Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2752
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: 500988
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.21
Warning! 175871 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:317888 original size:18 final size:18
Alignment explanation
Indices: 317865--317899 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
317855 TATTTGTATT
317865 ATATTATTATTAT-TTTTC
1 ATATTA-TATTATATTTTC
317883 ATATTATATTATATTTT
1 ATATTATATTATATTTT
317900 AATTATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTATATTATATTTTC
Found at i:319331 original size:2 final size:2
Alignment explanation
Indices: 319320--319361 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
319310 GAATGTATTT
319320 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319361 T
1 T
319362 GAAGAAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:319734 original size:2 final size:2
Alignment explanation
Indices: 319727--319765 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
319717 TGGATCCTTT
319727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
319766 GATTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:326506 original size:32 final size:32
Alignment explanation
Indices: 326463--326532 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
326453 AAACAGTAAC
* *
326463 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
326495 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
326527 TGTATC
1 TGTATC
326533 GCTATTGTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAA
Found at i:326736 original size:11 final size:10
Alignment explanation
Indices: 326718--326759 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
326708 CAAAAAGAAA
326718 AAAAAATAA-
1 AAAAAATAAT
326727 AATAATAATAAT
1 AA-AA-AATAAT
326739 AAAAAATAAAT
1 AAAAAAT-AAT
326750 AAAAAATAAT
1 AAAAAATAAT
326760 TTTTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.07
10 8 0.28
11 17 0.59
12 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:326741 original size:14 final size:15
Alignment explanation
Indices: 326722--326759 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
326712 AAGAAAAAAA
326722 AATAAAATAAT-AAT
1 AATAAAATAATAAAT
326736 AATAAAA-AATAAAT
1 AATAAAATAATAAAT
326750 AA-AAAATAAT
1 AATAAAATAAT
326760 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:326757 original size:21 final size:21
Alignment explanation
Indices: 326709--326759 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
326699 TTTGGAAGGC
* *
326709 AAAAAGAAAAAAAAATAAAAT
1 AAAAATAATAAAAAATAAAAT
*
326730 AATAATAATAAAAAAT-AAAT
1 AAAAATAATAAAAAATAAAAT
326750 AAAAAATAAT
1 -AAAAATAAT
326760 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (21 bp):
AAAAATAATAAAAAATAAAAT
Found at i:326908 original size:19 final size:18
Alignment explanation
Indices: 326880--326942 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
326870 AAACCGTAAA
*
326880 TGTATTGATACATAAGTGT
1 TGTATCGATACATAAGT-T
326899 TGTATCGATAC---A--T
1 TGTATCGATACATAAGTT
326912 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
326931 TGTATCGATACA
1 TGTATCGATACA
326943 ATGTATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 12 0.32
16 2 0.05
19 23 0.62
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:326916 original size:13 final size:13
Alignment explanation
Indices: 326898--326924 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
326888 TACATAAGTG
326898 TTGTATCGATACA
1 TTGTATCGATACA
326911 TTGTATCGATACA
1 TTGTATCGATACA
326924 T
1 T
326925 AAGTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:326922 original size:32 final size:32
Alignment explanation
Indices: 326878--326950 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
326868 ACAAACCGTA
*
326878 AATGTATTGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
* *
326910 ATTGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
326942 AATGTATCG
1 AATGTATCG
326951 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:326996 original size:21 final size:21
Alignment explanation
Indices: 326970--327029 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
326960 TACTACCAAA
326970 GAAATGTATCGATACATTAAG
1 GAAATGTATCGATACATTAAG
326991 GAAATGTATCGATACATTAAG
1 GAAATGTATCGATACATTAAG
327012 GAAATGTATCGATACATT
1 GAAATGTATCGATACATT
327030 GTATCGATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (21 bp):
GAAATGTATCGATACATTAAG
Found at i:327034 original size:13 final size:13
Alignment explanation
Indices: 327016--327042 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
327006 ATTAAGGAAA
327016 TGTATCGATACAT
1 TGTATCGATACAT
327029 TGTATCGATACAT
1 TGTATCGATACAT
327042 T
1 T
327043 AAGGAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:327038 original size:34 final size:34
Alignment explanation
Indices: 326995--327064 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
326985 ATTAAGGAAA
326995 TGTATCGATACATTAAGGAAATGTATCGATACAT
1 TGTATCGATACATTAAGGAAATGTATCGATACAT
327029 TGTATCGATACATTAAGGAAATGTATCGATACAT
1 TGTATCGATACATTAAGGAAATGTATCGATACAT
327063 TG
1 TG
327065 ATCTTTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (34 bp):
TGTATCGATACATTAAGGAAATGTATCGATACAT
Found at i:327125 original size:20 final size:20
Alignment explanation
Indices: 327100--327155 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
327090 GTTTACCCAG
* *
327100 ATGTATCGATATATTTTATA
1 ATGTATCGATACATTTTACA
327120 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
327140 ATGTATCGATACATTT
1 ATGTATCGATACATTT
327156 AGGCATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:328575 original size:21 final size:21
Alignment explanation
Indices: 328534--328572 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
328524 GTGATGTTTG
328534 CATTTGTTTTTTTATTATTAT
1 CATTTGTTTTTTTATTATTAT
328555 CATTT-TTTTTGTT-TTATT
1 CATTTGTTTTT-TTATTATT
328573 TATATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
CATTTGTTTTTTTATTATTAT
Found at i:328586 original size:2 final size:2
Alignment explanation
Indices: 328573--328607 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
328563 TTGTTTTATT
*
328573 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
328608 TTTGAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:333066 original size:52 final size:53
Alignment explanation
Indices: 333009--333132 Score: 171
Period size: 52 Copynumber: 2.4 Consensus size: 53
332999 CAATTGTTCA
* *
333009 TAATCGGGGATACTCTAACCCCGATTTTATTTTC-AAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* * *
333061 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* *
333113 CAATCGAGGATACTCCAACC
1 TAATCGGGGATACTCCAACC
333133 TCGTTATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 48 0.76
53 15 0.24
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (53 bp):
TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
Found at i:333281 original size:79 final size:77
Alignment explanation
Indices: 333141--333358 Score: 215
Period size: 79 Copynumber: 2.8 Consensus size: 77
333131 CCTCGTTATT
** * *
333141 TACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTCCCAAAATATTGATTT
1 TACTCCAA-CCCGTTATTTCTGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATATTGATTT
* *
333206 CTCATAATTGGGGA
64 CTCACAACTGGGGA
* ** *
333220 TACTCCAATCCCGTTATTTCTGAGGGGATACTCCAATCCCGATTCTATTTTC-TAATCATTGATT
1 TACTCCAA-CCCGTTATTTCTGAGGGGATACTCCAACCCCGATT-TATTCCCAAAAT-ATTGATT
*
333284 TTTCACAACTGGGGA
63 TCTCACAACTGGGGA
* * * *
333299 TACTCCAACCTCGTTATTT-TCAAGGGAATACTCCAACCCCGTTATTATTTCCAAAATATT
1 TACTCCAACC-CGTTATTTCT-GAGGGGATACTCCAACCCCGAT-TTATTCCCAAAATATT
333359 AAATTTTTCA
Statistics
Matches: 115, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
78 9 0.08
79 102 0.89
80 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (77 bp):
TACTCCAACCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATTGATTTCT
CACAACTGGGGA
Found at i:334373 original size:13 final size:13
Alignment explanation
Indices: 334355--334381 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
334345 ATTACTCAAG
334355 GTATCGATACATT
1 GTATCGATACATT
334368 GTATCGATACATT
1 GTATCGATACATT
334381 G
1 G
334382 ATCTTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:334391 original size:20 final size:20
Alignment explanation
Indices: 334366--334419 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
334356 TATCGATACA
334366 TTGTATCGATACATTGATCT
1 TTGTATCGATACATTGATCT
334386 TTGTATCGATACATTGATCT
1 TTGTATCGATACATTGATCT
334406 TTGTATCGATACAT
1 TTGTATCGATACAT
334420 CTAGGAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGATCT
Found at i:342602 original size:31 final size:31
Alignment explanation
Indices: 342561--342810 Score: 242
Period size: 31 Copynumber: 8.1 Consensus size: 31
342551 TTCAAATCTA
*
342561 TTTTC-TCAAAGTCCATGACTCAGTGGCATC
1 TTTTCTTCAAAGTCCACGACTCAGTGGCATC
* *
342591 TTTTCTTCAAAGTCCACGACCCAGTGGCAATA
1 TTTTCTTCAAAGTCCACGACTCAGTGGC-ATC
* *
342623 TCTT-TTCAAAGTCCACAACTCAGTGGCATC
1 TTTTCTTCAAAGTCCACGACTCAGTGGCATC
* * *
342653 CTTT-TTCTAAGTCCACGACTCACTGGCATCC
1 TTTTCTTCAAAGTCCACGACTCAGTGGCAT-C
* *
342684 TTTTCTTCCTAAAGTCCACGATTCAATGGCAATC
1 TTTTCTT-C-AAAGTCCACGACTCAGTGGC-ATC
* *
342718 TCTTC-TCAAAGTCCACGACTTAGTGGCATC
1 TTTTCTTCAAAGTCCACGACTCAGTGGCATC
* *
342748 TTCTTCCT-AAAGTCCATGACTCAGTGGCATC
1 TT-TTCTTCAAAGTCCACGACTCAGTGGCATC
* * * *
342779 TCTT-GTCCAAGTCCACGATTCAGTGGCATC
1 TTTTCTTCAAAGTCCACGACTCAGTGGCATC
342809 TT
1 TT
342811 GTCCCAAAAT
Statistics
Matches: 181, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
29 1 0.01
30 58 0.32
31 87 0.48
32 9 0.05
33 2 0.01
34 22 0.12
35 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (31 bp):
TTTTCTTCAAAGTCCACGACTCAGTGGCATC
Found at i:342793 original size:126 final size:124
Alignment explanation
Indices: 342568--342808 Score: 290
Period size: 126 Copynumber: 1.9 Consensus size: 124
342558 CTATTTTCTC
* * *
342568 AAAGTCCATGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACCCAGTGGCAATATCTTTTCAAA
1 AAAGTCCACGACTCAATGGCATCTCTTCTTCAAAGTCCACGACCCAGTGGC-A-ATCTTTTCAAA
* *
342633 GTCCACAACTCAGTGGCATCCTTTTTCTAAGTCCACGACTCACTGGCATCCTTTTCTTCCT
64 GTCCACAACTCAGTGGCATCCTTTGTCCAAGTCCACGACTCACTGGCATCCTTTTCTTCCT
* **
342694 AAAGTCCACGATTCAATGGCAATCTCTTC-TCAAAGTCCACGACTTAGTGGC-ATCTTCTTCCTA
1 AAAGTCCACGACTCAATGGC-ATCTCTTCTTCAAAGTCCACGACCCAGTGGCAATCTT-TT-C-A
** * *
342757 AAGTCCATGACTCAGTGGCAT-CTCTTGTCCAAGTCCACGATTCAGTGGCATC
62 AAGTCCACAACTCAGTGGCATCCT-TTGTCCAAGTCCACGACTCACTGGCATC
342809 TTGTCCCAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
123 5 0.05
124 2 0.02
125 3 0.03
126 81 0.83
127 7 0.07
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.30
Consensus pattern (124 bp):
AAAGTCCACGACTCAATGGCATCTCTTCTTCAAAGTCCACGACCCAGTGGCAATCTTTTCAAAGT
CCACAACTCAGTGGCATCCTTTGTCCAAGTCCACGACTCACTGGCATCCTTTTCTTCCT
Found at i:342894 original size:34 final size:34
Alignment explanation
Indices: 342838--343228 Score: 278
Period size: 34 Copynumber: 12.2 Consensus size: 34
342828 TCCATGGTAT
* *
342838 CCTTGTTCTTTTT-AAGTCCACAACTTTGTGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* *
342871 CATTTTTCTTTTTAAAGTCCACAACTCCGTGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
*
342905 CCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* *
342939 CC-----C-TTTT-AAGTCCATAACTCCGTGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
*
342966 CCTTTTTCTTTTTAAAGCCCACAACTCTGT-G-A
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* * *
342998 CC----CCCTTTT-AAGTCCACAACTCCGTGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* * *
343027 CCTTTTT-TTTTTAAAGCCCACAACTCCGTGGTA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* * *
343060 CTCCTTTTCCTTTT-AAGTCCACAACTCCGTGGCA
1 C-CTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* **
343094 CC-----C-TTTT-AAGTCCATAACTCCATGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* *
343121 TCCTTGTTCCTTTT-AAGTCCACAACTCTGTGGCA
1 -CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* * * *
343155 TCTTTTCCCTTTT-AAGTCCATAACTCTGTGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
* * * * * *
343188 TCTTTCTCCTTTT-AAGCCCACAAGTCAGTGGCA
1 CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
*
343221 CCCTTTTC
1 CCTTTTTC
343229 AAAAGCCCAC
Statistics
Matches: 291, Mismatches: 43, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
27 55 0.19
28 13 0.04
29 4 0.01
32 8 0.03
33 98 0.34
34 109 0.37
35 4 0.01
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.37
Consensus pattern (34 bp):
CCTTTTTCTTTTTAAAGTCCACAACTCTGTGGCA
Found at i:342950 original size:61 final size:61
Alignment explanation
Indices: 342880--343100 Score: 318
Period size: 61 Copynumber: 3.5 Consensus size: 61
342870 ACATTTTTCT
*
342880 TTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCCCCC
* *
342942 TTTTAAGTCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGACCCCC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCCCCC
*
343003 TTTTAAGTCCACAACTCCGTGGCACCTTTTT-TTTTTAAAGCCCACAACTCCGTGGTACTCCTTT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGG--C-CC---
343067 TCC
60 -CC
*
343070 TTTTAAGTCCACAACTCCGTGGCACCCTTTT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTT
343101 AAGTCCATAA
Statistics
Matches: 145, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
60 22 0.15
61 84 0.58
62 5 0.03
63 2 0.01
67 32 0.22
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (61 bp):
TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCCCCC
Found at i:342963 original size:27 final size:27
Alignment explanation
Indices: 342880--343125 Score: 123
Period size: 27 Copynumber: 8.1 Consensus size: 27
342870 ACATTTTTCT
342880 TTTTAAAGTCCACAACTCCGTGGCACCTTTTTC
1 TTTT-AAGTCCACAACTCCGTGGCACC-----C
* *
342913 TTTTTAAAGCCCACAACTCTGTGGCACCC
1 -TTTT-AAGTCCACAACTCCGTGGCACCC
*
342942 TTTTAAGTCCATAACTCCGTGGCACCTTTTTC
1 TTTTAAGTCCACAACTCCGTGGCACC-----C
* * * *
342974 TTTTTAAAGCCCACAACTCTGTGACCCCC
1 -TTTT-AAGTCCACAACTCCGTGGCACCC
*
343003 TTTTAAGTCCACAACTCCGTGGCACCTTTTTT
1 TTTTAAGTCCACAACTCCGTGGCACC-----C
* *
343035 TTTTAAAGCCCACAACTCCGTGGTACTCCTTTTCC
1 TTTT-AAGTCCACAACTCCGTGG--C-AC----CC
343070 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
343097 TTTTAAGTCCATAACTCCATGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
343124 TT
1 TT
343126 GTTCCTTTTA
Statistics
Matches: 169, Mismatches: 23, Indels: 47
0.71 0.10 0.20
Matches are distributed among these distances:
27 65 0.38
28 8 0.05
29 2 0.01
31 1 0.01
32 6 0.04
33 21 0.12
34 59 0.35
35 5 0.03
36 1 0.01
40 1 0.01
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:343072 original size:67 final size:65
Alignment explanation
Indices: 342820--343228 Score: 298
Period size: 61 Copynumber: 6.4 Consensus size: 65
342810 TGTCCCAAAA
* * * * * ** * *
342820 TCCATAACTCCATGGTATCCTTGTTCTTTTTAAGTCCACAACTTTGTGGCA-CATTTTTCTTTTT
1 TCCACAACTCCGTGGCA-CCTTTTTC-TTTTAAGTCCATAACTCCGTGGCATC-CTTTTCCTTTT
342884 AAAG
63 -AAG
* * *
342888 TCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCA--C----CCTTTTA
1 TCCACAACTCCGTGGCACCTTTTTC-TTTT-AAGTCCATAACTCCGTGGCATCCTTTTCCTTTTA
342947 AG
64 AG
* * * * *
342949 TCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGT-G-A-CC---CCCTTTTA
1 TCCACAACTCCGTGGCACCTTTTTC-TTTT-AAGTCCATAACTCCGTGGCATCCTTTTCCTTTTA
343008 AG
64 AG
* * * *
343010 TCCACAACTCCGTGGCACCTTTTTTTTTTAAAGCCCACAACTCCGTGGTACTCCTTTTCCTTTTA
1 TCCACAACTCCGTGGCACCTTTTTCTTTT-AAGTCCATAACTCCGTGGCA-TCCTTTTCCTTTTA
343075 AG
64 AG
*
343077 TCCACAACTCCGTGGCACC-----CTTTTAAGTCCATAACTCCATGGCATCCTTGTTCCTTTTAA
1 TCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCATAACTCCGTGGCATCCTT-TTCCTTTTAA
343137 G
65 G
* * * *
343138 TCCACAACTCTGTGGCATCTTTTCCCTTTTAAGTCCATAACTCTGTGGCAT-CTTTCTCCTTTTA
1 TCCACAACTCCGTGGCACCTTTT-TCTTTTAAGTCCATAACTCCGTGGCATCCTTT-TCCTTTTA
343202 AG
64 AG
* * * *
343204 CCCACAAGTCAGTGGCACCCTTTTC
1 TCCACAACTCCGTGGCACCTTTTTC
343229 AAAAGCCCAC
Statistics
Matches: 295, Mismatches: 28, Indels: 39
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.00
60 27 0.09
61 126 0.43
62 10 0.03
64 2 0.01
65 2 0.01
66 31 0.11
67 64 0.22
68 32 0.11
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (65 bp):
TCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCATAACTCCGTGGCATCCTTTTCCTTTTAAG
Found at i:343094 original size:155 final size:156
Alignment explanation
Indices: 342847--343228 Score: 468
Period size: 155 Copynumber: 2.4 Consensus size: 156
342837 TCCTTGTTCT
** * *
342847 TTTTAAGTCCACAACTTTGTGGCACATTTTTCTTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
1 TTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
* * * * *
342912 CTTTTTAAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCATAACTCCGTGGCA-CCTTTTTCTT
66 CCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCATCCTTGTTCCT
342976 TTTAAAGCCCACAACTCTGTGACCCCC
131 TTT-AAGCCCACAACTCTGTGACCCCC
* *
343003 TTTTAAGTCCACAACTCCGTGGCACCTTTTT-TTTTTAAAGCCCACAACTCCGTGGTACTCCTTT
1 TTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC-CCTTT
*
343067 TCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCATCCTTGTTCC
65 TCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCATCCTTGTTCC
* *
343131 TTTTAAGTCCACAACTCTGTGGCATCTTTTCCC
130 TTTTAAGCCCACAACTCTGT-G-A-C---CCCC
* * * * * *
343164 TTTTAAGTCCATAACTCTGTGGCATC-TTTCTCCTTTT-AAGCCCACAAGTCAGTGGCACCCTTT
1 TTTTAAGTCCACAACTCCGTGGCA-CATTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCCTTT
343227 TC
65 TC
343229 AAAAGCCCAC
Statistics
Matches: 195, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
155 84 0.43
156 50 0.26
157 1 0.01
158 1 0.01
160 7 0.04
161 47 0.24
162 5 0.03
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (156 bp):
TTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
CCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCATCCTTGTTCCT
TTTAAGCCCACAACTCTGTGACCCCC
Found at i:343098 original size:94 final size:95
Alignment explanation
Indices: 342940--343187 Score: 290
Period size: 94 Copynumber: 2.6 Consensus size: 95
342930 TCTGTGGCAC
* * * * * * *
342940 CCTTTTAAGTCCATAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCTGTGACCCCCT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCCTTTTCCTTTT-AAGTCCACAACTCTGTGGCACCCT
*
343004 TTTAAGTCCACAACTCCGTGGCA-CCTT-TT
65 TTTAAGTCCACAACTCCATGGCATCCTTGTT
** * *
343033 TTTTTTAAAGCCCACAACTCCGTGGTACTCCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCT
1 CCTTTT-AAGCCCACAACTCCGTGGCACTCCTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCT
*
343098 TTTAAGTCCATAACTCCATGGCATCCTTGTT
65 TTTAAGTCCACAACTCCATGGCATCCTTGTT
* * *
343129 CCTTTTAAGTCCACAACTCTGTGGCA-T-CTTTTCCCTTTTAAGTCCATAACTCTGTGGCA
1 CCTTTTAAGCCCACAACTCCGTGGCACTCCTTTT-CCTTTTAAGTCCACAACTCTGTGGCA
343188 TCTTTCTCCT
Statistics
Matches: 130, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
93 9 0.07
94 84 0.65
95 31 0.24
96 6 0.05
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.35
Consensus pattern (95 bp):
CCTTTTAAGCCCACAACTCCGTGGCACTCCTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTT
TTAAGTCCACAACTCCATGGCATCCTTGTT
Found at i:343269 original size:28 final size:30
Alignment explanation
Indices: 343201--343301 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 30
343191 TTCTCCTTTT
* *
343201 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCACACAAGTCAGTGGCAACCTTTTCAA
*
343231 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
1 AAGCACACAAGTCAGTGGCAACCTTTTCAA
* ** **
343259 AAGCATACAAGTTGGT-GCAACCCCTTCAA
1 AAGCACACAAGTCAGTGGCAACCTTTTCAA
343288 AAGCCCACACAAGT
1 AAG--CACACAAGT
343302 TGGTGGCATC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.10
28 16 0.27
29 8 0.13
30 22 0.37
31 8 0.13
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.18
Consensus pattern (30 bp):
AAGCACACAAGTCAGTGGCAACCTTTTCAA
Found at i:343386 original size:49 final size:48
Alignment explanation
Indices: 343313--344044 Score: 521
Period size: 49 Copynumber: 15.9 Consensus size: 48
343303 GGTGGCATCT
* *
343313 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTG
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTA
* * *
343363 TCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCATATTGG---C--A
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
*
343406 -C---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * * *
343450 TCTTTAAGACCAATGTCACTGGCCTTGACTCAGCACATTGG---C--A
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * *
343493 -C---AAGCCCAATATCGCTGGCCTTGAATCAGTATATTAGCACCTTG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * *
343537 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG---C--A
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * *
343580 -C---AAGACCAATGTCGCTGGCCTTGAATCAACACATTGG-----T-
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* *
343618 GC---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * *
343663 TGTTTAAGAT-CAATGTCGCTAGCCTTGAATCAGCACATTGG---C--A
1 TCTTTAAG-TCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * *
343706 -C---AAGCCCAGTATCACTGGCCTTGAATCAGCATATTGGCGCCTTCGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-T--T-A
* * * *
343754 TCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCATCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-A
** **
343803 TCTTTAAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGGTGCCTTCGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-T--T-A
* * * *
343855 TCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCATCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-A
** * * *
343904 TCTTTAAGTCCGGTATCGCTGGCTTTGAATCATCATATTGGCACCGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTA
** * *
343953 TCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-A
*
344002 TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
344045 TCTTTAACAT
Statistics
Matches: 539, Mismatches: 94, Indels: 99
0.74 0.13 0.14
Matches are distributed among these distances:
39 159 0.29
42 6 0.01
44 1 0.00
45 5 0.01
46 1 0.00
48 95 0.18
49 192 0.36
50 6 0.01
51 2 0.00
52 72 0.13
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (48 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTA
Found at i:343491 original size:87 final size:87
Alignment explanation
Indices: 343319--343616 Score: 479
Period size: 87 Copynumber: 3.4 Consensus size: 87
343309 ATCTTCTTCT
*
343319 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTGTCTTTAAGACCAATGTCGTTG
1 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACC-TTGTCTTTAAGACCAATGTCGCTG
*
343384 GCCTTGAATCAGCATATTGGCAC
65 GCCTTGAATCAGCACATTGGCAC
* *
343407 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGG
1 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
*
343472 CCTTGACTCAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
* ** *
343494 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTAGCACCTTGTCTTTAAGACCAATGTCGCTGG
1 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
343559 CCTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
* * *
343581 AAGACCAATGTCGCTGGCCTTGAATCAACACATTGG
1 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGG
343617 TGCAAGTCCA
Statistics
Matches: 194, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
87 155 0.80
88 39 0.20
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (87 bp):
AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
CCTTGAATCAGCACATTGGCAC
Found at i:343614 original size:126 final size:126
Alignment explanation
Indices: 343455--343743 Score: 443
Period size: 126 Copynumber: 2.3 Consensus size: 126
343445 CCTTGTCTTT
*
343455 AAGACCAATGTCACTGGCCTTGACTCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATC
1 AAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATC
* *
343520 AGTATATTAGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
66 AGCATATTAGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCAC
* * ** *
343581 AAGACCAATGTCGCTGGCCTTGAATCAACACATTGGTGCAAGTCCAATATCGCTGGCCTTGAATC
1 AAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATC
* * *
343646 AGCATATTGGCACCTTGTGTTTAAGATCAATGTCGCTAGCCTTGAATCAGCACATTGGCAC
66 AGCATATTAGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCAC
* * * *
343707 AAGCCCAGTATCACTGGCCTTGAATCAGCATATTGGC
1 AAGACCAATGTCACTGGCCTTGAATCAGCACATTGGC
343744 GCCTTCGTCA
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
126 145 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (126 bp):
AAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATC
AGCATATTAGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCAC
Found at i:343688 original size:87 final size:89
Alignment explanation
Indices: 343581--343996 Score: 320
Period size: 101 Copynumber: 4.4 Consensus size: 89
343571 ACATTGGCAC
* * ** * *
343581 AAGACCAATGTCGCTGGCCTTGAATCAACACATTGGTGCAAGTCCAATATCGCTGGCCTTGAATC
1 AAGATCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATC
*
343646 AGCATATTGGCACCTT-G-TGTTT
66 AGCATATTGGCACCTTCGATCTTT
* *
343668 AAGATCAATGTCGCTAGCCTTGAATCAGCACATTGGCACAAGCCCAGTATCACTGGCCTTGAATC
1 AAGATCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATC
*
343733 AGCATATTGGCGCCTTCGTCATCTTT
66 AGCATATTGGCACCTTCG--ATCTTT
* * ** *
343759 AAG-TCCAATGTTGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGCT
1 AAGAT-CAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-C---AAGCCCAATATCACT
**
343823 GGCCTTGAATCAGCATATTGGTGCCTTCGTCATCTTT
55 GGCCTTGAATCAGCATATTGGCACCTTCG--ATCTTT
* * ** *
343860 AAG-TCCAATGTCGCTGGCCTTGAATTAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGCT
1 AAGAT-CAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-C---AAGCCCAATATCACT
* * *
343924 GGCTTTGAATCATCATATTGGCACCGTC-ATCTTT
55 GGCCTTGAATCAGCATATTGGCACCTTCGATCTTT
* *
343958 AAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 AAGATCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
343997 CTTCATCTTT
Statistics
Matches: 287, Mismatches: 26, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
87 72 0.25
88 1 0.00
90 1 0.00
91 37 0.13
92 2 0.01
97 2 0.01
98 39 0.14
101 133 0.46
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (89 bp):
AAGATCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATC
AGCATATTGGCACCTTCGATCTTT
Found at i:343706 original size:213 final size:215
Alignment explanation
Indices: 343368--343796 Score: 673
Period size: 213 Copynumber: 2.0 Consensus size: 215
343358 CTTTGTCTTT
* * *
343368 AAGACCAATGTCGTTGGCCTTGAATCAGCATATTGGCACAAGTCCAATATCGCTGGCCTTGAATC
1 AAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACAAGTCCAATATCGCTGGCCTTGAATC
* *
343433 AGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGACTCAGCACATTGGCACAAGC
66 AGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTAGCCTTGAATCAGCACATTGGCACAAGC
* *
343498 CCAATATCGCTGGCCTTGAATCAGTATATTAGCACCTT-G-TCTTTAAGACCAATGTCGCTGGCC
131 CCAATATCACTGGCCTTGAATCAGCATATTAGCACCTTCGATCTTTAAGACCAATGTCGCTGGCC
343561 TTGAATCAGCACATTGGCAC
196 TTGAATCAGCACATTGGCAC
**
343581 AAGACCAATGTCGCTGGCCTTGAATCAACACATTGGTGCAAGTCCAATATCGCTGGCCTTGAATC
1 AAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACAAGTCCAATATCGCTGGCCTTGAATC
* * *
343646 AGCATATTGGCACCTTGTGTTTAAGATCAATGTCGCTAGCCTTGAATCAGCACATTGGCACAAGC
66 AGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTAGCCTTGAATCAGCACATTGGCACAAGC
* * * * *
343711 CCAGTATCACTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTTGCTGG
131 CCAATATCACTGGCCTTGAATCAGCATATTAGCACCTTCG--ATCTTTAAGACCAATGTCGCTGG
343776 CCTTGAATCAGCACATTGGCA
194 CCTTGAATCAGCACATTGGCA
343797 TCTTCATCTT
Statistics
Matches: 195, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
213 153 0.78
214 1 0.01
217 41 0.21
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (215 bp):
AAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACAAGTCCAATATCGCTGGCCTTGAATC
AGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTAGCCTTGAATCAGCACATTGGCACAAGC
CCAATATCACTGGCCTTGAATCAGCATATTAGCACCTTCGATCTTTAAGACCAATGTCGCTGGCC
TTGAATCAGCACATTGGCAC
Found at i:343890 original size:101 final size:100
Alignment explanation
Indices: 343714--344042 Score: 511
Period size: 101 Copynumber: 3.3 Consensus size: 100
343704 CACAAGCCCA
* *
343714 GTATCACTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTTGCTGGCCT
1 GTATCGCTGGCCTTGAATCAGCATATTGG-GCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCT
343779 TGAATCAGCACATTGGCATCTTCATCTTTAAGTCCG
65 TGAATCAGCACATTGGCATCTTCATCTTTAAGTCCG
343815 GTATCGCTGGCCTTGAATCAGCATATTGGTGCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCT
1 GTATCGCTGGCCTTGAATCAGCATATTGG-GCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCT
*
343880 TGAATTAGCACATTGGCATCTTCATCTTTAAGTCCG
65 TGAATCAGCACATTGGCATCTTCATCTTTAAGTCCG
* * **
343916 GTATCGCTGGCTTTGAATCATCATATT-GGCAC--CGTCATCTTTAAAACCAATGTCGCTGGCCT
1 GTATCGCTGGCCTTGAATCAGCATATTGGGC-CTTCGTCATCTTTAAGTCCAATGTCGCTGGCCT
* *
343978 TGAATCAGCACATTGGCACCTTCATCTTTAAGTCCA
65 TGAATCAGCACATTGGCATCTTCATCTTTAAGTCCG
* *
344014 ATATCGTTGGCCTTGAATCAGCATATTGG
1 GTATCGCTGGCCTTGAATCAGCATATTGG
344043 CATCTTTAAC
Statistics
Matches: 211, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
98 84 0.40
99 3 0.01
100 2 0.01
101 122 0.58
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (100 bp):
GTATCGCTGGCCTTGAATCAGCATATTGGGCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCTT
GAATCAGCACATTGGCATCTTCATCTTTAAGTCCG
Found at i:344069 original size:199 final size:202
Alignment explanation
Indices: 343714--344102 Score: 525
Period size: 199 Copynumber: 1.9 Consensus size: 202
343704 CACAAGCCCA
* ** *
343714 GTATCACTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTTGCTGGCCT
1 GTATCACTGGCCTTGAATCAGCATATTGGCGAC-TCGTCATCTTTAAAACCAATGTCGCTGGCCT
* **
343779 TGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGG
65 TGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
** ** * *
343844 TGCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCA-TCTTCATCTT
130 CACCTTCAACATCTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCATCTT
343908 TAAGTCCG
195 TAAGTCCG
* * *
343916 GTATCGCTGGCTTTGAATCATCATATTGGC-AC-CGTCATCTTTAAAACCAATGTCGCTGGCCTT
1 GTATCACTGGCCTTGAATCAGCATATTGGCGACTCGTCATCTTTAAAACCAATGTCGCTGGCCTT
*
343979 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGC
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
* * * * **
344044 ATCTTTAACAT-TCTTGAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCATTCTTC
131 ACCTTCAACATCT-TTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTC
344103 TTCAAGTCTA
Statistics
Matches: 162, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
198 1 0.01
199 128 0.79
200 5 0.03
201 1 0.01
202 27 0.17
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (202 bp):
GTATCACTGGCCTTGAATCAGCATATTGGCGACTCGTCATCTTTAAAACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
ACCTTCAACATCTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCATCTTT
AAGTCCG
Found at i:344094 original size:52 final size:50
Alignment explanation
Indices: 343721--344150 Score: 329
Period size: 49 Copynumber: 8.6 Consensus size: 50
343711 CCAGTATCAC
* * * * *
343721 TGGCCTTGAATCAGCATATTGGC-GCCTTCGTCATCTTTAAGTCCAATGTTGC
1 TGGCCTTGAATCAGCACATTGGCATCC-T--TCATCTTTAAGCCCAATGTCGT
* ** * *
343773 TGGCCTTGAATCAGCACATTGGCAT-CTTCATCTTTAAGTCCGGTATCGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTCATCTTTAAGCCCAATGTCGT
* * * * * *
343822 TGGCCTTGAATCAGCATATTGGTGCCTTCGTCATCTTTAAGTCCAATGTCGC
1 TGGCCTTGAATCAGCACATT-G-GCATCCTTCATCTTTAAGCCCAATGTCGT
* * ** * *
343874 TGGCCTTGAATTAGCACATTGGCAT-CTTCATCTTTAAGTCCGGTATCGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTCATCTTTAAGCCCAATGTCGT
* * * * ** *
343923 TGGCTTTGAATCATCATATTGGCA-CCGTCATCTTTAAAACCAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTCATCTTTAAGCCCAATGTCGT
* *
343972 TGGCCTTGAATCAGCACATTGGCA-CCTTCATCTTTAAGTCCAATATCGT
1 TGGCCTTGAATCAGCACATTGGCATCCTTCATCTTTAAGCCCAATGTCGT
* * *
344021 TGGCCTTGAATCAGCATATTGGCATCTTTAACAT-TCTTGAGCCCAATGTCGT
1 TGGCCTTGAATCAGCACATTGGCATCCTT--CATCT-TTAAGCCCAATGTCGT
** * * * * *
344073 TGGCCTTGTCTCAGCACATTGGCA---TTCTTCTTCAAGTCTAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTCATCTTTAAGCCCAATGTCGT
* * *
344120 TGGCCATGAATCAGCACATTGTCATTCTTCA
1 TGGCCTTGAATCAGCACATTGGCATCCTTCA
344151 CATCTTCGAG
Statistics
Matches: 309, Mismatches: 56, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
47 33 0.11
48 1 0.00
49 161 0.52
50 10 0.03
51 6 0.02
52 98 0.32
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (50 bp):
TGGCCTTGAATCAGCACATTGGCATCCTTCATCTTTAAGCCCAATGTCGT
Found at i:344938 original size:13 final size:13
Alignment explanation
Indices: 344920--344977 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
344910 CGATAAGTGT
344920 TGTATCGATACAA
1 TGTATCGATACAA
344933 TGTATCGATACATAA
1 TGTATCGATAC--AA
344948 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
344965 TGTATCGCTACAA
1 TGTATCGATACAA
344978 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:344953 original size:32 final size:32
Alignment explanation
Indices: 344912--344976 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
344902 AACTATATCG
344912 ATAAGTGTTGTATCGATACAATGTATCGATAC
1 ATAAGTGTTGTATCGATACAATGTATCGATAC
*
344944 ATAAGTGTTGTATCGATACAATGTATCGCTAC
1 ATAAGTGTTGTATCGATACAATGTATCGATAC
344976 A
1 A
344977 AAGCTACTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
ATAAGTGTTGTATCGATACAATGTATCGATAC
Found at i:348544 original size:97 final size:97
Alignment explanation
Indices: 348379--348614 Score: 278
Period size: 97 Copynumber: 2.4 Consensus size: 97
348369 TATTTATCGG
* * * *
348379 GGATACTCCAACCCCATTCTTCCGAAGGGATACTCCAACCCCGCTTTTAAACTCGTCAAAGTTTA
1 GGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTCGTCAAAGATCA
* * **
348444 AATCTCATTCTCACTCAAATTGTCTTCAT-TG
66 AATCTCATTCTCACTCAAATTATCATCATCAA
* *
348475 GGAATACTCCAACCCCATGCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTTGTCAACA-AT
1 GG-ATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTCGTCAA-AGAT
* * *
348539 CAAATCTTATTCTCGCTTAAATTATCATCATCAA
64 CAAATCTCATTCTCACTCAAATTATCATCATCAA
* * ** *
348573 GGACAGTCCAACCCCATTCCTTTGAGAGGATACTCCAACCCC
1 GGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCC
348615 ATTTTTTTCA
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
96 2 0.02
97 113 0.96
98 3 0.03
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (97 bp):
GGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTCGTCAAAGATCA
AATCTCATTCTCACTCAAATTATCATCATCAA
Found at i:353239 original size:50 final size:50
Alignment explanation
Indices: 353164--353472 Score: 478
Period size: 50 Copynumber: 6.2 Consensus size: 50
353154 AGTTGTTGCC
* * * *
353164 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
353214 ATTGTTGATGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
353264 ATTGTTGACGATTCTTTACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* * *
353314 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAAGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
353364 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
353414 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
353464 ATTATTGAC
1 ATTGTTGAC
353473 TCTAAGTATA
Statistics
Matches: 238, Mismatches: 17, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
49 1 0.00
50 237 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:357939 original size:50 final size:50
Alignment explanation
Indices: 357864--357972 Score: 182
Period size: 50 Copynumber: 2.2 Consensus size: 50
357854 AGTTGTTGCC
* * *
357864 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATCCATCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
*
357914 ATTGTTGACGATTCATCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
1 ATTGTTGACGATCCATCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
357964 ATTGTTGAC
1 ATTGTTGAC
357973 TCTGAGTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATCCATCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
Found at i:360437 original size:16 final size:16
Alignment explanation
Indices: 360408--360449 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
360398 CTTTTTTGTA
*
360408 TTTTTATCTGTTAATAT
1 TTTTTAT-TTTTAATAT
*
360425 TTTTTATTTTTAATTT
1 TTTTTATTTTTAATAT
360441 TTTTTATTT
1 TTTTTATTT
360450 ACGATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTATTTTTAATAT
Found at i:361602 original size:21 final size:21
Alignment explanation
Indices: 361578--361632 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
361568 TTATCCTTTC
361578 CTTCATCTAATTCTCTATT-TT
1 CTTC-TCTAATTCTCTATTCTT
*
361599 CTTCTCCAAATTCTCTATTCTT
1 CTTCT-CTAATTCTCTATTCTT
361621 C-TCTCTAATTCT
1 CTTCTCTAATTCT
361633 TTGTTCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 8 0.27
21 19 0.63
22 3 0.10
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (21 bp):
CTTCTCTAATTCTCTATTCTT
Found at i:364069 original size:43 final size:43
Alignment explanation
Indices: 364008--364092 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
363998 AAAACTGCAG
*
364008 AGAAGGAATCCAGACCATGCCTTACGAATAGAAACAACAAAAT
1 AGAAGGAATCCAGACCATGCCTTACAAATAGAAACAACAAAAT
*
364051 AGAAGGAATCCAGACCATGCCTTATAAATAGAAACAACAAAA
1 AGAAGGAATCCAGACCATGCCTTACAAATAGAAACAACAAAA
364093 AGTTGATCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.14
Consensus pattern (43 bp):
AGAAGGAATCCAGACCATGCCTTACAAATAGAAACAACAAAAT
Found at i:371988 original size:2 final size:2
Alignment explanation
Indices: 371981--372017 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
371971 AAAGTTACAA
371981 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
372018 AGACTTGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:372391 original size:12 final size:13
Alignment explanation
Indices: 372355--372394 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
372345 TAATAAAAAA
372355 TATTATAATT-TT
1 TATTATAATTATT
372367 TATTATAATTTATT
1 TATTATAA-TTATT
372381 TATTA-AATTATT
1 TATTATAATTATT
372393 TA
1 TA
372395 ATTTTTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 15 0.58
13 4 0.15
14 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATAATTATT
Found at i:372582 original size:19 final size:19
Alignment explanation
Indices: 372560--372628 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
372550 AAGTACAAAA
*
372560 TATTGTTATAATTACTTAT
1 TATTATTATAATTACTTAT
* * *
372579 TATTATTTTAAATAGTTACT
1 TATTATTATAATTACTTA-T
372599 TATTATTATAATTACTTAT
1 TATTATTATAATTACTTAT
*
372618 TGTTATTATAA
1 TATTATTATAA
372629 ATAACATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
TATTATTATAATTACTTAT
Found at i:376521 original size:20 final size:20
Alignment explanation
Indices: 376493--376564 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
376483 AACCTAGATA
376493 TATCAATACAATGATAAATG
1 TATCAATACAATGATAAATG
* *
376513 TATCGATACAATTTGA-AGCATG
1 TATCAATACAA--TGATA-AATG
* * * *
376535 TATCGATACATTTATTAATG
1 TATCAATACAATGATAAATG
376555 TATCAATACA
1 TATCAATACA
376565 TTTCCTTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
20 24 0.59
21 1 0.02
22 16 0.39
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (20 bp):
TATCAATACAATGATAAATG
Found at i:376724 original size:21 final size:21
Alignment explanation
Indices: 376694--376749 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
376684 GTTGGGACCT
376694 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
*
376715 TGTATTGATACATTCTAGAAA
1 TGTATCGATACATTCTAGAAA
376736 TGTATCGATACATT
1 TGTATCGATACATT
376750 TGAACAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTAGAAA
Found at i:377482 original size:52 final size:51
Alignment explanation
Indices: 377414--377718 Score: 246
Period size: 52 Copynumber: 6.0 Consensus size: 51
377404 CTTAAGGATG
* *
377414 AGAAAAATACCAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAAGATA
1 AGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGA-A
* * *
377466 AGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACA-TAGGGCTT-AGGAA
1 AGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTA-GACTTAAAGAA
* * * * * **
377516 TGTTAAAGATGCCAATATGTTGATTCAAGGCCAGCGATATCGGACTTAAA-AA
1 AG--AAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGAA
* ** * * ** *
377568 TG-AAGGTGCTAGTGTGCTGATTCAAGGTTAGTGACATTAGACTTAAAG-A
1 AGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGAA
* * * *
377617 TGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAGAA
1 AGA-AAA-ATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGAA
* * * *
377669 A-AAAAATGCCAATGTGCTAATTCAAGGCTAGTGACATTAGGCTTAGAAGA
1 AGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTA-AAGA
377719 GTTACCACTG
Statistics
Matches: 197, Mismatches: 44, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
49 69 0.35
50 5 0.03
51 15 0.08
52 107 0.54
53 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (51 bp):
AGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGAA
Found at i:377633 original size:101 final size:102
Alignment explanation
Indices: 377423--377718 Score: 321
Period size: 101 Copynumber: 2.9 Consensus size: 102
377413 GAGAAAAATA
* * * ** *
377423 CCAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAAGATAAGAAAAATGCCAATGTGCTGAT
1 CCAATATGCTGATTCAAGGCCAGCGATATCGGACTT-AAGA-AA-AAAAATGCCAATGTGCTAAT
* ** * * *
377488 TCAAGGCCAGCAACA-TAGGGCTTAGGA-ATGTTAAAGATG
63 TCAAGGCTAGTGACATTA-GACTTAGAAGATGATAAAGATG
* * ** * * *
377527 CCAATATGTTGATTCAAGGCCAGCGATATCGGACTTAA-AAATGAAGGTGCTAGTGTGCTGATTC
1 CCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAGAAA-AAAAATGCCAATGTGCTAATTC
*
377591 AAGGTTAGTGACATTAGACTTA-AAGATGATAAAGATG
65 AAGGCTAGTGACATTAGACTTAGAAGATGATAAAGATG
*
377628 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAAAAAAATGCCAATGTGCTAATTCA
1 CCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAGAAAAAAAATGCCAATGTGCTAATTCA
*
377693 AGGCTAGTGACATTAGGCTTAGAAGA
66 AGGCTAGTGACATTAGACTTAGAAGA
377719 GTTACCACTG
Statistics
Matches: 159, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
100 1 0.01
101 116 0.73
102 10 0.06
103 2 0.01
104 30 0.19
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (102 bp):
CCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAGAAAAAAAATGCCAATGTGCTAATTCA
AGGCTAGTGACATTAGACTTAGAAGATGATAAAGATG
Found at i:377817 original size:27 final size:27
Alignment explanation
Indices: 377787--377841 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
377777 AGAAGGAATA
*
377787 GGTGCCACGAAGTTGTAGACTTAAAAG
1 GGTGCCACGAAGTTATAGACTTAAAAG
* * * *
377814 GGTGCTATGGAGTTATGGACTTAAAAG
1 GGTGCCACGAAGTTATAGACTTAAAAG
377841 G
1 G
377842 AAAAAGAGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.25
Consensus pattern (27 bp):
GGTGCCACGAAGTTATAGACTTAAAAG
Found at i:377889 original size:34 final size:33
Alignment explanation
Indices: 377809--378122 Score: 243
Period size: 34 Copynumber: 9.4 Consensus size: 33
377799 TTGTAGACTT
* * *
377809 AAAAGGGTGCTATGGAGTTATGGAC-TTAAAAGG
1 AAAAAGGTGCCATGGAGTTATGGGCTTTAAAA-G
* *
377842 AAAAAGAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 -AAAA-AGGTGCCATGGAGTTATGGGCTTT-AAAAG
* * * *
377878 AAAAATGTGCCATAGAGTTGTGGAC-TTAAAAG
1 AAAAAGGTGCCATGGAGTTATGGGCTTTAAAAG
* *
377910 -----GGTGCCATGGAGTTATGGAC-ATAAAAGGG
1 AAAAAGGTGCCATGGAGTTATGGGCTTTAAAA--G
* *
377939 GAAAAGGTGCGATGGAGTTATGGGCTTTGAAAAG
1 AAAAAGGTGCCATGGAGTTATGGGCTTT-AAAAG
* * *
377973 AAAAAGATGCCATGGAGTTATGGAC-ATAAAAGGG
1 AAAAAGGTGCCATGGAGTTATGGGCTTTAAAA--G
*
378007 AAAAAGGTGCGATGGAGTTATGGGCTTTGAAAAG
1 AAAAAGGTGCCATGGAGTTATGGGCTTT-AAAAG
* *
378041 AAAAAGATGCCATGGAGTTAT-GGATTTAAAAGG
1 AAAAAGGTGCCATGGAGTTATGGGCTTTAAAA-G
*
378074 AAAAAATGGTGCCATGGAGTTGTGGGCTTTGAAAAG
1 -AAAAA-GGTGCCATGGAGTTATGGGCTTT-AAAAG
*
378110 AACAAGGTGCCAT
1 AAAAAGGTGCCAT
378123 TGAATTGTGG
Statistics
Matches: 227, Mismatches: 32, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
27 22 0.10
29 1 0.00
32 13 0.06
33 9 0.04
34 117 0.52
35 40 0.18
36 17 0.07
37 8 0.04
ACGTcount: A:0.37, C:0.09, G:0.32, T:0.22
Consensus pattern (33 bp):
AAAAAGGTGCCATGGAGTTATGGGCTTTAAAAG
Found at i:377916 original size:27 final size:27
Alignment explanation
Indices: 377884--377938 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
377874 AAAGAAAAAT
* *
377884 GTGCCATAGAGTTGTGGACTTAAAAGG
1 GTGCCATAGAGTTATGGACATAAAAGG
*
377911 GTGCCATGGAGTTATGGACATAAAAGG
1 GTGCCATAGAGTTATGGACATAAAAGG
377938 G
1 G
377939 GAAAAGGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.11, G:0.35, T:0.24
Consensus pattern (27 bp):
GTGCCATAGAGTTATGGACATAAAAGG
Found at i:377991 original size:95 final size:96
Alignment explanation
Indices: 377797--378006 Score: 298
Period size: 95 Copynumber: 2.2 Consensus size: 96
377787 GGTGCCACGA
* * *
377797 AGTTGTAGACTTAAAAGGGTGCTATGGAGTTATGGACTTAAAAGGAAAAAGAGGTGCCACGGAGT
1 AGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACATAAAAGGAAAAAGAGGTGCCACGGAGT
*
377862 TGTGGGCTTTGAAAAGAAAAATGTGCCATAG
66 TATGGGCTTTGAAAAGAAAAATGTGCCATAG
** * *
377893 AGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACATAAAAGGGGAAA-AGGTGCGATGGAGT
1 AGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACATAAAAGGAAAAAGAGGTGCCACGGAGT
*
377957 TATGGGCTTTGAAAAGAAAAA-GATGCCATGG
66 TATGGGCTTTGAAAAGAAAAATG-TGCCATAG
* *
377988 AGTTATGGACATAAAAGGG
1 AGTTGTGGACTTAAAAGGG
378007 AAAAAGGTGC
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 1 0.01
95 56 0.55
96 45 0.44
ACGTcount: A:0.36, C:0.09, G:0.33, T:0.23
Consensus pattern (96 bp):
AGTTGTGGACTTAAAAGGGTGCCATGGAGTTATGGACATAAAAGGAAAAAGAGGTGCCACGGAGT
TATGGGCTTTGAAAAGAAAAATGTGCCATAG
Found at i:378139 original size:69 final size:68
Alignment explanation
Indices: 377912--378122 Score: 341
Period size: 68 Copynumber: 3.1 Consensus size: 68
377902 CTTAAAAGGG
*
377912 TGCCATGGAGTTATGGACATAAAAGGGGAAAAGGTGCGATGGAGTTATGGGCTTTGAAAAGAAAA
1 TGCCATGGAGTTATGGACATAAAAGGGAAAAAGGTGCGATGGAGTTATGGGCTTTGAAAAGAAAA
377977 AGA
66 AGA
377980 TGCCATGGAGTTATGGACATAAAAGGGAAAAAGGTGCGATGGAGTTATGGGCTTTGAAAAGAAAA
1 TGCCATGGAGTTATGGACATAAAAGGGAAAAAGGTGCGATGGAGTTATGGGCTTTGAAAAGAAAA
378045 AGA
66 AGA
** * * * *
378048 TGCCATGGAGTTATGGATTTAAAAGGAAAAAATGGTGCCATGGAGTTGTGGGCTTTGAAAAGAAC
1 TGCCATGGAGTTATGGACATAAAAGGGAAAAA-GGTGCGATGGAGTTATGGGCTTTGAAAAGAAA
*
378113 AAGG
65 AAGA
378117 TGCCAT
1 TGCCAT
378123 TGAATTGTGG
Statistics
Matches: 134, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
68 96 0.72
69 38 0.28
ACGTcount: A:0.37, C:0.09, G:0.32, T:0.22
Consensus pattern (68 bp):
TGCCATGGAGTTATGGACATAAAAGGGAAAAAGGTGCGATGGAGTTATGGGCTTTGAAAAGAAAA
AGA
Found at i:378181 original size:27 final size:27
Alignment explanation
Indices: 378127--378221 Score: 131
Period size: 26 Copynumber: 3.6 Consensus size: 27
378117 TGCCATTGAA
*
378127 TTGTGGACTT-AAAGGGTGCTACAAAG
1 TTGTGGACTTAAAAGGGTGCCACAAAG
* ***
378153 TTGTGGACTTAAAAGGGTGGCATGGAG
1 TTGTGGACTTAAAAGGGTGCCACAAAG
378180 TTGTGGACTTAAAA-GGTGCCACAAAG
1 TTGTGGACTTAAAAGGGTGCCACAAAG
378206 TTGTGGACTTAAAAGG
1 TTGTGGACTTAAAAGG
378222 AAAAGGTGCT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
26 32 0.55
27 26 0.45
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.26
Consensus pattern (27 bp):
TTGTGGACTTAAAAGGGTGCCACAAAG
Found at i:378391 original size:26 final size:26
Alignment explanation
Indices: 378322--378392 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
378312 TTTGAAAAAA
378322 AAAAGGTGCCATAGAGTTGTGGACTT
1 AAAAGGTGCCATAGAGTTGTGGACTT
* * **
378348 AAGAGGCTGCCACAGAGTTGTGGTTTT
1 AAAAGG-TGCCATAGAGTTGTGGACTT
*
378375 AAAAGGTGCCATGGAGTT
1 AAAAGGTGCCATAGAGTT
378393 CTGGGCTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
26 15 0.41
27 22 0.59
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.27
Consensus pattern (26 bp):
AAAAGGTGCCATAGAGTTGTGGACTT
Found at i:378453 original size:155 final size:153
Alignment explanation
Indices: 378255--378533 Score: 396
Period size: 155 Copynumber: 1.8 Consensus size: 153
378245 CTTAAAAGGG
* * * *
378255 AAAGGTGACACGAAGTTATGGACTTAAAAGGGAAAAGGGTGCCACGGAGTTATGGGCTTTGAAAA
1 AAAGGTGACACGAAGTTATGGACTTAAAAGGAAAAACGATGCCACGAAGTTAT-GGCTTTGAAAA
* * **
378320 AAAAAAGGTGCCATAGAGTTGTGGACTTAAGAGGCTGCCACAGAGTTGTGGTTTTAAAAGGTGCC
65 AAAAAAGGTGCCACAGAGTTATGGACTTAA-AGGCTGCCACAGAGTTGTGGACTTAAAAGGTGCC
378385 ATGGAGTTCTGGGCTTTGAAAAGAA
129 ATGGAGTTCTGGGCTTTGAAAAGAA
* * * *
378410 AAAGGTGCCACGGAGTTATGGACTTAAAAGGAAAAACGATGCCACGAAGTTGTGGCTTTGAAAAG
1 AAAGGTGACACGAAGTTATGGACTTAAAAGGAAAAACGATGCCACGAAGTTATGGCTTTGAAAAA
* * **
378475 AAAAAGGTGCCACGGAGTTATGGACTTAAAGGGTGCCATGGAGTTGTGGACTTAAAAGG
66 AAAAAGGTGCCACAGAGTTATGGACTTAAAGGCTGCCACAGAGTTGTGGACTTAAAAGG
378534 AAAAAAAGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
153 25 0.23
154 37 0.34
155 46 0.43
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (153 bp):
AAAGGTGACACGAAGTTATGGACTTAAAAGGAAAAACGATGCCACGAAGTTATGGCTTTGAAAAA
AAAAAGGTGCCACAGAGTTATGGACTTAAAGGCTGCCACAGAGTTGTGGACTTAAAAGGTGCCAT
GGAGTTCTGGGCTTTGAAAAGAA
Found at i:378512 original size:26 final size:26
Alignment explanation
Indices: 378480--378530 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
378470 AAAAGAAAAA
378480 GGTGCCACGGAGTTATGGACTTAAAG
1 GGTGCCACGGAGTTATGGACTTAAAG
* *
378506 GGTGCCATGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTATGGACTTAAA
378531 AGGAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (26 bp):
GGTGCCACGGAGTTATGGACTTAAAG
Found at i:378593 original size:27 final size:27
Alignment explanation
Indices: 378534--378593 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
378524 ACTTAAAAGG
** *
378534 AAAAAAAGGTGCCATGGAGTTGTGGAC
1 AAAAAAAGGTGCCACAGAGTTGTAGAC
** *
378561 TTAAAATGGTGCCACAGAGTTGTAGAC
1 AAAAAAAGGTGCCACAGAGTTGTAGAC
378588 AAAAAA
1 AAAAAA
378594 GGGAAAAGGG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.20
Consensus pattern (27 bp):
AAAAAAAGGTGCCACAGAGTTGTAGAC
Found at i:378606 original size:61 final size:61
Alignment explanation
Indices: 378473--378619 Score: 170
Period size: 61 Copynumber: 2.4 Consensus size: 61
378463 GGCTTTGAAA
** * **
378473 AGAAAAAGGTGCCACGGAGTTATGGACTTAAAGGGTGCCATGGAGTTGTGGACTTAAAAGG
1 AGAAAAAGGTGCCACGGAGTTATGGACTTAAAGGGTGCCACAGAGTTGTAGACAAAAAAGG
* * * *
378534 AAAAAAAGGTGCCATGGAGTTGTGGACTTAAAATGGTGCCACAGAGTTGTAGACAAAAAAGG
1 AGAAAAAGGTGCCACGGAGTTATGGACTT-AAAGGGTGCCACAGAGTTGTAGACAAAAAAGG
* * *
378596 -GAAAAGGGTGCGACAGAGTTATGG
1 AGAAAAAGGTGCCACGGAGTTATGG
378620 GCTTTGAAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
61 44 0.63
62 26 0.37
ACGTcount: A:0.36, C:0.11, G:0.33, T:0.20
Consensus pattern (61 bp):
AGAAAAAGGTGCCACGGAGTTATGGACTTAAAGGGTGCCACAGAGTTGTAGACAAAAAAGG
Found at i:378719 original size:34 final size:32
Alignment explanation
Indices: 378190--379269 Score: 417
Period size: 34 Copynumber: 35.2 Consensus size: 32
378180 TTGTGGACTT
** *
378190 AAAAGGTGCCACAAAGTTGTGGACTTAAAAGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* * * *
378222 AAAAGGTGCTACGGACTTATGGACTTAAAAGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* * * *
378254 GAAAGGTGACACGAAGTTATGGACTTAAAAGGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAA--GA
* * * *
378288 AAAGGGTGCCACGGAGTTATGGGCTTTGAAAAAA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGA
**
378322 AAAAGGTGCCATAGAGTTGTGGACTT--AAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* **
378351 ---AGGCTGCCACAGAGTTGTGG--TT----TT
1 AAAAGG-TGCCACGGAGTTGTGGACTTAAAAGA
* * *
378375 AAAAGGTGCCATGGAGTTCTGGGCTTTGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGA
*
378409 AAAAGGTGCCACGGAGTTATGGACTTAAAAGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAA-GA
* *
378442 AAAACGATGCCACGAAGTTGTGG-CTTTGAAAAGA
1 AAAA-GGTGCCACGGAGTTGTGGAC-TT-AAAAGA
*
378476 AAAAGGTGCCACGGAGTTATGGACTT-AAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
378506 ----GGTGCCATGGAGTTGTGGACTTAAAAGGAAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAA-G--A
*
378537 AAAAGGTGCCATGGAGTTGTGGACTT-----A
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* * * **
378564 AAATGGTGCCACAGAGTTGTAGACAAAAAAGGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAA--GA
* * * * *
378598 AAAGGGTGCGACAGAGTTATGGGCTTTGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGA
* * * *
378632 AAAAGATGCCACGAAGTTATAGACTTAAAAGGAA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAA-G-A
* *
378666 AAAAGAGTGCCACGAAGTTGTGGGCTTTGAAAAGA
1 AAAAG-GTGCCACGGAGTTGTGGAC-TT-AAAAGA
*
378701 AAAAGGTGCCACGGAGTTGTAGACTT-AAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
378731 ----GGTGCCACAGAGTTGTGGACTTAAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* *
378758 ----GGTGCCATGGAGTTGTAGAC-T-----A
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* * *
378780 AAAAGGTGCCACAGAGTTGTGAACTTAAAAGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
378812 GAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAA--GA
* * * *
378846 AAAGGGTGCCATGGAGTTATGGGCTTTGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGA
* * *
378880 AAAAAGTGCCATGGAGTTGTAGACTTAAAAAGAAA
1 AAAAGGTGCCACGGAGTTGTGGACTT-AAAAG--A
* * *
378915 AAAAGGGTGCCACAGAATTGTGGGCTTTGAAAAGA
1 AAAA-GGTGCCACGGAGTTGTGGAC-TT-AAAAGA
** ** *
378950 AAAAAATGCCATAGAGTTATGGACTT-AAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
378980 ----GGTGCCACGAAGTTGTGGACTT-----A
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* *
379003 AAAAGGTGCCACAGAGTTGTGAACTT------
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
379029 AAAAGGTGTCACGGAGTTGTGG-CTTAAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
379059 ----GGTGCCACAGAGTTGTGGACTT-----A
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
379082 AAAA-GTGCCATGGAGTTGTGGACTTAAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* **
379112 ----GATGCCATAGAGTTGTGGACTT------
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
** *
379134 AAAAGGTGCCACAAAGTTATGGACTTAAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
* *
379165 ----GGTACCACAGAGTTGTGGACTTTGAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGA
* * * *
379195 AACAGGTGCCACAGAGTTTTGGACTTAAAGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
*
379227 AAAATGGTGCCACGGAGTT-TGGGCTTTGAAAAGA
1 AAAA-GGTGCCACGGAGTTGTGGAC-TT-AAAAGA
379261 AAAATGGTG
1 AAAA-GGTG
379270 GACTTGGAGA
Statistics
Matches: 804, Mismatches: 138, Indels: 210
0.70 0.12 0.18
Matches are distributed among these distances:
25 5 0.01
26 161 0.20
27 122 0.15
28 3 0.00
29 7 0.01
30 2 0.00
31 12 0.01
32 99 0.12
33 59 0.07
34 233 0.29
35 61 0.08
36 29 0.04
37 11 0.01
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (32 bp):
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGA
Found at i:378734 original size:225 final size:214
Alignment explanation
Indices: 378388--378799 Score: 626
Period size: 225 Copynumber: 1.9 Consensus size: 214
378378 AGGTGCCATG
* * * * *
378388 GAGTTCTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAAAAACGATGCC
1 GAGTTATGGGCTTTGAAAAGAAAAAGATGCCACGAAGTTATAGACTTAAAAGGAAAAAAGATGCC
* **
378453 ACGAAGTTGTGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTATGGACTTAAAGGGTGCCATGGAG
66 ACGAAGTTGTGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTATAGACTTAAAGGGTGCCACAGAG
* *
378518 TTGTGGACTTAAAAGGAAAAAAAGGTGCCATGGAGTTGTGGACTTAAAATGGTGCCACAGAGTTG
131 TTGTGGACTTAAAA-G-------GGTGCCATGGAGTTGTAGAC-TAAAAAGGTGCCACAGAGTTG
378583 TAGACAAAAAAGGGAAAAGGGTGCGACA
187 TAGACAAAAAAGGGAAAAGGGTGCGACA
378611 GAGTTATGGGCTTTGAAAAGAAAAAGATGCCACGAAGTTATAGACTTAAAAGGAAAAAAGAGTGC
1 GAGTTATGGGCTTTGAAAAGAAAAAGATGCCACGAAGTTATAGACTTAAAAGGAAAAAAGA-TGC
*
378676 CACGAAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTAGACTTAAAGGGTGCCACAG
65 CACGAAGTTGT-GGCTTTGAAAAGAAAAAGGTGCCACGGAGTTATAGACTTAAAGGGTGCCACAG
378741 AGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTAGACTAAAAAGGTGCCACAGAGTTGT
129 AGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTAGACTAAAAAGGTGCCACAGAGTTGT
378800 GAACTTAAAA
Statistics
Matches: 176, Mismatches: 11, Indels: 11
0.89 0.06 0.06
Matches are distributed among these distances:
216 21 0.12
217 19 0.11
223 56 0.32
224 15 0.09
225 65 0.37
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (214 bp):
GAGTTATGGGCTTTGAAAAGAAAAAGATGCCACGAAGTTATAGACTTAAAAGGAAAAAAGATGCC
ACGAAGTTGTGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTATAGACTTAAAGGGTGCCACAGAG
TTGTGGACTTAAAAGGGTGCCATGGAGTTGTAGACTAAAAAGGTGCCACAGAGTTGTAGACAAAA
AAGGGAAAAGGGTGCGACA
Found at i:378770 original size:27 final size:27
Alignment explanation
Indices: 378700--379186 Score: 268
Period size: 26 Copynumber: 17.0 Consensus size: 27
378690 CTTTGAAAAG
* *
378700 AAAAAGGTGCCACGGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
378727 -AAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
378753 AAAAGGGTGCCATGGAGTTGTAGAC-T
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
378779 AAAAAGGTGCCACAGAGTTGTGAACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
378806 AAAAGGGAAAGGTGCCACGGAGTTGTGGACTT
1 AAAA--G---GGTGCCACGGAGTTGTGGACTT
* * *
378838 AAAAGGGAAAAGGGTGCCATGGAGTTATGGGCTTT
1 -------AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * *
378873 GAAAAGAAAAAAGTGCCATGGAGTTGTAGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
* * *
378906 AAAAAGAAAAAAAGGGTGCCACAGAATTGTGGGCTTT
1 ---------AAAAGGGTGCCACGGAGTTGTGGAC-TT
** ** *
378943 GAAAAGAAAAAAATGCCATAGAGTTATGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
*
378976 -AAAGGGTGCCACGAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
379002 AAAAAGGTGCCACAGAGTTGTGAACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
379029 AAAA-GGTGTCACGGAGTTGTGG-CTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
379054 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
379081 AAAA-AGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* **
379107 AAAAGGATGCCATAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** *
379134 AAAA-GGTGCCACAAAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
379160 AAAAGGGTACCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
379187 TGAAAAGAAA
Statistics
Matches: 358, Mismatches: 63, Indels: 78
0.72 0.13 0.16
Matches are distributed among these distances:
25 7 0.02
26 136 0.38
27 101 0.28
29 11 0.03
31 4 0.01
32 20 0.06
33 4 0.01
34 47 0.13
35 2 0.01
36 14 0.04
37 3 0.01
39 4 0.01
41 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:378788 original size:53 final size:53
Alignment explanation
Indices: 378700--378812 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 53
378690 CTTTGAAAAG
* * * * *
378700 AAAAAGGTGCCACGGAGTTGTAGACTTAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGTGCCACAGAGTTGTGGACTT
** * *
378753 AAAAGGGTGCCATGGAGTTGTAGACTAAAAAGGTGCCACAGAGTTGTGAACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGTGCCACAGAGTTGTGGACTT
378806 AAAAGGG
1 AAAAGGG
378813 AAAGGTGCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (53 bp):
AAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGTGCCACAGAGTTGTGGACTT
Found at i:378946 original size:70 final size:69
Alignment explanation
Indices: 378779--378978 Score: 219
Period size: 70 Copynumber: 2.9 Consensus size: 69
378769 GTTGTAGACT
** ** * *
378779 AAAAA-GGTGCCACAGAGTTGTGAAC-TT-AAAAGGGAAAGGTGCCACGGAGTTGTGGACTT-AA
1 AAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTGTGGACTTAAA
*
378840 AAGG
66 AAGA
* ** * *
378844 GAAAAGGGTGCCATGGAGTTATGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTGTAGACTTAAA
1 AAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTGTGGACTTAAA
378909 AAGAA
66 AAG-A
* * * *
378914 AAAAAGGGTGCCACAGAATTGTGGGCTTTGAAAAGAAAAAAATGCCATAGAGTTATGGACTTAAA
1 AAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTGTGGACTTAAA
378979 GGGTGCCACG
Statistics
Matches: 109, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
65 4 0.04
66 15 0.14
67 2 0.02
68 27 0.25
69 5 0.05
70 56 0.51
ACGTcount: A:0.40, C:0.10, G:0.29, T:0.20
Consensus pattern (69 bp):
AAAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTGTGGACTTAAA
AAGA
Found at i:378993 original size:26 final size:27
Alignment explanation
Indices: 378956--379223 Score: 271
Period size: 26 Copynumber: 9.9 Consensus size: 27
378946 AAGAAAAAAA
* * *
378956 TGCCATAGAGTTATGGACTT-AAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAAGG
378982 TGCCAC-GAAGTTGTGGACTTAAAAAGG
1 TGCCACAG-AGTTGTGGACTTAAAAAGG
*
379009 TGCCACAGAGTTGTGAACTT-AAAAGG
1 TGCCACAGAGTTGTGGACTTAAAAAGG
* * *
379035 TGTCACGGAGTTGTGG-CTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAAGG
379061 TGCCACAGAGTTGTGGACTTAAAAA-G
1 TGCCACAGAGTTGTGGACTTAAAAAGG
**
379087 TGCCATGGAGTTGTGGACTT-AAAAGG
1 TGCCACAGAGTTGTGGACTTAAAAAGG
*
379113 ATGCCATAGAGTTGTGGACTT-AAAAGG
1 -TGCCACAGAGTTGTGGACTTAAAAAGG
* * *
379140 TGCCACAAAGTTATGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAAGG
*
379167 TACCACAGAGTTGTGGACTTTGAAAAGAAACAGG
1 TGCCACAGAGTTGTGGAC-TT----A-AAA-AGG
*
379201 TGCCACAGAGTTTTGGACTTAAA
1 TGCCACAGAGTTGTGGACTTAAA
379224 GGAAAAATGG
Statistics
Matches: 203, Mismatches: 24, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
25 8 0.04
26 91 0.45
27 74 0.36
28 5 0.02
29 1 0.00
32 1 0.00
33 5 0.02
34 18 0.09
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (27 bp):
TGCCACAGAGTTGTGGACTTAAAAAGG
Found at i:379013 original size:249 final size:242
Alignment explanation
Indices: 378536--379084 Score: 710
Period size: 249 Copynumber: 2.2 Consensus size: 242
378526 TTAAAAGGAA
** * * **
378536 AAAAAGGTGCCATGGAGTTGTGGACTTAAAATGGTGCCACAGAGTTGTAGACAAAAAAGGGAAAA
1 AAAAAGGTGCCACAGAGTTGT-GACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGAAAA
* *
378601 GGGTGCGACAGAGTTATGGGCTTTGAAAAGAAAAAGATGCCACGAAGTTATAGACTTAAAAGGAA
65 GGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAGATGCCACGAAGTTATAGACTTAAAAGAAA
** * *
378666 AAAAGAGTGCCACGAAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTAGACTTAAAG
130 AAAAGAGTGCCACGAAGTTGTGGGCTTTGAAAAGAAAAAAATGCCACAGAGTTATAGACTTAAAG
* **
378731 GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGT-AGACT
195 GGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGA-ACT
*
378779 AAAAAGGTGCCACAGAGTTGTGAACTTAAAAGGGAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACAGAGTTGTG-ACTTAAAA--G---GGTGCCACAGAGTTGTGGACTTAAAAGG
** * * *
378844 GAAAAGGGTGCCATGGAGTTATGGGCTTTGAAAAGAAAAA-AGTGCCATGGAGTTGTAGACTTAA
60 GAAAAGGGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAGA-TGCCACGAAGTTATAGACTT-A
* * *
378908 AAAGAAAAAAAGGGTGCCACAGAA-TTGTGGGCTTTGAAAAGAAAAAAATGCCATAGAGTTATGG
123 AAAGAAAAAAAGAGTGCCAC-GAAGTTGTGGGCTTTGAAAAGAAAAAAATGCCACAGAGTTATAG
378972 ACTTAAAGGGTGCCAC-GAAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGAACT
187 ACTTAAAGGGTGCCACAG-AGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGAACT
* * * *
379028 TAAAAGGTGTCACGGAGTTGTGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 AAAAAGGTGCCACAGAGTTGTGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
379085 AGTGCCATGG
Statistics
Matches: 266, Mismatches: 29, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
242 1 0.00
243 52 0.20
246 1 0.00
247 1 0.00
248 86 0.32
249 121 0.45
250 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (242 bp):
AAAAAGGTGCCACAGAGTTGTGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGAAAAG
GGTGCCACAGAGTTATGGGCTTTGAAAAGAAAAAGATGCCACGAAGTTATAGACTTAAAAGAAAA
AAAGAGTGCCACGAAGTTGTGGGCTTTGAAAAGAAAAAAATGCCACAGAGTTATAGACTTAAAGG
GTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGAACT
Found at i:379029 original size:53 final size:53
Alignment explanation
Indices: 378956--379186 Score: 304
Period size: 53 Copynumber: 4.4 Consensus size: 53
378946 AAGAAAAAAA
* * *
378956 TGCCATAGAGTTATGGACTTAAAGGGTGCCACGAAGTTGTGGACTTAAAAAGG
1 TGCCACAGAGTTGTGGACTTAAAAGGTGCCACGAAGTTGTGGACTTAAAAAGG
* * * *
379009 TGCCACAGAGTTGTGAACTTAAAAGGTGTCACGGAGTTGTGG-CTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGTGCCACGAAGTTGTGGACTTAAAAAGG
* * *
379061 TGCCACAGAGTTGTGGACTTAAAAAGTGCCATGGAGTTGTGGACTT-AAAAGG
1 TGCCACAGAGTTGTGGACTTAAAAGGTGCCACGAAGTTGTGGACTTAAAAAGG
* * * *
379113 ATGCCATAGAGTTGTGGACTTAAAAGGTGCCACAAAGTTATGGACTTAAAAGGG
1 -TGCCACAGAGTTGTGGACTTAAAAGGTGCCACGAAGTTGTGGACTTAAAAAGG
*
379167 TACCACAGAGTTGTGGACTT
1 TGCCACAGAGTTGTGGACTT
379187 TGAAAAGAAA
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
52 52 0.34
53 97 0.63
54 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (53 bp):
TGCCACAGAGTTGTGGACTTAAAAGGTGCCACGAAGTTGTGGACTTAAAAAGG
Found at i:379138 original size:105 final size:106
Alignment explanation
Indices: 378956--379186 Score: 322
Period size: 105 Copynumber: 2.2 Consensus size: 106
378946 AAGAAAAAAA
* * **
378956 TGCCATAGAGTTATGGACTTAAAGGGTGCCACGAAGTTGTGGACTTAAAAAGGTGCCACAGAGTT
1 TGCCACAGAGTTGTGGACTTAAAAAGTGCCACGAAGTTGTGGACTTAAAAAGGTGCCACAGAGTT
* ** *
379021 GTGAACTTAAAAGGTGTCACGGAGTTGTGG-CTTAAAAGGG
66 GTGAACTTAAAAGGTGCCACAAAGTTATGGACTTAAAAGGG
* * *
379061 TGCCACAGAGTTGTGGACTTAAAAAGTGCCATGGAGTTGTGGACTT-AAAAGGATGCCATAGAGT
1 TGCCACAGAGTTGTGGACTTAAAAAGTGCCACGAAGTTGTGGACTTAAAAAGG-TGCCACAGAGT
*
379125 TGTGGACTTAAAAGGTGCCACAAAGTTATGGACTTAAAAGGG
65 TGTGAACTTAAAAGGTGCCACAAAGTTATGGACTTAAAAGGG
*
379167 TACCACAGAGTTGTGGACTT
1 TGCCACAGAGTTGTGGACTT
379187 TGAAAAGAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
104 6 0.05
105 76 0.68
106 29 0.26
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (106 bp):
TGCCACAGAGTTGTGGACTTAAAAAGTGCCACGAAGTTGTGGACTTAAAAAGGTGCCACAGAGTT
GTGAACTTAAAAGGTGCCACAAAGTTATGGACTTAAAAGGG
Found at i:380556 original size:13 final size:13
Alignment explanation
Indices: 380538--380563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
380528 AATTTTTTTG
380538 TGTATCGATACAT
1 TGTATCGATACAT
380551 TGTATCGATACAT
1 TGTATCGATACAT
380564 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:381301 original size:21 final size:21
Alignment explanation
Indices: 381260--381303 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
381250 CTCCCCTTTA
* *
381260 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
381281 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
381302 TC
1 TC
381304 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:383124 original size:13 final size:13
Alignment explanation
Indices: 383106--383157 Score: 104
Period size: 13 Copynumber: 4.0 Consensus size: 13
383096 ATAATCACCC
383106 TGTATCGATACAA
1 TGTATCGATACAA
383119 TGTATCGATACAA
1 TGTATCGATACAA
383132 TGTATCGATACAA
1 TGTATCGATACAA
383145 TGTATCGATACAA
1 TGTATCGATACAA
383158 AGAAAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:383363 original size:8 final size:8
Alignment explanation
Indices: 383350--383383 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
383340 TATTAACAGC
383350 ATCACAAA
1 ATCACAAA
383358 ATCACAAA
1 ATCACAAA
383366 ATCACAAA
1 ATCACAAA
383374 ATCACAAA
1 ATCACAAA
383382 AT
1 AT
383384 TTAATCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:385257 original size:15 final size:15
Alignment explanation
Indices: 385237--385267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
385227 ATTTCTTGTG
*
385237 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
385252 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
385267 G
1 G
385268 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:387099 original size:21 final size:21
Alignment explanation
Indices: 387070--387114 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
387060 AAGTTTTCAT
*
387070 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
387090 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
387112 TTT
1 TTT
387115 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:389345 original size:13 final size:13
Alignment explanation
Indices: 389327--389352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
389317 AATTTTTTTG
389327 TGTATCGATACAT
1 TGTATCGATACAT
389340 TGTATCGATACAT
1 TGTATCGATACAT
389353 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:394779 original size:122 final size:123
Alignment explanation
Indices: 394536--394757 Score: 347
Period size: 122 Copynumber: 1.8 Consensus size: 123
394526 CACAACATGC
* *** * *
394536 GCTCGACCCCGGCGATAGGGCAAGTGAGGCGTGCCCAACTTAATATCCCTTATGATTGGGGATTT
1 GCTCGACCCCGACGATAGGGCAAGTGAGGCACACCCAACTTAATATCCCTCATGATTGGAGATTT
*
394601 TTATGGCATGATAAGGAATACGTTAATTGGAGGGGAGAGAGCGACACATGAATCGCCT
66 TTATGGCATGATAAGGAATACGTTAATTAGAGGGGAGAGAGCGACACATGAATCGCCT
*
394659 GCTCGA-CCCGACGATAGGGCAAGTGAGGCACACCCGACTTAATATCCCTCATGATTGGAGATTT
1 GCTCGACCCCGACGATAGGGCAAGTGAGGCACACCCAACTTAATATCCCTCATGATTGGAGATTT
* *
394723 TTATGGCATGATAAGGAATATGTTAGTTAGAGGGG
66 TTATGGCATGATAAGGAATACGTTAATTAGAGGGG
394758 GAAGATCGGT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
122 83 0.93
123 6 0.07
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (123 bp):
GCTCGACCCCGACGATAGGGCAAGTGAGGCACACCCAACTTAATATCCCTCATGATTGGAGATTT
TTATGGCATGATAAGGAATACGTTAATTAGAGGGGAGAGAGCGACACATGAATCGCCT
Found at i:395412 original size:387 final size:387
Alignment explanation
Indices: 394693--395417 Score: 1010
Period size: 387 Copynumber: 1.9 Consensus size: 387
394683 GAGGCACACC
* * * *
394693 CGACTTAATATCCCTCATGATTGGAGATTTTTATGGCATGATAAGGAATATGTTAGTTAGAGGGG
1 CGACTTAATATCCCTCACGATTGGAGATTTCTATAGCATGATAAGGAATATGTTAGTTAAAGGGG
* * *
394758 GAAGATCGGTAGATGAATCGCCCATCTAATCGATCTTCAATAGTCACCATGAAGTGACTGAAAAT
66 GAAGATCGATAAATGAATCGCCCATCTAATCGATCTTCAATAGTCACCACGAAGTGACTGAAAAT
* * *
394823 TTAGAGTCGTCACCTATCATTTCGGGCTAGACATGATCGAAAGCCTATTGAAACCTATGTCTTGA
131 TTAGAGTCGCCACCGATCATTTCGGGCTAGACATGATCGAAAGCCTATTGAAACCTATGCCTTGA
* * *
394888 GTTACGAAACTCAAGACATTGATCCCGTGGTCTACGGAATAGAGAGATTCGTTGGTTGGGTTTAG
196 GTTACGAAACTCAAAACATCGATCCCGTGGTCTACGGAATAGAGAGATTCATTGGTTGGGTTTAG
* * *
394953 GAGTTGGTTACGCGCAAAGAGGTATGAACCCCCTCGCGATACCCAAAATCGGTACCTTACTAGAT
261 GAGTTAGTTACGCGCAAAGAGGTATGAACCCCCTCGCGACACCCAAAATCAGTACCTTACTAGAT
*
395018 GTGTTTTGACTCGTGTCGCAACTGTGCGCTCGACCCCGGTGATAAGGCAAATGAGGCGCGCT
326 ATGTTTTGACTCGTGTCGCAACTGTGCGCTCGACCCCGGTGATAAGGCAAATGAGGCGCGCT
* * *
395080 CGACTTAATATCCTTCGCGATTAGG-GATTTCTATAGCATGAT-GGGAAGTATGTT-GATTAAAG
1 CGACTTAATATCCCTCACGATT-GGAGATTTCTATAGCATGATAAGGAA-TATGTTAG-TTAAAG
* * * * *
395142 GGGGAAGATCGATAAATGAATCGCCCGTCTAATTGATCTTGAATGGTCACTACGAAGTGA-TCGA
63 GGGGAAGATCGATAAATGAATCGCCCATCTAATCGATCTTCAATAGTCACCACGAAGTGACT-GA
* * * * * *
395206 AATTTTAGAGTCGCCACCGATCATTTTGGGTTAGGCATGATCGGATGCCTATTGAAACCTATGCC
127 AAATTTAGAGTCGCCACCGATCATTTCGGGCTAGACATGATCGAAAGCCTATTGAAACCTATGCC
* **
395271 TTGAGTTACGAAACTCAAAACATCGATCCCGTGGTCTACTGAATTTAGAGATTCATTGGTTGGGT
192 TTGAGTTACGAAACTCAAAACATCGATCCCGTGGTCTACGGAATAGAGAGATTCATTGGTTGGGT
* * * * * *
395336 TTGGGAGTTAGTTACGCGTAAAGAGGTATGAACCTCCTCGTGACGCCCGAAATCAGTACCTTACT
257 TTAGGAGTTAGTTACGCGCAAAGAGGTATGAACCCCCTCGCGACACCCAAAATCAGTACCTTACT
395401 AGCA-ATGTTTTGACTCG
322 AG-ATATGTTTTGACTCG
395418 ATATTGGTTA
Statistics
Matches: 293, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
386 6 0.02
387 284 0.97
388 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (387 bp):
CGACTTAATATCCCTCACGATTGGAGATTTCTATAGCATGATAAGGAATATGTTAGTTAAAGGGG
GAAGATCGATAAATGAATCGCCCATCTAATCGATCTTCAATAGTCACCACGAAGTGACTGAAAAT
TTAGAGTCGCCACCGATCATTTCGGGCTAGACATGATCGAAAGCCTATTGAAACCTATGCCTTGA
GTTACGAAACTCAAAACATCGATCCCGTGGTCTACGGAATAGAGAGATTCATTGGTTGGGTTTAG
GAGTTAGTTACGCGCAAAGAGGTATGAACCCCCTCGCGACACCCAAAATCAGTACCTTACTAGAT
ATGTTTTGACTCGTGTCGCAACTGTGCGCTCGACCCCGGTGATAAGGCAAATGAGGCGCGCT
Found at i:401442 original size:20 final size:20
Alignment explanation
Indices: 401367--401444 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 20
401357 AAAAACCAAG
* *
401367 ATGTATCGATACAATGATAA
1 ATGTATCGATACATTTATAA
401387 ATGTATCGATACAATTTA-AA
1 ATGTATCGATAC-ATTTATAA
* *
401407 GCATGTATCAATACATTTATTA
1 --ATGTATCGATACATTTATAA
401429 ATGTATCGATACATTT
1 ATGTATCGATACATTT
401445 TCTTGGCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 29 0.59
21 8 0.16
22 12 0.24
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTATAA
Found at i:402673 original size:31 final size:33
Alignment explanation
Indices: 402610--402677 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
402600 TGTTGTTGTT
*
402610 TTTTAGAGTTGTCTGTTTAGGTTTAGTTTTTTC
1 TTTTAGAGTTGTCTGGTTAGGTTTAGTTTTTTC
* *
402643 TTTTAG-GTTGTGTGGTTATGTTT-GTTTTTTC
1 TTTTAGAGTTGTCTGGTTAGGTTTAGTTTTTTC
402674 TTTT
1 TTTT
402678 TTGAGTTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 12 0.38
32 14 0.44
33 6 0.19
ACGTcount: A:0.09, C:0.04, G:0.22, T:0.65
Consensus pattern (33 bp):
TTTTAGAGTTGTCTGGTTAGGTTTAGTTTTTTC
Found at i:403766 original size:13 final size:13
Alignment explanation
Indices: 403748--403773 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
403738 TACACCAAGT
403748 ATGTATCGATACA
1 ATGTATCGATACA
403761 ATGTATCGATACA
1 ATGTATCGATACA
403774 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:403771 original size:32 final size:33
Alignment explanation
Indices: 403730--403793 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
403720 TAGCCAAACT
* **
403730 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
403762 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
403794 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:405987 original size:21 final size:21
Alignment explanation
Indices: 405954--405998 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
405944 TTGCAAGTTG
*
405954 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
405976 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
405996 AAA
1 AAA
405999 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:409879 original size:13 final size:13
Alignment explanation
Indices: 409861--409885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
409851 GGAAATTCAA
409861 TGTATCGATACAT
1 TGTATCGATACAT
409874 TGTATCGATACA
1 TGTATCGATACA
409886 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:410049 original size:20 final size:20
Alignment explanation
Indices: 410006--410051 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
409996 AAATCTTTTG
410006 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
410027 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
410047 CAAAA
1 CAAAA
410052 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:412443 original size:13 final size:13
Alignment explanation
Indices: 412425--412450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
412415 TACACCAAGT
412425 ATGTATCGATACA
1 ATGTATCGATACA
412438 ATGTATCGATACA
1 ATGTATCGATACA
412451 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:412448 original size:32 final size:33
Alignment explanation
Indices: 412407--412470 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
412397 TAGCCAAACT
* **
412407 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
412439 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
412471 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:414839 original size:51 final size:51
Alignment explanation
Indices: 414780--414914 Score: 164
Period size: 51 Copynumber: 2.6 Consensus size: 51
414770 GGAAAAAAAA
* * * *
414780 TATATCGATACTTTTTTCATTGTATCGATGCATTTTGGGTTTTGACCTAAT
1 TATATCGATACTTTTTTCATTGTATCGATACATTCTAGGTTTTGACCCAAT
* * *
414831 TATATCGATACATTCTTCATTGTATTGATACATTCTAGGTTTTGACCCAAT
1 TATATCGATACTTTTTTCATTGTATCGATACATTCTAGGTTTTGACCCAAT
* * *
414882 TGTATCGATACATTCTTT-ATTGTATTGATACAT
1 TATATCGATAC-TTTTTTCATTGTATCGATACAT
414915 CCAATTAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 69 0.96
52 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (51 bp):
TATATCGATACTTTTTTCATTGTATCGATACATTCTAGGTTTTGACCCAAT
Found at i:422095 original size:51 final size:50
Alignment explanation
Indices: 422035--422220 Score: 212
Period size: 51 Copynumber: 3.6 Consensus size: 50
422025 TTGAGTTTCT
* *
422035 CAATATTTCATAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCC-GGTTTTATTTCTAAAACAC
*
422086 TAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAA-CCCGGTTTTATTTCT-AAAACAC
* * ** * *
422137 CAACTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCCAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAAC-CCGGTTTTATTT-CTAAAACAC
**
422190 CAATTTTTCACAATTAGGGATACTCCAACCC
1 CAATTTTTCACAATCGGGGATACTCCAACCC
422221 CGTTAATCAT
Statistics
Matches: 113, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
50 1 0.01
51 51 0.45
52 47 0.42
53 14 0.12
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (50 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCGGTTTTATTTCTAAAACAC
Found at i:422176 original size:52 final size:50
Alignment explanation
Indices: 422043--422220 Score: 187
Period size: 52 Copynumber: 3.5 Consensus size: 50
422033 CTCAATATTT
* * *
422043 CATAATCGGGGATACTCCAACCCTGGTTTTA-TTTCTAAAACACTAATTTTT
1 CATAATCGGGGATACTCCAACCC-GGTTTTATTTTC-AAAACACCAACTTTC
*
422094 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAACTTTC
1 CATAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAACTTTC
* * * * *
422145 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCCAAAACACCAATTTTT
1 C-ATAATCGGGGATACTCCAAC-CCGGTTTTATTT-TCAAAACACCAACTTTC
* **
422198 CACAATTAGGGATACTCCAACCC
1 CATAATCGGGGATACTCCAACCC
422221 CGTTAATCAT
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
51 42 0.39
52 51 0.47
53 15 0.14
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (50 bp):
CATAATCGGGGATACTCCAACCCGGTTTTATTTTCAAAACACCAACTTTC
Found at i:422392 original size:80 final size:80
Alignment explanation
Indices: 422229--422405 Score: 214
Period size: 80 Copynumber: 2.2 Consensus size: 80
422219 CCCGTTAATC
* ** * *
422229 ATCGGGGATACTCCATCCCTGTTATTTTCGAGGGGATACTCTAACCCCCGATTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCGAACCCCAGATTTTATTTCTAAAA
* *
422294 CATCAAATTTTCATA
66 CATCAAATTTCCACA
* *
422309 ATCGGGGATACTCTAACCCCATTATTCTT-GAGGGGATACTCGAACCCCAGGTTTTATTTCTAAA
1 ATCGGGGATACTCCAACCCCATTATT-TTCGAGGGGATACTCGAACCCCAGATTTTATTTCTAAA
*
422373 ACA-CCAATTCTCCACA
65 ACATCAAATT-TCCACA
* *
422389 ATCGAGGATATTCCAAC
1 ATCGGGGATACTCCAAC
422406 TCCAATTTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 5 0.06
80 75 0.91
81 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCGAACCCCAGATTTTATTTCTAAAA
CATCAAATTTCCACA
Found at i:422491 original size:28 final size:29
Alignment explanation
Indices: 422440--422512 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
422430 GTTTTTCACA
* **
422440 ATCGAGGATACTCTAA-CCTCGTTATTTC
1 ATCGAGGATACTCCAACCCTCGTTACCTC
422468 ATCGAGGATACTCCAACCCT-GTTACCTC
1 ATCGAGGATACTCCAACCCTCGTTACCTC
422496 --CGAGGGATACTCCAACC
1 ATCGA-GGATACTCCAACC
422513 GCGGTTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
26 3 0.08
27 13 0.32
28 21 0.52
29 3 0.08
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
ATCGAGGATACTCCAACCCTCGTTACCTC
Found at i:422618 original size:79 final size:79
Alignment explanation
Indices: 422473--422670 Score: 211
Period size: 79 Copynumber: 2.5 Consensus size: 79
422463 ATTTCATCGA
* ** * * * *
422473 GGATACTCCAACCCTGTTACCTCCGA-GGGATACTCCAACCGCGGTTGTATTTTCAAAATATTGA
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCACGATTGTATTTTCAAAATATCGA
* **
422537 TTTCTCATAATTGG
66 TTTCTCAAAACCGG
* * **
422551 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCACGATTTTA-TTTCCTAATCATCG
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCACGATTGTATTTTCAAAAT-ATCG
*
422615 ATTTTTCAAAACCGG
65 ATTTCTCAAAACCGG
** *
422630 GGATACTCCAACCCCACTATTTTCAAGGGGATACTCCAACC
1 GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACC
422671 CCGTTATTAT
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
78 29 0.29
79 70 0.71
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCACGATTGTATTTTCAAAATATCGA
TTTCTCAAAACCGG
Found at i:435072 original size:1 final size:1
Alignment explanation
Indices: 435068--435141 Score: 67
Period size: 1 Copynumber: 74.0 Consensus size: 1
435058 ATTCTTTTTC
* * * * * * * *
435068 AAAAAAAAAATAAAAATAAAAACAAAAACAAAAAAAAATAAAAAAACAAAAACAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
435133 AAGAAAAAA
1 AAAAAAAAA
435142 GAGAGAAAAT
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.88, C:0.07, G:0.01, T:0.04
Consensus pattern (1 bp):
A
Found at i:435082 original size:6 final size:6
Alignment explanation
Indices: 435067--435134 Score: 79
Period size: 6 Copynumber: 11.7 Consensus size: 6
435057 CATTCTTTTT
* * *
435067 CAAAAA -AAAAA TAAAAA TAAAAA CAAAAA CAAAAA -AAAATA AAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAA-A CAAAAA
435114 CAAAAA CAAAAA -AAAAA CAAA
1 CAAAAA CAAAAA CAAAAA CAAA
435135 GAAAAAAGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
5 14 0.25
6 38 0.68
7 4 0.07
ACGTcount: A:0.87, C:0.09, G:0.00, T:0.04
Consensus pattern (6 bp):
CAAAAA
Found at i:435100 original size:24 final size:23
Alignment explanation
Indices: 435067--435130 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 23
435057 CATTCTTTTT
*
435067 CAAAAA-AAAAATAAAAATAAAAA
1 CAAAAACAAAAA-AAAAAAAAAAA
435090 CAAAAACAAAAAAAAATAAAAAAA
1 CAAAAACAAAAAAAAA-AAAAAAA
435114 CAAAAACAAAAAAAAAA
1 CAAAAACAAAAAAAAAA
435131 CAAAGAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.05
Consensus pattern (23 bp):
CAAAAACAAAAAAAAAAAAAAAA
Found at i:435141 original size:30 final size:30
Alignment explanation
Indices: 435067--435141 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 30
435057 CATTCTTTTT
* *
435067 CAAAAAAAAA-ATAAAAATAAAAACAAAAA
1 CAAAAAAAAATAAAAAAACAAAAACAAAAA
435096 CAAAAAAAAATAAAAAAACAAAAACAAAAA
1 CAAAAAAAAATAAAAAAACAAAAACAAAAA
* *
435126 -AAAAACAAAGAAAAAA
1 CAAAAAAAAATAAAAAA
435142 GAGAGAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.87, C:0.08, G:0.01, T:0.04
Consensus pattern (30 bp):
CAAAAAAAAATAAAAAAACAAAAACAAAAA
Found at i:436513 original size:61 final size:57
Alignment explanation
Indices: 436228--436589 Score: 400
Period size: 55 Copynumber: 6.4 Consensus size: 57
436218 TTCGCCCTTT
* *
436228 AGTCCTCAAAAAGTAGGATG--CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGATGCTCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCC
* * * *
436283 AGTCCTCAAAGAGCAGGA--CGCCTTTTAAAGCCCACACAAGTTAGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGATGCTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* * *
436338 AGTCCTCAAAGAGCAGGA--CACCTTTCAAAGCCCACACGAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGATGCTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * * *
436393 AGTCTTCAAAGAGCAAGA--CGCCTTTCAAAGCCCACACGAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGATGCTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
*
436448 AGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGATGC--TC-CTTT-CAAAGCCCACACAAGTTGGTGGCACTTTCC
* ** **
436509 AGTCCTCAAAGAGCAGGATACCTTTCCTTTTCAAAGCCCACATGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGAT-GC--TCC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
436570 AGTCCTCAAAGAGCAGGATG
1 AGTCCTCAAAGAGCAGGATG
436590 GACTTTATTT
Statistics
Matches: 271, Mismatches: 25, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
54 3 0.01
55 163 0.60
57 1 0.00
59 1 0.00
60 4 0.01
61 91 0.34
62 8 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (57 bp):
AGTCCTCAAAGAGCAGGATGCTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:436659 original size:42 final size:42
Alignment explanation
Indices: 436571--436663 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
436561 GCACTTTTTA
* *
436571 GTCCTCAAAGAGCAGGATGGACTTTATTTTCCTCTTTCTTTC
1 GTCCTCAAAGAGCAGGACGGACTTTATTTCCCTCTTTCTTTC
* * *
436613 GTCCTCAAAGAGCAGGACGTA-TTTCGTTTCCCTTTTTCCTTT-
1 GTCCTCAAAGAGCAGGACGGACTTT-ATTTCCCTCTTT-CTTTC
436655 GTCCTCAAA
1 GTCCTCAAA
436664 AAACGGGACG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 3 0.07
42 37 0.84
43 4 0.09
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACGGACTTTATTTCCCTCTTTCTTTC
Found at i:437503 original size:79 final size:78
Alignment explanation
Indices: 437369--437603 Score: 220
Period size: 79 Copynumber: 3.0 Consensus size: 78
437359 GTTATTTCAT
** ** * * *
437369 CGGGGATACTCCAACCTTGTTACCTCCGAGGGGATACTCCAACCCCGGCTGTATTTTCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCAGTTTTATTTTCAAAATAT
*
437434 TGATTTCTCATAAT
65 TGATTTCTCATAAC
* * **
437448 TGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCAATTTTA-TTTCCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCAGTTTTATTTTCAAAAT-A
* * *
437512 TCGATTTTTCACAAC
64 TTGATTTCTCATAAC
* * * * * *
437527 CGGGGATACTCCAACCCCATTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCAGTT-TTATTTTCAAAATAT
*
437592 TAAATTTCTCAT
65 T-GATTTCTCAT
437604 CGGGAAATAT
Statistics
Matches: 122, Mismatches: 30, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
78 12 0.10
79 98 0.80
80 12 0.10
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCAGTTTTATTTTCAAAATATT
GATTTCTCATAAC
Found at i:439091 original size:13 final size:13
Alignment explanation
Indices: 439073--439099 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
439063 ATACATTGCT
439073 TTGTATCGATACA
1 TTGTATCGATACA
439086 TTGTATCGATACA
1 TTGTATCGATACA
439099 T
1 T
439100 GGCCAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:446606 original size:13 final size:13
Alignment explanation
Indices: 446588--446612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
446578 CATTTTATGG
446588 TGTATCGATACAA
1 TGTATCGATACAA
446601 TGTATCGATACA
1 TGTATCGATACA
446613 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:446628 original size:32 final size:33
Alignment explanation
Indices: 446565--446632 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
446555 CGTTACAAGC
**
446565 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
446598 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
446630 CAA
1 CAA
446633 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:446708 original size:20 final size:20
Alignment explanation
Indices: 446662--446715 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
446652 TTGCCAATGA
*
446662 CATGTATCGATACATCTTTT
1 CATGTATCGATACATCTTGT
* *
446682 TAAGTATCGATACAT-TTGGT
1 CATGTATCGATACATCTT-GT
*
446702 CATGTATCAATACA
1 CATGTATCGATACA
446716 ATGTATCGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATCTTGT
Found at i:448572 original size:20 final size:22
Alignment explanation
Indices: 448533--448573 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
448523 GGCTAGTGTG
*
448533 GGGGCTGCCTGGTTGCGACCTA
1 GGGGCTGCCTGGTCGCGACCTA
448555 GGGG-TGCC-GGTCGCGACCT
1 GGGGCTGCCTGGTCGCGACCT
448574 GGTGGGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.07, C:0.29, G:0.44, T:0.20
Consensus pattern (22 bp):
GGGGCTGCCTGGTCGCGACCTA
Found at i:452211 original size:9 final size:9
Alignment explanation
Indices: 452197--452227 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
452187 TCTGAGTCAC
*
452197 CATCATCAT
1 CATCATCTT
452206 CATCATCTT
1 CATCATCTT
452215 CATCATCTT
1 CATCATCTT
452224 CATC
1 CATC
452228 GTCCTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (9 bp):
CATCATCTT
Found at i:453845 original size:13 final size:13
Alignment explanation
Indices: 453827--453851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
453817 CATTTTATGG
453827 TGTATCGATACAA
1 TGTATCGATACAA
453840 TGTATCGATACA
1 TGTATCGATACA
453852 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:453867 original size:32 final size:33
Alignment explanation
Indices: 453804--453871 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
453794 CGTTACAAGC
**
453804 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
453837 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
453869 CAA
1 CAA
453872 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:456798 original size:13 final size:13
Alignment explanation
Indices: 456780--456808 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
456770 ACAACATTCC
456780 TTGTATCGATACA
1 TTGTATCGATACA
456793 TTGTATCGATACA
1 TTGTATCGATACA
456806 TTG
1 TTG
456809 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:459269 original size:33 final size:32
Alignment explanation
Indices: 459227--459288 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
459217 CACACCCAGA
*
459227 TGTATCGATACATGCTGCTTTGTATCGATATAT
1 TGTATCGATACATG-TGCATTGTATCGATATAT
*
459260 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATGTGCATTGTATCGATA
459289 CATAGCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATATAT
Found at i:459282 original size:19 final size:19
Alignment explanation
Indices: 459258--459313 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
459248 GTATCGATAT
*
459258 ATTGTATCGATACATGTTC-
1 ATTGTATCGATACATG-CCA
459277 ATTGTATCGATACATAGCCAA
1 ATTGTATCGATACAT-GCC-A
459298 ATTGTATCGATACATG
1 ATTGTATCGATACATG
459314 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 16 0.48
20 2 0.06
21 15 0.45
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGCCA
Found at i:459379 original size:13 final size:13
Alignment explanation
Indices: 459358--459388 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
459348 TGATACATGG
*
459358 TACAATGTATCGA
1 TACATTGTATCGA
459371 TACATTGTATCGA
1 TACATTGTATCGA
459384 TACAT
1 TACAT
459389 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:459386 original size:33 final size:32
Alignment explanation
Indices: 459342--459408 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
459332 CTATCACTAT
*
459342 TTGTATTGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
459375 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
459408 T
1 T
459409 AGCATGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:460402 original size:21 final size:20
Alignment explanation
Indices: 460372--460410 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
460362 CACATTTTTG
460372 TCTAAATGTATCGATACATT
1 TCTAAATGTATCGATACATT
460392 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCGATACA
460411 AGGTCCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCGATACATT
Found at i:460465 original size:13 final size:13
Alignment explanation
Indices: 460447--460471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460437 TTCAACAATT
460447 TGTATCGATACAA
1 TGTATCGATACAA
460460 TGTATCGATACA
1 TGTATCGATACA
460472 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:467004 original size:21 final size:23
Alignment explanation
Indices: 466961--467011 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
466951 GTTTTAAAAA
* *
466961 TTTATTTATTTTCTTG-AGTTTT
1 TTTATTTATTTCCTTGAAATTTT
466983 TTTATTT-TTTCCTTGAAATTTT
1 TTTATTTATTTCCTTGAAATTTT
467005 TTTATTT
1 TTTATTT
467012 CCGATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.73
Consensus pattern (23 bp):
TTTATTTATTTCCTTGAAATTTT
Found at i:467064 original size:167 final size:166
Alignment explanation
Indices: 466695--467292 Score: 714
Period size: 167 Copynumber: 3.6 Consensus size: 166
466685 AAAAACACAA
* * *
466695 TTTTTTACTCTGTAAATATTTTC-AGAAGGATTTTTCTTGGTTTTTAATTTTT-AAATTCATCAA
1 TTTTTTACTCCGTAAATATTTTCAAG-GGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAA
*
466758 ATATTATTATTTAATTCATATTAAATTAGTTTAAAAAATTTATTTATTTTCATGAGTTTTTCT-T
65 ATATTATTATTTAATTCATATTAAATTAGTTTAAAAAATTTATTTATTTTCATGAGTTTTTTTAT
* **
466822 TTTTT-CTTGAAATTCTTTTATTTTCGAAAAACGGAG
130 TTTTTCCTTGAAATTCTTTTATTTCCGAAAAATAGAG
*
466858 CTTTTTT-CTTCC-TAAATATTTTTAAGGGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCA
1 -TTTTTTAC-TCCGTAAATATTTTCAAGGGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCA
* *
466921 AATATTATTATTTAATTCATATTAAATTATGTTTTAAAAATTTATTTATTTTCTTGAGTTTTTTT
64 AATATTATTATTTAATTCATATTAAATTA-GTTTAAAAAATTTATTTATTTTCATGAGTTTTTTT
* * *
466986 ATTTTTTCCTTGAAATTTTTTTATTTCCGATAAATAAAG
128 ATTTTTTCCTTGAAATTCTTTTATTTCCGAAAAATAGAG
* **
467025 TTTTTTACTCCGTAAATGTTTTCGGGGGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAA
1 TTTTTTACTCCGTAAATATTTTCAAGGGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAA
* * * *
467090 TACTATTATTTAATTCGTATTAAATTAGTTTCAAAAAATTCATTTATTTTCATGAG--TTTTCAT
66 TATTATTATTTAATTCATATTAAATTAGTTT-AAAAAATTTATTTATTTTCATGAGTTTTTTTAT
* * ** *
467153 TTTTTCTTTGAAA-TCTCTTATTTCTAAAAAATCGAG
130 TTTTTCCTTGAAATTCTTTTATTTCCGAAAAATAGAG
* * ** * * * *
467189 TTTTCTGCTCTATAAATGTTTTC-AGGGGATTTTTC-TCGTTTTAAAATTTTTAAAATTCATCTA
1 TTTTTTACTCCGTAAATATTTTCAAGGGGATTTTTCTTAGTTTT-TAATTTTTAAAATTCATCAA
* * * * *
467252 ATATTATTATTAAATTTACATTAAATCAGTTTTGAAAAATT
65 ATATTATTATTTAATTCATATTAAATTAG-TTTAAAAAATT
467293 CAAATTATTT
Statistics
Matches: 377, Mismatches: 46, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
162 6 0.02
163 94 0.25
164 87 0.23
165 50 0.13
166 19 0.05
167 121 0.32
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (166 bp):
TTTTTTACTCCGTAAATATTTTCAAGGGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAA
TATTATTATTTAATTCATATTAAATTAGTTTAAAAAATTTATTTATTTTCATGAGTTTTTTTATT
TTTTCCTTGAAATTCTTTTATTTCCGAAAAATAGAG
Done.