Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 85 of 131
Found at i:28576258 original size:17 final size:17
Alignment explanation
Indices: 28576236--28576275 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
28576226 TTAGAACCAT
28576236 GCTACTCACACTAAAAC
1 GCTACTCACACTAAAAC
28576253 GCTACTCACACTAAAAC
1 GCTACTCACACTAAAAC
28576270 GCTACT
1 GCTACT
28576276 AATCTACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.35, G:0.07, T:0.20
Consensus pattern (17 bp):
GCTACTCACACTAAAAC
Found at i:28578341 original size:31 final size:30
Alignment explanation
Indices: 28578240--28578341 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 30
28578230 AAAGAAAATT
* **
28578240 ATAGTTGGGTGACCAAAACGGAAAAGGAGCA
1 ATAGTTGGATGACCAAAAAAGAAAAGGAG-A
**
28578271 ATAGTT-GAGTGACCAAAAAA-AAATTG-G-
1 ATAGTTGGA-TGACCAAAAAAGAAAAGGAGA
*
28578298 -TAGTTGGGTGACCAAAAAAGAAAAGGAGTA
1 ATAGTTGGATGACCAAAAAAGAAAAGGAG-A
28578328 ATAGTTGGATGACC
1 ATAGTTGGATGACC
28578342 TACAGTGTAG
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
26 16 0.29
27 5 0.09
28 1 0.02
29 1 0.02
30 5 0.09
31 27 0.49
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.19
Consensus pattern (30 bp):
ATAGTTGGATGACCAAAAAAGAAAAGGAGA
Found at i:28578655 original size:15 final size:16
Alignment explanation
Indices: 28578604--28578658 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
28578594 TAAAATTTTA
*
28578604 ATAAATA-AAAAAGAAT
1 ATAAATATAAATA-AAT
*
28578620 ATAAA-ATTAATAAAT
1 ATAAATATAAATAAAT
28578635 ATTAAATATAAAT-AAT
1 A-TAAATATAAATAAAT
28578651 ATAAATAT
1 ATAAATAT
28578659 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 12 0.36
16 16 0.48
17 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
ATAAATATAAATAAAT
Found at i:28579790 original size:110 final size:110
Alignment explanation
Indices: 28579652--28579983 Score: 619
Period size: 110 Copynumber: 3.0 Consensus size: 110
28579642 AGACATGGAG
* * * *
28579652 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAGTTTTGGCTACTGACTTCCATGTCCCTAGTC
1 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTGGTC
*
28579717 ACTAGAGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
66 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
28579762 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTGGTC
1 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTGGTC
28579827 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
66 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
28579872 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTGGTC
1 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTGGTC
28579937 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
66 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
28579982 CC
1 CC
28579984 ATGGTATGTC
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 217 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (110 bp):
CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTGGTC
ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
Found at i:28580345 original size:40 final size:40
Alignment explanation
Indices: 28580288--28580448 Score: 160
Period size: 40 Copynumber: 4.0 Consensus size: 40
28580278 ACAAATGTCG
* * **
28580288 CTATAGGTCGAGTATTAGCGGCGCTTTTTAAAAAACGCCA
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
* * ** * **
28580328 CTATAGATTGAGCATTAGTGATGCTTTTTGAAAAACGCTG
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
* * * *
28580368 CTATAGATCAAGCATTAGCGGTGCTTCTCGAAAAATGCCA
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
* * *
28580408 CTATAGAACGAGCATTAGTGGGGCTTTTCGAAAAACGCCA
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
28580448 C
1 C
28580449 AAAAAAGTTG
Statistics
Matches: 97, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (40 bp):
CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
Found at i:28580385 original size:80 final size:80
Alignment explanation
Indices: 28580287--28580445 Score: 201
Period size: 80 Copynumber: 2.0 Consensus size: 80
28580277 AACAAATGTC
* * * * * ** *
28580287 GCTATAGGTCGAGTATTAGCGGCGCTTTTTAAAAAACGCCACTATAGATTGAGCATTAGTGATGC
1 GCTATAGATCAAGCATTAGCGGCGCTTCTCAAAAAACGCCACTATAGAACGAGCATTAGTGAGGC
*
28580352 TTTTTGAAAAACGCT
66 TTTTCGAAAAACGCT
* * * *
28580367 GCTATAGATCAAGCATTAGCGGTGCTTCTCGAAAAATGCCACTATAGAACGAGCATTAGTGGGGC
1 GCTATAGATCAAGCATTAGCGGCGCTTCTCAAAAAACGCCACTATAGAACGAGCATTAGTGAGGC
28580432 TTTTCGAAAAACGC
66 TTTTCGAAAAACGC
28580446 CACAAAAAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (80 bp):
GCTATAGATCAAGCATTAGCGGCGCTTCTCAAAAAACGCCACTATAGAACGAGCATTAGTGAGGC
TTTTCGAAAAACGCT
Found at i:28580924 original size:7 final size:7
Alignment explanation
Indices: 28580901--28581044 Score: 85
Period size: 7 Copynumber: 20.3 Consensus size: 7
28580891 ATTTTAGGGT
28580901 TTTAAGG
1 TTTAAGG
28580908 TTT-AGTG
1 TTTAAG-G
*
28580915 TTTATGG
1 TTTAAGG
28580922 TTTAAGG
1 TTTAAGG
*
28580929 TAT-AGTG
1 TTTAAG-G
* *
28580936 CTTATGG
1 TTTAAGG
*
28580943 TTTAGGG
1 TTTAAGG
**
28580950 TTTATTG
1 TTTAAGG
* *
28580957 TGTATGG
1 TTTAAGG
28580964 TTTAAGG
1 TTTAAGG
*
28580971 TTTAGGG
1 TTTAAGG
28580978 TTTAAGG
1 TTTAAGG
*
28580985 TTTAAGA
1 TTTAAGG
28580992 TTTAAGG
1 TTTAAGG
*
28580999 TTTTAAAG
1 -TTTAAGG
*
28581007 TTTAGGG
1 TTTAAGG
*
28581014 TTTATGG
1 TTTAAGG
**
28581021 TTTAAAC
1 TTTAAGG
*
28581028 TTTAGGG
1 TTTAAGG
28581035 TTTTAAGG
1 -TTTAAGG
28581043 TT
1 TT
28581045 CAATTACTTT
Statistics
Matches: 102, Mismatches: 29, Indels: 12
0.71 0.20 0.08
Matches are distributed among these distances:
6 4 0.04
7 84 0.82
8 14 0.14
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:28580927 original size:21 final size:21
Alignment explanation
Indices: 28580901--28580995 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
28580891 ATTTTAGGGT
28580901 TTTAAGGTTTAGTGTTTATGG
1 TTTAAGGTTTAGTGTTTATGG
* *
28580922 TTTAAGGTATAGTGCTTATGG
1 TTTAAGGTTTAGTGTTTATGG
* * *
28580943 TTTAGGGTTTATTGTGTATGG
1 TTTAAGGTTTAGTGTTTATGG
* *
28580964 TTTAAGGTTTAGGGTTTAAGG
1 TTTAAGGTTTAGTGTTTATGG
*
28580985 TTTAAGATTTA
1 TTTAAGGTTTA
28580996 AGGTTTTAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.48
Consensus pattern (21 bp):
TTTAAGGTTTAGTGTTTATGG
Found at i:28581011 original size:36 final size:36
Alignment explanation
Indices: 28580964--28581040 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
28580954 TTGTGTATGG
*
28580964 TTTAAGGTTTAGGGTTTAAGGTTTAAGA-TTTAAGGT
1 TTTAAAGTTTAGGGTTTAAGGTTTAA-ACTTTAAGGT
* *
28581000 TTTAAAGTTTAGGGTTTATGGTTTAAACTTTAGGGT
1 TTTAAAGTTTAGGGTTTAAGGTTTAAACTTTAAGGT
28581036 TTTAA
1 TTTAA
28581041 GGTTCAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (36 bp):
TTTAAAGTTTAGGGTTTAAGGTTTAAACTTTAAGGT
Found at i:28586419 original size:17 final size:17
Alignment explanation
Indices: 28586397--28586436 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
28586387 TTAGAACCAT
28586397 GCTACTCACACTAAAAC
1 GCTACTCACACTAAAAC
28586414 GCTACTCACACTAAAAC
1 GCTACTCACACTAAAAC
28586431 GCTACT
1 GCTACT
28586437 AATCTACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.35, G:0.07, T:0.20
Consensus pattern (17 bp):
GCTACTCACACTAAAAC
Found at i:28588502 original size:31 final size:30
Alignment explanation
Indices: 28588401--28588502 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 30
28588391 AAAGAAAATT
* **
28588401 ATAGTTGGGTGACCAAAACGGAAAAGGAGCA
1 ATAGTTGGATGACCAAAAAAGAAAAGGAG-A
**
28588432 ATAGTT-GAGTGACCAAAAAA-AAATTG-G-
1 ATAGTTGGA-TGACCAAAAAAGAAAAGGAGA
*
28588459 -TAGTTGGGTGACCAAAAAAGAAAAGGAGTA
1 ATAGTTGGATGACCAAAAAAGAAAAGGAG-A
28588489 ATAGTTGGATGACC
1 ATAGTTGGATGACC
28588503 TACAGTGTAG
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
26 16 0.29
27 5 0.09
28 1 0.02
29 1 0.02
30 5 0.09
31 27 0.49
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.19
Consensus pattern (30 bp):
ATAGTTGGATGACCAAAAAAGAAAAGGAGA
Found at i:28588816 original size:15 final size:16
Alignment explanation
Indices: 28588765--28588819 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
28588755 TAAAATTTTA
*
28588765 ATAAATA-AAAAAGAAT
1 ATAAATATAAATA-AAT
*
28588781 ATAAA-ATTAATAAAT
1 ATAAATATAAATAAAT
28588796 ATTAAATATAAAT-AAT
1 A-TAAATATAAATAAAT
28588812 ATAAATAT
1 ATAAATAT
28588820 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 12 0.36
16 16 0.48
17 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
ATAAATATAAATAAAT
Found at i:28589951 original size:110 final size:110
Alignment explanation
Indices: 28589813--28590034 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 110
28589803 AGACATGGAG
* * *
28589813 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAGTTTTGGCTACTGACTTCCATGTCCCTAGTC
1 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTAGTC
28589878 ACTAGAGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
66 ACTAGAGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
*
28589923 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTGGTC
1 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTAGTC
*
28589988 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
66 ACTAGAGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
28590033 CC
1 CC
28590035 ATGGTATGTC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (110 bp):
CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCAACTGACTCCCATGTCCCTAGTC
ACTAGAGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACAC
Found at i:28590396 original size:40 final size:40
Alignment explanation
Indices: 28590339--28590499 Score: 160
Period size: 40 Copynumber: 4.0 Consensus size: 40
28590329 ACAAATGTCG
* * **
28590339 CTATAGGTCGAGTATTAGCGGCGCTTTTTAAAAAACGCCA
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
* * ** * **
28590379 CTATAGATTGAGCATTAGTGATGCTTTTTGAAAAACGCTG
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
* * * *
28590419 CTATAGATCAAGCATTAGCGGTGCTTCTCGAAAAATGCCA
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
* * *
28590459 CTATAGAACGAGCATTAGTGGGGCTTTTCGAAAAACGCCA
1 CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
28590499 C
1 C
28590500 AAAAAAGTTG
Statistics
Matches: 97, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (40 bp):
CTATAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCA
Found at i:28590436 original size:80 final size:80
Alignment explanation
Indices: 28590338--28590496 Score: 201
Period size: 80 Copynumber: 2.0 Consensus size: 80
28590328 AACAAATGTC
* * * * * ** *
28590338 GCTATAGGTCGAGTATTAGCGGCGCTTTTTAAAAAACGCCACTATAGATTGAGCATTAGTGATGC
1 GCTATAGATCAAGCATTAGCGGCGCTTCTCAAAAAACGCCACTATAGAACGAGCATTAGTGAGGC
*
28590403 TTTTTGAAAAACGCT
66 TTTTCGAAAAACGCT
* * * *
28590418 GCTATAGATCAAGCATTAGCGGTGCTTCTCGAAAAATGCCACTATAGAACGAGCATTAGTGGGGC
1 GCTATAGATCAAGCATTAGCGGCGCTTCTCAAAAAACGCCACTATAGAACGAGCATTAGTGAGGC
28590483 TTTTCGAAAAACGC
66 TTTTCGAAAAACGC
28590497 CACAAAAAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (80 bp):
GCTATAGATCAAGCATTAGCGGCGCTTCTCAAAAAACGCCACTATAGAACGAGCATTAGTGAGGC
TTTTCGAAAAACGCT
Found at i:28590586 original size:114 final size:115
Alignment explanation
Indices: 28590431--28590707 Score: 340
Period size: 114 Copynumber: 2.4 Consensus size: 115
28590421 ATAGATCAAG
* * ** * * **
28590431 CATTAGCGGTGCTTCTCGAAAAATGCCACTATAGAACGAGCATTAGTGGGGCTTTTCGAAAAACG
1 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGAACGAGCATTAGCGACGCTTTTCGAAAAACG
*
28590496 CCACAAAAAAGTTGAGCAAAAC-ACGACATTTGTTGTTGAGCTTTAGTGA
66 CCACAAAAAAGTTGAGCAAAACAACGACATTTGTTATTGAGCTTTAGTGA
* ** *
28590545 CATTAGCGGCGCTTTTTAAAAAATGTCACAATAGATTGAGCATTAGCGACGCTTTTTGAAAAACG
1 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGAACGAGCATTAGCGACGCTTTTCGAAAAACG
* * * *
28590610 CCGCAAAAAAGTTGAGCAAAACAACGTCGTTTGTTATTGAGCTTTAGTGG
66 CCACAAAAAAGTTGAGCAAAACAACGACATTTGTTATTGAGCTTTAGTGA
* ** * * *
28590660 CATTAGCAGCGCTTTTTAAAAAACACCGCAATAGATCGAGAATTAGCG
1 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGAACGAGCATTAGCG
28590708 GCACTTTGTC
Statistics
Matches: 138, Mismatches: 24, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
114 74 0.54
115 64 0.46
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (115 bp):
CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGAACGAGCATTAGCGACGCTTTTCGAAAAACG
CCACAAAAAAGTTGAGCAAAACAACGACATTTGTTATTGAGCTTTAGTGA
Found at i:28590625 original size:41 final size:40
Alignment explanation
Indices: 28590545--28590627 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
28590535 GCTTTAGTGA
* * * * *
28590545 CATTAGCGGCGCTTTTTAAAAAATGTCACAATAGATTGAG
1 CATTAGCGACGCTTTTTAAAAAACGCCACAAAAAATTGAG
* *
28590585 CATTAGCGACGCTTTTTGAAAAACGCCGCAAAAAAGTTGAG
1 CATTAGCGACGCTTTTTAAAAAACGCCACAAAAAA-TTGAG
28590626 CA
1 CA
28590628 AAACAACGTC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
40 28 0.80
41 7 0.20
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (40 bp):
CATTAGCGACGCTTTTTAAAAAACGCCACAAAAAATTGAG
Found at i:28590693 original size:115 final size:114
Alignment explanation
Indices: 28590481--28590707 Score: 328
Period size: 115 Copynumber: 2.0 Consensus size: 114
28590471 CATTAGTGGG
*
28590481 GCTTTTCGAAAAACGCCACAAAAAAGTTGAGCAAAACACGACATTTGTTGTTGAGCTTTAGTGAC
1 GCTTTTCGAAAAACGCCACAAAAAAGTTGAGCAAAACACGACATTTGTTATTGAGCTTTAGTGAC
* *** * *
28590546 ATTAGCGGCGCTTTTTAAAAAATGTCACAATAGATTGAGCATTAGCGAC
66 ATTAGCAGCGCTTTTTAAAAAACACCACAATAGATCGAGAATTAGCGAC
* * * * *
28590595 GCTTTTTGAAAAACGCCGCAAAAAAGTTGAGCAAAACAACGTCGTTTGTTATTGAGCTTTAGTGG
1 GCTTTTCGAAAAACGCCACAAAAAAGTTGAGCAAAAC-ACGACATTTGTTATTGAGCTTTAGTGA
*
28590660 CATTAGCAGCGCTTTTTAAAAAACACCGCAATAGATCGAGAATTAGCG
65 CATTAGCAGCGCTTTTTAAAAAACACCACAATAGATCGAGAATTAGCG
28590708 GCACTTTGTC
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
114 35 0.35
115 64 0.65
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (114 bp):
GCTTTTCGAAAAACGCCACAAAAAAGTTGAGCAAAACACGACATTTGTTATTGAGCTTTAGTGAC
ATTAGCAGCGCTTTTTAAAAAACACCACAATAGATCGAGAATTAGCGAC
Found at i:28590775 original size:156 final size:156
Alignment explanation
Indices: 28590546--28590987 Score: 604
Period size: 157 Copynumber: 2.8 Consensus size: 156
28590536 CTTTAGTGAC
* * * * * * *
28590546 ATTAGCGGCGCTTT-TTAAAAAATGTCACAATAGATTGAGCATTAGCGACGCTTTTTGAAAAACG
1 ATTAGCGGCACTTTGTTAAAAAATGCCGCTATAGATAGAGCATTAGCGGCGCTTTTCGAAAAACG
* *
28590610 CCGCAAAAAAGTTGAGCAAAACAACGTCGTTTGTTATTGAGCTTTAGTGGCATTAGCAGCGCTTT
66 CCACAAAAAAGTTGAGCAAAACAACGTCGTTTGTTGTTGAGCTTTAGTGGCATTAGCAGCGCTTT
28590675 TTAAAAAACACCGCAATAGATCGAGA
131 TTAAAAAACACCGCAATAGATCGAGA
* *
28590701 ATTAGCGGCACTTTGTCAAAAAATGCCGCTATAGATAGAGCATTAGCGGTGCTTTTCGGAAAAAC
1 ATTAGCGGCACTTTGTTAAAAAATGCCGCTATAGATAGAGCATTAGCGGCGCTTTTC-GAAAAAC
*
28590766 GCCACAAAAAAGTTGAGCAAAACAACGTCGTTTGTTGTTGAGCTTTAGTGGCATTAGCAGCACTT
65 GCCACAAAAAAGTTGAGCAAAACAACGTCGTTTGTTGTTGAGCTTTAGTGGCATTAGCAGCGCTT
**
28590831 TTGTAAAAAATGCCGCAATAGATCGAGA
130 TT-TAAAAAACACCGCAATAGATCGAGA
* * * ** * * * *
28590859 ATTAGTGACAC-TTGTTGAAAAACACTGCTATAGATCGAGCATTAGCGGCGCTTTTCGCAAAATG
1 ATTAGCGGCACTTTGTTAAAAAATGCCGCTATAGATAGAGCATTAGCGGCGCTTTTCGAAAAACG
* * *
28590923 CCTCAAAAAAGTTGAG-AAAACGACGTCGTTTGTTGTTGAGCTTTAGTGGCATTAGCGGCG-TTT
66 CCACAAAAAAGTTGAGCAAAACAACGTCGTTTGTTGTTGAGCTTTAGTGGCATTAGCAGCGCTTT
28590986 TT
131 TT
28590988 GGTATAAATG
Statistics
Matches: 255, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
153 1 0.00
154 4 0.02
155 54 0.21
156 55 0.22
157 109 0.43
158 32 0.13
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (156 bp):
ATTAGCGGCACTTTGTTAAAAAATGCCGCTATAGATAGAGCATTAGCGGCGCTTTTCGAAAAACG
CCACAAAAAAGTTGAGCAAAACAACGTCGTTTGTTGTTGAGCTTTAGTGGCATTAGCAGCGCTTT
TTAAAAAACACCGCAATAGATCGAGA
Found at i:28591040 original size:14 final size:14
Alignment explanation
Indices: 28591018--28591071 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
28591008 ATTATTTTAT
* *
28591018 TTTAGGGTTTAGTA
1 TTTAAGGTTTAGTG
*
28591032 TTTAAGGTTTAATG
1 TTTAAGGTTTAGTG
* *
28591046 TCTATGGTTTAGTG
1 TTTAAGGTTTAGTG
28591060 TTTAAAGGTTTA
1 TTT-AAGGTTTA
28591072 TGATATAATG
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 24 0.77
15 7 0.23
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (14 bp):
TTTAAGGTTTAGTG
Found at i:28591114 original size:14 final size:14
Alignment explanation
Indices: 28591097--28591140 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
28591087 TATTTTGGGA
28591097 TTAGAGTTT-TGAGT
1 TTAGAGTTTATG-GT
*
28591111 TTAGGGTTTATGGT
1 TTAGAGTTTATGGT
*
28591125 TTATAGTTTATGGT
1 TTAGAGTTTATGGT
28591139 TT
1 TT
28591141 GGGGTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 24 0.92
15 2 0.08
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (14 bp):
TTAGAGTTTATGGT
Found at i:28591132 original size:21 final size:21
Alignment explanation
Indices: 28591108--28591149 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28591098 TAGAGTTTTG
*
28591108 AGTTTAGGGTTTATGGTTTAT
1 AGTTTAGGGTTTAGGGTTTAT
* *
28591129 AGTTTATGGTTTGGGGTTTAT
1 AGTTTAGGGTTTAGGGTTTAT
28591150 TATTTTATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (21 bp):
AGTTTAGGGTTTAGGGTTTAT
Found at i:28591147 original size:14 final size:14
Alignment explanation
Indices: 28591109--28591149 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28591099 AGAGTTTTGA
28591109 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
**
28591123 GTTTATAGTTTATG
1 GTTTAGGGTTTATG
*
28591137 GTTTGGGGTTTAT
1 GTTTAGGGTTTAT
28591150 TATTTTATAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.54
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:28591324 original size:7 final size:7
Alignment explanation
Indices: 28591314--28591545 Score: 117
Period size: 7 Copynumber: 33.1 Consensus size: 7
28591304 GTAATATATA
28591314 TTTAGGG
1 TTTAGGG
*
28591321 TTTAAGG
1 TTTAGGG
28591328 TTTAGGG
1 TTTAGGG
*
28591335 TATA-GG
1 TTTAGGG
*
28591341 TTTATGG
1 TTTAGGG
28591348 TTTAGGG
1 TTTAGGG
**
28591355 TTTAATG
1 TTTAGGG
*
28591362 TTTAAGG
1 TTTAGGG
* *
28591369 TTTATGA
1 TTTAGGG
*
28591376 TTTAGTG
1 TTTAGGG
* *
28591383 TTAAGAG
1 TTTAGGG
*
28591390 TTTAGTG
1 TTTAGGG
* *
28591397 TTTATAGT
1 TTTA-GGG
28591405 TTTAGGG
1 TTTAGGG
*
28591412 TGTA-GG
1 TTTAGGG
*
28591418 TTTATGG
1 TTTAGGG
***
28591425 TTTAATC
1 TTTAGGG
*
28591432 TTTAGTG
1 TTTAGGG
28591439 TTTAGGG
1 TTTAGGG
*
28591446 TTTAGGA
1 TTTAGGG
*
28591453 TTTAGGA
1 TTTAGGG
*
28591460 TTTAAGG
1 TTTAGGG
**
28591467 TTTAGAA
1 TTTAGGG
*
28591474 TTTAGGT
1 TTTAGGG
28591481 TTTAGGG
1 TTTAGGG
**
28591488 TTTAAAG
1 TTTAGGG
**
28591495 TTTATAG
1 TTTAGGG
28591502 TTTAGGG
1 TTTAGGG
*
28591509 TTTAAAGG
1 TTT-AGGG
* *
28591517 CTTAGGA
1 TTTAGGG
*
28591524 TTTATGG
1 TTTAGGG
*
28591531 TTTAGTG
1 TTTAGGG
28591538 TTTAGGG
1 TTTAGGG
28591545 T
1 T
28591546 CTGATTTTAA
Statistics
Matches: 167, Mismatches: 54, Indels: 8
0.73 0.24 0.03
Matches are distributed among these distances:
6 10 0.06
7 148 0.89
8 9 0.05
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:28591344 original size:20 final size:21
Alignment explanation
Indices: 28591319--28591372 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
28591309 ATATATTTAG
28591319 GGTTTAAGGTTTAGGGTAT-A
1 GGTTTAAGGTTTAGGGTATAA
* *
28591339 GGTTTATGGTTTAGGGTTTAA
1 GGTTTAAGGTTTAGGGTATAA
*
28591360 TGTTTAAGGTTTA
1 GGTTTAAGGTTTA
28591373 TGATTTAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
GGTTTAAGGTTTAGGGTATAA
Found at i:28592233 original size:22 final size:23
Alignment explanation
Indices: 28592197--28592239 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
28592187 ACTCTTTTTC
*
28592197 AAAAGGTTGATGGTCAAATTTGA
1 AAAAGATTGATGGTCAAATTTGA
28592220 AAAAGATTGA-GGTCAAATTT
1 AAAAGATTGATGGTCAAATTT
28592240 AACTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (23 bp):
AAAAGATTGATGGTCAAATTTGA
Found at i:28593186 original size:19 final size:20
Alignment explanation
Indices: 28593162--28593202 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28593152 CCTTTACATG
*
28593162 TTACATCCTT-TTGTCTTTT
1 TTACATACTTATTGTCTTTT
*
28593181 TTACATATTTATTGTCTTTT
1 TTACATACTTATTGTCTTTT
28593201 TT
1 TT
28593203 GGACATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TTACATACTTATTGTCTTTT
Found at i:28595365 original size:41 final size:41
Alignment explanation
Indices: 28595292--28595371 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
28595282 CCATAAACGC
* * * *
28595292 CGCTAAATATCATGCTCTTTAGTGGCGGTTGTGAAAAAAAT
1 CGCTAAAAATCATGCGCTATAGCGGCGGTTGTGAAAAAAAT
* * *
28595333 CGCTAAAAATCATTCGCTATAGCGGCGTTTGTGATAAAA
1 CGCTAAAAATCATGCGCTATAGCGGCGGTTGTGAAAAAA
28595372 GCGCCGCTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (41 bp):
CGCTAAAAATCATGCGCTATAGCGGCGGTTGTGAAAAAAAT
Found at i:28595382 original size:84 final size:85
Alignment explanation
Indices: 28595289--28595517 Score: 248
Period size: 86 Copynumber: 2.7 Consensus size: 85
28595279 TTTCCATAAA
* * * *
28595289 CGCCGCTAAATATCATGCTCTTTAGTGGCGGTTGTGA-AAAAAATCGCTAAAAATCAT-TCGCTA
1 CGCCGCTAAATGTCATGCTCTTTACTGGCGATTGTGATAAAAAATCGCTAAAGATCATGT-GCTA
*
28595352 TAGCGGCGTTTGTGATAAAAG
65 TAGCAGCGTTTGTGATAAAAG
* * * * * * *
28595373 CGCCGCTAAATGTCATGCTCTTTACCGGCGTTTGTGATAAAAGTACCGCTAAAGGTCATGTTCTT
1 CGCCGCTAAATGTCATGCTCTTTACTGGCGATTGTGATAAAA-AATCGCTAAAGATCATGTGCTA
*
28595438 TAGCAGTGTTTGTGATAAAAG
65 TAGCAGCGTTTGTGATAAAAG
* * * *
28595459 CACCACTAAAGGTCATGTTCTTTACTGGC-ATCTGTGATAAAAACATCGCTAAAGATCAT
1 CGCCGCTAAATGTCATGCTCTTTACTGGCGAT-TGTGATAAAAA-ATCGCTAAAGATCAT
28595518 ATTTTTTAGC
Statistics
Matches: 119, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
84 33 0.28
85 5 0.04
86 80 0.67
87 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (85 bp):
CGCCGCTAAATGTCATGCTCTTTACTGGCGATTGTGATAAAAAATCGCTAAAGATCATGTGCTAT
AGCAGCGTTTGTGATAAAAG
Found at i:28595402 original size:43 final size:43
Alignment explanation
Indices: 28595291--28595620 Score: 200
Period size: 43 Copynumber: 7.7 Consensus size: 43
28595281 TCCATAAACG
** * * *
28595291 CCGCTAAATATCATGCTCTTTAGTGGCGGTTGTGA-AAAA-AA
1 CCGCTAAAGGTCATGCTCTTTAGCGGCGTTTGTGATAAAAGCA
* ** * * * *
28595332 TCGCTAAAAATCATTCGCTATAGCGGCGTTTGTGATAAAAGCG
1 CCGCTAAAGGTCATGCTCTTTAGCGGCGTTTGTGATAAAAGCA
* * *
28595375 CCGCTAAATGTCATGCTCTTTACCGGCGTTTGTGATAAAAGTA
1 CCGCTAAAGGTCATGCTCTTTAGCGGCGTTTGTGATAAAAGCA
* * *
28595418 CCGCTAAAGGTCATGTTCTTTAGCAGTGTTTGTGATAAAAGCA
1 CCGCTAAAGGTCATGCTCTTTAGCGGCGTTTGTGATAAAAGCA
* * * * *
28595461 CCACTAAAGGTCATGTTCTTTA-CTGGCATCTGTGATAAAAACA
1 CCGCTAAAGGTCATGCTCTTTAGC-GGCGTTTGTGATAAAAGCA
* * ** * ** * **
28595504 TCGCTAAAGATCATATTTTTTAGCGATGTTTGTAGGT-AAAGTG
1 CCGCTAAAGGTCATGCTCTTTAGCGGCGTTTGT-GATAAAAGCA
* * * * * * *
28595547 TCGCTAAAGGTCATGTTCTTTAGCAGCATTTTTTATAAAAGCG
1 CCGCTAAAGGTCATGCTCTTTAGCGGCGTTTGTGATAAAAGCA
** * * * *
28595590 CCATTAAAGGTTATGTTCTATAACGGCGTTT
1 CCGCTAAAGGTCATGCTCTTTAGCGGCGTTT
28595621 TTTTCGCATA
Statistics
Matches: 221, Mismatches: 62, Indels: 10
0.75 0.21 0.03
Matches are distributed among these distances:
41 28 0.13
42 6 0.03
43 184 0.83
44 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (43 bp):
CCGCTAAAGGTCATGCTCTTTAGCGGCGTTTGTGATAAAAGCA
Found at i:28595554 original size:86 final size:86
Alignment explanation
Indices: 28595359--28595568 Score: 235
Period size: 86 Copynumber: 2.4 Consensus size: 86
28595349 CTATAGCGGC
* * * * * **
28595359 GTTTGTGATAAAAGCGCCGCTAAATGTCATGCTCTTTACCGGCGTTTGTGATAAAAGTACCGCTA
1 GTTTGTGATAAAAGCACCGCTAAAGGTCATGTTCTTTACCGGCATCTGTGATAAAAACACCGCTA
* *
28595424 AAGGTCATGTTCTTTAGCAGT
66 AAGATCATATTCTTTAGCAGT
* * *
28595445 GTTTGTGATAAAAGCACCACTAAAGGTCATGTTCTTTACTGGCATCTGTGATAAAAACATCGCTA
1 GTTTGTGATAAAAGCACCGCTAAAGGTCATGTTCTTTACCGGCATCTGTGATAAAAACACCGCTA
*
28595510 AAGATCATATTTTTTAGC-GAT
66 AAGATCATATTCTTTAGCAG-T
* ***
28595531 GTTTGTAGGT-AAAGTGTCGCTAAAGGTCATGTTCTTTA
1 GTTTGT-GATAAAAGCACCGCTAAAGGTCATGTTCTTTA
28595569 GCAGCATTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
85 1 0.01
86 101 0.97
87 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (86 bp):
GTTTGTGATAAAAGCACCGCTAAAGGTCATGTTCTTTACCGGCATCTGTGATAAAAACACCGCTA
AAGATCATATTCTTTAGCAGT
Found at i:28598553 original size:26 final size:26
Alignment explanation
Indices: 28598517--28598571 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
28598507 TTCCAGCATA
28598517 CATTGTTTCTTAGCTCTTCATCTTCT
1 CATTGTTTCTTAGCTCTTCATCTTCT
28598543 CATTGTTTCTTAGCTCTTCATCTTCT
1 CATTGTTTCTTAGCTCTTCATCTTCT
28598569 CAT
1 CAT
28598572 CTTTGTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.13, C:0.27, G:0.07, T:0.53
Consensus pattern (26 bp):
CATTGTTTCTTAGCTCTTCATCTTCT
Found at i:28601973 original size:10 final size:10
Alignment explanation
Indices: 28601916--28602000 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 10
28601906 CTTACACAGT
28601916 ATTATA-AAA
1 ATTATATAAA
* *
28601925 ATTTTAGAAA
1 ATTATATAAA
*
28601935 ACTATAGTAAA
1 ATTATA-TAAA
28601946 ATTATAT-AA
1 ATTATATAAA
28601955 ATTAT-TAAA
1 ATTATATAAA
*
28601964 ATTTTATAAAGA
1 ATTATAT-AA-A
28601976 ATTATA-AAA
1 ATTATATAAA
* *
28601985 ATAATAAAAA
1 ATTATATAAA
28601995 ATTATA
1 ATTATA
28602001 GAGAAAATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
8 1 0.02
9 24 0.40
10 19 0.32
11 10 0.17
12 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (10 bp):
ATTATATAAA
Found at i:28602033 original size:18 final size:19
Alignment explanation
Indices: 28601993--28602033 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28601983 AAATAATAAA
* *
28601993 AAATTATAGAGAAAATTTG
1 AAATTATAAAAAAAATTTG
28602012 AAATTATAAAAAAAATTT-
1 AAATTATAAAAAAAATTTG
28602030 AAAT
1 AAAT
28602034 AGCCGAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
AAATTATAAAAAAAATTTG
Found at i:28602656 original size:23 final size:24
Alignment explanation
Indices: 28602612--28602656 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
28602602 TTTTAATAAA
*
28602612 AATAAATATTTTAATCATATATTT
1 AATAAATATTTTAATCAAATATTT
* *
28602636 AATAAA-ATTTTCATTAAATAT
1 AATAAATATTTTAATCAAATAT
28602657 AATTTTTTTA
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:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
AATAAATATTTTAATCAAATATTT
Found at i:28602713 original size:61 final size:57
Alignment explanation
Indices: 28602577--28602739 Score: 138
Period size: 61 Copynumber: 2.8 Consensus size: 57
28602567 GTTATTAAAT
** * * *
28602577 TTTAATAGGATTATTATCAAATAT-ATTTTAATAAAAATAAATATTTTAATCATATA
1 TTTAATAAAATTATTATTAAATATAATTTTAATAAAAATAAATATTTTAATAACATA
**
28602633 TTTAATAAAATT-TTCATTAAATATAATTTTTTTAAAATATAATATATAATTTAATAACAT-
1 TTTAATAAAATTATT-ATTAAATATAATTTTAATAAAA-ATAA-ATAT--TTTAATAACATA
*
28602693 TCTTAATATAATTATTATTAAAATATGAA--TTAATAAAAATAATATAT
1 T-TTAATAAAATTATTATT-AAATAT-AATTTTAATAAAAATAA-ATAT
28602740 AGCCTACTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
55 2 0.02
56 18 0.21
57 10 0.11
58 4 0.05
59 4 0.05
60 10 0.11
61 29 0.33
62 8 0.09
63 2 0.02
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (57 bp):
TTTAATAAAATTATTATTAAATATAATTTTAATAAAAATAAATATTTTAATAACATA
Found at i:28612732 original size:5 final size:5
Alignment explanation
Indices: 28612722--28612746 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28612712 AATTTGTAAA
28612722 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
28612747 GAAGATGACA
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:28615873 original size:13 final size:13
Alignment explanation
Indices: 28615857--28615884 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28615847 TTTATAAAAC
28615857 TTGTTTATGTTAT
1 TTGTTTATGTTAT
28615870 TTGTTTATGTTAT
1 TTGTTTATGTTAT
28615883 TT
1 TT
28615885 CATCTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (13 bp):
TTGTTTATGTTAT
Found at i:28622978 original size:16 final size:16
Alignment explanation
Indices: 28622957--28622989 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28622947 TTCGCTGTAT
28622957 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28622973 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28622989 T
1 T
28622990 AGCAAATCAA
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:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:28623064 original size:44 final size:45
Alignment explanation
Indices: 28622971--28623065 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
28622961 ATAGAGGCGT
*
28622971 AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGG
* * *
28623016 AATGGAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAATGG
28623060 AATGGA
1 AATGGA
28623066 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGG
Found at i:28623218 original size:16 final size:16
Alignment explanation
Indices: 28623197--28623229 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28623187 CTCGCTGTAT
28623197 TGGAATAGAAGCGTAA
1 TGGAATAGAAGCGTAA
*
28623213 TGGAATAGAGGCGTAA
1 TGGAATAGAAGCGTAA
28623229 T
1 T
28623230 AGCAAATCAA
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:0.39, C:0.06, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGAAGCGTAA
Found at i:28623304 original size:44 final size:45
Alignment explanation
Indices: 28623211--28623305 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 45
28623201 ATAGAAGCGT
* *
28623211 AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAACGG
* * *
28623256 AATGGAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTGAACGG
1 AATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAACGG
28623300 AATGGA
1 AATGGA
28623306 TGTGTAATAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAACGG
Found at i:28623393 original size:240 final size:240
Alignment explanation
Indices: 28622934--28623414 Score: 883
Period size: 240 Copynumber: 2.0 Consensus size: 240
28622924 CTTTCAATTA
* *
28622934 AGGGCACGTTTGGTTCGCTGTATTGGAATAGAGGCGTAATGGAATAGAGGCGTAATAGCAAATCA
1 AGGGCACGTTTGGCTCGCTGTATTGGAATAGAAGCGTAATGGAATAGAGGCGTAATAGCAAATCA
*
28622999 ATTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAATGGAATG
66 ATTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAACGGAATG
28623064 GAGGTGTAATAGCATAAGGAAAAAAAACTAAAATGACTAGAATACCCTTAGCAGAAATTTGTTTA
131 GAGGTGTAATAGCATAAGGAAAAAAAACTAAAATGACTAGAATACCCTTAGCAGAAATTTGTTTA
*
28623129 GATAAATGATTATTGTTATTGTTATTAAATTTTAATAAGATTATT
196 GATAAATGATTATTGTTATTGTTATAAAATTTTAATAAGATTATT
28623174 AGGGCACGTTTGGCTCGCTGTATTGGAATAGAAGCGTAATGGAATAGAGGCGTAATAGCAAATCA
1 AGGGCACGTTTGGCTCGCTGTATTGGAATAGAAGCGTAATGGAATAGAGGCGTAATAGCAAATCA
28623239 ATTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAACGGAATG
66 ATTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAACGGAATG
* *
28623304 GATGTGTAATAGCATAAGGGAAAAAAAACTAAAATGATTAGAATACCCTTAGCAGAAATTTGTTT
131 GAGGTGTAATAGCATAA-GGAAAAAAAACTAAAATGACTAGAATACCCTTAGCAGAAATTTGTTT
*
28623369 AGATAAATTATTATTGTT-TTGTTATAAAATTTTAATAAGATTATT
195 AGATAAATGATTATTGTTATTGTTATAAAATTTTAATAAGATTATT
28623414 A
1 A
28623415 AAAATATAAT
Statistics
Matches: 233, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
240 170 0.73
241 63 0.27
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (240 bp):
AGGGCACGTTTGGCTCGCTGTATTGGAATAGAAGCGTAATGGAATAGAGGCGTAATAGCAAATCA
ATTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAACGGAATG
GAGGTGTAATAGCATAAGGAAAAAAAACTAAAATGACTAGAATACCCTTAGCAGAAATTTGTTTA
GATAAATGATTATTGTTATTGTTATAAAATTTTAATAAGATTATT
Found at i:28623548 original size:60 final size:56
Alignment explanation
Indices: 28623420--28623548 Score: 129
Period size: 57 Copynumber: 2.2 Consensus size: 56
28623410 TATTAAAAAT
28623420 ATAATATAAATATTTTAATCATAATTATTATTAAATATAATTTAATAAAAAATATATA
1 ATAATATAAA-ATTTTAATCATAATTATTATT-AATATAATTTAATAAAAAATATATA
* * *
28623478 AT-TTAATAAAATTCTTAAT-ATAATTATTCTT-ATATGAATTTACTAAAATCATGATATATA
1 ATAAT-ATAAAATT-TTAATCATAATTATTATTAATAT-AATTTAATAAAA--A--ATATATA
28623538 ATAATATAAAA
1 ATAATATAAAA
28623549 ATATATATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
55 4 0.07
56 11 0.19
57 15 0.25
58 13 0.22
60 15 0.25
61 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (56 bp):
ATAATATAAAATTTTAATCATAATTATTATTAATATAATTTAATAAAAAATATATA
Found at i:28625165 original size:12 final size:12
Alignment explanation
Indices: 28625148--28625177 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28625138 TGGTTTCTCC
*
28625148 AGAAGCTTGAGA
1 AGAAGCTTGAAA
28625160 AGAAGCTTGAAA
1 AGAAGCTTGAAA
28625172 AGAAGC
1 AGAAGC
28625178 ATTTGATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.30, T:0.13
Consensus pattern (12 bp):
AGAAGCTTGAAA
Found at i:28628477 original size:23 final size:23
Alignment explanation
Indices: 28628417--28628505 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
28628407 TCTACTCACT
*
28628417 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAACAACAATTTCCAG
*
28628440 CAGAC-TATCAA-AACAATTTCCAG
1 -A-ACAAATCAACAACAATTTCCAG
* *
28628463 AACAAATCAACAACAATAT-CAT
1 AACAAATCAACAACAATTTCCAG
*
28628485 AACAAAT--GCAACAATTTCCAG
1 AACAAATCAACAACAATTTCCAG
28628506 TTTCATTGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
20 8 0.15
21 4 0.07
22 15 0.28
23 19 0.35
24 6 0.11
25 2 0.04
ACGTcount: A:0.51, C:0.24, G:0.07, T:0.19
Consensus pattern (23 bp):
AACAAATCAACAACAATTTCCAG
Found at i:28630660 original size:20 final size:20
Alignment explanation
Indices: 28630617--28630662 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
28630607 CATGTTAGCA
*
28630617 AAAATTAAAAAATAAAACTC
1 AAAATTAAAAAATAAAAATC
*
28630637 AAAATTCAAAAAA-AAAAATT
1 AAAATT-AAAAAATAAAAATC
28630657 AAAATT
1 AAAATT
28630663 TCTTGTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATTAAAAAATAAAAATC
Found at i:28631102 original size:37 final size:37
Alignment explanation
Indices: 28631030--28631102 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
28631020 CTTTTATTAG
**
28631030 GTTACACATAAAAGAAAATAATTGATAGACTTTTTTA
1 GTTACACATAAAAGAAAATAATTGATAGAAATTTTTA
** * *
28631067 GTTACACATGTAAGAAAATAATTTATATAAATTTTT
1 GTTACACATAAAAGAAAATAATTGATAGAAATTTTT
28631103 TAATTGGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (37 bp):
GTTACACATAAAAGAAAATAATTGATAGAAATTTTTA
Found at i:28631460 original size:22 final size:22
Alignment explanation
Indices: 28631435--28631481 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
28631425 AAAAAAAGTT
28631435 AAAAATATTTTTTATAATTTAA
1 AAAAATATTTTTTATAATTTAA
28631457 AAAAATATTTTTTATAATTTAA
1 AAAAATATTTTTTATAATTTAA
28631479 AAA
1 AAA
28631482 CTAAATCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAAATATTTTTTATAATTTAA
Found at i:28631587 original size:17 final size:17
Alignment explanation
Indices: 28631565--28631599 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28631555 TGATGTGGCA
28631565 GTTCCATGTCAACAAAT
1 GTTCCATGTCAACAAAT
28631582 GTTCCATGTCAACAAAT
1 GTTCCATGTCAACAAAT
28631599 G
1 G
28631600 CCGCTAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (17 bp):
GTTCCATGTCAACAAAT
Found at i:28636274 original size:24 final size:24
Alignment explanation
Indices: 28636247--28636295 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28636237 AGGATGTGTA
28636247 TCGATTAGTAATAGTTGAATAACC
1 TCGATTAGTAATAGTTGAATAACC
28636271 TCGATTAGTAATAGTTGAATAACC
1 TCGATTAGTAATAGTTGAATAACC
28636295 T
1 T
28636296 GACTGTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (24 bp):
TCGATTAGTAATAGTTGAATAACC
Found at i:28640103 original size:45 final size:45
Alignment explanation
Indices: 28640034--28640126 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
28640024 CTTCCAACCT
*
28640034 TAACAACCTTCCAAGTTACTATAAAACAGGGGAAATAAAACAGAG
1 TAACAACCTTCCAAGTTACTATAAAACAGAGGAAATAAAACAGAG
*
28640079 TAACGACCTTCCAAGTTACTATAAAACAGAGGAAATAAAACAGAG
1 TAACAACCTTCCAAGTTACTATAAAACAGAGGAAATAAAACAGAG
28640124 TAA
1 TAA
28640127 GCATTTAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.18
Consensus pattern (45 bp):
TAACAACCTTCCAAGTTACTATAAAACAGAGGAAATAAAACAGAG
Found at i:28640553 original size:26 final size:26
Alignment explanation
Indices: 28640518--28640599 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 26
28640508 TATGCCCATA
28640518 CGAG-CATGTAATCGGGAAGCTCTTT
1 CGAGCCATGTAATCGGGAAGCTCTTT
* *
28640543 CGAGCCATGTAAT-AGGAAGCTCATGT
1 CGAGCCATGTAATCGGGAAGCTC-TTT
* *
28640569 -GA-CC-TGTATAACGGGAAGCTCTTG
1 CGAGCCATGTA-ATCGGGAAGCTCTTT
28640593 CGAGCCA
1 CGAGCCA
28640600 ATTATCGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
23 4 0.09
24 4 0.09
25 24 0.55
26 12 0.27
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (26 bp):
CGAGCCATGTAATCGGGAAGCTCTTT
Found at i:28647368 original size:25 final size:25
Alignment explanation
Indices: 28647325--28647446 Score: 95
Period size: 25 Copynumber: 4.9 Consensus size: 25
28647315 TATGCCCATA
* * *
28647325 CGAG-CATGTAATCGAGAAGCTCTTC
1 CGAGCCATGTAA-CGGGAAGCTCATG
28647350 CGAGCCATGTAACGGGAAGCTCATG
1 CGAGCCATGTAACGGGAAGCTCATG
* ** * * *
28647375 TGAGCTGTATAATGGGAAGCTCTTG
1 CGAGCCATGTAACGGGAAGCTCATG
* * * *
28647400 CGAGCCATTTATCGGGAAACTCATA
1 CGAGCCATGTAACGGGAAGCTCATG
*
28647425 CGAGCCAT-AAACGGGAAGCTCA
1 CGAGCCATGTAACGGGAAGCTCA
28647447 AGTGAGCTAA
Statistics
Matches: 75, Mismatches: 21, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
24 11 0.15
25 57 0.76
26 7 0.09
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (25 bp):
CGAGCCATGTAACGGGAAGCTCATG
Found at i:28647488 original size:24 final size:24
Alignment explanation
Indices: 28647335--28647493 Score: 90
Period size: 25 Copynumber: 6.5 Consensus size: 24
28647325 CGAGCATGTA
* * * *
28647335 ATCGAGAAGCTCTTCCGAGCCATGT
1 ATCGGGAAGCTCATGCGAGCCA-AT
* * **
28647360 AACGGGAAGCTCATGTGAGCTGTAT
1 ATCGGGAAGCTCATGCGAGC-CAAT
* *
28647385 AAT-GGGAAGCTCTTGCGAGCCATTT
1 -ATCGGGAAGCTCATGCGAGCCA-AT
* *
28647410 ATCGGGAAACTCATACGAGCC-AT
1 ATCGGGAAGCTCATGCGAGCCAAT
* * * *
28647433 AAACGGGAAGCTCAAGTGAGCTAA-
1 -ATCGGGAAGCTCATGCGAGCCAAT
*
28647457 ATTTGGGAAGCTCATGCGAGCCAAT
1 A-TCGGGAAGCTCATGCGAGCCAAT
28647482 ATCGGGAAGCTC
1 ATCGGGAAGCTC
28647494 CGGAGAGCCA
Statistics
Matches: 96, Mismatches: 30, Indels: 17
0.67 0.21 0.12
Matches are distributed among these distances:
23 2 0.02
24 44 0.46
25 49 0.51
26 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (24 bp):
ATCGGGAAGCTCATGCGAGCCAAT
Found at i:28648828 original size:13 final size:13
Alignment explanation
Indices: 28648810--28648836 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28648800 AGGACTCATG
28648810 TCTGTTTCTGTTC
1 TCTGTTTCTGTTC
28648823 TCTGTTTCTGTTC
1 TCTGTTTCTGTTC
28648836 T
1 T
28648837 GGTATACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.22, G:0.15, T:0.63
Consensus pattern (13 bp):
TCTGTTTCTGTTC
Found at i:28651114 original size:18 final size:19
Alignment explanation
Indices: 28651084--28651120 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
28651074 GTAACTACTC
28651084 ATTTTCCCTATTAT-AAAT
1 ATTTTCCCTATTATGAAAT
28651102 ATTTT-CCTCATTATGAAAT
1 ATTTTCCCT-ATTATGAAAT
28651121 TCTTTTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTTTCCCTATTATGAAAT
Found at i:28656016 original size:21 final size:21
Alignment explanation
Indices: 28655963--28656027 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
28655953 TTTTGATTTG
**
28655963 CTCTGCTTCCCTCGTTGCTG-
1 CTCTGCTTTACTCGTTGCTGC
* *
28655983 -TCTACTTTACTCGTTGTTGC
1 CTCTGCTTTACTCGTTGCTGC
*
28656003 CTCTGCTTTTCTCGTTGCTGC
1 CTCTGCTTTACTCGTTGCTGC
28656024 CTCT
1 CTCT
28656028 ATTTTAAGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.42
21 21 0.58
ACGTcount: A:0.03, C:0.34, G:0.17, T:0.46
Consensus pattern (21 bp):
CTCTGCTTTACTCGTTGCTGC
Found at i:28660881 original size:22 final size:22
Alignment explanation
Indices: 28660856--28660897 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28660846 TCTTCAATAT
28660856 TCTCTCTAACTCTTTTCAAAGC
1 TCTCTCTAACTCTTTTCAAAGC
* * *
28660878 TCTCTTTAATTTTTTTCAAA
1 TCTCTCTAACTCTTTTCAAA
28660898 AAATCTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50
Consensus pattern (22 bp):
TCTCTCTAACTCTTTTCAAAGC
Found at i:28660936 original size:14 final size:15
Alignment explanation
Indices: 28660907--28660935 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28660897 AAAATCTAAT
28660907 TTTATTTTTTTAAAA
1 TTTATTTTTTTAAAA
28660922 TTTATTTTTTTAAA
1 TTTATTTTTTTAAA
28660936 TAAAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTTTTTTAAAA
Found at i:28662133 original size:125 final size:126
Alignment explanation
Indices: 28661896--28662152 Score: 498
Period size: 125 Copynumber: 2.0 Consensus size: 126
28661886 ATAATATTTA
28661896 AAAATTAAATTTAATACTCACAATTTTCATTTGTTCGACGGATATGTGTATCATTGAGACGAATT
1 AAAA-TAAATTTAATACTCACAATTTTCATTTGTTCGACGGATATGTGTATCATTGAGACGAATT
28661961 AATTCTCCGGCTATTGCTAACATGATAAATTTTTTTGATTTAAAAAATAAATTTAAAAAAAT
65 AATTCTCCGGCTATTGCTAACATGATAAATTTTTTTGATTTAAAAAATAAATTTAAAAAAAT
28662023 AAAATAAATTTAAT-CTCACAATTTTCATTTGTTCGACGGATATGTGTATCATTGAGACGAATTA
1 AAAATAAATTTAATACTCACAATTTTCATTTGTTCGACGGATATGTGTATCATTGAGACGAATTA
28662087 ATTCTCCGGCTATTGCTAACATGATAAATTTTTTTGATTTAAAAAATAAATTTAAAAAAAT
66 ATTCTCCGGCTATTGCTAACATGATAAATTTTTTTGATTTAAAAAATAAATTTAAAAAAAT
28662148 AAAAT
1 AAAAT
28662153 TAGGGCTTTT
Statistics
Matches: 130, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
125 116 0.89
126 10 0.08
127 4 0.03
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (126 bp):
AAAATAAATTTAATACTCACAATTTTCATTTGTTCGACGGATATGTGTATCATTGAGACGAATTA
ATTCTCCGGCTATTGCTAACATGATAAATTTTTTTGATTTAAAAAATAAATTTAAAAAAAT
Found at i:28665109 original size:43 final size:43
Alignment explanation
Indices: 28665042--28665242 Score: 172
Period size: 43 Copynumber: 4.5 Consensus size: 43
28665032 AGATTTTATG
*
28665042 TTATGTATGTATGTGAGTTATGTAAGTAATGATCTGATATATAT
1 TTATGTAT-TATGTGAGTTATGTAAGTAATGATATGATATATAT
* * * *
28665086 TTATGTATTATGTAAGTTCTGTAAGTTATGGTATGATATATAT
1 TTATGTATTATGTGAGTTATGTAAGTAATGATATGATATATAT
* * * * * * *
28665129 AAATTATGAAGTTTTGTGAGTTATGATATGATATAT-ATAAGTTTTA-AG
1 ---TTATGTA-TTATGTGAGTTATG-TAAG-TA-ATGATATGATATATAT
*
28665177 TTATGTATGTATGTGAGTTATGTAAGTAATGATCTGATATATAT
1 TTATGTAT-TATGTGAGTTATGTAAGTAATGATATGATATATAT
* *
28665221 TTACGTATTATGTAAGTTATGT
1 TTATGTATTATGTGAGTTATGT
28665243 GTTTGTTTTG
Statistics
Matches: 121, Mismatches: 26, Indels: 21
0.72 0.15 0.12
Matches are distributed among these distances:
42 2 0.02
43 51 0.42
44 20 0.17
45 18 0.15
46 6 0.05
47 11 0.09
48 4 0.03
49 7 0.06
50 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (43 bp):
TTATGTATTATGTGAGTTATGTAAGTAATGATATGATATATAT
Found at i:28665151 original size:38 final size:39
Alignment explanation
Indices: 28665051--28665168 Score: 121
Period size: 38 Copynumber: 2.9 Consensus size: 39
28665041 GTTATGTATG
* * * * *
28665051 TATGTGAGTTATGTAAGTAATGATCTGATATATATTTATGTAT
1 TATGTAAGTTCTGTAAGTTATGATATGATATATA--TA--AAT
*
28665094 TATGTAAGTTCTGTAAGTTATGGTATGATATATATAAAT
1 TATGTAAGTTCTGTAAGTTATGATATGATATATATAAAT
* *
28665133 TATG-AAGTTTTGTGAGTTATGATATGATATATATAA
1 TATGTAAGTTCTGTAAGTTATGATATGATATATATAA
28665169 GTTTTAAGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
38 29 0.44
39 6 0.09
41 2 0.03
43 29 0.44
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.45
Consensus pattern (39 bp):
TATGTAAGTTCTGTAAGTTATGATATGATATATATAAAT
Found at i:28665215 original size:54 final size:54
Alignment explanation
Indices: 28665151--28665308 Score: 151
Period size: 54 Copynumber: 2.9 Consensus size: 54
28665141 TTTGTGAGTT
28665151 ATGATATGATATATATAAGTTTTAAGTTATGTATGTATGTGAGTTATGTAAGTA
1 ATGATATGATATATATAAGTTTTAAGTTATGTATGTATGTGAGTTATGTAAGTA
* * * * * ** * *
28665205 ATGATCTGATATATATTTACGTATTATG-TAAGTTATG--TGTTTGTTTTGTAAGTT
1 ATGATATGATATATA--TAAGTTTTAAGTTATG-TATGTATGTGAGTTATGTAAGTA
* *
28665259 ATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATG
1 ATGATATGATATATATAAGTT-TTAAGTTATGTATG-TATGTGAGTTATG
28665309 ATATGATATA
Statistics
Matches: 77, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
52 4 0.05
53 7 0.09
54 43 0.56
55 3 0.04
56 20 0.26
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (54 bp):
ATGATATGATATATATAAGTTTTAAGTTATGTATGTATGTGAGTTATGTAAGTA
Found at i:28665242 original size:9 final size:9
Alignment explanation
Indices: 28665228--28665422 Score: 99
Period size: 9 Copynumber: 20.9 Consensus size: 9
28665218 TATTTACGTA
28665228 TTATGTAAG
1 TTATGTAAG
**
28665237 TTATGTGTTTG
1 TTA--TGTAAG
*
28665248 TTTTGTAAG
1 TTATGTAAG
*
28665257 TTATGGTATG
1 TTAT-GTAAG
*
28665267 ATATATATAAG
1 -T-TATGTAAG
28665278 TTAT-TAAG
1 TTATGTAAG
28665286 TTATGTAAG
1 TTATGTAAG
*
28665295 TTATGTGAG
1 TTATGTAAG
*
28665304 TTATGATATG
1 TTATG-TAAG
* *
28665314 ATATATATATG
1 -T-TATGTAAG
*
28665325 TTAT-TATG
1 TTATGTAAG
28665333 TTATGTAAG
1 TTATGTAAG
*
28665342 TTATGTGAG
1 TTATGTAAG
*
28665351 TTATGATATG
1 TTATG-TAAG
* * *
28665361 ATATAATATG
1 TTAT-GTAAG
*
28665371 TTAT-TATG
1 TTATGTAAG
28665379 TTATGTAAG
1 TTATGTAAG
*
28665388 TTATGTGAG
1 TTATGTAAG
* *
28665397 TTATATAAA
1 TTATGTAAG
*
28665406 TTATATAAG
1 TTATGTAAG
28665415 TTATGTAA
1 TTATGTAA
28665423 TTTTTGATAT
Statistics
Matches: 146, Mismatches: 27, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
8 24 0.16
9 81 0.55
10 20 0.14
11 15 0.10
12 6 0.04
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28665328 original size:47 final size:47
Alignment explanation
Indices: 28665255--28665400 Score: 258
Period size: 47 Copynumber: 3.1 Consensus size: 47
28665245 TTGTTTTGTA
* * *
28665255 AGTTATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
1 AGTTATGATATGATATATATATGTTATTATGTTATGTAAGTTATGTG
28665302 AGTTATGATATGATATATATATGTTATTATGTTATGTAAGTTATGTG
1 AGTTATGATATGATATATATATGTTATTATGTTATGTAAGTTATGTG
28665349 AGTTATGATATGATATA-ATATGTTATTATGTTATGTAAGTTATGTG
1 AGTTATGATATGATATATATATGTTATTATGTTATGTAAGTTATGTG
28665395 AGTTAT
1 AGTTAT
28665401 ATAAATTATA
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 35 0.36
47 61 0.64
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (47 bp):
AGTTATGATATGATATATATATGTTATTATGTTATGTAAGTTATGTG
Found at i:28668799 original size:7 final size:7
Alignment explanation
Indices: 28668790--28668940 Score: 90
Period size: 7 Copynumber: 21.4 Consensus size: 7
28668780 CCCCAACCCT
*
28668790 TAAACCT
1 TAAACCA
28668797 TAAACCA
1 TAAACCA
*
28668804 TAAAGCA
1 TAAACCA
* *
28668811 TAATCCC
1 TAAACCA
28668818 TAAACTCA
1 TAAAC-CA
*
28668826 TAATCCA
1 TAAACCA
*
28668833 TAAACCT
1 TAAACCA
*
28668840 TAAA-TA
1 TAAACCA
*
28668846 GTATATCC-
1 -TA-AACCA
28668854 TAAACCA
1 TAAACCA
28668861 TAAACCA
1 TAAACCA
28668868 TAAACCA
1 TAAACCA
* *
28668875 TAATCCT
1 TAAACCA
*
28668882 TAAACCC
1 TAAACCA
* *
28668889 TAAATCT
1 TAAACCA
* *
28668896 TAAAACT
1 TAAACCA
28668903 TAAACCA
1 TAAACCA
** *
28668910 TATGCCT
1 TAAACCA
28668917 TAAACCA
1 TAAACCA
28668924 TAAACCA
1 TAAACCA
*
28668931 TAAACTA
1 TAAACCA
28668938 TAA
1 TAA
28668941 TGATAATTAA
Statistics
Matches: 108, Mismatches: 31, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
6 3 0.03
7 99 0.92
8 6 0.06
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (7 bp):
TAAACCA
Found at i:28668887 original size:21 final size:21
Alignment explanation
Indices: 28668762--28668940 Score: 110
Period size: 21 Copynumber: 8.5 Consensus size: 21
28668752 CTCTAAATTC
* * *
28668762 TAAACCCTAAACCTTAAGCCC
1 TAAACCATAAACCTTAAACCA
* * *
28668783 CAACCCTTAAACCTTAAACCA
1 TAAACCATAAACCTTAAACCA
* * *
28668804 TAAAGCATAATCCCTAAACTCA
1 TAAACCATAAACCTTAAAC-CA
* *
28668826 TAATCCATAAACCTTAAA-TA
1 TAAACCATAAACCTTAAACCA
* *
28668846 GTATATCC-TAAACCATAAACCA
1 -TA-AACCATAAACCTTAAACCA
* *
28668868 TAAACCATAATCCTTAAACCC
1 TAAACCATAAACCTTAAACCA
* * *
28668889 TAAATCTTAAAACTTAAACCA
1 TAAACCATAAACCTTAAACCA
** * *
28668910 TATGCCTTAAACCATAAACCA
1 TAAACCATAAACCTTAAACCA
*
28668931 TAAACTATAA
1 TAAACCATAA
28668941 TGATAATTAA
Statistics
Matches: 117, Mismatches: 36, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
20 4 0.03
21 92 0.79
22 21 0.18
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACCATAAACCTTAAACCA
Found at i:28669132 original size:103 final size:104
Alignment explanation
Indices: 28668995--28669206 Score: 410
Period size: 103 Copynumber: 2.1 Consensus size: 104
28668985 GATTATAAAG
28668995 AAAT-TATTTAATATATAAATTAAAAAACAACCAGTCATGTACCTAAAAAACCTTAAAATTTAAT
1 AAATATATTTAATATATAAATTAAAAAACAACCAGTCATGTACCTAAAAAACCTTAAAATTTAAT
28669059 ATATAAATAATAGTCTCTTAAATTTTTTGCGTTTTTAAC
66 ATATAAATAATAGTCTCTTAAATTTTTTGCGTTTTTAAC
28669098 AAATATATTTAATATA-AAATTAAAAAACAACCAGTCATGTACCTAAAAAACCTTAAAATTTAAT
1 AAATATATTTAATATATAAATTAAAAAACAACCAGTCATGTACCTAAAAAACCTTAAAATTTAAT
28669162 ATATAAATAATAGTCTCTTAAATTTTTTGCGTTTTTAAC
66 ATATAAATAATAGTCTCTTAAATTTTTTGCGTTTTTAAC
28669201 AAATAT
1 AAATAT
28669207 TTTTCTATGT
Statistics
Matches: 108, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 97 0.90
104 11 0.10
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (104 bp):
AAATATATTTAATATATAAATTAAAAAACAACCAGTCATGTACCTAAAAAACCTTAAAATTTAAT
ATATAAATAATAGTCTCTTAAATTTTTTGCGTTTTTAAC
Found at i:28669455 original size:116 final size:116
Alignment explanation
Indices: 28669320--28669573 Score: 336
Period size: 116 Copynumber: 2.2 Consensus size: 116
28669310 TCTTGCGGTG
* * **
28669320 TTTTTCAAAGAGCGTCGCTAATGCTCGACCTAT-AGCGGCGTTTTTTAAAAAGCGCTGCTAATGC
1 TTTTTCAAAGAGCGCCGCTAATGCTCGACCTATGA-CGGCGTTTTTCAAAAAGCGCCACTAATGC
*
28669384 CACTAAAGT-TCAACATAAAACGAGGTCATTGTGCTTAATTTTTTTTGCGGCA
65 CACTAAA-TCTCAACATAAAACGAGGCCATTGTGCTTAATTTTTTTTGCGGCA
* * *
28669436 TTTTTCAAAGGGTGCCGCTAATGCTCGACCTATGACGGCGTTTTTCAACAAGCGCCACTAATGCC
1 TTTTTCAAAGAGCGCCGCTAATGCTCGACCTATGACGGCGTTTTTCAAAAAGCGCCACTAATGCC
* * **
28669501 ACTAAATCTCAACATAAAACGATGCCGTTGTGCTTAA--TTTTTTGCGGTG
66 ACTAAATCTCAACATAAAACGAGGCCATTGTGCTTAATTTTTTTTGCGGCA
* *
28669550 TTTTTCAAAAAGCGTCGCTAATGC
1 TTTTTCAAAGAGCGCCGCTAATGC
28669574 CTCTAAAGCT
Statistics
Matches: 120, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
114 30 0.25
115 1 0.01
116 88 0.73
117 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (116 bp):
TTTTTCAAAGAGCGCCGCTAATGCTCGACCTATGACGGCGTTTTTCAAAAAGCGCCACTAATGCC
ACTAAATCTCAACATAAAACGAGGCCATTGTGCTTAATTTTTTTTGCGGCA
Found at i:28669605 original size:74 final size:74
Alignment explanation
Indices: 28669471--28669720 Score: 322
Period size: 74 Copynumber: 3.4 Consensus size: 74
28669461 CGACCTATGA
* * * * **
28669471 CGGCGTTTTTCAACAAGCGCCACTAATGCCACTAAATCTCAACATAAAACGATGCCGTTGTGCTT
1 CGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGATGTTGTGCTT
28669536 AATTTTTTG
66 AATTTTTTG
* * * *
28669545 CGGTGTTTTTCAAAAAGCGTCGCTAATGCCTCTAAAGCTCAACATAAAACAACGATGTTGTGCTT
1 CGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGATGTTGTGCTT
28669610 AATTTTTTG
66 AATTTTTTG
* * *
28669619 CGGCGTTTTTTAAAGAGCGCCGCTAATGCCACTAAAGCTTAACATAAAACGAC-AGTGTTGTGCT
1 CGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGA-TGTTGTGCT
*
28669683 TAATTTTTTA
65 TAATTTTTTG
* * * *
28669693 TGGCTTTTTTCAAAGAGTGCCGCTAATG
1 CGGCGTTTTTCAAAAAGCGCCGCTAATG
28669721 TTCGACCTAT
Statistics
Matches: 153, Mismatches: 22, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
73 1 0.01
74 152 0.99
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (74 bp):
CGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGATGTTGTGCTT
AATTTTTTG
Found at i:28669755 original size:40 final size:40
Alignment explanation
Indices: 28669698--28669782 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
28669688 TTTTATGGCT
*
28669698 TTTTTCAAAGAGTGCCGCTAATGTTCGACCTATAGCGGCG
1 TTTTTCAAAGAGTGCCGCTAATGCTCGACCTATAGCGGCG
* *
28669738 TTTTTCAAATA-TCGCCGCTAATGCTCGAGCTATAGCGGCG
1 TTTTTCAAAGAGT-GCCGCTAATGCTCGACCTATAGCGGCG
28669778 TTTTT
1 TTTTT
28669783 TGTCCAAACG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (40 bp):
TTTTTCAAAGAGTGCCGCTAATGCTCGACCTATAGCGGCG
Found at i:28671450 original size:54 final size:54
Alignment explanation
Indices: 28671392--28671504 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 54
28671382 AGTTATGTCT
*
28671392 GTGTGTGCATGAATCACATGGTCGTGTGGTTAGGACGTGTAACCATTTGTGTTC
1 GTGTGTGCATGAATCACATGGTCATGTGGTTAGGACGTGTAACCATTTGTGTTC
* * *
28671446 GTGTGTGCGTGAGTCACATGGTTATGTGGTTAGGACGTGTAACCATTTGTGTTC
1 GTGTGTGCATGAATCACATGGTCATGTGGTTAGGACGTGTAACCATTTGTGTTC
28671500 GTGTG
1 GTGTG
28671505 AAAAATATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.17, C:0.13, G:0.34, T:0.36
Consensus pattern (54 bp):
GTGTGTGCATGAATCACATGGTCATGTGGTTAGGACGTGTAACCATTTGTGTTC
Found at i:28676039 original size:12 final size:12
Alignment explanation
Indices: 28676022--28676082 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
28676012 TAAATGGATA
28676022 AAATATTTAATT
1 AAATATTTAATT
28676034 AAATATTT-ATCT
1 AAATATTTAAT-T
*
28676046 AAATTATCTAATT
1 AAA-TATTTAATT
*
28676059 AATTTTTATTTAATT
1 AA---ATATTTAATT
28676074 AAATATTTA
1 AAATATTTA
28676083 TCTAAATGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 2 0.05
12 18 0.46
13 7 0.18
14 2 0.05
15 10 0.26
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATATTTAATT
Found at i:28676322 original size:28 final size:28
Alignment explanation
Indices: 28676288--28676341 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
28676278 TATCATATTT
28676288 ATAAATAAAGTTAATATTTTATTTTATA
1 ATAAATAAAGTTAATATTTTATTTTATA
28676316 ATAAATAAAGTTAATATTTTATTTTA
1 ATAAATAAAGTTAATATTTTATTTTA
28676342 ACTTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
ATAAATAAAGTTAATATTTTATTTTATA
Found at i:28683846 original size:13 final size:14
Alignment explanation
Indices: 28683826--28683866 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
28683816 ATGTGAAGAA
28683826 TATTATTTAAAATT
1 TATTATTTAAAATT
28683840 T-TTATTTTTAAAATT
1 TATTA--TTTAAAATT
28683855 TATTA-TTAAAAT
1 TATTATTTAAAAT
28683867 AAAATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTTAAAATT
Found at i:28683851 original size:15 final size:17
Alignment explanation
Indices: 28683826--28683862 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
28683816 ATGTGAAGAA
28683826 TATTATTTAAAATTT-T
1 TATTATTTAAAATTTAT
28683842 TATT-TTTAAAATTTAT
1 TATTATTTAAAATTTAT
28683858 TATTA
1 TATTA
28683863 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTTAAAATTTAT
Found at i:28685232 original size:22 final size:21
Alignment explanation
Indices: 28685207--28685248 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
28685197 ATGAATTAAT
*
28685207 AAAAATAATATATAATATTACA
1 AAAAATAATATAAAAT-TTACA
28685229 AAAAATAATATAAAATTTAC
1 AAAAATAATATAAAATTTAC
28685249 TTTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATAATATAAAATTTACA
Found at i:28686130 original size:27 final size:27
Alignment explanation
Indices: 28686078--28686130 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28686068 AATTCTCATA
*
28686078 ATCAAGTATAGAAGCAGAATAGAATAT
1 ATCAAGTATAGAAGCAGAATACAATAT
* *
28686105 ATCAAGTTTAGATA-CAGATTACAATA
1 ATCAAGTATAGA-AGCAGAATACAATA
28686131 GATACAGATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.26
Consensus pattern (27 bp):
ATCAAGTATAGAAGCAGAATACAATAT
Found at i:28686857 original size:63 final size:63
Alignment explanation
Indices: 28686784--28686924 Score: 194
Period size: 63 Copynumber: 2.3 Consensus size: 63
28686774 AATACCTCTC
* * * *
28686784 ACACGGCCTGGACACACGCCCGTGTCCCTAGTCCGTGTGACTCTAATTCCAAAAAAGTGAGTT
1 ACACGGCCTGGACACACGCCCGTGTCACTAGCCCGCGTGACTCTAATTCCAAAAAAGTGAGTA
* * * *
28686847 ACACGGCCTGGACACATGCCCGTGTCATTGGCCCGCGTGACTCTAATTCCAAAATAGTGAGTA
1 ACACGGCCTGGACACACGCCCGTGTCACTAGCCCGCGTGACTCTAATTCCAAAAAAGTGAGTA
*
28686910 ACACAGCCT-GACACA
1 ACACGGCCTGGACACA
28686925 TAGTCGTGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
62 6 0.09
63 63 0.91
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (63 bp):
ACACGGCCTGGACACACGCCCGTGTCACTAGCCCGCGTGACTCTAATTCCAAAAAAGTGAGTA
Found at i:28695688 original size:15 final size:15
Alignment explanation
Indices: 28695668--28695696 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28695658 TTTATGCTAA
28695668 ATTGGAGATGTCAAT
1 ATTGGAGATGTCAAT
28695683 ATTGGAGATGTCAA
1 ATTGGAGATGTCAA
28695697 AAAATGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (15 bp):
ATTGGAGATGTCAAT
Found at i:28698753 original size:45 final size:44
Alignment explanation
Indices: 28698697--28698821 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 44
28698687 TTAGCTTGAG
* * * *
28698697 GAACGAGAAAGACCATGGTTGAAAGATATCATGGCATTATACCC
1 GAACAAGAAAGACCATAGTTGAAAGATATCATGGCATTAAACCA
*
28698741 GAAATAAGAAAGACCATAGTTGAAAGATA-CTATGGCATTAAACCA
1 G-AACAAGAAAGACCATAGTTGAAAGATATC-ATGGCATTAAACCA
* * * *
28698786 GAACAGGTAAGACCCTAGTTGAAAGATATTATGGCA
1 GAACAAGAAAGACCATAGTTGAAAGATATCATGGCA
28698822 CCACTTCGGG
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
44 31 0.46
45 37 0.54
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (44 bp):
GAACAAGAAAGACCATAGTTGAAAGATATCATGGCATTAAACCA
Found at i:28706620 original size:50 final size:49
Alignment explanation
Indices: 28706566--28706688 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 49
28706556 GAGGTTCCCC
*
28706566 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATA-TGAAAAC-TCCAAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCA--G-TACAGAAAACATCCAAT
* * * * * *
28706616 GTAAGACCATATCTGGGATATGACATTGGCAGTACAGGAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCAGTACAGAAAACATCCAAT
*
28706665 GTAAGACCATGTCTGGGGCATGGC
1 GTAAGACCATGTCTGGGACATGGC
28706689 TTTGGCATGT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.03
48 6 0.10
49 25 0.42
50 27 0.45
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCAGTACAGAAAACATCCAAT
Found at i:28706694 original size:49 final size:49
Alignment explanation
Indices: 28706566--28706695 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 49
28706556 GAGGTTCCCC
* * *
28706566 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAAAACTCCAAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAGGAAAACTCCAAT
* * * *
28706616 GTAAGACCATATCTGGGATATGACATTGGCA-GTACAGG-AAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACG-ACAGGAAAAC-TCCAAT
* *
28706665 GTAAGACCATGTCTGGGGCATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
28706696 TGTTATTATC
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
48 5 0.08
49 34 0.52
50 27 0.41
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGACAGGAAAACTCCAAT
Found at i:28706923 original size:20 final size:20
Alignment explanation
Indices: 28706898--28706946 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
28706888 TGAGTTATTT
28706898 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
28706918 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
28706938 AAG-AAGCAA
1 AAGTAAGCAA
28706947 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:28711250 original size:28 final size:31
Alignment explanation
Indices: 28711187--28711265 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 31
28711177 TTTCGAGTGT
28711187 CAGTGTGGGCCTTAGCCCAATACAATATCAATA
1 CAGTGTGGGCCTTAGCCCAAT--AATATCAATA
* *
28711220 CAGTGCGGGCCTTAGCCCAAT-ATA-GAA-A
1 CAGTGTGGGCCTTAGCCCAATAATATCAATA
*
28711248 CAGTGTGGGCCTAAGCCC
1 CAGTGTGGGCCTTAGCCC
28711266 GTTACAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 17 0.40
29 2 0.05
30 3 0.07
33 20 0.48
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (31 bp):
CAGTGTGGGCCTTAGCCCAATAATATCAATA
Found at i:28711635 original size:26 final size:26
Alignment explanation
Indices: 28711606--28711739 Score: 198
Period size: 26 Copynumber: 5.2 Consensus size: 26
28711596 TAACGGTCAT
* *
28711606 TTTACCCTTCGGGGGTATTTC-AGTAA
1 TTTACCCATCGAGGGTATTTCGA-TAA
* * *
28711632 TTTACCCATTGAGGCTATTTCGGTAA
1 TTTACCCATCGAGGGTATTTCGATAA
28711658 TTTACCCATCGAGGGTATTTCGATAA
1 TTTACCCATCGAGGGTATTTCGATAA
*
28711684 TTTACCCATCGAGGGTATTTCGATCA
1 TTTACCCATCGAGGGTATTTCGATAA
28711710 TTTACCCATCGAGGGTATTTCGATAA
1 TTTACCCATCGAGGGTATTTCGATAA
28711736 TTTA
1 TTTA
28711740 GGTCCATTAC
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
26 97 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (26 bp):
TTTACCCATCGAGGGTATTTCGATAA
Found at i:28718100 original size:21 final size:23
Alignment explanation
Indices: 28718074--28718119 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
28718064 TAAAGGGTAT
*
28718074 TTAC-AAATTAAATC-TCTAAGA
1 TTACAAAATCAAATCTTCTAAGA
*
28718095 TTACAAAATCATATCTTCTAAGA
1 TTACAAAATCAAATCTTCTAAGA
28718118 TT
1 TT
28718120 GCATATCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
23 9 0.43
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (23 bp):
TTACAAAATCAAATCTTCTAAGA
Found at i:28718110 original size:22 final size:21
Alignment explanation
Indices: 28718074--28718177 Score: 67
Period size: 19 Copynumber: 5.1 Consensus size: 21
28718064 TAAAGGGTAT
* *
28718074 TTACAAATTAAATCTCTAAGA
1 TTACAAATCATATCTCTAAGA
28718095 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATC-TCTAAGA
* *
28718118 TTGCATATCATA--TCTAAGA
1 TTACAAATCATATCTCTAAGA
** *
28718137 TTTTATATCATA--TCTAAGA
1 TTACAAATCATATCTCTAAGA
* *
28718156 TTGCATATCATA--TCTAAGA
1 TTACAAATCATATCTCTAAGA
28718175 TTA
1 TTA
28718178 TATATTATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
19 43 0.60
21 4 0.06
22 15 0.21
23 10 0.14
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (21 bp):
TTACAAATCATATCTCTAAGA
Found at i:28718118 original size:23 final size:22
Alignment explanation
Indices: 28718074--28718132 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
28718064 TAAAGGGTAT
* *
28718074 TTACAAATTAAATC-TCTAAGA
1 TTACAAATCATATCTTCTAAGA
28718095 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATCTTCTAAGA
* *
28718118 TTGCATATCATATCT
1 TTACAAATCATATCT
28718133 AAGATTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.56
23 10 0.31
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (22 bp):
TTACAAATCATATCTTCTAAGA
Found at i:28718135 original size:19 final size:19
Alignment explanation
Indices: 28718111--28718221 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
28718101 AATCATATCT
28718111 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
28718130 TCTAAGATTTTATATCATA
1 TCTAAGATTGCATATCATA
28718149 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
28718168 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
*
28718187 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
28718206 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28718222 CCTGAAGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28718711 original size:44 final size:45
Alignment explanation
Indices: 28718663--28718843 Score: 99
Period size: 44 Copynumber: 4.1 Consensus size: 45
28718653 ACTACTGCTT
*
28718663 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTC-C
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTATTGTCAC
* * * * ***
28718707 AGGGAAGTAGAATTA-CTG---GCTTCAATGTATTCCACTATAACCAC
1 AGGG-AG-ATAA-GACCTGAAATCTTCAATCTATTCCACTATTGTCAC
* * ** * ** * **
28718751 AGGGAGGTAAAATCC-GCCATCTTCGATCTGCTCCACTACTG-CTT
1 AGGGAGATAAGA-CCTGAAATCTTCAATCTATTCCACTATTGTCAC
*
28718795 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTC-C
1 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTATTGTCAC
28718839 AGGGA
1 AGGGA
28718844 AGTAGAATTA
Statistics
Matches: 95, Mismatches: 31, Indels: 22
0.64 0.21 0.15
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 23 0.24
44 44 0.46
45 17 0.18
46 6 0.06
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (45 bp):
AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTATTGTCAC
Found at i:28718754 original size:132 final size:132
Alignment explanation
Indices: 28718549--28719572 Score: 1635
Period size: 132 Copynumber: 7.8 Consensus size: 132
28718539 TAGGACTTAC
* * * * *
28718549 AATCTTCAACCTATTCCACTGCTGACTAGGG-AGATATG--TTACTGGCTTCAATGTATTCCACT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAG-TA-GAATTACTGGCTTCAATGTACTCCACT
28718611 ATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAC
64 ATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAC
28718676 CTGA
129 CTGA
*
28718680 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTATTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
28718745 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28718810 GA
131 GA
*
28718812 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTATTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
*
28718877 AACCACAGGGAGGTAAAATCCGCCATCTTCGATTTGCAT-CACTACTGCTTAGGGAGATAAGACC
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGC-TCCACTACTGCTTAGGGAGATAAGACC
28718941 TGA
130 TGA
*
28718944 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* * * *
28719009 AACCACAAGGAGGTAAAATCCACCATTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGTCCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
*
28719074 AA
131 GA
*
28719076 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* *
28719141 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28719206 GA
131 GA
* *
28719208 AATCTTCAATCTATTCCACTGTTGTTCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* * * * *
28719273 AACCACAGGGAGGTAAAATCCGCCATCTTTGATCTACACCACTACTGCTTAGGGAGAGAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28719338 GA
131 GA
* * * *
28719340 AATCTTCAATCTACTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* * *
28719405 AACCACAGGGAGGTAAAATCCGCCATCTTCGACCTGCTCCACTACTGCTTAGGGAGAGAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28719470 GA
131 GA
* * * * *
28719472 AATCTTCAA-CATATTCCACTGTTGTCTAGGGAAATAGAATTACTAGCTCCAATGTACTCCACTG
1 AATCTTCAATC-TATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTA
* *
28719536 TAACCACAAGGAGGTAAAATCTGCCATCTTCGATCTG
65 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
28719573 TTTCGCTGTC
Statistics
Matches: 841, Mismatches: 46, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
130 1 0.00
131 31 0.04
132 808 0.96
133 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
GA
Found at i:28719371 original size:44 final size:44
Alignment explanation
Indices: 28719323--28719495 Score: 104
Period size: 44 Copynumber: 3.9 Consensus size: 44
28719313 ACTACTGCTT
28719323 AGGGAGAGAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCC
1 AGGGAGAGAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCC
* * * * **
28719367 AGGGA-AGTAGAAT-T-ACTAGCTTCAATGTACTCCACTGTAACCAC
1 AGGGAGAGAAG-ATCTGA-AATCTTCAATCTACTCCACTGTTGCC-C
* * ** * * * ** **
28719411 AGGGAG-GTAAAATCCGCCATCTTCGACCTGCTCCACTACTGCTT
1 AGGGAGAG-AAGATCTGAAATCTTCAATCTACTCCACTGTTGCCC
*
28719455 AGGGAGAGAAGATCTGAAATCTTCAA-CATATTCCACTGTTG
1 AGGGAGAGAAGATCTGAAATCTTCAATC-TACTCCACTGTTG
28719496 TCTAGGGAAA
Statistics
Matches: 89, Mismatches: 31, Indels: 18
0.64 0.22 0.13
Matches are distributed among these distances:
42 1 0.01
43 27 0.30
44 44 0.49
45 17 0.19
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (44 bp):
AGGGAGAGAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCC
Found at i:28723576 original size:24 final size:24
Alignment explanation
Indices: 28723549--28723594 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28723539 TCATTTGTCG
* *
28723549 TTGAAGCTGCTCTTGCATTTCCTT
1 TTGAAACTGCTCTAGCATTTCCTT
*
28723573 TTGAAACTGCTCTAGCTTTTCC
1 TTGAAACTGCTCTAGCATTTCC
28723595 ATCATTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.43
Consensus pattern (24 bp):
TTGAAACTGCTCTAGCATTTCCTT
Found at i:28725853 original size:31 final size:31
Alignment explanation
Indices: 28725815--28725887 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
28725805 TTCAGTCACC
*
28725815 TCTAAAAATTTGGGGTTACACCAGAAATACT
1 TCTAAAAATTTGGGGCTACACCAGAAATACT
28725846 TCTAAAAATTTGGGGCTACACCAGAAATACT
1 TCTAAAAATTTGGGGCTACACCAGAAATACT
28725877 TCTAAAAATTT
1 TCTAAAAATTT
28725888 CCACTCTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (31 bp):
TCTAAAAATTTGGGGCTACACCAGAAATACT
Found at i:28727126 original size:28 final size:31
Alignment explanation
Indices: 28727095--28727175 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 31
28727085 CCCTTTCCAG
*
28727095 TATCAGTGTGGGCCTTAGCCCAATA-CAATA
1 TATCAGTGTGGGCCTTAGCCCAATATAAATA
28727125 TCAATACAGTGTGGGCCTTAGCCCAATATAAA-A
1 T--AT-CAGTGTGGGCCTTAGCCCAATATAAATA
*
28727158 -AT-AGTGTGGGCCTAAGCC
1 TATCAGTGTGGGCCTTAGCC
28727176 TGTTACAGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
28 15 0.33
30 3 0.07
32 2 0.04
33 23 0.51
34 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (31 bp):
TATCAGTGTGGGCCTTAGCCCAATATAAATA
Found at i:28727373 original size:27 final size:27
Alignment explanation
Indices: 28727337--28727402 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
28727327 CAGCAGAGCT
28727337 ACCAGT-ACAGT-ATATGTGCCAAAGCC
1 ACCAGTAACAGTAAT-TGTGCCAAAGCC
** *
28727363 ACCAGTAACAGTAATTGTGGTAGAGCC
1 ACCAGTAACAGTAATTGTGCCAAAGCC
28727390 ACCAGTAACAGTA
1 ACCAGTAACAGTA
28727403 CTTTCTCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 27 0.77
28 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (27 bp):
ACCAGTAACAGTAATTGTGCCAAAGCC
Found at i:28727666 original size:52 final size:52
Alignment explanation
Indices: 28727581--28727755 Score: 219
Period size: 52 Copynumber: 3.4 Consensus size: 52
28727571 CTGCCCTTCA
*
28727581 AAGG-TATTTCGATAATTTACCCATCAAGAGTATTTCGATAATTTACCCATC
1 AAGGCTATTTCGATAATTTACCCATCGAGAGTATTTCGATAATTTACCCATC
* * * *
28727632 GAGGCTCTTTCGATAATTTACCCATCGAGGGTATTTC-AGTAATTTACCTATC
1 AAGGCTATTTCGATAATTTACCCATCGAGAGTATTTCGA-TAATTTACCCATC
* * * * **
28727684 AAGGGTATTTTGGTAATTTACCCATCGAGAGTATTTCGGTAATTTAGGCATC
1 AAGGCTATTTCGATAATTTACCCATCGAGAGTATTTCGATAATTTACCCATC
*
28727736 AAGGTTATTTCGATAATTTA
1 AAGGCTATTTCGATAATTTA
28727756 GGCCCATTAC
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
51 4 0.04
52 99 0.96
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
AAGGCTATTTCGATAATTTACCCATCGAGAGTATTTCGATAATTTACCCATC
Found at i:28727712 original size:78 final size:78
Alignment explanation
Indices: 28727578--28727755 Score: 225
Period size: 78 Copynumber: 2.3 Consensus size: 78
28727568 ATTCTGCCCT
* *
28727578 TCAAAGGTATTTCGATAATTTACCCATCAAGAGTATTTCGATAATTTACCCATCGAG-GCTCTTT
1 TCAAGGGTATTTCGATAATTTACCCATCAAGAGTATTTCGATAATTTACCCATCGAGAG-TATTT
28727642 CGATAATTTACCCA
65 CGATAATTTACCCA
* * * * *
28727656 TCGAGGGTATTTC-AGTAATTTACCTATCAAGGGTATTTTGGTAATTTACCCATCGAGAGTATTT
1 TCAAGGGTATTTCGA-TAATTTACCCATCAAGAGTATTTCGATAATTTACCCATCGAGAGTATTT
* **
28727720 CGGTAATTTAGGCA
65 CGATAATTTACCCA
*
28727734 TCAAGGTTATTTCGATAATTTA
1 TCAAGGGTATTTCGATAATTTA
28727756 GGCCCATTAC
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
77 1 0.01
78 82 0.96
79 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (78 bp):
TCAAGGGTATTTCGATAATTTACCCATCAAGAGTATTTCGATAATTTACCCATCGAGAGTATTTC
GATAATTTACCCA
Found at i:28727758 original size:26 final size:25
Alignment explanation
Indices: 28727581--28727755 Score: 190
Period size: 26 Copynumber: 6.8 Consensus size: 25
28727571 CTGCCCTTCA
28727581 AAGGTATTTCGATAATTTACCCATC
1 AAGGTATTTCGATAATTTACCCATC
28727606 AAGAGTATTTCGATAATTTACCCATC
1 AAG-GTATTTCGATAATTTACCCATC
* *
28727632 GAGGCTCTTTCGATAATTTACCCATC
1 AAGG-TATTTCGATAATTTACCCATC
* *
28727658 GAGGGTATTTC-AGTAATTTACCTATC
1 -AAGGTATTTCGA-TAATTTACCCATC
* *
28727684 AAGGGTATTTTGGTAATTTACCCATC
1 AA-GGTATTTCGATAATTTACCCATC
* * **
28727710 GAGAGTATTTCGGTAATTTAGGCATC
1 AAG-GTATTTCGATAATTTACCCATC
28727736 AAGGTTATTTCGATAATTTA
1 AAGG-TATTTCGATAATTTA
28727756 GGCCCATTAC
Statistics
Matches: 126, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
25 8 0.06
26 116 0.92
27 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (25 bp):
AAGGTATTTCGATAATTTACCCATC
Found at i:28733763 original size:7 final size:7
Alignment explanation
Indices: 28733751--28733788 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
28733741 CTCATAAATA
28733751 TTATTAT
1 TTATTAT
28733758 TTATTAT
1 TTATTAT
28733765 TTATTAT
1 TTATTAT
28733772 TTATTAT
1 TTATTAT
28733779 TTATTAT
1 TTATTAT
28733786 TTA
1 TTA
28733789 CGAATCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:28735291 original size:77 final size:77
Alignment explanation
Indices: 28735204--28735380 Score: 345
Period size: 77 Copynumber: 2.3 Consensus size: 77
28735194 GAGAATTTTA
28735204 TTATTAAATTAATTACCCAAAATAATTATTAATCTAATCGAGTCATGAATTAGTAGTGTGAATCA
1 TTATTAAATTAATTACCCAAAATAATTATTAATCTAATCGAGTCATGAATTAGTAGTGTGAATCA
28735269 AAATTAAATTAT
66 AAATTAAATTAT
28735281 TTATTAAATTAATTACCCAAAATAATTATTAATCTAATCGAGTCATGAATTAGTAGTGTGAATCA
1 TTATTAAATTAATTACCCAAAATAATTATTAATCTAATCGAGTCATGAATTAGTAGTGTGAATCA
28735346 AAATTAAATTAT
66 AAATTAAATTAT
*
28735358 TTATTAAATTAATTACCCTAAAT
1 TTATTAAATTAATTACCCAAAAT
28735381 TAACCTAATG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 99 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (77 bp):
TTATTAAATTAATTACCCAAAATAATTATTAATCTAATCGAGTCATGAATTAGTAGTGTGAATCA
AAATTAAATTAT
Found at i:28738361 original size:17 final size:19
Alignment explanation
Indices: 28738325--28738362 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28738315 AAAATAAACC
28738325 AATTAAAAATAAATTTTAA
1 AATTAAAAATAAATTTTAA
*
28738344 AATTAAACA-AAA-TTTAA
1 AATTAAAAATAAATTTTAA
28738361 AA
1 AA
28738363 AAAGATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAAAATAAATTTTAA
Found at i:28738363 original size:18 final size:19
Alignment explanation
Indices: 28738325--28738363 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28738315 AAAATAAACC
*
28738325 AATTAAAAATAAATTTTAA
1 AATTAAAAATAAATTTAAA
*
28738344 AATTAAACA-AAATTTAAA
1 AATTAAAAATAAATTTAAA
28738362 AA
1 AA
28738364 AAGATCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAAAATAAATTTAAA
Found at i:28750422 original size:26 final size:26
Alignment explanation
Indices: 28750392--28750453 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
28750382 TTTCCCTAGC
28750392 AAAATTTTGACGATTTTGCCCCAAGT
1 AAAATTTTGACGATTTTGCCCCAAGT
*
28750418 AAAATTTTAACGATTTTGCCCCAAGT
1 AAAATTTTGACGATTTTGCCCCAAGT
28750444 AAAATTTTGA
1 AAAATTTTGA
28750454 AAAAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (26 bp):
AAAATTTTGACGATTTTGCCCCAAGT
Found at i:28758255 original size:28 final size:28
Alignment explanation
Indices: 28758200--28758253 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
28758190 TTAAAAAACC
*
28758200 ATAAATTTTTATAAAAAAATTATTTTTT
1 ATAAAGTTTTATAAAAAAATTATTTTTT
*
28758228 ATAAAGTTTTAT--AGAAATTATTTTTT
1 ATAAAGTTTTATAAAAAAATTATTTTTT
28758254 TTCTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.54
28 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
ATAAAGTTTTATAAAAAAATTATTTTTT
Found at i:28760257 original size:14 final size:14
Alignment explanation
Indices: 28760224--28760266 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
28760214 ATATAAAGAG
*
28760224 ATTAAATTCCAAAA
1 ATTAAATTCTAAAA
*
28760238 ATTTAAATTATAAAA
1 A-TTAAATTCTAAAA
28760253 ATTAAATTCTAAAA
1 ATTAAATTCTAAAA
28760267 CTAAGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTAAATTCTAAAA
Found at i:28760260 original size:29 final size:32
Alignment explanation
Indices: 28760204--28760266 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 32
28760194 TCGCACTAAC
28760204 AAATTTAACAATATAAAGAGATTAAATTCCAA
1 AAATTTAACAATATAAAGAGATTAAATTCCAA
* *
28760236 AAATTTAA-ATTATAAA-A-ATTAAATTCTAA
1 AAATTTAACAATATAAAGAGATTAAATTCCAA
28760265 AA
1 AA
28760267 CTAAGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.45
30 1 0.03
31 7 0.24
32 8 0.28
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (32 bp):
AAATTTAACAATATAAAGAGATTAAATTCCAA
Found at i:28760860 original size:19 final size:21
Alignment explanation
Indices: 28760838--28760882 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
28760828 AAATACATAT
* *
28760838 TTTTTATAAA-TATTTTGAA-
1 TTTTTAAAAATTACTTTGAAC
28760857 TTTTTAAAAATTACTTTGAAC
1 TTTTTAAAAATTACTTTGAAC
28760878 TTTTT
1 TTTTT
28760883 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 8 0.36
21 5 0.23
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTTAAAAATTACTTTGAAC
Found at i:28761700 original size:21 final size:21
Alignment explanation
Indices: 28761666--28761708 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28761656 ATTTGACCTA
*
28761666 TTTTTAAGTTTATTATATAAT
1 TTTTTAAGTATATTATATAAT
* *
28761687 TTTTTTAGTATATTATGTAAT
1 TTTTTAAGTATATTATATAAT
28761708 T
1 T
28761709 CATATCATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTTAAGTATATTATATAAT
Found at i:28769068 original size:88 final size:88
Alignment explanation
Indices: 28768919--28769094 Score: 289
Period size: 88 Copynumber: 2.0 Consensus size: 88
28768909 GTTTATTCGA
* * * * *
28768919 TGCTAAGTCGTTATGTCCATTGCTTTCGTCATTCCGAGCTCAAAGAAACCAGGGCGTAACTATAG
1 TGCTAAGTCGTTATGTCCAGTGCATTCGTCATTCCGAGCTCAAAGAAACAAGGACATAACTATAG
28768984 ATGGAAACGTGGCGGATATAATT
66 ATGGAAACGTGGCGGATATAATT
* *
28769007 TGCTAAGTCGTTATGTCCGGTGCATTCGTCATTCTGAGCTCAAAGAAACAAGGACATAACTATAG
1 TGCTAAGTCGTTATGTCCAGTGCATTCGTCATTCCGAGCTCAAAGAAACAAGGACATAACTATAG
28769072 ATGGAAACGTGGCGGATATAATT
66 ATGGAAACGTGGCGGATATAATT
28769095 CTTGTTAGTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (88 bp):
TGCTAAGTCGTTATGTCCAGTGCATTCGTCATTCCGAGCTCAAAGAAACAAGGACATAACTATAG
ATGGAAACGTGGCGGATATAATT
Found at i:28772119 original size:1 final size:1
Alignment explanation
Indices: 28772113--28772152 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
28772103 TCATTTTGCC
28772113 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28772153 GAAGATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28772214 original size:16 final size:17
Alignment explanation
Indices: 28772188--28772219 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28772178 AAAAAAAAAA
28772188 AAAGAAGAAGAAGAAAG
1 AAAGAAGAAGAAGAAAG
28772205 AAAG-AGAAGAAGAAA
1 AAAGAAGAAGAAGAAA
28772220 ATAACTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAGAAGAAAG
Found at i:28773932 original size:19 final size:20
Alignment explanation
Indices: 28773905--28773943 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
28773895 TAGTCAGACT
28773905 AAAAAAATTACAAAA-ATTC
1 AAAAAAATTACAAAATATTC
* *
28773924 AAAATAATTATAAAATATTC
1 AAAAAAATTACAAAATATTC
28773944 TTTTTTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAATTACAAAATATTC
Found at i:28774004 original size:10 final size:11
Alignment explanation
Indices: 28773983--28774031 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
28773973 TCAAATATTT
28773983 AAAATTATATA
1 AAAATTATATA
28773994 AAAATTA-AT-
1 AAAATTATATA
*
28774003 AAAATTATATTG
1 AAAATTATA-TA
28774015 AAAATTATATA
1 AAAATTATATA
*
28774026 ATAATT
1 AAAATT
28774032 CTAAGTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 7 0.21
10 3 0.09
11 14 0.42
12 9 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAATTATATA
Found at i:28774005 original size:20 final size:22
Alignment explanation
Indices: 28773982--28774031 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
28773972 TTCAAATATT
28773982 TAAAATTATA-TAAAAATTA-A
1 TAAAATTATATTAAAAATTATA
*
28774002 TAAAATTATATTGAAAATTATA
1 TAAAATTATATTAAAAATTATA
28774024 TAATAATT
1 TAA-AATT
28774032 CTAAGTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.38
21 8 0.31
22 4 0.15
23 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAATTATATTAAAAATTATA
Found at i:28774020 original size:12 final size:11
Alignment explanation
Indices: 28773981--28774024 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
28773971 ATTCAAATAT
28773981 TTAAAATTATA
1 TTAAAATTATA
*
28773992 TAAAAATTA-A
1 TTAAAATTATA
28774002 -TAAAATTATA
1 TTAAAATTATA
28774012 TTGAAAATTATA
1 TT-AAAATTATA
28774024 T
1 T
28774025 AATAATTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 9 0.32
12 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAAATTATA
Found at i:28784249 original size:103 final size:103
Alignment explanation
Indices: 28784058--28784591 Score: 536
Period size: 104 Copynumber: 5.2 Consensus size: 103
28784048 GATGAACATA
* * * * * * ** * *
28784058 GGTTGTGATCTTAACTCAACTAACCTTTAAACATCAGTTGGGAACATAAGTCCATGAGTTGTTTC
1 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCGTGAACTATTTT
*
28784123 GTAGTTGCGAGCTTAACTT-AGCTAACTCAAATAACTAGG
66 GGAGTTGCGAGCTTAA-TTCAGCTAACTCAAATAACT-GG
** * * * **
28784162 GGTTGCGAGCTTAACTCAACTAACC-TTAAGCATCAGCTAAGACCGTAGATTTGTGAACTATTTT
1 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCGTGAACTATTTT
* *
28784226 GGAGTTGCGAGCTTGATTCAGCTAACTCAAATAAATGTG
66 GGAGTTGCGAGCTTAATTCAGCTAACTCAAATAACTG-G
* * ** **
28784265 GGTTGCGAGCTTAAGTCATCTAACCTTTAAGCATCAGCTGGGAACATAGGTCCACGGCCTATTTT
1 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCGTGAACTATTTT
* * *
28784330 GGACTTACGAACTT-ATGTCAGCTAACTCAAATAACTGGG
66 GGAGTTGCGAGCTTAAT-TCAGCTAACTCAAATAACT-GG
* * * * * * * *
28784369 GGTTGTGAGCTTAACTTAGCTAACCTTTAAGCATCAGCTTGGAACGTTGGTCCGTGCACTGTTTT
1 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCGTGAACTATTTT
* * * * *
28784434 AGAGTTGTGAGCTTAACTT-AGCTAACTTAAATAATTGA
66 GGAGTTGCGAGCTTAA-TTCAGCTAACTCAAATAACTGG
* * *
28784472 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCTGTGAGCTGTTTT
1 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCGTGAACTATTTT
* * *
28784537 GGAGTTACGAGTTTAACTCAGCTAACTCAAATAACTGG
66 GGAGTTGCGAGCTTAATTCAGCTAACTCAAATAACTGG
*
28784575 AGGTTGCAAGCTTAACT
1 -GGTTGCGAGCTTAACT
28784592 TAGCTAACTC
Statistics
Matches: 346, Mismatches: 75, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
102 4 0.01
103 165 0.48
104 173 0.50
105 3 0.01
106 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (103 bp):
GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCGTGAACTATTTT
GGAGTTGCGAGCTTAATTCAGCTAACTCAAATAACTGG
Found at i:28784478 original size:207 final size:207
Alignment explanation
Indices: 28784058--28784599 Score: 624
Period size: 207 Copynumber: 2.6 Consensus size: 207
28784048 GATGAACATA
* * * * * * * * *
28784058 GGTTGTGATCTTAACTCAACTAACCTTTAAACATCAGTTGGGAACATAAGTCCATGAGTTGTTTC
1 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCACGAGCTATTTT
* * * * * * * *
28784123 GTAGTTGCGAGCTTAACTTAGCTAACTCAAATAACTAGGGGTTGCGAGCTTAACTCAACTAACCT
66 GGACTTACGAACTTAACTCAGCTAACTCAAATAACTGGGGGTTGCGAGCTTAACTTAGCTAACCT
* ** * *
28784188 TAAGCATCAGCTAAGACCGTAGATTTGTGAACTATTTTGGAGTTGCGAGCTTGATTCAGCTAACT
131 TAAGCATCAGCTAAGAACGTAGATCCGTGAACTATTTTAGAGTTGCGAGCTTAATTCAGCTAACT
28784253 CAAATAAATGTG
196 CAAATAAATGTG
* *
28784265 GGTTGCGAGCTTAAGTCATCTAACCTTTAAGCATCAGCTGGGAACATAGGTCCACG-GCCTATTT
1 GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCACGAG-CTATTT
** *
28784329 TGGACTTACGAACTTATGTCAGCTAACTCAAATAACTGGGGGTTGTGAGCTTAACTTAGCTAACC
65 TGGACTTACGAACTTAACTCAGCTAACTCAAATAACTGGGGGTTGCGAGCTTAACTTAGCTAACC
** * * * * *
28784394 TTTAAGCATCAGCTTGGAACGTTGGTCCGTGCACTGTTTTAGAGTTGTGAGCTTAACTT-AGCTA
130 -TTAAGCATCAGCTAAGAACGTAGATCCGTGAACTATTTTAGAGTTGCGAGCTTAA-TTCAGCTA
*
28784458 ACTTAAAT-AAT-TG
193 ACTCAAATAAATGTG
*** *
28784471 AGGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCTGTGAGCTGTTT
1 -GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCACGAGCTATTT
* ** * *
28784536 TGGAGTTACGAGTTTAACTCAGCTAACTCAAATAACTGGAGGTTGCAAGCTTAACTTAGCTAAC
65 TGGACTTACGAACTTAACTCAGCTAACTCAAATAACTGGGGGTTGCGAGCTTAACTTAGCTAAC
28784600 TCAAATTACT
Statistics
Matches: 281, Mismatches: 49, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
206 3 0.01
207 220 0.78
208 56 0.20
209 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (207 bp):
GGTTGCGAGCTTAACTCAACTAACCTTTAAGCATCAGCTGGGAACATAGGTCCACGAGCTATTTT
GGACTTACGAACTTAACTCAGCTAACTCAAATAACTGGGGGTTGCGAGCTTAACTTAGCTAACCT
TAAGCATCAGCTAAGAACGTAGATCCGTGAACTATTTTAGAGTTGCGAGCTTAATTCAGCTAACT
CAAATAAATGTG
Done.