Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 16 of 211
Found at i:5214482 original size:30 final size:30
Alignment explanation
Indices: 5214409--5214583 Score: 85
Period size: 30 Copynumber: 5.9 Consensus size: 30
5214399 TAGAGTGTGC
* * *
5214409 AAAGTTTTTGGGGCAAAAATGTGATTTTAGG
1 AAAG-TTTAGGGGCCAAAATGTAATTTTAGG
* *
5214440 AAAATATA-GGGCCAAAATGTAATTTCTA-G
1 AAAGTTTAGGGGCCAAAATGTAATTT-TAGG
* * *
5214469 AAAGTTTAGGGGCC-AACTATAA-TTTA-C
1 AAAGTTTAGGGGCCAAAATGTAATTTTAGG
* * * * *
5214496 AAAATATTAGGGGTCAAGATGTAAATTTAGAA
1 AAAGT-TTAGGGGCCAAAATGTAATTTTAG-G
* * ** * *
5214528 AAAG-TTGGGGGTCAAAAAATAATTTTTGA
1 AAAGTTTAGGGGCCAAAATGTAATTTTAGG
5214557 AAAGTTT-GGAGGCCAAAATGTAATTTT
1 AAAGTTTAGG-GGCCAAAATGTAATTTT
5214584 TATTTTTTGT
Statistics
Matches: 109, Mismatches: 26, Indels: 19
0.71 0.17 0.12
Matches are distributed among these distances:
27 6 0.06
28 10 0.09
29 40 0.37
30 47 0.43
31 3 0.03
32 3 0.03
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (30 bp):
AAAGTTTAGGGGCCAAAATGTAATTTTAGG
Found at i:5214599 original size:15 final size:14
Alignment explanation
Indices: 5214579--5214618 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
5214569 CCAAAATGTA
5214579 ATTTTTATTTTTTGT
1 ATTTTT-TTTTTTGT
*
5214594 ATTTTTTTTATTTTT
1 ATTTTTTTT-TTTGT
5214609 ATTTTTTTTT
1 ATTTTTTTTT
5214619 CAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (14 bp):
ATTTTTTTTTTTGT
Found at i:5214617 original size:9 final size:9
Alignment explanation
Indices: 5214580--5214618 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
5214570 CAAAATGTAA
5214580 TTTTTATTT
1 TTTTTATTT
*
5214589 TTTGTATTT
1 TTTTTATTT
5214598 TTTTTATTT
1 TTTTTATTT
5214607 TTATTT-TTT
1 TT-TTTATTT
5214616 TTT
1 TTT
5214619 CAAAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 1 0.04
9 23 0.85
10 3 0.11
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTTATTT
Found at i:5216165 original size:40 final size:41
Alignment explanation
Indices: 5216106--5216213 Score: 107
Period size: 40 Copynumber: 2.7 Consensus size: 41
5216096 GTTTGAATAA
* * * *
5216106 AAAATGCCTCTAAAGATCGAGCATTAGCGA-CTCTTT-TCGG
1 AAAACGCCGCTAAATATCGAGCATTAGCGATCGCTTTAT-GG
* * *
5216146 AAAACGCCGCTAAATATCGAACTTTAAC-ATCGCTTTATGG
1 AAAACGCCGCTAAATATCGAGCATTAGCGATCGCTTTATGG
*
5216186 AAAACGCCGCTAAATAT-AAGCATTAGCG
1 AAAACGCCGCTAAATATCGAGCATTAGCG
5216214 GCGTTTTCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
39 7 0.13
40 46 0.85
41 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (41 bp):
AAAACGCCGCTAAATATCGAGCATTAGCGATCGCTTTATGG
Found at i:5216303 original size:41 final size:40
Alignment explanation
Indices: 5216257--5216423 Score: 160
Period size: 41 Copynumber: 4.1 Consensus size: 40
5216247 CTTTCGGGGT
*
5216257 TTTAGCGGCGTTTTTAATGAAGCGCTGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTAA-GAAGCGCCGCTAATGCTCAGGGC
* ** *
5216298 TTTAGCGGCATGTTTTGGGAAGCGCCGCTAATGCTTAGGGC
1 TTTAGCGGCGT-TTTTAAGAAGCGCCGCTAATGCTCAGGGC
* * **
5216339 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATACTCTA--TT
1 TTTAGCGGCGTTTTTAAG-AAGCGCCGCTAATGCTC-AGGGC
* *
5216379 TTTAGCGGCGTTTTCTAA-AATGCGCTGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTT-TAAGAA-GCGCCGCTAATGCTCAGGGC
5216420 TTTA
1 TTTA
5216424 AAATAATCTA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
39 3 0.03
40 33 0.32
41 62 0.60
42 5 0.05
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTAAGAAGCGCCGCTAATGCTCAGGGC
Found at i:5217413 original size:14 final size:15
Alignment explanation
Indices: 5217396--5217452 Score: 73
Period size: 14 Copynumber: 3.9 Consensus size: 15
5217386 TGTGGTTTAT
5217396 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
*
5217410 GGTTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
*
5217425 GG-TTAGGGGTTAGG
1 GGTTTAAGGGTTAGG
*
5217439 GGTTTAGGGGTTAG
1 GGTTTAAGGGTTAG
5217453 TGCTTGCTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 23 0.61
15 15 0.39
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.35
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:5217430 original size:7 final size:7
Alignment explanation
Indices: 5217420--5217452 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
5217410 GGTTTAAGGT
5217420 TTAGGGG
1 TTAGGGG
5217427 TTAGGGG
1 TTAGGGG
5217434 TTAGGGG
1 TTAGGGG
5217441 TTTAGGGG
1 -TTAGGGG
5217449 TTAG
1 TTAG
5217453 TGCTTGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:5217442 original size:22 final size:22
Alignment explanation
Indices: 5217389--5217452 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
5217379 TATGAATTGT
* *
5217389 GGTTTATGGTTTAAGGGTT-GG
1 GGTTTAAGGTTTAGGGGTTAGG
5217410 GGTTTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGTTTAGGGGTTAGG
*
5217432 GG-TTAGGGGTTTAGGGGTTAG
1 GGTTTA-AGGTTTAGGGGTTAG
5217453 TGCTTGCTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.38
Consensus pattern (22 bp):
GGTTTAAGGTTTAGGGGTTAGG
Found at i:5220369 original size:43 final size:43
Alignment explanation
Indices: 5220321--5220571 Score: 299
Period size: 43 Copynumber: 5.9 Consensus size: 43
5220311 GTTTGTGATG
* * *
5220321 AAAGCGCCGTTAAAGATAATGTTCTCTAGCGGCGTTTGTGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
* * * *
5220364 CAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGTGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
* *
5220407 AAAGCGCCGCTAAAGCTCATGTTCTTTAGCAGCGTTTGTGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
** * *
5220450 AAAGCGCCATTAAAGGA-CATGTTCTTTAGCGGCGTTTGTAGCT
1 AAAGCGCCGCTAAA-GATCATGTTCTTTAGCGGCGTTTGTGGGT
* * * *
5220493 AAAGCGCCGCTAAAGGTTATGTTCTTTAG-TGCGTTTGTGGCT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
* * *
5220535 AAAGCGCCGCTAAAGATTAAGTTCTTTAGCGGTGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
5220572 TTTTCACATA
Statistics
Matches: 177, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 39 0.22
43 137 0.77
44 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
Found at i:5220463 original size:129 final size:128
Alignment explanation
Indices: 5220302--5220564 Score: 343
Period size: 129 Copynumber: 2.0 Consensus size: 128
5220292 AGTACGTACT
* * * * *
5220302 TTTAGTAGCGTTTGTGATGAAAGCGCCGTTAAA-GATAATGTTCTCTAGCGGCGTTTGTGGGTCA
1 TTTAGCAGCGTTTGTGATGAAAGCGCCATTAAAGGA-AATGTTCTCTAGCGGCGTTTGTAGCTAA
* * *
5220366 AGCGTCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGTG-TAAAGCGCCGCTAAAGCTCATGTT
65 AGCGCCGCTAAAGGTCATGTTCTTTAG-GGCGTTTGTG-GCTAAAGCGCCGCTAAAGATCAAGTT
5220430 C
128 C
* * *
5220431 TTTAGCAGCGTTTGTG-GGTAAAGCGCCATTAAAGGACATGTTCTTTAGCGGCGTTTGTAGCTAA
1 TTTAGCAGCGTTTGTGATG-AAAGCGCCATTAAAGGAAATGTTCTCTAGCGGCGTTTGTAGCTAA
* * *
5220495 AGCGCCGCTAAAGGTTATGTTCTTTAGTGCGTTTGTGGCTAAAGCGCCGCTAAAGATTAAGTTC
65 AGCGCCGCTAAAGGTCATGTTCTTTAGGGCGTTTGTGGCTAAAGCGCCGCTAAAGATCAAGTTC
5220559 TTTAGC
1 TTTAGC
5220565 GGTGTTTTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
127 1 0.01
128 38 0.32
129 76 0.65
130 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (128 bp):
TTTAGCAGCGTTTGTGATGAAAGCGCCATTAAAGGAAATGTTCTCTAGCGGCGTTTGTAGCTAAA
GCGCCGCTAAAGGTCATGTTCTTTAGGGCGTTTGTGGCTAAAGCGCCGCTAAAGATCAAGTTC
Found at i:5224486 original size:17 final size:17
Alignment explanation
Indices: 5224461--5224518 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 17
5224451 GAATGATATT
5224461 TTTGATTATTGAAAATA
1 TTTGATTATTGAAAATA
*
5224478 TTTGCTTATTGAAGAATGATA
1 TTTGATTATTG-A-AA--ATA
5224499 TTTTTGATTATTGAAAATA
1 --TTTGATTATTGAAAATA
5224518 T
1 T
5224519 CTGCTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 11 0.33
18 1 0.03
19 5 0.15
21 5 0.15
22 1 0.03
23 10 0.30
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (17 bp):
TTTGATTATTGAAAATA
Found at i:5224499 original size:40 final size:40
Alignment explanation
Indices: 5224444--5224527 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
5224434 AGAGAAATTC
*
5224444 TATTGAAGAATGATATTTTTGATTATTGAAAATATTTGCT
1 TATTGAAGAATGATATTTTTGATTATTGAAAATATCTGCT
5224484 TATTGAAGAATGATATTTTTGATTATTGAAAATATCTGCT
1 TATTGAAGAATGATATTTTTGATTATTGAAAATATCTGCT
5224524 TATT
1 TATT
5224528 ATCAGACGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.48
Consensus pattern (40 bp):
TATTGAAGAATGATATTTTTGATTATTGAAAATATCTGCT
Found at i:5224509 original size:23 final size:23
Alignment explanation
Indices: 5224444--5224513 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
5224434 AGAGAAATTC
5224444 TATTGAAGAATGATATTTTTGAT
1 TATTGAAGAATGATATTTTTGAT
*
5224467 TATTG-A-AA--ATA--TTTGCT
1 TATTGAAGAATGATATTTTTGAT
5224484 TATTGAAGAATGATATTTTTGAT
1 TATTGAAGAATGATATTTTTGAT
5224507 TATTGAA
1 TATTGAA
5224514 AATATCTGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
17 10 0.26
18 1 0.03
19 5 0.13
21 5 0.13
22 1 0.03
23 17 0.44
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (23 bp):
TATTGAAGAATGATATTTTTGAT
Found at i:5225663 original size:12 final size:12
Alignment explanation
Indices: 5225646--5225671 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5225636 AAACATTCCA
5225646 TATTTTTTATTT
1 TATTTTTTATTT
5225658 TATTTTTTATTT
1 TATTTTTTATTT
5225670 TA
1 TA
5225672 GTAAACCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:5231983 original size:20 final size:20
Alignment explanation
Indices: 5231947--5231986 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5231937 TCCTATTGTT
5231947 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
5231967 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
5231987 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:5232635 original size:44 final size:44
Alignment explanation
Indices: 5232521--5232637 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
5232511 TTTTAACCCA
* * ** * *
5232521 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
*
5232564 CTCCGCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
*
5232608 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
5232638 GTAATTTCCA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 4 0.07
43 19 0.32
44 32 0.53
45 5 0.08
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:5233151 original size:175 final size:173
Alignment explanation
Indices: 5232775--5233251 Score: 574
Period size: 175 Copynumber: 2.8 Consensus size: 173
5232765 TGTAACCTTT
* * * * *
5232775 AACCAGCTCCAAT-GCAACCAATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTACTGTTAATG
1 AACCAGCTCC-ATCACAACCAA-AGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCACTGTCAATG
** * * * * ** *
5232837 CAGGAAGGCAAGATCTGCT-TCTTTAACTAGCTCCA-CTGCAATCGATGGATGCAAGGCTTTGT-
63 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGAAAGAGGCAAGG-TTTGTG
* * * *
5232899 T-TTCGATCTGCTTCGCTGTTAATGTAGGAGGCAAGATCTGCTTCTTT
126 TCTTCGATCTGCTTCGCTGTCAATGCAGAAGGCAAGATCTGCTTCTTC
* * *
5232946 AACCAGCTCCA-CTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCAATGTCAATGC
1 AACCAGCTCCATC-ACAACC-AAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAATGC
*
5233010 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCT
64 AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCT
**
5233075 TCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
129 TCGATCTGCTTCGCTGTCAATGCAG-AAGGCAAGATCTGCT-TCTTC
*
5233122 AACCAGCTCCATCACAACCAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAG
1 AACCAGCTCCATCACAACCAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAATGCAG
* *
5233187 AAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGACTTC
66 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
5233252 ATTGATCTGT
Statistics
Matches: 263, Mismatches: 31, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
170 6 0.02
171 25 0.10
172 41 0.16
173 28 0.11
174 25 0.10
175 116 0.44
176 21 0.08
177 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (173 bp):
AACCAGCTCCATCACAACCAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAATGCAG
GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
GATCTGCTTCGCTGTCAATGCAGAAGGCAAGATCTGCTTCTTC
Found at i:5233187 original size:87 final size:88
Alignment explanation
Indices: 5232798--5233251 Score: 559
Period size: 88 Copynumber: 5.2 Consensus size: 88
5232788 GCAACCAATG
* ** * * **
5232798 GAGGCAAGGCTTTGT-T-TTTGATCTGCTTTACTGTTAATGCAGGAAGGCAAGATCTGCT-TCTT
1 GAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTT
* * * * **
5232860 TAACTAGCTCCA-CTGCAATCGATG
65 CAACCAGCTCCATC-ACAACCGAAA
* * * * **
5232884 GATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAG-GAGGCAAGATCTGCT-TCTT
1 GAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTT
* *
5232945 TAACCAGCTCCA-CTACAACCGAGA
65 CAACCAGCTCCATC-ACAACCGAAA
* ** *
5232969 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCAATGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
*
5233034 AACCAGCTCTATCACAACCGAAA
66 AACCAGCTCCATCACAACCGAAA
5233057 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
5233122 AACCAGCTCCATCACAACC-AAA
66 AACCAGCTCCATCACAACCGAAA
5233144 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
5233209 AACCAGCTCCATCACAACCGAAA
66 AACCAGCTCCATCACAACCGAAA
*
5233232 GAGGCAAGGTTTGTGACTTC
1 GAGGCAAGGTTTGTGTCTTC
5233252 ATTGATCTGT
Statistics
Matches: 333, Mismatches: 29, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
84 5 0.02
85 46 0.14
86 58 0.17
87 99 0.30
88 124 0.37
89 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (88 bp):
GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
AACCAGCTCCATCACAACCGAAA
Found at i:5234978 original size:12 final size:12
Alignment explanation
Indices: 5234934--5234978 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
5234924 TTGATTTCTC
5234934 TTTGTTTTT-AT
1 TTTGTTTTTGAT
*
5234945 TTTTTATTTTGAT
1 TTTGT-TTTTGAT
*
5234958 TTTGATTTTGAT
1 TTTGTTTTTGAT
5234970 TTTGTTTTT
1 TTTGTTTTT
5234979 TTTTTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 4 0.14
12 19 0.68
13 5 0.18
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (12 bp):
TTTGTTTTTGAT
Found at i:5234990 original size:18 final size:17
Alignment explanation
Indices: 5234934--5234989 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
5234924 TTGATTTCTC
*
5234934 TTTGTTTTTATTTTTTAT
1 TTTGTTTTT-TTTTTCAT
** *
5234952 TTTGATTTTGATTTTGAT
1 TTTG-TTTTTTTTTTCAT
5234970 TTTGTTTTTTTTTTCAT
1 TTTGTTTTTTTTTTCAT
5234987 TTT
1 TTT
5234990 TCCTTGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 13 0.42
18 14 0.45
19 4 0.13
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTGTTTTTTTTTTCAT
Found at i:5242858 original size:20 final size:20
Alignment explanation
Indices: 5242822--5242861 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5242812 TCCTATTGTT
5242822 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
5242842 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
5242862 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:5247807 original size:13 final size:13
Alignment explanation
Indices: 5247789--5247815 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5247779 ATTGAGTTGA
5247789 ATGTTAGTGGTAT
1 ATGTTAGTGGTAT
5247802 ATGTTAGTGGTAT
1 ATGTTAGTGGTAT
5247815 A
1 A
5247816 CATTTTAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (13 bp):
ATGTTAGTGGTAT
Found at i:5248137 original size:36 final size:36
Alignment explanation
Indices: 5248010--5248499 Score: 426
Period size: 38 Copynumber: 13.4 Consensus size: 36
5248000 CATTATACGT
* * * * *
5248010 GTCTATTCCAATC-TTTTTAAGATTACCTTAGACGG
1 GTCTATCCCAACCTTTTTTAAGGTTGCCTTAGACAG
*
5248045 GTTTATCCCAACCTTTTTTTAAAGGTTGCCTTAGACAAG
1 GTCTATCCCAACC-TTTTTT-AAGGTTGCCTTAGAC-AG
* * * *
5248084 ATTTATCCCAACC-TTTTTAAGGTTG-CTCTAAACGG
1 GTCTATCCCAACCTTTTTTAAGGTTGCCT-TAGACAG
*
5248119 GTCTATCCCAACCTTTTTTAAAAGTTGCCTTAGACAAG
1 GTCTATCCCAACCTTTTTT-AAGGTTGCCTTAGAC-AG
* *
5248157 GTCTATCCCAACC-TTTTTAAAGTTGCCTTAGACGG
1 GTCTATCCCAACCTTTTTTAAGGTTGCCTTAGACAG
5248192 GTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACATG
1 GTCTATCCCAACCTTTTTT-AAGGTTGCCTTAGACA-G
* * *
5248230 GTCTATTCCAACC-TGTTTAAGGTTGCCTTAGATAG
1 GTCTATCCCAACCTTTTTTAAGGTTGCCTTAGACAG
* *
5248265 GTCTATCCCAACCTTTTTTATAGGTTGTCTTAGACAAA
1 GTCTATCCCAACCTTTTTTA-AGGTTGCCTTAGAC-AG
*
5248303 GTCTATCCCAACC-TTTTTAAGGTTGTCTTAGAC-G
1 GTCTATCCCAACCTTTTTTAAGGTTGCCTTAGACAG
* * *
5248337 GCTCTAT-CCAAACTATTTTTAAAAGTTGCCTCAGACAAG
1 G-TCTATCCCAACCT-TTTTT-AAGGTTGCCTTAGAC-AG
** ** * *
5248376 AACTATATCAACC-TTTTTAAGGTTGTCTTAGATAG
1 GTCTATCCCAACCTTTTTTAAGGTTGCCTTAGACAG
* * *
5248411 GTCTATCTCAACCTTTTTCAAAGGTTGGCTGTA-ACTAG
1 GTCTATCCCAACCTTTTT-TAAGGTTGCCT-TAGAC-AG
*
5248449 GTCTATCCCAACCCTTTTTAATGGTTGGCCTT-GACTAG
1 GTCTATCCCAACCTTTTTTAA-GGTT-GCCTTAGAC-AG
*
5248487 GTCTTTCCCAACC
1 GTCTATCCCAACC
5248500 CTTCAATAAG
Statistics
Matches: 377, Mismatches: 49, Indels: 55
0.78 0.10 0.11
Matches are distributed among these distances:
34 6 0.02
35 68 0.18
36 90 0.24
37 90 0.24
38 102 0.27
39 21 0.06
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (36 bp):
GTCTATCCCAACCTTTTTTAAGGTTGCCTTAGACAG
Found at i:5248166 original size:73 final size:73
Alignment explanation
Indices: 5248010--5248499 Score: 556
Period size: 73 Copynumber: 6.7 Consensus size: 73
5248000 CATTATACGT
* * * * *
5248010 GTCTATTCCAATCTTTTTAAGATTACCTTAGACGGGTTTATCCCAACCTTTTTTTAAAGGTTGCC
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACC-TTTTTTAAAGGTTGCC
5248075 TTAGACAAG
65 TTAGACAAG
* * * *
5248084 ATTTATCCCAACCTTTTTAAGGTTG-CTCTAAACGGGTCTATCCCAACCTTTTTTAAAAGTTGCC
1 GTCTATCCCAACCTTTTTAAGGTTGCCT-TAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCC
5248148 TTAGACAAG
65 TTAGACAAG
*
5248157 GTCTATCCCAACCTTTTTAAAGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
*
5248222 TAGACATG
66 TAGACAAG
* * ** * *
5248230 GTCTATTCCAACCTGTTTAAGGTTGCCTTAGATAGGTCTATCCCAACCTTTTTTATAGGTTGTCT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
*
5248295 TAGACAAA
66 TAGACAAG
* * * *
5248303 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACGGCTCTAT-CCAAACTATTTTTAAAAGTTGCC
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCT-TTTTTAAAGGTTGCC
*
5248367 TCAGACAAG
65 TTAGACAAG
** ** * ** * * *
5248376 AACTATATCAACCTTTTTAAGGTTGTCTTAGATAGGTCTATCTCAACCTTTTTCAAAGGTTGGCT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
*
5248441 GTA-ACTAG
66 -TAGACAAG
* *
5248449 GTCTATCCCAACCCTTTTTAATGGTTGGCCTT-GACTAGGTCTTTCCCAACC
1 GTCTATCCCAA-CCTTTTTAA-GGTT-GCCTTAGAC-GGGTCTATCCCAACC
5248500 CTTCAATAAG
Statistics
Matches: 349, Mismatches: 58, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
72 6 0.02
73 266 0.76
74 54 0.15
75 6 0.02
76 17 0.05
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (73 bp):
GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
TAGACAAG
Found at i:5250983 original size:30 final size:30
Alignment explanation
Indices: 5250947--5251009 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
5250937 TTGGAGCTTC
5250947 ATCCCCGTCCCGACGCCAAGACCCGCGGTG
1 ATCCCCGTCCCGACGCCAAGACCCGCGGTG
5250977 ATCCCCGTCCCGACGCCAAGACCCGCGGTG
1 ATCCCCGTCCCGACGCCAAGACCCGCGGTG
5251007 ATC
1 ATC
5251010 TTCCACTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.17, C:0.46, G:0.25, T:0.11
Consensus pattern (30 bp):
ATCCCCGTCCCGACGCCAAGACCCGCGGTG
Found at i:5253709 original size:101 final size:102
Alignment explanation
Indices: 5253587--5253771 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 102
5253577 AAAGTGATGG
*
5253587 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCAG-GTGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCAC-GTGTGTAG
*
5253649 TACTATGTGCAGGTTACTATGCGTACCGGATAGCTTCGA
64 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* *
5253688 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACGTGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACGTGTGTAGTA
5253753 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
5253772 TGAACCGGTA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
101 41 0.53
102 32 0.42
103 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACGTGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:5253711 original size:51 final size:49
Alignment explanation
Indices: 5253586--5253779 Score: 223
Period size: 51 Copynumber: 3.9 Consensus size: 49
5253576 GAAAGTGATG
*
5253586 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-G---GATAGTTC
* * *
5253639 G-CA-G-GTGTAGTACTATGTGCAGGTTACTATGCGTACCGGATAGCTTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TTC
* *
5253686 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATG
1 G-TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT--TC
* *
5253738 GTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
5253780 TATCATTAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
46 5 0.04
47 3 0.02
49 3 0.02
50 32 0.26
51 74 0.61
52 4 0.03
53 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (49 bp):
GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTC
Found at i:5257472 original size:100 final size:100
Alignment explanation
Indices: 5257341--5257652 Score: 453
Period size: 100 Copynumber: 3.1 Consensus size: 100
5257331 ATTACAGTGG
*
5257341 AATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGTGGTGTAGTGGAACAAATTGAAGCTA
1 AATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAAATTGAAGCTA
* * *
5257406 CGATGGCGAATCTAGTTTCCCCGACACTGCAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * * * * * *
5257441 AATAGATTGAAGCCATAACGGTGAATTTTACTTCCCTGGCGGTGTAGTGGAACATATTAAAGCTA
1 AATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAAATTGAAGCTA
* *
5257506 CGACGCCAAATCTTGTTTCCCCGACATTGCAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * *
5257541 AATAGATTGAAGCTACAACAGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAAATTGAAGCTA
* *
5257606 CAACGGCGAATCTTGTTTCCCCGACATTACAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
*
5257641 AACAGATTGAAG
1 AATAGATTGAAG
5257653 ATGGCGAATC
Statistics
Matches: 185, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 185 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (100 bp):
AATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAAATTGAAGCTA
CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
Found at i:5257626 original size:50 final size:50
Alignment explanation
Indices: 5257335--5257619 Score: 230
Period size: 50 Copynumber: 5.7 Consensus size: 50
5257325 TTTGGCATTA
* * *
5257335 CAGTGGAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGTGGTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
* * * * * * * **
5257385 TAGTGGAACAAATTGAAGCTACGATGGCGAATC-TAGTTTCCCCGACACTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGAATCTTA-CTTCCCTGGCGGTG
** * * * * *
5257435 CAGTTAAATAGATTGAAGCCATAACGGTGAATTTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
* * * * * * ** * * **
5257485 TAGTGGAACATATTAAAGCTACGACGCCAAATCTTGTTTCCCCGACATTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
** * * *
5257535 CAGTTAAATAGATTGAAGCTACAACAGCAAATCTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
5257585 CAGTGGAACAGATTGAAGCTACAACGGCGAATCTT
1 CAGTGGAACAGATTGAAGCTACAACGGCGAATCTT
5257620 GTTTCCCCGA
Statistics
Matches: 166, Mismatches: 67, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
49 2 0.01
50 162 0.98
51 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
Found at i:5257645 original size:50 final size:50
Alignment explanation
Indices: 5257344--5257652 Score: 204
Period size: 50 Copynumber: 6.2 Consensus size: 50
5257334 ACAGTGGAAT
* ** * *** * **
5257344 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGTGGTGTAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAGTGCAGTTAAAC
* * * * * *
5257394 AAATTGAAGCTACGATGGCGAATCTAGTTTCCCCGACACTGCAGTTAAAT
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAGTGCAGTTAAAC
* * * * ** * * * * **
5257444 AGATTGAAGCCATAACGGTGAATTTTACTTCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAGTGCAGTTAAAC
* * * * * * *
5257494 ATATTAAAGCTACGACGCCAAATCTTGTTTCCCCGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAGTGCAGTTAAAC
* * ** * * * **
5257544 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAGTGCAGTTAAAC
* *
5257594 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACATTACAGTTAAAC
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAGTGCAGTTAAAC
5257644 AGATTGAAG
1 AGATTGAAG
5257653 ATGGCGAATC
Statistics
Matches: 181, Mismatches: 78, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
50 181 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAGTGCAGTTAAAC
Found at i:5257760 original size:43 final size:44
Alignment explanation
Indices: 5257659--5257779 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 44
5257649 GAAGATGGCG
* *
5257659 AATCTTATCTCTCTAAGGTTACAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCTCTGAGGTTACAGTAGAGCAGATTAAAGCCAAT
* * * * **
5257703 AATCCTATCTCTCTGAGGTTGCAGTAGAGCGGATTGAAG-TGAT
1 AATCTTATCTCTCTGAGGTTACAGTAGAGCAGATTAAAGCCAAT
* *
5257746 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGAT
1 AATCTTATCTCTCTGAGGTTACAGTAGAGCAGAT
5257780 CGCATCCAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 31 0.48
44 33 0.52
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCTCTGAGGTTACAGTAGAGCAGATTAAAGCCAAT
Found at i:5259953 original size:26 final size:26
Alignment explanation
Indices: 5259902--5259977 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
5259892 ATTGTTATTG
* * * *
5259902 TATTTTCTATACAT-ATAAATACGCA
1 TATTTTTTATATATAATATATAAGCA
5259927 TATTTTTTATATATAATATATAAGCA
1 TATTTTTTATATATAATATATAAGCA
* *
5259953 TATTTTTAATATATATATTTATAAG
1 TATTTTTTATATATA-ATATATAAG
5259978 TACGCATCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.28
26 23 0.53
27 8 0.19
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.49
Consensus pattern (26 bp):
TATTTTTTATATATAATATATAAGCA
Found at i:5266494 original size:44 final size:44
Alignment explanation
Indices: 5266406--5267017 Score: 625
Period size: 44 Copynumber: 13.9 Consensus size: 44
5266396 GTTGAAAAGC
** * * *
5266406 AGCAGATCTTGTCTTCCCGTACTGGTGACGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCG-TGAAGTAGATCGAAGAA
5266451 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *** * *
5266495 AGAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
* *
5266540 AGCAGATCTTGTCTTCATGTATTAGCGTGAAGCAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * * * * * *
5266584 AGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
* * *
5266629 AGCAGATCTTGTCTTCATGTATTGACGTGAAATAGATCAAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* *
5266673 AACAGATCTTGTCTTCATGTATTGGCGTGAAATAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*
5266717 AGCAGA--------TCATGTATTGGCGTGAAATAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * *
5266753 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
* * * *
5266797 AGCAGATCTTGTCTTTCCA--TACTGGTGGCGAAGTAGATCGAGGAA
1 AGCAGATCTTGTC-TT-CATGTATTGG-CGTGAAGTAGATCGAAGAA
* * *
5266842 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGAG
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
*** * * *
5266886 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG-A
1 AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAA
* * * *
5266930 TGACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGGAT
1 AG-CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA-GAA
**
5266976 AGCAGATCTTGTCTTCATGTATCAGCAGTGAAGTAGATCGAA
1 AGCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCGAA
5267018 AATACAAGTC
Statistics
Matches: 463, Mismatches: 84, Indels: 39
0.79 0.14 0.07
Matches are distributed among these distances:
36 36 0.08
43 2 0.00
44 226 0.49
45 183 0.40
46 16 0.03
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAA
Found at i:5266521 original size:89 final size:88
Alignment explanation
Indices: 5266435--5267017 Score: 605
Period size: 89 Copynumber: 6.6 Consensus size: 88
5266425 TACTGGTGAC
5266435 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGAAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGAAG
*** * **
5266500 ATCTTGTCTTCCCATACTGGTGGT
66 ATCTTGTCTTCATGTATTGG-CAT
* * *
5266524 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGCAGATCGAAGAAAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGAAG
* * * * *
5266589 ATCCTGTCTTCCTATATTGGTAGC
66 ATCTTGTCTTCATGTATTGGCA-T
* * * * *
5266613 GAAGTGGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACGTGAAATAGATCAAAGAAA-ACA
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGA-A
*
5266677 GATCTTGTCTTCATGTATTGGCGT
65 GATCTTGTCTTCATGTATTGGCAT
* * *
5266701 GAAATAGATCGAAGAAAGCAGA--------TCATGTATTGGCGTGAAATAGATCGAAGAAAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGAAG
5266758 ATCTTGTCTTCATGTATTGGCAT
66 ATCTTGTCTTCATGTATTGGCAT
* * * * * *
5266781 GAAGTAGATCAAAGATAGCAGATCTTGTCTTTCCA--TACTGGTGGCGAAGTAGATCGAGGAAAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTC-TT-CATGTATTGG-CGTGAAGTAGATCGAAGAAAG
*
5266844 CAGATCTTGTCTTCATGTATTGGCAT
63 AAGATCTTGTCTTCATGTATTGGCAT
* * *** * * * *
5266870 GAAGTAGATCAAAGAGAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG-ATGAC
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGA-
5266934 AGATCTTGTCTTCATGTATTGGCAT
64 AGATCTTGTCTTCATGTATTGGCAT
* * **
5266959 GAAGTAGATCAAAGGATAGCAGATCTTGTCTTCATGTATCAGCAGTGAAGTAGATCGAA
1 GAAGTAGATCGAA-GAAAGCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCGAA
5267018 AATACAAGTC
Statistics
Matches: 423, Mismatches: 52, Indels: 37
0.83 0.10 0.07
Matches are distributed among these distances:
80 72 0.17
87 1 0.00
88 28 0.07
89 285 0.67
90 37 0.09
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (88 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGAAG
ATCTTGTCTTCATGTATTGGCAT
Found at i:5266734 original size:36 final size:36
Alignment explanation
Indices: 5266687--5266760 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5266677 GATCTTGTCT
5266687 TCATGTATTGGCGTGAAATAGATCGAAGAAAGCAGA
1 TCATGTATTGGCGTGAAATAGATCGAAGAAAGCAGA
5266723 TCATGTATTGGCGTGAAATAGATCGAAGAAAGCAGA
1 TCATGTATTGGCGTGAAATAGATCGAAGAAAGCAGA
5266759 TC
1 TC
5266761 TTGTCTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (36 bp):
TCATGTATTGGCGTGAAATAGATCGAAGAAAGCAGA
Found at i:5270652 original size:23 final size:21
Alignment explanation
Indices: 5270624--5270671 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
5270614 AAATTTAGTA
5270624 TATTTTAA-ATTTATTAACAATAT
1 TATTTTAATA-TTA-TAAC-ATAT
5270647 TATTTTAATATTATAACATAT
1 TATTTTAATATTATAACATAT
5270668 TATT
1 TATT
5270672 ATTCTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.33
22 4 0.17
23 11 0.46
24 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTTAATATTATAACATAT
Found at i:5271699 original size:7 final size:8
Alignment explanation
Indices: 5271687--5271720 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5271677 ATAATAAAAT
5271687 ATAT-AAA
1 ATATCAAA
5271694 ATAT-AAA
1 ATATCAAA
5271701 ATATCAAA
1 ATATCAAA
5271709 ATATCAAA
1 ATATCAAA
5271717 ATAT
1 ATAT
5271721 TAGAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATCAAA
Found at i:5271727 original size:16 final size:15
Alignment explanation
Indices: 5271680--5271727 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
5271670 GATGTGAATA
5271680 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
*
5271696 ATAAAATATCAAAAT
1 ATAAAATATTAAAAT
*
5271711 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
5271727 A
1 A
5271728 ATAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:5271894 original size:20 final size:20
Alignment explanation
Indices: 5271842--5271898 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
5271832 ATACTACATT
*
5271842 AATATGTACATATATAAAAAA
1 AATATGTACATA-ATATAAAA
* * *
5271863 AATACGT-GATAATATTAAA
1 AATATGTACATAATATAAAA
5271882 AATATGTACATAATATA
1 AATATGTACATAATATA
5271899 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AATATGTACATAATATAAAA
Found at i:5271987 original size:25 final size:25
Alignment explanation
Indices: 5271871--5272089 Score: 129
Period size: 25 Copynumber: 9.0 Consensus size: 25
5271861 AAAATACGTG
* *
5271871 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
5271896 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
5271921 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
5271943 ATAACATGTAAAAAAAATATATAAATAAT
1 ATAATAT-T---AAAGATATATACATAAT
*
5271972 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
5271997 ATAGTA-TAAATATATATACGTAAT
1 ATAATATTAAAGATATATACATAAT
* *
5272021 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
5272044 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
5272066 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
5272089 A
1 A
5272090 ACAAAAAAGG
Statistics
Matches: 152, Mismatches: 28, Indels: 30
0.72 0.13 0.14
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 28 0.18
24 27 0.18
25 46 0.30
28 1 0.01
29 19 0.12
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:5272012 original size:47 final size:44
Alignment explanation
Indices: 5271956--5272087 Score: 108
Period size: 47 Copynumber: 2.9 Consensus size: 44
5271946 ACATGTAAAA
5271956 AAAATATATAAATAATATAATATTAAAGATATATACATAAAATAGT
1 AAAATATATAAATAATATAATATT-AAGA-ATATACATAAAATAGT
* * * *
5272002 ATAAATATATATACGTAATATAGA-ATTTAA-AATATACCTAATATATT
1 A-AAATATATA-A-ATAATATA-ATA-TTAAGAATATACATAAAATAGT
* *
5272049 AAAAGAATATATATAATATAATATTAAGAAATATA-ATAA
1 AAAA-TATATAAATAATATAATATTAAG-AATATACATAA
5272088 TAACAAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
44 5 0.07
45 11 0.16
46 10 0.14
47 28 0.41
48 2 0.03
49 10 0.14
50 3 0.04
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (44 bp):
AAAATATATAAATAATATAATATTAAGAATATACATAAAATAGT
Found at i:5272089 original size:45 final size:46
Alignment explanation
Indices: 5271871--5272089 Score: 128
Period size: 49 Copynumber: 4.5 Consensus size: 46
5271861 AAAATACGTG
* *
5271871 ATAATATTAA-AAATATGTACATAATATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAGAAATA--TACATAATATAGT-ATAAAAAT--ATATATAAT
* * * *
5271921 AT-A-GTTAAGATATATACATAAGATAACATGTAAAAAAAATATATAAATAAT
1 ATAATATTAAGAAATATACAT-A-AT-ATA-GT-ATAAAAATATAT--ATAAT
* * *
5271972 ATAATATTAAAGATATATACATAAAATAGTATAAATATATATACGTAAT
1 ATAATATT-AAGAAATATACATAATATAGTATAAAAATATATA--TAAT
* * *
5272021 ATAGA-ATTTA-AAATATACCTAATATATTA-AAAGAATATATATAAT
1 ATA-ATATTAAGAAATATACATAATATAGTATAAA-AATATATATAAT
5272066 ATAATATTAAGAAATATA-ATAATA
1 ATAATATTAAGAAATATACATAATA
5272090 ACAAAAAAGG
Statistics
Matches: 133, Mismatches: 20, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
44 1 0.01
45 16 0.12
46 10 0.08
47 28 0.21
48 6 0.05
49 30 0.23
50 7 0.05
51 17 0.13
52 2 0.02
53 3 0.02
54 13 0.10
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (46 bp):
ATAATATTAAGAAATATACATAATATAGTATAAAAATATATATAAT
Found at i:5272728 original size:30 final size:30
Alignment explanation
Indices: 5272578--5272752 Score: 237
Period size: 30 Copynumber: 5.8 Consensus size: 30
5272568 TAGGTACAAG
* *
5272578 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
5272608 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
5272638 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
5272668 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
5272698 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
5272728 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
5272753 TGAGAAAAGT
Statistics
Matches: 131, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
29 2 0.02
30 129 0.98
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:5273559 original size:75 final size:75
Alignment explanation
Indices: 5273459--5273712 Score: 343
Period size: 75 Copynumber: 3.3 Consensus size: 75
5273449 CGACATGTAA
* *
5273459 ACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGA-TTTTTGAAAAGCAGAAATTGAAAA-CG
1 ACCC-AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAATAG
**
5273522 CCTCAGCGTGTG
65 -CTCAGCACGTG
*
5273534 ACCCGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATA
1 ACCC-AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAGCAGAAATTGAAAATA
5273599 GCTCAGCACGTG
64 GCTCAGCACGTG
* *
5273611 A-GCAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAG
1 ACCCAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAAAGCAGAAATTGAAAATAG
5273675 CTCAGCACGTG
65 CTCAGCACGTG
** *
5273686 AGCAAAGGCTCAACTCACTTCTCGCAA
1 A-CCCAGGCTCAACTCACCTCTCGCAA
5273713 AAGTAGATTT
Statistics
Matches: 160, Mismatches: 13, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
74 2 0.01
75 102 0.64
76 1 0.01
77 54 0.34
78 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (75 bp):
ACCCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAATAGC
TCAGCACGTG
Found at i:5273803 original size:14 final size:14
Alignment explanation
Indices: 5273784--5273834 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
5273774 GAGTTGATTT
*
5273784 TTGAAAAATATAAA
1 TTGAAAAATAGAAA
5273798 TTGAAAAAAATAGAAA
1 TTG--AAAAATAGAAA
**
5273814 TTGAAAAGCAGAAA
1 TTGAAAAATAGAAA
5273828 TT-AAAAA
1 TTGAAAAA
5273835 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 14 0.45
16 13 0.42
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.22
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:5273808 original size:16 final size:16
Alignment explanation
Indices: 5273787--5273820 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5273777 TTGATTTTTG
*
5273787 AAAAATATAAATTGAA
1 AAAAATAGAAATTGAA
5273803 AAAAATAGAAATTGAA
1 AAAAATAGAAATTGAA
5273819 AA
1 AA
5273821 GCAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAATAGAAATTGAA
Found at i:5274001 original size:72 final size:73
Alignment explanation
Indices: 5273857--5274030 Score: 260
Period size: 72 Copynumber: 2.4 Consensus size: 73
5273847 TGAGCCGAGA
* * * * * *
5273857 CTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGTACCTCAACGTG
5273922 TCCTGAGG
66 TCCTGAGG
*
5273930 CTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGTACCTCAACGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGTACCTCAACGTG
*
5273994 TCTTGAGG
66 TCCTGAGG
*
5274002 CTCAACTCATCTCTCGCAATATGAGTTGA
1 CTCAACTCACCTCTCGCAATATGAGTTGA
5274031 CTTTCCTTGA
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 64 0.70
73 27 0.30
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (73 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGTACCTCAACGTG
TCCTGAGG
Found at i:5282356 original size:7 final size:7
Alignment explanation
Indices: 5282344--5282376 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
5282334 ATAATAAAAT
5282344 ATATAAA
1 ATATAAA
5282351 ATATAAA
1 ATATAAA
5282358 ATATAAA
1 ATATAAA
5282365 ATATCAAA
1 ATAT-AAA
5282373 ATAT
1 ATAT
5282377 TAGAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
ATATAAA
Found at i:5282383 original size:23 final size:23
Alignment explanation
Indices: 5282332--5282383 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
5282322 ATAATGATGT
*
5282332 GAATAATAAAATATATAAAATATA
1 GAAT-ATAAAATATACAAAATATA
*
5282356 AAATATAAAATAT-CAAAATATTA
1 GAATATAAAATATACAAAATA-TA
5282379 GAATA
1 GAATA
5282384 ATAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 6 0.25
23 15 0.62
24 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
GAATATAAAATATACAAAATATA
Found at i:5282551 original size:20 final size:20
Alignment explanation
Indices: 5282499--5282555 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
5282489 ATACTACATC
*
5282499 AATATGTACATATATAAAAAA
1 AATATGTACATA-ATATAAAA
* * *
5282520 AATACGT-GATAATATTAAA
1 AATATGTACATAATATAAAA
5282539 AATATGTACATAATATA
1 AATATGTACATAATATA
5282556 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AATATGTACATAATATAAAA
Found at i:5282562 original size:25 final size:25
Alignment explanation
Indices: 5282534--5282582 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5282524 CGTGATAATA
**
5282534 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATACATACATAATATAGTG
5282559 TTAAAAATACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
5282583 TAAGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:5282627 original size:29 final size:29
Alignment explanation
Indices: 5282595--5282653 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5282585 AGATATATGC
*
5282595 ATAAGATAACATGTAAA-ATATATATATAA
1 ATAAGATAACAT-TAAAGATATATACATAA
* *
5282624 ATAATATAATATTAAAGATATATACATAA
1 ATAAGATAACATTAAAGATATATACATAA
5282653 A
1 A
5282654 ATAGTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (29 bp):
ATAAGATAACATTAAAGATATATACATAA
Found at i:5282644 original size:25 final size:25
Alignment explanation
Indices: 5282616--5282749 Score: 77
Period size: 25 Copynumber: 5.6 Consensus size: 25
5282606 TGTAAAATAT
5282616 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * * *
5282641 ATATATACATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
5282666 ATATATATACGTAATATAGA-ATTTAA-
1 ATATATA-A-ATAATATA-ATATTAAAG
** *
5282692 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
5282714 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
5282737 AAATAT-AATAATA
1 ATATATAAATAATA
5282750 ACAAAAAAGG
Statistics
Matches: 82, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.15
23 18 0.22
24 5 0.06
25 32 0.39
26 1 0.01
27 10 0.12
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:5282671 original size:27 final size:27
Alignment explanation
Indices: 5282540--5282684 Score: 92
Period size: 25 Copynumber: 5.6 Consensus size: 27
5282530 AATATTAAAA
* * *
5282540 ATATGTACATAATATAGTGTTAAA-A-
1 ATATATACATAATATAGTATAAAATAT
* *
5282565 ATACATACATAATATAGT-TAAGATAT
1 ATATATACATAATATAGTATAAAATAT
* *
5282591 ATGCATA-AGATAACAT-G--TAAAATAT
1 AT--ATATACATAATATAGTATAAAATAT
* * * *
5282616 ATATATAAATAATATAATAT-TAA-AG
1 ATATATACATAATATAGTATAAAATAT
*
5282641 ATATATACATAAAATAGTATAAAATAT
1 ATATATACATAATATAGTATAAAATAT
*
5282668 ATATATACGTAATATAG
1 ATATATACATAATATAG
5282685 AATTTAAAAT
Statistics
Matches: 90, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
23 3 0.03
24 10 0.11
25 44 0.49
26 7 0.08
27 24 0.27
28 2 0.02
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (27 bp):
ATATATACATAATATAGTATAAAATAT
Found at i:5283278 original size:30 final size:30
Alignment explanation
Indices: 5283244--5283355 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 30
5283234 AGTGGTGGTA
*
5283244 GAGCAAGTGTGGTTAGTGGAGTAGGTAATG
1 GAGCAAGTGTGGCTAGTGGAGTAGGTAATG
* * **
5283274 GAGCAAGTGTGGCTAGTGGATTTGGTGGTG
1 GAGCAAGTGTGGCTAGTGGAGTAGGTAATG
* **
5283304 GAG-AAGGTGTGGCTAGTGGAGTTGGTGGTG
1 GAGCAA-GTGTGGCTAGTGGAGTAGGTAATG
*
5283334 GA-AAAGGTGTGGCTAGTGGAGT
1 GAGCAA-GTGTGGCTAGTGGAGT
5283356 TGGTGGTGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
29 2 0.03
30 72 0.97
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.27
Consensus pattern (30 bp):
GAGCAAGTGTGGCTAGTGGAGTAGGTAATG
Found at i:5283344 original size:60 final size:60
Alignment explanation
Indices: 5283236--5283380 Score: 186
Period size: 60 Copynumber: 2.4 Consensus size: 60
5283226 TAGGTACAAG
* * * *
5283236 TGGTGGTAGAGCAA-GTGTGGTTAGTGGAGTAGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAG-AAGGTGTGGCTAGTGGAGTAGGTAATGGAGAAAGTGTGGCTAGTGGAGT
* **
5283296 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTAGGTAATGGAGAAA-GTGTGGCTAGTGGAGT
*
5283356 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAGAAGGTGTGGCTAGT
5283381 TGAGAAAAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 4 0.05
60 71 0.95
ACGTcount: A:0.21, C:0.04, G:0.48, T:0.28
Consensus pattern (60 bp):
TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTAGGTAATGGAGAAAGTGTGGCTAGTGGAGT
Found at i:5283356 original size:30 final size:30
Alignment explanation
Indices: 5283280--5283380 Score: 184
Period size: 30 Copynumber: 3.4 Consensus size: 30
5283270 AATGGAGCAA
* *
5283280 GTGTGGCTAGTGGATTTGGTGGTGGAGAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
5283310 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
5283340 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
5283370 GTGTGGCTAGT
1 GTGTGGCTAGT
5283381 TGAGAAAAGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.18, C:0.04, G:0.50, T:0.29
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
Found at i:5285583 original size:19 final size:20
Alignment explanation
Indices: 5285561--5285598 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5285551 AGGTATATGT
5285561 ATCAACTAAAAA-ATAAAAA
1 ATCAACTAAAAATATAAAAA
**
5285580 ATCATTTAAAAATATAAAA
1 ATCAACTAAAAATATAAAA
5285599 CTCTCACGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (20 bp):
ATCAACTAAAAATATAAAAA
Found at i:5289031 original size:43 final size:43
Alignment explanation
Indices: 5288935--5289258 Score: 271
Period size: 43 Copynumber: 7.7 Consensus size: 43
5288925 ATCCGTTACT
* *
5288935 CGGTGGATTAAGCACTTAGCAACCACC-TT-A-AATTC-AGTGATA
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTCACAA-TCAAG-GATA
* *
5288977 C-GTGGAATCAGCACATAGCAACCCCTTTCACAGTCAAGGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTTCACAATCAAGGATA
* * *
5289019 CGGTGGAATCAGCACTTAGCAACCACCTCT-ATATTC-AGTGATA
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTCACAATCAAG-GATA
* *
5289062 CGG-GGAATCAGCA-TATAGTAACCCCTTTCACAATCAAAGATA
1 CGGTGGAATCAGCACT-TAGCAACCCCTTTCACAATCAAGGATA
* * *
5289104 CGGTGGAATCAGCACTTAGCAACCACCTCT-ATATTC-AGTGATA
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTCACAATCAAG-GATA
* *
5289147 CGG-GGAATCAGCACATAGCAACCCCTTTCACAATCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTTCACAATCAAGGATA
* * * ** *
5289189 CGGTAGAATCAGCACTTAGCAACCACCTTTGA-AGTCAATAATT
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTCACAATCAAGGATA
* *
5289232 CAG-GGAATCAACACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCCCTT
5289259 GGGAAATCTG
Statistics
Matches: 231, Mismatches: 33, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
40 2 0.01
41 34 0.15
42 88 0.38
43 92 0.40
44 15 0.06
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCCCTTTCACAATCAAGGATA
Found at i:5289240 original size:170 final size:169
Alignment explanation
Indices: 5288935--5289258 Score: 472
Period size: 170 Copynumber: 1.9 Consensus size: 169
5288925 ATCCGTTACT
* *
5288935 CGGTGGATTAAGCACTTAGCAACCACCTTAAATTCAGTGATACGTGGAATCAGCACATAGCAACC
1 CGGTGGAATAAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
* * * * * * *
5289000 CCTTTCACAGTCAAGGATACGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGG
66 CCTTTCACAATCAAAGATACGGTAGAATCAGCACTTAGCAACCACCTCTATAGTCAATAATACAG
* *
5289065 GGAATCAGCA-TATAGTAACCCCTTTCACAATCAAAGATA
131 GGAATCAACACT-TAGCAACCCCTTTCACAATCAAAGATA
* *
5289104 CGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATAAGCACTTAGCAACCACCT-TAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
* *
5289169 CCCTTTCACAATCAAAGATACGGTAGAATCAGCACTTAGCAACCACCTTTGA-AGTCAATAATTC
65 CCCTTTCACAATCAAAGATACGGTAGAATCAGCACTTAGCAACCACCTCT-ATAGTCAATAATAC
5289233 AGGGAATCAACACTTAGCAACCCCTT
129 AGGGAATCAACACTTAGCAACCCCTT
5289259 GGGAAATCTG
Statistics
Matches: 137, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
169 26 0.19
170 109 0.80
171 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (169 bp):
CGGTGGAATAAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAAGATACGGTAGAATCAGCACTTAGCAACCACCTCTATAGTCAATAATACAG
GGAATCAACACTTAGCAACCCCTTTCACAATCAAAGATA
Found at i:5289258 original size:85 final size:85
Alignment explanation
Indices: 5288935--5289216 Score: 476
Period size: 85 Copynumber: 3.3 Consensus size: 85
5288925 ATCCGTTACT
* * * *
5288935 CGGTGGATTAAGCACTTAGCAACCACCT-TAAATTCAGTGATACGTGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGGGGAATCAGCACATAGCAAC
* *
5288999 CCCTTTCACAGTCAAGGATA
66 CCCTTTCACAATCAAAGATA
* *
5289019 CGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGGGGAATCAGCATATAGTAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGGGGAATCAGCACATAGCAAC
5289084 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
5289104 CGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGGGGAATCAGCACATAGCAAC
5289169 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
*
5289189 CGGTAGAATCAGCACTTAGCAACCACCT
1 CGGTGGAATCAGCACTTAGCAACCACCT
5289217 TTGAAGTCAA
Statistics
Matches: 186, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
84 26 0.14
85 160 0.86
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTCTATATTCAGTGATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:5293714 original size:18 final size:18
Alignment explanation
Indices: 5293691--5293754 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
5293681 ACATATCAAC
5293691 ATTTAATTAATTTTTAAA
1 ATTTAATTAATTTTTAAA
* *
5293709 ATTTAAGTATTTTTTAAA
1 ATTTAATTAATTTTTAAA
* * *
5293727 TATTT-TTTATTTTTTGAA
1 -ATTTAATTAATTTTTAAA
*
5293745 ATTTATTTAA
1 ATTTAATTAA
5293755 AAAATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 4 0.11
18 30 0.79
19 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTTAATTAATTTTTAAA
Found at i:5295670 original size:19 final size:21
Alignment explanation
Indices: 5295646--5295685 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5295636 TTAAGATATT
5295646 ATTTCA-ATAAAATAT-TTAA
1 ATTTCATATAAAATATATTAA
5295665 ATTTCATATAAAATATATTAA
1 ATTTCATATAAAATATATTAA
5295686 TTATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTCATATAAAATATATTAA
Found at i:5295687 original size:20 final size:19
Alignment explanation
Indices: 5295641--5295687 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
5295631 TTTAATTAAG
5295641 ATATT-ATTTCAATAAAAT
1 ATATTAATTTCAATAAAAT
5295659 AT-TTAAATTTCATATAAAAT
1 ATATT-AATTTCA-ATAAAAT
5295679 ATATTAATT
1 ATATTAATT
5295688 ATATTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 2 0.08
19 6 0.24
20 13 0.52
21 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTAATTTCAATAAAAT
Found at i:5309935 original size:44 final size:44
Alignment explanation
Indices: 5309813--5309943 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 44
5309803 TGACCTACTG
* * * * * *
5309813 CAACTTCAGAG-GTATATGATTCATCGTTTTAATCCGCTCCACTT
1 CAACTTCAGAGAG-ATAAGATTAATAGCTTTAATCTGCTCCACTA
* * * *
5309857 CAACTTCAGGGAGATAGGATTAATAGCTTCAATCTACTCCACTA
1 CAACTTCAGAGAGATAAGATTAATAGCTTTAATCTGCTCCACTA
** *
5309901 CAACTTCAGAGAGATAAGATTTGTGGCTTTAATCTGCTCCACT
1 CAACTTCAGAGAGATAAGATTAATAGCTTTAATCTGCTCCACT
5309944 GCTCTACTGC
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
44 69 0.99
45 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATTAATAGCTTTAATCTGCTCCACTA
Found at i:5310191 original size:55 final size:55
Alignment explanation
Indices: 5310107--5310218 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
5310097 ATTTTTTAAC
* *
5310107 CTGCTCCACTGCAACTTCAAGGAGATAAGGTTTGATGTGATCTGCTCTACTGCAA
1 CTGCTCCACTACAACTTCAAGGAGATAAGGTTTGATGTGATCTACTCTACTGCAA
*
5310162 CTGCTCCACTACAACTTCAGGGAGATAAGGTTTGATGTGATCTACTCTACTGCAA
1 CTGCTCCACTACAACTTCAAGGAGATAAGGTTTGATGTGATCTACTCTACTGCAA
5310217 CT
1 CT
5310219 TCAAAGAGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (55 bp):
CTGCTCCACTACAACTTCAAGGAGATAAGGTTTGATGTGATCTACTCTACTGCAA
Found at i:5321136 original size:36 final size:36
Alignment explanation
Indices: 5321089--5321160 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
5321079 TGAATTCTAT
5321089 CGAGTTCCGGTGGTAATGCCAATCGATAAGCGACCG
1 CGAGTTCCGGTGGTAATGCCAATCGATAAGCGACCG
5321125 CGAGTTCCGGTGGTAATGCCAATCGATAAGCGACCG
1 CGAGTTCCGGTGGTAATGCCAATCGATAAGCGACCG
5321161 GTCTAATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (36 bp):
CGAGTTCCGGTGGTAATGCCAATCGATAAGCGACCG
Found at i:5323734 original size:22 final size:22
Alignment explanation
Indices: 5323706--5323751 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
5323696 ATTCACATAC
5323706 AATTGGCACTGCCTGTATATTT
1 AATTGGCACTGCCTGTATATTT
*
5323728 AATTGGCACTGCCTGTATCTTT
1 AATTGGCACTGCCTGTATATTT
5323750 AA
1 AA
5323752 CTCAGATACC
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:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
AATTGGCACTGCCTGTATATTT
Found at i:5325318 original size:3 final size:3
Alignment explanation
Indices: 5325310--5325334 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5325300 GGGAATCGGT
5325310 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
5325335 CTTGAGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:5326309 original size:5 final size:5
Alignment explanation
Indices: 5326299--5326323 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5326289 CTAATATTTT
5326299 CAATA CAATA CAATA CAATA CAATA
1 CAATA CAATA CAATA CAATA CAATA
5326324 AACATTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
CAATA
Found at i:5335015 original size:12 final size:12
Alignment explanation
Indices: 5335000--5335032 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5334990 GTAATTAAAA
5335000 ACTTGATT-AATG
1 ACTTGATTCAA-G
5335012 ACTTGATTCAAG
1 ACTTGATTCAAG
5335024 ACTTGATTC
1 ACTTGATTC
5335033 CTAAATGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.90
13 2 0.10
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (12 bp):
ACTTGATTCAAG
Found at i:5338277 original size:12 final size:12
Alignment explanation
Indices: 5338262--5338294 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5338252 GTAATTAAAA
5338262 ACTTGATT-AATG
1 ACTTGATTCAA-G
5338274 ACTTGATTCAAG
1 ACTTGATTCAAG
5338286 ACTTGATTC
1 ACTTGATTC
5338295 CTAAATGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.90
13 2 0.10
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (12 bp):
ACTTGATTCAAG
Found at i:5339535 original size:22 final size:25
Alignment explanation
Indices: 5339510--5339561 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5339500 ACATTTACTT
* *
5339510 TATAATT-TTT-TAA-TAAATTTCA
1 TATAATTATTTGTAATTAAATCTAA
5339532 TATAATTATTTGTAATTAAATCTAA
1 TATAATTATTTGTAATTAAATCTAA
5339557 TATAA
1 TATAA
5339562 ATAAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 3 0.12
24 3 0.12
25 12 0.48
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (25 bp):
TATAATTATTTGTAATTAAATCTAA
Found at i:5340665 original size:17 final size:16
Alignment explanation
Indices: 5340620--5340653 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5340610 CAGATCATTT
*
5340620 AATTAAATTTTTTTAA
1 AATTTAATTTTTTTAA
5340636 AATTTAAGTTTTTTTAA
1 AATTTAA-TTTTTTTAA
5340653 A
1 A
5340654 TTTCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AATTTAATTTTTTTAA
Found at i:5341610 original size:28 final size:29
Alignment explanation
Indices: 5341572--5341646 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
5341562 AAAAAATGTA
5341572 TAAAATTTATATATTATCTCTTGAATA-AT
1 TAAAA-TTATATATTATCTCTTGAATATAT
* * * * *
5341601 TTAAATTATA-ATGATATTTTTAATATAT
1 TAAAATTATATATTATCTCTTGAATATAT
5341629 TAAAATTAATATATTATC
1 TAAAATT-ATATATTATC
5341647 ACTTTTACTA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
27 11 0.31
28 13 0.37
29 7 0.20
30 4 0.11
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (29 bp):
TAAAATTATATATTATCTCTTGAATATAT
Found at i:5351004 original size:23 final size:23
Alignment explanation
Indices: 5350960--5351004 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5350950 TCTTATTTTG
* *
5350960 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
5350983 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
5351005 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:5351481 original size:19 final size:19
Alignment explanation
Indices: 5351457--5351498 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5351447 TATCCTTTTT
*
5351457 TATAATCTA-TATATATGTA
1 TATAAT-TATTATATATATA
5351476 TATAATTATTATATATATA
1 TATAATTATTATATATATA
5351495 TATA
1 TATA
5351499 TGTACATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TATAATTATTATATATATA
Found at i:5351878 original size:4 final size:4
Alignment explanation
Indices: 5351869--5351903 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
5351859 TTGCATGTCA
*
5351869 TTAT TTAT TTAT TTAT TTAT TTAT TCAT ATTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TT
5351904 CTATATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:5353094 original size:28 final size:28
Alignment explanation
Indices: 5353041--5353101 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
5353031 ATCAAACATG
* * *
5353041 AATGATATAAATAGTCTTTAAATTTTTA
1 AATGATATAAATAGTATATAAATTTTAA
*
5353069 AATGATATAAATA-TATATATATTTTTAA
1 AATGATATAAATAGTATATA-AATTTTAA
5353097 AATGA
1 AATGA
5353102 ACAAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.44
Consensus pattern (28 bp):
AATGATATAAATAGTATATAAATTTTAA
Found at i:5354293 original size:26 final size:26
Alignment explanation
Indices: 5354264--5354323 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
5354254 TTAGAATGTA
* * *
5354264 AAAATTACATTAAAAACAAAAATATC
1 AAAATTAAAATAAAAACAAAAATAGC
* *
5354290 AAAATAAAAATAAAAATAAAAATAGC
1 AAAATTAAAATAAAAACAAAAATAGC
*
5354316 TAAATTAA
1 AAAATTAA
5354324 TAGAAATAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAATTAAAATAAAAACAAAAATAGC
Found at i:5354331 original size:6 final size:6
Alignment explanation
Indices: 5354274--5354313 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
5354264 AAAATTACAT
*
5354274 TAAAAA CAAAAA TATCAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TA--AAAA TAAAAA TAAAAA TAAAAA TA
5354314 GCTAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 24 0.80
8 6 0.20
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:5360457 original size:18 final size:18
Alignment explanation
Indices: 5360434--5360470 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5360424 AAACTCTTTC
5360434 AAGAGTAATTGAATCCTA
1 AAGAGTAATTGAATCCTA
5360452 AAGAGTAATTGAATCCTA
1 AAGAGTAATTGAATCCTA
5360470 A
1 A
5360471 TAAAACTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (18 bp):
AAGAGTAATTGAATCCTA
Found at i:5366032 original size:20 final size:20
Alignment explanation
Indices: 5366007--5366046 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5365997 AAGGTAGTCA
*
5366007 ACTTTTTTTTTGCTCTTTTT
1 ACTTTTTTTGTGCTCTTTTT
*
5366027 ACTTTTTTTGTGCTGTTTTT
1 ACTTTTTTTGTGCTCTTTTT
5366047 TTTTTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.12, G:0.10, T:0.72
Consensus pattern (20 bp):
ACTTTTTTTGTGCTCTTTTT
Found at i:5366052 original size:20 final size:19
Alignment explanation
Indices: 5366009--5366052 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5365999 GGTAGTCAAC
5366009 TTTTTTTTTGCTCTTTTTA
1 TTTTTTTTTGCTCTTTTTA
* *
5366028 CTTTTTTTGTGCTGTTTTT-
1 -TTTTTTTTTGCTCTTTTTA
5366047 TTTTTT
1 TTTTTT
5366053 AAAGAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTGCTCTTTTTA
Found at i:5366676 original size:29 final size:31
Alignment explanation
Indices: 5366612--5366705 Score: 156
Period size: 29 Copynumber: 3.1 Consensus size: 31
5366602 GGCAAATTAC
*
5366612 AAGAGTAATTGAATCCTAATTAAAACTCTTTC
1 AAGAGTAATTGAATCCTAA-TAAAACTCTTTA
5366644 AAGAGTAATTGAATCCT-A-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
5366673 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
5366704 AA
1 AA
5366706 ATTATCTAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
29 27 0.46
30 1 0.02
31 14 0.24
32 17 0.29
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:5370131 original size:18 final size:18
Alignment explanation
Indices: 5370093--5370132 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5370083 ATAAATATGA
*
5370093 TTGTATTGAATATTGCTT
1 TTGTATTGAATATTGATT
5370111 TTGTATTGAAT-TTGATAT
1 TTGTATTGAATATTGAT-T
5370129 TTGT
1 TTGT
5370133 CTATGTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (18 bp):
TTGTATTGAATATTGATT
Found at i:5376348 original size:25 final size:25
Alignment explanation
Indices: 5376320--5376370 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5376310 TGTAATTACG
5376320 TATGTAATCATTTTAACTCTCACCC
1 TATGTAATCATTTTAACTCTCACCC
5376345 TATGTAATCATTTTAACTCTCACCC
1 TATGTAATCATTTTAACTCTCACCC
5376370 T
1 T
5376371 CCCCTAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.41
Consensus pattern (25 bp):
TATGTAATCATTTTAACTCTCACCC
Found at i:5377160 original size:30 final size:30
Alignment explanation
Indices: 5377119--5377226 Score: 104
Period size: 30 Copynumber: 3.8 Consensus size: 30
5377109 AAAAAAAATT
5377119 ATTACATTTTGACCCCTAAACTTT-TCTAAA
1 ATTACATTTTGACCCCTAAACTTTCTC-AAA
*
5377149 ATTATATTTTGACCCCTAAACTTTCTC--A
1 ATTACATTTTGACCCCTAAACTTTCTCAAA
* *
5377177 A--A-A-TTTGACCCCGAAACTTCCTCAAA
1 ATTACATTTTGACCCCTAAACTTTCTCAAA
* * *
5377203 ATTACACTTTGGCCCCAAAACTTT
1 ATTACATTTTGACCCCTAAACTTT
5377227 TGCTGCATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
24 18 0.28
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
30 37 0.57
31 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (30 bp):
ATTACATTTTGACCCCTAAACTTTCTCAAA
Found at i:5377187 original size:24 final size:24
Alignment explanation
Indices: 5377156--5377205 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
5377146 AAAATTATAT
* *
5377156 TTTGACCCCTAAACTTTCTCAAAA
1 TTTGACCCCGAAACTTCCTCAAAA
5377180 TTTGACCCCGAAACTTCCTCAAAA
1 TTTGACCCCGAAACTTCCTCAAAA
5377204 TT
1 TT
5377206 ACACTTTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (24 bp):
TTTGACCCCGAAACTTCCTCAAAA
Found at i:5377554 original size:3 final size:3
Alignment explanation
Indices: 5377546--5377649 Score: 82
Period size: 3 Copynumber: 36.3 Consensus size: 3
5377536 GGCCGAACGG
5377546 AGA AGA AGA AGA A-A A-A AGA AGA A-A A-A AG- AGAA AGAA AGA AGGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AG-A AGA A-GA
* *
5377589 AGA AGA AGA AGA AGA AGA AGA AGAA AGA AAA AGA A-A A-A AGA AAA
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA
*
5377633 AGA A-A A-A AGA AAA AGA A
1 AGA AGA AGA AGA AGA AGA A
5377650 AAAAAATAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
2 18 0.21
3 57 0.66
4 12 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5377566 original size:13 final size:13
Alignment explanation
Indices: 5377546--5377653 Score: 112
Period size: 13 Copynumber: 8.1 Consensus size: 13
5377536 GGCCGAACGG
5377546 AGAAGAAGAAGAAA
1 AGAAGAAGAA-AAA
5377560 A-AAGAAGAAAAA
1 AGAAGAAGAAAAA
5377572 AG-AGAAAGAAAGAA
1 AGAAG-AAGAAA-AA
*
5377586 GGAAGAAGAAGAAGA
1 AGAAGAAGAA-AA-A
*
5377601 AGAAGAAGAAGAA
1 AGAAGAAGAAAAA
*
5377614 AGAAAAAGAAAAA
1 AGAAGAAGAAAAA
*
5377627 AGAAAAAGAAAAA
1 AGAAGAAGAAAAA
*
5377640 AGAAAAAGAAAAA
1 AGAAGAAGAAAAA
5377653 A
1 A
5377654 AATAAAAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
12 6 0.07
13 53 0.64
14 11 0.13
15 13 0.16
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAAAA
Found at i:5378479 original size:18 final size:18
Alignment explanation
Indices: 5378453--5378625 Score: 108
Period size: 17 Copynumber: 9.8 Consensus size: 18
5378443 ATCGAAAAAT
5378453 TCGTGTTTCAAAAAATTC
1 TCGTGTTTCAAAAAATTC
* *
5378471 TCTTGTTTC-AAAAATTT
1 TCGTGTTTCAAAAAATTC
*
5378488 TCGTGTTTTC-AAAAATTG
1 TCGTG-TTTCAAAAAATTC
* * *
5378506 TTGTGTTT-TAAAAATTT
1 TCGTGTTTCAAAAAATTC
* **
5378523 TCATGTTT-TTAAAATTC
1 TCGTGTTTCAAAAAATTC
* * * **
5378540 TTGTATTTGAAAAGTTTC
1 TCGTGTTTCAAAAAATTC
*
5378558 -CGTGTTTC-AAAAATTT
1 TCGTGTTTCAAAAAATTC
*
5378574 TCGTGTTTC-TAAAATTC
1 TCGTGTTTCAAAAAATTC
*
5378591 TCGTGTTTCAAAAAAAATC
1 TCGTGTTTC-AAAAAATTC
*
5378610 CCGTGTTTTCAAAAAA
1 TCGTG-TTTCAAAAAA
5378626 AATGTTGTGT
Statistics
Matches: 120, Mismatches: 28, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
16 5 0.04
17 67 0.56
18 28 0.23
19 16 0.13
20 4 0.03
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
TCGTGTTTCAAAAAATTC
Found at i:5378483 original size:17 final size:17
Alignment explanation
Indices: 5378453--5378604 Score: 135
Period size: 17 Copynumber: 8.8 Consensus size: 17
5378443 ATCGAAAAAT
5378453 TCGTGTTTCAAAAAATTC
1 TCGTGTTTC-AAAAATTC
* *
5378471 TCTTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTC
*
5378488 TCGTGTTTTCAAAAATTG
1 TCGTG-TTTCAAAAATTC
* * *
5378506 TTGTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTC
* **
5378523 TCATGTTTTTAAAATTC
1 TCGTGTTTCAAAAATTC
* * * *
5378540 TTGTATTTGAAAAGTT-
1 TCGTGTTTCAAAAATTC
*
5378556 TCCGTGTTTCAAAAATTT
1 T-CGTGTTTCAAAAATTC
*
5378574 TCGTGTTTCTAAAATTC
1 TCGTGTTTCAAAAATTC
5378591 TCGTGTTTCAAAAA
1 TCGTGTTTCAAAAA
5378605 AAATCCCGTG
Statistics
Matches: 107, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
16 1 0.01
17 82 0.77
18 24 0.22
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTC
Found at i:5378638 original size:19 final size:19
Alignment explanation
Indices: 5378592--5378642 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
5378582 CTAAAATTCT
5378592 CGTGTTTCAAAAAAAATCC
1 CGTGTTTCAAAAAAAATCC
**
5378611 CGTGTTTTCAAAAAAAATGT
1 CGTG-TTTCAAAAAAAATCC
*
5378631 TGTGTTTCAAAA
1 CGTGTTTCAAAA
5378643 TTCTTGCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (19 bp):
CGTGTTTCAAAAAAAATCC
Found at i:5386544 original size:16 final size:16
Alignment explanation
Indices: 5386523--5386558 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5386513 TTTGGTTCGT
5386523 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5386539 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5386555 TGTA
1 TGTA
5386559 ATAGCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5386815 original size:18 final size:17
Alignment explanation
Indices: 5386794--5386828 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5386784 TTATTATTAA
*
5386794 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5386812 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5386829 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5386942 original size:162 final size:163
Alignment explanation
Indices: 5386708--5387002 Score: 556
Period size: 162 Copynumber: 1.8 Consensus size: 163
5386698 TGGTAAATGA
* *
5386708 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATA
1 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATA
*
5386773 TTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT-ATAA
66 TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
5386837 TTAGCAGATATTTGTTTTGGTAAATTATTATTG
131 TTAGCAGATATTTGTTTTGGTAAATTATTATTG
5386870 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATA
1 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATA
5386935 TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
66 TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
5387000 TTA
131 TTA
5387003 ATATTCTTAT
Statistics
Matches: 129, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
162 122 0.95
163 7 0.05
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (163 bp):
TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATA
TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAGCAGATATTTGTTTTGGTAAATTATTATTG
Found at i:5386973 original size:16 final size:16
Alignment explanation
Indices: 5386936--5386977 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5386926 TTAATCATAT
*
5386936 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5386952 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5386967 TTAAAATATAT
1 TTAAAATATAT
5386978 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5386984 original size:14 final size:15
Alignment explanation
Indices: 5386945--5386986 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5386935 TTTAAACATA
*
5386945 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5386960 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5386974 A-TATAATTTAATA
1 ATTATAATTAAATA
5386987 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5387072 original size:162 final size:161
Alignment explanation
Indices: 5386733--5387073 Score: 377
Period size: 162 Copynumber: 2.1 Consensus size: 161
5386723 TTTAAATTTT
* * * *
5386733 AATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATAT
1 AATAACATAATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATAT
* * * * * ** *
5386798 ATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGATATTTGTTTTGGTAAATT
66 ATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTAACACATATATGATTTACTAAATC
* * * * * * *
5386863 ATTATTGTTATTGTTATTGTTATTTAAATTTT
131 ATTAATGATATTGATACTGTTA-TAAAATATA
* *
5386895 AATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATAT
1 AATAACATAATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATAT
* *
5386960 ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTC
66 ATTATAATTAAAATATATAATTTAATAAAATTCTT-ATAATTAACA--CATATATG-ATTTACT-
5387025 AAATCA-TAAT-ATA-TGATACTG-TA-AAAATATA
126 AAATCATTAATGATATTGATACTGTTATAAAATATA
5387056 AATTAACATAATTATTAT
1 AA-TAACATAATTATTAT
5387074 TAAATATATT
Statistics
Matches: 152, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
161 7 0.05
162 110 0.72
163 10 0.07
164 6 0.04
165 7 0.05
166 7 0.05
167 5 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (161 bp):
AATAACATAATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATAT
ATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTAACACATATATGATTTACTAAATC
ATTAATGATATTGATACTGTTATAAAATATA
Found at i:5387105 original size:14 final size:15
Alignment explanation
Indices: 5387056--5387107 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5387046 TAAAAATATA
5387056 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5387071 TATTAAATATATTAT
1 AATTAAATATATTAT
5387086 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5387099 AATTTAATA
1 AATTAAATA
5387108 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5387225 original size:14 final size:15
Alignment explanation
Indices: 5387176--5387227 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5387166 GTAAAATATA
5387176 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5387191 TATTAAATATATTAT
1 AATTAAATATATTAT
5387206 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5387219 AATTTAATA
1 AATTAAATA
5387228 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5387261 original size:120 final size:120
Alignment explanation
Indices: 5386939--5387465 Score: 961
Period size: 120 Copynumber: 4.4 Consensus size: 120
5386929 ATCATATTTA
5386939 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
5387004 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGT-AAAATATAAATT
5387060 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
5387125 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5387180 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
5387245 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
5387300 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
5387365 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* * *
5387420 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAA
5387466 AATAATTTAA
Statistics
Matches: 399, Mismatches: 4, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
119 7 0.02
120 282 0.71
121 110 0.28
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:5387345 original size:14 final size:15
Alignment explanation
Indices: 5387296--5387347 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5387286 GTAAAATATA
5387296 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5387311 TATTAAATATATTAT
1 AATTAAATATATTAT
5387326 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5387339 AATTTAATA
1 AATTAAATA
5387348 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5387559 original size:24 final size:25
Alignment explanation
Indices: 5387513--5387560 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
5387503 TATGAATTTG
5387513 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
5387539 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
5387561 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:5387565 original size:92 final size:91
Alignment explanation
Indices: 5387469--5387691 Score: 221
Period size: 92 Copynumber: 2.5 Consensus size: 91
5387459 GATTTAAAAT
* * *
5387469 AATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAA
1 AATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTT-AAATAATTAA
*
5387531 TTATTACATATAATTTAATAATTAATATTA
63 -TATTAAATATAATTTAATAATTAATATTA
* * * * *
5387561 AATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAATAATTAATAT
1 AATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAATAATTAATAT
5387626 TAAATATAATTTAATAA-T-ATA-T-
66 TAAATATAATTTAATAATTAATATTA
* * *
5387648 -ATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
5387692 CTAAAATCAA
Statistics
Matches: 116, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
86 21 0.18
87 19 0.16
88 2 0.02
89 3 0.03
90 1 0.01
91 25 0.22
92 40 0.34
93 5 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
AATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAATAATTAATAT
TAAATATAATTTAATAATTAATATTA
Found at i:5390613 original size:5 final size:5
Alignment explanation
Indices: 5390603--5390634 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5390593 CTTTTCAATC
5390603 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
5390635 AACATTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:5396721 original size:145 final size:144
Alignment explanation
Indices: 5396499--5397001 Score: 509
Period size: 145 Copynumber: 3.6 Consensus size: 144
5396489 TTCATCCTAT
* * * * * * * *
5396499 CCCACAGCAACTTCAGGGGTATAGGAATTGT-AGTTTCAATATACTCCACTACAACGTCAAGGAG
1 CCCACTGCAACTTCAGAGGTATAGGACTTATCA-TTTCAATCTACTCCACTGCAACTTCAGGGAG
* *
5396563 ATAAGATTTGTAGCTTGTAGCTTTAGTCTATTCCACTGCAACTTCAGAGAGATAAGACCTGCTAT
65 ATAAGATTAGTAGCTTGTAGCTTTAGTCTATTCCACTGCAACTTCAGGGAGATAAGACCT-CTAT
5396628 GGTAGATTTAATCTGA
129 GGTAGATTTAATCTGA
*
5396644 CCCACTGCAACTTCAGAGGTATAGGACTTATCGTTTCAATCTACTCCACTGCAACTTCAGGGAGA
1 CCCACTGCAACTTCAGAGGTATAGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGA
* **
5396709 TAAGATTAGTAGC-T-T--C---AATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-T-T-G
66 TAAGATTAGTAGCTTGTAGCTTTAGTCTATTCCACTGCAACTTCAGGGAGATAAGACCTCTATGG
* * *
5396762 TAGCTTCAATATG-
131 TAGATTTAATCTGA
* * * * * * * *
5396775 CTCTACTGCAATTTCAGAGAG-ATAAGA-TT-TGCTATCTTCGATCCACTCCGCTGGAATTTCAG
1 C-CCACTGCAACTTCAGAG-GTATAGGACTTAT-C-AT-TTCAATCTACTCCACTGCAACTTCAG
* * * * * *
5396837 AGAGATAAGATTTGTAGCTTGTAGTTTTAGTTTATTCTACTACAACTTCAGGGAGATAAGACCTA
61 GGAGATAAGATTAGTAGCTTGTAGCTTTAGTCTATTCCACTGCAACTTCAGGGAGATAAGACCT-
5396902 CTATGGTAGATTTAATCTGA
125 CTATGGTAGATTTAATCTGA
* *
5396922 CCCACTACAACTTCAGAGGTATCGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGA
1 CCCACTGCAACTTCAGAGGTATAGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGA
*
5396987 TAAGATTATTAGCTT
66 TAAGATTAGTAGCTT
5397002 CAATCTGCTC
Statistics
Matches: 284, Mismatches: 51, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
130 1 0.00
131 4 0.01
132 32 0.11
133 39 0.14
134 2 0.01
135 1 0.00
136 1 0.00
138 29 0.10
140 27 0.10
141 1 0.00
142 1 0.00
143 1 0.00
144 2 0.01
145 107 0.38
146 31 0.11
147 4 0.01
148 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (144 bp):
CCCACTGCAACTTCAGAGGTATAGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGA
TAAGATTAGTAGCTTGTAGCTTTAGTCTATTCCACTGCAACTTCAGGGAGATAAGACCTCTATGG
TAGATTTAATCTGA
Found at i:5397063 original size:89 final size:88
Alignment explanation
Indices: 5396955--5397360 Score: 320
Period size: 89 Copynumber: 4.4 Consensus size: 88
5396945 GGACTTATCA
* * *
5396955 TTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTAGCTTCAATCTGCTCTACTGCAA
1 TTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT-CTAACTTCAATCTGCTCCACTGCAA
*
5397020 CTTTAGAGAGATAAGATTTGCT-AT
65 CTTTAGGGAGATAAGATTTG-TAAT
* * * * *
5397044 TTTCAATCCACTCCACTGCAATTTCAAGGAGATAAGATCTGTAACTTCAATCTGCTCCACTACAA
1 TTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGAT-TCTAACTTCAATCTGCTCCACTGCAA
*
5397109 CTTCAGGGAGATAAGATTTGTAAT
65 CTTTAGGGAGATAAGATTTGTAAT
* * * * * *
5397133 TTGTAGCTTTAATCAATTCCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCC
1 TT-T--C---AATCTACTCCACTGCAACTTCAGGGAGATAAGATT--CTAACTTCAATCTGCTCC
***
5397198 ACTGCAACTTTAGGGAGATAAGATTTGTGGC
58 ACTGCAACTTTAGGGAGATAAGATTTGTAAT
* * *
5397229 TTT-AATCTGCTCCACTACAACTTCAGAGAGATAAGATTCACCATGATGACTTCAATC--CATCC
1 TTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT---C-T-A--ACTTCAATCTGC-T-C
* * ***
5397291 CACTGTAACTTCAGGG-GTATAAGATTTGTGGC
57 CACTGCAACTTTAGGGAG-ATAAGATTTGTAAT
* *
5397323 TTT-AATCTGCTCCACTGCAACTTCAGAGAGATAAGATT
1 TTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
5397361 TGCCATGATA
Statistics
Matches: 262, Mismatches: 37, Indels: 31
0.79 0.11 0.09
Matches are distributed among these distances:
88 1 0.00
89 106 0.40
90 3 0.01
91 1 0.00
92 3 0.01
93 2 0.01
94 74 0.28
95 29 0.11
96 43 0.16
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (88 bp):
TTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCTAACTTCAATCTGCTCCACTGCAAC
TTTAGGGAGATAAGATTTGTAAT
Found at i:5397122 original size:278 final size:278
Alignment explanation
Indices: 5396533--5397175 Score: 912
Period size: 278 Copynumber: 2.3 Consensus size: 278
5396523 GAATTGTAGT
* * *
5396533 TTCAATATACTCCACTACAACGTCAAGGAGATAAGATTTGTAGCTTGTAGCTTTAGTCTATTCCA
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAGTCTATTCCA
* * *
5396598 CTGCAACTTCAGAGAGATAAGACCTGCTATGGTAGATTTAATCTGACCCACTGCAACTTCAGAGG
66 CTGCAACTTCAGGGAGATAAGACCTACTATGGTAGATTTAATCTGACCCACTACAACTTCAGAGG
*
5396663 TATAGGACTTATCGTTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAAT
131 TATAGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAAT
* ** *
5396728 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATATGCTCTACTGCAATTTCAGA
196 CTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATACACTCCACTGCAATTTCAGA
* *
5396793 GAGATAAGATTTGCTATC
261 GAGATAAGATCTGCTAAC
* * * ** * * * * *
5396811 TTCGATCCACTCCGCTGGAATTTCAGAGAGATAAGATTTGTAGCTTGTAGTTTTAGTTTATTCTA
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAGTCTATTCCA
*
5396876 CTACAACTTCAGGGAGATAAGACCTACTATGGTAGATTTAATCTGACCCACTACAACTTCAGAGG
66 CTGCAACTTCAGGGAGATAAGACCTACTATGGTAGATTTAATCTGACCCACTACAACTTCAGAGG
* *
5396941 TATCGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTAGCTTCAAT
131 TATAGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAAT
* * ** *
5397006 CTGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTATTTTCAATCCACTCCACTGCAATTTCA-
196 CTGCTCCACTGCAACTTCAGAGAGATAAGATTTG-TAGCTTCAATACACTCCACTGCAATTTCAG
5397070 AGGAGATAAGATCTG-TAAC
260 A-GAGATAAGATCTGCTAAC
* ** * *
5397089 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAATTTGTAGCTTTAATCAATTCCA
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAGTCTATTCCA
* *
5397154 TTGCAACTTCAGGGAAATAAGA
66 CTGCAACTTCAGGGAGATAAGA
5397176 TTCGCTATCT
Statistics
Matches: 314, Mismatches: 49, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
278 279 0.89
279 35 0.11
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (278 bp):
TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAGCTTGTAGCTTTAGTCTATTCCA
CTGCAACTTCAGGGAGATAAGACCTACTATGGTAGATTTAATCTGACCCACTACAACTTCAGAGG
TATAGGACTTATCATTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAAT
CTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTCAATACACTCCACTGCAATTTCAGA
GAGATAAGATCTGCTAAC
Found at i:5397202 original size:140 final size:140
Alignment explanation
Indices: 5397015--5397266 Score: 362
Period size: 140 Copynumber: 1.8 Consensus size: 140
5397005 TCTGCTCTAC
* * * *
5397015 TGCAACTTTAGAGAGATAAGATTTGCTATTTTCAATCCACTCCACTGCAA-TTTCAAGGAGATAA
1 TGCAACTTCAGAGAAATAAGATTCGCTATCTTCAATCCACTCCACTGCAACTTT-AAGGAGATAA
*
5397079 GATCTGTAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAATTTGTAGCTTTA
65 GATCTGTAACTTCAATCTGCTCCACTACAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTA
5397144 ATCAATTCCAT
130 ATCAATTCCAT
* * ** *
5397155 TGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAG
1 TGCAACTTCAGAGAAATAAGATTCGCTATCTTCAATCCACTCCACTGCAACTTTAAGGAGATAAG
* ** *
5397220 ATTTGTGGCTTTAATCTGCTCCACTACAACTTCAGAGAGATAAGATT
66 ATCTGTAACTTCAATCTGCTCCACTACAACTTCAGAGAGATAAGATT
5397267 CACCATGATG
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
140 94 0.97
141 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (140 bp):
TGCAACTTCAGAGAAATAAGATTCGCTATCTTCAATCCACTCCACTGCAACTTTAAGGAGATAAG
ATCTGTAACTTCAATCTGCTCCACTACAACTTCAGAGAGATAAGATTTGTAATTTGTAGCTTTAA
TCAATTCCAT
Found at i:5397319 original size:94 final size:94
Alignment explanation
Indices: 5397196--5397508 Score: 441
Period size: 94 Copynumber: 3.3 Consensus size: 94
5397186 TCAGTCTGCT
*
5397196 CCACTGCAACTTTAGGGAG-ATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTCAGAGAGA
1 CCACTGCAACTTCAGGG-GTATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTCAGAGAGA
*
5397260 TAAGATTCACCATGATGACTTCAATCCATC
65 TAAGATTCACCATGATAACTTCAATCCATC
* *
5397290 CCACTGTAACTTCAGGGGTATAAGATTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGAT
1 CCACTGCAACTTCAGGGGTATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTCAGAGAGAT
** * *
5397355 AAGATTTGCCATGATAACTTCAATTCATT
66 AAGATTCACCATGATAACTTCAATCCATC
* * * * *
5397384 TCACTACAACTTCAGGGGTATAGGATTTGCGGCTTTAATCTACTCCACTACAACTTCAG-GAAGA
1 CCACTGCAACTTCAGGGGTATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTCAGAG-AGA
* *
5397448 TAAAATTCACCATGATAACTTCAATCCGTC
65 TAAGATTCACCATGATAACTTCAATCCATC
* *
5397478 CTACTGCAACTTCAGGGGTATAGGATTTGTG
1 CCACTGCAACTTCAGGGGTATAAGATTTGTG
5397509 ATTTCACTGA
Statistics
Matches: 192, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
93 2 0.01
94 190 0.99
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (94 bp):
CCACTGCAACTTCAGGGGTATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTCAGAGAGAT
AAGATTCACCATGATAACTTCAATCCATC
Found at i:5397361 original size:44 final size:44
Alignment explanation
Indices: 5396577--5397362 Score: 412
Period size: 44 Copynumber: 17.1 Consensus size: 44
5396567 GATTTGTAGC
* **
5396577 TTGTAGCTTTAGTCTATTCCACTGCAACTTCAGAGAGATAAGACCT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGA--T
* * *
5396623 GCTATGGTAGATTTAATCTGAC-CCACTGCAACTTCAGAG-GTATAGGAC
1 --T-T-GTAGCTTTAATCTG-CTCCACTGCAACTTCAGAGAG-ATAAGAT
* * * *
5396671 TTATCG-TTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGAT
1 TTGTAGCTTT-AATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* * *
5396715 TAGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* * * *
5396759 TTGTAGCTTCAATATGCTCTACTGCAATTTCAGAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* ** ** * * *
5396803 TTGCTATCTTCGATCCACTCCGCTGGAATTTCAGAGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* ** * * *
5396848 TTGTAGCTTGTAGTTTTAGTTTATTCTACTACAACTTCAGGGAGATAAGACCT
1 TTGTAGCTT-TA-----A-TCTGCTCCACTGCAACTTCAGAGAGATAAGA--T
* * **
5396901 ACTATGGTAGATTTAATCTGAC-CCACTACAACTTCAGAG-GTATCGGA-
1 --T-T-GTAGCTTTAATCTG-CTCCACTGCAACTTCAGAGAG-ATAAGAT
* * * *
5396948 CT-TATCATTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGAT
1 TTGTAGC-TTT-AATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* * *
5396993 TAT-TAGCTTCAATCTGCTCTACTGCAACTTTAGAGAGATAAGAT
1 T-TGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* ** *
5397037 TTGCTA-TTTTCAATCCACTCCACTGCAATTTCA-AGGAGATAAGAT
1 TTG-TAGCTTT-AATCTGCTCCACTGCAACTTCAGA-GAGATAAGAT
* * * * *
5397082 CTGTAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGAT-A-A---G--AT
*** * * *
5397133 TTGTAGCTTTAATCAATTCCATTGCAACTTCAGGGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* * * * * *
5397177 TCGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* *
5397222 TTGTGGCTTTAATCTGCTCCACTACAACTTCAGAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* * *
5397266 TCACCATG-ATGACTTCAATC--CATCCCACTGTAACTTCAG-GGGTATAAGAT
1 T-----TGTA-G-CTTTAATCTGC-T-CCACTGCAACTTCAGAGAG-ATAAGAT
*
5397316 TTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
5397360 TTG
1 TTG
5397363 CCATGATAAC
Statistics
Matches: 564, Mismatches: 116, Indels: 120
0.70 0.14 0.15
Matches are distributed among these distances:
42 2 0.00
43 9 0.02
44 265 0.47
45 117 0.21
46 8 0.01
48 2 0.00
49 11 0.02
50 84 0.15
51 55 0.10
53 1 0.00
55 1 0.00
56 3 0.01
57 6 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
Found at i:5402290 original size:12 final size:12
Alignment explanation
Indices: 5402273--5402298 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5402263 ATGATCGGGT
5402273 TTAAAAAAATTA
1 TTAAAAAAATTA
5402285 TTAAAAAAATTA
1 TTAAAAAAATTA
5402297 TT
1 TT
5402299 TATTTCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:5402860 original size:11 final size:11
Alignment explanation
Indices: 5402840--5402872 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5402830 TTTATCAACT
5402840 AAATAATAAAA
1 AAATAATAAAA
*
5402851 AAATATTAAAA
1 AAATAATAAAA
5402862 AAATAA-AAAA
1 AAATAATAAAA
5402872 A
1 A
5402873 TTCCTACAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:5403038 original size:43 final size:43
Alignment explanation
Indices: 5402986--5403071 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
5402976 AGAGCAATAA
*
5402986 TTTGAAGCAGTCAATAAACTTGTAGAAAGGGTATAGCAAGAGG
1 TTTGAAGCAGGCAATAAACTTGTAGAAAGGGTATAGCAAGAGG
5403029 TTTGAAGCAGGCAATAAACTTGTAGAAAGGGTATAGCAAGAGG
1 TTTGAAGCAGGCAATAAACTTGTAGAAAGGGTATAGCAAGAGG
5403072 ATGGAAGCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (43 bp):
TTTGAAGCAGGCAATAAACTTGTAGAAAGGGTATAGCAAGAGG
Found at i:5407434 original size:3 final size:3
Alignment explanation
Indices: 5407404--5407492 Score: 65
Period size: 3 Copynumber: 30.0 Consensus size: 3
5407394 TTCGTGAAAG
* * * * ** *
5407404 TAA TAT TAA TAC TAA CAA TAA TAG TAA TAA TAA CCA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5407452 TAG TAA -AC TAA TAA TAA TATT TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
5407493 ATTGCTAAAA
Statistics
Matches: 63, Mismatches: 20, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
2 3 0.05
3 58 0.92
4 2 0.03
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5407543 original size:29 final size:28
Alignment explanation
Indices: 5407498--5407561 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
5407488 AATAAATTGC
* *
5407498 TAAAATATGGGCTAAATCAAAATAAAAA
1 TAAAATATGGGCGAAATCAAAAGAAAAA
* **
5407526 TAAAATGTAGGGCGAAATTGAAAGAAAAA
1 TAAAATAT-GGGCGAAATCAAAAGAAAAA
5407555 TAAAATA
1 TAAAATA
5407562 AAAGGGACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (28 bp):
TAAAATATGGGCGAAATCAAAAGAAAAA
Found at i:5409055 original size:9 final size:9
Alignment explanation
Indices: 5409038--5409074 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5409028 TGAGTTTTCG
5409038 AATTCGAAT
1 AATTCGAAT
*
5409047 AACTCGAAT
1 AATTCGAAT
5409056 AATTCGAAT
1 AATTCGAAT
5409065 AATTCGAAT
1 AATTCGAAT
5409074 A
1 A
5409075 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5410235 original size:14 final size:13
Alignment explanation
Indices: 5410195--5410245 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
5410185 TAAAGTATGT
*
5410195 TATTATTTTATTA
1 TATTATTATATTA
* *
5410208 TATT-GTAAATTA
1 TATTATTATATTA
5410220 TATTAATTATATTA
1 TATT-ATTATATTA
5410234 TATTATTATATT
1 TATTATTATATT
5410246 TTAAATAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Done.