Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 21 of 29
Found at i:8153520 original size:24 final size:24
Alignment explanation
Indices: 8153469--8153520 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
8153459 AATAATTATT
* *
8153469 TTATTAAAATATAATTTTTAAAAG
1 TTATTAAAATATAATATTTAAAAA
8153493 TTATT-AAATATAATATTTAAATAA
1 TTATTAAAATATAATATTTAAA-AA
8153517 TTAT
1 TTAT
8153521 ATTATAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTATTAAAATATAATATTTAAAAA
Found at i:8154252 original size:20 final size:24
Alignment explanation
Indices: 8154206--8154253 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
8154196 GCACTTGAGT
8154206 AAATGTACAAAAAAGAGAAGAAAG
1 AAATGTACAAAAAAGAGAAGAAAG
*
8154230 AAATGTACAAAAAGGAGAAGAAAG
1 AAATGTACAAAAAAGAGAAGAAAG
8154254 GTACGGACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.23, T:0.08
Consensus pattern (24 bp):
AAATGTACAAAAAAGAGAAGAAAG
Found at i:8154263 original size:24 final size:24
Alignment explanation
Indices: 8154212--8154264 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
8154202 GAGTAAATGT
* *
8154212 ACAAAAAAGAGAAGAAAGAAATGT
1 ACAAAAAAGAGAAGAAAGAAACGG
* **
8154236 ACAAAAAGGAGAAGAAAGGTACGG
1 ACAAAAAAGAGAAGAAAGAAACGG
8154260 ACAAA
1 ACAAA
8154265 TTTCTTGCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.08, G:0.25, T:0.06
Consensus pattern (24 bp):
ACAAAAAAGAGAAGAAAGAAACGG
Found at i:8158830 original size:17 final size:16
Alignment explanation
Indices: 8158792--8158830 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
8158782 AGTCATACTC
8158792 TTTCTTCTTCTCTAAA
1 TTTCTTCTTCTCTAAA
*
8158808 TATTCTTCTTCTTCTACA
1 T-TTCTTCTTC-TCTAAA
8158826 TTTCT
1 TTTCT
8158831 AACAGGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 13 0.65
18 6 0.30
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTCTTCTTCTCTAAA
Found at i:8172384 original size:19 final size:19
Alignment explanation
Indices: 8172354--8172410 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
8172344 CATTTCTCAT
8172354 ATTT-TTTA-TTTGATTCA
1 ATTTATTTATTTTGATTCA
* * **
8172371 ATTTTTTTCTTTTGATTTT
1 ATTTATTTATTTTGATTCA
*
8172390 ATTTATTTATTTTTATTCA
1 ATTTATTTATTTTGATTCA
8172409 AT
1 AT
8172411 AAAAAATTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
19 23 0.77
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (19 bp):
ATTTATTTATTTTGATTCA
Found at i:8175913 original size:22 final size:24
Alignment explanation
Indices: 8175869--8175917 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
8175859 AATATTATTT
8175869 TAATATATTATAACTAAATTATTAA
1 TAATATATTATAAC-AAATTATTAA
*
8175894 TAATTTATTATAA-AAA-TATTAA
1 TAATATATTATAACAAATTATTAA
8175916 TA
1 TA
8175918 TGATTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 3 0.13
25 12 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATATTATAACAAATTATTAA
Found at i:8176021 original size:22 final size:22
Alignment explanation
Indices: 8175996--8176046 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
8175986 AATATGTGAT
*
8175996 TAAAGTATCAATAATTTATTAC
1 TAAAATATCAATAATTTATTAC
* * *
8176018 TAAAATATTAATAATTTGTTAT
1 TAAAATATCAATAATTTATTAC
8176040 TAAAATA
1 TAAAATA
8176047 CTAATATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
TAAAATATCAATAATTTATTAC
Found at i:8176051 original size:22 final size:22
Alignment explanation
Indices: 8176005--8176052 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
8175995 TTAAAGTATC
*
8176005 AATAATTTATTACTAAAATATT
1 AATAATTTATTACTAAAATACT
* *
8176027 AATAATTTGTTATTAAAATACT
1 AATAATTTATTACTAAAATACT
8176049 AATA
1 AATA
8176053 TGATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
AATAATTTATTACTAAAATACT
Found at i:8176280 original size:21 final size:21
Alignment explanation
Indices: 8176256--8176313 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
8176246 TACATTTAAT
8176256 TTAATAATTTATTTTTAAATA
1 TTAATAATTTATTTTTAAATA
** * *
8176277 TTAATAATAAATTATGAAATA
1 TTAATAATTTATTTTTAAATA
8176298 TTAATAATTTATTTTT
1 TTAATAATTTATTTTT
8176314 TCTTTTTTCT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAATAATTTATTTTTAAATA
Found at i:8176333 original size:107 final size:110
Alignment explanation
Indices: 8176191--8176389 Score: 323
Period size: 107 Copynumber: 1.8 Consensus size: 110
8176181 AATTTATTAA
8176191 TAATAATTTATTTTTTCCTTTTTTCTCTTTCAATTTATTTTTCAAAAATATT-AAATACATTTAA
1 TAATAATTTATTTTTTCCTTTTTTCTCTTTCAATTTATTTTTCAAAAATATTAAAATACATTTAA
*
8176255 TTTAATAATTTATT-TTTAAATATTAATAATAAATTATGAAATAT
66 TTTAATAATTTATTATTAAAATATTAATAATAAATTATGAAATAT
* * * *
8176299 TAATAATTTATTTTTT-CTTTTTTCTCTTTTAATTTATTTTTTAAAATTATTAAAAATATATTTA
1 TAATAATTTATTTTTTCCTTTTTTCTCTTTCAATTTATTTTTCAAAAATATT-AAAATACATTTA
8176363 ATTTAATAATTTATTATTAAAATATTA
65 ATTTAATAATTTATTATTAAAATATTA
8176390 TTATGATTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 32 0.39
108 16 0.19
109 25 0.30
110 10 0.12
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (110 bp):
TAATAATTTATTTTTTCCTTTTTTCTCTTTCAATTTATTTTTCAAAAATATTAAAATACATTTAA
TTTAATAATTTATTATTAAAATATTAATAATAAATTATGAAATAT
Found at i:8176489 original size:19 final size:22
Alignment explanation
Indices: 8176467--8176515 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
8176457 TTTAACTTTT
8176467 TATTAA-AATTT-T-ATTAAAA
1 TATTAATAATTTATCATTAAAA
*
8176486 TATTAATTATTTATCATTAAAA
1 TATTAATAATTTATCATTAAAA
*
8176508 TATAAATA
1 TATTAATA
8176516 TAATATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 4 0.17
21 1 0.04
22 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTAATAATTTATCATTAAAA
Found at i:8181553 original size:37 final size:37
Alignment explanation
Indices: 8181507--8181582 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
8181497 ATTCTACTAA
8181507 TCATGTAAGTGGTCCACACATGGTATAATCTATTCTT
1 TCATGTAAGTGGTCCACACATGGTATAATCTATTCTT
*
8181544 TCATTTAAGTGGTCCACACATGGTATAATCTATTCTT
1 TCATGTAAGTGGTCCACACATGGTATAATCTATTCTT
8181581 TC
1 TC
8181583 TTTTTCCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
TCATGTAAGTGGTCCACACATGGTATAATCTATTCTT
Found at i:8197444 original size:2 final size:2
Alignment explanation
Indices: 8197437--8197468 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8197427 GTTCTGTCTC
8197437 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
8197469 GTGGTGGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:8219988 original size:2 final size:2
Alignment explanation
Indices: 8219983--8220018 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8219973 AGGGGGGGGA
8219983 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8220019 TATCAAGCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8238361 original size:45 final size:46
Alignment explanation
Indices: 8238296--8238393 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 46
8238286 CTCTCCCCAT
*
8238296 ATTTTCAGATTTCTCTTTCCAACACTTTGAAGACAC-AAAACGAT-
1 ATTTTCAGATTTCTCTTTCCAACACTTTGAAAACACAAAAACGATG
*
8238340 AGTTTTCAGATTTCTCTTTCCAGCACTTTGAAAACACAAAAACGATG
1 A-TTTTCAGATTTCTCTTTCCAACACTTTGAAAACACAAAAACGATG
8238387 ATTTTCA
1 ATTTTCA
8238394 TTGCTTGAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 1 0.02
45 33 0.67
46 14 0.29
47 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (46 bp):
ATTTTCAGATTTCTCTTTCCAACACTTTGAAAACACAAAAACGATG
Found at i:8238957 original size:45 final size:45
Alignment explanation
Indices: 8238892--8239229 Score: 199
Period size: 45 Copynumber: 7.5 Consensus size: 45
8238882 AACAATAGTT
* * * *
8238892 TATTTTTTTAACATGACGTGTAACAATTTAACCAAGACATGTAACA
1 TATTTTTGT-ACATGGCGTGTAACAATTTAACCATGACGTGTAACA
* * *
8238938 TATTTTTGTACATGGCGTGTAACAATTTAATCATGGCGTGTCACA
1 TATTTTTGTACATGGCGTGTAACAATTTAACCATGACGTGTAACA
* * *
8238983 TGTTTTTGTACATGGTGTGTAACAACTTAACCATGACGTGTAACA
1 TATTTTTGTACATGGCGTGTAACAATTTAACCATGACGTGTAACA
* * * * ** ** * * *
8239028 TATTTCTGTATATGGAGTGTAATAACCTAATTATAACGTATCACA
1 TATTTTTGTACATGGCGTGTAACAATTTAACCATGACGTGTAACA
* * * * * ** * *
8239073 TGTTTTTGTATATCGCATATAACAACCTAACCATAACGTGTAAGA
1 TATTTTTGTACATGGCGTGTAACAATTTAACCATGACGTGTAACA
* * * * * ** * * * *
8239118 TGTTTCTGTATATGACGTGTAATAACCTAACTATAACGTATCACA
1 TATTTTTGTACATGGCGTGTAACAATTTAACCATGACGTGTAACA
* * * * ** * * *
8239163 TATTTTTGTATATTGCATATAACAACCTAACCATAACATATAACA
1 TATTTTTGTACATGGCGTGTAACAATTTAACCATGACGTGTAACA
* *
8239208 TGTTTTTGTACATGACGTGTAA
1 TATTTTTGTACATGGCGTGTAA
8239230 TATCATATTA
Statistics
Matches: 230, Mismatches: 62, Indels: 1
0.78 0.21 0.00
Matches are distributed among these distances:
45 222 0.97
46 8 0.03
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (45 bp):
TATTTTTGTACATGGCGTGTAACAATTTAACCATGACGTGTAACA
Found at i:8238958 original size:24 final size:24
Alignment explanation
Indices: 8238931--8239006 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 24
8238921 AACCAAGACA
8238931 TGTAACATATTTTTGTACATGGCG
1 TGTAACATATTTTTGTACATGGCG
**
8238955 TGTAACA-A-TTTAAT-CATGGCG
1 TGTAACATATTTTTGTACATGGCG
* * *
8238976 TGTCACATGTTTTTGTACATGGTG
1 TGTAACATATTTTTGTACATGGCG
8239000 TGTAACA
1 TGTAACA
8239007 ACTTAACCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
21 13 0.32
22 4 0.10
23 5 0.12
24 19 0.46
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (24 bp):
TGTAACATATTTTTGTACATGGCG
Found at i:8238974 original size:21 final size:22
Alignment explanation
Indices: 8238898--8239032 Score: 71
Period size: 21 Copynumber: 6.1 Consensus size: 22
8238888 AGTTTATTTT
8238898 TTTAA-CATGACGTGTAACA-A
1 TTTAATCATGACGTGTAACATA
* * *
8238918 TTTAACCAAGACATGTAACATA
1 TTTAATCATGACGTGTAACATA
** *
8238940 TTTTTGTACATGGCGTGTAACA-A
1 -TTTAAT-CATGACGTGTAACATA
* * *
8238963 TTTAATCATGGCGTGTCACATGT
1 TTTAATCATGACGTGTAACAT-A
** **
8238986 TTTTGTACATGGTGTGTAACA-A
1 TTTAAT-CATGACGTGTAACATA
* *
8239008 CTTAACCATGACGTGTAACATA
1 TTTAATCATGACGTGTAACATA
8239030 TTT
1 TTT
8239033 CTGTATATGG
Statistics
Matches: 83, Mismatches: 24, Indels: 14
0.69 0.20 0.12
Matches are distributed among these distances:
20 5 0.06
21 37 0.45
22 10 0.12
23 8 0.10
24 23 0.28
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (22 bp):
TTTAATCATGACGTGTAACATA
Found at i:8239003 original size:90 final size:90
Alignment explanation
Indices: 8238909--8239229 Score: 256
Period size: 90 Copynumber: 3.6 Consensus size: 90
8238899 TTAACATGAC
* * * ** **
8238909 GTGTAACAATTTAACCAAGACATGTAACATATTTTTGTACATGGCGTGTAACAATTTAATCATGG
1 GTGTAACAACTTAACCAAGACATGTAACATATTTCTGTACATGGAGTGTAACAACCTAATCATAA
*
8238974 CGTGTCACATGTTTTTGTACATGGT
66 CGTATCACATGTTTTTGTACATGGT
* * * * *
8238999 GTGTAACAACTTAACCATGACGTGTAACATATTTCTGTATATGGAGTGTAATAACCTAATTATAA
1 GTGTAACAACTTAACCAAGACATGTAACATATTTCTGTACATGGAGTGTAACAACCTAATCATAA
* * *
8239064 CGTATCACATGTTTTTGTATATCGC
66 CGTATCACATGTTTTTGTACATGGT
* * * * * * * *
8239089 ATATAACAACCTAACCATA-ACGTGTAAGATGTTTCTGTATAT-GACGTGTAATAACCTAA-CTA
1 GTGTAACAACTTAACCA-AGACATGTAACATATTTCTGTACATGGA-GTGTAACAACCTAATC-A
* * * *
8239151 TAACGTATCACATATTTTTGTATATTGC
63 TAACGTATCACATGTTTTTGTACATGGT
* * * * * *
8239179 ATATAACAACCTAACCATA-ACATATAACATGTTTTTGTACAT-GACGTGTAA
1 GTGTAACAACTTAACCA-AGACATGTAACATATTTCTGTACATGGA-GTGTAA
8239230 TATCATATTA
Statistics
Matches: 198, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
89 2 0.01
90 196 0.99
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (90 bp):
GTGTAACAACTTAACCAAGACATGTAACATATTTCTGTACATGGAGTGTAACAACCTAATCATAA
CGTATCACATGTTTTTGTACATGGT
Found at i:8239230 original size:90 final size:90
Alignment explanation
Indices: 8239002--8239231 Score: 345
Period size: 90 Copynumber: 2.6 Consensus size: 90
8238992 ACATGGTGTG
* * * *
8239002 TAACAACTTAACCATGACGTGTAACATATTTCTGTATATGGA-GTGTAATAACCTAATTATAACG
1 TAACAACCTAACCATAACGTGTAACATGTTTCTGTATAT-GACGTGTAATAACCTAACTATAACG
*
8239066 TATCACATGTTTTTGTATATCGCATA
65 TATCACATATTTTTGTATATCGCATA
*
8239092 TAACAACCTAACCATAACGTGTAAGATGTTTCTGTATATGACGTGTAATAACCTAACTATAACGT
1 TAACAACCTAACCATAACGTGTAACATGTTTCTGTATATGACGTGTAATAACCTAACTATAACGT
*
8239157 ATCACATATTTTTGTATATTGCATA
66 ATCACATATTTTTGTATATCGCATA
* * * *
8239182 TAACAACCTAACCATAACATATAACATGTTTTTGTACATGACGTGTAATA
1 TAACAACCTAACCATAACGTGTAACATGTTTCTGTATATGACGTGTAATA
8239232 TCATATTATG
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
89 2 0.02
90 125 0.98
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (90 bp):
TAACAACCTAACCATAACGTGTAACATGTTTCTGTATATGACGTGTAATAACCTAACTATAACGT
ATCACATATTTTTGTATATCGCATA
Found at i:8243010 original size:18 final size:18
Alignment explanation
Indices: 8242975--8243011 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8242965 ATGAAGACGA
*
8242975 TTAATTTTTTTATGATTT
1 TTAATTTTTTTATAATTT
*
8242993 TTAATTTTTTTTTAATTT
1 TTAATTTTTTTATAATTT
8243011 T
1 T
8243012 GATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTAATTTTTTTATAATTT
Found at i:8251701 original size:2 final size:2
Alignment explanation
Indices: 8251696--8251721 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8251686 GAATATATGA
8251696 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8251722 GATAAGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8253258 original size:2 final size:2
Alignment explanation
Indices: 8253253--8253292 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
8253243 GTGTCCTCAA
8253253 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G A- AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8253293 GGTCACGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8253701 original size:2 final size:2
Alignment explanation
Indices: 8253691--8253721 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8253681 AGAGAAATGA
*
8253691 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8253722 AAAGTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8256531 original size:2 final size:2
Alignment explanation
Indices: 8256524--8256555 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8256514 TCTTTTCTTT
8256524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8256556 AAACAACAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8257184 original size:30 final size:28
Alignment explanation
Indices: 8257148--8257222 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
8257138 AATTATTAAT
* *
8257148 TATAAAAAATTATTTGATTTAAAATAAAAA
1 TATAAAAATTTATTTAATTT--AATAAAAA
*
8257178 TATAAAAATTTGATTAAATTTAATAAAAA
1 TATAAAAATTT-ATTTAATTTAATAAAAA
8257207 -ATAAAAATTTATTTAA
1 TATAAAAATTTATTTAA
8257223 AATTTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.12
28 10 0.25
29 8 0.20
30 10 0.25
31 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
TATAAAAATTTATTTAATTTAATAAAAA
Found at i:8257225 original size:29 final size:29
Alignment explanation
Indices: 8257170--8257253 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
8257160 TTTGATTTAA
8257170 AATAAAAATATAAAAATTTGA-TT-AAATTT
1 AATAAAAA-ATAAAAATTT-ATTTAAAATTT
8257199 AATAAAAAATAAAAATTTATTTAAAATTT
1 AATAAAAAATAAAAATTTATTTAAAATTT
* * *
8257228 -TTAAAATAATTTAAAATTTATCTAAA
1 AATAAAA-AA-TAAAAATTTATTTAAA
8257254 TATTATGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 1 0.02
28 17 0.35
29 16 0.33
30 14 0.29
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (29 bp):
AATAAAAAATAAAAATTTATTTAAAATTT
Found at i:8273035 original size:74 final size:74
Alignment explanation
Indices: 8272885--8273027 Score: 189
Period size: 74 Copynumber: 1.9 Consensus size: 74
8272875 TTTTAAATAT
* * * * *
8272885 ATTTTTAATATCATATATTTTATTTTTATTTCTTATTATAATCTTATATATTTTATTTTTATTTT
1 ATTTTTAATATCATATATTTTATTTTAATTCCTAATTATAATATTATATATTTTATTTTAATTTT
8272950 TTTAATCTA
66 TTTAATCTA
* * * *
8272959 ATTTTTTATATTATATATTTTATTTTAATTCCTAATTCTTATATTATAT-TTTTATTTTAATATT
1 ATTTTTAATATCATATATTTTATTTTAATTCCTAATTATAATATTATATATTTTATTTTAAT-TT
8273023 TTTTA
65 TTTTA
8273028 TTTTAATTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
73 11 0.19
74 48 0.81
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (74 bp):
ATTTTTAATATCATATATTTTATTTTAATTCCTAATTATAATATTATATATTTTATTTTAATTTT
TTTAATCTA
Found at i:8287808 original size:50 final size:51
Alignment explanation
Indices: 8287706--8287808 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
8287696 TATGTTTGAG
8287706 TTTATTGGGTTTATTGGTATATTCATAAACCCCAAAGTTAAAGAGTTAAAA
1 TTTATTGGGTTTATTGGTATATTCATAAACCCCAAAGTTAAAGAGTTAAAA
*
8287757 TTTATTGGGTTTATTGGTATATTCAT-AACCCCAAAGTTGAAGAGTTAAAA
1 TTTATTGGGTTTATTGGTATATTCATAAACCCCAAAGTTAAAGAGTTAAAA
8287807 TT
1 TT
8287809 GATTTTTAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 25 0.49
51 26 0.51
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (51 bp):
TTTATTGGGTTTATTGGTATATTCATAAACCCCAAAGTTAAAGAGTTAAAA
Found at i:8287875 original size:21 final size:21
Alignment explanation
Indices: 8287834--8287879 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
8287824 CAGGATTAAT
*
8287834 TTTTAGGCATTATGTGACTAG
1 TTTTAGGCATTATATGACTAG
*
8287855 TTTTAGGTATTATAT-ACCTAG
1 TTTTAGGCATTATATGA-CTAG
8287876 TTTT
1 TTTT
8287880 TATGTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTTAGGCATTATATGACTAG
Found at i:8289114 original size:101 final size:101
Alignment explanation
Indices: 8288938--8289145 Score: 292
Period size: 101 Copynumber: 2.1 Consensus size: 101
8288928 AATAGTTCAA
* * * * ** *
8288938 GGAATAGTTATTTTCTTACAATAATTAATTTTTAAAATCTTCTAAAAACAAGGCTTAACTAATTC
1 GGAATAATTATCTTCTTACAATAACTAATCTCCAAAATCTTCTAAAAACAAGGCTTAACTAATCC
*
8289003 CGACCTTCTCTTGAGATTTGCTATTTTATGGTTGGG
66 CGACCTTCTCTTGAGATTTGCTATTCTATGGTTGGG
* *
8289039 GGAATAATTATCTTCTTATAATAACTAATCTCCAAAATCTTCTAAGAACAAGGCTTAACTAATCC
1 GGAATAATTATCTTCTTACAATAACTAATCTCCAAAATCTTCTAAAAACAAGGCTTAACTAATCC
* *
8289104 CTA-TTCTCTCTTGAGATTTGCTATTCTATGGTTGGG
66 CGACCT-TCTCTTGAGATTTGCTATTCTATGGTTGGG
8289140 GGAATA
1 GGAATA
8289146 GCTTTTAAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 1 0.01
101 93 0.99
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (101 bp):
GGAATAATTATCTTCTTACAATAACTAATCTCCAAAATCTTCTAAAAACAAGGCTTAACTAATCC
CGACCTTCTCTTGAGATTTGCTATTCTATGGTTGGG
Found at i:8289386 original size:16 final size:16
Alignment explanation
Indices: 8289362--8289396 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8289352 ATTTTAATAA
* *
8289362 TAAATTTTTAAACTTT
1 TAAACTTTTAAAATTT
8289378 TAAACTTTTAAAATTT
1 TAAACTTTTAAAATTT
8289394 TAA
1 TAA
8289397 TGAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAACTTTTAAAATTT
Found at i:8289550 original size:29 final size:28
Alignment explanation
Indices: 8289510--8289569 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
8289500 ATAAATCTTA
*
8289510 TTATAATAAAAA-GTCTAAAATTTTAATT
1 TTATAATAAAAATGT-TAAAATTTTAAAT
* *
8289538 TTATATTATAAAATGTTAAGATTTTAAAT
1 TTATAATA-AAAATGTTAAAATTTTAAAT
8289567 TTA
1 TTA
8289570 AAAATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 18 0.67
30 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (28 bp):
TTATAATAAAAATGTTAAAATTTTAAAT
Found at i:8289695 original size:41 final size:40
Alignment explanation
Indices: 8289616--8289709 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 40
8289606 AATATTGTTA
* * * **
8289616 TTATAAATAAATATTAGTATTTTAATTTTTGATGATTAAG
1 TTATAAATAAATATTAATATTTAAATTATAAATGATTAAG
* *
8289656 TTATAAATAAAATATTAATATTTAAATTATAAATTATTAATA
1 TTATAAAT-AAATATTAATATTTAAATTATAAATGATTAA-G
*
8289698 TTTTAAATAAAT
1 TTATAAATAAAT
8289710 GATAAATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
40 8 0.18
41 29 0.66
42 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (40 bp):
TTATAAATAAATATTAATATTTAAATTATAAATGATTAAG
Found at i:8289714 original size:27 final size:28
Alignment explanation
Indices: 8289678--8289736 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
8289668 TATTAATATT
*
8289678 TAAATTATAAATTATTAATATTTTAAA-
1 TAAATGATAAATTATTAATATTTTAAAC
8289705 TAAATGATAAATTATTAATATTTTAAAC
1 TAAATGATAAATTATTAATATTTTAAAC
8289733 TAAA
1 TAAA
8289737 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
TAAATGATAAATTATTAATATTTTAAAC
Found at i:8290211 original size:20 final size:20
Alignment explanation
Indices: 8290186--8290226 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
8290176 CCAAGGCATC
*
8290186 CCCTTGTAATTAATTAACGT
1 CCCTTGTAATTAAATAACGT
8290206 CCCTTGTAATTAAATAACGT
1 CCCTTGTAATTAAATAACGT
8290226 C
1 C
8290227 GCATGCACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (20 bp):
CCCTTGTAATTAAATAACGT
Found at i:8291856 original size:38 final size:39
Alignment explanation
Indices: 8291790--8291868 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
8291780 CTTCTTTTTC
*
8291790 GGAAAGAAATAGTCTATGTTTTGACTTTGCACTTTAAACA
1 GGAAAGAAAGAG-CTATGTTTTGACTTTGCACTTTAAACA
** * *
8291830 GGAAAGAAAGAG-TATGTTTTTCCTTTGGACTTTAGACA
1 GGAAAGAAAGAGCTATGTTTTGACTTTGCACTTTAAACA
8291868 G
1 G
8291869 CTATATAGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 23 0.68
40 11 0.32
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (39 bp):
GGAAAGAAAGAGCTATGTTTTGACTTTGCACTTTAAACA
Found at i:8292803 original size:28 final size:28
Alignment explanation
Indices: 8292772--8292848 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
8292762 TATTCACAAA
*
8292772 TTTTTAAATAAA-TATCTATTTTTTATTC
1 TTTTTAAATAAATTAT-TATATTTTATTC
*
8292800 TTTTTAATTAAATTATTATATTTTATT-
1 TTTTTAAATAAATTATTATATTTTATTC
* *
8292827 TTAAATTAAATAATTTATTATA
1 TT--TTTAAATAAATTATTATA
8292849 AGTAATAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.05
28 21 0.51
29 18 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTAAATAAATTATTATATTTTATTC
Found at i:8292843 original size:19 final size:20
Alignment explanation
Indices: 8292807--8292845 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
8292797 TTCTTTTTAA
* *
8292807 TTAAATTATTATATTTTATT
1 TTAAATTATAATAATTTATT
8292827 TTAAATTA-AATAATTTATT
1 TTAAATTATAATAATTTATT
8292846 ATAAGTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAAATTATAATAATTTATT
Found at i:8294096 original size:3 final size:3
Alignment explanation
Indices: 8294088--8294113 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8294078 TATAAATAGG
8294088 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
8294114 CTTATACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:8294546 original size:15 final size:15
Alignment explanation
Indices: 8294528--8294560 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
8294518 TCATATAAAT
8294528 ATTAGTGCTAATCAA
1 ATTAGTGCTAATCAA
8294543 ATTAGTGCTAATCAA
1 ATTAGTGCTAATCAA
8294558 ATT
1 ATT
8294561 TAAAAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (15 bp):
ATTAGTGCTAATCAA
Found at i:8303474 original size:50 final size:49
Alignment explanation
Indices: 8303415--8303509 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 49
8303405 AAATGCCATC
* *
8303415 CTAAACACTTTTGCTAACAGAAATAAAAATATGAATTTGTTCTAAAGTAT
1 CTAAACACTTTTGCTAACACAAATAAAAATATGAAATTGTT-TAAAGTAT
*
8303465 CTAAACACTTTTGCTAACACAAATGAAAATATGAAATTGTTTAAA
1 CTAAACACTTTTGCTAACACAAATAAAAATATGAAATTGTTTAAA
8303510 AAATATGAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 4 0.10
50 38 0.90
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (49 bp):
CTAAACACTTTTGCTAACACAAATAAAAATATGAAATTGTTTAAAGTAT
Found at i:8309144 original size:33 final size:33
Alignment explanation
Indices: 8309072--8309157 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
8309062 TTTTAATATC
* *
8309072 ATATATTTTATTTTCATTTCTTATTATAATCTT
1 ATATATTTTATTTTCATTTCTTAATACAATCTT
*
8309105 ACATATTTTATTTTCATTTCTTTAATACAAT-TT
1 ATATATTTTATTTTCATTTC-TTAATACAATCTT
* *
8309138 TTATATTATATATTTCATTT
1 ATATATTTTAT-TTTCATTT
8309158 TAATTTCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 29 0.64
34 16 0.36
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTCTTAATACAATCTT
Found at i:8309225 original size:6 final size:7
Alignment explanation
Indices: 8309209--8309234 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8309199 ATTTTATTTA
8309209 TTTTAAT
1 TTTTAAT
8309216 TTTTAAT
1 TTTTAAT
8309223 TTTTAAT
1 TTTTAAT
8309230 TTTTA
1 TTTTA
8309235 TATAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:8315179 original size:104 final size:103
Alignment explanation
Indices: 8314976--8315169 Score: 275
Period size: 104 Copynumber: 1.9 Consensus size: 103
8314966 TTAATAATAT
* * * *
8314976 TTTTCCTTTTTAATCTTTTAATTTTATTTTTATTAAAATTTTAAAATTTTAATAATTTATTATTA
1 TTTTCATTTTTAATATTTTAATTTTATTTTCATTAAAATTTTAAAATTTTAATAATGTATTATTA
8315041 AATTATTAACATAATTTTTTATTTTTTCTATTTATGTA
66 AATTATTAACATAATTTTTTATTTTTTCTATTTATGTA
* * *
8315079 TTTTCATTTTTAAATATTTTAATTTTTATTTTCATTAAAAATTTTGACA-TTT-ATAATGTATTC
1 TTTTCATTTTT-AATATTTTAA-TTTTATTTTCATT-AAAATTTTAAAATTTTAATAATGTATTA
*
8315142 TTAAATTATTAATATAATTTTTTATTTT
63 TTAAATTATTAACATAATTTTTTATTTT
8315170 AATTTTTTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
103 10 0.12
104 45 0.56
105 15 0.19
106 10 0.12
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (103 bp):
TTTTCATTTTTAATATTTTAATTTTATTTTCATTAAAATTTTAAAATTTTAATAATGTATTATTA
AATTATTAACATAATTTTTTATTTTTTCTATTTATGTA
Found at i:8315182 original size:12 final size:13
Alignment explanation
Indices: 8315156--8315181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8315146 ATTATTAATA
8315156 TAATTTTTTATTT
1 TAATTTTTTATTT
8315169 TAATTTTTTATTT
1 TAATTTTTTATTT
8315182 ATAAGTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TAATTTTTTATTT
Found at i:8318249 original size:2 final size:2
Alignment explanation
Indices: 8318244--8318275 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8318234 ATATATATAT
8318244 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8318276 TCAATACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8330808 original size:17 final size:17
Alignment explanation
Indices: 8330783--8330815 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8330773 ATTTTCAAGC
8330783 TTATATATAAAAAGAAA
1 TTATATATAAAAAGAAA
*
8330800 TTATCTATAAAAAGAA
1 TTATATATAAAAAGAA
8330816 TGTGCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
TTATATATAAAAAGAAA
Found at i:8337885 original size:133 final size:132
Alignment explanation
Indices: 8337674--8338014 Score: 319
Period size: 133 Copynumber: 2.6 Consensus size: 132
8337664 TTAGGTTTTT
* * * * * * **
8337674 TTTTATTTTGGTTAGATTTAAATGTCATA-CTAAGCACTTTAAAGAAAATAAGTAGGGTGTTTCA
1 TTTTCTTTT-GTTAGGTTTAAATGTCACATC-AAACAC-TTAAAAAAAATAAATAAAGTGTTTCA
* * * *** * ** * *
8337738 ATTTTACATTTAGTAGGTAGGTGGATTTTGGAAAAGAGTAAAAAA-TG-AGGAGAAATTAAAAAT
63 ATTTCACATCTAGTAAGTAGCAAGATTTTGAAAAAGAG-AAAAAAGTGAACAAAAAATGAAAAAT
8337801 TAAAAAA
127 T-AAAAA
* * * * *
8337808 TTTTCTTTTGTTAGGTTTAAATGTCACATTAAATATTTTTAAAAAAGTAAATAAAGTGTTTCAAT
1 TTTTCTTTTGTTAGGTTTAAATGTCACATCAAACA-CTTAAAAAAAATAAATAAAGTGTTTCAAT
* * **
8337873 TTCACATCTAGTAAGTAGCAAGATTTTGAAAAAGAGAAAAAAGTGAACAAAAAATGAGAACTTGG
65 TTCACATCTAGTAAGTAGCAAGATTTTGAAAAAGAGAAAAAAGTGAACAAAAAATGAAAAATTAA
**
8337938 AGT
130 AAA
*
8337941 TTTTCTTTTGTTAGGTTTAAATGTCACATCAAACACTTAAAAAAAATAAATAGAGTGTTTCAATT
1 TTTTCTTTTGTTAGGTTTAAATGTCACATCAAACACTTAAAAAAAATAAATAAAGTGTTTCAATT
*
8338006 ACACATCTA
66 TCACATCTA
8338015 AATAGGTAAG
Statistics
Matches: 166, Mismatches: 37, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
132 40 0.24
133 107 0.64
134 19 0.11
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (132 bp):
TTTTCTTTTGTTAGGTTTAAATGTCACATCAAACACTTAAAAAAAATAAATAAAGTGTTTCAATT
TCACATCTAGTAAGTAGCAAGATTTTGAAAAAGAGAAAAAAGTGAACAAAAAATGAAAAATTAAA
AA
Found at i:8354707 original size:4 final size:4
Alignment explanation
Indices: 8354693--8354724 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
8354683 ACTTCCTCAA
*
8354693 AGCC GGCC AGCC AGCC AGCC AGCC AGCC AGCC
1 AGCC AGCC AGCC AGCC AGCC AGCC AGCC AGCC
8354725 CCAACATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.50, G:0.28, T:0.00
Consensus pattern (4 bp):
AGCC
Found at i:8356321 original size:3 final size:3
Alignment explanation
Indices: 8356313--8356343 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8356303 AAAAATTCAT
8356313 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
8356344 GAAACACCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:8356630 original size:7 final size:7
Alignment explanation
Indices: 8356618--8356643 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8356608 CTTTTAATAT
8356618 TATATTA
1 TATATTA
8356625 TATATTA
1 TATATTA
8356632 TATATTA
1 TATATTA
8356639 TATAT
1 TATAT
8356644 ATCATCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:8363514 original size:22 final size:22
Alignment explanation
Indices: 8363467--8363516 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
8363457 ATATATAACG
*
8363467 TAATTAAAATATAATTTCATAA
1 TAATTAAAATATAATTTCAAAA
*
8363489 TAATTAAAA-ATAATTTTAAAA
1 TAATTAAAATATAATTTCAAAA
8363510 TTAATTA
1 -TAATTA
8363517 GATCTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATTAAAATATAATTTCAAAA
Found at i:8363530 original size:17 final size:17
Alignment explanation
Indices: 8363508--8363545 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
8363498 ATAATTTTAA
* *
8363508 AATTAATTAGATCTCAT
1 AATTAACTAAATCTCAT
8363525 AATTAACTAAATCTCAT
1 AATTAACTAAATCTCAT
8363542 AATT
1 AATT
8363546 TTGTAGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTAACTAAATCTCAT
Found at i:8380197 original size:33 final size:33
Alignment explanation
Indices: 8380155--8380231 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
8380145 TTATTTGACA
* *
8380155 TTATCTTTTA-AATATATTGTTAATGTTATATATT
1 TTAT-TTTTATAATATATT-ATAATCTTATATATT
** *
8380189 TTATTTTTATTTTTTATTATAATCTTATATATT
1 TTATTTTTATAATATATTATAATCTTATATATT
8380222 TTATTTTTAT
1 TTATTTTTAT
8380232 TTCTTAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (33 bp):
TTATTTTTATAATATATTATAATCTTATATATT
Found at i:8380232 original size:33 final size:33
Alignment explanation
Indices: 8380175--8380269 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
8380165 AATATATTGT
* *
8380175 TAATGTTATATATTTTATTTTTATTTTTTATTA
1 TAATCTTATATATTTTATTTTTATTTTTTAATA
*
8380208 TAATCTTATATATTTTATTTTTATTTCTTAATA
1 TAATCTTATATATTTTATTTTTATTTTTTAATA
* * * *
8380241 TAATTTTTTATATTATATATTTTAATTTT
1 TAATCTTATATATTTTAT-TTTTATTTTT
8380270 AATTTTTTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 45 0.85
34 8 0.15
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (33 bp):
TAATCTTATATATTTTATTTTTATTTTTTAATA
Found at i:8380236 original size:22 final size:22
Alignment explanation
Indices: 8380196--8380270 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 22
8380186 ATTTTATTTT
*
8380196 TATTTT-TTATTATAATCTTATA
1 TATTTTATTTTTAT-ATCTTATA
*
8380218 TATTTTATTTTTATTTCTTA-A
1 TATTTTATTTTTATATCTTATA
* *
8380239 TA--TAATTTTT-TATATTATA
1 TATTTTATTTTTATATCTTATA
*
8380258 TATTTTAATTTTA
1 TATTTTATTTTTA
8380271 ATTTTTTCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 5 0.12
19 10 0.24
21 9 0.22
22 11 0.27
23 6 0.15
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTATTTTTATATCTTATA
Found at i:8384008 original size:18 final size:18
Alignment explanation
Indices: 8383968--8384030 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 18
8383958 TTAAATCAAA
8383968 TATAATAATGTA-ATTTTT
1 TATAATAAT-TATATTTTT
8383986 T-TAATAATTATATTTTT
1 TATAATAATTATATTTTT
8384003 TATAATAA-T-TATTTTT
1 TATAATAATTATATTTTT
8384019 TATAATATATTA
1 TATAATA-ATTA
8384031 AATATTACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
16 16 0.40
17 16 0.40
18 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TATAATAATTATATTTTT
Found at i:8384027 original size:21 final size:18
Alignment explanation
Indices: 8383968--8384019 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
8383958 TTAAATCAAA
*
8383968 TATAATAATGTA-ATTTTT
1 TATAATAAT-TATTTTTTT
*
8383986 T-TAATAATTATATTTTT
1 TATAATAATTATTTTTTT
8384003 TATAATAATTATTTTTT
1 TATAATAATTATTTTTT
8384020 ATAATATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 2 0.06
17 14 0.45
18 15 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TATAATAATTATTTTTTT
Found at i:8387383 original size:2 final size:2
Alignment explanation
Indices: 8387376--8387400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8387366 CCCTAAACAA
8387376 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
8387401 AACATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:8390006 original size:26 final size:25
Alignment explanation
Indices: 8389964--8390013 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
8389954 TCAAATCAGT
* * *
8389964 ATATCATGTCATCATCAATTATAAC
1 ATATCATATCATAATCAATGATAAC
8389989 ATATCCATATCATAATCAATGATAA
1 ATAT-CATATCATAATCAATGATAA
8390014 TATTTTAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (25 bp):
ATATCATATCATAATCAATGATAAC
Found at i:8390121 original size:25 final size:25
Alignment explanation
Indices: 8390090--8390141 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
8390080 AATTAATCAT
8390090 AAAAATTTATTT-ATCTCAAAATAAA
1 AAAAATTTATTTAAT-TCAAAATAAA
*
8390115 AAAAATTTATTTAATTTAAAATAAA
1 AAAAATTTATTTAATTCAAAATAAA
8390140 AA
1 AA
8390142 TATAAGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAAATTTATTTAATTCAAAATAAA
Found at i:8391026 original size:17 final size:17
Alignment explanation
Indices: 8391004--8391039 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
8390994 GGTGGATGGC
8391004 GTGGTGGTGCAGCTGGG
1 GTGGTGGTGCAGCTGGG
*
8391021 GTGGTGGTGGAGCTGGG
1 GTGGTGGTGCAGCTGGG
8391038 GT
1 GT
8391040 TGCGGCCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.08, G:0.61, T:0.25
Consensus pattern (17 bp):
GTGGTGGTGCAGCTGGG
Found at i:8393476 original size:16 final size:15
Alignment explanation
Indices: 8393453--8393490 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
8393443 TGTTTGTACT
8393453 TTTTTTTTCTTTTAA
1 TTTTTTTTCTTTTAA
*
8393468 TTCTTTTTTTTTTTAA
1 TT-TTTTTTCTTTTAA
8393484 TTTTTTT
1 TTTTTTT
8393491 GTTACTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTTCTTTTAA
Found at i:8397904 original size:22 final size:22
Alignment explanation
Indices: 8397873--8397931 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
8397863 GGAATTATCG
8397873 ATCAA-TTTAAAGGTTTAGGGA
1 ATCAATTTTAAAGGTTTAGGGA
* * *
8397894 ATTAATTTTAAAGTTTTAGTGA
1 ATCAATTTTAAAGGTTTAGGGA
*
8397916 ATCGATTTT-AAGGTTT
1 ATCAATTTTAAAGGTTT
8397932 GGTTAATTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (22 bp):
ATCAATTTTAAAGGTTTAGGGA
Found at i:8397972 original size:21 final size:21
Alignment explanation
Indices: 8397892--8397972 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 21
8397882 AAGGTTTAGG
* *
8397892 GAATTAATTTTAAAGTTTTAGT
1 GAATTGATTTTAAAGTTTCA-T
* * **
8397914 GAATCGATTTTAAGGTTTGGT
1 GAATTGATTTTAAAGTTTCAT
* * **
8397935 TAATTG-GTTTAGGGTTTCAT
1 GAATTGATTTTAAAGTTTCAT
8397955 GAATTGATTTTAAAGTTT
1 GAATTGATTTTAAAGTTT
8397973 TGTGAACTTG
Statistics
Matches: 43, Mismatches: 15, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
20 15 0.35
21 13 0.30
22 15 0.35
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.48
Consensus pattern (21 bp):
GAATTGATTTTAAAGTTTCAT
Found at i:8397978 original size:21 final size:21
Alignment explanation
Indices: 8397878--8397978 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 21
8397868 TATCGATCAA
* * *
8397878 TTTAAAGGTTTAGGGAATTAAT
1 TTTAAA-GTTTTGTGAATTGAT
*
8397900 TTTAAAGTTTTAGTGAATCGAT
1 TTTAAAGTTTT-GTGAATTGAT
* * * *
8397922 TTTAAGGTTTGGTTAATTG-G
1 TTTAAAGTTTTGTGAATTGAT
** **
8397942 TTTAGGGTTTCATGAATTGAT
1 TTTAAAGTTTTGTGAATTGAT
8397963 TTTAAAGTTTTGTGAA
1 TTTAAAGTTTTGTGAA
8397979 CTTGTTGGTG
Statistics
Matches: 59, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
20 15 0.25
21 22 0.37
22 22 0.37
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.47
Consensus pattern (21 bp):
TTTAAAGTTTTGTGAATTGAT
Found at i:8398013 original size:21 final size:21
Alignment explanation
Indices: 8397987--8398026 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8397977 AACTTGTTGG
8397987 TGAATTGGTTTTAAGATTTAA
1 TGAATTGGTTTTAAGATTTAA
* *
8398008 TGAATTTGTTTTAGGATTT
1 TGAATTGGTTTTAAGATTT
8398027 TGTGTGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
TGAATTGGTTTTAAGATTTAA
Found at i:8398247 original size:20 final size:21
Alignment explanation
Indices: 8398200--8398247 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
8398190 TGGTGAACTA
8398200 ATTTTAGGATTTAGTGAATCG
1 ATTTTAGGATTTAGTGAATCG
*
8398221 GTTTTAGGATTTCA-TGAA-CG
1 ATTTTAGGATTT-AGTGAATCG
8398241 ATTTTAG
1 ATTTTAG
8398248 AGTGTGGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (21 bp):
ATTTTAGGATTTAGTGAATCG
Found at i:8398443 original size:23 final size:23
Alignment explanation
Indices: 8398411--8398466 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
8398401 GAGTTCAGTG
*
8398411 TTTTGGTGAACTAGGCTTAGGGT
1 TTTTGATGAACTAGGCTTAGGGT
* * * *
8398434 TTTTGTTGAATTGGGTTTAGGGT
1 TTTTGATGAACTAGGCTTAGGGT
8398457 TTTTGATGAA
1 TTTTGATGAA
8398467 TCGAATTGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.18, C:0.04, G:0.32, T:0.46
Consensus pattern (23 bp):
TTTTGATGAACTAGGCTTAGGGT
Found at i:8400445 original size:33 final size:33
Alignment explanation
Indices: 8400403--8400465 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
8400393 TACGGGTTGT
8400403 AAGGTTTTCTCCTTGAGAGCGAATCATCAATGC
1 AAGGTTTTCTCCTTGAGAGCGAATCATCAATGC
*
8400436 AAGGTTTTCTCCTTGAGAGCGAATTATCAA
1 AAGGTTTTCTCCTTGAGAGCGAATCATCAA
8400466 AACTGTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (33 bp):
AAGGTTTTCTCCTTGAGAGCGAATCATCAATGC
Found at i:8442563 original size:12 final size:12
Alignment explanation
Indices: 8442542--8442579 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
8442532 ATAAATAATA
*
8442542 ATAATAATTATT
1 ATAATTATTATT
8442554 ATAATTATTATT
1 ATAATTATTATT
8442566 ATAATTATTATT
1 ATAATTATTATT
8442578 AT
1 AT
8442580 CTATCAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:8445578 original size:3 final size:3
Alignment explanation
Indices: 8445570--8445654 Score: 89
Period size: 3 Copynumber: 28.3 Consensus size: 3
8445560 GAGGCATGCT
* * * * * * *
8445570 CAG CAG CAG CAG CAA CAA CAA CAA CAA CAG CAA CAG CAG CAG CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* *
8445618 CAG CAA CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
8445655 GAAGAGAAGG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.44, C:0.34, G:0.22, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:8445600 original size:27 final size:27
Alignment explanation
Indices: 8445571--8445643 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
8445561 AGGCATGCTC
* * *
8445571 AGCAGCAGCAGCAACAACAACAACAAC
1 AGCAACAGCAGCAGCAGCAACAACAAC
*
8445598 AGCAACAGCAGCAGCAGCAACAGCAAC
1 AGCAACAGCAGCAGCAGCAACAACAAC
8445625 AGCAACAGCAGCAGCAGCA
1 AGCAACAGCAGCAGCAGCA
8445644 GCAGCAGCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.47, C:0.33, G:0.21, T:0.00
Consensus pattern (27 bp):
AGCAACAGCAGCAGCAGCAACAACAAC
Found at i:8459207 original size:16 final size:17
Alignment explanation
Indices: 8459175--8459208 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
8459165 TTTAGAGTAG
*
8459175 TGAAATTAAAAATAATT
1 TGAAATTAAAAAGAATT
8459192 TGAAATT-AAAAGAATT
1 TGAAATTAAAAAGAATT
8459208 T
1 T
8459209 TTTAAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
TGAAATTAAAAAGAATT
Found at i:8461155 original size:2 final size:2
Alignment explanation
Indices: 8461148--8461177 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8461138 ACTATCCATC
8461148 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8461178 ATGTTCCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8483371 original size:40 final size:41
Alignment explanation
Indices: 8483324--8483453 Score: 122
Period size: 41 Copynumber: 3.1 Consensus size: 41
8483314 TTATATAATA
* *
8483324 TCATTTC-TTAGATAT-ATTTTTAATGTCATATATTTTGTTT
1 TCATTTCTTTA-ATATAATTTTTAATATCATATATTTTATTT
* *
8483364 TCATTTCTTTAATATAATTTTTTATATTATATATTTTATTT
1 TCATTTCTTTAATATAATTTTTAATATCATATATTTTATTT
* * * * *
8483405 TAATTTTTTTACTTATATAAATTTTAATTTCTTATATTTTATTT
1 TCATTTCTTTA---ATATAATTTTTAATATCATATATTTTATTT
8483449 T-ATTT
1 TCATTT
8483454 TAATTTCTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
40 11 0.15
41 33 0.45
43 4 0.05
44 26 0.35
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (41 bp):
TCATTTCTTTAATATAATTTTTAATATCATATATTTTATTT
Found at i:8483401 original size:27 final size:28
Alignment explanation
Indices: 8483371--8483432 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
8483361 TTTTCATTTC
8483371 TTTAATATAATTTTTTATA-TTATAT-AT
1 TTTAATATAATTTTTT-TACTTATATAAT
* *
8483398 TTTATTTTAATTTTTTTACTTATATAAAT
1 TTTAATATAATTTTTTTACTTATAT-AAT
8483427 TTTAAT
1 TTTAAT
8483433 TTCTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 20 0.69
29 7 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTAATATAATTTTTTTACTTATATAAT
Found at i:8483403 original size:5 final size:5
Alignment explanation
Indices: 8483395--8483502 Score: 62
Period size: 5 Copynumber: 21.4 Consensus size: 5
8483385 TTATATTATA
* * * * * * *
8483395 TATTT TATTT TAATT T-TTT TA-CT TATATA AATTT TAATT TCTTA TATTT
1 TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT
* *
8483444 TATTT TATTT TAATTTCT TATTCT TATAT TA-TA TATTT TATTT TATTT
1 TATTT TATTT T-A-TT-T TATT-T TATTT TATTT TATTT TATTT TATTT
8483492 T-TTT TATTT TA
1 TATTT TATTT TA
8483503 ATTATAACAT
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
4 12 0.16
5 50 0.65
6 10 0.13
7 3 0.04
8 2 0.03
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:8483475 original size:24 final size:24
Alignment explanation
Indices: 8483399--8483475 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
8483389 ATTATATATT
8483399 TTATTTTAATTT-TT-TTACTTATA
1 TTATTTTAATTTCTTATT-CTTATA
* * *
8483422 TAAATTTTAATTTCTTATATTTTATT
1 T-TATTTTAATTTCTTAT-TCTTATA
8483448 TTATTTTAATTTCTTATTCTTATA
1 TTATTTTAATTTCTTATTCTTATA
8483472 TTAT
1 TTAT
8483476 ATATTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 1 0.02
24 19 0.43
25 17 0.39
26 6 0.14
27 1 0.02
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATTTTAATTTCTTATTCTTATA
Found at i:8485506 original size:2 final size:2
Alignment explanation
Indices: 8485499--8485524 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8485489 AAGAAAAGGA
8485499 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
8485525 ACACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8498412 original size:64 final size:64
Alignment explanation
Indices: 8498333--8498456 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
8498323 TAGAAAATTT
* * *
8498333 CGATCTAGCATAGCAATCTAAGTTAGATAATATAACAACTATCAGATACTAGAATTTAGCGTTC
1 CGATCTACCATAGCAATCCAAGCTAGATAATATAACAACTATCAGATACTAGAATTTAGCGTTC
* * *
8498397 CGATCTACCATAGCAATCCAAGCTAGATCATCTAACAACTATTAGATACTAGAATTTAGC
1 CGATCTACCATAGCAATCCAAGCTAGATAATATAACAACTATCAGATACTAGAATTTAGC
8498457 TTTCATCCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (64 bp):
CGATCTACCATAGCAATCCAAGCTAGATAATATAACAACTATCAGATACTAGAATTTAGCGTTC
Found at i:8500430 original size:5 final size:5
Alignment explanation
Indices: 8500420--8500452 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
8500410 TTGTCAGTCG
8500420 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA- AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
8500453 TAAAGGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:8508171 original size:14 final size:14
Alignment explanation
Indices: 8508152--8508180 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8508142 TAATTTTGAG
8508152 TAGAAGACCTAAAT
1 TAGAAGACCTAAAT
8508166 TAGAAGACCTAAAT
1 TAGAAGACCTAAAT
8508180 T
1 T
8508181 GAACAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (14 bp):
TAGAAGACCTAAAT
Found at i:8516894 original size:69 final size:68
Alignment explanation
Indices: 8516686--8516975 Score: 212
Period size: 69 Copynumber: 4.2 Consensus size: 68
8516676 CACACCAAGC
* * ** * * * * **
8516686 TTAGGAGGGAAAAAAATGAATACATTCACTTAACTAGACC-CGTGCTATTCTTACCCCCACATCG
1 TTAGAAGGG-AAAAAATGGATACATTCACCCAACTAGACCTTGTGATATTTTTACCCCCATATTA
*
8516750 GGCT
65 GACT
* * * * * * *
8516754 TT--AAGAGAAAAAAAGATGAGTACATTCCCCCAACTAGACCTTGTGGTATTCTTACCTCCACA-
1 TTAGAAGGGAAAAAATG--GA-TACATTCACCCAACTAGACCTTGTGATATTTTTACCCCCATAT
*
8516816 TAGGGCT
63 TA-GACT
* * *
8516823 TTATGAAGGGAAAAAATGGATACGTTCACTCAACTAGACCTTGTGATATTTTTACTCCCATACTT
1 TTA-GAAGGGAAAAAATGGATACATTCACCCAACTAGACCTTGTGATATTTTTACCCCCATA-TT
8516888 A-ACT
64 AGACT
* * * * *
8516892 TTAGGAGGGAAAAAGATGGGTATATTCACCCAATTAGACTTTGTGATATTTTTACCCCCATATTA
1 TTAGAAGGGAAAAA-ATGGATACATTCACCCAACTAGACCTTGTGATATTTTTACCCCCATATTA
*
8516957 GGCT
65 GACT
*
8516961 TTAGAAGGGGAAAAA
1 TTAGAAGGGAAAAAA
8516976 GATAAGTATA
Statistics
Matches: 176, Mismatches: 34, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
65 7 0.04
66 3 0.02
67 1 0.01
68 33 0.19
69 117 0.66
70 2 0.01
71 2 0.01
72 11 0.06
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (68 bp):
TTAGAAGGGAAAAAATGGATACATTCACCCAACTAGACCTTGTGATATTTTTACCCCCATATTAG
ACT
Found at i:8520847 original size:29 final size:29
Alignment explanation
Indices: 8520815--8520902 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
8520805 CTATTTAGAA
*
8520815 ACATTCAAATAAATTTTTATACTTTTATT
1 ACATTCAAATAAATTTTTATATTTTTATT
* *
8520844 ACATTC-AATCAAACTCTTATATTTTTATTTT
1 ACATTCAAAT-AAATTTTTATATTTTTA--TT
* *
8520875 GCACT-AAATAAATTTTTATATTTTTATT
1 ACATTCAAATAAATTTTTATATTTTTATT
8520903 TTGAATCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 5 0.10
29 20 0.42
30 15 0.31
31 8 0.17
ACGTcount: A:0.35, C:0.11, G:0.01, T:0.52
Consensus pattern (29 bp):
ACATTCAAATAAATTTTTATATTTTTATT
Found at i:8520896 original size:30 final size:30
Alignment explanation
Indices: 8520821--8520905 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
8520811 AGAAACATTC
* * *
8520821 AAATAAATTTTTATACTTTTA--TTACATT
1 AAATAAATTTTTATATTTTTATTTTGCACT
* * *
8520849 CAATCAAACTCTTATATTTTTATTTTGCACT
1 AAAT-AAATTTTTATATTTTTATTTTGCACT
8520880 AAATAAATTTTTATATTTTTATTTTG
1 AAATAAATTTTTATATTTTTATTTTG
8520906 AATCAAATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
28 3 0.07
29 14 0.31
30 20 0.44
31 8 0.18
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.54
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTTATTTTGCACT
Found at i:8520914 original size:30 final size:30
Alignment explanation
Indices: 8520819--8520915 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
8520809 TTAGAAACAT
* ** *
8520819 TCAAATAAATTTTTATACTTTTA-TTACAT
1 TCAAATAAATTTTTATATTTTTATTTTGAA
* * *
8520848 TC-AATCAAACTCTTATATTTTTATTTTGCA
1 TCAAAT-AAATTTTTATATTTTTATTTTGAA
8520878 -CTAAATAAATTTTTATATTTTTATTTTGAA
1 TC-AAATAAATTTTTATATTTTTATTTTGAA
8520908 TCAAATAA
1 TCAAATAA
8520916 TCTCTTATAA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 3 0.06
29 17 0.32
30 29 0.55
31 4 0.08
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (30 bp):
TCAAATAAATTTTTATATTTTTATTTTGAA
Found at i:8520924 original size:30 final size:31
Alignment explanation
Indices: 8520857--8520924 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
8520847 TTCAATCAAA
*
8520857 CTCTTATATTTTTATTTTGCACTAAATAAAT
1 CTCTTATATTTTTATTTTGAACTAAATAAAT
*
8520888 -TTTTATATTTTTATTTTGAA-TCAAAT-AAT
1 CTCTTATATTTTTATTTTGAACT-AAATAAAT
8520917 CTCTTATA
1 CTCTTATA
8520925 ATTAATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.54
Consensus pattern (31 bp):
CTCTTATATTTTTATTTTGAACTAAATAAAT
Found at i:8521052 original size:33 final size:33
Alignment explanation
Indices: 8520991--8521059 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
8520981 TGTAATATAC
* * *
8520991 TAACATATCATAATTAATGATAATATGACATGT
1 TAACATATCATAATTAATAATAACATGACATAT
* *
8521024 TAACATATCATAATTGATAATGACATGACATAT
1 TAACATATCATAATTAATAATAACATGACATAT
8521057 TAA
1 TAA
8521060 TTTGACATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (33 bp):
TAACATATCATAATTAATAATAACATGACATAT
Found at i:8527794 original size:5 final size:5
Alignment explanation
Indices: 8527784--8527808 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
8527774 TAATTAACTT
8527784 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
8527809 AAGAGTTTAC
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:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:8530386 original size:2 final size:2
Alignment explanation
Indices: 8530373--8530404 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8530363 CGTGATAACA
*
8530373 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8530405 GCAAATAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8549042 original size:29 final size:29
Alignment explanation
Indices: 8548982--8549043 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
8548972 AGTTAATAAA
**
8548982 AAAAGTTTATTTGAGAAAAATAAAAATTT
1 AAAAGTTTATTTGAGAAAAATAAAAAAAT
***
8549011 AAAAGTTTATTTGAGTGTAATAAAAAAAT
1 AAAAGTTTATTTGAGAAAAATAAAAAAAT
8549040 AAAA
1 AAAA
8549044 ATTAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.32
Consensus pattern (29 bp):
AAAAGTTTATTTGAGAAAAATAAAAAAAT
Found at i:8549837 original size:11 final size:11
Alignment explanation
Indices: 8549821--8549846 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8549811 TTAATAATTT
8549821 TAAATAGAAGA
1 TAAATAGAAGA
8549832 TAAATAGAAGA
1 TAAATAGAAGA
8549843 TAAA
1 TAAA
8549847 CAAAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.19
Consensus pattern (11 bp):
TAAATAGAAGA
Found at i:8554026 original size:3 final size:3
Alignment explanation
Indices: 8554012--8554044 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
8554002 AGCTCAGATG
*
8554012 CAA CAA CGA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
8554045 TTTAAATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.33, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:8589652 original size:60 final size:58
Alignment explanation
Indices: 8589517--8589692 Score: 300
Period size: 58 Copynumber: 3.0 Consensus size: 58
8589507 GCAATTATAA
* *
8589517 ATATATGTAAATGTGAACTAAAAATGTGTCAGGCTAATTAGGATATTCTCTTAATTAC
1 ATATATGTAAATGTGAACTAAAAATGTGTTAGGCTAATTAGGATATTCTTTTAATTAC
8589575 ATATATGTAAATGTGAACTAAAAATGTGTTAGGCTAATTAGGATATATTCTTTTAATTAC
1 ATATATGTAAATGTGAACTAAAAATGTGTTAGGCTAATTAGG--ATATTCTTTTAATTAC
8589635 ATATATGTAAATGTGAACTAAAAATGTGGTT-GGCTAATTAGGATATTCTTTTAATTAC
1 ATATATGTAAATGTGAACTAAAAATGT-GTTAGGCTAATTAGGATATTCTTTTAATTAC
8589693 GTGCAGTTTT
Statistics
Matches: 113, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
58 57 0.50
60 53 0.47
61 3 0.03
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (58 bp):
ATATATGTAAATGTGAACTAAAAATGTGTTAGGCTAATTAGGATATTCTTTTAATTAC
Found at i:8605781 original size:24 final size:22
Alignment explanation
Indices: 8605754--8605810 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
8605744 TGAAAATATA
8605754 TAAATAAATAATATTATTGATAAC
1 TAAATAAATAATATTA-T-ATAAC
* * *
8605778 TAAATTATTAATATTATATAAT
1 TAAATAAATAATATTATATAAC
*
8605800 TAAATATATAA
1 TAAATAAATAA
8605811 AAGTATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 12 0.44
23 1 0.04
24 14 0.52
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAATAAATAATATTATATAAC
Found at i:8606254 original size:2 final size:2
Alignment explanation
Indices: 8606247--8606274 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8606237 TGCTATAGAA
8606247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8606275 GTTGGTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8606813 original size:22 final size:22
Alignment explanation
Indices: 8606788--8606831 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8606778 ATTAAATAGA
* * *
8606788 TTTGAATTTAATTTTTTAATAT
1 TTTGAATCTAAATTATTAATAT
*
8606810 TTTGTATCTAAATTATTAATAT
1 TTTGAATCTAAATTATTAATAT
8606832 ATTTAAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTGAATCTAAATTATTAATAT
Found at i:8606950 original size:16 final size:15
Alignment explanation
Indices: 8606929--8607019 Score: 60
Period size: 15 Copynumber: 5.7 Consensus size: 15
8606919 AATAATCAAA
8606929 TATTATTTTAGTTTAT
1 TATTATTTTAGTTT-T
8606945 TATTATTTT-GTTTT
1 TATTATTTTAGTTTT
8606959 TATTATATTTA-TTAGTCT
1 TATTAT-TTTAGTT--T-T
* **
8606977 TATTATGTTAAATTT
1 TATTATTTTAGTTTT
*
8606992 TATTATATTTGATGTTAT
1 TATTAT-TTT-A-GTTTT
8607010 TATTATTTTA
1 TATTATTTTA
8607020 TTATAATTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
14 7 0.12
15 16 0.27
16 13 0.22
17 8 0.13
18 16 0.27
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.66
Consensus pattern (15 bp):
TATTATTTTAGTTTT
Found at i:8607030 original size:50 final size:51
Alignment explanation
Indices: 8606940--8607042 Score: 124
Period size: 51 Copynumber: 2.0 Consensus size: 51
8606930 ATTATTTTAG
* *
8606940 TTTATTATTATTTTGTTTTTATTATATTTATTAGTCTTATT-ATGTTAAAT
1 TTTATTATTATTTTGTTATTATTATATTTATTAGTATTATTAATGTTAAAT
*
8606990 TTTATTA-TATTTGATGTTATTATTAT-TTTATTA-TAATTATTAATTTTAAAT
1 TTTATTATTATTT--TGTTATTATTATATTTATTAGT-ATTATTAATGTTAAAT
8607041 TT
1 TT
8607043 AAATAATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
49 6 0.13
50 19 0.41
51 21 0.46
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (51 bp):
TTTATTATTATTTTGTTATTATTATATTTATTAGTATTATTAATGTTAAAT
Found at i:8607374 original size:29 final size:29
Alignment explanation
Indices: 8607318--8607375 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
8607308 TCATGTTATG
* *
8607318 TTTATATTTATTCATATAATTATTAATAT
1 TTTATATTAATTCATATAATTATAAATAT
*
8607347 TTTATATTAATATGATATAATTA-AAATAT
1 TTTATATTAAT-TCATATAATTATAAATAT
8607376 AAAATTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTATATTAATTCATATAATTATAAATAT
Found at i:8644182 original size:6 final size:6
Alignment explanation
Indices: 8644171--8644196 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8644161 AGAAGTAGCT
8644171 TTCCTC TTCCTC TTCCTC TTCCTC TT
1 TTCCTC TTCCTC TTCCTC TTCCTC TT
8644197 TTTCCACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
TTCCTC
Found at i:8645351 original size:15 final size:15
Alignment explanation
Indices: 8645331--8645360 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8645321 AGATTAAGTA
8645331 GATCTTTGAAAATTC
1 GATCTTTGAAAATTC
8645346 GATCTTTGAAAATTC
1 GATCTTTGAAAATTC
8645361 ATAGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
GATCTTTGAAAATTC
Found at i:8653235 original size:2 final size:2
Alignment explanation
Indices: 8653230--8653277 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
8653220 TGATATATAT
8653230 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC ATC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A-C AC AC AC AC AC
8653273 AC AC A
1 AC AC A
8653278 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:8653282 original size:2 final size:2
Alignment explanation
Indices: 8653277--8653303 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8653267 ACACACACAC
8653277 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8653304 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8660385 original size:16 final size:16
Alignment explanation
Indices: 8660364--8660402 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
8660354 CATGTCTCGT
8660364 GATACATATACCATAG
1 GATACATATACCATAG
8660380 GATACATATACCATAG
1 GATACATATACCATAG
8660396 GAATACA
1 G-ATACA
8660403 ATGTCGAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
GATACATATACCATAG
Found at i:8660752 original size:2 final size:2
Alignment explanation
Indices: 8660745--8660780 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
8660735 TCTGCAGTAA
*
8660745 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8660781 ATCATTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8665582 original size:13 final size:13
Alignment explanation
Indices: 8665564--8665590 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8665554 CTGGCAGAGA
8665564 CTTAAGAACAAGT
1 CTTAAGAACAAGT
8665577 CTTAAGAACAAGT
1 CTTAAGAACAAGT
8665590 C
1 C
8665591 CATATAAAAA
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:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (13 bp):
CTTAAGAACAAGT
Found at i:8687329 original size:2 final size:2
Alignment explanation
Indices: 8687316--8687353 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
8687306 CCATGTAACT
*
8687316 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8687354 CACATTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8693261 original size:24 final size:24
Alignment explanation
Indices: 8693234--8693285 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
8693224 GCAAAAATAA
8693234 AGGAAGAG-GATGATG-CTGATGATG
1 AGGAAGAGAG-TGATGAC-GATGATG
*
8693258 AGGAGGAGAGTGATGACGATGATG
1 AGGAAGAGAGTGATGACGATGATG
8693282 AGGA
1 AGGA
8693286 CAATGACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.44, T:0.17
Consensus pattern (24 bp):
AGGAAGAGAGTGATGACGATGATG
Found at i:8695229 original size:13 final size:14
Alignment explanation
Indices: 8695198--8695230 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8695188 TTGAGGTCCT
*
8695198 ATACATTTAGAGAA
1 ATACTTTTAGAGAA
8695212 ATACTTTTAGAG-A
1 ATACTTTTAGAGAA
8695225 ATACTT
1 ATACTT
8695231 AAATATCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (14 bp):
ATACTTTTAGAGAA
Found at i:8716997 original size:45 final size:45
Alignment explanation
Indices: 8716929--8717025 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 45
8716919 CACGCTATGA
* * * * * * *
8716929 TGTTACATACCATGTACAGAAACATGTTACATGTCATGATTAAGT
1 TGTTACACACCATATACAAAAACATGTGACACGCCATAATTAAGT
*
8716974 TGTTACACACCATATACAAAAACATGTGACACGCCATAATTAGGT
1 TGTTACACACCATATACAAAAACATGTGACACGCCATAATTAAGT
8717019 TGTTACA
1 TGTTACA
8717026 AGTCATTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (45 bp):
TGTTACACACCATATACAAAAACATGTGACACGCCATAATTAAGT
Found at i:8717113 original size:66 final size:66
Alignment explanation
Indices: 8716953--8717130 Score: 182
Period size: 66 Copynumber: 2.7 Consensus size: 66
8716943 TACAGAAACA
* * * * * *
8716953 TGTTACATGTCATGATTAAGTTGTTACACACCATATACAAAAACATGTGACACGCCATAATTAGG
1 TGTTACAAGCCATGATTAAGTTGTTACATACTATGTACAAAAATATGTGACACGCCATAATTAGG
8717018 T
66 T
* * ** *
8717019 TGTTACAAGTCATTG-TTAAGTTGGTACATACTATGTACAAAAATATGTGACACGTTATGATTAG
1 TGTTACAAGCCA-TGATTAAGTTGTTACATACTATGTACAAAAATATGTGACACGCCATAATTAG
8717083 GT
65 GT
* * *
8717085 TGTTGCACA-CCATGATTAAATTGTTACAT-GTCATGTACAAAAATAT
1 TGTTACA-AGCCATGATTAAGTTGTTACATACT-ATGTACAAAAATAT
8717131 ATTATACACC
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
65 3 0.03
66 88 0.94
67 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (66 bp):
TGTTACAAGCCATGATTAAGTTGTTACATACTATGTACAAAAATATGTGACACGCCATAATTAGG
T
Found at i:8717235 original size:28 final size:25
Alignment explanation
Indices: 8717176--8717231 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
8717166 TGTTATGTGT
*
8717176 AAAAATATGTTACACGCTATAATTA
1 AAAAATATGTTACACACTATAATTA
8717201 AAAAATATTGTTACACACTAT-ATTGA
1 AAAAATA-TGTTACACACTATAATT-A
8717227 AAAAA
1 AAAAA
8717232 AATACTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (25 bp):
AAAAATATGTTACACACTATAATTA
Found at i:8717289 original size:29 final size:29
Alignment explanation
Indices: 8717227--8717290 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
8717217 ACTATATTGA
* * *
8717227 AAAAAAATACTATTATTACATGTCATGTT
1 AAAAAAATACTATTATTACACGCCATATT
*
8717256 AAAAAAATATTATTATTACACGCCATATT
1 AAAAAAATACTATTATTACACGCCATATT
*
8717285 TAAAAA
1 AAAAAA
8717291 CATTTTGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAAAATACTATTATTACACGCCATATT
Found at i:8731751 original size:24 final size:24
Alignment explanation
Indices: 8731715--8731760 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
8731705 AATTCTAAAA
*
8731715 TTTTTTCTCGTTTTTCCTTTTTCC
1 TTTTTTATCGTTTTTCCTTTTTCC
*
8731739 TTTTTTATTGTTTTTCCTTTTT
1 TTTTTTATCGTTTTTCCTTTTT
8731761 TGCTGACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTTATCGTTTTTCCTTTTTCC
Found at i:8747350 original size:41 final size:41
Alignment explanation
Indices: 8747293--8747375 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
8747283 GAACGCTGAT
*
8747293 AGAATCTGCTGTTTCCCCTTGTTTCACTTGTTGTTCAGCGA
1 AGAATCCGCTGTTTCCCCTTGTTTCACTTGTTGTTCAGCGA
8747334 AGAATCCGCTGTTTCCCCTTGTTTCACTTGTTGTTCAGCGA
1 AGAATCCGCTGTTTCCCCTTGTTTCACTTGTTGTTCAGCGA
8747375 A
1 A
8747376 TCTTCCTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (41 bp):
AGAATCCGCTGTTTCCCCTTGTTTCACTTGTTGTTCAGCGA
Found at i:8748195 original size:28 final size:27
Alignment explanation
Indices: 8748116--8748225 Score: 82
Period size: 28 Copynumber: 4.0 Consensus size: 27
8748106 CATGGTTAGG
* *
8748116 TTGTTACATGCCATATTAAAAAAAATACT
1 TTGTTACACGCCATGTTAAAAAAAA-A-T
* *
8748145 GTTGTTACACGTCATG-T--ACAAAAAT
1 -TTGTTACACGCCATGTTAAAAAAAAAT
* *
8748170 TTGTTACACGTCATAGTTAAAAAAAAAG
1 TTGTTACACGCCAT-GTTAAAAAAAAAT
* *
8748198 TTATTACACGCCATGTTGAAAAACAAAT
1 TTGTTACACGCCATGTT-AAAAAAAAAT
8748226 ACTGTTATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
24 14 0.22
25 2 0.03
26 2 0.03
27 8 0.12
28 26 0.40
29 1 0.02
30 12 0.18
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (27 bp):
TTGTTACACGCCATGTTAAAAAAAAAT
Found at i:8756437 original size:2 final size:2
Alignment explanation
Indices: 8756430--8756454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8756420 CCCCTTCATT
8756430 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
8756455 GTCACTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.