Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, 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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 55
Found at i:4302917 original size:14 final size:15
Alignment explanation
Indices: 4302898--4302928 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4302888 ATTGAAAATA
4302898 AATTAAAAG-AAACG
1 AATTAAAAGAAAACG
4302912 AATTAAAAGAAAACG
1 AATTAAAAGAAAACG
4302927 AA
1 AA
4302929 ATAAGTTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.68, C:0.06, G:0.13, T:0.13
Consensus pattern (15 bp):
AATTAAAAGAAAACG
Found at i:4309440 original size:13 final size:13
Alignment explanation
Indices: 4309422--4309455 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4309412 ATTCAAAACA
4309422 AAAGATAATTACT
1 AAAGATAATTACT
*
4309435 AAAGATAATTCCT
1 AAAGATAATTACT
*
4309448 AAAAATAA
1 AAAGATAA
4309456 AATTAAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (13 bp):
AAAGATAATTACT
Found at i:4312758 original size:2 final size:2
Alignment explanation
Indices: 4312751--4312778 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4312741 CTAACTATTA
4312751 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
4312779 TACAAGTCAA
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:4312927 original size:2 final size:2
Alignment explanation
Indices: 4312920--4312950 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4312910 AATGACGATG
4312920 AT AT 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 AT AT A
4312951 GTAAGCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4313548 original size:23 final size:23
Alignment explanation
Indices: 4313503--4313548 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4313493 TCAAAACAAC
* * *
4313503 TTAAGTTTTGGTCACTTATTTAA
1 TTAAGTTTTGATCAATTAGTTAA
4313526 TTAAGTTTTGATCAATTAGTTAA
1 TTAAGTTTTGATCAATTAGTTAA
4313549 AAAGGTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (23 bp):
TTAAGTTTTGATCAATTAGTTAA
Found at i:4314095 original size:17 final size:17
Alignment explanation
Indices: 4314023--4314103 Score: 53
Period size: 17 Copynumber: 4.8 Consensus size: 17
4314013 TCATAATATT
* *
4314023 AATTATAAATTTTAAAT
1 AATTATAAATATTAAAG
*
4314040 ATTTATAAATATTAAAG
1 AATTATAAATATTAAAG
4314057 -ATGTGATATAATA--AAA-
1 AAT-T-ATA-AATATTAAAG
* *
4314073 ATTTATATATATTAAAG
1 AATTATAAATATTAAAG
*
4314090 AATTATAATTATTA
1 AATTATAAATATTA
4314104 TTATAAACGT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
14 3 0.06
15 3 0.06
16 5 0.10
17 30 0.62
18 3 0.06
19 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
AATTATAAATATTAAAG
Found at i:4317317 original size:19 final size:18
Alignment explanation
Indices: 4317273--4317329 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 18
4317263 TTATTCAACT
4317273 AAAAATAATGTAAATATA
1 AAAAATAATGTAAATATA
4317291 ATATAAATATATG-AATATATA
1 A-A-AAATA-ATGTAA-ATATA
*
4317312 AAAAATAATATAAA-ATA
1 AAAAATAATGTAAATATA
4317329 A
1 A
4317330 TTTTTTGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 8 0.24
20 8 0.24
21 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
AAAAATAATGTAAATATA
Found at i:4319888 original size:12 final size:12
Alignment explanation
Indices: 4319868--4319898 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4319858 AAAAATATAT
*
4319868 ATACTCGGCCCG
1 ATACCCGGCCCG
4319880 ATACCCGGCCCG
1 ATACCCGGCCCG
4319892 ATACCCG
1 ATACCCG
4319899 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:4325134 original size:40 final size:40
Alignment explanation
Indices: 4325076--4325189 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 40
4325066 TCCGATCATT
* * * * * *
4325076 TTATTATATATTACTAATTTTATAGATTTAAGAATTAATC
1 TTATTATACATTAATAATTGTATAGATTAAAAAATTAATA
4325116 TTATTATACATTAATAATTGTATAGATTAAAAAATTAATA
1 TTATTATACATTAATAATTGTATAGATTAAAAAATTAATA
** **
4325156 TTATTATGTATTCTTAATT-TCATAGATTAAAAAA
1 TTATTATACATTAATAATTGT-ATAGATTAAAAAA
4325190 ATTAGTCTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.02
40 62 0.98
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (40 bp):
TTATTATACATTAATAATTGTATAGATTAAAAAATTAATA
Found at i:4332925 original size:17 final size:15
Alignment explanation
Indices: 4332889--4332927 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
4332879 TTGCTTACAA
*
4332889 ATGAATGAAAATATG
1 ATGAATGAAAATAGG
4332904 ATGAATGAAAACATAGG
1 ATGAATG-AAA-ATAGG
4332921 ATGAATG
1 ATGAATG
4332928 TGGACATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 3 0.14
17 11 0.52
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (15 bp):
ATGAATGAAAATAGG
Found at i:4333420 original size:17 final size:16
Alignment explanation
Indices: 4333400--4333471 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
4333390 ATTAAAGAGT
*
4333400 TAATTAGATTAATGAAC
1 TAATTA-ATTAATAAAC
* *
4333417 TAATTAAATGAATTAAC
1 TAATT-AATTAATAAAC
*
4333434 TAGTTTAATTAATAAAC
1 TA-ATTAATTAATAAAC
*
4333451 TAACTTTATTGAATAAAC
1 TAA-TTAATT-AATAAAC
4333469 TAA
1 TAA
4333472 GGTGCATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 31 0.70
18 13 0.30
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (16 bp):
TAATTAATTAATAAAC
Found at i:4333515 original size:17 final size:17
Alignment explanation
Indices: 4333495--4333536 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
4333485 AGTAGCTTAC
4333495 TAAATGAATTAAATTCA
1 TAAATGAATTAAATTCA
*
4333512 TAAACGAATTAAATTCA
1 TAAATGAATTAAATTCA
4333529 TAAATGAA
1 TAAATGAA
4333537 CTACTTCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
TAAATGAATTAAATTCA
Found at i:4333817 original size:45 final size:45
Alignment explanation
Indices: 4333753--4333843 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
4333743 AGATAATCAA
*
4333753 GTAAAAGATGAAGAAAGGAATAACTCCCTTTGTATCAGCCTTGGT
1 GTAAAAGATGAAGAAAGGAAGAACTCCCTTTGTATCAGCCTTGGT
* *
4333798 GTAAAGGATGAAGAAAGGAAGAATTCCCTTTGTATCAGCCTTGGT
1 GTAAAAGATGAAGAAAGGAAGAACTCCCTTTGTATCAGCCTTGGT
4333843 G
1 G
4333844 AACTTCAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (45 bp):
GTAAAAGATGAAGAAAGGAAGAACTCCCTTTGTATCAGCCTTGGT
Found at i:4334824 original size:13 final size:13
Alignment explanation
Indices: 4334808--4334832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4334798 TTTATTAAGT
4334808 ATTTTTTAATTTC
1 ATTTTTTAATTTC
4334821 ATTTTTTAATTT
1 ATTTTTTAATTT
4334833 AGAACCTCGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTAATTTC
Found at i:4339796 original size:238 final size:238
Alignment explanation
Indices: 4339365--4339842 Score: 875
Period size: 238 Copynumber: 2.0 Consensus size: 238
4339355 TTTATGGTGA
* *
4339365 AAATGCTTTTGTTTTTAGATTGAGAATTAAGGTTTATGTAGGGCTTTTGAATTTTGAAGAATTAA
1 AAATGATTTTGTGTTTAGATTGAGAATTAAGGTTTATGTAGGGCTTTTGAATTTTGAAGAATTAA
* * *
4339430 TGAAAGATTATTATATCGTTGATTTTGGAGATTAATTTTCAAGCATGTATGATGTTTAAAATCAA
66 TGAAAGATTATTATATCATTGATGTTGGAGATAAATTTTCAAGCATGTATGATGTTTAAAATCAA
*
4339495 GTGTAGGATGATTTAAAGTATTTGGCCTAATTAGGGTTTTGGTGATTGATTGGATTTTGGTTCAA
131 GTGTAGGATGATTTAAAGTATTTGACCTAATTAGGGTTTTGGTGATTGATTGGATTTTGGTTCAA
4339560 TTTGATGTTGTGTTGATTAGAATAGCATGAATTTGAAGTAAGG
196 TTTGATGTTGTGTTGATTAGAATAGCATGAATTTGAAGTAAGG
* *
4339603 AAATGATTTTGTGTTTAGATTGAGAATTAGGGTTTCTGTAGGGCTTTTGAATTTTGAAGAATTAA
1 AAATGATTTTGTGTTTAGATTGAGAATTAAGGTTTATGTAGGGCTTTTGAATTTTGAAGAATTAA
4339668 TGAAAGATTATTATATCATTGATGTTGGAGATAAATTTTCAAGCATGTATGATGTTTAAAATCAA
66 TGAAAGATTATTATATCATTGATGTTGGAGATAAATTTTCAAGCATGTATGATGTTTAAAATCAA
*
4339733 GTGTATGATGATTTAAAGTATTTGACCTAATTAGGGTTTTGGTGATTGATTGGATTTTGGTTCAA
131 GTGTAGGATGATTTAAAGTATTTGACCTAATTAGGGTTTTGGTGATTGATTGGATTTTGGTTCAA
4339798 TTTGATGTTGTGTTGATTAGAATAGCATGAATTTGAAGTAAGG
196 TTTGATGTTGTGTTGATTAGAATAGCATGAATTTGAAGTAAGG
4339841 AA
1 AA
4339843 GTTGAATTTA
Statistics
Matches: 231, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
238 231 1.00
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (238 bp):
AAATGATTTTGTGTTTAGATTGAGAATTAAGGTTTATGTAGGGCTTTTGAATTTTGAAGAATTAA
TGAAAGATTATTATATCATTGATGTTGGAGATAAATTTTCAAGCATGTATGATGTTTAAAATCAA
GTGTAGGATGATTTAAAGTATTTGACCTAATTAGGGTTTTGGTGATTGATTGGATTTTGGTTCAA
TTTGATGTTGTGTTGATTAGAATAGCATGAATTTGAAGTAAGG
Found at i:4341189 original size:2 final size:2
Alignment explanation
Indices: 4341182--4341217 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4341172 CAATTTTTCA
4341182 AT AT AT AT 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 AT AT AT AT
4341218 TAATACAGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4341572 original size:18 final size:18
Alignment explanation
Indices: 4341551--4341590 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4341541 ATGTTTACAA
*
4341551 TTATCAGACATTTTATAG
1 TTATCAAACATTTTATAG
*
4341569 TTATCAAACATTTTTTAG
1 TTATCAAACATTTTATAG
4341587 TTAT
1 TTAT
4341591 GAGATTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (18 bp):
TTATCAAACATTTTATAG
Found at i:4343090 original size:24 final size:24
Alignment explanation
Indices: 4343063--4343117 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
4343053 TTCCCACTTT
4343063 CATATTCATTCACATATTCATTCA
1 CATATTCATTCACATATTCATTCA
**
4343087 CATATTCATTCACATATTCATTTT
1 CATATTCATTCACATATTCATTCA
4343111 CATATTC
1 CATATTC
4343118 CATGTTCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.00, T:0.45
Consensus pattern (24 bp):
CATATTCATTCACATATTCATTCA
Found at i:4343117 original size:12 final size:12
Alignment explanation
Indices: 4343063--4343108 Score: 92
Period size: 12 Copynumber: 3.8 Consensus size: 12
4343053 TTCCCACTTT
4343063 CATATTCATTCA
1 CATATTCATTCA
4343075 CATATTCATTCA
1 CATATTCATTCA
4343087 CATATTCATTCA
1 CATATTCATTCA
4343099 CATATTCATT
1 CATATTCATT
4343109 TTCATATTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (12 bp):
CATATTCATTCA
Found at i:4343205 original size:19 final size:19
Alignment explanation
Indices: 4343152--4343211 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
4343142 ATTTCAAAAT
* *
4343152 TTATTTTCTGAATCAGAAC
1 TTATTTTCAGAATCATAAC
* *
4343171 TTATTTCCAGATTCATAAC
1 TTATTTTCAGAATCATAAC
* *
4343190 TTATTTTCAGACTCATAGC
1 TTATTTTCAGAATCATAAC
4343209 TTA
1 TTA
4343212 CTGTTATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (19 bp):
TTATTTTCAGAATCATAAC
Found at i:4343223 original size:38 final size:38
Alignment explanation
Indices: 4343181--4343265 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
4343171 TTATTTCCAG
* *
4343181 ATTCATAACTTATTTTCAGACTCATAGCTTACTGTTAT
1 ATTCATAACTTATTTTCAAACTCATAGCTTACTGTTAA
* * * * *
4343219 ATTCATAGCTTATTTTCAAATTCATAGTTTATTTTTAA
1 ATTCATAACTTATTTTCAAACTCATAGCTTACTGTTAA
4343257 ATTCATAAC
1 ATTCATAAC
4343266 CCAATACATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (38 bp):
ATTCATAACTTATTTTCAAACTCATAGCTTACTGTTAA
Found at i:4343241 original size:19 final size:19
Alignment explanation
Indices: 4343170--4343263 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
4343160 TGAATCAGAA
* * *
4343170 CTTATTTCCAGATTCATAA
1 CTTATTTTCAAATTCATAG
* *
4343189 CTTATTTTCAGACTCATAG
1 CTTATTTTCAAATTCATAG
* *
4343208 CTTACTGTT-ATATTCATAG
1 CTTA-TTTTCAAATTCATAG
4343227 CTTATTTTCAAATTCATAG
1 CTTATTTTCAAATTCATAG
* *
4343246 TTTATTTTTAAATTCATA
1 CTTATTTTCAAATTCATA
4343264 ACCCAATACA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
18 3 0.05
19 57 0.90
20 3 0.05
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (19 bp):
CTTATTTTCAAATTCATAG
Found at i:4344928 original size:20 final size:20
Alignment explanation
Indices: 4344903--4344941 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4344893 TCCAAAATAG
*
4344903 TCAAATTTCACATTCTAACA
1 TCAAATTTAACATTCTAACA
*
4344923 TCAAATTTAATATTCTAAC
1 TCAAATTTAACATTCTAAC
4344942 TTTCAATTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (20 bp):
TCAAATTTAACATTCTAACA
Found at i:4346972 original size:20 final size:20
Alignment explanation
Indices: 4346947--4347006 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
4346937 AGGCAGATTG
4346947 CCCAGAGGGTACCGATACCC
1 CCCAGAGGGTACCGATACCC
4346967 CCCAGAGGGTACCGATA-CC
1 CCCAGAGGGTACCGATACCC
*
4346986 CCCTGAGGGTACCGATACCC
1 CCCAGAGGGTACCGATACCC
4347006 C
1 C
4347007 TATGTAAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.47
20 20 0.53
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (20 bp):
CCCAGAGGGTACCGATACCC
Found at i:4346993 original size:19 final size:19
Alignment explanation
Indices: 4346947--4347006 Score: 102
Period size: 19 Copynumber: 3.1 Consensus size: 19
4346937 AGGCAGATTG
4346947 CCCAGAGGGTACCGATACCC
1 CCCAGAGGGTACCGATA-CC
4346967 CCCAGAGGGTACCGATACC
1 CCCAGAGGGTACCGATACC
*
4346986 CCCTGAGGGTACCGATACC
1 CCCAGAGGGTACCGATACC
4347005 CC
1 CC
4347007 TATGTAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (19 bp):
CCCAGAGGGTACCGATACC
Found at i:4349026 original size:21 final size:22
Alignment explanation
Indices: 4348988--4349030 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4348978 TATAAGACTT
4348988 TATTTTCAAAATACAAAAATGA
1 TATTTTCAAAATACAAAAATGA
**
4349010 TATTTT-AAAATTGAAAAATGA
1 TATTTTCAAAATACAAAAATGA
4349031 AAATAGTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (22 bp):
TATTTTCAAAATACAAAAATGA
Found at i:4352879 original size:22 final size:22
Alignment explanation
Indices: 4352836--4352894 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 22
4352826 TAGTGCAGGA
*
4352836 GGTATCGATACGCCTTTTGAATG
1 GGTATCGATAC-CCCTTTGAATG
4352859 GGTATCGATACCCCTTTGAATG
1 GGTATCGATACCCCTTTGAATG
4352881 GGTATCGATACCCC
1 GGTATCGATACCCC
4352895 CATGTGAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 24 0.69
23 11 0.31
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (22 bp):
GGTATCGATACCCCTTTGAATG
Found at i:4352906 original size:22 final size:23
Alignment explanation
Indices: 4352836--4352901 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
4352826 TAGTGCAGGA
* * *
4352836 GGTATCGATACGCCTTTTGAATG
1 GGTATCGATACCCCCTGTGAATG
*
4352859 GGTATCGATA-CCCCTTTGAATG
1 GGTATCGATACCCCCTGTGAATG
4352881 GGTATCGATACCCCCATGTGA
1 GGTATCGATACCCCC-TGTGA
4352902 GGGTACTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.53
23 14 0.37
24 4 0.11
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (23 bp):
GGTATCGATACCCCCTGTGAATG
Found at i:4353411 original size:20 final size:23
Alignment explanation
Indices: 4353364--4353411 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
4353354 TTATTTAATT
4353364 GTTTTTGAAAACTACTAATCATTA
1 GTTTTTGAAAACTAC-AATCATTA
4353388 -TTTTTGAAAACTA-AA-CA-TA
1 GTTTTTGAAAACTACAATCATTA
4353407 GTTTT
1 GTTTT
4353412 CAAAATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.09
20 6 0.26
21 2 0.09
23 13 0.57
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (23 bp):
GTTTTTGAAAACTACAATCATTA
Found at i:4355179 original size:13 final size:14
Alignment explanation
Indices: 4355153--4355185 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
4355143 GGGAGTAATA
4355153 ATTTTCTCAAAATG
1 ATTTTCTCAAAATG
4355167 ATTTTCT-AAAATG
1 ATTTTCTCAAAATG
4355180 ATTTTC
1 ATTTTC
4355186 AATAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (14 bp):
ATTTTCTCAAAATG
Found at i:4355533 original size:20 final size:20
Alignment explanation
Indices: 4355508--4355548 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4355498 AGGTAGATTG
4355508 CCCAGAGGGTACCGATACCC
1 CCCAGAGGGTACCGATACCC
4355528 CCCAGAGGGTACCGATACCC
1 CCCAGAGGGTACCGATACCC
4355548 C
1 C
4355549 TATGTAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.10
Consensus pattern (20 bp):
CCCAGAGGGTACCGATACCC
Found at i:4360213 original size:20 final size:20
Alignment explanation
Indices: 4360188--4360240 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
4360178 TTCAAAGTGA
4360188 GTAGTATCGATACTCTACTT
1 GTAGTATCGATACTCTACTT
4360208 GTAGTATCGATACTCTACTT
1 GTAGTATCGATACTCTACTT
4360228 GTAGTATCGATAC
1 GTAGTATCGATAC
4360241 CCTAGGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
GTAGTATCGATACTCTACTT
Found at i:4361964 original size:40 final size:41
Alignment explanation
Indices: 4361916--4361994 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
4361906 ATCCTATTTT
* *
4361916 TTAATATTTTTGATT-CAACTTAAAATATTATAAAAAAAAG
1 TTAATATTTTCGATTGCAACATAAAATATTATAAAAAAAAG
*
4361956 TTAATATTTTCGATTGCAACATAAAATATTATGAAAAAA
1 TTAATATTTTCGATTGCAACATAAAATATTATAAAAAAA
4361995 GTTTGCAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 14 0.40
41 21 0.60
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (41 bp):
TTAATATTTTCGATTGCAACATAAAATATTATAAAAAAAAG
Found at i:4362468 original size:23 final size:23
Alignment explanation
Indices: 4362442--4362491 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4362432 ATCAAGCACA
*
4362442 ATAACATATTAGGTACCGCTTAT
1 ATAACATAGTAGGTACCGCTTAT
** *
4362465 ATAATGTAGTAGGTAGCGCTTAT
1 ATAACATAGTAGGTACCGCTTAT
4362488 ATAA
1 ATAA
4362492 TAAATGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAACATAGTAGGTACCGCTTAT
Found at i:4362488 original size:87 final size:86
Alignment explanation
Indices: 4362342--4362591 Score: 396
Period size: 84 Copynumber: 2.9 Consensus size: 86
4362332 AACCGAAAAT
* * *
4362342 ATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATATGTAACACTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATA
4362407 AAATAGGTTAATTACTGGAAAC
66 AAATA-GTTAATTACTGGAAAC
*
4362429 ATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAGTAGGTAGCGCTTATATAAT-
1 ATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATA
*
4362493 AAAT-GTTAATCACTGGAAAC
66 AAATAGTTAATTACTGGAAAC
* *
4362513 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATA
*
4362578 AAATATATTAATTA
66 AAATA-GTTAATTA
4362592 TTTAATTTGT
Statistics
Matches: 150, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
84 76 0.51
85 4 0.03
86 4 0.03
87 66 0.44
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (86 bp):
ATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATA
AAATAGTTAATTACTGGAAAC
Found at i:4362552 original size:23 final size:23
Alignment explanation
Indices: 4362526--4362575 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
4362516 ATCAAGCACA
*
4362526 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
4362549 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
4362572 ATAA
1 ATAA
4362576 TAAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:4362582 original size:23 final size:23
Alignment explanation
Indices: 4362526--4362582 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
4362516 ATCAAGCACA
* *
4362526 ATAACATATTAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCGCTTAT
**
4362549 ATAACGTAATAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCGCTTAT
*
4362572 ATAATAAAATA
1 ATAACAAAATA
4362583 TATTAATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAACAAAATAGGTAGCGCTTAT
Found at i:4363111 original size:112 final size:111
Alignment explanation
Indices: 4362875--4363240 Score: 608
Period size: 112 Copynumber: 3.3 Consensus size: 111
4362865 CAGGTAAAAA
* * *
4362875 TATGACAAAACCGGTAAAATTTACCGGATAGGTTGAAAGTATCGATCTTTTTTATAAAAATGCAT
1 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATC-TTTTTATAAAAA-GGAT
* *
4362940 TGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCAT
64 CGATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
*
4362988 TATGACAAAACCCGTAAAATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAGGATC
1 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATC-TTTTTATAAAAAGGATC
* *
4363053 GATATTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCAT
65 GATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
4363100 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGAT-TCTTTTATAAAAAGGATC
1 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCT-TTTTATAAAAAGGATC
4363164 GATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
65 GATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
*
4363211 TTTGACAAAACCGGTAAAATTTACCTGATA
1 TATGACAAAACCGGTAAAATTTACCTGATA
4363241 CTTTAAAATA
Statistics
Matches: 239, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
110 1 0.00
111 90 0.38
112 92 0.38
113 56 0.23
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (111 bp):
TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCTTTTTATAAAAAGGATCG
ATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
Found at i:4363203 original size:111 final size:111
Alignment explanation
Indices: 4362875--4363240 Score: 599
Period size: 111 Copynumber: 3.3 Consensus size: 111
4362865 CAGGTAAAAA
* * * *
4362875 TATGACAAAACCGGTAAAATTTACCGGATAGGTTGAAAGTATCGATCTTTTTTATAAAAATGCAT
1 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGAT-TCTTTTATAAAAA-GGAT
* *
4362940 TGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCAT
64 CGATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
*
4362988 TATGACAAAACCCGTAAAATTTACCTGATATGTTGAAAGTATCGA-TCATTTTTATAAAAAGGAT
1 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATTC--TTTTATAAAAAGGAT
* *
4363052 CGATATTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCAT
64 CGATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
4363100 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATTCTTTTATAAAAAGGATCG
1 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATTCTTTTATAAAAAGGATCG
4363165 ATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
66 ATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
*
4363211 TTTGACAAAACCGGTAAAATTTACCTGATA
1 TATGACAAAACCGGTAAAATTTACCTGATA
4363241 CTTTAAAATA
Statistics
Matches: 237, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
111 91 0.38
112 91 0.38
113 55 0.23
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (111 bp):
TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATTCTTTTATAAAAAGGATCG
ATACTTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCAT
Found at i:4363251 original size:73 final size:73
Alignment explanation
Indices: 4363164--4363313 Score: 266
Period size: 73 Copynumber: 2.1 Consensus size: 73
4363154 AAAAAGGATC
* *
4363164 GATACTTTACAATATAACAGGTAAAAATATGACAAAA-TCAGTTTCATTTTGACAAAACCGGTAA
1 GATACTTTAAAATATAACAGGTAAAAATATGACAAAACT-AGTTTCATTATGACAAAACCGGTAA
4363228 AATTTACCT
65 AATTTACCT
4363237 GATACTTTAAAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
1 GATACTTTAAAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
4363302 ATTTACCT
66 ATTTACCT
4363310 GATA
1 GATA
4363314 TGTTGAAAGT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
73 73 0.99
74 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.29
Consensus pattern (73 bp):
GATACTTTAAAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
ATTTACCT
Found at i:4363381 original size:113 final size:112
Alignment explanation
Indices: 4363237--4363919 Score: 1048
Period size: 113 Copynumber: 6.1 Consensus size: 112
4363227 AAATTTACCT
*
4363237 GATACTTTAAAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
*
4363302 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAATGCATC
66 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAA-GGATC
* *
4363350 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCCGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
*
4363415 ATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAGGATC
66 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAAGGATC
* *
4363462 GATATTTTACAATATAACATGTAAAAATATGACAAAA-TCAGTTTCATTATGACAAAACCGGTAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACT-AGTTTCATTATGACAAAACCGGTAA
4363526 AATTTACCTGATATGTTGAAAGTATCGATCC-TTTTATAAAAAGGATC
65 AATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAAGGATC
* * * * *
4363573 GACACTTTACAATATAATATGTAAAAATATGACAAAACCAGTTTCATTATGAAAAAACCGGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
*
4363638 ATTTACCTAATATGTTGAAAGTATCGATCCTTTTTTATAAAAAGGATC
66 ATTTACCTGATATGTTGAAAGTATCGATCC-TTTTTATAAAAAGGATC
* *
4363686 GATACTTTAAAATATAACAGGTAAAAATATGACAAAACTAGTTTTATTATGACAAAACCGGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
* *
4363751 ATTTACCTGATATGTTGAAAGTATTGATCCTTTTTTATAAAAAGAATC
66 ATTTACCTGATATGTTGAAAGTATCGATCC-TTTTTATAAAAAGGATC
* * * * * *
4363799 AATAATTTATAATATAACATGTAAAAATATGACAAAA-TCAGTTTCATTATGATAAAACCAGTAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACT-AGTTTCATTATGACAAAACCGGTAA
* * * *
4363863 AATTTACCTGATATGTTGAGAGTATAGATACTTTTTATAAAAATGTATC
65 AATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAA-GGATC
4363912 GATACTTT
1 GATACTTT
4363920 GTTAAAAGTT
Statistics
Matches: 525, Mismatches: 39, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
111 104 0.20
112 106 0.20
113 315 0.60
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (112 bp):
GATACTTTACAATATAACAGGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAA
ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAAGGATC
Found at i:4363634 original size:409 final size:409
Alignment explanation
Indices: 4362875--4363645 Score: 1443
Period size: 409 Copynumber: 1.9 Consensus size: 409
4362865 CAGGTAAAAA
*
4362875 TATGACAAAACCGGTAAAATTTACCGGATAGGTTGAAAGTATCGATCTTTTTTATAAAAATGCAT
1 TATGACAAAACCGGTAAAATTTACCGGATAGGTTGAAAGTATCGATCCTTTTTATAAAAATGCAT
*
4362940 TGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCCGTAA
66 CGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCCGTAA
4363005 AATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAGGATCGATATTTTACAATATAA
131 AATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAGGATCGATATTTTACAATATAA
4363070 CATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
196 CATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
* *
4363135 AAAGTATCGATTCTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
261 AAAGTATCGATCCTTTTATAAAAAGGATCGACACTTTACAATATAACAGGTAAAAATATGACAAA
* * *
4363200 ATCAGTTTCATTTTGACAAAACCGGTAAAATTTACCTGATACTTTAAAATATAACAGGTAAAAAT
326 ACCAGTTTCATTATGAAAAAACCGGTAAAATTTACCTGATACTTTAAAATATAACAGGTAAAAAT
4363265 ATGACAAAACTAGTTTCAT
391 ATGACAAAACTAGTTTCAT
* *
4363284 TATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAATGCAT
1 TATGACAAAACCGGTAAAATTTACCGGATAGGTTGAAAGTATCGATCCTTTTTATAAAAATGCAT
4363349 CGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCCGTAA
66 CGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCCGTAA
4363414 AATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAGGATCGATATTTTACAATATAA
131 AATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAGGATCGATATTTTACAATATAA
4363479 CATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
196 CATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
* *
4363544 AAAGTATCGATCCTTTTATAAAAAGGATCGACACTTTACAATATAATATGTAAAAATATGACAAA
261 AAAGTATCGATCCTTTTATAAAAAGGATCGACACTTTACAATATAACAGGTAAAAATATGACAAA
4363609 ACCAGTTTCATTATGAAAAAACCGGTAAAATTTACCT
326 ACCAGTTTCATTATGAAAAAACCGGTAAAATTTACCT
4363646 AATATGTTGA
Statistics
Matches: 351, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
409 351 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (409 bp):
TATGACAAAACCGGTAAAATTTACCGGATAGGTTGAAAGTATCGATCCTTTTTATAAAAATGCAT
CGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCCGTAA
AATTTACCTGATATGTTGAAAGTATCGATCATTTTTATAAAAAGGATCGATATTTTACAATATAA
CATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
AAAGTATCGATCCTTTTATAAAAAGGATCGACACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGAAAAAACCGGTAAAATTTACCTGATACTTTAAAATATAACAGGTAAAAAT
ATGACAAAACTAGTTTCAT
Found at i:4364322 original size:23 final size:23
Alignment explanation
Indices: 4364296--4364355 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
4364286 ATCAAGTACA
* *
4364296 ATAATATATTAGGTACCGGTTAT
1 ATAATATAATAGGTACCGCTTAT
* * *
4364319 ATAATGTAATATGTAGCGCTTAT
1 ATAATATAATAGGTACCGCTTAT
*
4364342 ATAATAAAATAGGT
1 ATAATATAATAGGT
4364356 TAATTACTGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTACCGCTTAT
Found at i:4364348 original size:87 final size:87
Alignment explanation
Indices: 4364244--4364410 Score: 262
Period size: 87 Copynumber: 1.9 Consensus size: 87
4364234 TTCCACAGAG
* *
4364244 GTAGCACTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAGTACAATAATATATTAGG
1 GTAGCACTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAGCACAATAACATATTAGG
*
4364309 TACCGGTTATATAATGTAATAT
66 TACCGCTTATATAATGTAATAT
* * * *
4364331 GTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
1 GTAGCACTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAGCACAATAACATATTAGG
*
4364396 TAGCGCTTATATAAT
66 TACCGCTTATATAAT
4364411 AAAATATGAT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
GTAGCACTTATATAATAAAATAGATTAATTACTAGAAACATTATCAAGCACAATAACATATTAGG
TACCGCTTATATAATGTAATAT
Found at i:4364767 original size:113 final size:113
Alignment explanation
Indices: 4364645--4365110 Score: 740
Period size: 112 Copynumber: 4.1 Consensus size: 113
4364635 GTATCGATAC
* *
4364645 TTTATAAAAATGTATCGATACTTTACAATATAACAAGTAAAATTATGACAAAACCAGTTTCATTA
1 TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
* *
4364710 TGACAAAATCGGTAAAATTTACCGGATATGTTGAAAGTATCGATCATT
66 TGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCATT
*
4364758 TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTTATTA
1 TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
* *
4364823 TGACAAAACCGGTAAATTTTACCTGATATGTTGAAAGTATCGATCCTT
66 TGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCATT
* * *
4364871 TTTATAAAAA-GGATCGATACTTTACAATATAACAGGTAAAAATATGAAAAAATCAGTTTCATTA
1 TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
* *
4364935 TGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTT
66 TGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCATT
* * *
4364983 TTTATAAAAATG-ATCGATATTTTACAATATAACACGCAAAAATATGACAAAACCAGTTTCATTA
1 TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
* **
4365047 TGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTATATAT-ACTT
66 TGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCA-TT
4365095 TTTATAAAAATGTATC
1 TTTATAAAAATGTATC
4365111 AATATTTTGT
Statistics
Matches: 327, Mismatches: 23, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
112 207 0.63
113 120 0.37
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (113 bp):
TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
TGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCATT
Found at i:4365747 original size:17 final size:17
Alignment explanation
Indices: 4365722--4365760 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4365712 CATTTTAAAA
*
4365722 ATTTAAAATTATTATAT
1 ATTTTAAATTATTATAT
*
4365739 ATTTTAAATTTTTATAT
1 ATTTTAAATTATTATAT
4365756 ATTTT
1 ATTTT
4365761 TATTAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTAAATTATTATAT
Found at i:4369718 original size:20 final size:20
Alignment explanation
Indices: 4369693--4369730 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4369683 TATAATATTA
4369693 TAATATTCTAAAAATATTCT
1 TAATATTCTAAAAATATTCT
*
4369713 TAATATTCTTAAAATATT
1 TAATATTCTAAAAATATT
4369731 TTCCAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATTCTAAAAATATTCT
Found at i:4371657 original size:17 final size:17
Alignment explanation
Indices: 4371635--4371669 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4371625 TGATTCCTTT
4371635 GGAAAAGTAAGTAGGTG
1 GGAAAAGTAAGTAGGTG
4371652 GGAAAAGTAAGTAGGTG
1 GGAAAAGTAAGTAGGTG
4371669 G
1 G
4371670 TTGTAGACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (17 bp):
GGAAAAGTAAGTAGGTG
Found at i:4371847 original size:36 final size:36
Alignment explanation
Indices: 4371749--4371950 Score: 166
Period size: 38 Copynumber: 5.4 Consensus size: 36
4371739 TTGCAAATTG
4371749 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT---TATATAATATATAGTTTTTAAAACA
* *
4371786 TTTTTTGAAAA-TATGTATATCATATAGTTTTTAAAATA
1 -TTTTTGAAAATTATATA-AT-ATATAGTTTTTAAAACA
*
4371824 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTTTGAAAATTATATAATATATAGTTTTT-AAAACA
* *
4371861 TTTTT-AAAATATATATAATATATACTTTTGAAAAC-
1 TTTTTGAAAAT-TATATAATATATAGTTTTTAAAACA
* * *
4371896 GTTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTTG-AAA-A-TTATATAATATATAGTTTTT-AAAA-CA
4371937 -TTTTGAAAA-TATAT
1 TTTTTGAAAATTATAT
4371951 TTTTTGAAAA
Statistics
Matches: 138, Mismatches: 12, Indels: 30
0.77 0.07 0.17
Matches are distributed among these distances:
34 5 0.04
35 5 0.04
36 32 0.23
37 41 0.30
38 42 0.30
39 8 0.06
40 5 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATAGTTTTTAAAACA
Found at i:4371859 original size:75 final size:72
Alignment explanation
Indices: 4371721--4371950 Score: 200
Period size: 75 Copynumber: 3.1 Consensus size: 72
4371711 ATATATACAC
* * *
4371721 ATATATATATTATATAGTTTGCAAATTGTTTTTGAAAATACATATATAATATATAG--TTTAAAA
1 ATATATATA-TATATAGTTTTCAAAATATTTTTGAAAAT---TATATAATATATAGTTTTTAAAA
4371784 CATTTTTTGAAA
62 CA-TTTTTGAAA
* * *
4371796 ATATGTATATCATATAGTTTTTAAAATATTTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 ATATATATAT-ATATAGTTTTCAAAATATTTTTGAAAATTATATAATATATAGTTTTT-AAAACA
4371861 TTTTT-AAA
64 TTTTTGAAA
* * ** * *
4371869 ATATATATAATATATACTTTTGAAAA-CGTTATGAAAACATTTATATAATATATAATTTTTAAAA
1 ATATATAT-ATATATAGTTTTCAAAATATTTTTG-AAA-A-TTATATAATATATAGTTTTT-AAA
4371933 ACCA-TTTTGAAA
61 A-CATTTTTGAAA
4371945 ATATAT
1 ATATAT
4371951 TTTTTGAAAA
Statistics
Matches: 130, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
72 18 0.14
73 26 0.20
74 12 0.09
75 64 0.49
76 10 0.08
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (72 bp):
ATATATATATATATAGTTTTCAAAATATTTTTGAAAATTATATAATATATAGTTTTTAAAACATT
TTTGAAA
Found at i:4371932 original size:27 final size:28
Alignment explanation
Indices: 4371902--4371985 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 28
4371892 AAACGTTATG
4371902 AAAACATTTATATAATATATAATTTTTA
1 AAAACATTTATATAATATATAATTTTTA
*
4371930 AAAACCATTT-TGA-AA-ATAT-ATTTTTT
1 AAAA-CATTTAT-ATAATATATAATTTTTA
* * *
4371956 GAAA-A-TTATATAATATATAGTTTTTG
1 AAAACATTTATATAATATATAATTTTTA
4371982 AAAA
1 AAAA
4371986 TGTTTTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
23 3 0.07
24 4 0.09
25 4 0.09
26 17 0.38
27 4 0.09
28 7 0.16
29 6 0.13
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (28 bp):
AAAACATTTATATAATATATAATTTTTA
Found at i:4371957 original size:15 final size:16
Alignment explanation
Indices: 4371937--4371966 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4371927 TTAAAAACCA
4371937 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
4371952 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
4371967 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:4371964 original size:127 final size:127
Alignment explanation
Indices: 4371824--4372077 Score: 499
Period size: 127 Copynumber: 2.0 Consensus size: 127
4371814 TTTTAAAATA
4371824 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
4371889 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
66 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
*
4371951 TTTTTGAAAATTATATAATATATAGTTTTTGAAAATGTTTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
4372016 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
66 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
4372078 ATAATATATA
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (127 bp):
TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
Found at i:4371973 original size:25 final size:25
Alignment explanation
Indices: 4371909--4371986 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
4371899 ATGAAAACAT
*
4371909 TTATATAATATATAATTTTTAAAAA
1 TTATATAATATATAATTTTTGAAAA
** * * *
4371934 CCATTTTGAAAATATATTTTTTGAAAA
1 TTA-TAT-AATATATAATTTTTGAAAA
*
4371961 TTATATAATATATAGTTTTTGAAAA
1 TTATATAATATATAATTTTTGAAAA
4371986 T
1 T
4371987 GTTTTTAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
25 19 0.47
26 4 0.10
27 17 0.43
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (25 bp):
TTATATAATATATAATTTTTGAAAA
Found at i:4372017 original size:36 final size:36
Alignment explanation
Indices: 4371951--4372140 Score: 175
Period size: 38 Copynumber: 5.1 Consensus size: 36
4371941 GAAAATATAT
*
4371951 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAATG
1 TTTTT-AAAATATATATAATATATA-TTTTTGAAAACG
*
4371988 TTTTTAAAATATATATAATATATACTTTTGAAAACG
1 TTTTTAAAATATATATAATATATATTTTTGAAAACG
** * * *
4372024 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TT-TTTAAA-ATATATATAATATAT-ATTTTTGAAAA-CG
* * *
4372064 TTTTGAAAATATATATAATATATAGTTTTTTTAAAACA
1 TTTTTAAAATATATATAATATATA--TTTTTGAAAACG
* * * *
4372102 TTTTAAAAATTTATATATTATATGTTTTTGAAAACG
1 TTTTTAAAATATATATAATATATATTTTTGAAAACG
4372138 TTT
1 TTT
4372141 ATATATATAA
Statistics
Matches: 128, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
36 30 0.23
37 23 0.18
38 50 0.39
39 22 0.17
40 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (36 bp):
TTTTTAAAATATATATAATATATATTTTTGAAAACG
Found at i:4372987 original size:22 final size:22
Alignment explanation
Indices: 4372953--4373009 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
4372943 TGGGTTGGTC
*
4372953 CGGCCGCCGGAGCGACTGAGAG
1 CGGCGGCCGGAGCGACTGAGAG
*
4372975 CGGCGGCCAGAGCGACTGAGAG
1 CGGCGGCCGGAGCGACTGAGAG
4372997 CGGCGGCCGGAGC
1 CGGCGGCCGGAGC
4373010 TACACCGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.32, G:0.47, T:0.04
Consensus pattern (22 bp):
CGGCGGCCGGAGCGACTGAGAG
Found at i:4373472 original size:23 final size:24
Alignment explanation
Indices: 4373424--4373473 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
4373414 ATTTCGTCTT
* *
4373424 TTTTTTTATTTTATTATTCTATTG
1 TTTTGTTATTTTATTATTCTAATG
4373448 TTTTGTTA-TTTATTTATT-TAATG
1 TTTTGTTATTTTA-TTATTCTAATG
4373471 TTT
1 TTT
4373474 AATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTGTTATTTTATTATTCTAATG
Found at i:4374555 original size:17 final size:17
Alignment explanation
Indices: 4374535--4374567 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4374525 CTCACTAACC
*
4374535 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
4374552 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
4374568 ATCGTTTGCA
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:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:4375201 original size:18 final size:19
Alignment explanation
Indices: 4375180--4375216 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4375170 ATTTAGACAT
4375180 TTTGAATTTT-TTATTTTC
1 TTTGAATTTTGTTATTTTC
*
4375198 TTTGCATTTTGTTATTTTC
1 TTTGAATTTTGTTATTTTC
4375217 ATTGCATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.70
Consensus pattern (19 bp):
TTTGAATTTTGTTATTTTC
Found at i:4375214 original size:19 final size:18
Alignment explanation
Indices: 4375180--4375224 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
4375170 ATTTAGACAT
*
4375180 TTTGAATTTTTTATTTTC
1 TTTGCATTTTTTATTTTC
4375198 TTTGCATTTTGTTATTTTC
1 TTTGCATTTT-TTATTTTC
*
4375217 ATTGCATT
1 TTTGCATT
4375225 CACATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.67
Consensus pattern (18 bp):
TTTGCATTTTTTATTTTC
Found at i:4378808 original size:84 final size:83
Alignment explanation
Indices: 4378614--4379397 Score: 712
Period size: 84 Copynumber: 9.5 Consensus size: 83
4378604 TTTTTAAACA
* * * ** *
4378614 ATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
* * * * *
4378676 CACTCAACTTCGAGGGAAC
66 CGCTCAGC-TCCAAGGCAC
4378695 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACT
*
4378760 ACGCTCAGCTCCAAGGCAT
65 ACGCTCAGCTCCAAGGCAC
* * * * * *
4378779 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACT
*
4378844 ACGCTCAGCT-CAACGTCAC
65 ACGCTCAGCTCCAA-GGCAC
* * * * ** * *
4378863 ATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGATTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
* * *
4378925 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
* * * * ** *
4378944 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGACT
*
4379009 ACGCTCAGCTCCAAGGTAC
65 ACGCTCAGCTCCAAGGCAC
* * * * ** *
4379028 ATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTA--T-CAGCCAAAGACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
* ** *
4379090 CACTCAGCTTTGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
* * * * ** *
4379109 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGACT
4379174 ACGCTCAGCTCCAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
* * * ** *
4379193 ATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
* * *
4379255 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
* * * * ** *
4379274 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGACT
4379339 ACGCTCAGCTCCAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
* * *
4379358 ATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
4379398 CAAAGACTCC
Statistics
Matches: 554, Mismatches: 128, Indels: 39
0.77 0.18 0.05
Matches are distributed among these distances:
80 71 0.13
81 150 0.27
82 2 0.00
83 4 0.01
84 230 0.42
85 97 0.18
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (83 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCAC
Found at i:4378950 original size:165 final size:165
Alignment explanation
Indices: 4378693--4379474 Score: 1190
Period size: 165 Copynumber: 4.7 Consensus size: 165
4378683 CTTCGAGGGA
* * * **
4378693 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
1 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGA
* * * * * * * * * * ** *
4378758 CTACGCTCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
62 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
* *
4378822 CAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGTC
127 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGC
* * * *
4378861 ACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGATTTCGATTAC
1 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
4378926 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
66 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
*
4378991 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGT
131 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
*
4379026 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCAGCCAAAGACCCCCGAGTTCGATTAC
1 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
*
4379091 ACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
66 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
4379156 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
131 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
4379191 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
1 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
4379256 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
66 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
4379321 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
131 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
*
4379356 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCCCGAGTTCGATTAC
1 ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
* * * * * * *
4379421 ACTCAACTTCGAGGTCATATCATTTACAACATAACTCATGGCAAGAAAGGTTAT
66 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
4379475 TTGTCAATAA
Statistics
Matches: 572, Mismatches: 40, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
164 26 0.05
165 506 0.88
166 3 0.01
168 37 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
ACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAA
AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
Found at i:4379059 original size:249 final size:245
Alignment explanation
Indices: 4378614--4379474 Score: 924
Period size: 249 Copynumber: 3.5 Consensus size: 245
4378604 TTTTTAAACA
*
4378614 ATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
* * * * **
4378679 TCAACTTCGAGGGAACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG-TGACCAAAG
* *
4378744 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAG
130 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAG
* * *
4378809 GGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGTCAC
195 GGTTATCTG-C-ACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCAC
* * *
4378863 ATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGATTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
* *
4378928 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAG
66 TCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACC-AAAG
* * * * *
4378993 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATATGCAGCATAGCTTAAGTCGAGAAG
130 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAG
* * *** * * * *
4379058 GGCTATCAGC-C-AAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCAC
195 GGTTATCTGCACAAAAGACCTTTGAGTTCGACTACGCTCAGC--TCAAGGCAC
* * * * * * *** *
4379109 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCGATT
* * * * * * * * * *
4379174 ACGCTCAGC-TCCAAGGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CCA
62 ACACTCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCA
** * * * * * * *
4379235 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
127 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
*
4379300 GAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
191 GAAGGGTTATCTG-CA-CAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCAC
* *
4379358 ATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
* * * * * *
4379423 TCAACTTCGAGGTCATATCATTTACAACATAACTCATGGCAAGAAAGGTTAT
66 TCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTAT
4379475 TTGTCAATAA
Statistics
Matches: 492, Mismatches: 106, Indels: 31
0.78 0.17 0.05
Matches are distributed among these distances:
245 69 0.14
246 108 0.22
247 6 0.01
248 7 0.01
249 255 0.52
250 47 0.10
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (245 bp):
ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
TCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTGACCAAAGA
CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGG
GTTATCTGCACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCAC
Found at i:4380156 original size:36 final size:36
Alignment explanation
Indices: 4380058--4380259 Score: 166
Period size: 38 Copynumber: 5.4 Consensus size: 36
4380048 TTGCAAATTG
4380058 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT---TATATAATATATAGTTTTTAAAACA
* *
4380095 TTTTTTGAAAA-TATGTATATCATATAGTTTTTAAAATA
1 -TTTTTGAAAATTATATA-AT-ATATAGTTTTTAAAACA
*
4380133 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTTTGAAAATTATATAATATATAGTTTTT-AAAACA
* *
4380170 TTTTT-AAAATATATATAATATATACTTTTGAAAAC-
1 TTTTTGAAAAT-TATATAATATATAGTTTTTAAAACA
* * *
4380205 GTTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTTG-AAA-A-TTATATAATATATAGTTTTT-AAAA-CA
4380246 -TTTTGAAAA-TATAT
1 TTTTTGAAAATTATAT
4380260 TTTTTGAAAA
Statistics
Matches: 138, Mismatches: 12, Indels: 30
0.77 0.07 0.17
Matches are distributed among these distances:
34 5 0.04
35 5 0.04
36 32 0.23
37 41 0.30
38 42 0.30
39 8 0.06
40 5 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATAGTTTTTAAAACA
Found at i:4380168 original size:75 final size:72
Alignment explanation
Indices: 4380032--4380259 Score: 198
Period size: 75 Copynumber: 3.1 Consensus size: 72
4380022 ATATATACAC
* * *
4380032 ATATATAT-TATATAGTTTGCAAATTGTTTTTGAAAATACATATATAATATATAG--TTTAAAAC
1 ATATATATATATATAGTTTTCAAAATATTTTTGAAAAT---TATATAATATATAGTTTTTAAAAC
4380094 ATTTTTTGAAA
63 A-TTTTTGAAA
* * *
4380105 ATATGTATATCATATAGTTTTTAAAATATTTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 ATATATATAT-ATATAGTTTTCAAAATATTTTTGAAAATTATATAATATATAGTTTTT-AAAACA
4380170 TTTTT-AAA
64 TTTTTGAAA
* * ** * *
4380178 ATATATATAATATATACTTTTGAAAA-CGTTATGAAAACATTTATATAATATATAATTTTTAAAA
1 ATATATAT-ATATATAGTTTTCAAAATATTTTTG-AAA-A-TTATATAATATATAGTTTTT-AAA
4380242 ACCA-TTTTGAAA
61 A-CATTTTTGAAA
4380254 ATATAT
1 ATATAT
4380260 TTTTTGAAAA
Statistics
Matches: 129, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
72 18 0.14
73 33 0.26
74 12 0.09
75 56 0.43
76 10 0.08
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (72 bp):
ATATATATATATATAGTTTTCAAAATATTTTTGAAAATTATATAATATATAGTTTTTAAAACATT
TTTGAAA
Found at i:4380241 original size:27 final size:28
Alignment explanation
Indices: 4380211--4380294 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 28
4380201 AAACGTTATG
4380211 AAAACATTTATATAATATATAATTTTTA
1 AAAACATTTATATAATATATAATTTTTA
*
4380239 AAAACCATTT-TGA-AA-ATAT-ATTTTTT
1 AAAA-CATTTAT-ATAATATATAATTTTTA
* * *
4380265 GAAA-A-TTATATAATATATAGTTTTTG
1 AAAACATTTATATAATATATAATTTTTA
4380291 AAAA
1 AAAA
4380295 TGTTTTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
23 3 0.07
24 4 0.09
25 4 0.09
26 17 0.38
27 4 0.09
28 7 0.16
29 6 0.13
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (28 bp):
AAAACATTTATATAATATATAATTTTTA
Found at i:4380266 original size:15 final size:16
Alignment explanation
Indices: 4380246--4380275 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4380236 TTAAAAACCA
4380246 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
4380261 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
4380276 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:4380267 original size:127 final size:127
Alignment explanation
Indices: 4380133--4380386 Score: 499
Period size: 127 Copynumber: 2.0 Consensus size: 127
4380123 TTTTAAAATA
4380133 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
4380198 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
66 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
*
4380260 TTTTTGAAAATTATATAATATATAGTTTTTGAAAATGTTTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
4380325 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
66 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
4380387 ATAATATATA
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (127 bp):
TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
Found at i:4380282 original size:25 final size:25
Alignment explanation
Indices: 4380218--4380295 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
4380208 ATGAAAACAT
*
4380218 TTATATAATATATAATTTTTAAAAA
1 TTATATAATATATAATTTTTGAAAA
** * * *
4380243 CCATTTTGAAAATATATTTTTTGAAAA
1 TTA-TAT-AATATATAATTTTTGAAAA
*
4380270 TTATATAATATATAGTTTTTGAAAA
1 TTATATAATATATAATTTTTGAAAA
4380295 T
1 T
4380296 GTTTTTAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
25 19 0.47
26 4 0.10
27 17 0.43
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (25 bp):
TTATATAATATATAATTTTTGAAAA
Found at i:4380326 original size:36 final size:36
Alignment explanation
Indices: 4380260--4380449 Score: 175
Period size: 38 Copynumber: 5.1 Consensus size: 36
4380250 GAAAATATAT
*
4380260 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAATG
1 TTTTT-AAAATATATATAATATATA-TTTTTGAAAACG
*
4380297 TTTTTAAAATATATATAATATATACTTTTGAAAACG
1 TTTTTAAAATATATATAATATATATTTTTGAAAACG
** * * *
4380333 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TT-TTTAAA-ATATATATAATATAT-ATTTTTGAAAA-CG
* * *
4380373 TTTTGAAAATATATATAATATATAGTTTTTTTAAAACA
1 TTTTTAAAATATATATAATATATA--TTTTTGAAAACG
* * * *
4380411 TTTTAAAAATTTATATATTATATGTTTTTGAAAACG
1 TTTTTAAAATATATATAATATATATTTTTGAAAACG
4380447 TTT
1 TTT
4380450 ATATATATAA
Statistics
Matches: 128, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
36 30 0.23
37 23 0.18
38 50 0.39
39 22 0.17
40 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (36 bp):
TTTTTAAAATATATATAATATATATTTTTGAAAACG
Found at i:4381295 original size:22 final size:22
Alignment explanation
Indices: 4381261--4381317 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
4381251 TGGGTTGGTC
*
4381261 CGGCCGCCGGAGCAACTGAGAG
1 CGGCGGCCGGAGCAACTGAGAG
* *
4381283 CGGCGGCCAGAGCGACTGAGAG
1 CGGCGGCCGGAGCAACTGAGAG
4381305 CGGCGGCCGGAGC
1 CGGCGGCCGGAGC
4381318 TACACCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.32, G:0.46, T:0.04
Consensus pattern (22 bp):
CGGCGGCCGGAGCAACTGAGAG
Found at i:4381777 original size:23 final size:24
Alignment explanation
Indices: 4381729--4381778 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
4381719 CAATTTCGTC
* *
4381729 TTTTTTTATTTTATTATTCTATTG
1 TTTTGTTATTTTATTATTCTAATG
4381753 TTTTGTTA-TTTATTTATT-TAATG
1 TTTTGTTATTTTA-TTATTCTAATG
4381776 TTT
1 TTT
4381779 AATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTGTTATTTTATTATTCTAATG
Found at i:4387339 original size:10 final size:10
Alignment explanation
Indices: 4387294--4387340 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
4387284 CATTATTTTA
4387294 TAAAAATATG
1 TAAAAATATG
*
4387304 TAAATA-ATG
1 TAAAAATATG
* *
4387313 TAAAAAGATC
1 TAAAAATATG
*
4387323 TAAAAATATT
1 TAAAAATATG
4387333 TAAAAATA
1 TAAAAATA
4387341 ATATTATTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (10 bp):
TAAAAATATG
Found at i:4395267 original size:23 final size:23
Alignment explanation
Indices: 4395240--4395286 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4395230 ATTAAATTAT
4395240 AATTCAGA-AAAGAAAGATGCATA
1 AATTC-GACAAAGAAAGATGCATA
**
4395263 AATTCGACAAAGAAATTTGCATA
1 AATTCGACAAAGAAAGATGCATA
4395286 A
1 A
4395287 GGTAAAGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.21
Consensus pattern (23 bp):
AATTCGACAAAGAAAGATGCATA
Found at i:4403865 original size:3 final size:3
Alignment explanation
Indices: 4403859--4403919 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
4403849 AAAAAATATG
* **
4403859 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4403903 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
4403920 CGATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:4403896 original size:29 final size:30
Alignment explanation
Indices: 4403864--4403926 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
4403854 ATATGTAATA
*
4403864 ATAAATAATAATAA-AATAATAAGATAACG
1 ATAAATAATAATAATAATAATAAAATAACG
4403893 AT-AATAATAATAATAATAATAAAATAACG
1 ATAAATAATAATAATAATAATAAAATAACG
4403922 ATAAA
1 ATAAA
4403927 AAAACCCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 11 0.35
29 18 0.58
30 2 0.06
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (30 bp):
ATAAATAATAATAATAATAATAAAATAACG
Found at i:4404141 original size:43 final size:44
Alignment explanation
Indices: 4404072--4404456 Score: 218
Period size: 46 Copynumber: 9.0 Consensus size: 44
4404062 TCTGTTGGTG
* * ** * *
4404072 GGGACGACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTAA
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
* *
4404116 GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG---TC--G
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
* ** * *
4404154 GGGAATGACACGACTCATACGCAATGAAGAGTTCTGG-CTATCTAAA
1 GGG-ATGACACGGCTCATACGTGATGAGGAGATCTGGTC-ATCT-AA
* * * * *
4404200 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-A
1 GG-GATGACACGGCTCATACGTGATGAGGA-GATCTGGTCATCTAA
* * *
4404244 GGG-TGACACGACTCATACGTGATGAAGAGATCTGG---TCT-G
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
* * * * *
4404283 GGGATGACACGGTTCCTACATGATGAGGACG-GCTGGCCATCTAAA
1 GGGATGACACGGCTCATACGTGATGAGGA-GATCTGGTCATCT-AA
* * * * *
4404328 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-A
1 GG-GATGACACGGCTCATACGTGATGAGGA-GATCTGGTCATCTAA
* * * *
4404372 TGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG---TCT-G
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
4404412 GGGAATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
1 GGG-ATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
4404457 AGGAGTTATG
Statistics
Matches: 267, Mismatches: 48, Indels: 51
0.73 0.13 0.14
Matches are distributed among these distances:
38 3 0.01
39 6 0.02
40 59 0.22
41 33 0.12
42 25 0.09
43 61 0.23
44 11 0.04
45 2 0.01
46 65 0.24
47 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (44 bp):
GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
Found at i:4404269 original size:88 final size:82
Alignment explanation
Indices: 4404159--4404318 Score: 212
Period size: 82 Copynumber: 1.9 Consensus size: 82
4404149 GGTCGGGGAA
* * *
4404159 TGACACGACTCATACGCAATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGACTCATACGCAATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATGA
4404224 TGAGGACGGCTGGTTATCTAGGG
60 TGAGGACGGCTGGTTATCTAGGG
** *
4404247 TGACACGACTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGACTCATACGCAATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
4404312 CGGCTGG
66 CGGCTGG
4404319 CCATCTAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
82 34 0.52
85 3 0.05
88 29 0.44
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (82 bp):
TGACACGACTCATACGCAATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
CGGCTGGTTATCTAGGG
Found at i:4404343 original size:128 final size:129
Alignment explanation
Indices: 4404104--4404459 Score: 520
Period size: 128 Copynumber: 2.8 Consensus size: 129
4404094 ATGAAGAGGT
* *
4404104 CTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGAC
1 CTGGTTATCT-AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGC
** * * *
4404168 TCATACGCAATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
65 TCATACGTGATGAGGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* *
4404233 CTGGTTATCTAGGGTGACACGACTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGTT
1 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCT
* * *
4404297 CCTACATGATGAGGACG-GCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
66 CATACGTGATGAGGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* * *
4404361 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGC
1 CTGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGC
*
4404426 TCATACGTGATGAGGAGATCTGGTCATCTAAAGG
65 TCATACGTGATGAGGAGATCTGGCCATCTAAAGG
4404460 AGTTATGGTT
Statistics
Matches: 202, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
128 112 0.55
129 53 0.26
130 37 0.18
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (129 bp):
CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCT
CATACGTGATGAGGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
Found at i:4404605 original size:63 final size:62
Alignment explanation
Indices: 4404537--4404654 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 62
4404527 TTTCAAAAGC
*
4404537 AACTGTCTC-AAAAGAGACAAAATTTTGTTTCAAA-GGAAATGA-CTCAAAGATTGTTTAAAGGA
1 AACTGTCTCGAAAA-AGACAAAA-TTCGTTT-AAAGGGAAATGATCTCAAAGA-TGTTTAAAGGA
4404599 A
62 A
*
4404600 AACTGTCTCGAATAAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCGAAAAAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
4404655 GTTTTGTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 3 0.06
62 19 0.38
63 25 0.50
64 3 0.06
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (62 bp):
AACTGTCTCGAAAAAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTTAAAGGAA
Found at i:4404819 original size:64 final size:64
Alignment explanation
Indices: 4404722--4404964 Score: 256
Period size: 67 Copynumber: 3.7 Consensus size: 64
4404712 ACTCAAAGAT
* * ** * * * *
4404722 TTTCAAAATGAACATATTCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTTAT
1 TTTCAAAA-AAACAGATTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTT-T
4404787 -
64 G
*
4404787 TTT-AAGAAAAACAGATTCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTG
1 TTTCAA-AAAAACAGATTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTG
* *
4404851 TTTCCAAAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTT
1 TTT-CAAAAAAACAGATTCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTT
4404916 TG
63 TG
* * * * *
4404918 TTCCCAAAGAAACAAACTCAAAGATTTTTTTCCAAAAGAAACAATCT
1 TT-TCAAAAAAACAGATTCAAAGATTTTTTT-CAAAAGAAACTATCT
4404965 CAAAGATTTT
Statistics
Matches: 155, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
63 1 0.01
64 50 0.32
65 23 0.15
66 24 0.15
67 57 0.37
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (64 bp):
TTTCAAAAAAACAGATTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTG
Found at i:4404860 original size:37 final size:37
Alignment explanation
Indices: 4404804--4404929 Score: 103
Period size: 37 Copynumber: 3.6 Consensus size: 37
4404794 AAAACAGATT
4404804 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGATTTTGTTTCAAAAGAAA-TATCTTAAGAGAGA
* **
4404841 CAAA-ATTTTGTTTCCAAAG-AA-A-C-----AGACT
1 CAAAGATTTTGTTTCAAAAGAAATATCTTAAGAGAGA
4404869 CAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCAAAAGAAA-TATCTTAAGAGAGA
* *
4404908 CAAA-ATTTTGTTCCCAAAGAAA
1 CAAAGATTTTGTTTCAAAAGAAA
4404930 CAAACTCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
28 7 0.10
29 1 0.01
30 13 0.19
31 2 0.03
33 2 0.03
34 2 0.03
36 7 0.10
37 27 0.39
38 1 0.01
39 7 0.10
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (37 bp):
CAAAGATTTTGTTTCAAAAGAAATATCTTAAGAGAGA
Found at i:4404877 original size:29 final size:28
Alignment explanation
Indices: 4404841--4404974 Score: 92
Period size: 29 Copynumber: 4.4 Consensus size: 28
4404831 TTAAGAGAGA
4404841 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTGTTTCCAAAGAAACA-ACT
* *
4404869 CAAAGATTTTTGTTTCAAAAGAAACTATCTT
1 CAAAGA-TTTTGTTTCCAAAGAAAC-AAC-T
* *
4404900 AAGAGAGACAAAATTTTGTTCCCAAAGAAACAAACT
1 CA-A-AG-----ATTTTGTTTCCAAAGAAAC-AACT
4404936 CAAAGATTTT-TTTCCAAAAGAAACAATCT
1 CAAAGATTTTGTTTCC-AAAGAAACAA-CT
4404965 CAAAGATTTT
1 CAAAGATTTT
4404975 TTCACAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
28 10 0.12
29 26 0.31
30 18 0.21
31 3 0.04
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 2 0.02
37 18 0.21
38 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (28 bp):
CAAAGATTTTGTTTCCAAAGAAACAACT
Found at i:4404898 original size:67 final size:66
Alignment explanation
Indices: 4404751--4404964 Score: 274
Period size: 67 Copynumber: 3.3 Consensus size: 66
4404741 AAAGATTTAC
* * * * * *
4404751 TTCAAGAGAAACTGTCTCAAGAGATACAAAATTTAT-TTT--AAGAAAAACAGATTCAAAGA-TT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTT-TGTTTCCAA-AGAAACAGACTCAAAGATTT
4404812 TTT
64 TTT
*
4404815 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
4404880 GT
66 -T
* *
4404882 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTCCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
4404947 T
66 T
* *
4404948 TCCAAAAGAAACAATCT
1 TTCAAAAGAAACTATCT
4404965 CAAAGATTTT
Statistics
Matches: 133, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 32 0.24
65 15 0.11
66 22 0.17
67 63 0.47
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (66 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
T
Found at i:4404983 original size:29 final size:29
Alignment explanation
Indices: 4404908--4404976 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
4404898 TTAAGAGAGA
* *
4404908 CAAA-ATTTTGTTCCCAAAGAAACAAACT
1 CAAAGATTTTTTTCCAAAAGAAACAAACT
*
4404936 CAAAGATTTTTTTCCAAAAGAAACAATCT
1 CAAAGATTTTTTTCCAAAAGAAACAAACT
4404965 CAAAGATTTTTT
1 CAAAGATTTTTT
4404977 CACAAAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 4 0.11
29 33 0.89
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.32
Consensus pattern (29 bp):
CAAAGATTTTTTTCCAAAAGAAACAAACT
Found at i:4405020 original size:53 final size:53
Alignment explanation
Indices: 4404963--4405068 Score: 151
Period size: 55 Copynumber: 2.0 Consensus size: 53
4404953 AAGAAACAAT
*
4404963 CTCAAAGATTTTTTC-ACAAAATTGTCTAAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTCAACAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAGA
* *
4405016 CTCAAAGATTTTTCAAAAGAAAACTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTC--AACAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCA
4405069 AAATAAATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
52 6 0.13
53 8 0.17
55 33 0.70
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (53 bp):
CTCAAAGATTTTTCAACAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAGA
Found at i:4405093 original size:26 final size:25
Alignment explanation
Indices: 4405064--4405185 Score: 100
Period size: 28 Copynumber: 4.5 Consensus size: 25
4405054 CAAAACTTTG
* *
4405064 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
4405090 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
4405117 TATTCAAAAGGAACAAACTCCAAGATTT
1 T-TTCAAAAGAAAC-AACTCAAAGA-TT
* *
4405145 TATTTAAAAGGAACTAACTCAAAGATTT
1 T-TTCAAAAGAAAC-AACTCAAAGA-TT
*
4405173 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
4405186 TGTCTCAAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
25 8 0.10
26 12 0.15
27 14 0.17
28 39 0.48
29 8 0.10
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:4405124 original size:54 final size:55
Alignment explanation
Indices: 4405064--4405185 Score: 133
Period size: 54 Copynumber: 2.2 Consensus size: 55
4405054 CAAAACTTTG
* * *
4405064 TTTCAAAATAAATAGACTCAAAGA-TTT-TTCAAAAGAAAC-AACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATTTTATTCAAAAGAAACTAACTCAAAGAT-TT
* * * *
4405117 TATTCAAAAGGAACAAACTCCAAGATTTTATTTAAAAGGAACTAACTCAAAGATTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTTATTCAAAAGAAACTAACTCAAAGATTT
*
4405173 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
4405186 TGTCTCAAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
53 1 0.02
54 18 0.32
55 13 0.23
56 13 0.23
57 11 0.20
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (55 bp):
TTTCAAAAGAAACAAACTCAAAGATTTTATTCAAAAGAAACTAACTCAAAGATTT
Found at i:4405131 original size:28 final size:27
Alignment explanation
Indices: 4405079--4405178 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 27
4405069 AAATAAATAG
*
4405079 ACTCAAAGA-TTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGGAACAA
4405104 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGGAACAA
* * *
4405133 ACTCCAAGATTTTATTTAAAAGGAACTA
1 ACTCAAAGATTTT-TTCAAAAGGAACAA
4405161 ACTCAAAGATTTTTTCAA
1 ACTCAAAGATTTTTTCAA
4405179 GAGAAACTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.14
27 7 0.11
28 39 0.60
29 10 0.15
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:4405509 original size:36 final size:35
Alignment explanation
Indices: 4405425--4405555 Score: 117
Period size: 36 Copynumber: 3.7 Consensus size: 35
4405415 GAGAAAATGA
* *
4405425 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGAC-AAATTTGTTTTTAGAGAAAT
* **
4405459 AGTCTCAAATGAGACAACATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAA-ATTTGTTTTTAGAGAAAT
4405495 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA-
1 TGTCTCAAGCGAGACAAA-TTTGTTTTTAGAGAAAT
* * *
4405529 CGATCTCAAGTGAGATCAACTTTGTTT
1 TG-TCTCAAGCGAGA-CAAATTTGTTT
4405556 AATGTGAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
33 2 0.03
34 18 0.22
35 29 0.36
36 31 0.39
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAATTTGTTTTTAGAGAAAT
Found at i:4406195 original size:4 final size:4
Alignment explanation
Indices: 4406179--4406224 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
4406169 ATACAAATTT
*
4406179 TATG TAT- TATG TATG TATG --TG TATT TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4406224 T
1 T
4406225 TTTCTCGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:4406208 original size:18 final size:17
Alignment explanation
Indices: 4406181--4406216 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
4406171 ACAAATTTTA
4406181 TGTATTATGTATGTATG
1 TGTATTATGTATGTATG
4406198 TGTATTTATGTATGTATG
1 TGTA-TTATGTATGTATG
4406216 T
1 T
4406217 ATGTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (17 bp):
TGTATTATGTATGTATG
Found at i:4413356 original size:3 final size:3
Alignment explanation
Indices: 4413350--4413411 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
4413340 AAAAAATATG
* * **
4413350 TAA TAA TAA -AT TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4413395 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
4413412 CGATAAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:4413366 original size:11 final size:11
Alignment explanation
Indices: 4413350--4413411 Score: 70
Period size: 11 Copynumber: 5.3 Consensus size: 11
4413340 AAAAAATATG
*
4413350 TAATAATAAAT
1 TAATAATAAAA
4413361 TAATAATAAAA
1 TAATAATAAAA
*
4413372 TAATAAGATAACGA
1 TAAT-A-ATAA-AA
4413386 TAATAATAATAA
1 TAATAATAA-AA
4413398 TAATAATAAAA
1 TAATAATAAAA
4413409 TAA
1 TAA
4413412 CGATAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
11 19 0.43
12 15 0.34
13 5 0.11
14 5 0.11
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:4413403 original size:29 final size:28
Alignment explanation
Indices: 4413361--4413417 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
4413351 AATAATAAAT
*
4413361 TAATAATAAAATAATAAGATAACGATAA
1 TAATAATAAAATAATAAAATAACGATAA
4413389 TAATAATAATAATAATAAAATAACGATAA
1 TAATAATAA-AATAATAAAATAACGATAA
4413418 AAAAACCCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (28 bp):
TAATAATAAAATAATAAAATAACGATAA
Found at i:4416211 original size:22 final size:22
Alignment explanation
Indices: 4416186--4416241 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
4416176 CTTAGCGTTA
4416186 ATACTAAAGTGC-CTCAACACTG
1 ATACTAAAGTGCACTC-ACACTG
* *
4416208 ATACTAAAGTGCATTCGCACTG
1 ATACTAAAGTGCACTCACACTG
*
4416230 ATACAAAAGTGC
1 ATACTAAAGTGC
4416242 TATAACACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (22 bp):
ATACTAAAGTGCACTCACACTG
Found at i:4416250 original size:22 final size:22
Alignment explanation
Indices: 4416186--4416250 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
4416176 CTTAGCGTTA
* * *
4416186 ATACTAAAGTGCCTCAACACTG
1 ATACAAAAGTGCATTAACACTG
* **
4416208 ATACTAAAGTGCATTCGCACTG
1 ATACAAAAGTGCATTAACACTG
4416230 ATACAAAAGTGC-TATAACACT
1 ATACAAAAGTGCAT-TAACACT
4416251 AGGGAGAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (22 bp):
ATACAAAAGTGCATTAACACTG
Found at i:4416623 original size:17 final size:16
Alignment explanation
Indices: 4416601--4416647 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 16
4416591 TTCAAATTAA
4416601 TTCCCAGTATCGATAC
1 TTCCCAGTATCGATAC
4416617 TTTCCCAGTATCGATAC
1 -TTCCCAGTATCGATAC
4416634 --CCCAGTATCGATAC
1 TTCCCAGTATCGATAC
4416648 CCCGATGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.47
17 16 0.53
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.30
Consensus pattern (16 bp):
TTCCCAGTATCGATAC
Found at i:4416639 original size:14 final size:14
Alignment explanation
Indices: 4416603--4416650 Score: 69
Period size: 14 Copynumber: 3.2 Consensus size: 14
4416593 CAAATTAATT
4416603 CCCAGTATCGATAC
1 CCCAGTATCGATAC
4416617 TTTCCCAGTATCGATAC
1 ---CCCAGTATCGATAC
4416634 CCCAGTATCGATAC
1 CCCAGTATCGATAC
4416648 CCC
1 CCC
4416651 GATGGAGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.55
17 14 0.45
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (14 bp):
CCCAGTATCGATAC
Found at i:4419054 original size:59 final size:60
Alignment explanation
Indices: 4418985--4419098 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
4418975 AACGTTTGAC
* *
4418985 AGTTAGTAGAG-TTTATGGCTAAAAAACATTTTGTGGGAATTAGAATTTATGGGCTTAAG
1 AGTTAGTAGAGTTTTATGGCTAAAAAACATTTTATGGGAATTAAAATTTATGGGCTTAAG
* *
4419044 AGTTATTAGAGTTTTATGGCTAAAATACATTTTATGGGAATTAAAATTTATGGGC
1 AGTTAGTAGAGTTTTATGGCTAAAAAACATTTTATGGGAATTAAAATTTATGGGC
4419099 CCTGGGCAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 10 0.20
60 40 0.80
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (60 bp):
AGTTAGTAGAGTTTTATGGCTAAAAAACATTTTATGGGAATTAAAATTTATGGGCTTAAG
Found at i:4424505 original size:17 final size:17
Alignment explanation
Indices: 4424485--4424519 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4424475 TTATTGATTC
*
4424485 TTTTTTTAAATATTATA
1 TTTTATTAAATATTATA
*
4424502 TTTTATTATATATTATA
1 TTTTATTAAATATTATA
4424519 T
1 T
4424520 ATATTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATATTATA
Found at i:4424523 original size:26 final size:26
Alignment explanation
Indices: 4424501--4424551 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4424491 TAAATATTAT
4424501 ATTTTATTATATA-TTATATATATTTA
1 ATTTTATTATATATTTAT-TATATTTA
* *
4424527 ATTTTTTTATCTATTTATTATATTT
1 ATTTTATTATATATTTATTATATTT
4424552 CTCTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
ATTTTATTATATATTTATTATATTTA
Found at i:4424666 original size:15 final size:14
Alignment explanation
Indices: 4424626--4424722 Score: 76
Period size: 15 Copynumber: 6.7 Consensus size: 14
4424616 ATATATATAT
4424626 TATTTTTATTATTA
1 TATTTTTATTATTA
* *
4424640 TATCTTTCTTATGTA
1 TATTTTTATTAT-TA
4424655 TATTTTTATTA-TA
1 TATTTTTATTATTA
4424668 TATTTTTACTTA-T-
1 TATTTTTA-TTATTA
4424681 TA-TTTTATTATTCAA
1 TATTTTTATTATT--A
4424696 TATTTGGTTATTATGTA
1 TATTT--TTATTAT-TA
*
4424713 TATATTTATT
1 TATTTTTATT
4424723 CGTTTTTTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
11 3 0.04
12 6 0.09
13 12 0.18
14 14 0.21
15 18 0.26
16 2 0.03
17 5 0.07
18 7 0.10
19 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (14 bp):
TATTTTTATTATTA
Found at i:4424670 original size:28 final size:29
Alignment explanation
Indices: 4424626--4424692 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 29
4424616 ATATATATAT
4424626 TATTTTTATTATTATATCTTT-CTTATGTA
1 TATTTTTATTATTATATCTTTACTTAT-TA
*
4424655 TATTTTTATTA-TATATTTTTACTTATTA
1 TATTTTTATTATTATATCTTTACTTATTA
4424683 T-TTTATTATT
1 TATTT-TTATT
4424693 CAATATTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.46
29 16 0.46
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (29 bp):
TATTTTTATTATTATATCTTTACTTATTA
Found at i:4424684 original size:26 final size:25
Alignment explanation
Indices: 4424623--4424691 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 25
4424613 CATATATATA
4424623 TATTATTTTTATTATTATATCTTTCT
1 TATTATTTTTATTA-TATATCTTTCT
*
4424649 TATGTATATTTTTATTATATATTTTTACT
1 TA--T-TATTTTTATTATATATCTTT-CT
4424678 TATTA-TTTTATTAT
1 TATTATTTTTATTAT
4424692 TCAATATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 9 0.24
26 4 0.11
27 1 0.03
28 9 0.24
29 15 0.39
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (25 bp):
TATTATTTTTATTATATATCTTTCT
Found at i:4424698 original size:28 final size:26
Alignment explanation
Indices: 4424623--4424700 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 26
4424613 CATATATATA
*
4424623 TATTATTTTTATTATT-ATATCTTTCT
1 TATTA-TTTTATTATTAATATTTTTCT
4424649 TATGTATATTT-TTATTATATATTTTTACT
1 TAT-TAT-TTTATTATTA-ATATTTTT-CT
4424678 TATTATTTTATTATTCAATATTT
1 TATTATTTTATTATT-AATATTT
4424701 GGTTATTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
26 9 0.20
27 8 0.18
28 21 0.48
29 6 0.14
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (26 bp):
TATTATTTTATTATTAATATTTTTCT
Found at i:4435246 original size:48 final size:49
Alignment explanation
Indices: 4435175--4435268 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 49
4435165 AATACTTCGC
* *
4435175 TTAGGATGAAAACCCGAGAGGGCGTCCTAAATTGA-AAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAAAAAAACGT
* * *
4435223 TTAGGGTGAAAACCTGAAAGGGCGCCCTAAATTGAGAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAAAAAAA
4435269 GAGGAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 31 0.77
49 9 0.22
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (49 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAAAAAAACGT
Found at i:4436203 original size:105 final size:105
Alignment explanation
Indices: 4436021--4436786 Score: 1309
Period size: 105 Copynumber: 7.3 Consensus size: 105
4436011 TTTTACCCAA
4436021 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
4436086 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
4436126 AGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
4436191 AAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
**
4436231 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
4436296 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
4436336 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACA
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
4436401 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
4436441 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
4436506 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
** ** * *
4436546 AAACAATTTCTGCTTCACAACAAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
4436611 AAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTTTAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* * * * *
4436651 AGCCAATTTTAACTTCACAACGAAGGATGTTAGACTCGAGACAACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
4436716 AAGGGGCCGCTGGTTGTCAACAAACACTTTC-CAAGTTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACA-TTTCTCAA-TTTCAG
* * *
4436757 AGTCAATTTCAACTTCACACCGAATGATAT
1 AGCCAATTTCAACTTCACAACGAAGGATAT
4436787 CGGCCTTGAA
Statistics
Matches: 622, Mismatches: 37, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
105 588 0.95
106 34 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
Found at i:4438838 original size:15 final size:14
Alignment explanation
Indices: 4438798--4438894 Score: 76
Period size: 15 Copynumber: 6.7 Consensus size: 14
4438788 ATATATATAT
4438798 TATTTTTATTATTA
1 TATTTTTATTATTA
* *
4438812 TATCTTTCTTATGTA
1 TATTTTTATTAT-TA
4438827 TATTTTTATTA-TA
1 TATTTTTATTATTA
4438840 TATTTTTACTTA-T-
1 TATTTTTA-TTATTA
4438853 TA-TTTTATTATTCAA
1 TATTTTTATTATT--A
4438868 TATTTGGTTATTATGTA
1 TATTT--TTATTAT-TA
*
4438885 TATATTTATT
1 TATTTTTATT
4438895 CGTTTTTTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
11 3 0.04
12 6 0.09
13 12 0.18
14 14 0.21
15 18 0.26
16 2 0.03
17 5 0.07
18 7 0.10
19 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (14 bp):
TATTTTTATTATTA
Found at i:4438842 original size:28 final size:29
Alignment explanation
Indices: 4438798--4438864 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 29
4438788 ATATATATAT
4438798 TATTTTTATTATTATATCTTT-CTTATGTA
1 TATTTTTATTATTATATCTTTACTTAT-TA
*
4438827 TATTTTTATTA-TATATTTTTACTTATTA
1 TATTTTTATTATTATATCTTTACTTATTA
4438855 T-TTTATTATT
1 TATTT-TTATT
4438865 CAATATTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.46
29 16 0.46
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (29 bp):
TATTTTTATTATTATATCTTTACTTATTA
Found at i:4438856 original size:26 final size:25
Alignment explanation
Indices: 4438795--4438863 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 25
4438785 TATATATATA
4438795 TATTATTTTTATTATTATATCTTTCT
1 TATTATTTTTATTA-TATATCTTTCT
*
4438821 TATGTATATTTTTATTATATATTTTTACT
1 TA--T-TATTTTTATTATATATCTTT-CT
4438850 TATTA-TTTTATTAT
1 TATTATTTTTATTAT
4438864 TCAATATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 9 0.24
26 4 0.11
27 1 0.03
28 9 0.24
29 15 0.39
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (25 bp):
TATTATTTTTATTATATATCTTTCT
Found at i:4438870 original size:28 final size:26
Alignment explanation
Indices: 4438795--4438872 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 26
4438785 TATATATATA
*
4438795 TATTATTTTTATTATT-ATATCTTTCT
1 TATTA-TTTTATTATTAATATTTTTCT
4438821 TATGTATATTT-TTATTATATATTTTTACT
1 TAT-TAT-TTTATTATTA-ATATTTTT-CT
4438850 TATTATTTTATTATTCAATATTT
1 TATTATTTTATTATT-AATATTT
4438873 GGTTATTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
26 9 0.20
27 8 0.18
28 21 0.48
29 6 0.14
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (26 bp):
TATTATTTTATTATTAATATTTTTCT
Found at i:4438930 original size:23 final size:24
Alignment explanation
Indices: 4438887--4438938 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
4438877 ATTATGTATA
* *
4438887 TATTTATTCGTTTTTTTATTC-TT
1 TATTTATTCGTTCTTTCATTCATT
4438910 TATTTATT-GTTACTTTCATTCATT
1 TATTTATTCGTT-CTTTCATTCATT
4438934 TATTT
1 TATTT
4438939 CACTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.12
23 15 0.60
24 7 0.28
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (24 bp):
TATTTATTCGTTCTTTCATTCATT
Found at i:4441787 original size:24 final size:24
Alignment explanation
Indices: 4441755--4441800 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4441745 CAATTGCTCC
4441755 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
4441779 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
4441801 TTCTACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:4446903 original size:24 final size:24
Alignment explanation
Indices: 4446871--4446916 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4446861 CAATTGCTCC
4446871 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
4446895 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
4446917 TTCTACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:4452175 original size:2 final size:2
Alignment explanation
Indices: 4452170--4452197 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4452160 AAAAAAGTAT
4452170 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
4452198 AATCTTATAT
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):
TA
Found at i:4454484 original size:30 final size:30
Alignment explanation
Indices: 4454420--4454514 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 30
4454410 ATTAAATTTT
* *
4454420 AAAATTACGCCATTAATAATAAATATTG-A
1 AAAATTAGGCCACTAATAATAAATATTGAA
*
4454449 AAAATTAGGCCACTAATAATAAGTATTGAA
1 AAAATTAGGCCACTAATAATAAATATTGAA
*
4454479 AAAATT-GGACC-CTTAATAATAAATGTTAGAA
1 AAAATTAGG-CCAC-TAATAATAAATATT-GAA
4454510 AAAAT
1 AAAAT
4454515 ATTGGAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
29 28 0.49
30 21 0.37
31 8 0.14
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (30 bp):
AAAATTAGGCCACTAATAATAAATATTGAA
Found at i:4455984 original size:5 final size:5
Alignment explanation
Indices: 4455974--4456024 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
4455964 CAATGTAGCC
4455974 GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG
1 GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG
4456024 G
1 G
4456025 GGGAAAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (5 bp):
GTTAG
Found at i:4457414 original size:12 final size:11
Alignment explanation
Indices: 4457399--4457423 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4457389 TTTAAAATAT
4457399 AAAAAAAAACC
1 AAAAAAAAACC
4457410 AAAAAAAAACC
1 AAAAAAAAACC
4457421 AAA
1 AAA
4457424 CTCCATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:4459290 original size:3 final size:3
Alignment explanation
Indices: 4459276--4459362 Score: 86
Period size: 3 Copynumber: 29.0 Consensus size: 3
4459266 TTGGCCTGTT
* * * *
4459276 TTA TTT TTA TTA TTA TAA TTA TAA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
4459324 TTA TCA TTA -TA TTT TTA TTA TTA CTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
4459363 CATATTACAG
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
2 2 0.03
3 62 0.94
4 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Done.