Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 181 of 207
Found at i:55462645 original size:7 final size:7
Alignment explanation
Indices: 55462635--55462670 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
55462625 TTATATACAT
55462635 AATACTA
1 AATACTA
55462642 AATACTA
1 AATACTA
55462649 AATACTA
1 AATACTA
55462656 AATACTA
1 AATACTA
55462663 AATA-TA
1 AATACTA
55462669 AA
1 AA
55462671 ACGACTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:55465325 original size:11 final size:11
Alignment explanation
Indices: 55465311--55465354 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
55465301 AGATAAATAT
55465311 TATTTTATTAA
1 TATTTTATTAA
*
55465322 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
55465335 TATTTTATTAT
1 TATTTTATTAA
55465346 TATTTTATT
1 TATTTTATT
55465355 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:55467337 original size:35 final size:34
Alignment explanation
Indices: 55467298--55467457 Score: 128
Period size: 35 Copynumber: 4.7 Consensus size: 34
55467288 ACTATGAACA
* * *
55467298 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGTTGGGCTATGGCAGT-TTTATATG
* * *
55467333 TAAGACTATAGTTGGGCTATGGCA-TTCT-GATG
1 TAAGACCATAGTTGGGCTATGGCAGTTTTATATG
** * * * * *
55467365 ATAAGACCATAACTGGGTTATGGCACTATGA-ACG
1 -TAAGACCATAGTTGGGCTATGGCAGTTTTATATG
* * *
55467399 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGTTGGGCTATGGCAGT-TTTATATG
55467434 TAAGACCATAGTTGGGCTATGGCA
1 TAAGACCATAGTTGGGCTATGGCA
55467458 TTCTGATGAT
Statistics
Matches: 93, Mismatches: 27, Indels: 10
0.72 0.21 0.08
Matches are distributed among these distances:
32 3 0.03
33 41 0.44
34 6 0.06
35 43 0.46
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (34 bp):
TAAGACCATAGTTGGGCTATGGCAGTTTTATATG
Found at i:55467387 original size:33 final size:32
Alignment explanation
Indices: 55467330--55467490 Score: 115
Period size: 33 Copynumber: 4.8 Consensus size: 32
55467320 CAGTGTTTAT
* **
55467330 ATGTAAGACTATAGTTGGGCTATGGCATTCTG
1 ATGTAAGACCATAACTGGGCTATGGCATTCTG
* * *
55467362 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAACTGGGCTATGGCATTCTG
* *** * * * *
55467395 AACGTAAGACCATGGTTGGACCATGGCAGTGTTTAT
1 -ATGTAAGACCATAACTGGGCTATGGCA-T-TCT-G
**
55467431 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
1 ATGTAAGACCATAACTGGGCTATGGCATTCTG
*
55467463 ATGATAAGACCATAACTGGGTTATGGCA
1 ATG-TAAGACCATAACTGGGCTATGGCA
55467491 CTACAAATGT
Statistics
Matches: 98, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
32 6 0.06
33 64 0.65
34 3 0.03
35 25 0.26
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGGCATTCTG
Found at i:55467438 original size:101 final size:101
Alignment explanation
Indices: 55467263--55467493 Score: 408
Period size: 101 Copynumber: 2.3 Consensus size: 101
55467253 TGAATTCACG
* ** *
55467263 GATAATACCATAACTAAGTTATGGAACTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
*
55467328 ATATGTAAGACTATAGTTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGTTGGGCTATGGCATTCTGAT
*
55467364 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
55467429 ATATGTAAGACCATAGTTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGTTGGGCTATGGCATTCTGAT
55467465 GATAAGACCATAACTGGGTTATGGCACTA
1 GATAAGACCATAACTGGGTTATGGCACTA
55467494 CAAATGTAAA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 124 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
ATATGTAAGACCATAGTTGGGCTATGGCATTCTGAT
Found at i:55467546 original size:24 final size:25
Alignment explanation
Indices: 55467493--55467546 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
55467483 TTATGGCACT
55467493 ACAAATGTAAAGGATGAATTGACGG
1 ACAAATGTAAAGGATGAATTGACGG
*
55467518 A-AAATGTAAATGATGAATTGAC-G
1 ACAAATGTAAAGGATGAATTGACGG
55467541 ACAAAT
1 ACAAAT
55467547 TACCCAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 2 0.07
24 24 0.89
25 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (25 bp):
ACAAATGTAAAGGATGAATTGACGG
Found at i:55471011 original size:97 final size:97
Alignment explanation
Indices: 55470845--55471038 Score: 370
Period size: 97 Copynumber: 2.0 Consensus size: 97
55470835 CCCCAGTACG
55470845 TATTTCCAGCATTGAACATTGACCCACCGAGGTGCAAGTCCCATCCACTAACCGAGTGTCGTGTA
1 TATTTCCAGCATTGAACATTGACCCACCGAGGTGCAAGTCCCATCCACTAACCGAGTGTCGTGTA
55470910 AGAGTTGTGTATTCCATACTGCCACCAAACAC
66 AGAGTTGTGTATTCCATACTGCCACCAAACAC
* *
55470942 TATTTCCAGCATTGAACATTGACCCATCGAGGTGCATGTCCCATCCACTAACCGAGTGTCGTGTA
1 TATTTCCAGCATTGAACATTGACCCACCGAGGTGCAAGTCCCATCCACTAACCGAGTGTCGTGTA
55471007 AGAGTTGTGTATTCCATACTGCCACCAAACAC
66 AGAGTTGTGTATTCCATACTGCCACCAAACAC
55471039 GGGTGTTTCC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (97 bp):
TATTTCCAGCATTGAACATTGACCCACCGAGGTGCAAGTCCCATCCACTAACCGAGTGTCGTGTA
AGAGTTGTGTATTCCATACTGCCACCAAACAC
Found at i:55494973 original size:46 final size:46
Alignment explanation
Indices: 55494901--55494993 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
55494891 AGGGATAGAC
*
55494901 TATGATGAAACATATGCTCCCGTAGCTAGAATGGAAACCATTAGGA
1 TATGATGAAACATATGCTCCCATAGCTAGAATGGAAACCATTAGGA
55494947 TATGATGAAACATATGCTCCCATAGCTAGAATGGAAACCATTAGGA
1 TATGATGAAACATATGCTCCCATAGCTAGAATGGAAACCATTAGGA
55494993 T
1 T
55494994 GCTTTTAGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (46 bp):
TATGATGAAACATATGCTCCCATAGCTAGAATGGAAACCATTAGGA
Found at i:55512330 original size:15 final size:15
Alignment explanation
Indices: 55512293--55512331 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
55512283 CATAGCAGTG
55512293 TTTTAAGAAATATATA
1 TTTTAA-AAATATATA
* *
55512309 ATCTAAAAATATATA
1 TTTTAAAAATATATA
55512324 TTTTAAAA
1 TTTTAAAA
55512332 TTTATAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTTAAAAATATATA
Found at i:55512571 original size:21 final size:21
Alignment explanation
Indices: 55512547--55512606 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
55512537 AGGTGAAAAA
*
55512547 ATAAAAATATATGAA-ATTATC
1 ATAAAAATAAAT-AATATTATC
*
55512568 ATAAATATAAATAATATTATC
1 ATAAAAATAAATAATATTATC
* *
55512589 ATAAATATAAATATTATT
1 ATAAAAATAAATAATATT
55512607 TAATTATCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAAAATAAATAATATTATC
Found at i:55512616 original size:26 final size:26
Alignment explanation
Indices: 55512561--55512634 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
55512551 AAATATATGA
55512561 AATTATCATAAATATAAATA--A--T
1 AATTATCATAAATATAAATATTATTT
55512583 -ATTATCATAAATATAAATATTATTT
1 AATTATCATAAATATAAATATTATTT
* *
55512608 AATTATCATAAAGATAAAAATTATTT
1 AATTATCATAAATATAAATATTATTT
55512634 A
1 A
55512635 CCTTAACATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 19 0.42
23 1 0.02
25 1 0.02
26 24 0.53
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (26 bp):
AATTATCATAAATATAAATATTATTT
Found at i:55515274 original size:12 final size:12
Alignment explanation
Indices: 55515241--55515274 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
55515231 AGACCAATGG
55515241 GAGCATAACAAA
1 GAGCATAACAAA
*
55515253 GAGCACAACAAA
1 GAGCATAACAAA
*
55515265 GAGTATAACA
1 GAGCATAACA
55515275 TAAGCACGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.18, G:0.18, T:0.09
Consensus pattern (12 bp):
GAGCATAACAAA
Found at i:55515442 original size:55 final size:55
Alignment explanation
Indices: 55515376--55515488 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
55515366 CCCCTAGAAG
55515376 AAAAAGTAAAGCTTCTTTATTATGGATTCAAATAACCCAGAAAAGGAAACATCAA
1 AAAAAGTAAAGCTTCTTTATTATGGATTCAAATAACCCAGAAAAGGAAACATCAA
55515431 AAAAAGTAAAGCTTCTTTATTATGGATTCAAATAACCCAGAAAAGGAAACATCAA
1 AAAAAGTAAAGCTTCTTTATTATGGATTCAAATAACCCAGAAAAGGAAACATCAA
55515486 AAA
1 AAA
55515489 GCACTTACCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.23
Consensus pattern (55 bp):
AAAAAGTAAAGCTTCTTTATTATGGATTCAAATAACCCAGAAAAGGAAACATCAA
Found at i:55516797 original size:26 final size:26
Alignment explanation
Indices: 55516752--55516815 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
55516742 ATTATATATT
55516752 AAATATATA-TTTTTTATTTTTAATC
1 AAATATATATTTTTTTATTTTTAATC
55516777 AAATATATATTTTTTTATTTTTAATC
1 AAATATATATTTTTTTATTTTTAATC
55516803 AAATATATATTTT
1 AAATATATATTTT
55516816 ATATATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 9 0.24
26 29 0.76
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (26 bp):
AAATATATATTTTTTTATTTTTAATC
Found at i:55518150 original size:42 final size:43
Alignment explanation
Indices: 55518102--55518183 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
55518092 CCGGCACTAA
*
55518102 TTCAAATTTTAA-AAAAATT-ATTTTTTTACTTTTTGGGTGTAT
1 TTCAAATTTAAAGAAAAATTGATTTTTTT-CTTTTTGGGTGTAT
*
55518144 TTCAAATTTAAAGAAAAATTGATTTTTTTCTTTTTTGGTG
1 TTCAAATTTAAAGAAAAATTGATTTTTTTCTTTTTGGGTG
55518184 CCAATGTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 11 0.31
43 17 0.47
44 8 0.22
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (43 bp):
TTCAAATTTAAAGAAAAATTGATTTTTTTCTTTTTGGGTGTAT
Found at i:55534097 original size:19 final size:20
Alignment explanation
Indices: 55534075--55534113 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
55534065 ATTTTTTTTA
55534075 ATTTAATAAAATTTT-ATAT
1 ATTTAATAAAATTTTCATAT
**
55534094 ATTTTTTAAAATTTTCATAT
1 ATTTAATAAAATTTTCATAT
55534114 TGATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTAATAAAATTTTCATAT
Found at i:55537320 original size:4 final size:4
Alignment explanation
Indices: 55537313--55537337 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55537303 ATGTGCTTAT
55537313 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
55537338 AATACAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:55537706 original size:22 final size:22
Alignment explanation
Indices: 55537681--55537725 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
55537671 ATGTTATAAC
55537681 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
55537703 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
55537725 T
1 T
55537726 AAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTTTATTTACCAAAATATA
Found at i:55537826 original size:27 final size:27
Alignment explanation
Indices: 55537796--55537863 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
55537786 ACGCCAATGG
55537796 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* *
55537823 CATTGGCGGCACCAATGGTGCCAATAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
55537850 CATTGGCGGCACCA
1 CATTGGCGGCACCA
55537864 GTTGATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:55537920 original size:8 final size:8
Alignment explanation
Indices: 55537906--55538038 Score: 75
Period size: 8 Copynumber: 16.5 Consensus size: 8
55537896 GAAGGAGAGG
55537906 GAAAGAAA
1 GAAAGAAA
*
55537914 TAAAGAAA
1 GAAAGAAA
*
55537922 GAAAGGAGAG
1 GAAA-GA-AA
55537932 GAAAGAAA
1 GAAAGAAA
55537940 G-AA-AAA
1 GAAAGAAA
*
55537946 GAAGGAAA
1 GAAAGAAA
55537954 GAAAAGGAAA
1 G-AAA-GAAA
*
55537964 G-GAGAAGA
1 GAAAGAA-A
55537972 GAAA-AAA
1 GAAAGAAA
*
55537979 -AAAGAAG
1 GAAAGAAA
55537986 GAAAG-AA
1 GAAAGAAA
55537993 G-AAGAAAA
1 GAAAG-AAA
55538001 GGAAAGGAGAA
1 -GAAA-GA-AA
55538012 GAAA-AAA
1 GAAAGAAA
55538019 GAAAGAAA
1 GAAAGAAA
*
55538027 GAAGGAAA
1 GAAAGAAA
55538035 GAAA
1 GAAA
55538039 AGGAAAGGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
6 10 0.10
7 17 0.18
8 41 0.43
9 8 0.08
10 17 0.18
11 3 0.03
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (8 bp):
GAAAGAAA
Found at i:55537938 original size:18 final size:18
Alignment explanation
Indices: 55537915--55538057 Score: 74
Period size: 21 Copynumber: 7.3 Consensus size: 18
55537905 GGAAAGAAAT
55537915 AAAGAAAGAAAGGAGAGG
1 AAAGAAAGAAAGGAGAGG
*
55537933 AAAGAAAGAAA-AAGAAGG
1 AAAGAAAGAAAGGAG-AGG
55537951 AAAGAAAAGGAAAGGAGAAGAG
1 AAAG-AAA-GAAAGGAG-AG-G
* * * *
55537973 AAAAAAAAAGAAGGAAAGA
1 AAAGAAAGA-AAGGAGAGG
*
55537992 AGAAGAAAAGGAAAGGAGAAG
1 A-AAG-AAA-GAAAGGAGAGG
*
55538013 AAA-AAAGAAAGAAAGAAGG
1 AAAGAAAGAAAG-GAG-AGG
*
55538032 AAAGAAAAGGAAAGGAAAGG
1 AAAG-AAA-GAAAGGAGAGG
55538052 AGAAGA
1 A-AAGA
55538058 GAAAAAAAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
17 7 0.07
18 23 0.24
19 9 0.09
20 16 0.17
21 30 0.32
22 10 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAGGAGAGG
Found at i:55537964 original size:5 final size:5
Alignment explanation
Indices: 55537918--55538052 Score: 68
Period size: 5 Copynumber: 27.4 Consensus size: 5
55537908 AAGAAATAAA
* * * *
55537918 GAAA- GAAAG GAGAG GAAA- GAAAG AAAAA G-AAG GAAAG AAAAG GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
* * * * *
55537965 GAGAAG AGAAAA AAAAA G-AAG GAAAG AAGAAG AAAAG GAAAG GAGAAG
1 GA-AAG -GAAAG GAAAG GAAAG GAAAG GA-AAG GAAAG GAAAG GA-AAG
* * *
55538013 AAAAAA GAAA- GAAA- G-AAG GAAAG AAAAG GAAAG GAAAG GA
1 -GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GA
55538053 GAAGAGAAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
3 2 0.02
4 20 0.20
5 61 0.60
6 15 0.15
7 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:55538040 original size:81 final size:77
Alignment explanation
Indices: 55537922--55538108 Score: 236
Period size: 81 Copynumber: 2.4 Consensus size: 77
55537912 AATAAAGAAA
55537922 GAAAGGAGAGGAAAGAAAG-AAAAAGAAGGAAAGAAAAGGAAAGGAGAA-GAGAAAAAAAAAGAA
1 GAAAGGAGAGGAAA-AAAGAAAAAAGAAGGAAAGAAAAGGAAAGGA-AAGGAGAAAAAAAAA-AA
55537985 GGAAAGAAGAAGAAAAG
63 --AAAGAAGAAGAAAAG
* * *
55538002 GAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAAAGGAGAAGAGAAAAAAAA
1 GAAAGGAGAGGAAAAAAGAAA-AAAGAAGGAAAGAAAAGGAAAGGAAAGGAGAAAAAAAAAAAAA
*
55538067 AGAAGAAGAAGAG
65 AGAAGAAGAAAAG
* *
55538080 GGAAGGA-AGGAAAAAAAGAAAAAAAAAGG
1 GAAAGGAGAGG-AAAAAAGAAAAAAGAAGG
55538109 TAATTTTTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
77 9 0.09
78 30 0.31
79 4 0.04
80 19 0.20
81 34 0.35
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (77 bp):
GAAAGGAGAGGAAAAAAGAAAAAAGAAGGAAAGAAAAGGAAAGGAAAGGAGAAAAAAAAAAAAAA
GAAGAAGAAAAG
Found at i:55538086 original size:39 final size:41
Alignment explanation
Indices: 55537956--55538107 Score: 184
Period size: 39 Copynumber: 3.7 Consensus size: 41
55537946 GAAGGAAAGA
*
55537956 AAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAGAAGA
1 AAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAG-AGG
* *
55537998 AAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGG
1 AAAGGAAAGGAGAAG-AGAAA-AAA-AAAGAAGGAAAGAAGAGG
55538042 AAAGGAAAGGAGAAGAGAAAAAAAAAGAA-G-AAGAAGAGG
1 AAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAGAGG
* * *
55538081 GAAGG-AAGGAAAAAAAGAAAAAAAAAG
1 AAAGGAAAGG-AGAAGAGAAAAAAAAAG
55538108 GTAATTTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
38 4 0.04
39 27 0.28
40 1 0.01
41 6 0.06
42 18 0.18
43 8 0.08
44 20 0.20
45 14 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (41 bp):
AAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAGAGG
Found at i:55538103 original size:86 final size:82
Alignment explanation
Indices: 55537933--55538107 Score: 223
Period size: 86 Copynumber: 2.1 Consensus size: 82
55537923 AAAGGAGAGG
*
55537933 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAGAAGA
1 AAAGAAAGAAAAAGAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAGAAGA
*
55537998 AAAGGAAAGGAGAAGAAA
66 AAAGGAAA-GAAAAGAAA
*
55538016 AAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAAAGGAGAAGAGAAAAAAAAAGAA-G-AAGAAGA
1 AAAGAAAGAAA-AA-G-AAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAGA
*
55538079 GGGAAGGAAGGAAA-AAAAGAAA
63 -AGAA--AAGGAAAGAAAAGAAA
55538101 AAA-AAAG
1 AAAGAAAG
55538108 GTAATTTTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
83 11 0.13
84 13 0.16
85 15 0.18
86 36 0.44
87 7 0.09
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (82 bp):
AAAGAAAGAAAAAGAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAGGAAAGAAGAAGA
AAAGGAAAGAAAAGAAA
Found at i:55538980 original size:161 final size:160
Alignment explanation
Indices: 55538582--55539031 Score: 388
Period size: 161 Copynumber: 2.8 Consensus size: 160
55538572 TATTCTCCCT
* *
55538582 TAACACACTAAATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAAGACTA
1 TAACACACT-AATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATA-GA
* *
55538647 AGTTTATGATA--TTT-TTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAGAAG
64 A-ATTATGATATTTTTATTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCAGAAG
**** *
55538709 TAAGAGTGTATTACTAACTTTTTTAAAATTTAGA
128 TAAGAGTGTATTACTAACCAAATT-AAATTTAAA
* * * * ** * * ** *
55538743 -AATA-ATTAA-TACAAAATATTTCAAAGAAAATGTACTGAAATAATTTAAAACAATAACATACG
1 TAACACACTAATTA-ATAA-ATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATA-G
* * * *
55538805 AGAATAAT-ATATTTTTATTTAAAGTAATAAAAAT-C-GAGAAAATAATACGAGCAAAGGGCAGG
63 A-AATTATGATATTTTTATTTAAAGTAAT-AAAATGCGGAGAAAAAAATACGAACAAAGGGCAGA
* * * * **
55538867 GGTAAGGGTTTTTTTTTACACCAAATT-AATTTAAA
126 AGTAAGAGTGTATTACTA-ACCAAATTAAATTTAAA
55538902 TAACACACTAGATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGA
1 TAACACACTA-ATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAA-TAGA
* * * *
55538967 AATTATGATA---TT-TTTAAAGGAATAAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGT
64 AATTATGATATTTTTATTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCAGAAGT
55539028 AAGA
129 AAGA
55539032 TTTTTTTACT
Statistics
Matches: 222, Mismatches: 51, Indels: 35
0.72 0.17 0.11
Matches are distributed among these distances:
156 5 0.02
157 13 0.06
158 36 0.16
159 48 0.22
160 50 0.23
161 57 0.26
162 11 0.05
163 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (160 bp):
TAACACACTAATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATAGAAA
TTATGATATTTTTATTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCAGAAGTAA
GAGTGTATTACTAACCAAATTAAATTTAAA
Found at i:55541276 original size:11 final size:11
Alignment explanation
Indices: 55541257--55541312 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
55541247 TAACTTAATC
*
55541257 TGGAAACAATT
1 TGGATACAATT
55541268 TGGATACAATT
1 TGGATACAATT
*
55541279 T--ATAACTTAATC
1 TGGAT-AC--AATT
55541291 TGGATACAATT
1 TGGATACAATT
55541302 TGGATACAATT
1 TGGATACAATT
55541313 ACCTTTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
9 2 0.05
10 2 0.05
11 25 0.68
12 4 0.11
13 2 0.05
14 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (11 bp):
TGGATACAATT
Found at i:55541282 original size:34 final size:34
Alignment explanation
Indices: 55541243--55541312 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
55541233 CACATGGTAT
55541243 TTTATAACTTAATCTGGAAACAATTTGGATACAA
1 TTTATAACTTAATCTGGAAACAATTTGGATACAA
*
55541277 TTTATAACTTAATCTGGATACAATTTGGATACAA
1 TTTATAACTTAATCTGGAAACAATTTGGATACAA
55541311 TT
1 TT
55541313 ACCTTTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (34 bp):
TTTATAACTTAATCTGGAAACAATTTGGATACAA
Found at i:55544295 original size:63 final size:66
Alignment explanation
Indices: 55544228--55544350 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
55544218 AAAATTATTA
* *
55544228 ATTTTACTAAA-AATAATAACTAATTAA-C-T-ATAATAATAATACTAGTTTTTTACTAACTAGT
1 ATTTTACTAAATAAAAATAA-TAAGTAACCATAATAATAATAATACTAGTTTTTTACTAACTAGT
55544289 TT
65 TT
** *
55544291 ATTTTGGTAAATAAAAATAATAAGTAACCATAATAATAATAATACTAGTTTTTTGCTAAC
1 ATTTTACTAAATAAAAATAATAAGTAACCATAATAATAATAATACTAGTTTTTTACTAAC
55544351 AATAATATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
63 15 0.29
64 8 0.16
65 1 0.02
66 27 0.53
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (66 bp):
ATTTTACTAAATAAAAATAATAAGTAACCATAATAATAATAATACTAGTTTTTTACTAACTAGTT
T
Found at i:55544408 original size:3 final size:3
Alignment explanation
Indices: 55544400--55544443 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
55544390 TCTTAATACT
*
55544400 AAC AAC AAC AAC AAC AAC AAC AGC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
55544444 TAATAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.32, G:0.02, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:55544534 original size:19 final size:21
Alignment explanation
Indices: 55544510--55544548 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55544500 ACTAAAACAA
*
55544510 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
55544529 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
55544549 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:55544753 original size:27 final size:27
Alignment explanation
Indices: 55544697--55544755 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
55544687 CCAATCAGTA
***
55544697 TGGCACCATTGGTGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGCCAT
*
55544724 TGGCACCTTTGGTGCCGCCAATGCCAT
1 TGGCACCATTGGTGCCGCCAATGCCAT
55544751 TGGCA
1 TGGCA
55544756 TAACCAAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGCCAT
Found at i:55544862 original size:28 final size:28
Alignment explanation
Indices: 55544814--55544883 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 28
55544804 TTTTGTTTTT
55544814 TATATATTTTGGTAAAT-AAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
55544840 TATATATTTTGGTAAATAAAAAAAAAGTTA
1 TATATATTTTGGTAAAT--AAAAAAAGTTA
*
55544870 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
55544884 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 17 0.44
29 17 0.44
30 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAGTTA
Found at i:55546299 original size:113 final size:112
Alignment explanation
Indices: 55546160--55546375 Score: 263
Period size: 113 Copynumber: 1.9 Consensus size: 112
55546150 TCTCAAGACC
* * * * ** * *
55546160 AAAACGCATCGTTTTTGTCTTGATGTATACAATAATTAGTGGCGATTATGATAAAACGCC-GCTA
1 AAAACGCATCGTTTTGGTATCGATGTATACAAGAATTAGTGGCGATTACAAAAAAAAGCCAG-TA
* * * *
55546224 AAGCAAGTATTAGCGGCGCATTGCGGGAAGCGCCGCAAAAATCTTAACG
65 AAACAAGTATTAGCGGCGC-TTACGGAAAGCGCCACAAAAATCTTAACG
** *
55546273 AAAACGCATCGTTTTGGTATCGATGTATAGTAGAATTAGTGGCGTTTACAAAAAAAAGCCAGTAA
1 AAAACGCATCGTTTTGGTATCGATGTATACAAGAATTAGTGGCGATTACAAAAAAAAGCCAGTAA
*
55546338 AACAAGTCTTAGCGGCGCTTACGGAAAGCGCCACAAAA
66 AACAAGTATTAGCGGCGCTTACGGAAAGCGCCACAAAA
55546376 TATGATAACC
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
112 17 0.20
113 68 0.79
114 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (112 bp):
AAAACGCATCGTTTTGGTATCGATGTATACAAGAATTAGTGGCGATTACAAAAAAAAGCCAGTAA
AACAAGTATTAGCGGCGCTTACGGAAAGCGCCACAAAAATCTTAACG
Found at i:55546726 original size:115 final size:113
Alignment explanation
Indices: 55546431--55547029 Score: 495
Period size: 115 Copynumber: 5.2 Consensus size: 113
55546421 GCAAAAAATG
* * * * *
55546431 TTAACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCG-TTAGGGAAAAACGC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTACGG-AAAACGC
* * * * *
55546495 CGCTAGAGCATA-TAATTAGCGGCGATTTTCTAGAATCGCCGCAAGATATGC
65 CGCTAAAGCATACT-ATTAGCGGCGCTTTTATAGAAGCGCCGCAA-AT-TTC
* * * *
55546546 --ACACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACTGTAAAACG
1 TTA-ACCAAAACGCAGCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTAC-GGAAAACG
* * *
55546608 CCGCTAAAGCGTACTATTAGCGGTGCTTTTAGAGAAGCGCCGCTAAATTTC
64 CCGCTAAAGCATACTATTAGCGGCGCTTTTATAGAAGCGCCGC-AAATTTC
* * * *
55546659 TTAACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGCTTACGAGAAAAAGC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTACG-GAAAACGC
** * * * ** *
55546724 CGCTAAATAATAGTATTAGCGGCGATTTGATTTAAGCGCCGCAAGATATGC
65 CGCTAAAGCATACTATTAGCGGCGCTTTTATAGAAGCGCCGCAA-AT-TTC
* * * *
55546775 --ACACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTGGAAAACG
1 TTA-ACCAAAACGCAGCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTA-CGGAAAACG
* * * * *
55546837 CCGCTAAAGTATACTATTAGCGGCGCGTTTT-TAGATGCGCCGTAGAATATA
64 CCGCTAAAGCATACTATTAGCGGCGC-TTTTATAGAAGCGCCGCA-AATTTC
* * * *** *
55546888 TTAACCGAAACGCTGTGTTTAAATCTTGATGTATATTGGAATTAGTGGCG-TTCAC-GATAAATC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTT-ACGGA-AAA-C
* * *
55546951 GCCGCTAAAGCATATTATTAGCGGCGCTTTT-TGGTAAGCGCCGCAAAATATC
63 GCCGCTAAAGCATACTATTAGCGGCGCTTTTATAG-AAGCGCCGC-AAATTTC
55547003 TTAACCAAAACGCA-CAGTTTTGGTCTT
1 TTAACCAAAACGCAGC-GTTTTGGTCTT
55547030 AACCATGCAT
Statistics
Matches: 383, Mismatches: 77, Indels: 48
0.75 0.15 0.09
Matches are distributed among these distances:
113 32 0.08
114 166 0.43
115 182 0.48
116 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (113 bp):
TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTACGGAAAACGCC
GCTAAAGCATACTATTAGCGGCGCTTTTATAGAAGCGCCGCAAATTTC
Found at i:55546837 original size:229 final size:225
Alignment explanation
Indices: 55546431--55547029 Score: 677
Period size: 229 Copynumber: 2.6 Consensus size: 225
55546421 GCAAAAAATG
* * *
55546431 TTAACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCGTTA-GGGAAAAACGC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATAATACAATTAGTGGCGTTACGAGAAAAA-GC
* * *
55546495 CGCTAGAGCATATAATTAGCGGCGATTTTCTAGAATCGCCGCAAGATATGCACACCAAAACGCAG
65 CGCTAAAGCATAT-ATTAGCGGCGATTTT-T-TAAGCGCCGCAAGATATGCACACCAAAACGCAG
* * * *
55546560 AGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACTGTAAAACGCCGCTAAAGCGTACTAT
127 AGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAAACGCCGCTAAAGCATACTAT
* * *
55546625 TAGCGGTGC-TTTTAGAGAAGCGCCGCTA-AATTTC
192 TAGCGGCGCGTTTT-GAGAAGCGCCG-TAGAATATA
* * *
55546659 TTAACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGCTTACGAGAAAAAGC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATAATACAATTAGTGGCG-TTACGAGAAAAAGC
**
55546724 CGCTAAATAATAGTATTAGCGGCGATTTGATTTAAGCGCCGCAAGATATGCACACCAAAACGCAG
65 CGCTAAAGCATA-TATTAGCGGCGATTT--TTTAAGCGCCGCAAGATATGCACACCAAAACGCAG
* *
55546789 AGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTGGAAAACGCCGCTAAAGTATACTAT
127 AGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAAACGCCGCTAAAGCATACTAT
* *
55546854 TAGCGGCGCGTTTTTAGATGCGCCGTAGAATATA
192 TAGCGGCGCGTTTTGAGAAGCGCCGTAGAATATA
* * * *** * ** * **
55546888 TTAACCGAAACGCTGTGTTTAAATCTTGATGTATATTGGAATTAGTGGCGTTCACGATAAATCGC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATAATACAATTAGTGGCGTT-ACGAGAAAAAGC
* *
55546953 CGCTAAAGCATATTATTAGCGGCGCTTTTTGGTAAGCGCCGCAAAATAT-CTTA-ACCAAAACGC
65 CGCTAAAGCATA-TATTAGCGGCGATTTTT--TAAGCGCCGCAAGATATGC--ACACCAAAACGC
*
55547016 ACAGTTTTGGTCTT
125 AGAG-TTTGGTCTT
55547030 AACCATGCAT
Statistics
Matches: 317, Mismatches: 41, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
227 2 0.01
228 50 0.16
229 241 0.76
230 23 0.07
231 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (225 bp):
TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATAATACAATTAGTGGCGTTACGAGAAAAAGCC
GCTAAAGCATATATTAGCGGCGATTTTTTAAGCGCCGCAAGATATGCACACCAAAACGCAGAGTT
TGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAAACGCCGCTAAAGCATACTATTAGC
GGCGCGTTTTGAGAAGCGCCGTAGAATATA
Found at i:55547796 original size:23 final size:24
Alignment explanation
Indices: 55547747--55547810 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
55547737 TATAATACAT
* *
55547747 TAATTTAATAA-TATAAATAATTTA
1 TAATTT-ATAATTTTAAATAATTGA
55547771 TAATTTATAATTTTAAAT-ATTGA
1 TAATTTATAATTTTAAATAATTGA
55547794 TAATATT-TAAATTTTAA
1 TAAT-TTAT-AATTTTAA
55547811 TGTATGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 13 0.37
24 22 0.63
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TAATTTATAATTTTAAATAATTGA
Found at i:55548484 original size:44 final size:44
Alignment explanation
Indices: 55548434--55548527 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
55548424 AATTCTTGCG
* * *
55548434 TCCTTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAATGGCC
1 TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC
*
55548478 TCCTTCTTGCCGAATTTCTTGAAATCCCAAATCCCTAAATCGCC
1 TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC
55548522 TCCTTC
1 TCCTTC
55548528 CTCCTTCCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34
Consensus pattern (44 bp):
TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC
Found at i:55550176 original size:19 final size:19
Alignment explanation
Indices: 55550152--55550213 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
55550142 TTTAAAGTTA
55550152 TATTTTAAATATTTTATTT
1 TATTTTAAATATTTTATTT
** *
55550171 TATTTT-AATCA--CGAATT
1 TATTTTAAAT-ATTTTATTT
55550188 T-TTTTAAATATTTTATTT
1 TATTTTAAATATTTTATTT
55550206 TATTTTAA
1 TATTTTAA
55550214 TCACGAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 5 0.16
17 7 0.22
18 7 0.22
19 13 0.41
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTAAATATTTTATTT
Found at i:55550198 original size:35 final size:35
Alignment explanation
Indices: 55550154--55550241 Score: 158
Period size: 35 Copynumber: 2.5 Consensus size: 35
55550144 TAAAGTTATA
*
55550154 TTTTAAATATTTTATTTTATTTTAATCACGAATTT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATAT
55550189 TTTTAAATATTTTATTTTATTTTAATCACGAATAT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATAT
*
55550224 TTTTAAATATTTAATTTT
1 TTTTAAATATTTTATTTT
55550242 TTTAAAGTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (35 bp):
TTTTAAATATTTTATTTTATTTTAATCACGAATAT
Found at i:55550285 original size:9 final size:9
Alignment explanation
Indices: 55550261--55550338 Score: 63
Period size: 9 Copynumber: 8.7 Consensus size: 9
55550251 CAAATTTCAC
*
55550261 AACTTACGT
1 AACTTACAT
*
55550270 AATTTACAT
1 AACTTACAT
55550279 AACTTACAT
1 AACTTACAT
55550288 AA-TT-CAT
1 AACTTACAT
55550295 AACTTACAT
1 AACTTACAT
* *
55550304 AATTTAAATTT
1 AACTTACA--T
*
55550315 ATA-ATACAT
1 A-ACTTACAT
55550324 AACTTACAT
1 AACTTACAT
55550333 AACTTA
1 AACTTA
55550339 TTAATATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
7 5 0.09
8 5 0.09
9 39 0.71
11 5 0.09
12 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.38
Consensus pattern (9 bp):
AACTTACAT
Found at i:55550297 original size:16 final size:16
Alignment explanation
Indices: 55550256--55550334 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
55550246 AAGTTCAAAT
* *
55550256 TTCACAACTTACGTAA
1 TTCATAACTTACATAA
55550272 TTTACATAACTTACATAA
1 -TT-CATAACTTACATAA
55550290 TTCATAACTTACATAA
1 TTCATAACTTACATAA
* *
55550306 TT--TAAATT-TATAA
1 TTCATAACTTACATAA
*
55550319 TACATAACTTACATAA
1 TTCATAACTTACATAA
55550335 CTTATTAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 20 0.39
17 4 0.08
18 12 0.24
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.38
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:55550450 original size:23 final size:22
Alignment explanation
Indices: 55550400--55550463 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
55550390 TTAAAAATTG
55550400 ATACATTACATAACTTACATAAC
1 ATACA-TACATAACTTACATAAC
*
55550423 CTACATACATAAGCTTACAT---
1 ATACATACATAA-CTTACATAAC
*
55550443 ATA-ATACATAACTTATATAAC
1 ATACATACATAACTTACATAAC
55550464 TTAAATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 2 0.06
22 7 0.21
23 11 0.32
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (22 bp):
ATACATACATAACTTACATAAC
Found at i:55550602 original size:9 final size:9
Alignment explanation
Indices: 55550588--55550767 Score: 70
Period size: 9 Copynumber: 19.2 Consensus size: 9
55550578 CAAAAACAAA
55550588 AACTTACAT
1 AACTTACAT
55550597 AACTTACAT
1 AACTTACAT
55550606 AATATCTTACATAAT
1 -A-A-CTTAC---AT
55550621 AACTTACAT
1 AACTTACAT
55550630 AA-TAATACAT
1 AACT--TACAT
* *
55550640 ACCCTACAT
1 AACTTACAT
* *
55550649 AAATTAAAT
1 AACTTACAT
*
55550658 AAGTTACAT
1 AACTTACAT
*
55550667 AA--TACAC
1 AACTTACAT
** *
55550674 AA-AAACAA
1 AACTTACAT
55550682 AAACTTACAT
1 A-ACTTACAT
55550692 AACTTACAT
1 AACTTACAT
55550701 AATATCTTACAT
1 -A-A-CTTACAT
55550713 AATGACTTACAT
1 -A--ACTTACAT
55550725 AA--TACAT
1 AACTTACAT
*
55550732 AATTTACAT
1 AACTTACAT
55550741 AACTTACAT
1 AACTTACAT
*
55550750 AA--AACAT
1 AACTTACAT
55550757 AACTTACAT
1 AACTTACAT
55550766 AA
1 AA
55550768 TACATTAGTT
Statistics
Matches: 133, Mismatches: 18, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
7 19 0.14
8 5 0.04
9 63 0.47
10 12 0.09
11 3 0.02
12 26 0.20
13 2 0.02
14 1 0.01
15 2 0.02
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:55550616 original size:12 final size:12
Alignment explanation
Indices: 55550595--55550728 Score: 73
Period size: 12 Copynumber: 11.2 Consensus size: 12
55550585 AAAAACTTAC
55550595 ATAACTTACATA
1 ATAACTTACATA
*
55550607 ATATCTTACATA
1 ATAACTTACATA
55550619 ATAACTTACATA
1 ATAACTTACATA
55550631 ATAA--TACATA
1 ATAACTTACATA
* * *
55550641 CCCT-ACATAAATTAA
1 --ATAACTTACA-T-A
*
55550656 ATAAGTTACATA
1 ATAACTTACATA
** * *
55550668 ATACACAAAAACA
1 ATA-ACTTACATA
*
55550681 AAAACTTAC---
1 ATAACTTACATA
55550690 ATAACTTACATA
1 ATAACTTACATA
*
55550702 ATATCTTACATA
1 ATAACTTACATA
*
55550714 ATGACTTACATA
1 ATAACTTACATA
55550726 ATA
1 ATA
55550729 CATAATTTAC
Statistics
Matches: 89, Mismatches: 22, Indels: 22
0.67 0.17 0.17
Matches are distributed among these distances:
9 8 0.09
10 6 0.07
11 1 0.01
12 57 0.64
13 11 0.12
14 5 0.06
15 1 0.01
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:55550641 original size:95 final size:95
Alignment explanation
Indices: 55550524--55550728 Score: 374
Period size: 95 Copynumber: 2.2 Consensus size: 95
55550514 CACAACTTGC
*
55550524 ATAACTTACATAATAATACATACCGTACATAAAATAAATAAGTTACAGAATACACAAAAACAAAA
1 ATAACTTACATAATAATACATACCCTACATAAAATAAATAAGTTACAGAATACACAAAAACAAAA
55550589 ACTTACATAACTTACATAATATCTTACATA
66 ACTTACATAACTTACATAATATCTTACATA
* *
55550619 ATAACTTACATAATAATACATACCCTACATAAATTAAATAAGTTACATAATACACAAAAACAAAA
1 ATAACTTACATAATAATACATACCCTACATAAAATAAATAAGTTACAGAATACACAAAAACAAAA
55550684 ACTTACATAACTTACATAATATCTTACATA
66 ACTTACATAACTTACATAATATCTTACATA
*
55550714 ATGACTTACATAATA
1 ATAACTTACATAATA
55550729 CATAATTTAC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 106 1.00
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (95 bp):
ATAACTTACATAATAATACATACCCTACATAAAATAAATAAGTTACAGAATACACAAAAACAAAA
ACTTACATAACTTACATAATATCTTACATA
Found at i:55550672 original size:25 final size:25
Alignment explanation
Indices: 55550644--55550767 Score: 88
Period size: 25 Copynumber: 4.6 Consensus size: 25
55550634 ATACATACCC
* *
55550644 TACATAAATTAAATAAGTTACATAA
1 TACATAAATTACATAACTTACATAA
* * *
55550669 TACACAAA-AACAAAAACTTACATAA
1 TACATAAATTAC-ATAACTTACATAA
55550694 CTTACATAATATCTTACATAATGACTTACATAA
1 --TACATAA-A--TTACAT-A--ACTTACATAA
*
55550727 TACATAATTTACATAACTTACATAA
1 TACATAAATTACATAACTTACATAA
* *
55550752 AACATAACTTACATAA
1 TACATAAATTACATAA
55550768 TACATTAGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
24 1 0.01
25 42 0.54
27 7 0.09
28 7 0.09
30 1 0.01
31 10 0.13
33 10 0.13
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (25 bp):
TACATAAATTACATAACTTACATAA
Found at i:55550691 original size:43 final size:43
Alignment explanation
Indices: 55550549--55550702 Score: 128
Period size: 43 Copynumber: 3.4 Consensus size: 43
55550539 ATACATACCG
* *
55550549 TACATAAAATAAATAAGTTACAGAATACACAAAAACAAAAACT
1 TACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACT
* ** * * * *
55550592 TACATAACTTACATAATATCTTACATAATAACTTACATAATAATACATACCC
1 TACATAAATT--A-AATAAGTTACATAAT-AC--ACA-AA-AACA-AAAACT
55550644 TACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACT
1 TACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACT
* *
55550687 TACATAACTTACATAA
1 TACATAAATTAAATAA
55550703 TATCTTACAT
Statistics
Matches: 84, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
43 25 0.30
44 3 0.04
45 3 0.04
46 15 0.18
47 2 0.02
48 2 0.02
49 16 0.19
50 3 0.04
51 3 0.04
52 12 0.14
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (43 bp):
TACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACT
Found at i:55550756 original size:16 final size:16
Alignment explanation
Indices: 55550737--55550772 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
55550727 TACATAATTT
55550737 ACATAACTTACATAAA
1 ACATAACTTACATAAA
*
55550753 ACATAACTTACATAAT
1 ACATAACTTACATAAA
55550769 ACAT
1 ACAT
55550773 TAGTTATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (16 bp):
ACATAACTTACATAAA
Found at i:55556249 original size:21 final size:21
Alignment explanation
Indices: 55556223--55556291 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
55556213 TAACAACTTA
*
55556223 AAGCAGAGGCGGCAGCAAGGG
1 AAGCAGAGGCCGCAGCAAGGG
* * **
55556244 AAGCAGAGGCTGCAGCGAGAA
1 AAGCAGAGGCCGCAGCAAGGG
** *
55556265 AAGCAGTTGCCGCAGCAAAGG
1 AAGCAGAGGCCGCAGCAAGGG
55556286 AAGCAG
1 AAGCAG
55556292 CGAGAGAAGC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.20, G:0.39, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCAAGGG
Found at i:55556861 original size:42 final size:42
Alignment explanation
Indices: 55556740--55556989 Score: 290
Period size: 42 Copynumber: 5.9 Consensus size: 42
55556730 GTTTGTGAAA
*
55556740 TAAGCGCCGCGAAAGAACACT-A-CTTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTT-TTCC
* * *
55556783 TAAGCGCAGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* ** * * *
55556825 AAAGCGTTGCTAAAGAACATGATCTTCAGCGACGTTTTTCCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* *
55556867 TAAGCTCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* *
55556909 TAAGCGCCGCTGAAGAACATGATCTTTAGCGGCGTTTTTTCGG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC-C
* * *
55556952 T-AGCGCCGCTGAAGAACATGAGCTTTAGCGGCATTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
55556990 AACGACGTTG
Statistics
Matches: 180, Mismatches: 24, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
42 148 0.82
43 31 0.17
44 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:55558530 original size:31 final size:29
Alignment explanation
Indices: 55558495--55558566 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 29
55558485 TTTTTGTACC
55558495 AAAATGAAAGCAATCC-AAAAGTTGAGTGACT
1 AAAATGAAAGC--TCCTAAAAGTTGAGTGA-T
55558526 AAAATGAAAGCTCCTTAAAAGTTGAGTGAT
1 AAAATGAAAGCTCC-TAAAAGTTGAGTGAT
55558556 AAAATTGAAAG
1 AAAA-TGAAAG
55558567 GATTTTCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.08
30 5 0.13
31 30 0.79
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (29 bp):
AAAATGAAAGCTCCTAAAAGTTGAGTGAT
Found at i:55563224 original size:27 final size:27
Alignment explanation
Indices: 55563186--55563262 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
55563176 CCCTGGGTAG
*
55563186 AGGGAACACTGTTGGCGGCACCAAACA
1 AGGGAACCCTGTTGGCGGCACCAAACA
55563213 AGGGAACCCTGTTGGCGGCACCAAACA
1 AGGGAACCCTGTTGGCGGCACCAAACA
** *
55563240 AGGGTTCCCTGTTGGTGGCACCA
1 AGGGAACCCTGTTGGCGGCACCA
55563263 CTCGTGTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.26, C:0.27, G:0.31, T:0.16
Consensus pattern (27 bp):
AGGGAACCCTGTTGGCGGCACCAAACA
Found at i:55564554 original size:14 final size:14
Alignment explanation
Indices: 55564537--55564565 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55564527 TTTTTGTATC
55564537 AATTTAATTATTCT
1 AATTTAATTATTCT
55564551 AATTTAATTATTCT
1 AATTTAATTATTCT
55564565 A
1 A
55564566 GTTCCAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:55565055 original size:27 final size:27
Alignment explanation
Indices: 55564982--55565058 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
55564972 ATAACACGAG
**
55564982 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
55565009 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
55565036 TGGTGCCGCCAACAGTGTTCCCT
1 TGGTGCCGCCAACAGGGTTCCCT
55565059 CCACCCAGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:55565155 original size:27 final size:29
Alignment explanation
Indices: 55565122--55565190 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
55565112 TATTTTTTTG
55565122 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
55565149 ATATATTTTGTTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
55565178 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
55565191 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.41
28 17 0.46
29 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:55569174 original size:17 final size:18
Alignment explanation
Indices: 55569152--55569187 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55569142 CCTCAATAAG
55569152 CATTTATA-AAAATCAAA
1 CATTTATATAAAATCAAA
*
55569169 CATTTATATAAACTCAAA
1 CATTTATATAAAATCAAA
55569187 C
1 C
55569188 CTTTCCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (18 bp):
CATTTATATAAAATCAAA
Found at i:55569453 original size:42 final size:40
Alignment explanation
Indices: 55569387--55569530 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 40
55569377 TATCCCAGAT
* *
55569387 ATGGTCTTACATGCTATCATATATCGATGCCAATAG-CCCAGC
1 ATGGTCTTACACG-AATC-TATATCGATGCCAAT-GTCCCAGC
* *
55569429 TATGGTCTTACACGAATCTCATATCCATGCCAATGTCCCAAAC
1 -ATGGTCTTACACGAATCT-ATATCGATGCCAATGTCCC-AGC
*
55569472 ATGGTCTTACACGAATCTTATATCGGTGCCAATGTCCCAGAC
1 ATGGTCTTACACGAATC-TATATCGATGCCAATGTCCCAG-C
55569514 ATGGTCTTACACGAATC
1 ATGGTCTTACACGAATC
55569531 ACATCTCAGT
Statistics
Matches: 89, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.03
42 71 0.80
43 15 0.17
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (40 bp):
ATGGTCTTACACGAATCTATATCGATGCCAATGTCCCAGC
Found at i:55573456 original size:31 final size:31
Alignment explanation
Indices: 55573421--55573479 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
55573411 GTGTTTTACC
55573421 ATTTTGCCCCTTCAAAAAATAATATAAAACT
1 ATTTTGCCCCTTCAAAAAATAATATAAAACT
*
55573452 ATTTTGCCCCTTCAGAAAATAATATAAA
1 ATTTTGCCCCTTCAAAAAATAATATAAA
55573480 TAGCAGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (31 bp):
ATTTTGCCCCTTCAAAAAATAATATAAAACT
Found at i:55575015 original size:29 final size:32
Alignment explanation
Indices: 55574980--55575046 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
55574970 CAATAAAAAT
*
55574980 AAAATTTATATTTAAAATATA-T-ATTA-ATG
1 AAAATTTATATTTAAAATAAATTAATTATATG
* *
55575009 AAAATTTATTTTTATAATAAATTAATTATATG
1 AAAATTTATATTTAAAATAAATTAATTATATG
55575041 AAAATT
1 AAAATT
55575047 AAATATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 18 0.56
30 1 0.03
31 4 0.12
32 9 0.28
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
AAAATTTATATTTAAAATAAATTAATTATATG
Found at i:55575074 original size:25 final size:25
Alignment explanation
Indices: 55575046--55575094 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55575036 ATATGAAAAT
* * *
55575046 TAAATATACATAATTTAAAAATATG
1 TAAATATAAAAAATTAAAAAATATG
*
55575071 TAAATTTAAAAAATTAAAAAATAT
1 TAAATATAAAAAATTAAAAAATAT
55575095 TGTTGAGGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAATATAAAAAATTAAAAAATATG
Found at i:55578916 original size:42 final size:43
Alignment explanation
Indices: 55578808--55579015 Score: 226
Period size: 42 Copynumber: 4.9 Consensus size: 43
55578798 AGCTCGTATA
* * ***
55578808 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCA-ACTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATA-TATCG
* * *
55578851 ATGCCACTGTCCCAAACAGGGTCTTACACAAAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATATATCG
*
55578893 ATGCCAATGTCCCACACATGGTCTTACACAAAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATATATCG
* *
55578935 ATGTCAATGTCCCAGACATGGTCTTACACATAAATC-TCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACA-AAATCAT-ATATCG
* * * *
55578979 ATGCCAACGTCCCAGACGTGGTCTTATACGAAATCAT
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCAT
55579016 GTACTGCCAT
Statistics
Matches: 141, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
42 70 0.50
43 42 0.30
44 29 0.21
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACAAAATCATATATCG
Found at i:55583954 original size:16 final size:16
Alignment explanation
Indices: 55583933--55583996 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 16
55583923 TTCATACTAA
55583933 ATAAATTATATAAAAT
1 ATAAATTATATAAAAT
*
55583949 ATAAATTATATATAAT
1 ATAAATTATATAAAAT
*
55583965 ATAAA-TAGTTTAATATAT
1 ATAAATTA-TATAA-A-AT
55583983 ATAAATTATA-AAAA
1 ATAAATTATATAAAA
55583997 AAAATTCAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.08
16 24 0.60
17 3 0.08
18 8 0.20
19 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAAATTATATAAAAT
Found at i:55586726 original size:22 final size:22
Alignment explanation
Indices: 55586701--55586742 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55586691 GTCTTAACAT
55586701 TTTTAATTTT-TTTAAATATTTA
1 TTTT-ATTTTATTTAAATATTTA
*
55586723 TTTTATTTTATTTTAATATT
1 TTTTATTTTATTTAAATATT
55586743 GAATATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTTTATTTAAATATTTA
Found at i:55588940 original size:17 final size:17
Alignment explanation
Indices: 55588918--55588981 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
55588908 AATCTTAGAG
55588918 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
55588935 TTCTAATTGTGTCTTAAAG-
1 TTCTAA-T-TGT-ATACAGC
55588954 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
55588971 TTTTAATTGTA
1 TTCTAATTGTA
55588982 GCCTTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 4 0.11
17 19 0.50
18 2 0.05
19 9 0.24
20 4 0.11
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:55588957 original size:36 final size:36
Alignment explanation
Indices: 55588910--55588980 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
55588900 GATTATATAA
*
55588910 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
*
55588946 TCTTAAAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGT
55588981 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAAAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:55589250 original size:48 final size:48
Alignment explanation
Indices: 55589175--55589269 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
55589165 TGAGGGAATT
* *
55589175 CTGTTGAATCCTTTATCATTGTAAGTTAGGCCGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTG
* *
55589223 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCATTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTT
55589270 AAGCAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTG
Found at i:55594329 original size:48 final size:48
Alignment explanation
Indices: 55594254--55594348 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
55594244 TGAGGGAATT
55594254 CTGTTGAATCCTTTATCATAGCAAGTTAGGCCGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATAGCAAGTTAGGCCGACTTAGGCGTTTTTG
* * *
55594302 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATAGCAAGTTAGGCCGACTTAGGCGTTTTT
55594349 AAGTAAAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATAGCAAGTTAGGCCGACTTAGGCGTTTTTG
Found at i:55595456 original size:31 final size:31
Alignment explanation
Indices: 55595418--55595481 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
55595408 CGGCCCATTT
55595418 TTATTTTAAAAAT-TTTAAAAAATTAAAAAAA
1 TTATTTTAAAAATATTT-AAAAATTAAAAAAA
*
55595449 TTATTTTAAAAATATTTTAAAATTAAAAAAA
1 TTATTTTAAAAATATTTAAAAATTAAAAAAA
55595480 TT
1 TT
55595482 TAAAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TTATTTTAAAAATATTTAAAAATTAAAAAAA
Found at i:55595459 original size:11 final size:11
Alignment explanation
Indices: 55595445--55595513 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 11
55595435 AAAAATTAAA
55595445 AAAATTATTTT
1 AAAATTATTTT
*
55595456 AAAAATATTTT
1 AAAATTATTTT
55595467 AAAATTA----
1 AAAATTATTTT
* *
55595474 AAAA-AATTTAA
1 AAAATTATTT-T
55595485 AAAATTATTTT
1 AAAATTATTTT
*
55595496 AAAAATATTTT
1 AAAATTATTTT
55595507 AAAATTA
1 AAAATTA
55595514 AAAAAATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
11 36 0.80
12 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:55595489 original size:40 final size:40
Alignment explanation
Indices: 55595419--55595558 Score: 210
Period size: 40 Copynumber: 3.5 Consensus size: 40
55595409 GGCCCATTTT
* *
55595419 TATTTTAAAAATTTTAAAAAATTAAAAAAATTATTTTAAAAA
1 TATTTT-AAAA-TTAAAAAAATTTAAAAAATTATTTTAAAAA
55595461 TATTTTAAAATTAAAAAAATTTAAAAAATTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAAATTATTTTAAAAA
* * *
55595501 TATTTTAAAATTAAAAAAA-TTAAAAAAGTATGTCAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAAATTATTTTAAAAA
55595540 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
55595559 ATAAATATAT
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 36 0.39
40 47 0.51
41 4 0.04
42 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTTAAAAAATTATTTTAAAAA
Found at i:55606322 original size:21 final size:21
Alignment explanation
Indices: 55606296--55606336 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55606286 AGACGAGCAA
* *
55606296 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
55606317 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
55606337 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:55614436 original size:15 final size:15
Alignment explanation
Indices: 55614416--55614462 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
55614406 TGGTTACTAG
*
55614416 TAATAATAAGGTTAA
1 TAATAATAAGGATAA
*
55614431 TAATAATAATGATAA
1 TAATAATAAGGATAA
* *
55614446 TAATAATGATGATAA
1 TAATAATAAGGATAA
55614461 TA
1 TA
55614463 TATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (15 bp):
TAATAATAAGGATAA
Found at i:55614445 original size:12 final size:12
Alignment explanation
Indices: 55614430--55614462 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
55614420 AATAAGGTTA
55614430 ATAATAATAATG
1 ATAATAATAATG
55614442 ATAATAATAATG
1 ATAATAATAATG
*
55614454 ATGATAATA
1 ATAATAATA
55614463 TATTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:55616104 original size:87 final size:87
Alignment explanation
Indices: 55615999--55616368 Score: 251
Period size: 87 Copynumber: 4.3 Consensus size: 87
55615989 GACCTACTCT
* * * * * *
55615999 GCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATA
1 GCTGTAATCTCAGGGAGATAAGATCTC-TGACTTCAATCCACTCCACTGTAACCTCAGGGAGATA
* *
55616063 GGATAGTG-TCTTTGATCTGCTCC
65 AGAT-CTGATCTTTGATCTGCTCC
* **
55616086 GCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAA
1 GCTGTAATCTCAGGGAGATAAGATCTCTGACTTCAATCCACTCCACTGTAACCTCAGGGAGATAA
* *
55616151 GATCTGAAATTCTTTGGTCTGTTCC
66 GATCTG--A-TCTTTGATCTGCTCC
* * ** * * *
55616176 ACTGTAATCTCAGGGAGATAAGA-C-CTGA-TGT-GATCTTCTCTACTGTAACTTCAGAGAGATA
1 GCTGTAATCTCAGGGAGATAAGATCTCTGACT-TCAATCCACTCCACTGTAACCTCAGGGAGATA
* *
55616237 AGATC----CTTTAATCCGCTCC
65 AGATCTGATCTTTGATCTGCTCC
** * * ** * * * *
55616256 ATTGTAATCTCAAGGAGATAGGAT-TACT-ATCTTTGATCCGCTCCGCCGTAATCTCAGGGAGAT
1 GCTGTAATCTCAGGGAGATAAGATCT-CTGA-CTTCAATCCACTCCACTGTAACCTCAGGGAGAT
*
55616319 AAGATCTGAAATTCTTTGATCTGTTCC
64 AAGATCTG--A-TCTTTGATCTGCTCC
*
55616346 ACTGTAATCTCAGGGAGATAAGA
1 GCTGTAATCTCAGGGAGATAAGA
55616369 CCTGTATAAT
Statistics
Matches: 223, Mismatches: 41, Indels: 35
0.75 0.14 0.12
Matches are distributed among these distances:
80 30 0.13
81 1 0.00
82 3 0.01
83 28 0.13
86 2 0.01
87 87 0.39
88 5 0.02
89 1 0.00
90 66 0.30
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (87 bp):
GCTGTAATCTCAGGGAGATAAGATCTCTGACTTCAATCCACTCCACTGTAACCTCAGGGAGATAA
GATCTGATCTTTGATCTGCTCC
Found at i:55616135 original size:44 final size:44
Alignment explanation
Indices: 55616039--55616368 Score: 247
Period size: 44 Copynumber: 7.6 Consensus size: 44
55616029 TTTTAATCCA
* *
55616039 CTCCACTGTAA-CTTCAGGGAGATAGGA--TAGTGTCTTTGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTACT-TCTTTGATCTG
* * **
55616082 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTACT-TCTTTGATCTG
* * *
55616126 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT--ACTTCTTTGATCTG
* ** * *
55616172 TTCCACTGTAATCTCAGGGAGATAAGA-C--CTGATGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTACTTCTTTGATCTG
* * * *
55616213 CTCTACTGTAA-CTTCAGAGAGATAAGA--T-C--CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTACTTCTTTGATCTG
* * * *
55616252 CTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTACT-TCTTTGATCTG
* * *
55616296 CTCCGCCGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT--ACTTCTTTGATCTG
*
55616342 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
55616369 CCTGTATAAT
Statistics
Matches: 225, Mismatches: 45, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
39 25 0.11
40 3 0.01
41 31 0.14
43 23 0.10
44 71 0.32
45 3 0.01
46 66 0.29
47 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTACTTCTTTGATCTG
Found at i:55617584 original size:1 final size:1
Alignment explanation
Indices: 55617578--55617606 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
55617568 CTCTCCAAAA
55617578 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
55617607 AGGAAGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:55624747 original size:29 final size:29
Alignment explanation
Indices: 55624705--55624771 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
55624695 CTATTTGCTC
55624705 TTTCATTTGCGCCTGCAACTGGTCTTGCA
1 TTTCATTTGCGCCTGCAACTGGTCTTGCA
55624734 TTTCATTTGCGCCTGCAACTGGTCTTGCA
1 TTTCATTTGCGCCTGCAACTGGTCTTGCA
*
55624763 TTTCTTTTG
1 TTTCATTTG
55624772 AATCGCTCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.43
Consensus pattern (29 bp):
TTTCATTTGCGCCTGCAACTGGTCTTGCA
Found at i:55629342 original size:15 final size:15
Alignment explanation
Indices: 55629322--55629368 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
55629312 TGGTTACTAG
*
55629322 TAATAATAAGGTTAA
1 TAATAATAAGGATAA
*
55629337 TAATAATAATGATAA
1 TAATAATAAGGATAA
* *
55629352 TAATAATGATGATAA
1 TAATAATAAGGATAA
55629367 TA
1 TA
55629369 TATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (15 bp):
TAATAATAAGGATAA
Found at i:55629351 original size:12 final size:12
Alignment explanation
Indices: 55629336--55629368 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
55629326 AATAAGGTTA
55629336 ATAATAATAATG
1 ATAATAATAATG
55629348 ATAATAATAATG
1 ATAATAATAATG
*
55629360 ATGATAATA
1 ATAATAATA
55629369 TATTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:55631955 original size:125 final size:124
Alignment explanation
Indices: 55631680--55631966 Score: 448
Period size: 124 Copynumber: 2.3 Consensus size: 124
55631670 ATTTATTAAG
* * *
55631680 GAAATCGCTCCCACGTGGACGCGCTTTTGATACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
*
55631745 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* * *
55631804 AAAATCGCTTCCACGTGGACACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
* * *
55631869 GTTTCTAAGCAAATAGTATAAAAAAGGTTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
66 GTTTCTAAGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* * *
55631929 GAAATTGCTCCCACGTGGATATGCTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACACGCTTTTGCTACAGTAG
55631967 CATGTTTGGG
Statistics
Matches: 147, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
124 77 0.52
125 70 0.48
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (124 bp):
GAAATCGCTCCCACGTGGACACGCTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
Found at i:55635117 original size:49 final size:49
Alignment explanation
Indices: 55635062--55635359 Score: 269
Period size: 49 Copynumber: 6.5 Consensus size: 49
55635052 TAAGAATATT
* *
55635062 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
55635111 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATG
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
* * *
55635160 AACTATTTTGTATTTTATTACATC--A-AATAT-AAACTATT----TTG
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
* * ** *** * *
55635201 TA-TTTTATTAAATGAAATAATATC-AA-AATATTCAAAATA---------
1 AACTATT-TTGTATTTTATTACATCAAATAATA-TCAAAATATTCAAAATA
* *
55635240 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
*
55635289 AACTATTTTGTATTTTATTA-ATCAAATAATATCAAAATATTCAAAATG
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
55635337 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
55635360 TAATATAAAC
Statistics
Matches: 205, Mismatches: 27, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
39 10 0.05
40 16 0.08
41 17 0.08
42 5 0.02
43 1 0.00
44 5 0.02
45 7 0.03
46 5 0.02
47 1 0.00
48 46 0.22
49 92 0.45
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:55635195 original size:31 final size:31
Alignment explanation
Indices: 55635152--55635219 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
55635142 ATCAAAATAT
* *
55635152 TCAAA-ATGAACTATTTTGTATTTTATTACA
1 TCAAATATAAACTATTTTGTATTTTATTAAA
55635182 TCAAATATAAACTATTTTGTATTTTATTAAA
1 TCAAATATAAACTATTTTGTATTTTATTAAA
*
55635213 TGAAATA
1 TCAAATA
55635220 ATATCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (31 bp):
TCAAATATAAACTATTTTGTATTTTATTAAA
Found at i:55635208 original size:129 final size:128
Alignment explanation
Indices: 55635056--55635443 Score: 513
Period size: 129 Copynumber: 3.0 Consensus size: 128
55635046 TATTATTAAG
55635056 AATATTAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
1 AATA-TAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
* * *
55635121 TATTTTATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATCA
65 TATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACATCA
55635185 AATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
1 AATAT-AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
55635250 TATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTA-ATC-
65 TATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACATCA
**** * * * * * ***
55635312 AA-ATAA-TA-TCAAAATATTCA--AAATGAACTATTTTGTATTTTATTACATTAATATAAACTA
1 AATATAACTATTTTGTAT-TTTATTAAATGAAATAATAT-CAAAATATT-CA--AA-ATAAACTA
55635372 TTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGT-TTTTATTAC
60 TTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTAC
55635436 ATCA
125 ATCA
55635440 AATA
1 AATA
55635444 ATATCAAAAT
Statistics
Matches: 234, Mismatches: 15, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
122 11 0.05
123 8 0.03
124 7 0.03
125 2 0.01
126 12 0.05
127 68 0.29
128 6 0.03
129 120 0.51
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (128 bp):
AATATAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGT
ATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACATCA
Found at i:55635373 original size:78 final size:78
Alignment explanation
Indices: 55635286--55635437 Score: 270
Period size: 79 Copynumber: 1.9 Consensus size: 78
55635276 AATATTCAAA
*
55635286 ATAAACTATTTTGTATTTTATT-AATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTAT
1 ATAAACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATAAACTATTTTGT-T
55635350 TTTATTACATTAAT
65 TTTATTACATTAAT
*
55635364 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTTT
1 ATAAACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTTT
55635429 TTATTACAT
66 TTATTACAT
55635438 CAAATAATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 33 0.46
79 38 0.54
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (78 bp):
ATAAACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTTT
TTATTACATTAAT
Found at i:55635407 original size:127 final size:126
Alignment explanation
Indices: 55635106--55635493 Score: 491
Period size: 127 Copynumber: 3.0 Consensus size: 126
55635096 AAAATATTCA
* * *
55635106 AAATAAACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGT
1 AAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGT
**** * * * * * ***
55635171 ATTTTATTACATCAAATATAAACTAT-TTTGTATTTTATTAAATGAAATAATAT-CAAAATATT-
66 ATTTTATTACATC-AA-AT-AA-TATCAAAATA-TTCA--AAATGAACTATTTTGTATTTTATTA
55635233 CA-
124 CAT
55635235 AAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGT
1 AAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGT
55635300 ATTTTATTA-ATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATT
66 ATTTTATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACA-T
55635361 AATATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
1 AA-ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTG
* *
55635426 T-TTTTATTACATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTGATTACAT
65 TATTTTATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACAT
55635487 CAAATAA
1 -AAATAA
55635494 TATCAAAATA
Statistics
Matches: 234, Mismatches: 17, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
122 11 0.05
123 5 0.02
124 8 0.03
125 4 0.02
126 17 0.07
127 115 0.49
128 3 0.01
129 71 0.30
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (126 bp):
AAATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGT
ATTTTATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACAT
Found at i:55635419 original size:49 final size:49
Alignment explanation
Indices: 55635364--55635535 Score: 310
Period size: 49 Copynumber: 3.5 Consensus size: 49
55635354 TTACATTAAT
* *
55635364 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAA
1 ATAAACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAA
55635413 ATAAACTATTTTGT-TTTTATTACATCAAATAATATCAAAATATTCAAA
1 ATAAACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAA
*
55635461 ATAAACTATTTTGTATTTGATTACATCAAATAATATCAAAATATTCAAA
1 ATAAACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAA
55635510 ATAAACTATTTTGTATTTTATTACAT
1 ATAAACTATTTTGTATTTTATTACAT
55635536 TAATACAAAC
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
48 46 0.39
49 72 0.61
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (49 bp):
ATAAACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAA
Found at i:55635491 original size:176 final size:177
Alignment explanation
Indices: 55635062--55635554 Score: 900
Period size: 176 Copynumber: 2.8 Consensus size: 177
55635052 TAAGAATATT
55635062 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
*
55635127 ATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATCAAATATAA
66 ATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACAT-TAATATAA
55635192 ACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
130 ACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
55635240 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
55635305 ATTA-ATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATTAATATAAA
66 ATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATTAATATAAA
55635369 CTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
131 CTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
* * *
55635416 AACTATTTTGT-TTTTATTACATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTG
1 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
* *
55635480 ATTACATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACATTAATACAAA
66 ATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATTAATATAAA
*
55635545 CTACTTTGTA
131 CTATTTTGTA
55635555 CAAATAAATT
Statistics
Matches: 307, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
175 54 0.18
176 133 0.43
177 51 0.17
178 69 0.22
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (177 bp):
AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTT
ATTACATCAAATAATATCAAAATATTCAAAATGAACTATTTTGTATTTTATTACATTAATATAAA
CTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
Found at i:55635562 original size:97 final size:94
Alignment explanation
Indices: 55635364--55635544 Score: 285
Period size: 97 Copynumber: 1.9 Consensus size: 94
55635354 TTACATTAAT
* *
55635364 ATAAACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATAAACTATTTTGTTT
1 ATAAACTATTTTGTATTTGATTAAATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTTT
55635429 TTATTACATCAAATAATATCAAAATATTCAAA
66 TTATTACAT---ATAATATCAAAATATTCAAA
*
55635461 ATAAACTATTTTGTATTTGATTACATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTAT
1 ATAAACTATTTTGTATTTGATTAAATCAAATAATATCAAAATATTCAAAATAAACTATTTTGT-T
55635526 TTTATTACAT-TAATA-CAAA
65 TTTATTACATATAATATCAAA
55635545 CTACTTTGTA
Statistics
Matches: 80, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
93 4 0.05
94 5 0.06
97 60 0.75
98 11 0.14
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.41
Consensus pattern (94 bp):
ATAAACTATTTTGTATTTGATTAAATCAAATAATATCAAAATATTCAAAATAAACTATTTTGTTT
TTATTACATATAATATCAAAATATTCAAA
Found at i:55635967 original size:18 final size:18
Alignment explanation
Indices: 55635941--55635983 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55635931 GACTAGGAAA
* * *
55635941 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
55635959 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
55635977 AGGATAC
1 AGGATAC
55635984 GCATCTGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:55637848 original size:22 final size:22
Alignment explanation
Indices: 55637822--55637896 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
55637812 AAATAGGAAT
55637822 TTGAGAGAATATTAGAGAGAAA
1 TTGAGAGAATATTAGAGAGAAA
*
55637844 TTGAGATAATATTAGAGAGAAA
1 TTGAGAGAATATTAGAGAGAAA
*
55637866 TTGAGAGAATATTAGTGAGAAA
1 TTGAGAGAATATTAGAGAGAAA
55637888 TTGAGAGAA
1 TTGAGAGAA
55637897 AAGATTTAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (22 bp):
TTGAGAGAATATTAGAGAGAAA
Found at i:55637897 original size:10 final size:10
Alignment explanation
Indices: 55637822--55637897 Score: 80
Period size: 10 Copynumber: 7.0 Consensus size: 10
55637812 AAATAGGAAT
55637822 TTGAGAGAATA
1 TTGAGAGAA-A
55637833 TTAGAGAGAAA
1 TT-GAGAGAAA
*
55637844 TTGAGATAATA
1 TTGAGAGAA-A
55637855 TTAGAGAGAAA
1 TT-GAGAGAAA
55637866 TTGAGAGAATA
1 TTGAGAGAA-A
*
55637877 TTAGTGAGAAA
1 TT-GAGAGAAA
55637888 TTGAGAGAAA
1 TTGAGAGAAA
55637898 AGATTTAGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
10 20 0.36
11 17 0.30
12 19 0.34
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.25
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:55639762 original size:35 final size:34
Alignment explanation
Indices: 55639723--55639816 Score: 100
Period size: 33 Copynumber: 2.7 Consensus size: 34
55639713 AGATATAATA
55639723 AAAAATATAAGTATGTATATATATAAATAAATTAT
1 AAAAATAT-AGTATGTATATATATAAATAAATTAT
* * ** *
55639758 AAAAATAT-GTACGTGTATATATATGTATATTAT
1 AAAAATATAGTATGTATATATATAAATAAATTAT
* *
55639791 AAAAATGTATGTATTTATATATATAA
1 AAAAATATA-GTATGTATATATATAA
55639817 CGAAATTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
33 27 0.57
35 20 0.43
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (34 bp):
AAAAATATAGTATGTATATATATAAATAAATTAT
Found at i:55639799 original size:31 final size:31
Alignment explanation
Indices: 55639715--55639815 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 31
55639705 AAATTATAAG
*
55639715 ATATAATA-AAAAATATAAGTATGTATATATAT
1 ATATATTATAAAAATAT--GTATGTATATATAT
*
55639747 AAATAAATTATAAAAATATGTACGTGTATATATAT
1 --ATATATTATAAAAATATGTA--TGTATATATAT
* *
55639782 GTATATTAT-AAAA-ATGTATGTATTTATAT
1 ATATATTATAAAAATATGTATGTATATATAT
55639811 ATATA
1 ATATA
55639816 ACGAAATTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
29 14 0.24
31 5 0.09
32 4 0.07
33 10 0.17
34 6 0.10
35 19 0.33
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (31 bp):
ATATATTATAAAAATATGTATGTATATATAT
Found at i:55639878 original size:19 final size:19
Alignment explanation
Indices: 55639850--55639886 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55639840 TAAATGAGTA
55639850 AATAACAATAATAATAATT
1 AATAACAATAATAATAATT
* *
55639869 AATAATAATAGTAATAAT
1 AATAACAATAATAATAAT
55639887 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAACAATAATAATAATT
Found at i:55641048 original size:13 final size:13
Alignment explanation
Indices: 55641030--55641054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55641020 GGGCTGAGGG
55641030 TTTTGGGTTGTTA
1 TTTTGGGTTGTTA
55641043 TTTTGGGTTGTT
1 TTTTGGGTTGTT
55641055 GTTAAGTTTG
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:0.04, C:0.00, G:0.32, T:0.64
Consensus pattern (13 bp):
TTTTGGGTTGTTA
Found at i:55641756 original size:44 final size:44
Alignment explanation
Indices: 55641697--55641859 Score: 218
Period size: 44 Copynumber: 3.7 Consensus size: 44
55641687 TGTCTTCAGT
*
55641697 CTGCTCCGCTGCAACTTCAGGGAGATAAGACTTGTATCTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTTAAC
* ** * **
55641741 CTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTTTCTTTAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TATCTTTAAC
* * *
55641786 CTGCTCCACTGCAACTTTAAGGAGATAAGACTTGTATCTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTTAAC
*
55641830 GTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA
55641860 TTCGCCATGA
Statistics
Matches: 99, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 63 0.64
45 36 0.36
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTTAAC
Found at i:55641763 original size:89 final size:89
Alignment explanation
Indices: 55641669--55641864 Score: 293
Period size: 89 Copynumber: 2.2 Consensus size: 89
55641659 ACTACAGCGC
* * *
55641669 CAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACTTGTAT
1 CAGGGAGATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAT
*
55641734 CTTTAACCTGCTCCACTACAACTT
66 CTTCAACCTGCTCCACTACAACTT
* * * * *
55641758 CAGGGAGATAAGGTTTGCTTTCTTTAGTCTGCTCCACTGCAACTTTAAGGAGATAAGACTTGTAT
1 CAGGGAGATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAT
* *
55641823 CTTCAACGTGCTCCACTGCAACTT
66 CTTCAACCTGCTCCACTACAACTT
55641847 CAGGGAGATAAGATTCGC
1 CAGGGAGATAAGATTCGC
55641865 CATGATAACT
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 94 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (89 bp):
CAGGGAGATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAT
CTTCAACCTGCTCCACTACAACTT
Found at i:55651331 original size:41 final size:41
Alignment explanation
Indices: 55651274--55651534 Score: 249
Period size: 41 Copynumber: 6.4 Consensus size: 41
55651264 ATTTTTAAAC
* * * *
55651274 CTTTAGCGGCGTTTTTATTTTAGCGCCGCTAATGGTCCGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCCGAT
* * **
55651315 CTTTAGCGGCATTTTTATCTGAGCGCCACTAATGCTCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCCGAT
* * *
55651356 CTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCT-CGTAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCCG-AT
* * * **
55651397 CTTTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCCGAT
* * * * **
55651438 CTTTAGCGGTGTTTTTTTCTAAGCGCCGCTAATG-TTAGTAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCCG-AT
* * *
55651479 CTTTAGTGGCGTTTTTATCTGAGCGCCACTAATGCTCTG-G
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCCGAT
55651519 CTTTTAGCGGCGTTTT
1 C-TTTAGCGGCGTTTT
55651535 ATAGGTAAGC
Statistics
Matches: 173, Mismatches: 42, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
40 4 0.02
41 166 0.96
42 3 0.02
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCCGAT
Found at i:55651412 original size:82 final size:82
Alignment explanation
Indices: 55651273--55651534 Score: 400
Period size: 82 Copynumber: 3.2 Consensus size: 82
55651263 GATTTTTAAA
* * * * *
55651273 CCTTTAGCGGCGTTTTTATTTTAGCGCCGCTAATGGTCCG-ATCTTTAGCGGCATTTTTATCTGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
55651337 GCGCCACTAATGCTCTGG
65 GCGCCACTAATGCTCTGG
*
55651355 CCTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
55651420 CGCCACTAATTCTCTGG
66 CGCCACTAATGCTCTGG
* * * *
55651437 CCTTTAGCGGTGTTTTTTTCTAAGCGCCGCTAATGTTAGTATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
55651502 CGCCACTAATGCTCTGG
66 CGCCACTAATGCTCTGG
*
55651519 CTTTTAGCGGCGTTTT
1 CCTTTAGCGGCGTTTT
55651535 ATAGGTAAGC
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
81 2 0.01
82 163 0.99
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATGCTCTGG
Found at i:55654005 original size:8 final size:10
Alignment explanation
Indices: 55653983--55654019 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
55653973 TATTTTTACT
55653983 TATATATGGA
1 TATATATGGA
*
55653993 TATATATGAA
1 TATATATGGA
55654003 TATATATGGA
1 TATATATGGA
55654013 TATATAT
1 TATATAT
55654020 AATTATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:55654699 original size:8 final size:10
Alignment explanation
Indices: 55654677--55654713 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
55654667 TATTTTTACT
55654677 TATATATGGA
1 TATATATGGA
*
55654687 TATATATGAA
1 TATATATGGA
55654697 TATATATGGA
1 TATATATGGA
55654707 TATATAT
1 TATATAT
55654714 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:55654822 original size:27 final size:27
Alignment explanation
Indices: 55654781--55654832 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
55654771 AATAAACAAA
* *
55654781 TAAATAAGTTAGTAATGATTTATTTGT
1 TAAATAAATTAGTAATGAATTATTTGT
* *
55654808 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATTAGTAATGAATTATTT
55654833 AAAAGTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (27 bp):
TAAATAAATTAGTAATGAATTATTTGT
Found at i:55656037 original size:11 final size:11
Alignment explanation
Indices: 55656021--55656057 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
55656011 TTGACTTTTC
55656021 TAATTTGATTA
1 TAATTTGATTA
55656032 TAATTTGATTA
1 TAATTTGATTA
*
55656043 TAATTTCATTA
1 TAATTTGATTA
55656054 TAAT
1 TAAT
55656058 GTAGTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (11 bp):
TAATTTGATTA
Found at i:55656379 original size:38 final size:38
Alignment explanation
Indices: 55656331--55656408 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
55656321 CATAACTTAC
* *
55656331 ATTAATATTATACATAAATTACATAACTTAATTAATTA
1 ATTAATATTATACATAAATTACATAACTTAAATAAGTA
*
55656369 ATTAGTATTATACATAAATTACATAACTTAAATAAGTA
1 ATTAATATTATACATAAATTACATAACTTAAATAAGTA
55656407 AT
1 AT
55656409 ATTATACATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.40
Consensus pattern (38 bp):
ATTAATATTATACATAAATTACATAACTTAAATAAGTA
Found at i:55656393 original size:9 final size:9
Alignment explanation
Indices: 55656379--55656777 Score: 104
Period size: 9 Copynumber: 43.2 Consensus size: 9
55656369 ATTAGTATTA
55656379 TACATAAAT
1 TACATAAAT
*
55656388 TACATAACT
1 TACATAAAT
* *
55656397 TAAAT-AAG
1 TACATAAAT
*
55656405 TA-AT-ATT
1 TACATAAAT
*
55656412 ATACATAACT
1 -TACATAAAT
55656422 TACATTAATATT
1 TACA-TAA-A-T
55656434 ATACATAAAT
1 -TACATAAAT
*
55656444 TACATAACT
1 TACATAAAT
*
55656453 TA-ATTAAT
1 TACATAAAT
55656461 TA-ATTAATATT
1 TACA-TAA-A-T
55656472 ATACATAAAT
1 -TACATAAAT
55656482 TACATAACA-
1 TACATAA-AT
*
55656491 TA-ATTAAT
1 TACATAAAT
*
55656499 TA-AT-ATT
1 TACATAAAT
*
55656506 ATACATAACT
1 -TACATAAAT
55656516 TACATTAATATT
1 TACA-TAA-A-T
55656528 ATACATAAAT
1 -TACATAAAT
*
55656538 TACATAACT
1 TACATAAAT
55656547 TA-ATAAAT
1 TACATAAAT
*
55656555 TA-AT-ATT
1 TACATAAAT
*
55656562 ATACATAACT
1 -TACATAAAT
55656572 TACATTAATATT
1 TACA-TAA-A-T
55656584 ATACATAAAT
1 -TACATAAAT
*
55656594 TACATAACT
1 TACATAAAT
* *
55656603 TA-GTTAAT
1 TACATAAAT
*
55656611 TA-AT-ATT
1 TACATAAAT
*
55656618 ATACATAACT
1 -TACATAAAT
*
55656628 TACATAACT
1 TACATAAAT
*
55656637 TAC--AACT
1 TACATAAAT
*
55656644 TACATAACT
1 TACATAAAT
55656653 TACATTAATATT
1 TACA-TAA-A-T
*
55656665 ATACAT-ATT
1 -TACATAAAT
*
55656674 ATACATAACT
1 -TACATAAAT
55656684 TACATTAATATT
1 TACA-TAA-A-T
55656696 ATACATAAAT
1 -TACATAAAT
*
55656706 TACATAACT
1 TACATAAAT
*
55656715 TA-ATTAAT
1 TACATAAAT
55656723 ATACATAAAT
1 -TACATAAAT
*
55656733 TACATAACT
1 TACATAAAT
*
55656742 TA-ATTAAT
1 TACATAAAT
*
55656750 TA-AT-ATT
1 TACATAAAT
55656757 ATACATAAAT
1 -TACATAAAT
55656767 TACATAAAT
1 TACATAAAT
55656776 TA
1 TA
55656778 GTTAATTAAT
Statistics
Matches: 302, Mismatches: 41, Indels: 94
0.69 0.09 0.22
Matches are distributed among these distances:
7 19 0.06
8 54 0.18
9 139 0.46
10 39 0.13
11 7 0.02
12 23 0.08
13 21 0.07
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (9 bp):
TACATAAAT
Found at i:55656417 original size:34 final size:33
Alignment explanation
Indices: 55656308--55656811 Score: 194
Period size: 34 Copynumber: 14.7 Consensus size: 33
55656298 AATTAATTAA
* *
55656308 TATACATAGATTACATAACTTACAT--TAATAT
1 TATACATAAATTACATAACTTAAATAATAATAT
*
55656339 TATACATAAATTACATAACTTAATTAATTAATTAGTAT
1 TATACATAAATTACATAACTT-A--AA-TAA-TAATAT
55656377 TATACATAAATTACATAACTTAAATAAGTAATAT
1 TATACATAAATTACATAACTTAAATAA-TAATAT
* *
55656411 TATACATAACTTACATTAA--TATTATACATAA-A-
1 TATACATAAATTACA-TAACTTA-AATA-ATAATAT
*
55656443 T-TACATAACTTA-ATTAA-TT-AAT--TAATAT
1 TATACATAAATTACA-TAACTTAAATAATAATAT
* *
55656471 TATACATAAATTACATAACATAATTAATTAATAT
1 TATACATAAATTACATAACTTAAATAA-TAATAT
* * *
55656505 TATACATAACTTACATTAATATTATACATAAATTACATAAC
1 TATACATAAATTACA-TAA-CTTA-A-AT-AA-TA-AT-AT
* *
55656546 T-TA-ATAAATTA-AT-A-TTATACATAACTTACAT
1 TATACATAAATTACATAACTTA-A-ATAA-TAATAT
* * * **
55656577 TAATATTATACATAAATTACATAACTTAGTTAATTAATAT
1 T-ATA-CATAAATT----ACATAACTTAAATAA-TAATAT
*
55656617 TATACATAACTTACATAACTTACAACTTACATAACTTACAT
1 TATACATAAATTACATAACTTA-AA--TA-ATAA--T--AT
* *
55656658 TAATATTATACATATTATACATAACTTACAT--TAATAT
1 T-ATA-CATA-A-A-T-TACATAACTTAAATAATAATAT
55656695 TATACATAAATTACATAACTT-AAT--T-A-A-
1 TATACATAAATTACATAACTTAAATAATAATAT
*
55656722 TATACATAAATTACATAACTTAATTAATTAATAT
1 TATACATAAATTACATAACTTAAATAA-TAATAT
* **
55656756 TATACATAAATTACATAAATTAGTTAATTAATAT
1 TATACATAAATTACATAACTTAAATAA-TAATAT
*
55656790 TATACATAACTTACATAACTTA
1 TATACATAAATTACATAACTTA
55656812 CAACTTACAT
Statistics
Matches: 370, Mismatches: 44, Indels: 115
0.70 0.08 0.22
Matches are distributed among these distances:
26 3 0.01
27 22 0.06
28 4 0.01
29 16 0.04
30 10 0.03
31 47 0.13
32 5 0.01
33 10 0.03
34 120 0.32
35 18 0.05
36 6 0.02
37 11 0.03
38 33 0.09
39 18 0.05
40 14 0.04
41 9 0.02
42 6 0.02
43 3 0.01
44 2 0.01
46 2 0.01
47 11 0.03
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.39
Consensus pattern (33 bp):
TATACATAAATTACATAACTTAAATAATAATAT
Found at i:55656433 original size:22 final size:22
Alignment explanation
Indices: 55656405--55656486 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 22
55656395 CTTAAATAAG
*
55656405 TAATATTATACATAACTTACAT
1 TAATATTATACATAAATTACAT
55656427 TAATATTATACATAAATTACA-
1 TAATATTATACATAAATTACAT
* *
55656448 T-A-ACT-TA-ATTAATTA-AT
1 TAATATTATACATAAATTACAT
55656465 TAATATTATACATAAATTACAT
1 TAATATTATACATAAATTACAT
55656487 AACATAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.02
17 8 0.16
18 3 0.06
19 4 0.08
20 3 0.06
21 8 0.16
22 22 0.45
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATATTATACATAAATTACAT
Found at i:55656445 original size:56 final size:56
Alignment explanation
Indices: 55656364--55656807 Score: 297
Period size: 56 Copynumber: 7.8 Consensus size: 56
55656354 TAACTTAATT
* *
55656364 AATTA-ATTAGTATTATACATAAAT-TACATAACTTAAATAAGTAATATTATACATA
1 AATTACATTAATATTATACATAAATATACATAACTTACATAA-TAATATTATACATA
* *
55656419 ACTTACATTAATATTATACATAAAT-TACATAACTTAATTAATTAATTAATATTATACATA
1 AATTACATTAATATTATACATAAATATACATAACTT-A--CA-TAA-TAATATTATACATA
* *
55656479 AATTACATAACATAATTAATTA-AT-ATTATACATAACTTACAT--TAATATTATACATA
1 AATTACATTA-AT-ATT-A-TACATAAATATACATAACTTACATAATAATATTATACATA
* *
55656535 AATTACA-TAACT-TAATAAATTAATATTATACATAACTTACAT--TAATATTATACATA
1 AATTACATTAA-TATTATACA-TAA-A-TATACATAACTTACATAATAATATTATACATA
* *
55656591 AATTACA-TAACTTAGTTAATTA-AT-ATTATACATAACTTACATAACTTACA-ACT-TACATA
1 AATTACATTAA--TA-TT-A-TACATAAATATACATAACTTACATAA--TA-ATATTATACATA
* *
55656650 ACTTACATTAATATTATACAT-ATTATACATAACTTACAT--TAATATTATACATA
1 AATTACATTAATATTATACATAAATATACATAACTTACATAATAATATTATACATA
*
55656703 AATTACATAACTTAATTAATATACATAAAT-TACATAACTTA-ATTAATTAATATTATACATA
1 AATTAC---A-TTAA-TATTATACATAAATATACATAACTTACA-TAA-TAATATTATACATA
55656764 AATTACA-TAA-ATTAGTTA-ATTAATATTATACATAACTTACATAA
1 AATTACATTAATATTA--TACA-TAA-A-TATACATAACTTACATAA
55656808 CTTACAACTT
Statistics
Matches: 322, Mismatches: 20, Indels: 90
0.75 0.05 0.21
Matches are distributed among these distances:
51 3 0.01
52 6 0.02
53 13 0.04
54 5 0.02
55 9 0.03
56 135 0.42
57 10 0.03
58 26 0.08
59 33 0.10
60 36 0.11
61 25 0.08
62 6 0.02
63 13 0.04
64 2 0.01
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (56 bp):
AATTACATTAATATTATACATAAATATACATAACTTACATAATAATATTATACATA
Found at i:55656480 original size:94 final size:93
Alignment explanation
Indices: 55656319--55656805 Score: 520
Period size: 94 Copynumber: 5.2 Consensus size: 93
55656309 ATACATAGAT
*
55656319 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATTAGTATTATACAT
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATTAATATTATACAT
55656384 AAATTACATAACTTAAATAAGTAATATTA
66 AAATTACATAACTTAAATAA-TAATATTA
55656413 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATTAATATTATACAT
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATTAATATTATACAT
* *
55656478 AAATTACATAACATAATTAATTAATATTA
66 AAATTACATAACTTAAATAA-TAATATTA
55656507 TACATAACTTACATTAATATTATACATAAATTACATAACTTAA-T-A--AATTAATATTATACAT
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATTAATATTATACAT
* *
55656568 AACTTACATTAA--TATTATACATAA-A-T-
66 AAATTACA-TAACTTA-AATA-ATAATATTA
* *
55656594 TACATAACTTAGTTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATT
1 TACATAACTTA---CATTAATATTATACATAAATTACATAACTT--AA--T---TAA-TTA-ATT
* *
55656659 AATATTATACAT-ATTATACATAACTTACAT--TAATATTA
54 AATATTATACATAAAT-TACATAACTTAAATAATAATATTA
* *
55656697 TACATAAATTACATAACTTAATTAATATACATAAATTACATAAC----TTAATTAATTAATATTA
1 TACATAACTTAC---A-TTAA-TATTATACATAAATTACATAACTTAATTAATTAATTAATATTA
* **
55656758 TACATAAATTACATAAATTAGTTAATTAATATTA
61 TACATAAATTACATAACTTAAATAA-TAATATTA
55656792 TACATAACTTACAT
1 TACATAACTTACAT
55656806 AACTTACAAC
Statistics
Matches: 339, Mismatches: 20, Indels: 71
0.79 0.05 0.17
Matches are distributed among these distances:
87 11 0.03
88 1 0.00
89 3 0.01
90 56 0.17
91 5 0.01
92 30 0.09
93 6 0.02
94 136 0.40
95 19 0.06
97 1 0.00
98 1 0.00
99 1 0.00
100 3 0.01
101 1 0.00
102 7 0.02
103 32 0.09
104 6 0.02
105 20 0.06
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (93 bp):
TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATTAATATTATACAT
AAATTACATAACTTAAATAATAATATTA
Found at i:55656525 original size:22 final size:21
Alignment explanation
Indices: 55656488--55656542 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
55656478 AAATTACATA
55656488 ACATAATTA-ATTAATATTAT
1 ACATAATTACATTAATATTAT
55656508 ACATAACTTACATTAATATTAT
1 ACATAA-TTACATTAATATTAT
55656530 ACATAAATTACAT
1 ACAT-AATTACAT
55656543 AACTTAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.19
21 3 0.09
22 21 0.66
23 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (21 bp):
ACATAATTACATTAATATTAT
Found at i:55656581 original size:22 final size:22
Alignment explanation
Indices: 55656553--55656598 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
55656543 AACTTAATAA
*
55656553 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
55656575 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
55656597 AT
1 AT
55656599 AACTTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:55656645 original size:16 final size:16
Alignment explanation
Indices: 55656624--55656656 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55656614 TATTATACAT
55656624 AACTTACATAACTTAC
1 AACTTACATAACTTAC
55656640 AACTTACATAACTTAC
1 AACTTACATAACTTAC
55656656 A
1 A
55656657 TTAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:55656694 original size:22 final size:22
Alignment explanation
Indices: 55656669--55656737 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 22
55656659 AATATTATAC
*
55656669 ATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATTA
55656691 ATATTATACATAAATTACATAACTTA
1 ATATTATACATAAATTAC---A-TTA
*
55656717 ATTAATATACATAAATTACAT
1 A-TATTATACATAAATTACAT
55656738 AACTTAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 17 0.43
23 1 0.03
24 1 0.03
25 1 0.03
26 4 0.10
27 16 0.40
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTATACATAAATTACATTA
Found at i:55656719 original size:13 final size:13
Alignment explanation
Indices: 55656703--55656747 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
55656693 ATTATACATA
55656703 AATTACATAACTT
1 AATTACATAACTT
*
55656716 AATTA-ATATACATA
1 AATTACATA-AC-TT
55656730 AATTACATAACTT
1 AATTACATAACTT
55656743 AATTA
1 AATTA
55656748 ATTAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 3 0.11
13 13 0.48
14 8 0.30
15 3 0.11
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTACATAACTT
Found at i:55656806 original size:9 final size:9
Alignment explanation
Indices: 55656792--55657009 Score: 114
Period size: 9 Copynumber: 26.2 Consensus size: 9
55656782 ATTAATATTA
55656792 TACATAACT
1 TACATAACT
55656801 TACATAACT
1 TACATAACT
55656810 TAC--AACT
1 TACATAACT
55656817 TACATAACT
1 TACATAACT
***
55656826 TACATTTTTT
1 TACA-TAACT
*
55656836 TA-ATTA-T
1 TACATAACT
* *
55656843 T-CGTAAAT
1 TACATAACT
55656851 TACATAACT
1 TACATAACT
* *
55656860 TACTTAATT
1 TACATAACT
*
55656869 TGCATAA--
1 TACATAACT
*
55656876 TAAATAACT
1 TACATAACT
55656885 TACATAACT
1 TACATAACT
55656894 TACATAA--
1 TACATAACT
55656901 TACATAACT
1 TACATAACT
* *
55656910 TATATGACT
1 TACATAACT
55656919 TACATAACT
1 TACATAACT
55656928 TACAT-A--
1 TACATAACT
* *
55656934 -GCATAATT
1 TACATAACT
*
55656942 TTCATAA--
1 TACATAACT
*
55656949 TACACAACT
1 TACATAACT
*
55656958 TACATAATT
1 TACATAACT
*
55656967 TTCATAA--
1 TACATAACT
*
55656974 TAAATAACT
1 TACATAACT
55656983 TACATAA--
1 TACATAACT
55656990 TACATAACT
1 TACATAACT
*
55656999 TACATAGCT
1 TACATAACT
55657008 TA
1 TA
55657010 ATTATACTTA
Statistics
Matches: 159, Mismatches: 30, Indels: 40
0.69 0.13 0.17
Matches are distributed among these distances:
5 3 0.02
6 1 0.01
7 40 0.25
8 5 0.03
9 106 0.67
10 4 0.03
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:55656818 original size:16 final size:16
Alignment explanation
Indices: 55656797--55656829 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55656787 TATTATACAT
55656797 AACTTACATAACTTAC
1 AACTTACATAACTTAC
55656813 AACTTACATAACTTAC
1 AACTTACATAACTTAC
55656829 A
1 A
55656830 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:55656820 original size:25 final size:25
Alignment explanation
Indices: 55656792--55656933 Score: 80
Period size: 25 Copynumber: 5.6 Consensus size: 25
55656782 ATTAATATTA
55656792 TACATAACTTACATAACTTACAACT
1 TACATAACTTACATAACTTACAACT
** **
55656817 TACATAACTTACAT-TTTTTTAA-T
1 TACATAACTTACATAACTTACAACT
* * *
55656840 TATTCGTAAATTACATAACTTACTTAATT
1 TA--CATAACTTACATAACTTAC--AACT
* *
55656869 TGCATAA--TAAATAACTTACATAACT
1 TACATAACTTACATAACTTAC--AACT
*
55656894 TACATAA--TACATAACTTATATGACT
1 TACATAACTTACATAACTTACA--ACT
55656919 TACATAACTTACATA
1 TACATAACTTACATA
55656934 GCATAATTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
23 4 0.04
24 4 0.04
25 65 0.73
26 2 0.02
27 10 0.11
28 2 0.02
29 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39
Consensus pattern (25 bp):
TACATAACTTACATAACTTACAACT
Found at i:55656830 original size:34 final size:33
Alignment explanation
Indices: 55656792--55656933 Score: 94
Period size: 34 Copynumber: 4.2 Consensus size: 33
55656782 ATTAATATTA
*
55656792 TACATAACTTACATAACTTACAACTTACATAACT
1 TACATAATTTACATAA-TTACAACTTACATAACT
** * *
55656826 TACATTTTTTTA-ATTATT-CGTAAATTACATAACT
1 TACA-TAATTTACATAATTAC--AACTTACATAACT
* * * *
55656860 TACTTAATTTGCATAATAAATAACTTACATAACT
1 TACATAATTTACATAAT-TACAACTTACATAACT
*
55656894 TACATAA--TACATAACTTATATGACTTACATAACT
1 TACATAATTTACATAA-TTACA--ACTTACATAACT
55656928 TACATA
1 TACATA
55656934 GCATAATTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
32 10 0.12
33 7 0.08
34 62 0.75
35 4 0.05
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39
Consensus pattern (33 bp):
TACATAATTTACATAATTACAACTTACATAACT
Found at i:55656904 original size:16 final size:16
Alignment explanation
Indices: 55656885--55657004 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
55656875 ATAAATAACT
55656885 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
55656901 TACATAACTTATATGACT
1 TACATAACTTACAT-A-A
55656919 TACATAACTTACAT-A
1 TACATAACTTACATAA
* * *
55656934 -GCATAATTTTCATAA
1 TACATAACTTACATAA
*
55656949 TACACAACTTACATAA
1 TACATAACTTACATAA
55656965 T---T---TT-CATAA
1 TACATAACTTACATAA
*
55656974 TAAATAACTTACATAA
1 TACATAACTTACATAA
55656990 TACATAACTTACATA
1 TACATAACTTACATA
55657005 GCTTAATTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 10 0.12
15 3 0.04
16 44 0.55
17 1 0.01
18 13 0.16
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (16 bp):
TACATAACTTACATAA
Done.