Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 93 of 182
Found at i:28115236 original size:21 final size:22
Alignment explanation
Indices: 28115208--28115260 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
28115198 TAAATTTTTC
* *
28115208 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAAATGTATAT
*
28115229 ATATATAT-TAAAAATGTATAT
1 AAATATATATAAAAATGTATAT
28115250 AAATATATATA
1 AAATATATATA
28115261 TCAAAGATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATATATAAAAATGTATAT
Found at i:28117830 original size:4 final size:4
Alignment explanation
Indices: 28117821--28117850 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
28117811 AATTTCACAT
*
28117821 TTTA TTTA TTTA TTTA TATA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
28117851 GTATGTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:28117928 original size:21 final size:21
Alignment explanation
Indices: 28117862--28117928 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
28117852 TATGTTTCAT
28117862 TAAAA-TTTTAAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
28117884 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
28117904 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
28117925 TAAA
1 TAAA
28117929 TCTTAGTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.41
21 7 0.19
22 6 0.16
23 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:28117963 original size:11 final size:11
Alignment explanation
Indices: 28117947--28117979 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28117937 TTCTATTTCC
28117947 TTTTTATATTT
1 TTTTTATATTT
28117958 TTTTTATA-TT
1 TTTTTATATTT
*
28117968 TTCTTATATTT
1 TTTTTATATTT
28117979 T
1 T
28117980 GGTCCTGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:28118633 original size:15 final size:16
Alignment explanation
Indices: 28118613--28118677 Score: 73
Period size: 15 Copynumber: 4.2 Consensus size: 16
28118603 ACCCTTGACA
28118613 CCTTAAA-CCCTAAAC
1 CCTTAAATCCCTAAAC
*
28118628 CCTT-AACCCCT-AAC
1 CCTTAAATCCCTAAAC
28118642 CCTTAAATCCCTTAAAC
1 CCTTAAATCCC-TAAAC
* *
28118659 CCCTAAATCCCTAACC
1 CCTTAAATCCCTAAAC
28118675 CCT
1 CCT
28118678 AACCCTTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.21
15 13 0.31
16 7 0.17
17 13 0.31
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (16 bp):
CCTTAAATCCCTAAAC
Found at i:28118670 original size:8 final size:7
Alignment explanation
Indices: 28118616--28118683 Score: 50
Period size: 8 Copynumber: 9.1 Consensus size: 7
28118606 CTTGACACCT
28118616 TAAACCC
1 TAAACCC
28118623 TAAACCC
1 TAAACCC
*
28118630 TTAACCCC
1 -TAAACCC
28118638 T-AACCC
1 TAAACCC
28118644 TTAAATCCC
1 -TAAA-CCC
28118653 TTAAACCCC
1 -TAAA-CCC
28118662 TAAATCCC
1 TAAA-CCC
*
28118670 TAACCCC
1 TAAACCC
28118677 T-AACCC
1 TAAACCC
28118683 T
1 T
28118684 TGAACCTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
6 9 0.18
7 13 0.25
8 18 0.35
9 11 0.22
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:28118689 original size:8 final size:8
Alignment explanation
Indices: 28118613--28118670 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 8
28118603 ACCCTTGACA
28118613 CCTTAAAC
1 CCTTAAAC
28118621 CC-TAAAC
1 CCTTAAAC
28118628 CCTT-AAC
1 CCTTAAAC
*
28118635 CCCT-AAC
1 CCTTAAAC
28118642 CCTTAAATC
1 CCTTAAA-C
28118651 CCTTAAAC
1 CCTTAAAC
*
28118659 CCCTAAATC
1 CCTTAAA-C
28118668 CCT
1 CCT
28118671 AACCCCTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 19 0.45
8 12 0.29
9 11 0.26
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (8 bp):
CCTTAAAC
Found at i:28118689 original size:15 final size:16
Alignment explanation
Indices: 28118638--28118679 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
28118628 CCTTAACCCC
*
28118638 TAACCCTTAAATCCCT
1 TAACCCCTAAATCCCT
28118654 TAAACCCCTAAATCCC-
1 T-AACCCCTAAATCCCT
28118670 TAACCCCTAA
1 TAACCCCTAA
28118680 CCCTTGAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 2 0.08
17 13 0.54
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (16 bp):
TAACCCCTAAATCCCT
Found at i:28118849 original size:33 final size:36
Alignment explanation
Indices: 28118782--28118855 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 36
28118772 CATGAATCTT
* *
28118782 TAAACCCTAAATCACTAACTCTTAACCTCAAACCCC
1 TAAACCCTAAATCACTAACCCTTAACCACAAACCCC
* *
28118818 -AAACCCT-AA-CACTAACCCTTAACGACTAACCCC
1 TAAACCCTAAATCACTAACCCTTAACCACAAACCCC
28118851 TAAAC
1 TAAAC
28118856 ATTATTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 20 0.61
34 6 0.18
35 7 0.21
ACGTcount: A:0.41, C:0.39, G:0.01, T:0.19
Consensus pattern (36 bp):
TAAACCCTAAATCACTAACCCTTAACCACAAACCCC
Found at i:28118943 original size:88 final size:88
Alignment explanation
Indices: 28118843--28119086 Score: 443
Period size: 88 Copynumber: 2.8 Consensus size: 88
28118833 CCCTTAACGA
28118843 CTAACCCCTAAACATTATTTAATATATAAATTAAAAATACTAAATAATCTAAATCCTAAACCCTA
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAAATACTAAATAATCTAAATCCTAAACCCTA
28118908 ACTCGACCCCGAATCACTAACCC
66 ACTCGACCCCGAATCACTAACCC
28118931 CTAACCCCTAAACATTATTTAATATATAAATTAAAAATACTAAATAATCTAAATCCTAAACCCTA
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAAATACTAAATAATCTAAATCCTAAACCCTA
28118996 ACTCGACCCCGAATCACTAACCC
66 ACTCGACCCCGAATCACTAACCC
* * * *
28119019 CTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTAAACTCT
1 CTAACCCCTAAACATTATTTAATATATAAATTAAAA-ATACTAAATAATCTAAATCCTAAACCCT
28119084 AAC
65 AAC
28119087 CTAACACCAA
Statistics
Matches: 151, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
88 124 0.82
89 27 0.18
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (88 bp):
CTAACCCCTAAACATTATTTAATATATAAATTAAAAATACTAAATAATCTAAATCCTAAACCCTA
ACTCGACCCCGAATCACTAACCC
Found at i:28119200 original size:14 final size:15
Alignment explanation
Indices: 28119181--28119213 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
28119171 CTTAAATTAG
28119181 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
28119195 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
28119210 AATC
1 AATC
28119214 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:28119670 original size:41 final size:41
Alignment explanation
Indices: 28119529--28119780 Score: 269
Period size: 41 Copynumber: 6.2 Consensus size: 41
28119519 AAATGTTTTT
* * * * *
28119529 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATTTGACCA-TC
1 GCGGCGCTTATACAAAAACGCCGCTAAAGATCTGAGCATTA
* ** * *
28119569 GCGGCGATCT-TGGAAAAACACCGATAAAGATCTGAGCATTA
1 GCGGCGCT-TATACAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
28119610 GCAGCGCTTCTACAGAAACGCCGCTAAATATCTGAGCATTA
1 GCGGCGCTTATACAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
28119651 TCGGCACTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTATACAAAAACGCCGCTAAAGATCTGAGCATTA
* *
28119692 GCGGCGCTTATAAAAAAACGCAGCTAAAGATCTGAGCATTA
1 GCGGCGCTTATACAAAAACGCCGCTAAAGATCTGAGCATTA
* *
28119733 GCGGCGCTTAT--AAAAACGCCGCTAAAGATCTGGGAATTA
1 GCGGCGCTTATACAAAAACGCCGCTAAAGATCTGAGCATTA
28119772 GCGGCGCTT
1 GCGGCGCTT
28119781 TTTTTTAAAA
Statistics
Matches: 177, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
39 34 0.19
40 30 0.17
41 113 0.64
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTATACAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:28122516 original size:17 final size:17
Alignment explanation
Indices: 28122494--28122531 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28122484 AGACACCGAT
* *
28122494 CTTCCCTTTCCCTTTCC
1 CTTCCCCTTCCCCTTCC
28122511 CTTCCCCTTCCCCTTCC
1 CTTCCCCTTCCCCTTCC
28122528 CTTC
1 CTTC
28122532 GCTTGACACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (17 bp):
CTTCCCCTTCCCCTTCC
Found at i:28125573 original size:22 final size:24
Alignment explanation
Indices: 28125523--28125573 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
28125513 TTGCAATGCT
28125523 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
28125548 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
28125569 TTTAT
1 TTTAT
28125574 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:28130102 original size:6 final size:6
Alignment explanation
Indices: 28130093--28130122 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28130083 CACCGATCTT
*
28130093 CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
28130123 GCTTGACACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCCTTC
Found at i:28133164 original size:22 final size:24
Alignment explanation
Indices: 28133114--28133164 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
28133104 TTGCAATGCT
28133114 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
28133139 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
28133160 TTTAT
1 TTTAT
28133165 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:28133333 original size:20 final size:20
Alignment explanation
Indices: 28133308--28133347 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28133298 AATATTTTCC
*
28133308 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28133328 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
28133348 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28133349 original size:34 final size:35
Alignment explanation
Indices: 28133296--28133362 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28133286 CAAACACTAG
*
28133296 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
28133331 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28133363 CATTTTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28133354 original size:14 final size:14
Alignment explanation
Indices: 28133331--28133370 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28133321 ACAGAAAAGT
*
28133331 AAAACATTTTTCAG
1 AAAACATTTTACAG
* *
28133345 AAATCATTTTACGG
1 AAAACATTTTACAG
28133359 AAAACATTTTAC
1 AAAACATTTTAC
28133371 TAGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28135477 original size:2 final size:2
Alignment explanation
Indices: 28135465--28135500 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28135455 TTTGTACTAT
*
28135465 GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28135501 CCATATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28148944 original size:28 final size:28
Alignment explanation
Indices: 28148868--28148945 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
28148858 TATAATATGT
*
28148868 ATAAATTAAAAGGTTAAAATAAGTTTGA
1 ATAAATTAAAATGTTAAAATAAGTTTGA
* *
28148896 ATAAATTAACAATATTGAAATAAG-TTGAA
1 ATAAATTAA-AATGTTAAAATAAGTTTG-A
28148925 ATAAATTAAAATGTTAAAATA
1 ATAAATTAAAATGTTAAAATA
28148946 TTGGAAAGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.56, C:0.01, G:0.10, T:0.32
Consensus pattern (28 bp):
ATAAATTAAAATGTTAAAATAAGTTTGA
Found at i:28149246 original size:23 final size:24
Alignment explanation
Indices: 28149211--28149255 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
28149201 TGGAAATTTA
*
28149211 AATAATGATACATAATAAATTTTG
1 AATAATGAAACATAATAAATTTTG
**
28149235 AATAAT-AAACATGGTAAATTT
1 AATAATGAAACATAATAAATTT
28149256 ATATAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (24 bp):
AATAATGAAACATAATAAATTTTG
Found at i:28149972 original size:20 final size:19
Alignment explanation
Indices: 28149938--28149993 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
28149928 TTTTTCATAT
*
28149938 AGAAAATAGAAAGAAACAA
1 AGAAAACAGAAAGAAACAA
**
28149957 AGAAAACAGTAAAGAAACGC
1 AGAAAACAG-AAAGAAACAA
*
28149977 AGAGAAAGAGAAAGAAA
1 AGA-AAACAGAAAGAAA
28149994 AAGAGAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 8 0.26
20 18 0.58
21 5 0.16
ACGTcount: A:0.68, C:0.07, G:0.21, T:0.04
Consensus pattern (19 bp):
AGAAAACAGAAAGAAACAA
Found at i:28151116 original size:164 final size:171
Alignment explanation
Indices: 28150851--28151543 Score: 1026
Period size: 174 Copynumber: 4.0 Consensus size: 171
28150841 TGTTCCACTG
28150851 TAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGAT-CGATCTA
* * *
28150916 TTCTACTATAACTTCAGAGTGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTTAAGGAA
65 --CTAC-GTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAA
*
28150981 ATAGGATTACTGGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGA
127 ATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
* * *
28151026 TAAGATTTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACTTGAT-G-T-GA-
1 TAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATCGATCTAC
* * * *
28151087 T-C-T-ACTTCAGAGAGATAAGATCTTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATAT
66 TACGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAAATA-
28151149 GG-TTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
130 GGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
*
28151190 TAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGAT-CGATCTA
* * *
28151255 CTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCATTCCACTATAATCTCAAGGAA
65 --CTAC-GTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAA
*
28151320 ATAGGATTACT-GCTTCAATTTGCTCCGCTGTAATCTCAGGGAGA
127 ATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
*
28151364 TAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTA
1 TAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGAT-CGATCTA
*
28151429 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTTAAGGAA
65 --CTAC-GTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAA
* *
28151494 ATAGGATTACTGGCTTCAATCTGCTCTGCTATAATCTCAGGGAGA
127 ATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
28151539 TAAGA
1 TAAGA
28151544 CCTGATGTGA
Statistics
Matches: 474, Mismatches: 30, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
164 144 0.30
165 3 0.01
166 1 0.00
167 2 0.00
168 2 0.00
171 2 0.00
172 2 0.00
173 1 0.00
174 170 0.36
175 147 0.31
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (171 bp):
TAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATCGATCTAC
TACGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAAATAG
GATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
Found at i:28151223 original size:46 final size:46
Alignment explanation
Indices: 28151173--28151414 Score: 184
Period size: 46 Copynumber: 5.5 Consensus size: 46
28151163 ATCTGCTCCG
28151173 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
* * * * *
28151219 CTGTAATCTCAGGGAGATAAGACCTG--ATGC--GA-TCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
* * * *
28151260 CTGTAA-CTTCAGAGAGATAAGATCAT-TTATT-TTAATTC-ATTCCA
1 CTGTAATC-TCAGGGAGATAAGATC-TGTAATTCTTCAGTCTATTCCA
* * * * * * * * ** *
28151304 CTATAATCTCAAGGAAATAGGA--T-TACTGCTTCAATTTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
*
28151347 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
*
28151393 CTGTAATCTCAAGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
28151415 CCTGATGCGA
Statistics
Matches: 145, Mismatches: 38, Indels: 26
0.69 0.18 0.12
Matches are distributed among these distances:
40 1 0.01
41 30 0.21
42 6 0.04
43 23 0.16
44 23 0.16
45 4 0.03
46 58 0.40
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (46 bp):
CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
Found at i:28151584 original size:118 final size:118
Alignment explanation
Indices: 28151439--28151661 Score: 365
Period size: 118 Copynumber: 1.9 Consensus size: 118
28151429 CTCTACTGTA
* *
28151439 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTTAAGGAAATAGGATTAC
1 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATATCAAGGAAATAGGATTAC
* * *
28151504 TGGCTTCAATCTGCTCTGCTATAATCTCAGGGAGATAAGACCTGATGTGATCT
66 TGGCTTCAATCTGCTCCGCTATAATCTCAAGAAGATAAGACCTGATGTGATCT
* * *
28151557 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATATGATTAC
1 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATATCAAGGAAATAGGATTAC
*
28151622 TGGCTTCAATCTGCTCCGCTGTAATCTCAAGAAGATAAGA
66 TGGCTTCAATCTGCTCCGCTATAATCTCAAGAAGATAAGA
28151662 TCTGTAATTC
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 96 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (118 bp):
ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATATCAAGGAAATAGGATTAC
TGGCTTCAATCTGCTCCGCTATAATCTCAAGAAGATAAGACCTGATGTGATCT
Found at i:28151693 original size:46 final size:46
Alignment explanation
Indices: 28151640--28151882 Score: 136
Period size: 46 Copynumber: 5.5 Consensus size: 46
28151630 ATCTGCTCCG
28151640 CTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCA
1 CTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCA
* * * * * * *
28151686 CTGTAATCTCAGGGAGATAAGACCTG--ATGC--GA-TCTACTCTA
1 CTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCA
* * * *
28151727 CTGTAA-CTTC-AGAGAGATAAGATCAT-TTATT-TTAATTC-GTTCCA
1 CTGTAATC-TCAAGA-AGATAAGATC-TGTAATTCTTCAGTCTATTCCA
* * * ** *
28151771 CTGTAATCTCAAGGAA-ATAAGA--T-TACTGGCTTCAATCTGCTCCG
1 CTGTAATCTCAA-GAAGATAAGATCTGTAAT-TCTTCAGTCTATTCCA
* * *
28151815 CTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCA
1 CTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCA
* * *
28151861 CTGTAATATCTAGGAGATAAGA
1 CTGTAATCTCAAGAAGATAAGA
28151883 CCTGATGCGA
Statistics
Matches: 145, Mismatches: 34, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
40 2 0.01
41 27 0.19
42 2 0.01
43 9 0.06
44 42 0.29
45 5 0.03
46 55 0.38
47 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (46 bp):
CTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCA
Found at i:28151753 original size:467 final size:468
Alignment explanation
Indices: 28151058--28152011 Score: 1739
Period size: 467 Copynumber: 2.0 Consensus size: 468
28151048 TATTCCACTG
* *
28151058 TAATCTCAGGGAGATAAGACTTGATGTGATCTACTTCAGAGAGATAAGATCTTTTATTTTAATCC
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTACTTCAGAGAGATAAGATCCTTTATTTTAATCC
* * *
28151123 GTTCCACTGTAATATCAGGGAAATATGGTTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGA
66 GTTCCACTGTAATATCAGGGAAATATGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAAGAA
28151188 GATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATC
131 GATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATC
28151253 TACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCATTCCACTATAATCTCAAGG
196 TACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCATTCCACTATAATCTCAAGG
* *
28151318 AAATAGGATTACT-GCTTCAATTTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
261 AAATAAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
*
28151382 GGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGA
326 GGTCTATTCCACTGTAATATCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGA
*
28151447 GAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTTAAGGAAATAGGATTACTGGCTTCA
391 GAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAAATAGGATTACTGGCTTCA
*
28151512 ATCTGCTCTGCTA
456 ATCTGCTCCGCTA
28151525 TAATCTCAGGGAGATAAGACCTGATGTGATCTACTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTACTTCAGAGAGATAAGATCCTTTATTTTAATCC
28151590 GTTCCACTGTAATATCAGGGAAATATGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAAGAA
66 GTTCCACTGTAATATCAGGGAAATATGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAAGAA
28151655 GATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATC
131 GATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATC
* *
28151720 TACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCGTTCCACTGTAATCTCAAGG
196 TACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCATTCCACTATAATCTCAAGG
28151785 AAATAAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
261 AAATAAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
*
28151850 GGTCTATTCCACTGTAATATCTAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGA
326 GGTCTATTCCACTGTAATATCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGA
* ** *
28151915 GAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCGGGGATATAGGATTACTGGCTTCA
391 GAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAAATAGGATTACTGGCTTCA
*
28151980 ATCTGCTCCGCTG
456 ATCTGCTCCGCTA
28151993 TAATCTCAGGGAGATAAGA
1 TAATCTCAGGGAGATAAGA
28152012 TCTGTAATTC
Statistics
Matches: 468, Mismatches: 18, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
467 265 0.57
468 203 0.43
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (468 bp):
TAATCTCAGGGAGATAAGACCTGATGTGATCTACTTCAGAGAGATAAGATCCTTTATTTTAATCC
GTTCCACTGTAATATCAGGGAAATATGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAAGAA
GATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATC
TACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCATTCCACTATAATCTCAAGG
AAATAAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
GGTCTATTCCACTGTAATATCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGA
GAGATAAGATCCTTTATTTTAATCCGTTCCACTATAATCTCAAGGAAATAGGATTACTGGCTTCA
ATCTGCTCCGCTA
Found at i:28151759 original size:293 final size:292
Alignment explanation
Indices: 28151265--28151836 Score: 964
Period size: 293 Copynumber: 2.0 Consensus size: 292
28151255 CTCTACTGTA
* *
28151265 ACTTCAGAGAGATAAGATCATTTATTTTAATTCATTCCACTATAATCTCAAGGAAATAGGATTAC
1 ACTTCAGAGAGATAAGATCATTTATTTTAATCCATTCCACTATAATATCAAGGAAATAGGATTAC
* * * *
28151330 TGCTTCAATTTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCACT
66 TGCTTCAATCTGCTCCGCTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCACT
*
28151395 GTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT
131 GTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCAT
* * *
28151460 TTATTTTAATCCGTTCCACTATAATCTTAAGGAAATAGGATTACTGGCTTCAATCTGCTCTGCTA
196 TTATTTTAATCCGTTCCACTATAATCTCAAGGAAATAAGATTACTGGCTTCAATCTGCTCCGCTA
28151525 TAATCTCAGGGAGATAAGACCTGATGTGATCT
261 TAATCTCAGGGAGATAAGACCTGATGTGATCT
* * * * *
28151557 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATATGATTAC
1 ACTTCAGAGAGATAAGATCATTTATTTTAATCCATTCCACTATAATATCAAGGAAATAGGATTAC
28151622 TGGCTTCAATCTGCTCCGCTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
66 T-GCTTCAATCTGCTCCGCTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
*
28151687 TGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCA
130 TGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCA
* *
28151752 TTTATTTTAATTCGTTCCACTGTAATCTCAAGGAAATAAGATTACTGGCTTCAATCTGCTCCGCT
195 TTTATTTTAATCCGTTCCACTATAATCTCAAGGAAATAAGATTACTGGCTTCAATCTGCTCCGCT
*
28151817 GTAATCTCAGGGAGATAAGA
260 ATAATCTCAGGGAGATAAGA
28151837 TCTGTAATTC
Statistics
Matches: 260, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
292 59 0.23
293 201 0.77
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (292 bp):
ACTTCAGAGAGATAAGATCATTTATTTTAATCCATTCCACTATAATATCAAGGAAATAGGATTAC
TGCTTCAATCTGCTCCGCTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCACT
GTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCAT
TTATTTTAATCCGTTCCACTATAATCTCAAGGAAATAAGATTACTGGCTTCAATCTGCTCCGCTA
TAATCTCAGGGAGATAAGACCTGATGTGATCT
Found at i:28151848 original size:175 final size:175
Alignment explanation
Indices: 28151557--28152197 Score: 1079
Period size: 175 Copynumber: 3.7 Consensus size: 175
28151547 GATGTGATCT
* *
28151557 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATATGATTAC
1 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAAGATTAC
* * *
28151622 TGGCTTCAATCTGCTCCGCTGTAATCTCAAGAAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
66 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
28151687 TGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
131 TGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
* * *
28151732 ACTTCAGAGAGATAAGATCATTTATTTTAATTCGTTCCACTGTAATCTCAAGGAAATAAGATTAC
1 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAAGATTAC
28151797 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
66 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
*
28151862 TGTAATATCTA-GGAGATAAGACCTGATGCGATCTACTCTACTGTA
131 TGTAATCTC-AGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
* * *
28151907 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCGGGGATATAGGATTAC
1 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAAGATTAC
*
28151972 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTACTCCAC
66 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
* *
28152037 TGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTATA
131 TGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
* *
28152082 ACTTCAGAGAGATAAGATCCTTTATTTTATTCCGTTCCACTGTAATCACAGGGAAA-AATGATTA
1 ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAA-GATTA
* *
28152146 TTGGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTCT
65 CTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCT
28152198 CTGATCTGTT
Statistics
Matches: 437, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
174 2 0.00
175 434 0.99
176 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (175 bp):
ACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAAGATTAC
TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
TGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
Found at i:28152057 original size:46 final size:46
Alignment explanation
Indices: 28151625--28152197 Score: 238
Period size: 44 Copynumber: 13.0 Consensus size: 46
28151615 TGATTACTGG
* * * *
28151625 CTTCAATCTGCTCCGCTGTAATCTCAAGAAGATAAGATCTGTAATT
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
* * *
28151671 CTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTG--A--
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
* * * * *
28151713 -TGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCAT-TTATT
1 CTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATC-TGTAATT
* * * *
28151758 -TT-AAT-T-CGTTCCACTGTAATCTCAAGGAAATAAGA--T-TACTGG
1 CTTCAATCTAC--TCCACTGTAATCTCAGGGAGATAAGATCTGTAAT-T
* *
28151800 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATT
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
** * * *
28151846 CTTCGGTCTATTCCACTGTAATATCTA-GGAGATAAGACCTG--A--
1 CTTCAATCTACTCCACTGTAATCTC-AGGGAGATAAGATCTGTAATT
* * * * *
28151888 -TGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTATT
1 CTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGAT-CTGTAATT
*** * * * * *
28151933 -TT-AATCCGTTCCACTGTAATCTCGGGGATATAGGA--T-TACTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAAT-T
* *
28151975 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATT
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
** * *
28152021 CTTCGGTCTACTCCACTGTAATCTCAGGGAAATAAGACCTG--A--
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
* * * * * *
28152063 -TGCGATCTACTCTACTATAA-CTTCAGAGAGATAAGATCCT-TTATT
1 CTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGAT-CTGTAATT
* *** * *
28152108 -TT-ATTCCGTTCCACTGTAATCACAGGGA-A-AA-A--TGATTATT
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTG-TAATT
*
28152148 GGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
1 --CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
28152196 CT
1 CT
28152198 CTGATCTGTT
Statistics
Matches: 386, Mismatches: 91, Indels: 100
0.67 0.16 0.17
Matches are distributed among these distances:
38 1 0.00
40 8 0.02
41 91 0.24
42 8 0.02
43 11 0.03
44 137 0.35
45 8 0.02
46 108 0.28
47 8 0.02
48 4 0.01
49 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (46 bp):
CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTGTAATT
Found at i:28154345 original size:210 final size:210
Alignment explanation
Indices: 28153983--28154402 Score: 786
Period size: 210 Copynumber: 2.0 Consensus size: 210
28153973 ATAGCTTTTC
*
28153983 ATGCCAATCCTTGTAGGTTTCAGTCATTTTGCCCACAATTCTCTTAATATTCTTATTGGCCGCCT
1 ATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAATATTCTTATTGGCCGCCT
* *
28154048 CCACTGCACCATTCATTTTTGGGTGATATAGTGACGAGTTATGGTGACTGATCTTGAACTGACTA
66 CCACTGCACCATTCATTTTTGGGCGATATAGCGACGAGTTATGGTGACTGATCTTGAACTGACTA
28154113 CAAACTTCCGCTATTGTGCTATTATTCAAATTCAACGCATTGTCGGATATGATTCTTTCAGGCAT
131 CAAACTTCCGCTATTGTGCTATTATTCAAATTCAACGCATTGTCGGATATGATTCTTTCAGGCAT
28154178 TCCATATCGACAAAT
196 TCCATATCGACAAAT
*
28154193 ATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAATATTTTTATTGGCCGCCT
1 ATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAATATTCTTATTGGCCGCCT
*
28154258 CCACTGCACCATTCATTTTTGGGCGATATGGCGACGAGTTATGGTGACTGATCTTGAACTGACTA
66 CCACTGCACCATTCATTTTTGGGCGATATAGCGACGAGTTATGGTGACTGATCTTGAACTGACTA
*
28154323 CAAACTTCCGCTATTGTGCTATTGTTCAAATTCAACGCATTGTCGGATATGATTCTTTCAGGCAT
131 CAAACTTCCGCTATTGTGCTATTATTCAAATTCAACGCATTGTCGGATATGATTCTTTCAGGCAT
28154388 TCCATATCGACAAAT
196 TCCATATCGACAAAT
28154403 TGTCTCATTT
Statistics
Matches: 204, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
210 204 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (210 bp):
ATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAATATTCTTATTGGCCGCCT
CCACTGCACCATTCATTTTTGGGCGATATAGCGACGAGTTATGGTGACTGATCTTGAACTGACTA
CAAACTTCCGCTATTGTGCTATTATTCAAATTCAACGCATTGTCGGATATGATTCTTTCAGGCAT
TCCATATCGACAAAT
Found at i:28158738 original size:40 final size:40
Alignment explanation
Indices: 28158683--28158909 Score: 391
Period size: 40 Copynumber: 5.7 Consensus size: 40
28158673 AACATTGGAT
28158683 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
28158723 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28158763 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28158803 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
28158843 TATATCCGGGCTAAGACCTGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
28158883 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
28158910 ATGTGTTGCG
Statistics
Matches: 175, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 175 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:28167514 original size:40 final size:40
Alignment explanation
Indices: 28167456--28167602 Score: 249
Period size: 40 Copynumber: 3.7 Consensus size: 40
28167446 AACATTGGAT
28167456 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
28167496 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
28167536 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
28167576 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
28167603 ATGTGTTGCG
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 99 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:28175522 original size:25 final size:25
Alignment explanation
Indices: 28175475--28175522 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28175465 TTTTGTATTA
* **
28175475 AAAAACAAAAATTTTAGTTGTCGAC
1 AAAAACAAAAAATTTAGGAGTCGAC
*
28175500 AAAAACAAAAAATTTGGGAGTCG
1 AAAAACAAAAAATTTAGGAGTCG
28175523 CCACTGATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (25 bp):
AAAAACAAAAAATTTAGGAGTCGAC
Found at i:28176535 original size:28 final size:28
Alignment explanation
Indices: 28176504--28176581 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
28176494 TATAATATGT
*
28176504 ATAAATTAAAAGGTTAAAATAAGTTTGA-
1 ATAAATTAAAATGTTAAAATAAG-TTGAG
* *
28176532 ATAAATTAACAATATTGAAATAAGTTGAG
1 ATAAATTAA-AATGTTAAAATAAGTTGAG
28176561 ATAAATTAAAATGTTAAAATA
1 ATAAATTAAAATGTTAAAATA
28176582 TTGGAAAGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 23 0.53
29 20 0.47
ACGTcount: A:0.55, C:0.01, G:0.12, T:0.32
Consensus pattern (28 bp):
ATAAATTAAAATGTTAAAATAAGTTGAG
Found at i:28176876 original size:23 final size:24
Alignment explanation
Indices: 28176841--28176885 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
28176831 TGGAAATTTA
*
28176841 AATAATGATACATAATAAATTTTG
1 AATAATGAAACATAATAAATTTTG
**
28176865 AATAAT-AAACATGGTAAATTT
1 AATAATGAAACATAATAAATTT
28176886 ATATAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (24 bp):
AATAATGAAACATAATAAATTTTG
Found at i:28178190 original size:15 final size:14
Alignment explanation
Indices: 28178145--28178191 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
28178135 ACTTTTAATA
28178145 ATTTTGTTTTTATTT
1 ATTTT-TTTTTATTT
* *
28178160 -TTATTTTTTATAT
1 ATTTTTTTTTATTT
28178173 ATTTTTTGTTTATTT
1 ATTTTTT-TTTATTT
28178188 ATTT
1 ATTT
28178192 GATTTGGGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.31
14 8 0.31
15 10 0.38
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (14 bp):
ATTTTTTTTTATTT
Found at i:28189035 original size:16 final size:16
Alignment explanation
Indices: 28189014--28189046 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28189004 CATCAGTTTA
28189014 TTGCAATAGGCATTCC
1 TTGCAATAGGCATTCC
*
28189030 TTGCAATAGGCTTTCC
1 TTGCAATAGGCATTCC
28189046 T
1 T
28189047 GCTAGCGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (16 bp):
TTGCAATAGGCATTCC
Found at i:28192979 original size:17 final size:17
Alignment explanation
Indices: 28192959--28192996 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28192949 GGTTGTCTAT
*
28192959 TTTTCTTTATTTATTTA
1 TTTTCATTATTTATTTA
28192976 TTTTCATTATTTATTTA
1 TTTTCATTATTTATTTA
28192993 TTTT
1 TTTT
28192997 TATTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCATTATTTATTTA
Found at i:28194133 original size:18 final size:18
Alignment explanation
Indices: 28194105--28194146 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28194095 CAAATATACA
*
28194105 AATACTAAATAAAATTAAT
1 AATA-TAAATAAAAATAAT
*
28194124 TATATAAATAAAAATAAT
1 AATATAAATAAAAATAAT
28194142 AATAT
1 AATAT
28194147 GTGGGAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAAATAAAAATAAT
Found at i:28199900 original size:12 final size:12
Alignment explanation
Indices: 28199875--28199913 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
28199865 CACATGATTG
*
28199875 TGTCCTCACCCA
1 TGTCCTCAACCA
28199887 TGTCC-CAACTCA
1 TGTCCTCAAC-CA
28199899 TGTCCTCAACCA
1 TGTCCTCAACCA
28199911 TGT
1 TGT
28199914 AACTCTCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.12
12 17 0.71
13 4 0.17
ACGTcount: A:0.21, C:0.41, G:0.10, T:0.28
Consensus pattern (12 bp):
TGTCCTCAACCA
Found at i:28200177 original size:23 final size:24
Alignment explanation
Indices: 28200150--28200197 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
28200140 CATTATCAAG
* *
28200150 TCATTCCAAACTTGC-CATAAGAT
1 TCATTCAAAACATGCACATAAGAT
28200173 TCATTCAAAACATGCATCATAAGAT
1 TCATTCAAAACATGCA-CATAAGAT
28200198 AACCAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (24 bp):
TCATTCAAAACATGCACATAAGAT
Found at i:28200850 original size:42 final size:42
Alignment explanation
Indices: 28200789--28200890 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
28200779 TTTACATCAT
*
28200789 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTATACGATAC
1 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC
* * *
28200831 TGCTCTCACGAGCTGTGGGTCAAAATGTAAGCTACATGATAC
1 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC
28200873 TGCTCACACGAGCTATGG
1 TGCTCACACGAGCTATGG
28200891 AGTATCCGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (42 bp):
TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC
Found at i:28212304 original size:19 final size:19
Alignment explanation
Indices: 28212275--28212366 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
28212265 AATCTTCAAG
28212275 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
28212294 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* * *
28212313 GATATGCGACCTTAGAAAT
1 GATATGCAATCTTAGATAT
*
28212332 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28212351 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
28212367 ATATATGATT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28212327 original size:38 final size:38
Alignment explanation
Indices: 28212275--28212367 Score: 150
Period size: 38 Copynumber: 2.4 Consensus size: 38
28212265 AATCTTCAAG
*
28212275 GATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 GATATGCAATCTTAGAAATGATATATAATCTTAGATAT
* * *
28212313 GATATGCGACCTTAGAAATGATATGTAATCTTAGATAT
1 GATATGCAATCTTAGAAATGATATATAATCTTAGATAT
28212351 GATATGCAATCTTAGAA
1 GATATGCAATCTTAGAA
28212368 TATATGATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGAAATGATATATAATCTTAGATAT
Found at i:28212621 original size:23 final size:23
Alignment explanation
Indices: 28212577--28212621 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28212567 TCTTATTTTG
* *
28212577 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
28212600 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
28212622 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:28212855 original size:3 final size:3
Alignment explanation
Indices: 28212847--28212887 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28212837 ATCTTGTATC
28212847 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28212888 ATTCATGCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28213477 original size:64 final size:64
Alignment explanation
Indices: 28213376--28213502 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
28213366 TTGCTTATTG
28213376 ATTTATGTTTTCATTTATATTTTGTTCATTTGATACTTTACATGTCGTTATTTTTTATGTACAC
1 ATTTATGTTTTCATTTATATTTTGTTCATTTGATACTTTACATGTCGTTATTTTTTATGTACAC
*
28213440 ATTTATGTTTTCATTTATATTTTGTTCATTTGATACTTTACATGTCGTTGTTTTTTATGTACA
1 ATTTATGTTTTCATTTATATTTTGTTCATTTGATACTTTACATGTCGTTATTTTTTATGTACA
28213503 TTAATTTCGT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.58
Consensus pattern (64 bp):
ATTTATGTTTTCATTTATATTTTGTTCATTTGATACTTTACATGTCGTTATTTTTTATGTACAC
Found at i:28219670 original size:26 final size:28
Alignment explanation
Indices: 28219641--28219692 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
28219631 TTGTTCAAAC
*
28219641 TCTTCTAAA-AAAAACTCA-AGAGAAAT
1 TCTTCAAAAGAAAAACTCAGAGAGAAAT
*
28219667 TCTTGAAAAGAAAAACTCAGAGAGAA
1 TCTTCAAAAGAAAAACTCAGAGAGAA
28219693 TTTATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (28 bp):
TCTTCAAAAGAAAAACTCAGAGAGAAAT
Found at i:28222709 original size:304 final size:304
Alignment explanation
Indices: 28222160--28222767 Score: 1189
Period size: 304 Copynumber: 2.0 Consensus size: 304
28222150 AAATATTGTC
28222160 ATGTATCATTCTCCCAGGGATAAACGCACTCTAATTTGGACTTATGCAATTAGGGAGGACTACTT
1 ATGTATCATTCTCCCAGGGATAAACGCACTCTAATTTGGACTTATGCAATTAGGGAGGACTACTT
28222225 TGAGTCAGTTGGCAAGAACTTTGGAGATGACCTTATAAATGAACCTGCATAAGCTAATCGAGCAG
66 TGAGTCAGTTGGCAAGAACTTTGGAGATGACCTTATAAATGAACCTGCATAAGCTAATCGAGCAG
28222290 TAATTAGTAATATCATTAGGGTCACAAATTTTTGGGATTAGGATTATCATAGTTTCATTTAAAAA
131 TAATTAGTAATATCATTAGGGTCACAAATTTTTGGGATTAGGATTATCATAGTTTCATTTAAAAA
28222355 TGGAACATCTTTATTCCCGTTCAGAATATCTAGGCAAAATTGAATAGTGTCCCTGCCAACAATCT
196 TGGAACATCTTTATTCCCGTTCAGAATATCTAGGCAAAATTGAATAGTGTCCCTGCCAACAATCT
*
28222420 CCCAGTTGTACTTGAAGAAACTCCCCGAGAGACCATCCACTCCA
261 CCCAGTTGTACTTGAAGAAACCCCCCGAGAGACCATCCACTCCA
28222464 ATGTATCATTCTCCCAGGGATAAACGCACTCTAATTTGGACTTATGCAATTAGGGAGGACTACTT
1 ATGTATCATTCTCCCAGGGATAAACGCACTCTAATTTGGACTTATGCAATTAGGGAGGACTACTT
28222529 TGAGTCAGTTGGCAAGAACTTTGGAGATGACCTTATAAATGAACCTGCATAAGCTAATCGAGCAG
66 TGAGTCAGTTGGCAAGAACTTTGGAGATGACCTTATAAATGAACCTGCATAAGCTAATCGAGCAG
28222594 TAATTAGTAATATCATTAGGGTCACAAATTTTTGGGATTAGGATTATCATAGTTTCATTTAAAAA
131 TAATTAGTAATATCATTAGGGTCACAAATTTTTGGGATTAGGATTATCATAGTTTCATTTAAAAA
28222659 TGGAACATCTTTATTCCCGTTCAGAATATCTAGGCAAAATTGAATAGTGTCCCTGCCAACAATCT
196 TGGAACATCTTTATTCCCGTTCAGAATATCTAGGCAAAATTGAATAGTGTCCCTGCCAACAATCT
* *
28222724 CCCAGTTGTACTTGAAGAACCCCCCCGAGAGCCCATCCACTCCA
261 CCCAGTTGTACTTGAAGAAACCCCCCGAGAGACCATCCACTCCA
28222768 GGGGCCTTCC
Statistics
Matches: 301, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
304 301 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (304 bp):
ATGTATCATTCTCCCAGGGATAAACGCACTCTAATTTGGACTTATGCAATTAGGGAGGACTACTT
TGAGTCAGTTGGCAAGAACTTTGGAGATGACCTTATAAATGAACCTGCATAAGCTAATCGAGCAG
TAATTAGTAATATCATTAGGGTCACAAATTTTTGGGATTAGGATTATCATAGTTTCATTTAAAAA
TGGAACATCTTTATTCCCGTTCAGAATATCTAGGCAAAATTGAATAGTGTCCCTGCCAACAATCT
CCCAGTTGTACTTGAAGAAACCCCCCGAGAGACCATCCACTCCA
Found at i:28226777 original size:29 final size:29
Alignment explanation
Indices: 28226735--28226796 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
28226725 ACAAGACACA
28226735 AGTT-CAAGCAAGAACCAGACAAGCATAG
1 AGTTCCAAGCAAGAACCAGACAAGCATAG
28226763 AGTTCCAAGCAAGAACCAGACAAGCATAG
1 AGTTCCAAGCAAGAACCAGACAAGCATAG
28226792 AGTTC
1 AGTTC
28226797 AAATTCATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.13
Consensus pattern (29 bp):
AGTTCCAAGCAAGAACCAGACAAGCATAG
Found at i:28227846 original size:25 final size:25
Alignment explanation
Indices: 28227749--28227872 Score: 76
Period size: 25 Copynumber: 5.0 Consensus size: 25
28227739 AATGGGTAGG
*
28227749 TCCGAAGAGCCATTAA-CGGGAAGC
1 TCCGGAGAGCCATTAATCGGGAAGC
* * *
28227773 TTCGGATAGCCA-TATATCGGGAAGT
1 TCCGGAGAGCCATTA-ATCGGGAAGC
** * * * *
28227798 TCAAGTGACCCA-T-ATCAGGTAGC
1 TCCGGAGAGCCATTAATCGGGAAGC
28227821 TCCGGAGAGCCATTAATCGGGAAGC
1 TCCGGAGAGCCATTAATCGGGAAGC
** * *
28227846 TCACAAAAAGCCTTTAATCGGGAAGC
1 TC-CGGAGAGCCATTAATCGGGAAGC
28227872 T
1 T
28227873 TACGAAGAGC
Statistics
Matches: 72, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
23 17 0.24
24 11 0.15
25 24 0.33
26 20 0.28
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (25 bp):
TCCGGAGAGCCATTAATCGGGAAGC
Found at i:28227883 original size:26 final size:26
Alignment explanation
Indices: 28227826--28227885 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
28227816 GTAGCTCCGG
28227826 AGAGCCATTAATCGGGAAGCTCACAA
1 AGAGCCATTAATCGGGAAGCTCACAA
* * * *
28227852 AAAGCCTTTAATCGGGAAGCTTACGA
1 AGAGCCATTAATCGGGAAGCTCACAA
28227878 AGAGCCAT
1 AGAGCCAT
28227886 ATAACATGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCGGGAAGCTCACAA
Found at i:28237797 original size:31 final size:31
Alignment explanation
Indices: 28237759--28237822 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
28237749 CATACTTACA
*
28237759 AAATTTAATAACTCCACTACCACAGAATGAG
1 AAATTTAATAACTCCACTACCACAAAATGAG
28237790 AAATTTAATAACTCCACTACCACAAAATGAG
1 AAATTTAATAACTCCACTACCACAAAATGAG
28237821 AA
1 AA
28237823 TATAGATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.22
Consensus pattern (31 bp):
AAATTTAATAACTCCACTACCACAAAATGAG
Found at i:28242220 original size:21 final size:19
Alignment explanation
Indices: 28242194--28242266 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
28242184 ATCTAATTAC
28242194 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TAT-TTT
*
28242215 AAATATTTAAATATATTTT
1 AAATATTTAATTATATTTT
* *
28242234 ATATATTCTAATTAAATTTAAT
1 AAATATT-TAATTATATTT--T
*
28242256 AAATAATTAAT
1 AAATATTTAAT
28242267 ATTAATTACT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.21
20 12 0.28
21 16 0.37
22 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATATTTT
Found at i:28245821 original size:16 final size:16
Alignment explanation
Indices: 28245800--28245832 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28245790 GGACATGATA
28245800 GACTCTTTGACACATT
1 GACTCTTTGACACATT
28245816 GACTCTTTGACACATT
1 GACTCTTTGACACATT
28245832 G
1 G
28245833 GTGTCTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (16 bp):
GACTCTTTGACACATT
Found at i:28251166 original size:24 final size:24
Alignment explanation
Indices: 28251124--28251177 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
28251114 AATGAAAGTC
** **
28251124 AAATATATTATGTTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
28251148 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
28251172 AAATAT
1 AAATAT
28251178 TCTAGAAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:28251459 original size:20 final size:20
Alignment explanation
Indices: 28251418--28251459 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
28251408 TCATAACACA
* *
28251418 TCTCTCATTCTATATTCTTT
1 TCTCTCATTCCATATTCGTT
28251438 TCTCTCATTCCAT-TTCCGTT
1 TCTCTCATTCCATATT-CGTT
28251458 TC
1 TC
28251460 CTTTTTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.12, C:0.31, G:0.02, T:0.55
Consensus pattern (20 bp):
TCTCTCATTCCATATTCGTT
Found at i:28254294 original size:25 final size:25
Alignment explanation
Indices: 28254223--28254294 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
28254213 AATTTTCTTG
** *
28254223 AAATTTTACCGGGAGTAAAATCGTCA
1 AAATTTTACTAGG-GTAAAATCATCA
*
28254249 AATTTTTACTAAGGGTAAAATCATCA
1 AAATTTTACT-AGGGTAAAATCATCA
28254275 AAATTTTACTAGGGTAAAAT
1 AAATTTTACTAGGGTAAAAT
28254295 TAGGATGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
25 10 0.25
26 28 0.70
27 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (25 bp):
AAATTTTACTAGGGTAAAATCATCA
Found at i:28268407 original size:15 final size:15
Alignment explanation
Indices: 28268387--28268417 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28268377 TATAATACAC
28268387 TTATTACTGGAGTGA
1 TTATTACTGGAGTGA
*
28268402 TTATTAGTGGAGTGA
1 TTATTACTGGAGTGA
28268417 T
1 T
28268418 AATAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (15 bp):
TTATTACTGGAGTGA
Found at i:28269040 original size:93 final size:93
Alignment explanation
Indices: 28268920--28269094 Score: 350
Period size: 93 Copynumber: 1.9 Consensus size: 93
28268910 ATAGATCTTG
28268920 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
1 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
28268985 ACAGACTATGTATGCATACCTAAATTCA
66 ACAGACTATGTATGCATACCTAAATTCA
28269013 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
1 AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
28269078 ACAGACTATGTATGCAT
66 ACAGACTATGTATGCAT
28269095 GACCCGTATA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (93 bp):
AACTGTTTATGGATTTATTCACTTATGACGTTCAAAGTGTGGCATACCTAAATTCTGAGTGGATG
ACAGACTATGTATGCATACCTAAATTCA
Found at i:28274550 original size:21 final size:21
Alignment explanation
Indices: 28274524--28274564 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28274514 TCAACAATTG
28274524 ATGAGACTTTGGGTACTCATA
1 ATGAGACTTTGGGTACTCATA
28274545 ATGAGACTTTGGGTACTCAT
1 ATGAGACTTTGGGTACTCAT
28274565 GATGGGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (21 bp):
ATGAGACTTTGGGTACTCATA
Found at i:28280081 original size:21 final size:20
Alignment explanation
Indices: 28280055--28280146 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 20
28280045 GAGGTTGAGA
28280055 TTTAGGGTTTGAGGTTATGGG
1 TTTAGGGTTT-AGGTTATGGG
* *
28280076 TTTAGGGATCTAGGTTTTGGG
1 TTTAGGG-TTTAGGTTATGGG
* * * * *
28280097 TTTATGGTTAAGGATTCTTGA
1 TTTAGGGTTTAGG-TTATGGG
*
28280118 TTTAGGGTTCAGGGTT-TGGG
1 TTTAGGGTTTA-GGTTATGGG
28280138 TTTTAGGGT
1 -TTTAGGGT
28280147 AAAAAATAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
20 6 0.11
21 45 0.82
22 4 0.07
ACGTcount: A:0.15, C:0.03, G:0.37, T:0.45
Consensus pattern (20 bp):
TTTAGGGTTTAGGTTATGGG
Found at i:28281194 original size:27 final size:27
Alignment explanation
Indices: 28281153--28281221 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
28281143 TGGGGTTTGT
* * *
28281153 GTTTAGGATTTAAGGTTGAAGGTTCAA
1 GTTTAGGGTTCAAGGTTCAAGGTTCAA
*
28281180 GTTTGGGGTTCAAGGTTCAAGGTTCAA
1 GTTTAGGGTTCAAGGTTCAAGGTTCAA
*
28281207 GTTTAGTGTTCAAGG
1 GTTTAGGGTTCAAGG
28281222 GTTTGGGGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.07, G:0.32, T:0.36
Consensus pattern (27 bp):
GTTTAGGGTTCAAGGTTCAAGGTTCAA
Found at i:28297095 original size:44 final size:44
Alignment explanation
Indices: 28297032--28297534 Score: 287
Period size: 44 Copynumber: 11.6 Consensus size: 44
28297022 CCACTAATCC
* *
28297032 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTAACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
* * * ** * * *
28297076 TATCTCACTGAAGTGGCAGTAGAGTGGA-T--CGTATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
* * * *
28297117 TATCTCCCTGAAGGTGCAGCGGAGCAGACT-AAGTAAGCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-CAGATCT
* * * ** *
28297161 TATCCCCCTGAAGTTGCAGTGGGGCAGATCAAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAACAGATCT
* * ** * *
28297206 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAACAGATCT
* ** *
28297250 TATCTCCCTGAAGTTGCAG-CGAGC-GAATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGTAACAGATCT
* * * * * ** *
28297293 TATC-CCTTGAAGTTGCAGTGGGGTAGATCGAAGGTGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGTAACAGATCT
* * * * *
28297337 TATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-AACAGATCT
* * * ** *
28297381 TATCTCCCTGAAGTTGTAGCGGAGCGGATTAAAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
* * * * * *
28297425 TATCTCTCTGAAGTTGTACTAGAGCAGA-T--CGCAACCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-CAGATCT
* * * * *
28297466 CATCTCCCTGAAGTTGCAGTGGAGCAGA-CACAAGAAACAAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AAGTAACAGATCT
*
28297510 TATCTCCCTGAAGTTGCAGCGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
28297535 GGATCAAAAT
Statistics
Matches: 344, Mismatches: 97, Indels: 36
0.72 0.20 0.08
Matches are distributed among these distances:
41 58 0.17
42 20 0.06
43 28 0.08
44 176 0.51
45 61 0.18
46 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAACAGATCT
Found at i:28297321 original size:131 final size:132
Alignment explanation
Indices: 28297117--28297535 Score: 469
Period size: 131 Copynumber: 3.2 Consensus size: 132
28297107 TATCAGGTCT
* * * * * *
28297117 TATCTCCCTGAAGGTGCAGCGGAGC-AGACTAAGTA-AGCAGGTCTTATCCCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGCGGAGCGA-ATTAA-AACATCAGATCTTAT-CCCTTGAAGTTGCAG
*
28297180 TGGGGCAGATCAAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
63 TGGGGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
28297245 AATCC
128 AATCC
28297250 TATCTCCCTGAAGTTGCAGC-GAGCGAATTAAAACATCAGATCTTATCCCTTGAAGTTGCAGTGG
1 TATCTCCCTGAAGTTGCAGCGGAGCGAATTAAAACATCAGATCTTATCCCTTGAAGTTGCAGTGG
* * * * *
28297314 GGTAGATCGAAGGTGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGATAAT
66 GGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGATAAT
28297379 CC
131 CC
* * * * * *
28297381 TATCTCCCTGAAGTTGTAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTACTA
1 TATCTCCCTGAAGTTGCAGCGGAGCGAATTAAAACATCAGATCTTATCCCT-TGAAGTTGCAGTG
* ** * * * *** *
28297446 GAGCAGATCGCA-A---CCAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAAC-A-
65 GGGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--CCGAT
28297505 AATCC
128 AATCC
28297510 TATCTCCCTGAAGTTGCAGCGGAGCG
1 TATCTCCCTGAAGTTGCAGCGGAGCG
28297536 GATCAAAATG
Statistics
Matches: 249, Mismatches: 31, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
129 64 0.26
130 1 0.00
131 99 0.40
132 46 0.18
133 39 0.16
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (132 bp):
TATCTCCCTGAAGTTGCAGCGGAGCGAATTAAAACATCAGATCTTATCCCTTGAAGTTGCAGTGG
GGCAGATCAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGATAAT
CC
Found at i:28297509 original size:129 final size:129
Alignment explanation
Indices: 28297198--28297583 Score: 406
Period size: 129 Copynumber: 3.0 Consensus size: 129
28297188 ATCAAAGATG
* * *** *
28297198 GCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAG
1 GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGACGATAATCCTATCTCCCTGAAG
* * * * *
28297263 TTGCAGC-GAGCGAATTAAAACATCAGATCTTATCCCT-TGAAGTTGCAGTGGGGTAGATCGAA
66 TTGCAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGAA
* * *** *
28297325 GGTGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCT
1 ----GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGACGATAATCCTATCTCCCT
* * *
28297390 GAAGTTGTAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTACTAGAGCAGATC
62 GAAGTTGCAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATC
28297455 GCAA
127 G-AA
* *
28297459 -CCAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAAC-A-AATCCTATCTCCCTGA
1 GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAG--ACGATAATCCTATCTCCCTGA
* * * * * *
28297521 AGTTGCAGCGGAGCGGATCAAAATGAT-GGGTCTCATCTATCTGAAGTTGTAGTAGAGTAGATC
64 AGTTGCAGCGGAGCGGATTAAAA-CATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATC
28297584 ATATCAGTCT
Statistics
Matches: 221, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
129 101 0.46
130 3 0.01
131 69 0.31
132 28 0.13
133 18 0.08
134 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (129 bp):
GCAAATCTCATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGACGATAATCCTATCTCCCTGAAG
TTGCAGCGGAGCGGATTAAAACATCAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGAA
Found at i:28300783 original size:28 final size:29
Alignment explanation
Indices: 28300725--28300784 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
28300715 TGCATATATT
* *
28300725 TATTATATATAATAAAACCCACACATATA
1 TATTATATATAACAAAACCCACACAAATA
* *
28300754 TATTATATATAGCAAAA-CCACGCAAATA
1 TATTATATATAACAAAACCCACACAAATA
28300782 TAT
1 TAT
28300785 GCTGTATGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (29 bp):
TATTATATATAACAAAACCCACACAAATA
Found at i:28302468 original size:12 final size:12
Alignment explanation
Indices: 28302451--28302498 Score: 87
Period size: 12 Copynumber: 3.9 Consensus size: 12
28302441 CTCGAGCCCA
28302451 CAATCTAATACC
1 CAATCTAATACC
28302463 CAATCTAATACC
1 CAATCTAATACC
28302475 CAATCTAATACC
1 CAATCTAATACC
28302487 ACAATCTAATAC
1 -CAATCTAATAC
28302499 ACATAATCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (12 bp):
CAATCTAATACC
Found at i:28304078 original size:7 final size:6
Alignment explanation
Indices: 28304033--28304077 Score: 63
Period size: 6 Copynumber: 7.0 Consensus size: 6
28304023 TGACTAGATT
28304033 AAAATA AAAATA AAAATA AAAATA AAATATA AAATATA TAAAATA
1 AAAATA AAAATA AAAATA AAAATA AAA-ATA AAA-ATA -AAAATA
28304078 TTATTTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
6 21 0.57
7 13 0.35
8 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:28309119 original size:19 final size:19
Alignment explanation
Indices: 28309095--28309136 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
28309085 GAGTTGTCTT
28309095 AAAAGAGTAAAAAAATCCA
1 AAAAGAGTAAAAAAATCCA
28309114 AAAAGAGTAAAAAAATCCA
1 AAAAGAGTAAAAAAATCCA
28309133 AAAA
1 AAAA
28309137 TCTTGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAAGAGTAAAAAAATCCA
Found at i:28323711 original size:5 final size:5
Alignment explanation
Indices: 28323701--28323725 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28323691 TTCTATATTG
28323701 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
28323726 TGTCTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:28324832 original size:33 final size:33
Alignment explanation
Indices: 28324788--28324953 Score: 224
Period size: 33 Copynumber: 5.0 Consensus size: 33
28324778 TCAACATAAG
* *
28324788 TGATTGGAACATCTATTAGGGCAGCTTCATCAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
28324821 TGATTGAAACATCTATCAGGGTAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
28324854 TGATTGGGACATCTATCAAGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* **
28324887 TGAGTGGAACATCTATTGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* * *
28324920 TGATTGCAGCATCTATCAGGGCAACTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
28324953 T
1 T
28324954 CTATTCGACT
Statistics
Matches: 114, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAT
Found at i:28330032 original size:21 final size:23
Alignment explanation
Indices: 28330006--28330050 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
28329996 GAAAGGTATC
* *
28330006 TACAAATTAA-ATC-TCTATGAT
1 TACAAAATAATATCTTCTAAGAT
28330027 TACAAAATAATATCTTCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
28330050 T
1 T
28330051 GCATATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 8 0.40
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (23 bp):
TACAAAATAATATCTTCTAAGAT
Found at i:28330713 original size:131 final size:132
Alignment explanation
Indices: 28330499--28330886 Score: 609
Period size: 131 Copynumber: 2.9 Consensus size: 132
28330489 CAGTGAAACT
* ** * *
28330499 TCAGGGAGATAAGG-CTAGTGGCTTAAATCTGCTTCCCTACTACCTCGAAAAGGTAAGACTCGCC
1 TCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACC
* *
28330563 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATACAATCTTCAACCTACTCCACTAC
65 GTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTAC
28330628 TGC
130 TGC
* * *
28330631 TCAGGGAGATAGGACTGGTGGCTTAAATCTGGTT-CCTATTATCTCGGGAAGATAAGACTCACCG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACCG
28330695 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
28330760 GC
131 GC
* * * * * *
28330762 TCAAGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAGGATAAGATTCACTG
1 TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACCG
28330827 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCA
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCA
28330887 TTGCAAACTC
Statistics
Matches: 236, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
131 124 0.53
132 112 0.47
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (132 bp):
TCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGACTCACCG
TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTACT
GC
Found at i:28331013 original size:89 final size:89
Alignment explanation
Indices: 28330890--28331238 Score: 439
Period size: 89 Copynumber: 3.9 Consensus size: 89
28330880 TACTCCATTG
* * * * * *
28330890 CAAACTCAGAGAGGCAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTAAAGGAAGACAAGATC
1 CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
* * *
28330955 CGCTATTTTCACTCTGCTCCGCTA
66 TGCTATCTTCAGTCTGCTCCGCTA
* * * *
28330979 CAAAGTCAGGGAAGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGAAAGACAAGATC
1 CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
28331044 TGCTATCTTCAGTCTGCTCCGCTA
66 TGCTATCTTCAGTCTGCTCCGCTA
* * *
28331068 CAAACTCA-GGAAGACAAGGCTGGTGTCTTCGATCTGTTTCACTGCCAATATAGGATGACAAGAT
1 CAAACTCAGGGAAG-CAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGAT
* ** *
28331132 CTGCTATCTTCAGTCTACTCTACTG
65 CTGCTATCTTCAGTCTGCTCCGCTA
* * * * *
28331157 TAAACTCAGGGACGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGCCAATACAGGAAGACAAGATC
1 CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
* *
28331222 TGTTATCTTTAGTCTGC
66 TGCTATCTTCAGTCTGC
28331239 CCTGTTGCAA
Statistics
Matches: 223, Mismatches: 35, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
88 5 0.02
89 214 0.96
90 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (89 bp):
CAAACTCAGGGAAGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATC
TGCTATCTTCAGTCTGCTCCGCTA
Found at i:28331082 original size:45 final size:44
Alignment explanation
Indices: 28330941--28331147 Score: 131
Period size: 45 Copynumber: 4.7 Consensus size: 44
28330931 CTGCCAGTAA
* * *
28330941 AGGAAGACAAGATCCGCTATTTTCACTCTGCTCCGCTACAAAGTC
1 AGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAA-TC
* * * * *
28330986 AGGGAAG-CAAG-GCTAG-TGTCTTC-GATCTGCTTCGCTGCCAATAC
1 A-GGAAGACAAGATCT-GCTATCTTCAG-TCTGCTCCGCTACAAAT-C
*
28331030 AGAAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAACTC
1 AGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAA-TC
* * * * * * *
28331075 AGGAAGACAAG-GCTGGTGTCTTC-GATCTGTTTCACTGCCAATAT-
1 AGGAAGACAAGATCTGCTATCTTCAG-TCTGCTCCGCT-ACAA-ATC
*
28331119 AGGATGACAAGATCTGCTATCTTCAGTCT
1 AGGAAGACAAGATCTGCTATCTTCAGTCT
28331148 ACTCTACTGT
Statistics
Matches: 122, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
43 6 0.05
44 53 0.43
45 54 0.44
46 9 0.07
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCGCTACAAATC
Found at i:28331252 original size:178 final size:177
Alignment explanation
Indices: 28330882--28331263 Score: 487
Period size: 178 Copynumber: 2.1 Consensus size: 177
28330872 CTTCAACCTA
* * * *
28330882 CTCCATTGCAAACTCAGAGAGGCAAGGCTGGTGTTTTTGATCTGCTTCACTGCCAGTAAAGGAAG
1 CTCCGTTGCAAACTCAGA-AGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATAAAGGAAG
* * * *
28330947 ACAAGATCCGCTATTTTCACTCTGCTCCGCTACAAAGTCAGGGAAGCAAGGCTAGTGTCTTCGAT
65 ACAAGATCCGCTATCTTCACTCTACTCCACTACAAACTCAGGGAAGCAAGGCTAGTGTCTTCGAT
28331012 CTGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
130 CTGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
* * * * * *
28331060 CTCCGCTACAAACTCAGGAAGACAAGGCTGGTGTCTTCGATCTGTTTCACTGCCAATATAGGATG
1 CTCCGTTGCAAACTCA-GAAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATAAAGGAAG
* * * ** * * * *
28331125 ACAAGATCTGCTATCTTCAGTCTACTCTACTGTAAACTCAGGGACGCAAGGTTGGTGTCTTTGAT
65 ACAAGATCCGCTATCTTCACTCTACTCCACTACAAACTCAGGGAAGCAAGGCTAGTGTCTTCGAT
* * *
28331190 CTGCTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTTAGTCTG
130 CTGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
28331238 C-CCTGTTGCAAACTCAAGAAGGCAAG
1 CTCC-GTTGCAAACTC-AGAAGGCAAG
28331264 ACTTGTAACT
Statistics
Matches: 172, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
177 2 0.01
178 167 0.97
179 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (177 bp):
CTCCGTTGCAAACTCAGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGCCAATAAAGGAAGA
CAAGATCCGCTATCTTCACTCTACTCCACTACAAACTCAGGGAAGCAAGGCTAGTGTCTTCGATC
TGCTTCGCTGCCAATACAGAAAGACAAGATCTGCTATCTTCAGTCTG
Found at i:28331492 original size:177 final size:178
Alignment explanation
Indices: 28331261--28331660 Score: 529
Period size: 177 Copynumber: 2.3 Consensus size: 178
28331251 TCAAGAAGGC
* * *
28331261 AAGACTTGTAACTTTAATTTGCTCCACTGCAACTTCAGGGAGATAGCATTATTGGCTTTAATCTT
1 AAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAAGGAGATAGCATTATTGGCTTTAATCTA
* * ** * * * * * *
28331326 CTCCATTGCAACTTCAGGGAGATAAGATTTTCCATCTTCTGTCTACCTCACTGCAGCTTTA-GGG
66 CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTACCCCACTACAACTTCAGGGG
*
28331390 GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAACCTT-AGGGATAT
131 GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAA-CTTCAGGGAGAT
* * *
28331438 AAGACTTGTAACTTTAATTCGCTCCATTGTAACTTCAAGGAGATAGGATTATTGGCTTTAATCTA
1 AAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAAGGAGATAGCATTATTGGCTTTAATCTA
* *
28331503 CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTGCCCCATTACAACTTCAGGGG
66 CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTACCCCACTACAACTTCAGGGG
*
28331568 GATAAGACTTGTTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGAT
131 GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGAT
* ** *
28331616 AAGA-TTATTGGCTTTAATAT-GCTCCACTGCAACTTCAGGGAGATA
1 AAGACTT-GTAACTTTAAT-TCGCTCCACTGCAACTTCAAGGAGATA
28331661 AGATTCACCA
Statistics
Matches: 193, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
177 113 0.59
178 79 0.41
179 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (178 bp):
AAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAAGGAGATAGCATTATTGGCTTTAATCTA
CTCCACTGCAACCTCAGGGAGATAAGATTCGCCATATTCAGTCTACCCCACTACAACTTCAGGGG
GATAAGACTTGCTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGAT
Found at i:28331654 original size:44 final size:43
Alignment explanation
Indices: 28331272--28331665 Score: 239
Period size: 44 Copynumber: 8.9 Consensus size: 43
28331262 AGACTTGTAA
*
28331272 CTTTAATTTGCTCCACTGCAACTTCAGGGAGAT-AGCATTATTGG
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG-ATT-TTGG
* * *
28331316 CTTTAATCTTCTCCATTGCAACTTCAGGGAGATAAGATTTT-C
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTGG
* * * *
28331358 CATCT--TCTGTCTACCTCACTGCAGCTTTAGGG-GATAAGACTTGCTT-T
1 C-TTTAATCTG-CT--C-CACTGCAACTTCAGGGAGATAAGA-TT--TTGG
* * * * * **
28331405 CTTCAGTCTACTCCACTGCAACCTT-AGGGATATAAGACTTGTAA
1 CTTTAATCTGCTCCACTGCAA-CTTCAGGGAGATAAGA-TTTTGG
* * * *
28331449 CTTTAAT-TCGCTCCATTGTAACTTCAAGGAGATAGGATTATTGG
1 CTTTAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATT-TTGG
* * * *
28331493 CTTTAATCTACTCCACTGCAACCTCAGGGAGATAAGA-TTCGC
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTGG
* * * * * **
28331535 CATATTCAGTCTGCCCCATTACAACTTCAGGGGGATAAGACTTGTTTT
1 C-T-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-TTGG
* * *
28331583 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGG
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TTGG
*
28331627 CTTTAATATGCTCCACTGCAACTTCAGGGAGATAAGATT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
28331666 CACCATCTTC
Statistics
Matches: 267, Mismatches: 59, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
41 3 0.01
42 6 0.02
43 13 0.05
44 146 0.55
45 85 0.32
46 2 0.01
47 7 0.03
48 5 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (43 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTGG
Found at i:28332976 original size:9 final size:9
Alignment explanation
Indices: 28332962--28332987 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28332952 TCTTTCTTCT
28332962 TTTTTTTGA
1 TTTTTTTGA
28332971 TTTTTTTGA
1 TTTTTTTGA
28332980 TTTTTTTG
1 TTTTTTTG
28332988 TCTCAAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.81
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:28335528 original size:29 final size:31
Alignment explanation
Indices: 28335492--28335564 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 31
28335482 CGACAGAATC
28335492 TTAACATAGTC-G-GTATTAACAGATGATTA
1 TTAACATAGTCGGAGTATTAACAGATGATTA
*
28335521 TTAACATAGTCTGGCAATGTATTAGCAGATGATTA
1 TTAACATAGTC-GG--A-GTATTAACAGATGATTA
28335556 TTAACATAG
1 TTAACATAG
28335565 CTGGTGTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 11 0.30
31 1 0.03
35 25 0.68
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (31 bp):
TTAACATAGTCGGAGTATTAACAGATGATTA
Found at i:28343813 original size:15 final size:15
Alignment explanation
Indices: 28343775--28343813 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
28343765 CAAAACATCT
*
28343775 TAAAAATAAATGGTA
1 TAAAAATAAATAGTA
*
28343790 TATAAAATAGATAGTA
1 TA-AAAATAAATAGTA
28343806 TAAAAATA
1 TAAAAATA
28343814 TTTGCAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
TAAAAATAAATAGTA
Found at i:28344438 original size:23 final size:22
Alignment explanation
Indices: 28344408--28344453 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
28344398 TGAATTAAAT
28344408 TTCTAAGATTACAAAATCATATC
1 TTCTAAGATTAC-AAATCATATC
* *
28344431 TTCTAAGATTGCATATCATATC
1 TTCTAAGATTACAAATCATATC
28344453 T
1 T
28344454 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (22 bp):
TTCTAAGATTACAAATCATATC
Found at i:28352677 original size:11 final size:11
Alignment explanation
Indices: 28352661--28352685 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28352651 ATTGAATTGA
28352661 ATTTTTAGTTT
1 ATTTTTAGTTT
28352672 ATTTTTAGTTT
1 ATTTTTAGTTT
28352683 ATT
1 ATT
28352686 ATCATGTATT
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (11 bp):
ATTTTTAGTTT
Found at i:28356165 original size:93 final size:93
Alignment explanation
Indices: 28356006--28356191 Score: 309
Period size: 93 Copynumber: 2.0 Consensus size: 93
28355996 AAAGGCAATG
* * * *
28356006 TTTGTTCATTGATCGTTGTAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGGGAC
1 TTTGTTCATTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
*
28356071 ATTCGACCAATATTTCTCCAAGTACCAT
66 ATTCGACCAACATTTCTCCAAGTACCAT
*
28356099 TTTGTTCGTTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
1 TTTGTTCATTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
*
28356164 ATTCGACCAACGTTTCTCCAAGTACCAT
66 ATTCGACCAACATTTCTCCAAGTACCAT
28356192 AAGAGTTGTC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (93 bp):
TTTGTTCATTAATCGCTGCAGAGGTGCTACTGCTTTGATCATTGTGTTGTTGTATCCTGGGAGAC
ATTCGACCAACATTTCTCCAAGTACCAT
Found at i:28356853 original size:87 final size:86
Alignment explanation
Indices: 28356666--28357059 Score: 325
Period size: 87 Copynumber: 4.5 Consensus size: 86
28356656 CTTTGCTTCC
* * * * * ** *
28356666 AAATTAAAAGTAAATAAAATCAGTTTTGGGATTTCTTGCCGCTGTTCAACGGATTTTATTCCATT
1 AAATTAAAATTAAATAAAATTAGTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATT-CAAT
* ***
28356731 TTTTATTTTATTTCCAAATGGG
65 TTTGATTTTATTTCCAAAAACG
* * *
28356753 AAATTTAAGTTAAATAAAATTCA-TTTCGGGATTTATTCCCGCCATTCAACGAATTTTATTCGAA
1 AAATTAAAATTAAATAAAATT-AGTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTC-AA
* *
28356817 TTTCGATTTTATTT-CTAAAACG
64 TTTTGATTTTATTTCCAAAAACG
* * * * *
28356839 ATTATTAAAATTAAAATAAAA-TATGTTTCAGGATTTATTCCCGCCGTTCAATGGAGTTTATTCC
1 A-AATTAAAATT-AAATAAAATTA-GTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATT-C
* *
28356903 AAATTTGTTTTTATTTCCAAAAACG
62 AATTTTGATTTTATTTCCAAAAACG
* * *
28356928 AGTATTAAAATTAAA-ATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACGGA-TTTATT-A
1 A-AATTAAAATTAAATA-AAATTA-GTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTCA
* *
28356990 CATTTTTATTTTGTTTCCAAAAACGAG
63 -ATTTTGATTTTATTTCCAAAAAC--G
** *
28357017 AAATTAAAATTAAATAAAATCT-GTTTCAAGATTTATTCTCGCC
1 AAATTAAAATTAAATAAAAT-TAGTTTCGGGATTTATTCCCGCC
28357060 GTTTGACAAG
Statistics
Matches: 250, Mismatches: 42, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
86 8 0.03
87 108 0.43
88 82 0.33
89 52 0.21
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (86 bp):
AAATTAAAATTAAATAAAATTAGTTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTCAATT
TTGATTTTATTTCCAAAAACG
Found at i:28356902 original size:175 final size:175
Alignment explanation
Indices: 28356666--28357062 Score: 405
Period size: 175 Copynumber: 2.3 Consensus size: 175
28356656 CTTTGCTTCC
* ** * * * *
28356666 AAATTAAAAGTAAATAAAATCA-GTTTTGGGATTTCTTGCCGCTGTTCAACGGATTTTATTCC-A
1 AAATTAAAATTAAATAAAAT-ATGTTTCAGGATTTATTCCCGCCGTTCAACGGAGTTTATTCCAA
* * *** * *
28356729 TTTTTTATTTTATTTCCAAATGGGA-AATTTAAGTT-AAATAAAATTCA-TTTCGGGATTTATTC
65 ATTTGT-TTTTATTTCCAAAAACGAGAATTAAAATTAAAAT-AAATT-AGTTTCGGGATTTATTC
*
28356791 CCGCCATTCAACGAATTTTATT-CGAATTTCGATTTTATTT-CTAAAACGA-
127 CCGCCATTCAACGAA-TTTATTAC--ATTTCGATTTTATTTCCAAAAACGAG
** *
28356840 TTATTAAAATTAAAATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAATGGAGTTTATTCCAA
1 AAATTAAAATT-AAATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGAGTTTATTCCAA
* *
28356905 ATTTGTTTTTATTTCCAAAAACGAGTATTAAAATTAAAATAAATTATGTTTCGGGATTTATTCTC
65 ATTTGTTTTTATTTCCAAAAACGAGAATTAAAATTAAAATAAATTA-GTTTCGGGATTTATTCCC
* * ** *
28356970 GCCATTTAACGGATTTATTACATTTTTATTTTGTTTCCAAAAACGAG
129 GCCATTCAACGAATTTATTACATTTCGATTTTATTTCCAAAAACGAG
* * *
28357017 AAATTAAAATTAAATAAAATCTGTTTCAAGATTTATTCTCGCCGTT
1 AAATTAAAATTAAATAAAATATGTTTCAGGATTTATTCCCGCCGTT
28357063 TGACAAGATT
Statistics
Matches: 183, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
174 9 0.05
175 70 0.38
176 63 0.34
177 41 0.22
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (175 bp):
AAATTAAAATTAAATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGAGTTTATTCCAAA
TTTGTTTTTATTTCCAAAAACGAGAATTAAAATTAAAATAAATTAGTTTCGGGATTTATTCCCGC
CATTCAACGAATTTATTACATTTCGATTTTATTTCCAAAAACGAG
Found at i:28356954 original size:89 final size:87
Alignment explanation
Indices: 28356776--28357059 Score: 322
Period size: 89 Copynumber: 3.2 Consensus size: 87
28356766 ATAAAATTCA
* * * * *
28356776 TTTCGGGATTTATTCCCGCCATTCAACGAATTTTATTCGAATTTCGATTTTATTT-CTAAAACGA
1 TTTCAGGATTTATTCCCGCCATTCAACGGA-TTTATTCAAATTT-GTTTTTATTTCCAAAAACGA
*
28356840 TTATTAAAATTAAAATAAAATATG
64 GTATTAAAATTAAAATAAAATATG
* *
28356864 TTTCAGGATTTATTCCCGCCGTTCAATGGAGTTTATTCCAAATTTGTTTTTATTTCCAAAAACGA
1 TTTCAGGATTTATTCCCGCCATTCAACGGA-TTTATT-CAAATTTGTTTTTATTTCCAAAAACGA
*
28356929 GTATTAAAATTAAAATAAATTATG
64 GTATTAAAATTAAAATAAAATATG
* * * * * *
28356953 TTTCGGGATTTATTCTCGCCATTTAACGGATTTATT-ACATTTTTATTTTGTTTCCAAAAACGAG
1 TTTCAGGATTTATTCCCGCCATTCAACGGATTTATTCAAATTTGT-TTTTATTTCCAAAAACGAG
* *
28357017 AAATTAAAATT-AAATAAAATCTG
65 -TATTAAAATTAAAATAAAATATG
* *
28357040 TTTCAAGATTTATTCTCGCC
1 TTTCAGGATTTATTCCCGCC
28357060 GTTTGACAAG
Statistics
Matches: 169, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
86 6 0.04
87 46 0.27
88 56 0.33
89 61 0.36
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (87 bp):
TTTCAGGATTTATTCCCGCCATTCAACGGATTTATTCAAATTTGTTTTTATTTCCAAAAACGAGT
ATTAAAATTAAAATAAAATATG
Found at i:28357188 original size:157 final size:160
Alignment explanation
Indices: 28356935--28357231 Score: 367
Period size: 161 Copynumber: 1.9 Consensus size: 160
28356925 ACGAGTATTA
*
28356935 AAATTAAAATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACGGATTTATTACATTTTTATT
1 AAATTAAAATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACAGATTTATTACATTTTTATT
* * * * *
28357000 TTGTTTCCAAAAACGAGAAATTAAAATTAAATAAAATCTGTTTCAAGATTTATTCTCGCCGTTTG
66 TTGTTTCC-AAAACGAGAAACTAAAATTAAATAAAATCT-TTTCAAGATTCATTCCCACCGTTTA
28357065 ACAAGATTTTAGTTTGCTTCCAAAGTAGAATT
129 ACAAGATTTTAGTTTGCTTCCAAAGTAGAATT
* **
28357097 AAATT-AAATAATATT-TGTTTCGGGATTTATTCTCG-CAGTTTAACAATATTTTATTTGA-TTT
1 AAATTAAAATAA-ATTATGTTTCGGGATTTATTCTCGCCA-TTTAAC-AGA-TTTATTACATTTT
** **
28357158 TATTTTGTTT-C-AAATTAG-AACT-AAATTAAATAAAATCTTTTCGGGATTCATTCCCACCGTT
62 TATTTTGTTTCCAAAACGAGAAACTAAAATTAAATAAAATCTTTTCAAGATTCATTCCCACCGTT
28357219 TAACAAGATTTTA
127 TAACAAGATTTTA
28357232 TTCGATATTG
Statistics
Matches: 118, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
156 30 0.25
157 16 0.14
158 3 0.03
159 5 0.04
160 2 0.02
161 33 0.28
162 22 0.19
163 7 0.06
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (160 bp):
AAATTAAAATAAATTATGTTTCGGGATTTATTCTCGCCATTTAACAGATTTATTACATTTTTATT
TTGTTTCCAAAACGAGAAACTAAAATTAAATAAAATCTTTTCAAGATTCATTCCCACCGTTTAAC
AAGATTTTAGTTTGCTTCCAAAGTAGAATT
Found at i:28357222 original size:82 final size:84
Alignment explanation
Indices: 28357069--28357233 Score: 217
Period size: 82 Copynumber: 2.0 Consensus size: 84
28357059 CGTTTGACAA
* * * * * *
28357069 GATTTTAGTTTGCTTCCAAAGTAGAATTAAATTAAATAATATTTGTTTCGGGATTTATTCTCGCA
1 GATTTTAGTTTGCTTCCAAAGTAGAACTAAATTAAATAAAATCTGTTTCGGGATTCATTCCCACA
*
28357134 GTTTAACAATATTTTATTT
66 GTTTAACAAGATTTTATTT
* * * *
28357153 GATTTTATTTTG-TTTCAAATTAGAACTAAATTAAATAAAATCT-TTTCGGGATTCATTCCCACC
1 GATTTTAGTTTGCTTCCAAAGTAGAACTAAATTAAATAAAATCTGTTTCGGGATTCATTCCCACA
28357216 GTTTAACAAGATTTTATT
66 GTTTAACAAGATTTTATT
28357234 CGATATTGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
82 33 0.47
83 26 0.37
84 11 0.16
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (84 bp):
GATTTTAGTTTGCTTCCAAAGTAGAACTAAATTAAATAAAATCTGTTTCGGGATTCATTCCCACA
GTTTAACAAGATTTTATTT
Found at i:28358727 original size:50 final size:51
Alignment explanation
Indices: 28358644--28358746 Score: 120
Period size: 50 Copynumber: 2.0 Consensus size: 51
28358634 TTTGAAATTT
* *
28358644 TGGGCCCACATGCCCGTGTGGCCCACATAGCCCAAAATAGCTT-GCCCGTG
1 TGGGCCCACACGCCCGTGTGGCCCACATAGCCCAAAATAGCTTAGACCGTG
* * * * *
28358694 TGGGCCCACACGTCTGTGTGGCCCATACT-GCCCAATATGGCTTAGACCGTG
1 TGGGCCCACACGCCCGTGTGGCCCACA-TAGCCCAAAATAGCTTAGACCGTG
28358745 TG
1 TG
28358747 TCACACACGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 35 0.80
51 9 0.20
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.21
Consensus pattern (51 bp):
TGGGCCCACACGCCCGTGTGGCCCACATAGCCCAAAATAGCTTAGACCGTG
Found at i:28362508 original size:27 final size:27
Alignment explanation
Indices: 28362470--28362524 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
28362460 GCACATTGCG
**
28362470 TGGAATGCATGGTTTACATGAAATGCA
1 TGGAATGCATGGGATACATGAAATGCA
* *
28362497 TGGATTGCATGGGATGCATGAAATGCA
1 TGGAATGCATGGGATACATGAAATGCA
28362524 T
1 T
28362525 TTTTTGCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (27 bp):
TGGAATGCATGGGATACATGAAATGCA
Found at i:28362513 original size:18 final size:18
Alignment explanation
Indices: 28362464--28362516 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
28362454 CATGCAGCAC
*
28362464 ATTGCGTGGAATGCATGG
1 ATTGCATGGAATGCATGG
* * *
28362482 TTTACATGAAATGCATGG
1 ATTGCATGGAATGCATGG
*
28362500 ATTGCATGGGATGCATG
1 ATTGCATGGAATGCATG
28362517 AAATGCATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.30
Consensus pattern (18 bp):
ATTGCATGGAATGCATGG
Found at i:28374519 original size:28 final size:28
Alignment explanation
Indices: 28374487--28374580 Score: 161
Period size: 28 Copynumber: 3.4 Consensus size: 28
28374477 CAACATGCAA
28374487 TAACAGTGTGGGCCTTAGCCCGATACAG
1 TAACAGTGTGGGCCTTAGCCCGATACAG
28374515 TAACAGTGTGGGCCTTAGCCCGATACAG
1 TAACAGTGTGGGCCTTAGCCCGATACAG
* *
28374543 GAACAGTGTGGGCCTTAGCCCAATACAG
1 TAACAGTGTGGGCCTTAGCCCGATACAG
*
28374571 TAACAATGTG
1 TAACAGTGTG
28374581 ATAATGCAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (28 bp):
TAACAGTGTGGGCCTTAGCCCGATACAG
Found at i:28374655 original size:21 final size:21
Alignment explanation
Indices: 28374605--28374656 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
28374595 CTCAATCCAG
* *
28374605 CCAACACAACGCTTTGTACCG
1 CCAACACACCGCTTTGTACCA
28374626 CCAACACACCGCTTTGTACCA
1 CCAACACACCGCTTTGTACCA
28374647 CCAACACACC
1 CCAACACACC
28374657 ATGTGGGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.44, G:0.10, T:0.15
Consensus pattern (21 bp):
CCAACACACCGCTTTGTACCA
Found at i:28374957 original size:27 final size:27
Alignment explanation
Indices: 28374897--28375124 Score: 275
Period size: 27 Copynumber: 8.4 Consensus size: 27
28374887 AGAGGTATAG
**
28374897 TAGTCATTTTACCCTATGGGGGGTATTT
1 TAGTCATTTTACCCT-TCAGGGGTATTT
** *
28374925 CGGTCATTTTACCCTAT-GGGGGTATTT
1 TAGTCATTTTACCCT-TCAGGGGTATTT
28374952 TAGTCATTTTACCCTTC-GGGAGTATTT
1 TAGTCATTTTACCCTTCAGGG-GTATTT
*
28374979 CAGTCATTTTACCCTTCAGGGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
*
28375006 TAGTCATTTTACCCTTCAGAGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
* *
28375033 T-GATTATTTTACCTTTC-GCGGGTATTT
1 TAG-TCATTTTACCCTTCAG-GGGTATTT
* *
28375060 TAGTCATTTTACCCTTTAGAGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
28375087 TAGTCATTTTACCCTTCAGGGGTATTT
1 TAGTCATTTTACCCTTCAGGGGTATTT
*
28375114 CAGTCATTTTA
1 TAGTCATTTTA
28375125 TTGACCCTAC
Statistics
Matches: 176, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
26 6 0.03
27 150 0.85
28 20 0.11
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.45
Consensus pattern (27 bp):
TAGTCATTTTACCCTTCAGGGGTATTT
Found at i:28376289 original size:13 final size:13
Alignment explanation
Indices: 28376271--28376316 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
28376261 CTACACAGCT
28376271 AGTATAACCAAAA
1 AGTATAACCAAAA
*
28376284 AGTATAATCAAAA
1 AGTATAACCAAAA
*
28376297 AGTATAACCGAAA
1 AGTATAACCAAAA
28376310 AGTATAA
1 AGTATAA
28376317 TCAGCAGCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.20
Consensus pattern (13 bp):
AGTATAACCAAAA
Found at i:28387649 original size:11 final size:11
Alignment explanation
Indices: 28387633--28387677 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
28387623 TATTTCCTTC
28387633 TTTTTTTCAAA
1 TTTTTTTCAAA
*
28387644 TTTTTTTCGAA
1 TTTTTTTCAAA
**
28387655 TTTTTTTTGAA
1 TTTTTTTCAAA
*
28387666 TTTTTTTGAAA
1 TTTTTTTCAAA
28387677 T
1 T
28387678 ACCAATCCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:28388149 original size:66 final size:65
Alignment explanation
Indices: 28388067--28388230 Score: 238
Period size: 66 Copynumber: 2.5 Consensus size: 65
28388057 TCAACATATG
* *
28388067 TGATTGGAACATCTATCAGGGCACCTTCATCAATGATTGGAACATCTATCGAGGCAACTTCATCA
1 TGATTGGAACATCTATC-GGGCAACTTCATCAATGATTGGAACATCTATCGAGGCAACTTAATCA
28388132 T
65 T
* * * **
28388133 TGATTGGAACATCTATCGGGCCAGCTTCATCAATGATTGGAACATCTATCGGGGTAGTTTAATCA
1 TGATTGGAACATCTATCGGG-CAACTTCATCAATGATTGGAACATCTATCGAGGCAACTTAATCA
28388198 T
65 T
28388199 TGATTGGAACATCTATCGGTGCAACTTCATCA
1 TGATTGGAACATCTATCGG-GCAACTTCATCA
28388231 TTCTGTTCGA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
65 3 0.03
66 85 0.96
67 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (65 bp):
TGATTGGAACATCTATCGGGCAACTTCATCAATGATTGGAACATCTATCGAGGCAACTTAATCAT
Found at i:28388231 original size:33 final size:32
Alignment explanation
Indices: 28388067--28388232 Score: 215
Period size: 33 Copynumber: 5.0 Consensus size: 32
28388057 TCAACATATG
* *
28388067 TGATTGGAACATCTATCAGGGCACCTTCATCAA
1 TGATTGGAACATCTATC-GGGCAACTTCATCAT
28388100 TGATTGGAACATCTATCGAGGCAACTTCATCAT
1 TGATTGGAACATCTATCG-GGCAACTTCATCAT
* *
28388133 TGATTGGAACATCTATCGGGCCAGCTTCATCAA
1 TGATTGGAACATCTATCGGG-CAACTTCATCAT
* ** *
28388166 TGATTGGAACATCTATCGGGGTAGTTTAATCAT
1 TGATTGGAACATCTATC-GGGCAACTTCATCAT
28388199 TGATTGGAACATCTATCGGTGCAACTTCATCAT
1 TGATTGGAACATCTATCGG-GCAACTTCATCAT
28388232 T
1 T
28388233 CTGTTCGACT
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.04
33 109 0.93
34 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (32 bp):
TGATTGGAACATCTATCGGGCAACTTCATCAT
Found at i:28394132 original size:27 final size:27
Alignment explanation
Indices: 28393544--28394139 Score: 661
Period size: 27 Copynumber: 22.3 Consensus size: 27
28393534 GAGTATAACA
* *
28393544 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28393571 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28393598 GTCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
28393625 TTCATTTTACCGTATGGGGATATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28393652 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
28393679 GACACTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * ** *
28393706 GTTATTTTACCCTACGAAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* **
28393733 GTTATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28393760 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
28393787 GTCATTTTACCTTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28393814 GTCA-TTTACCCTATGGGTGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
28393840 GTTATTTTACCTTATGGGGTTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* **
28393867 GTTATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
28393894 GTCATTTTACCCTATGAGGGTATTTCT
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28393921 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
28393948 ATCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28393975 ATCATTTTACCCTATGGGGGTACTTT-G
1 GTCATTTTACCCTATGGGGGTA-TTTCG
*
28394002 GTCATTTTACCCTATGGGGGTACTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
28394029 ATCATTTTACCCTAT----GTACTTT-G
1 GTCATTTTACCCTATGGGGGTA-TTTCG
* *
28394052 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
28394079 GTCATTTTATCCC-ATGGGGGTATTTCG
1 GTCATTTTA-CCCTATGGGGGTATTTCG
28394106 GTCATTTTA-CCTCATGGGGGTATTTCG
1 GTCATTTTACCCT-ATGGGGGTATTTCG
*
28394133 GTTATTT
1 GTCATTT
28394140 ATTGACCTCT
Statistics
Matches: 491, Mismatches: 66, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.04
24 2 0.00
25 2 0.00
26 26 0.05
27 437 0.89
28 6 0.01
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:28401031 original size:25 final size:24
Alignment explanation
Indices: 28400971--28401058 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 24
28400961 GTACATATAG
*
28400971 GCTCATACGAGC-GATAAATGGTAA
1 GCTCATACGAGCTGA-ATATGGTAA
*
28400995 GCTCCT-CTGAGCTGAATATCGGTAA
1 GCTCATAC-GAGCTGAATAT-GGTAA
28401020 GCTCATACGAGCTGTGAAT-TGGTAA
1 GCTCATACGAGC--TGAATATGGTAA
28401045 GCTCATACGAGCTG
1 GCTCATACGAGCTG
28401059 TGGTGAGTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
23 3 0.05
24 12 0.22
25 33 0.60
26 2 0.04
27 5 0.09
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (24 bp):
GCTCATACGAGCTGAATATGGTAA
Found at i:28415484 original size:15 final size:15
Alignment explanation
Indices: 28415464--28415495 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28415454 AGGGGAAAGG
28415464 TTTTTTGTTTCTATT
1 TTTTTTGTTTCTATT
28415479 TTTTTTGTTTCTATT
1 TTTTTTGTTTCTATT
28415494 TT
1 TT
28415496 CCTTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTGTTTCTATT
Found at i:28415504 original size:15 final size:15
Alignment explanation
Indices: 28415467--28415505 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
28415457 GGAAAGGTTT
*
28415467 TTTGTTTCTATTTTT
1 TTTGTTTCTATTTTC
28415482 TTTGTTTCTATTTTCC
1 TTTGTTTCTATTTT-C
28415498 TTT-TTTCT
1 TTTGTTTCT
28415506 TCAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTGTTTCTATTTTC
Found at i:28415704 original size:46 final size:46
Alignment explanation
Indices: 28415649--28415738 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
28415639 ATAAAAAAGA
*
28415649 AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATTAGTCAGG
1 AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATCAGTCAGG
*
28415695 AAAAGAAAAAGAAAAGCTTTAAAAATGATATTTTTTATCAGTCA
1 AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATCAGTCA
28415739 CTATATATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (46 bp):
AAAAGAAAAAGAAAAGCGTTAAAAATGATATTTTTTATCAGTCAGG
Found at i:28416210 original size:11 final size:11
Alignment explanation
Indices: 28416167--28416218 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
28416157 ATTCAAATAA
28416167 ATTTTA-TTTT
1 ATTTTATTTTT
* *
28416177 ATTTCTCTTTTA
1 ATTT-TATTTTT
*
28416189 ATTTAATTTTT
1 ATTTTATTTTT
28416200 ATTTTATTTTT
1 ATTTTATTTTT
*
28416211 AGTTTATT
1 ATTTTATT
28416219 ATCATGTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 4 0.12
11 22 0.67
12 7 0.21
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:28422624 original size:22 final size:22
Alignment explanation
Indices: 28422596--28422649 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
28422586 CCTCTCAGTT
*
28422596 TCAGTTTTAGTTAAGACAATTC
1 TCAGTTTCAGTTAAGACAATTC
28422618 TCAGTTTCAGTTAAGACAATTC
1 TCAGTTTCAGTTAAGACAATTC
28422640 TCAGTTTCAG
1 TCAGTTTCAG
28422650 AAAACTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (22 bp):
TCAGTTTCAGTTAAGACAATTC
Found at i:28422980 original size:27 final size:28
Alignment explanation
Indices: 28422950--28423003 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
28422940 ATCATGTTAA
*
28422950 TTAATC-ATTCGAAAGCTTTCAAAACAT
1 TTAATCTATACGAAAGCTTTCAAAACAT
*
28422977 TTAATCTATACGAAAGCTTTTAAAACA
1 TTAATCTATACGAAAGCTTTCAAAACA
28423004 AATTGTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (28 bp):
TTAATCTATACGAAAGCTTTCAAAACAT
Found at i:28427730 original size:20 final size:20
Alignment explanation
Indices: 28427705--28427768 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
28427695 TTTCTTAATA
28427705 TTCAAATTTATATTTTTTGT
1 TTCAAATTTATATTTTTTGT
* *
28427725 TTCAAATTTATACTTTTT-A
1 TTCAAATTTATATTTTTTGT
* *
28427744 CTCCAATTT-T-TTTTTTGT
1 TTCAAATTTATATTTTTTGT
28427762 TTCAAAT
1 TTCAAAT
28427769 CCTCATTCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 5 0.14
18 6 0.17
19 7 0.20
20 17 0.49
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (20 bp):
TTCAAATTTATATTTTTTGT
Found at i:28427863 original size:19 final size:20
Alignment explanation
Indices: 28427817--28427870 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
28427807 CAAAAATTAT
28427817 GAAGTACTGAAAATTTTGAAC
1 GAAGTACT-AAAATTTTGAAC
* *
28427838 G-ATTACTAAAATTTTG-AG
1 GAAGTACTAAAATTTTGAAC
28427856 GAAGTACTAAGAATT
1 GAAGTACTAA-AATT
28427871 ATCCCGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 16 0.57
20 9 0.32
21 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (20 bp):
GAAGTACTAAAATTTTGAAC
Found at i:28427912 original size:20 final size:19
Alignment explanation
Indices: 28427883--28427945 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
28427873 CCCGAATACG
28427883 AAAAAACATGAGGGAGTAC
1 AAAAAACATGAGGGAGTAC
* **
28427902 TAAAAACCATGAGAAAGTACC
1 -AAAAAACATGAGGGAGTA-C
* **
28427923 AATAATTATGAGGGAGTAC
1 AAAAAACATGAGGGAGTAC
28427942 AAAA
1 AAAA
28427946 TAGAGAGAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 4 0.12
20 28 0.85
21 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
AAAAAACATGAGGGAGTAC
Found at i:28429688 original size:3 final size:3
Alignment explanation
Indices: 28429682--28429719 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28429672 TTAATTTAGT
28429682 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
28429720 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:28429724 original size:3 final size:3
Alignment explanation
Indices: 28429718--28429800 Score: 103
Period size: 3 Copynumber: 27.7 Consensus size: 3
28429708 CATCATCATC
* *
28429718 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** ** *
28429766 ATT ATT ATT GGT ATT ATT GGT ATT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28429801 CAACTTATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28430197 original size:29 final size:27
Alignment explanation
Indices: 28430159--28430236 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 27
28430149 CTCTTTCAAA
28430159 TATTTTAATATCTTTAATTTATTTCAACT
1 TATTTTAATAT-TTTAATTTATTT-AACT
* *
28430188 TATTTCAATATTGTTAATTTATTTAAGT
1 TATTTTAATATT-TTAATTTATTTAACT
*
28430216 TATTTTAACATTTTAATTTAT
1 TATTTTAATATTTTAATTTAT
28430237 ATATATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.20
28 14 0.32
29 21 0.48
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (27 bp):
TATTTTAATATTTTAATTTATTTAACT
Found at i:28435131 original size:21 final size:21
Alignment explanation
Indices: 28435107--28435152 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28435097 ATATTTCAAA
*
28435107 AAAATGATGAATAAA-AAAATG
1 AAAATGATGAA-AAAGAAAAAG
28435128 AAAATGATGAAAAAGAAAAAG
1 AAAATGATGAAAAAGAAAAAG
28435149 AAAA
1 AAAA
28435153 AGGAAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (21 bp):
AAAATGATGAAAAAGAAAAAG
Found at i:28435159 original size:17 final size:17
Alignment explanation
Indices: 28435139--28435173 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28435129 AAATGATGAA
28435139 AAAGAAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAGG
*
28435156 AAAGGAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAGG
28435173 A
1 A
28435174 GAGGCTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAGG
Found at i:28436604 original size:44 final size:43
Alignment explanation
Indices: 28436542--28436864 Score: 160
Period size: 44 Copynumber: 7.5 Consensus size: 43
28436532 ATCGAAGAAA
* * *
28436542 CCAATCCTATCTCCCTGAAGTTGTAGTGGAGTGA-ATTAAAAC
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* * *** *
28436584 CACAGATCTTATCTCTCTGAAGTTGCAGTAGAG-CAGA-TCGCAT
1 C-CA-ATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* ** *
28436627 CCAATCTTATCTCCCTGAAGTTGCAGTGGAGT-AGACGAAGAAA
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAA-AAC
* * * * *
28436670 CCAATCATCTCTCTCTAAAGTTGAAGTGGAGCG-GATTAAAAC
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* * * * *** *
28436712 CACAGATCTTATCTCTCTGAAGTTGCAATAGAG-CATA-TCGCAT
1 C-CA-ATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* * * ** *
28436755 CCAGTCTTATCTCTCTGAAGATGCAGTGGAG-CAGACAGAAGAAA
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGA-TTAA-AAC
* * * *
28436799 CCAATCCTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAAAC
1 CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
* *
28436841 CACAGATCTTATCCCTTTGAAGTT
1 C-CA-ATCTTATCTCTCTGAAGTT
28436865 TTAGTAGAGC
Statistics
Matches: 205, Mismatches: 60, Indels: 30
0.69 0.20 0.10
Matches are distributed among these distances:
41 56 0.27
42 11 0.05
43 46 0.22
44 91 0.44
45 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (43 bp):
CCAATCTTATCTCTCTGAAGTTGCAGTGGAGTGAGATTAAAAC
Found at i:28436645 original size:41 final size:41
Alignment explanation
Indices: 28436589--28436918 Score: 148
Period size: 41 Copynumber: 7.8 Consensus size: 41
28436579 AAAACCACAG
* *
28436589 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATCCA
* * *
28436630 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CGAAGAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC---GAATCCA
* * * * * * * ** *
28436673 ATCATCTCTCTCTAAAGTTGAAGTGGAGCGGATTAAAACCACA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TCGAATC-CA
* * * *
28436716 GATCTTATCTCTCTGAAGTTGCAATAGAGCATATCGCATCCA
1 -ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATCCA
* * * * *
28436758 GTCTTATCTCTCTGAAGATGCAGTGGAGCAGACAGA-AGAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGT--AG-AG-CAGATCGAATCCA
* * * ** *
28436802 ATCCTATCTCCCTGAAGTTACAGTGGAGC-GAATTAAAACCACA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAG-A-TCGAATC-CA
* ** * * *
28436845 GATCTTATC-CCTTTGAAGTTTTAGTAGAGCATATCGCATCTA
1 -ATCTTATCTCC-CTGAAGTTGCAGTAGAGCAGATCGAATCCA
*
28436887 GTCTTATCTCCCTGAAGTTGCAG-AGAAGCAGA
1 ATCTTATCTCCCTGAAGTTGCAGTAG-AGCAGA
28436919 CAGAAGAAAC
Statistics
Matches: 211, Mismatches: 58, Indels: 40
0.68 0.19 0.13
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 73 0.35
42 13 0.06
43 44 0.21
44 72 0.34
45 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (41 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATCCA
Done.