAA
28585795 ACATGAATGA
Statistics
Matches: 275, Mismatches: 54, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
129 1 0.00
130 39 0.14
131 164 0.60
132 60 0.22
133 11 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (131 bp):
AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTTATTTTATAG
AATTTTTAAGAAACATAAGTGAAATTCTAAAGGGATATTCGATTATTTTGAACAAACGGAAATCG
C
Found at i:28588954 original size:133 final size:133
Alignment explanation
Indices: 28588795--28589100 Score: 418
Period size: 133 Copynumber: 2.3 Consensus size: 133
28588785 AAGATTGTGA
* * * * ** * *
28588795 CTTCGATCCGCTCCACTGTAATTTCAGGGAGATAAGATCTAC-ACTCTTCGGTTTGCTCCACTGC
1 CTTCGATCTGCTCCACTGCAATTTCAGGGAGACAAGATCTACAAC-CTTCAGCCTACTCCACTAC
*
28588859 AACTTCAGAGAGATAAGATGGTGGCTCAAATCTGCTTCAATGCAACTTCAGG-AGAGCGAGATTC
65 AACTTCAGAGAGATAAGATGGTGGCTCAAATCTGCTTCAATACAACTTCAGGAAG-GCGAGATTC
28588923 GCCAT
129 GCCAT
* *
28588928 CTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAACCTTCAGCCTACTCCACTACA
1 CTTCGATCTGCTCCACTGCAATTTCAGGGAGACAAGATCTACAACCTTCAGCCTACTCCACTACA
* * * * * *
28588993 ACTTTAGGGAGATAGGGTGGTGGCTTAAATCTGCTTCACTACAACTTCAGGAAGGCGAGATTCGC
66 ACTTCAGAGAGATAAGATGGTGGCTCAAATCTGCTTCAATACAACTTCAGGAAGGCGAGATTCGC
28589058 CAT
131 CAT
*
28589061 TTTCGATCTGCTCCACTGCAATTTCAGGGAGACAAGATCT
1 CTTCGATCTGCTCCACTGCAATTTCAGGGAGACAAGATCT
28589101 GTAGAGTCGA
Statistics
Matches: 151, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
133 147 0.97
134 4 0.03
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (133 bp):
CTTCGATCTGCTCCACTGCAATTTCAGGGAGACAAGATCTACAACCTTCAGCCTACTCCACTACA
ACTTCAGAGAGATAAGATGGTGGCTCAAATCTGCTTCAATACAACTTCAGGAAGGCGAGATTCGC
CAT
Found at i:28598732 original size:20 final size:22
Alignment explanation
Indices: 28598691--28598744 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
28598681 TAATAATAGA
28598691 ATATTTTA-A-TTTTAAGACAT
1 ATATTTTATATTTTTAAGACAT
28598711 ATATTTTATATTTTTAA-A-AT
1 ATATTTTATATTTTTAAGACAT
*
28598731 ATAATTATATATTT
1 AT-ATTTTATATTT
28598745 CTTATTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.40
21 12 0.40
22 6 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTTTATATTTTTAAGACAT
Found at i:28598741 original size:21 final size:22
Alignment explanation
Indices: 28598700--28598744 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
28598690 AATATTTTAA
*
28598700 TTTTAAGACATATATTTTATAT
1 TTTTAAGACATATATTATATAT
28598722 TTTTAA-A-ATATAATTATATAT
1 TTTTAAGACATAT-ATTATATAT
28598743 TT
1 TT
28598745 CTTATTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTAAGACATATATTATATAT
Found at i:28600081 original size:34 final size:34
Alignment explanation
Indices: 28600030--28600094 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
28600020 ATAATGCATA
28600030 AAAAAAAGATCCTGATAATATTAATGATACAGAT
1 AAAAAAAGATCCTGATAATATTAATGATACAGAT
* *
28600064 AAAAAATGAT-CTCGATAATGTTAATGATACA
1 AAAAAAAGATCCT-GATAATATTAATGATACA
28600095 TATTCAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (34 bp):
AAAAAAAGATCCTGATAATATTAATGATACAGAT
Found at i:28603254 original size:10 final size:10
Alignment explanation
Indices: 28603224--28603264 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
28603214 ATCACAAGTC
28603224 TTGTGATATA
1 TTGTGATATA
*
28603234 GTGTGATATA
1 TTGTGATATA
28603244 TTGTGATATA
1 TTGTGATATA
*
28603254 TATATGATATA
1 T-TGTGATATA
28603265 CGTAGAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (10 bp):
TTGTGATATA
Found at i:28606073 original size:10 final size:10
Alignment explanation
Indices: 28606058--28606090 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
28606048 TGATTTCACT
28606058 TTTGATTGTA
1 TTTGATTGTA
28606068 TTTGATTGTA
1 TTTGATTGTA
*
28606078 TTTGATTCTA
1 TTTGATTGTA
28606088 TTT
1 TTT
28606091 AATCGGCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (10 bp):
TTTGATTGTA
Found at i:28611695 original size:73 final size:73
Alignment explanation
Indices: 28611591--28611735 Score: 272
Period size: 73 Copynumber: 2.0 Consensus size: 73
28611581 AAGAAATTCT
* *
28611591 GCATATTTTGACCGATTCAAGGTAAAAAATGGGGTTGCTCCCTCGGTAAAACTGGGATAAAGTTG
1 GCATATTTTGACCAATTCAAGGTAAAAAATGGGGTTGCTCCCTCGGCAAAACTGGGATAAAGTTG
28611656 AGCCAAAC
66 AGCCAAAC
28611664 GCATATTTTGACCAATTCAAGGTAAAAAATGGGGTTGCTCCCTCGGCAAAACTGGGATAAAGTTG
1 GCATATTTTGACCAATTCAAGGTAAAAAATGGGGTTGCTCCCTCGGCAAAACTGGGATAAAGTTG
28611729 AGCCAAA
66 AGCCAAA
28611736 AGATCACGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (73 bp):
GCATATTTTGACCAATTCAAGGTAAAAAATGGGGTTGCTCCCTCGGCAAAACTGGGATAAAGTTG
AGCCAAAC
Found at i:28612602 original size:15 final size:15
Alignment explanation
Indices: 28612584--28612614 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28612574 ATCTCTCATC
28612584 TATCTATCTATTTTT
1 TATCTATCTATTTTT
28612599 TATCTATCTATTTTT
1 TATCTATCTATTTTT
28612614 T
1 T
28612615 CTTTAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATCTATCTATTTTT
Found at i:28612734 original size:56 final size:56
Alignment explanation
Indices: 28612648--28612758 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
28612638 TATGATCTGA
*
28612648 AAGTCGATCCGGGGCAAGTGTTCGGATCTATTATGACATATCCATGAGGCGCTCAG
1 AAGTCGATCCGAGGCAAGTGTTCGGATCTATTATGACATATCCATGAGGCGCTCAG
28612704 AAGTCGATCCGAGGCAAGTGTTCGGATCTATTATGACATATCCATGAGGCGCTCA
1 AAGTCGATCCGAGGCAAGTGTTCGGATCTATTATGACATATCCATGAGGCGCTCA
28612759 ACGGACCTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (56 bp):
AAGTCGATCCGAGGCAAGTGTTCGGATCTATTATGACATATCCATGAGGCGCTCAG
Found at i:28613339 original size:74 final size:76
Alignment explanation
Indices: 28613251--28613401 Score: 270
Period size: 74 Copynumber: 2.0 Consensus size: 76
28613241 TAAATATTCA
28613251 ATTCAAATTGACTAGAAAATCGAATTTAATAATTTAAATAGTACCGTAATTTATTTAATTAAATT
1 ATTCAAATTGACTAGAAAATCGAATTTAATAATTTAAATAGTACCGTAATTTATTTAATTAAATT
28613316 -AAT-TTAAAT
66 AAATATTAAAT
* *
28613325 ATTCAAATTTACTAGAAAATCGAATTTAATAATTTAAATGGTACCGTAATTTATTTAATTAAATT
1 ATTCAAATTGACTAGAAAATCGAATTTAATAATTTAAATAGTACCGTAATTTATTTAATTAAATT
28613390 AAATATTAAAT
66 AAATATTAAAT
28613401 A
1 A
28613402 AATGGATTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 63 0.86
75 3 0.04
76 7 0.10
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (76 bp):
ATTCAAATTGACTAGAAAATCGAATTTAATAATTTAAATAGTACCGTAATTTATTTAATTAAATT
AAATATTAAAT
Found at i:28615528 original size:71 final size:71
Alignment explanation
Indices: 28615412--28615553 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
28615402 GCCGAAGGCA
*
28615412 GGGCTAGTGACTGGAGTGAAGTCGTAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTC
1 GGGCTAGTGACTGGAGTGAAGTCATAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTC
28615477 CTTTTC
66 CTTTTC
28615483 GGGCTAGTGACTGGAGTGAAGTCATAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTC
1 GGGCTAGTGACTGGAGTGAAGTCATAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTC
28615548 CTTTTC
66 CTTTTC
28615554 AGGGAGAGCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (71 bp):
GGGCTAGTGACTGGAGTGAAGTCATAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTC
CTTTTC
Found at i:28621058 original size:32 final size:32
Alignment explanation
Indices: 28621017--28621078 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
28621007 CATCTATTTT
28621017 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
28621049 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
28621079 ACCAAGAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:28628655 original size:93 final size:93
Alignment explanation
Indices: 28628533--28628706 Score: 255
Period size: 93 Copynumber: 1.9 Consensus size: 93
28628523 TCACATACCT
28628533 ATGCCGATGCCATGTCCCAGACATGGTCTTTACACTGACACATC-T-CGTAGCCA-ATGCATGTC
1 ATGCCGATGCCATGTCCCAGACATGGTC-TTACACTGACAC-TCATACGT-GCCAGATGCATGTC
28628595 CCAGACATGTCTTACACTGGTTCTCGTCTCA
63 CCAGACATGTCTTACACTGGTTCTCGTCTCA
* * * *
28628626 ATGCCGATGCCATGTCCCATACATGGTCTTACACTGACTCTCATAATGTGGCAGATGCATGTCCC
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCAT-ACGTGCCAGATGCATGTCCC
28628691 AGACATGTCTTACACT
65 AGACATGTCTTACACT
28628707 AGCACACACA
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
91 2 0.03
92 12 0.16
93 30 0.41
94 29 0.40
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (93 bp):
ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACTCATACGTGCCAGATGCATGTCCCA
GACATGTCTTACACTGGTTCTCGTCTCA
Found at i:28632456 original size:24 final size:24
Alignment explanation
Indices: 28632424--28632524 Score: 184
Period size: 24 Copynumber: 4.2 Consensus size: 24
28632414 AAGTCTGTCA
28632424 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
28632448 GGAGAGGATTTAGGAGCTAATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
28632472 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
28632496 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
28632520 GGAGA
1 GGAGA
28632525 ACAGTGTTGG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.34, C:0.04, G:0.42, T:0.21
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:28633966 original size:27 final size:27
Alignment explanation
Indices: 28633928--28634030 Score: 147
Period size: 27 Copynumber: 3.8 Consensus size: 27
28633918 AAGCATCCTG
*
28633928 GTGGCTATGCCACA-ATTATCTGATCTA
1 GTGGCTCTGCCACATA-TATCTGATCTA
28633955 GTGGCTCTGCCACATATATCTGATCTA
1 GTGGCTCTGCCACATATATCTGATCTA
* *
28633982 GTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTCTGCCACATATATCTGATCTA
28634009 GTGGCTCTGCCACGAT-TATCTG
1 GTGGCTCTGCCAC-ATATATCTG
28634031 TTCTGGCAGC
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
27 68 0.96
28 3 0.04
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
GTGGCTCTGCCACATATATCTGATCTA
Found at i:28640323 original size:24 final size:24
Alignment explanation
Indices: 28640290--28640390 Score: 157
Period size: 24 Copynumber: 4.2 Consensus size: 24
28640280 AAGTCTGTCA
*
28640290 GGAGAGGATTTAGAAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
28640314 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
28640338 GGAGAGGATTTAGGAGCTAATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
28640362 GGAGAGGGTTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
28640386 GGAGA
1 GGAGA
28640391 ACAGTGTTGG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.35, C:0.04, G:0.41, T:0.21
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:28641855 original size:27 final size:26
Alignment explanation
Indices: 28641817--28641930 Score: 138
Period size: 27 Copynumber: 4.3 Consensus size: 26
28641807 TATGCCCGCA
28641817 ATTATCTGATCTAGTGGCTCTGCCAC
1 ATTATCTGATCTAGTGGCTCTGCCAC
*
28641843 ATATATCTGATCTAGTGTCTCTGCCAC
1 AT-TATCTGATCTAGTGGCTCTGCCAC
* *
28641870 ATATATCTGTTCTGGTGGCTCTGCCAC
1 AT-TATCTGATCTAGTGGCTCTGCCAC
* * * *
28641897 GATTATCTGTTCTGGTGACTCTGTCAC
1 -ATTATCTGATCTAGTGGCTCTGCCAC
28641924 ATTATCT
1 ATTATCT
28641931 ATTTTGGCAG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.11
27 69 0.86
28 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (26 bp):
ATTATCTGATCTAGTGGCTCTGCCAC
Found at i:28648997 original size:33 final size:33
Alignment explanation
Indices: 28648960--28649058 Score: 189
Period size: 33 Copynumber: 3.0 Consensus size: 33
28648950 GGCTAGCTAG
28648960 AACATGAAGCAAGGATCATAAAAACATAGAAAT
1 AACATGAAGCAAGGATCATAAAAACATAGAAAT
28648993 AACATGAAGCAAGGATCATAAAAACATAGAAAT
1 AACATGAAGCAAGGATCATAAAAACATAGAAAT
*
28649026 GACATGAAGCAAGGATCATAAAAACATAGAAAT
1 AACATGAAGCAAGGATCATAAAAACATAGAAAT
28649059 TATCAAAAAC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.15
Consensus pattern (33 bp):
AACATGAAGCAAGGATCATAAAAACATAGAAAT
Found at i:28651990 original size:13 final size:13
Alignment explanation
Indices: 28651972--28651999 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28651962 ACATATTATA
28651972 AATATTTTGTGTT
1 AATATTTTGTGTT
28651985 AATATTTTGTGTT
1 AATATTTTGTGTT
28651998 AA
1 AA
28652000 AAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (13 bp):
AATATTTTGTGTT
Found at i:28653462 original size:40 final size:40
Alignment explanation
Indices: 28653414--28653524 Score: 204
Period size: 40 Copynumber: 2.8 Consensus size: 40
28653404 GGACTAAGAT
28653414 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
28653454 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* *
28653494 CCGAAGGCATTTGTGCGAGTTGCTATATCCG
1 CCGAAGGCATTTGTGCTAGTTACTATATCCG
28653525 ACTAAATCCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
Found at i:28668615 original size:50 final size:49
Alignment explanation
Indices: 28668505--28668786 Score: 248
Period size: 50 Copynumber: 5.6 Consensus size: 49
28668495 CTGGTATGCA
* * *
28668505 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATCT-AGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAAC-ATTTGA-TACACG
* * * *
28668554 TAGTAGCCTGCAGTTAGTACTACACACGTGACCTGACCATTTGATATACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT-AACATTTGATACACG
* * * * *
28668604 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAA-GTTGTCGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACATT-T-GA-TACACG
* * *
28668655 TAGTAGCCTGCGCTTAGTACTACACATGCGACCTAACTATTTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAAC-ATTTGATACACG
* * * *
28668705 TAGTAGCCTGCACTTTGTACTACACACGTGACCTAAAACCATCTT-AAACACA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT--AA-CAT-TTGATACACG
* *
28668757 TAGTAGCCTGCACATAGTACTATACATGTG
1 TAGTAGCCTGCACTTAGTACTACACATGTG
28668787 TTCTTACAAT
Statistics
Matches: 186, Mismatches: 35, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
48 2 0.01
49 32 0.17
50 73 0.39
51 39 0.21
52 35 0.19
53 5 0.03
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACATTTGATACACG
Found at i:28668679 original size:101 final size:99
Alignment explanation
Indices: 28668505--28668737 Score: 279
Period size: 101 Copynumber: 2.3 Consensus size: 99
28668495 CTGGTATGCA
* * **
28668505 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTAGTACATGTAGTAGCCTGCAGTTA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAATCGAGTACACATAGTAGCCTGCAGTTA
* * *
28668570 GTACTACACACGTGACCTGACCATTTGATATACG
66 GTACTACACACGCGACCTAACCATTTGATACACG
* *** *
28668604 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTGTCGAGTACGCATAGTAGCCTGC-GC
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-CAATCGAGTACACATAGTAGCCTGCAG-
* * *
28668668 TTAGTACTACACATGCGACCTAACTATTTGGTACACG
63 TTAGTACTACACACGCGACCTAACCATTTGATACACG
* *
28668705 TAGTAGCCTGCACTTTGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
28668738 TAAAACCATC
Statistics
Matches: 113, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
99 30 0.27
100 5 0.04
101 78 0.69
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAATCGAGTACACATAGTAGCCTGCAGTTA
GTACTACACACGCGACCTAACCATTTGATACACG
Found at i:28670363 original size:12 final size:12
Alignment explanation
Indices: 28670346--28670406 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
28670336 ATTTTAAGAC
28670346 TTATATATATAT
1 TTATATATATAT
28670358 TTATATATAAATAGT
1 TTATATAT--ATA-T
*
28670373 AATTATATATATAA
1 --TTATATATATAT
*
28670387 TAATATATATAT
1 TTATATATATAT
*
28670399 TGATATAT
1 TTATATAT
28670407 GTCTTTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 25 0.62
14 3 0.08
15 4 0.10
17 8 0.20
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
TTATATATATAT
Found at i:28678130 original size:23 final size:23
Alignment explanation
Indices: 28678104--28678149 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28678094 ACGCATATTA
* *
28678104 CTGATGATATAAGGCAAGGACTG
1 CTGATGACACAAGGCAAGGACTG
28678127 CTGATGACACAAGGCAAGGACTG
1 CTGATGACACAAGGCAAGGACTG
28678150 ATTGAGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.17
Consensus pattern (23 bp):
CTGATGACACAAGGCAAGGACTG
Found at i:28682611 original size:44 final size:44
Alignment explanation
Indices: 28682555--28682992 Score: 300
Period size: 44 Copynumber: 9.9 Consensus size: 44
28682545 AATCTAAGAT
* * *
28682555 GATTTGGTGTCTCTGTATTGTCAGAGAGTAGATCAAAGATAGTA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* *
28682599 GATTTGGCGTCTCTGTATTTGCCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTA-TTGTCAGAGAGCAGATCAAAGATAGCA
* * * * *
28682644 GATTTGGCGACCCTGTATTGTCAGGGAACAGATCGAAGACATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATC-AA-AGATAGCA
* * * * *
28682690 GATTTGGCTTTCACGTGT-TTACG-CTGA-AGCAAATCTAAGAT----
1 GATTTGGC-GTCTC-TGTATT--GTCAGAGAGCAGATCAAAGATAGCA
* * *
28682731 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATTGTA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * *
28682775 GATTTGGCGTCTCTGTATTTGTCAGGGAGCAGATCGAGGTTAGCA
1 GATTTGGCGTCTCTGTA-TTGTCAGAGAGCAGATCAAAGATAGCA
* * * * * *
28682820 GATTTGGCATCTCTGTATGGTCAGAGAGTAAATCAGAGATAGTA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
** * * * * * *
28682864 GATTTCACATCTTTGTATTCGAC-GAGGAGCAAATCCAAGA-AACA
1 GATTTGGCGTCTCTGTATT-GTCAGA-GAGCAGATCAAAGATAGCA
* ** * * ** *
28682908 TATTTGGCAACCCTGTATTGTCAGGGAGCAGATTGAGGATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* * *
28682952 GATTTGGCGTCTCTGTATTGTCAAAGAGTAGATCGAAGATA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATA
28682993 ATATGGTGTC
Statistics
Matches: 300, Mismatches: 75, Indels: 38
0.73 0.18 0.09
Matches are distributed among these distances:
38 1 0.00
39 6 0.02
40 17 0.06
41 8 0.03
43 12 0.04
44 132 0.44
45 92 0.31
46 16 0.05
47 10 0.03
48 5 0.02
49 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
Found at i:28682766 original size:176 final size:176
Alignment explanation
Indices: 28682496--28682827 Score: 574
Period size: 176 Copynumber: 1.9 Consensus size: 176
28682486 TTACAAGGAG
*
28682496 CAGATCAAAGACGTAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTG
1 CAGATCAAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTG
** *
28682561 GTGTCTCTGTATTGTCAGAGAGTAGATCAAAGATAGTAGATTTGGCGTCTCTGTATTTGCCAGAG
66 GCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGTAGATTTGGCGTCTCTGTATTTGCCAGAG
28682626 AGCAGATCGAAGATAGCAGATTTGGCGACCCTGTATTGTCAGGGAA
131 AGCAGATCGAAGATAGCAGATTTGGCGACCCTGTATTGTCAGGGAA
*
28682672 CAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTG
1 CAGATCAAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTG
* * *
28682737 GCATCTCTGTATTGTCAGAGAGCAGATCAAAGATTGTAGATTTGGCGTCTCTGTATTTGTCAGGG
66 GCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGTAGATTTGGCGTCTCTGTATTTGCCAGAG
* *
28682802 AGCAGATCGAGGTTAGCAGATTTGGC
131 AGCAGATCGAAGATAGCAGATTTGGC
28682828 ATCTCTGTAT
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
176 146 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (176 bp):
CAGATCAAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTG
GCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGTAGATTTGGCGTCTCTGTATTTGCCAGAG
AGCAGATCGAAGATAGCAGATTTGGCGACCCTGTATTGTCAGGGAA
Found at i:28704399 original size:40 final size:39
Alignment explanation
Indices: 28704354--28704452 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
28704344 CACCAACACA
*
28704354 AAGCCTACGAGACTTTAAG-CTCGGATATAGTACCAGTACG
1 AAGCCTAC-AGACCTTAAGTC-CGGATATAGTACCAGTACG
*
28704394 AAGCCTGCAGACCTTAAGTCCGGATATAGTACCAGTACG
1 AAGCCTACAGACCTTAAGTCCGGATATAGTACCAGTACG
* * *
28704433 AAGCCTGCGGATCTTAAGTC
1 AAGCCTACAGACCTTAAGTC
28704453 TAGATACAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
39 46 0.85
40 8 0.15
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (39 bp):
AAGCCTACAGACCTTAAGTCCGGATATAGTACCAGTACG
Found at i:28704501 original size:40 final size:40
Alignment explanation
Indices: 28704366--28704540 Score: 149
Period size: 39 Copynumber: 4.4 Consensus size: 40
28704356 GCCTACGAGA
* * * * * *
28704366 CTTTAAGCTCGGATATAGTACCAGTACGAAGCCTGC-AGA
1 CTTTAAGCCCGGATACAATACCAGCACGAAGCCTGCGGGT
* * * * * *
28704405 CCTTAAGTCCGGATATAGTACCAGTACGAAGCCTGCGGAT
1 CTTTAAGCCCGGATACAATACCAGCACGAAGCCTGCGGGT
* ** *
28704445 C-TTAAGTCTAGATACAATTCCAGCACGAAGCCTGCGGGT
1 CTTTAAGCCCGGATACAATACCAGCACGAAGCCTGCGGGT
* * *
28704484 CTTTAAGCCCGGATACAATTCCAGCA-TATAGCCTGCAGGT
1 CTTTAAGCCCGGATACAATACCAGCACGA-AGCCTGCGGGT
28704524 CTTTAAGCCCGGATACA
1 CTTTAAGCCCGGATACA
28704541 CATCAAATAT
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 66 0.57
40 49 0.43
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTTAAGCCCGGATACAATACCAGCACGAAGCCTGCGGGT
Found at i:28723721 original size:25 final size:25
Alignment explanation
Indices: 28723687--28723740 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
28723677 TTTTCTTAAA
*
28723687 TTTTAATTTAATCAATTATCTAAT-T
1 TTTTAATTTAATAAATTATC-AATAT
* *
28723712 TTTCAATTTATTAAATTATCAATAT
1 TTTTAATTTAATAAATTATCAATAT
28723737 TTTT
1 TTTT
28723741 TATTAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTAATTTAATAAATTATCAATAT
Found at i:28724536 original size:33 final size:33
Alignment explanation
Indices: 28724488--28724576 Score: 81
Period size: 33 Copynumber: 2.6 Consensus size: 33
28724478 GTTAGGAGCA
*
28724488 TTAACCCCTTTTCAGTAACAGTACCAGTGT-GGCC
1 TTAA-CCCATTTCAGT-ACAGTACCAGTGTGGGCC
** * *
28724522 TTAACCCATTTCAGTGACAAAAGCAGTTTGGGCC
1 TTAACCCATTTCAGT-ACAGTACCAGTGTGGGCC
* *
28724556 TTAGCCCATATCAGTACAGTA
1 TTAACCCATTTCAGTACAGTA
28724577 TGTAGACAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
33 23 0.52
34 21 0.48
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (33 bp):
TTAACCCATTTCAGTACAGTACCAGTGTGGGCC
Found at i:28726583 original size:27 final size:27
Alignment explanation
Indices: 28726548--28726659 Score: 95
Period size: 27 Copynumber: 4.1 Consensus size: 27
28726538 AGCATGGCTG
*
28726548 CCAGAACAGATAAT-GTGACAGAGTCA
1 CCAGAACAGATAATCGTGACAGAGCCA
*
28726574 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATCGTGACAGAGCCA
* *
28726602 CCAGAATAGA-AATATGTCG-CAGAGCCA
1 CCAGAACAGATAAT-CGT-GACAGAGCCA
* * * * *
28726629 CCAGATCAGAGAATTGTGGCATAGCCA
1 CCAGAACAGATAATCGTGACAGAGCCA
28726656 CCAG
1 CCAG
28726660 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
26 9 0.12
27 45 0.62
28 19 0.26
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATCGTGACAGAGCCA
Found at i:28734479 original size:28 final size:28
Alignment explanation
Indices: 28734429--28734535 Score: 132
Period size: 27 Copynumber: 3.9 Consensus size: 28
28734419 GGCTACCGAA
* *
28734429 ACAGATAA-TGTGACAGAGTCACCAGAT
1 ACAGATAATTGTGGCAGAGCCACCAGAT
*
28734456 ACAGATAATCGTGGCAGAGCCACCAGA-
1 ACAGATAATTGTGGCAGAGCCACCAGAT
*
28734483 ACAGA-AATATGTGGCAAAGCCACCAGAT
1 ACAGATAAT-TGTGGCAGAGCCACCAGAT
*
28734511 -CAGATAATTGTGGCATAGCCACCAG
1 ACAGATAATTGTGGCAGAGCCACCAG
28734536 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.04
27 49 0.70
28 18 0.26
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (28 bp):
ACAGATAATTGTGGCAGAGCCACCAGAT
Found at i:28743760 original size:27 final size:26
Alignment explanation
Indices: 28743704--28743809 Score: 97
Period size: 27 Copynumber: 4.0 Consensus size: 26
28743694 CATGGCTGCC
* * *
28743704 AGAACAGATAATGTGACAGAGTCACC
1 AGAACAGATAATGTGGCAGAGCCACA
28743730 AGAACAGATAATCGTGGCAGAGCCACA
1 AGAACAGATAAT-GTGGCAGAGCCACA
* *
28743757 AGAACGGATATATGTGGCACAGCCA-A
1 AGAACAGATA-ATGTGGCAGAGCCACA
* * *
28743783 CAGATCACATAATTGTGGCATAGCCAC
1 -AGAACAGATAA-TGTGGCAGAGCCAC
28743810 CAGGACGCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
26 14 0.21
27 50 0.76
28 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.16
Consensus pattern (26 bp):
AGAACAGATAATGTGGCAGAGCCACA
Found at i:28744242 original size:8 final size:8
Alignment explanation
Indices: 28744226--28744257 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
28744216 CTCAAAATAC
28744226 CGGCTTTT
1 CGGCTTTT
*
28744234 CGGCATTT
1 CGGCTTTT
28744242 CGGCTTTT
1 CGGCTTTT
28744250 CGGCTTTT
1 CGGCTTTT
28744258 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:28745259 original size:24 final size:24
Alignment explanation
Indices: 28745227--28745292 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
28745217 CTGTTCTTCC
*
28745227 TCAGCTCCTAAATCGTCTCCCTTA
1 TCAGCTCCTAAATCCTCTCCCTTA
28745251 TCAGCTCCTAAATCCTCTCCCTTA
1 TCAGCTCCTAAATCCTCTCCCTTA
*
28745275 TCAGCTCTTAAATCCTCT
1 TCAGCTCCTAAATCCTCT
28745293 TCTGACAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.21, C:0.38, G:0.06, T:0.35
Consensus pattern (24 bp):
TCAGCTCCTAAATCCTCTCCCTTA
Found at i:28748946 original size:46 final size:46
Alignment explanation
Indices: 28748896--28749067 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
28748886 TGAGCATCCG
*
28748896 AACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
* * * * *
28748942 AACTCGTTGAGTTGAGTTCAAGTTC-GTGA--GATG-TAACTAGGCATCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCA
* * *
28748989 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
28749035 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28749068 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 57 0.55
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
Found at i:28749059 original size:93 final size:93
Alignment explanation
Indices: 28748889--28749059 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
28748879 GGATGGTTGA
* * * *
28748889 GCATCCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
*
28748954 TGAGTTCAAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
*
28748982 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
*
28749047 TGAGTCCGAGTTC
66 TGAGTCCAAGTTC
28749060 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:28754298 original size:40 final size:40
Alignment explanation
Indices: 28754237--28754421 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
28754227 TTATTCAAAT
* * *
28754237 TATATTCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGAC
** * * *
28754277 TATATCCGAACTAAGATCCGAAGGCATTTGTGCGAGTTG-C
1 TATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGAC
* *
28754317 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGAC
*
28754357 TATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGAC
*
28754397 CATATCCGGGCTAAGACCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
28754422 CTTGTGCGAG
Statistics
Matches: 125, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 122 0.98
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGAC
Found at i:28757730 original size:27 final size:26
Alignment explanation
Indices: 28757673--28757784 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
28757663 CACCATGGCT
* * *
28757673 ACCAGAATAGATAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
28757699 ACCAGAACAGATAATCGTGGCAGAGCC
1 ACCAGAACAGATAAT-GTGGCAGAGCC
28757726 ACCAGAACAGATATATGTGGCAGAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* * *
28757753 AACAGATCAGATAATTGTGGCATAGCC
1 ACCAGAACAGATAA-TGTGGCAGAGCC
28757780 ACCAG
1 ACCAG
28757785 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 15 0.20
27 59 0.78
28 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.16
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:28759227 original size:24 final size:24
Alignment explanation
Indices: 28759191--28759292 Score: 177
Period size: 24 Copynumber: 4.2 Consensus size: 24
28759181 GCCAACACTG
* *
28759191 CTCTCCCTAATCAGCTCCTAAATC
1 CTCTCCCTTATCAGCTTCTAAATC
28759215 CTCTCCCTTATCAGCTTCTAAATC
1 CTCTCCCTTATCAGCTTCTAAATC
*
28759239 CTCTCCCTTATCAGCTTTTAAATC
1 CTCTCCCTTATCAGCTTCTAAATC
28759263 CTCTCCCTTATCAGCTTCTAAATC
1 CTCTCCCTTATCAGCTTCTAAATC
28759287 CTCTCC
1 CTCTCC
28759293 TGACAGACTT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.21, C:0.39, G:0.04, T:0.36
Consensus pattern (24 bp):
CTCTCCCTTATCAGCTTCTAAATC
Found at i:28771785 original size:40 final size:40
Alignment explanation
Indices: 28771737--28771812 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
28771727 GCTAAAAAAA
*
28771737 TGGCACTTAATGTGCGGTTCGAAATAGCTTCGGCTAAATG
1 TGGCACTTAATGTGCGATTCGAAATAGCTTCGGCTAAATG
* * *
28771777 TGGCACTTAGTGTGCGATTGGAGATAGCTTCGGCTA
1 TGGCACTTAATGTGCGATTCGAAATAGCTTCGGCTA
28771813 TATATGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (40 bp):
TGGCACTTAATGTGCGATTCGAAATAGCTTCGGCTAAATG
Found at i:28775470 original size:39 final size:40
Alignment explanation
Indices: 28775425--28775556 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
28775415 GCTCCTCGTT
* * *
28775425 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
28775465 C-AATGCCTTCGGGACATAACCCAGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
28775504 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
28775544 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
28775557 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 34 0.43
40 46 0.57
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28775569 original size:40 final size:40
Alignment explanation
Indices: 28775425--28775609 Score: 151
Period size: 40 Copynumber: 4.7 Consensus size: 40
28775415 GCTCCTCGTT
* * * * * *
28775425 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
28775465 C-AATGCCTTCGGGACATAACCCAGATTTAATAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * *
28775504 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
** * * * *
28775544 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
28775585 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
28775610 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:28775618 original size:41 final size:41
Alignment explanation
Indices: 28775541--28775618 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28775531 TTAGTATCTC
* * *
28775541 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28775582 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28775619 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28778944 original size:60 final size:60
Alignment explanation
Indices: 28778871--28778999 Score: 204
Period size: 60 Copynumber: 2.1 Consensus size: 60
28778861 TCACCAAACA
* * *
28778871 GATAATGTCGCCATATTTTTAAAGCAAACACGATGGCAGCTAGTTCGAGATCATGGGTCG
1 GATAATTTCGCCATATTTTCAAAGCAAACACAATGGCAGCTAGTTCGAGATCATGGGTCG
* * *
28778931 GATAATTTCGCCATATTTTCAATGCAAGCACAATGGCGGCTAGTTCGAGATCATGGGTCG
1 GATAATTTCGCCATATTTTCAAAGCAAACACAATGGCAGCTAGTTCGAGATCATGGGTCG
28778991 GATAATTTC
1 GATAATTTC
28779000 TCTCGTGTGG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (60 bp):
GATAATTTCGCCATATTTTCAAAGCAAACACAATGGCAGCTAGTTCGAGATCATGGGTCG
Found at i:28783855 original size:39 final size:40
Alignment explanation
Indices: 28783810--28783981 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
28783800 GCTCCTCGTT
* * *
28783810 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
28783850 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
28783889 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
28783929 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
28783969 CAAATGCCTTCGG
1 CAAATGCCTTCGG
28783982 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28783910 original size:40 final size:39
Alignment explanation
Indices: 28783812--28784034 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
28783802 TCCTCGTTCA
* * * *
28783812 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
28783851 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28783890 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
28783930 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
28783970 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
28784011 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28784035 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:28783994 original size:80 final size:79
Alignment explanation
Indices: 28783810--28784034 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
28783800 GCTCCTCGTT
* * * * *
28783810 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
28783874 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
28783889 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
28783954 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
28783969 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
28784033 GA
63 GA
28784035 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:28784043 original size:41 final size:41
Alignment explanation
Indices: 28783966--28784043 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28783956 TTTGTATCTC
* * *
28783966 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28784007 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28784044 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28785018 original size:19 final size:19
Alignment explanation
Indices: 28784994--28785032 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28784984 TAAAATTATT
28784994 GGCCAAGGATGAACCAAAG
1 GGCCAAGGATGAACCAAAG
28785013 GGCCAAGGATGAACCAAAG
1 GGCCAAGGATGAACCAAAG
28785032 G
1 G
28785033 ATGAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.33, T:0.05
Consensus pattern (19 bp):
GGCCAAGGATGAACCAAAG
Found at i:28785192 original size:16 final size:16
Alignment explanation
Indices: 28785171--28785203 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28785161 CCTTTTTTTT
28785171 TGTGTAATCATCATAC
1 TGTGTAATCATCATAC
28785187 TGTGTAATCATCATAC
1 TGTGTAATCATCATAC
28785203 T
1 T
28785204 CCTTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (16 bp):
TGTGTAATCATCATAC
Found at i:28787533 original size:30 final size:30
Alignment explanation
Indices: 28787489--28787548 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28787479 TAGCAGTACA
* **
28787489 GTGTGAGCCTTAGCCCATTACAGTAACAGT
1 GTGTGAGCCCTAGCCCAACACAGTAACAGT
*
28787519 GTGTGGGCCCTAGCCCAACACAGTAACAGT
1 GTGTGAGCCCTAGCCCAACACAGTAACAGT
28787549 ACAATGCAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (30 bp):
GTGTGAGCCCTAGCCCAACACAGTAACAGT
Found at i:28787742 original size:52 final size:52
Alignment explanation
Indices: 28787654--28787777 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 52
28787644 ACACCAATAT
* *
28787654 CGCAGCAAAGCTGCCTGTAATAATAACGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAACAAAGCTACCTGTAATAATAACGCAGCAAAGCTGCCAGTAACAGTAA
* * * *
28787706 CGCAACAAAGCTACTTGTAATAGTAACGCAGTAAAGCTGCCAGTAATAGTAA
1 CGCAACAAAGCTACCTGTAATAATAACGCAGCAAAGCTGCCAGTAACAGTAA
*
28787758 CGCAACAAAGCTACCGGTAA
1 CGCAACAAAGCTACCTGTAA
28787778 CAGTATGTGG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (52 bp):
CGCAACAAAGCTACCTGTAATAATAACGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:28787782 original size:26 final size:26
Alignment explanation
Indices: 28787654--28787769 Score: 151
Period size: 26 Copynumber: 4.5 Consensus size: 26
28787644 ACACCAATAT
* *
28787654 CGCAGCAAAGCTGCCTGTAATAATAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
*
28787680 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* * **
28787706 CGCAACAAAGCTACTTGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
*
28787732 CGCAGTAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
*
28787758 CGCAACAAAGCT
1 CGCAGCAAAGCT
28787770 ACCGGTAACA
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:28787986 original size:27 final size:27
Alignment explanation
Indices: 28787953--28788389 Score: 391
Period size: 27 Copynumber: 16.2 Consensus size: 27
28787943 GGCATAACAA
* *
28787953 TCATTTTACCCTAT-GGGGCTATTTTGG
1 TCATTTTACCCTTTCGGGG-TATTTCGG
* *
28787980 TCATTTTACCC-TTCTAGGGTATTTCGA
1 TCATTTTACCCTTTC-GGGGTATTTCGG
*
28788007 TCATTTTACCCTTTGGGGGTATTTCGG
1 TCATTTTACCCTTTCGGGGTATTTCGG
* *
28788034 TCATTTTACTCTTT-GAGGGTATTTCGA
1 TCATTTTACCCTTTCG-GGGTATTTCGG
**
28788061 TCATTTTA-CCTTTCAGGGGTATTTTAG
1 TCATTTTACCCTTTC-GGGGTATTTCGG
*
28788088 TCATTTTACCC-TTCAGGGGTATTTTGG
1 TCATTTTACCCTTTC-GGGGTATTTCGG
*
28788115 TCATTTTA-CCTTTTGAGGGTATTTCGG
1 TCATTTTACCCTTTCG-GGGTATTTCGG
*
28788142 TCATTTTA-CCTTTCGAGGGTATTTCGA
1 TCATTTTACCCTTTCG-GGGTATTTCGG
* * **
28788169 TTATTTTACCCTTT-GAGGTTATTTTAG
1 TCATTTTACCCTTTCG-GGGTATTTCGG
* *
28788196 TTATTTTACCC-TTCGAGGGTATTTCGA
1 TCATTTTACCCTTTCG-GGGTATTTCGG
* *
28788223 TCATTTTATCC-TTCAGGGGTATTTCGA
1 TCATTTTACCCTTTC-GGGGTATTTCGG
* **
28788250 TCATTTTACCC-TTCAAGGGTATTTTAG
1 TCATTTTACCCTTTC-GGGGTATTTCGG
* *
28788277 TTATTTTACCCTTT-GAGGGTATTTCAG
1 TCATTTTACCCTTTCG-GGGTATTTCGG
*
28788304 TCATTTTACCCTTT-GAGGGTATTTCAG
1 TCATTTTACCCTTTCG-GGGTATTTCGG
**
28788331 TCATTTTACCC-TTCGCGGGTATTTCAA
1 TCATTTTACCCTTTCG-GGGTATTTCGG
28788358 TCATTTTACCC-TTCGGGGTATTTCGG
1 TCATTTTACCCTTTCGGGGTATTTCGG
28788384 TCATTT
1 TCATTT
28788390 AGGCCCATTA
Statistics
Matches: 353, Mismatches: 42, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
26 28 0.08
27 309 0.88
28 16 0.05
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (27 bp):
TCATTTTACCCTTTCGGGGTATTTCGG
Found at i:28788010 original size:54 final size:53
Alignment explanation
Indices: 28787952--28788389 Score: 451
Period size: 54 Copynumber: 8.1 Consensus size: 53
28787942 GGGCATAACA
* **
28787952 ATCATTTTACCCTATGGGGCTATTTTGGTCATTTTACCCTTCTAGGGTATTTCG
1 ATCATTTTACCCTTTGGGG-TATTTCAGTCATTTTACCCTTCTAGGGTATTTCG
* *
28788006 ATCATTTTACCCTTTGGGGGTATTTCGGTCATTTTACTCTT-TGAGGGTATTTCG
1 ATCATTTTACCCTTT-GGGGTATTTCAGTCATTTTACCCTTCT-AGGGTATTTCG
* *
28788060 ATCATTTTA-CCTTTCAGGGGTATTTTAGTCATTTTACCCTTC-AGGGGTATTTTG
1 ATCATTTTACCCTTT--GGGGTATTTCAGTCATTTTACCCTTCTA-GGGTATTTCG
* * * * *
28788114 GTCATTTTACCTTTTGAGGGTATTTCGGTCATTTTACCTTTCGAGGGTATTTCG
1 ATCATTTTACCCTTTG-GGGTATTTCAGTCATTTTACCCTTCTAGGGTATTTCG
* * * * *
28788168 ATTATTTTACCCTTTGAGGTTATTTTAGTTATTTTACCCTTCGAGGGTATTTCG
1 ATCATTTTACCCTTTG-GGGTATTTCAGTCATTTTACCCTTCTAGGGTATTTCG
* * * *
28788222 ATCATTTTATCCTTCAGGGGTATTTC-GATCATTTTACCCTTCAAGGGTATTT-T
1 ATCATTTTACCCTT-TGGGGTATTTCAG-TCATTTTACCCTTCTAGGGTATTTCG
*
28788275 AGTTATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTT-TGAGGGTATTTC-
1 A-TCATTTTACCCTTTG-GGGTATTTCAGTCATTTTACCCTTCT-AGGGTATTTCG
* * *
28788329 AGTCATTTTACCCTTCGCGGGTATTTCAATCATTTTACCCTTC-GGGGTATTTCG
1 A-TCATTTTACCCTTTG-GGGTATTTCAGTCATTTTACCCTTCTAGGGTATTTCG
*
28788383 GTCATTT
1 ATCATTT
28788390 AGGCCCATTA
Statistics
Matches: 327, Mismatches: 40, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
53 26 0.08
54 290 0.89
55 11 0.03
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (53 bp):
ATCATTTTACCCTTTGGGGTATTTCAGTCATTTTACCCTTCTAGGGTATTTCG
Found at i:28788068 original size:81 final size:80
Alignment explanation
Indices: 28787953--28788389 Score: 490
Period size: 81 Copynumber: 5.4 Consensus size: 80
28787943 GGCATAACAA
* * *
28787953 TCATTTTACCCTATG-GGGCTATTTTGGTCATTTTACCCTTCTAGGGTATTTCGATCATTTTACC
1 TCATTTTACCCTTTGAGGG-TATTTCGATCATTTTACCCTTC-AGGGTATTTCGATCATTTTACC
* * **
28788017 CTTTGGGGGTATTTCGG
64 CTTCGAGGGTATTTTAG
* * *
28788034 TCATTTTACTCTTTGAGGGTATTTCGATCATTTTACCTTTCAGGGGTATTT-TAGTCATTTTACC
1 TCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCA-GGGTATTTCGA-TCATTTTACC
*
28788098 CTTC-AGGGGTATTTTGG
64 CTTCGA-GGGTATTTTAG
* * * *
28788115 TCATTTTACCTTTTGAGGGTATTTCGGTCATTTTACCTTTCGAGGGTATTTCGATTATTTTACCC
1 TCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTC-AGGGTATTTCGATCATTTTACCC
* *
28788180 TTTGAGGTTATTTTAG
65 TTCGAGGGTATTTTAG
* * *
28788196 TTATTTTACCCTTCGAGGGTATTTCGATCATTTTATCCTTCAGGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCA-GGGTATTTCGATCATTTTACCC
*
28788261 TTCAAGGGTATTTTAG
65 TTCGAGGGTATTTTAG
* *
28788277 TTATTTTACCCTTTGAGGGTATTTC-AGTCATTTTACCCTTTGAGGGTATTTC-AGTCATTTTAC
1 TCATTTTACCCTTTGAGGGTATTTCGA-TCATTTTACCC-TTCAGGGTATTTCGA-TCATTTTAC
* * *
28788340 CCTTCGCGGGTATTTCAA
63 CCTTCGAGGGTATTTTAG
* *
28788358 TCATTTTACCCTTCG-GGGTATTTCGGTCATTT
1 TCATTTTACCCTTTGAGGGTATTTCGATCATTT
28788390 AGGCCCATTA
Statistics
Matches: 307, Mismatches: 37, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
80 20 0.07
81 278 0.91
82 9 0.03
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (80 bp):
TCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTTCAGGGTATTTCGATCATTTTACCCT
TCGAGGGTATTTTAG
Found at i:28790553 original size:19 final size:19
Alignment explanation
Indices: 28790529--28790621 Score: 86
Period size: 19 Copynumber: 5.1 Consensus size: 19
28790519 AATAAATTAC
*
28790529 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
28790548 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * * *
28790567 TGC-T-GGAATAAATT-A-C
1 T-CATCTTAGTTAATTAAGT
28790583 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
28790602 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
28790621 T
1 T
28790622 GCTTAAATCA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 7 0.12
18 7 0.12
19 39 0.68
20 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:28790576 original size:54 final size:54
Alignment explanation
Indices: 28790508--28790624 Score: 200
Period size: 54 Copynumber: 2.2 Consensus size: 54
28790498 GAATAAGTAT
*
28790508 TTAA-TTGCTAGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAA
1 TTAAGTTGCTAGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAA
*
28790561 TTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAA
1 TTAAGTTGCTAGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAA
*
28790615 TTTAGTTGCT
1 TTAAGTTGCT
28790625 TAAATCATTA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 4 0.07
54 56 0.93
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (54 bp):
TTAAGTTGCTAGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAA
Found at i:28790843 original size:20 final size:20
Alignment explanation
Indices: 28790818--28790855 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28790808 AGCTGTTATG
*
28790818 AAGTTGAATTAATGGCCAAA
1 AAGTTGAATTAAAGGCCAAA
28790838 AAGTTGAATTAAAGGCCA
1 AAGTTGAATTAAAGGCCA
28790856 GCAGCTGTTA
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:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (20 bp):
AAGTTGAATTAAAGGCCAAA
Found at i:28793404 original size:18 final size:18
Alignment explanation
Indices: 28793383--28793423 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28793373 ATTCTTTGTT
*
28793383 TTTTCTTTTTCACTTTTC
1 TTTTCTTTTTCACTTATC
*
28793401 TTTTCTTTTTCTCTTATC
1 TTTTCTTTTTCACTTATC
28793419 TTTTC
1 TTTTC
28793424 ATACGACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCTTTTTCACTTATC
Found at i:28796739 original size:14 final size:14
Alignment explanation
Indices: 28796720--28796754 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28796710 CACTGATTGA
28796720 GCTTCAATGAATCG
1 GCTTCAATGAATCG
*
28796734 GCTTCATTGAATCG
1 GCTTCAATGAATCG
28796748 GCTTCAA
1 GCTTCAA
28796755 GTACATGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (14 bp):
GCTTCAATGAATCG
Found at i:28798801 original size:17 final size:16
Alignment explanation
Indices: 28798779--28798817 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28798769 AATTAAGAGA
28798779 AGAAAAAAAGAAATGTG
1 AGAAAAAAAG-AATGTG
*
28798796 AGAAAAAGAGAATGTG
1 AGAAAAAAAGAATGTG
28798812 AGAAAA
1 AGAAAA
28798818 GAAGTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (16 bp):
AGAAAAAAAGAATGTG
Found at i:28798803 original size:15 final size:16
Alignment explanation
Indices: 28798783--28798817 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28798773 AAGAGAAGAA
28798783 AAAAAGA-AATGTGAG
1 AAAAAGAGAATGTGAG
28798798 AAAAAGAGAATGTGAG
1 AAAAAGAGAATGTGAG
28798814 AAAA
1 AAAA
28798818 GAAGTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (16 bp):
AAAAAGAGAATGTGAG
Found at i:28798835 original size:31 final size:33
Alignment explanation
Indices: 28798798--28798861 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
28798788 GAAATGTGAG
*
28798798 AAAAAGAGAATGTGA-G-AAAAGAAGTTGAAAT
1 AAAAAGAGAATGTGAGGAAAAAGAAATTGAAAT
* *
28798829 AAAAAGATAGTGTGAGGAAAAAGAAATTGAAAT
1 AAAAAGAGAATGTGAGGAAAAAGAAATTGAAAT
28798862 CGAAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.46
32 1 0.04
33 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (33 bp):
AAAAAGAGAATGTGAGGAAAAAGAAATTGAAAT
Found at i:28807455 original size:21 final size:21
Alignment explanation
Indices: 28807431--28807471 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28807421 TTATAATTAA
*
28807431 ATTTAAAGTGTCTTAATGGTT
1 ATTTAAAGTGTCCTAATGGTT
**
28807452 ATTTATTGTGTCCTAATGGT
1 ATTTAAAGTGTCCTAATGGT
28807472 ACACCAATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (21 bp):
ATTTAAAGTGTCCTAATGGTT
Found at i:28810715 original size:15 final size:16
Alignment explanation
Indices: 28810695--28810725 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28810685 GATGAAAAAA
28810695 AAGAGAA-AAAGGAAG
1 AAGAGAATAAAGGAAG
28810710 AAGAGAATAAAGGAAG
1 AAGAGAATAAAGGAAG
28810726 TGAAATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (16 bp):
AAGAGAATAAAGGAAG
Done.