Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold488
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: 2093548
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2023853 original size:13 final size:13
Alignment explanation
Indices: 2023835--2023859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2023825 ACCTTTGGTC
2023835 ATGTATCGATACA
1 ATGTATCGATACA
2023848 ATGTATCGATAC
1 ATGTATCGATAC
2023860 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2023892 original size:20 final size:19
Alignment explanation
Indices: 2023869--2023907 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
2023859 CTGTGCATTA
2023869 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
2023889 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
2023908 GTTTTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:2024522 original size:20 final size:22
Alignment explanation
Indices: 2024482--2024522 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2024472 TAGCCTTTGA
*
2024482 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
2024504 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
2024523 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:2038923 original size:28 final size:29
Alignment explanation
Indices: 2038882--2039775 Score: 787
Period size: 28 Copynumber: 30.8 Consensus size: 29
2038872 ACATTCACCA
* *
2038882 TTTCAAAGCCCACAAGTCGGTGGCAACCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2038911 TTTC-AAGCCCACAAGTCAGTGGTAACCCT
1 TTTCAAAGCCCACAAGTCAGTGG-CATCCT
*
2038940 CTTCAAAGCCCACAAGTCA-TGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
2038967 TTTCAAAAGCCCACACAAGTCAGTGGCATCC-
1 TTTC-AAAG-CC-CACAAGTCAGTGGCATCCT
* *
2038998 TTTCAAAAGCCCACACAAGTCAATAGCATCC-
1 TTTC-AAAG-CC-CACAAGTCAGTGGCATCCT
*
2039029 TTTCAAAAGCCCACACAAGTTAGTGGCATCCT
1 TTTC-AAAG-CC-CACAAGTCAGTGGCATCCT
* * *
2039061 TTT-AAAGCCTACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCCT
* * * * *
2039090 TTT-GAAGACCATAGGTTAGTGGCA-CCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
*
2039117 CTTTCAAAGCCCACAAGTTAGTGGCAT-CT
1 -TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2039146 TTTCAAAAGCCCACAAGTTAGTGGCAT-CA
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
2039175 TTTCAAAAGCCCACCAGTTAGTGGCATCC-
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCT
2039204 TTTCAAAGCCCACAAGTCAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2039232 TTTCAAAGCCCACAAGTTAATGGCATCCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2039261 TTT-AAAGCCCATAAGACAGTGGCATCCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
2039289 TTTAAAAGCCCACTAGTTAGTGGCA-CCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
*
2039317 TTTCAAAGCCCAAAAGTCAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2039345 TTTCAAAAGCCCACCAGTTAGTGGCATCC-
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCT
*
2039374 TTTCAAAGCCTACAAGTCAGTGGCAT-C-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2039401 TTTCTAAAGCCCATAAGTCAGTGGCCTCC-
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCT
*
2039430 TTTCAAAGCCCACAAGTCAGTGGCAACC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2039458 TTTCAAAAGCCTACTAGTCAGTGGCATCC-
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCT
*
2039487 TTTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
2039516 TTT-AAAGCCCATAAGCCGGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
*
2039543 TTTCAAAGCCCACAAGCCAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2039571 TTTCAAAGCCCATAAGTTAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
2039599 TTTCAAAGCCTAGAAGTTAGTGGCAACCCT
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCCT
* * * * *
2039629 CTTCAAAGCCCATAAGGCGGTGGCAACCCT
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCCT
* *
2039659 TTT-AAAGACCACAGGTCAGTGGCATCCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
2039687 TTTCAAAATCCACACAAGTTAGTGGTAACCTT
1 TTTC-AAAGCC-CACAAGTCAGTGGCATCC-T
* * *
2039719 TTTCAAGGCCACACAAGTCGGTGGCACTTCT
1 TTTCAAAGCC-CACAAGTCAGTGGCA-TCCT
*
2039750 TTTTAAAGGCCCACACAAGTCAGTGG
1 TTTCAAA-G-CC-CACAAGTCAGTGG
2039776 TGACCCTTTT
Statistics
Matches: 729, Mismatches: 105, Indels: 58
0.82 0.12 0.07
Matches are distributed among these distances:
27 14 0.02
28 322 0.44
29 208 0.29
30 58 0.08
31 102 0.14
32 10 0.01
33 15 0.02
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:2039218 original size:57 final size:56
Alignment explanation
Indices: 2038882--2039744 Score: 841
Period size: 57 Copynumber: 14.9 Consensus size: 56
2038872 ACATTCACCA
* * * *
2038882 TTTCAAAGCCCACAAGTCGGTGGCAACCTTTTC-AAGCCCACAAGTCAGTGGTAACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGG-CATCC
2038939 TCTTCAAAGCCCACAAGTCA-TGGCATCCTTTCAAAAGCCCACACAAGTCAGTGGCATCC
1 T-TTCAAAGCCCACAAGTCAGTGGCATCCTTTC-AAAG-CC-CACAAGTCAGTGGCATCC
* * *
2038998 TTTCAAAAGCCCACACAAGTCAATAGCATCCTTTCAAAAGCCCACACAAGTTAGTGGCATCC
1 TTTC-AAAG-CC-CACAAGTCAGTGGCATCCTTTC-AAAG-CC-CACAAGTCAGTGGCATCC
* * * * ** * * * * *
2039060 TTTTAAAGCCTACAAGTCGGTGGCAACCCTTTTGAAGACCATAGGTTAGTGGCACCTC
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCCTTTCAAAGCCCACAAGTCAGTGGCATC-C
* * * *
2039118 TTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCAGTGGCATCC
* *
2039175 TTTCAAAAGCCCACCAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
2039232 TTTCAAAGCCCACAAGTTAATGGCATCCTTTTAAAGCCCATAAGACAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
2039288 TTTTAAAAGCCCACTAGTTAGTGGCACCCTTTCAAAGCCCAAAAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
2039345 TTTCAAAAGCCCACCAGTTAGTGGCATCCTTTCAAAGCCTACAAGTCAGTGGCAT-C
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
2039401 TTTCTAAAGCCCATAAGTCAGTGGCCTCCTTTCAAAGCCCACAAGTCAGTGGCAACC
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
2039458 TTTCAAAAGCCTACTAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
2039515 TTTTAAAGCCCATAAGCCGGTGGCATCCTTTCAAAGCCCACAAGCCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * * *
2039571 TTTCAAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCTAGAAGTTAGTGGCAACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC-ATCC
* * * * * * *
2039628 TCTTCAAAGCCCATAAGGCGGTGGCAACCCTTTTAAAGACCACAGGTCAGTGGCATCC
1 T-TTCAAAGCCCACAAGTCAGTGGC-ATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * * *
2039686 TTTTCAAAATCCACACAAGTTAGTGGTAACCTTTTTCAAGGCCACACAAGTCGGTGGCA
1 -TTTC-AAAGCC-CACAAGTCAGTGGCATCC--TTTCAAAGCC-CACAAGTCAGTGGCA
2039745 CTTCTTTTTA
Statistics
Matches: 675, Mismatches: 106, Indels: 45
0.82 0.13 0.05
Matches are distributed among these distances:
56 192 0.28
57 210 0.31
58 115 0.17
59 53 0.08
60 32 0.05
61 20 0.03
62 53 0.08
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (56 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:2039301 original size:113 final size:113
Alignment explanation
Indices: 2038882--2039775 Score: 875
Period size: 113 Copynumber: 7.7 Consensus size: 113
2038872 ACATTCACCA
** * * * * *
2038882 TTTC-AAAGCCCACAAGTCGGTGGCAACCTTTTC-AAGCCCACAAGTCAGTGGTAACCCTCTTCA
1 TTTCAAAAGCCCACAAGTTAGTGGCATCC-TTTCAAAGCCCACAAGTTAGTGG-CATCCT-TTTA
2038945 AAGCCCACAAGTCA-TGGCATCCTTTCAAAAGCCCACACAAGTCAGTGGCATCC
63 AAGCCCACAAGTCAGTGGCATCCTTTC-AAAG-CC-CACAAGTCAGTGGCATCC
* * *
2038998 TTTCAAAAGCCCACACAAGTCAATAGCATCCTTTCAAAAGCCCACACAAGTTAGTGGCATCCTTT
1 TTTCAAAAG-CC-CACAAGTTAGTGGCATCCTTTC-AAAG-CC-CACAAGTTAGTGGCATCCTTT
* * * ** * * * * *
2039063 TAAAGCCTACAAGTCGGTGGCAACCCTTTTGAAGACCATAGGTTAGTGGCACCTC
61 TAAAGCCCACAAGTCAGTGGC-ATCCTTTCAAAGCCCACAAGTCAGTGGCATC-C
* * *
2039118 TTTC-AAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCATCATTTCAAA
1 TTTCAAAAGCCCACAAGTTAGTGGCATCCTTTC-AAAGCCCACAAGTTAGTGGCATCCTTT-TAA
* *
2039182 AGCCCACCAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
64 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * **
2039232 TTTC-AAAGCCCACAAGTTAATGGCATCCTTTTAAAGCCCATAAGACAGTGGCATCCTTTTAAAA
1 TTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTT-AAA
* * * *
2039296 GCCCACTAGTTAGTGGCACCCTTTCAAAGCCCAAAAGTCAGTGGCATCC
65 GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
2039345 TTTCAAAAGCCCACCAGTTAGTGGCATCCTTTCAAAGCCTACAAGTCAGTGGCAT-CTTTCTAAA
1 TTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTT-TAAA
* * *
2039409 GCCCATAAGTCAGTGGCCTCCTTTCAAAGCCCACAAGTCAGTGGCAACC
65 GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
2039458 TTTCAAAAGCCTACTAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAG
1 TTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAG
* * * *
2039523 CCCATAAGCCGGTGGCATCCTTTCAAAGCCCACAAGCCAGTGGCATCC
66 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
2039571 TTTC-AAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCTAGAAGTTAGTGGCAACCCTCTTCAA
1 TTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGC-ATCCT-TTTAA
* * * * * * *
2039635 AGCCCATAAGGCGGTGGCAACCCTTTTAAAGACCACAGGTCAGTGGCATCC
64 AGCCCACAAGTCAGTGGC-ATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * ** *
2039686 TTTTCAAAATCCACACAAGTTAGTGGTAACCTTTTTCAAGGCCACACAAGTCGGTGGCACTTCTT
1 -TTTCAAAAGCC-CACAAGTTAGTGGCATCC--TTTCAAAGCC-CACAAGTTAGTGGCA--TCCT
2039751 TTTAAAGGCCCACACAAGTCAGTGG
59 TTTAAA-G-CC-CACAAGTCAGTGG
2039776 TGACCCTTTT
Statistics
Matches: 650, Mismatches: 99, Indels: 50
0.81 0.12 0.06
Matches are distributed among these distances:
112 42 0.06
113 231 0.36
114 100 0.15
115 70 0.11
116 26 0.04
117 32 0.05
118 23 0.04
119 31 0.05
120 34 0.05
121 28 0.04
122 21 0.03
123 2 0.00
124 10 0.02
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (113 bp):
TTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAG
CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:2039785 original size:33 final size:31
Alignment explanation
Indices: 2039668--2039785 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 31
2039658 TTTTAAAGAC
* * * * **
2039668 CACAGGTCAGTGGCATCCTTTTCAAAATCCA
1 CACAAGTCAGTGGTACCCTTTTTAAAGGCCA
* * *
2039699 CACAAGTTAGTGGTAACCTTTTTCAAGGCCA
1 CACAAGTCAGTGGTACCCTTTTTAAAGGCCA
* * *
2039730 CACAAGTCGGTGGCACTTCTTTTTAAAGGCCCA
1 CACAAGTCAGTGGTAC-CCTTTTTAAAGG-CCA
2039763 CACAAGTCAGTGGTGACCCTTTT
1 CACAAGTCAGTGGT-ACCCTTTT
2039786 CGAAACACCA
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
31 35 0.52
32 10 0.15
33 20 0.30
34 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (31 bp):
CACAAGTCAGTGGTACCCTTTTTAAAGGCCA
Found at i:2040742 original size:20 final size:20
Alignment explanation
Indices: 2040717--2040771 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2040707 TTTTTACCCA
*
2040717 AATGTATTGATACATTATGC
1 AATGTATCGATACATTATGC
* *
2040737 AATGTATCGACACATTTTGC
1 AATGTATCGATACATTATGC
2040757 AATGTATCGATACAT
1 AATGTATCGATACAT
2040772 CTATTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTATGC
Found at i:2043990 original size:52 final size:51
Alignment explanation
Indices: 2043907--2044045 Score: 201
Period size: 51 Copynumber: 2.7 Consensus size: 51
2043897 ATTTAACTAG
* * *
2043907 ATGTATCGATACATTAAAGAATATATTGATACATTTTGG-TCAAAAACCCAGA
1 ATGTATCGATACAATAAA-AATGTATCGATACATTTTGGATC-AAAACCCAGA
*
2043959 ATGTATAGATACAATGAAAAATGTATCGATACA-TTTGGATCAAAACCCAGA
1 ATGTATCGATACAAT-AAAAATGTATCGATACATTTTGGATCAAAACCCAGA
2044010 ATGTATCGATACAATAAAAATGTATCGATACATTTT
1 ATGTATCGATACAATAAAAATGTATCGATACATTTT
2044046 CTTTCCAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
50 17 0.22
51 32 0.41
52 27 0.34
53 3 0.04
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACAATAAAAATGTATCGATACATTTTGGATCAAAACCCAGA
Found at i:2044097 original size:20 final size:20
Alignment explanation
Indices: 2044072--2044135 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
2044062 ATTTGCTTCA
2044072 ACATTCACTTATGTATCGAT
1 ACATTCACTTATGTATCGAT
*
2044092 ACATTCACTTATGTATCAAT
1 ACATTCACTTATGTATCGAT
*
2044112 ACATTCACTTATTGTATTGAT
1 ACATTCACTTA-TGTATCGAT
2044133 ACA
1 ACA
2044136 AATTGTAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 30 0.75
21 10 0.25
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (20 bp):
ACATTCACTTATGTATCGAT
Found at i:2048283 original size:79 final size:80
Alignment explanation
Indices: 2047925--2048301 Score: 406
Period size: 79 Copynumber: 4.8 Consensus size: 80
2047915 TTCTCATCTC
*
2047925 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTT-TCATAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTCATAATCAGGGATACTCCAA
* *
2047989 TCCCGTTATTTCCAA
66 CCCCGTTATTTCCGA
* * * * * * *
2048004 AGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGA-TTTCTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTCATAATCAGGGATACTCCAA
** *
2048068 CCCCGTTATTTTGGT
66 CCCCGTTATTTCCGA
** * * * * *
2048083 GGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATTGATTTT-TCACAATC-GAGGATACTTCA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTCATAATCAG-GGATACTCCA
*
2048146 ACCCCGTTATTTTCGA
65 ACCCCGTTATTTCCGA
* * * *
2048162 GGGGATACTCCAACCCTGATTTTATTTTCAAAACATCGATTTTCT-ATAACCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTCATAATCAGGGATACTCCAA
**
2048226 CCTTGTTATTTCCGA
66 CCCCGTTATTTCCGA
* ** * * *
2048241 GGGGATACTCCAACCCCGATTTTATTTCCAGGACACCAATTTTC-CATAATCGGGGATACTC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTCATAATCAGGGATACTC
2048302 TAGCCCTATT
Statistics
Matches: 250, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
78 4 0.02
79 241 0.96
80 5 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTCTCATAATCAGGGATACTCCAA
CCCCGTTATTTCCGA
Found at i:2060960 original size:19 final size:19
Alignment explanation
Indices: 2060936--2060985 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2060926 ATCGATATAA
*
2060936 TGTATCGATGCATAAGTGT
1 TGTATCGATACATAAGTGT
*
2060955 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
2060974 TGTATCGATACA
1 TGTATCGATACA
2060986 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:2061033 original size:13 final size:13
Alignment explanation
Indices: 2061015--2061041 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2061005 CTGCCAAGGA
2061015 AATGTATCGATAC
1 AATGTATCGATAC
2061028 AATGTATCGATAC
1 AATGTATCGATAC
2061041 A
1 A
2061042 TTGATCTTTT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2064194 original size:9 final size:9
Alignment explanation
Indices: 2064180--2064219 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
2064170 ACGTTACGAC
2064180 AACAAAAAA
1 AACAAAAAA
*
2064189 AACAAAAGA
1 AACAAAAAA
2064198 AACAAAACAA
1 AACAAAA-AA
2064208 AACAAAGAAA
1 AACAAA-AAA
2064218 AA
1 AA
2064220 AAAGAGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 15 0.56
10 11 0.41
11 1 0.04
ACGTcount: A:0.82, C:0.12, G:0.05, T:0.00
Consensus pattern (9 bp):
AACAAAAAA
Found at i:2064203 original size:18 final size:17
Alignment explanation
Indices: 2064180--2064222 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2064170 ACGTTACGAC
2064180 AACAAAAAAAACAAAAGA
1 AACAAAAAAAAC-AAAGA
2064198 AACAAAACAAAACAAAGA
1 AACAAAA-AAAACAAAGA
2064216 AA-AAAAA
1 AACAAAAA
2064223 GAGAGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.04
17 4 0.17
18 14 0.58
19 5 0.21
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (17 bp):
AACAAAAAAAACAAAGA
Found at i:2064206 original size:14 final size:14
Alignment explanation
Indices: 2064187--2064224 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2064177 GACAACAAAA
2064187 AAAACAAAAGAAAC
1 AAAACAAAAGAAAC
* *
2064201 AAAACAAAACAAAG
1 AAAACAAAAGAAAC
2064215 AAAA-AAAAGA
1 AAAACAAAAGA
2064225 GAGAAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.82, C:0.11, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAACAAAAGAAAC
Found at i:2065720 original size:61 final size:61
Alignment explanation
Indices: 2065301--2065769 Score: 538
Period size: 62 Copynumber: 7.7 Consensus size: 61
2065291 TCTCTCTTTT
* * * * * *
2065301 CACCCTTTCGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAACGCCCACACAAATTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
** *
2065362 CATTTTTCTAGTCCTCAAAGAGCAGAACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTT-TAGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGG
* * * *
2065425 CACC-TTCAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGCTT-GTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAG-TTGGTGG
*
2065485 CACC-TTCAGTCCTCAAAGAGCAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGG
* * * *
2065545 CACCCTTGAGTCC-CTAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACATGTTGGTGG
1 CACCTTTTAGTCCTC-AAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGG
* * * * * *
2065607 CACCTCTTCGTCCTCAAAAAGCATGACGCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGG
* *
2065669 CACCTTTTAGTCCTTAAAGAGCAGGAC-ACTTTTTCTTTTCAAAGCCCACACGAA-TTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACAC-AAGTTGGTGG
* * * *
2065730 CACTTTTTAGTCTTCAAAGAGCAGGACACCTTTTCCTTTT
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT
2065770 CTCCTTTGCC
Statistics
Matches: 350, Mismatches: 44, Indels: 27
0.83 0.10 0.06
Matches are distributed among these distances:
59 7 0.02
60 80 0.23
61 102 0.29
62 130 0.37
63 31 0.09
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (61 bp):
CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:2065868 original size:82 final size:84
Alignment explanation
Indices: 2065737--2065921 Score: 230
Period size: 82 Copynumber: 2.2 Consensus size: 84
2065727 TGGCACTTTT
* * ** * * * * *
2065737 TAGTCTTCAAAGAGCAGGACACCTTTTCCTTTTCTCCTTTGCCCTCAAAGAGTAGGATATATTTC
1 TAGTCCTCAAAGAGCATGATTCATTTTCCTTTTCTCCTTTGCCCTCAAAGAGCAGGACACACTTC
2065802 ATTTCCTTCTTTTCCCTT-
66 ATTTCCTTCTTTTCCCTTC
* * * *
2065820 TTGTCCTCAAAGAGCATGATTCATTTTTCTTTT-TCCTTTGTCCTCAAAGAGCAGGACGCACTTC
1 TAGTCCTCAAAGAGCATGATTCATTTTCCTTTTCTCCTTTGCCCTCAAAGAGCAGGACACACTTC
2065884 ATTTCCTTCTTTTCCCTTC
66 ATTTCCTTCTTTTCCCTTC
*
2065903 TAGTTCTCAAAGAGCATGA
1 TAGTCCTCAAAGAGCATGA
2065922 CGCACTTCAT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
82 43 0.50
83 43 0.50
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (84 bp):
TAGTCCTCAAAGAGCATGATTCATTTTCCTTTTCTCCTTTGCCCTCAAAGAGCAGGACACACTTC
ATTTCCTTCTTTTCCCTTC
Found at i:2065914 original size:46 final size:45
Alignment explanation
Indices: 2065799--2066133 Score: 259
Period size: 46 Copynumber: 7.9 Consensus size: 45
2065789 TAGGATATAT
* *
2065799 TTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGC---ATG-A-
1 TTCATTTCCTTCTTTTCCCTTTAGTCCTCAAAGAGCAGGACGCAC
*
2065839 TTCATTT--TTCTTTTTCCTTT-GTCCTCAAAGAGCAGGACGCAC
1 TTCATTTCCTTCTTTTCCCTTTAGTCCTCAAAGAGCAGGACGCAC
* *
2065881 TTCATTTCCTTCTTTTCCCTTCTAGTTCTCAAAGAGCATGACGCAC
1 TTCATTTCCTTCTTTTCCCTT-TAGTCCTCAAAGAGCAGGACGCAC
*
2065927 TTCATTTCCTTCTTTTCCCTTCTAGTTCTCAAAGAGCAGGACGCAC
1 TTCATTTCCTTCTTTTCCCTT-TAGTCCTCAAAGAGCAGGACGCAC
* * * * * * *
2065973 TTTA-TT-CTTCTTTTTCCTTT-GTCCTTAAAAAGTAGGACACAT
1 TTCATTTCCTTCTTTTCCCTTTAGTCCTCAAAGAGCAGGACGCAC
* * * * *
2066015 TTAATTTCC-T-TTTT-CCTTT-GT-CTCCAAAGGGCATGATGCAT
1 TTCATTTCCTTCTTTTCCCTTTAGTCCT-CAAAGAGCAGGACGCAC
* * *
2066056 TTTATTTCCTT-TTTT-CCTTT-GTCCTCAAGGAGCAGGAC-CTAT
1 TTCATTTCCTTCTTTTCCCTTTAGTCCTCAAAGAGCAGGACGC-AC
* *
2066098 TTCA-TT-CTCCTTTT-CC-TTAATCCTCAAAGAGCAGGA
1 TTCATTTCCTTCTTTTCCCTTTAGTCCTCAAAGAGCAGGA
2066134 TGCTCTCTTC
Statistics
Matches: 247, Mismatches: 31, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
37 13 0.05
38 12 0.05
40 15 0.06
41 50 0.20
42 56 0.23
43 6 0.02
44 24 0.10
45 3 0.01
46 68 0.28
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (45 bp):
TTCATTTCCTTCTTTTCCCTTTAGTCCTCAAAGAGCAGGACGCAC
Found at i:2065958 original size:92 final size:82
Alignment explanation
Indices: 2065735--2065997 Score: 244
Period size: 83 Copynumber: 3.1 Consensus size: 82
2065725 GGTGGCACTT
* * ** * * * * *** *
2065735 TTTAGTCTTCAAAGAGCAGGACACCTTTTCCTTTTCTCCTTTGCCCTCAAAGAGTAGGATATATT
1 TTTAGTCCTCAAAGAGCATGATTCATTTTTCTTTTC-CCTTTGTCCTCAAAGAGCAGGACGCACT
2065800 TCATTTCCTTCTTTTCCC
65 TCATTTCCTTCTTTTCCC
* *
2065818 TTTTGTCCTCAAAGAGCATGATTCATTTTTCTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTT
1 TTTAGTCCTCAAAGAGCATGATTCATTTTTCTTTTCCCTTTGTCCTCAAAGAGCAGGACGCACTT
2065883 CATTTCCTTCTTTTCCC
66 CATTTCCTTCTTTTCCC
* *
2065900 TTCTAGTTCTCAAAGAGCATGACGCACTTCATTTCCTTCTTTTCCCTTCTAGTTCTCAAAGAGCA
1 TT-TAGTCCTCAAAGAGCAT---G-A-TTCATTT--TTCTTTTCCCTT-T-GTCCTCAAAGAGCA
* *
2065965 GGACGCACTTTA-TT-CTTCTTTTTCC
56 GGACGCACTTCATTTCCTTCTTTTCCC
2065990 TTT-GTCCT
1 TTTAGTCCT
2065998 TAAAAAGTAG
Statistics
Matches: 149, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
82 42 0.28
83 43 0.29
86 1 0.01
87 1 0.01
88 11 0.07
89 1 0.01
90 23 0.15
91 3 0.02
92 24 0.16
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (82 bp):
TTTAGTCCTCAAAGAGCATGATTCATTTTTCTTTTCCCTTTGTCCTCAAAGAGCAGGACGCACTT
CATTTCCTTCTTTTCCC
Found at i:2066126 original size:83 final size:83
Alignment explanation
Indices: 2065782--2066136 Score: 190
Period size: 83 Copynumber: 4.2 Consensus size: 83
2065772 CCTTTGCCCT
* ** * * * **
2065782 CAAAGAGTAGGATATATTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCATGATTCA-TT-
1 CAAAGAGCAGGATGCATTTTATTTCCTT-TTTT-CC-TTTGTCCTCAAAAAGCAGGACACATTTA
**
2065845 -TTT-CTTTTTCCTTTGTC-C
63 ATTTCCTTTTTCCTTAATCTC
* * * * * * * *
2065863 TCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCCCTTCTAGTTCTCAAAGAGCATGACGCACT
1 -CAAAGAGCAGGATGCATTTTATTTCCTT-TTTT-CCTT-T-GTCCTCAAAAAGCAGGACACATT
* *
2065928 TCATTTCCTTCTTTTCCCTTCTAGT-TC
61 TAATTTCC-T-TTTT-CC-T-TAATCTC
* * * * *
2065955 TCAAAGAGCAGGACGCACTTTA-TTCTTCTTTTTCCTTTGTCCTTAAAAAGTAGGACACATTTAA
1 -CAAAGAGCAGGATGCATTTTATTTCCT-TTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAA
**
2066019 TTTCCTTTTTCCTTTGTCTC
64 TTTCCTTTTTCCTTAATCTC
* * ** *
2066039 CAAAGGGCATGATGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAGGAGCAGGAC-CTATTTCAT
1 CAAAGAGCAGGATGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACAC-ATTTAAT
2066103 TCTCC-TTTTCCTTAATC-C
65 T-TCCTTTTTCCTTAATCTC
2066121 TCAAAGAGCAGGATGC
1 -CAAAGAGCAGGATGC
2066137 TCTCTTCCTT
Statistics
Matches: 221, Mismatches: 34, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
81 2 0.01
82 34 0.15
83 92 0.42
84 12 0.05
85 2 0.01
86 7 0.03
87 2 0.01
88 24 0.11
89 5 0.02
90 6 0.03
91 9 0.04
92 26 0.12
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (83 bp):
CAAAGAGCAGGATGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAATT
TCCTTTTTCCTTAATCTC
Found at i:2066762 original size:20 final size:20
Alignment explanation
Indices: 2066737--2066808 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
2066727 TCACAATTTA
2066737 TATCGATACATTATTCATTG
1 TATCGATACATTATTCATTG
*
2066757 TATCGATACATTGTTCATTG
1 TATCGATACATTATTCATTG
* * *
2066777 TATCAATACATTTTTCAATG
1 TATCGATACATTATTCATTG
2066797 TATCGATACATT
1 TATCGATACATT
2066809 CAGGCATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
TATCGATACATTATTCATTG
Found at i:2069194 original size:79 final size:78
Alignment explanation
Indices: 2069103--2069564 Score: 421
Period size: 79 Copynumber: 5.9 Consensus size: 78
2069093 TTTTCATCTC
* * * *
2069103 GGGGATACTCCAA-CCCTAGTTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCTAA
1 GGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACCGATTTTTCATAATCGAGGATACTCCAA
2069167 TCCCGTTATTTTCGA
65 -CCCGTTATTTTCGA
* * * * * ** * *
2069182 GGGGATACTCCAAACCTGACTTTATTTCTAAAATATTGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGAGGATACTCCAAC
* *
2069247 CCTGTTATTTTGGC
66 CC-GTTATTTTCGA
* ** * * * * * * *
2069261 GGGGACACTCCAACCCCGACCTTATTTCTAAAGCATCAATTTTCCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGAGGATACTCCAA-
*
2069326 CCCGTTATTTTTGA
65 CCCGTTATTTTCGA
* * *
2069340 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGA-TTCTCTATAAT-AAGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTC-ATAATCGA-GGATACTCCA
*
2069403 ACCTTGTTATTTTCGA
64 ACC-CGTTATTTTCGA
* * * *
2069419 GGAGATACTTCAACCCCGATTTTATTTTCAAAACACCGA-TTCTCTATAATC-AGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTC-ATAATCGA-GGATACTCCA
**
2069482 ACCTTATTATTTTCGA
64 ACC-CGTTATTTTCGA
* * * * * *
2069498 GGAGATACTTCAACCTCGATTTTATTTCCAGAACACCGATTTTCCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGAGGATACTCCAAC
2069563 CC
66 CC
2069565 CGTTGTTATC
Statistics
Matches: 326, Mismatches: 48, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
78 8 0.02
79 309 0.95
80 9 0.03
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCGAGGATACTCCAAC
CCGTTATTTTCGA
Found at i:2074448 original size:165 final size:162
Alignment explanation
Indices: 2073958--2074545 Score: 573
Period size: 165 Copynumber: 3.6 Consensus size: 162
2073948 CATCGGATTA
* * * * * * **
2073958 AAATTTTTAAAATTCATCAAATATTATTATCT-AATCACCATTTAATCT-GTTTTGAAATTTTCA
1 AAATTTTTAATATTCATCAAATATCATCATTTAAATCA-TATTAAAT-TAGTTTTGAAAAATTCA
* * * * *
2074021 TTTATTTTCATTAGTTTTTCAATTTTTCCTTAAAA-TTTCTTTTTTTCCAAAAAACTAAGTTTTC
64 TTTATTTTCATGAGTTTTTCAATTTTTTCTTAAAATTTTCTATTTTT--GAAAAACTGAGTTTT-
2074085 TATTCTATAAATGTTTTTCGAGGGGGTTTTTCTTGGTTC
126 TATTCTATAAATGTTTTT-GA-GGGGTTTTTCTTGGTTC
* * *
2074124 AAAGTTTTTAATATTCATCGAATATCATCATTTTAAATCATAATAAATCAGTTTTGAAAAATTCA
1 AAA-TTTTTAATATTCATCAAATATCATCA-TTTAAATCATATTAAATTAGTTTTGAAAAATTCA
* * * * * *
2074189 TTTATTTTCATGAGTTTTTCATTTTTTTCTTGAAATTCTCTTATTTCTGAAAAACCGAGTTTTCA
64 TTTATTTTCATGAGTTTTTCAATTTTTTCTTAAAATTTTC-TATTTTTGAAAAACTGAGTTTTTA
2074254 TTCTATAAATGTTTTTGAAGGGGTTTTTCTTGGTTC
128 TTCTATAAATGTTTTTG-AGGGGTTTTTCTTGGTTC
*
2074290 AAATTTTTCAATATTCATCAAATATCACCATTTAAATCATATTAAATTAGTTTTGAAAAATTCAT
1 AAATTTTT-AATATTCATCAAATATCATCATTTAAATCATATTAAATTAGTTTTGAAAAATTCAT
* * *
2074355 TTA-TTTCATAAGTTTTTTC-CTTTTTTCTTAAAATTTTGCTATTTTTGAAAAATTGAGGTTTTT
65 TTATTTTCATGAG-TTTTTCAATTTTTTCTTAAAATTTT-CTATTTTTGAAAAACTGA-GTTTTT
* ** *
2074418 ATTCTATAAATGTTTTT-AGGATGATTTTTCTCAGTCTA
127 ATTCTATAAATGTTTTTGAGG--GGTTTTTCTTGGT-TC
* ** * * ** **
2074456 AAATTTTT-ATATTTCATCTAATATTGTCATTGAATTCCCATTAAATTAGTTTCAAAAAATTCAA
1 AAATTTTTAATA-TTCATCAAATATCATCATTTAAATCATATTAAATTAGTTTTGAAAAATTC-A
*
2074520 TTTATTTT-ATGAG-TTTTGAATTTTTT
64 TTTATTTTCATGAGTTTTTCAATTTTTT
2074546 TGTGTTTATT
Statistics
Matches: 353, Mismatches: 51, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
163 3 0.01
164 44 0.12
165 126 0.36
166 61 0.17
167 43 0.12
168 63 0.18
169 8 0.02
170 5 0.01
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (162 bp):
AAATTTTTAATATTCATCAAATATCATCATTTAAATCATATTAAATTAGTTTTGAAAAATTCATT
TATTTTCATGAGTTTTTCAATTTTTTCTTAAAATTTTCTATTTTTGAAAAACTGAGTTTTTATTC
TATAAATGTTTTTGAGGGGTTTTTCTTGGTTC
Found at i:2075048 original size:10 final size:10
Alignment explanation
Indices: 2075033--2075100 Score: 93
Period size: 10 Copynumber: 6.8 Consensus size: 10
2075023 AACAAAGTGG
2075033 AGAAAAAAAA
1 AGAAAAAAAA
2075043 AGAAAAAAAA
1 AGAAAAAAAA
2075053 AGAAAGAAAAA
1 AGAAA-AAAAA
*
2075064 AGAAAGAAAA
1 AGAAAAAAAA
*
2075074 A-AAAAAGAA
1 AGAAAAAAAA
*
2075083 AGAAAAAGAA
1 AGAAAAAAAA
2075093 AGAAAAAA
1 AGAAAAAA
2075101 GAGAGAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
9 7 0.13
10 35 0.67
11 10 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:2075051 original size:11 final size:11
Alignment explanation
Indices: 2075033--2075119 Score: 86
Period size: 11 Copynumber: 7.8 Consensus size: 11
2075023 AACAAAGTGG
2075033 AGAAAAAAAAA
1 AGAAAAAAAAA
*
2075044 GAAAAAAAAAGAA
1 -AGAAAAAAA-AA
*
2075057 AGAAAAAAGAA
1 AGAAAAAAAAA
2075068 AGAAAAAAAAA
1 AGAAAAAAAAA
*
2075079 AG-AAAGAAAA
1 AGAAAAAAAAA
*
2075089 AGAAAGAAAAA
1 AGAAAAAAAAA
* * *
2075100 AGAGAGAAAAT
1 AGAAAAAAAAA
2075111 AGAAAAAAA
1 AGAAAAAAA
2075120 CAAACTAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
10 9 0.15
11 36 0.58
12 15 0.24
13 2 0.03
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:2075054 original size:25 final size:24
Alignment explanation
Indices: 2075033--2075100 Score: 109
Period size: 26 Copynumber: 2.8 Consensus size: 24
2075023 AACAAAGTGG
2075033 AGAAAAAAAAAGAAAAAAAAAGAA
1 AGAAAAAAAAAGAAAAAAAAAGAA
2075057 AGAAAAAAGAAAGAAAAAAAAAAGAA
1 AGAAAAAA-AAAG-AAAAAAAAAGAA
*
2075083 AGAAAAAGAAAGAAAAAA
1 AGAAAAAAAAAGAAAAAA
2075101 GAGAGAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
24 14 0.34
25 8 0.20
26 19 0.46
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AGAAAAAAAAAGAAAAAAAAAGAA
Found at i:2075081 original size:36 final size:36
Alignment explanation
Indices: 2075035--2075109 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
2075025 CAAAGTGGAG
2075035 AAAAAAAAAGAAAAAAAAAGAAAGAAAAAAGAAAGA
1 AAAAAAAAAGAAAAAAAAAGAAAGAAAAAAGAAAGA
* *
2075071 AAAAAAAAAGAAAGAAAAAGAAAGAAAAAAGAGAGA
1 AAAAAAAAAGAAAAAAAAAGAAAGAAAAAAGAAAGA
2075107 AAA
1 AAA
2075110 TAGAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (36 bp):
AAAAAAAAAGAAAAAAAAAGAAAGAAAAAAGAAAGA
Found at i:2075108 original size:15 final size:15
Alignment explanation
Indices: 2075041--2075102 Score: 85
Period size: 15 Copynumber: 4.3 Consensus size: 15
2075031 GGAGAAAAAA
2075041 AAAGAAAAAA-AAAG
1 AAAGAAAAAAGAAAG
2075055 AAAGAAAAAAGAAAG
1 AAAGAAAAAAGAAAG
*
2075070 AAAAAAAAAAGAAAG
1 AAAGAAAAAAGAAAG
*
2075085 AAA-AAGAAAGAAA-
1 AAAGAAAAAAGAAAG
2075098 AAAGA
1 AAAGA
2075103 GAGAAAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.07
14 20 0.45
15 21 0.48
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAG
Found at i:2075108 original size:25 final size:24
Alignment explanation
Indices: 2075033--2075100 Score: 109
Period size: 25 Copynumber: 2.8 Consensus size: 24
2075023 AACAAAGTGG
*
2075033 AGAAAAAAAAAGAAAAAAAAAGAA
1 AGAAAAAGAAAGAAAAAAAAAGAA
2075057 AGAAAAAAGAAAGAAAAAAAAAAGAA
1 AG-AAAAAGAAAG-AAAAAAAAAGAA
2075083 AGAAAAAGAAAGAAAAAA
1 AGAAAAAGAAAGAAAAAA
2075101 GAGAGAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
24 8 0.20
25 19 0.46
26 14 0.34
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AGAAAAAGAAAGAAAAAAAAAGAA
Found at i:2075119 original size:1 final size:1
Alignment explanation
Indices: 2075035--2075100 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
2075025 CAAAGTGGAG
* * * * * * * * *
2075035 AAAAAAAAAGAAAAAAAAAGAAAGAAAAAAGAAAGAAAAAAAAAAGAAAGAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2075100 A
1 A
2075101 GAGAGAAAAT
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:2075119 original size:10 final size:9
Alignment explanation
Indices: 2075036--2075119 Score: 80
Period size: 10 Copynumber: 8.8 Consensus size: 9
2075026 AAAGTGGAGA
2075036 AAAAAAAAG
1 AAAAAAAAG
2075045 AAAAAAAAAG
1 -AAAAAAAAG
2075055 AAAGAAAAAAG
1 -AA-AAAAAAG
2075066 AAAGAAAAA-
1 AAA-AAAAAG
2075075 AAAAAGAAAG
1 AAAAA-AAAG
2075085 AAAAAGAAAG
1 AAAAA-AAAG
*
2075095 AAAAAAGAG
1 AAAAAAAAG
* *
2075104 AGAAAATAG
1 AAAAAAAAG
2075113 AAAAAAA
1 AAAAAAA
2075120 CAAACTAAAC
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
8 2 0.03
9 22 0.34
10 34 0.52
11 7 0.11
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:2076274 original size:142 final size:142
Alignment explanation
Indices: 2076011--2076275 Score: 372
Period size: 142 Copynumber: 1.9 Consensus size: 142
2076001 TTATTTTATC
* *
2076011 ATTAAATAAAAATTATTAACTTAATTTTTCAAGACTCCTAATATTCCTATAGTTTTCTATAAGGG
1 ATTAAATAAAAATTATTAACTTAATTTCTCAAGACTCCTAATATTCCTATAGTTTTCTATAAGAG
*
2076076 TATAAAAATCTTCAAAACCTTTCATATCTTTTCGGTTCTCAATTAAGGTTCAAAATGAATATTCT
66 TATAAAAATCTTCAAAACCTTTCATATCTTTTCGGTTCTCAATTAAGGTACAAAATGAATATTCT
2076141 TAAAAATTAAAA
131 TAAAAATTAAAA
* * * *
2076153 ATTAAATAAAAATTATTATCTTAATTTCTCAAGATTTCTAATATTCCTATGGTTTGTC-ATAAGA
1 ATTAAATAAAAATTATTAACTTAATTTCTCAAGACTCCTAATATTCCTATAGTTT-TCTATAAGA
* * * * * * *
2076217 GTATAGAAATTTTTAAAACTTTTCGTATCTTTTCGGTTTTTC-ATTAAGGTACGAAATGA
65 GTATAAAAATCTTCAAAACCTTTCATATCTTTTCGG-TTCTCAATTAAGGTACAAAATGA
2076276 GATTTTAGAA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
142 101 0.94
143 6 0.06
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (142 bp):
ATTAAATAAAAATTATTAACTTAATTTCTCAAGACTCCTAATATTCCTATAGTTTTCTATAAGAG
TATAAAAATCTTCAAAACCTTTCATATCTTTTCGGTTCTCAATTAAGGTACAAAATGAATATTCT
TAAAAATTAAAA
Found at i:2077301 original size:20 final size:20
Alignment explanation
Indices: 2077257--2077314 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2077247 ATTTCAACGA
***
2077257 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
2077277 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
2077297 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
2077315 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:2077371 original size:13 final size:13
Alignment explanation
Indices: 2077353--2077377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2077343 ATCACTTAAA
2077353 TGTATCGATACAT
1 TGTATCGATACAT
2077366 TGTATCGATACA
1 TGTATCGATACA
2077378 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2077442 original size:52 final size:52
Alignment explanation
Indices: 2077386--2077514 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2077376 CACTGATCTT
*
2077386 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
* **
2077438 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
2077490 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2077515 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:2080986 original size:22 final size:22
Alignment explanation
Indices: 2080961--2081004 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2080951 AATAATAAGA
2080961 TACCCTTCTCGAAATAAAAATC
1 TACCCTTCTCGAAATAAAAATC
*
2080983 TACCCTTTTCGAAATAAAAATC
1 TACCCTTCTCGAAATAAAAATC
2081005 GAGAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (22 bp):
TACCCTTCTCGAAATAAAAATC
Found at i:2081013 original size:22 final size:22
Alignment explanation
Indices: 2080969--2081013 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2080959 GATACCCTTC
* **
2080969 TCGAAATAAAAATCTACCCTTT
1 TCGAAATAAAAATCGACAATTT
*
2080991 TCGAAATAAAAATCGAGAATTT
1 TCGAAATAAAAATCGACAATTT
2081013 T
1 T
2081014 TATAATTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (22 bp):
TCGAAATAAAAATCGACAATTT
Found at i:2084915 original size:20 final size:20
Alignment explanation
Indices: 2084892--2084964 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
2084882 ACAATTCAAA
2084892 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
2084912 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
2084933 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2084953 GTATCGATACAT
1 GTATCGATACAT
2084965 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2084936 original size:21 final size:21
Alignment explanation
Indices: 2084910--2084985 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
2084900 ACATGTTGCA
2084910 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
2084931 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
2084949 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
2084972 ATGTATCGATACAT
1 ATGTATCGATACAT
2084986 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:2084943 original size:41 final size:41
Alignment explanation
Indices: 2084892--2084985 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2084882 ACAATTCAAA
* *
2084892 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2084933 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2084974 GTATCGATACAT
1 GTATCGATACAT
2084986 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2085042 original size:13 final size:13
Alignment explanation
Indices: 2085024--2085049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2085014 TACAGCAAGT
2085024 ATGTATCGATACA
1 ATGTATCGATACA
2085037 ATGTATCGATACA
1 ATGTATCGATACA
2085050 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2088650 original size:11 final size:12
Alignment explanation
Indices: 2088621--2088664 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2088611 TTTTTGGCTA
2088621 AAAAAACAAAAG
1 AAAAAACAAAAG
*
2088633 CAAAAAAAAAAAAG
1 --AAAAAACAAAAG
*
2088647 AAAAAACAATAG
1 AAAAAACAAAAG
2088659 AAAAAA
1 AAAAAA
2088665 GAGAACCAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (12 bp):
AAAAAACAAAAG
Found at i:2090103 original size:28 final size:28
Alignment explanation
Indices: 2090063--2090134 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2090053 GGAATAAAGC
** *
2090063 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2090091 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2090119 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2090135 TCGATTATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2090192 original size:52 final size:52
Alignment explanation
Indices: 2090123--2090560 Score: 292
Period size: 52 Copynumber: 8.3 Consensus size: 52
2090113 AAATAACGAG
*
2090123 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * ** * *
2090175 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
*
2090228 -TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * * * * * * * *
2090279 ATTGGAGTATCCCCGATTAAAGGAGAAATTGGT-GTTGTGAAAATGAAACCGGG
1 GTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * * * *
2090332 GTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* **** * * *
2090383 GTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTATGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
* * *
2090438 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
*
2090492 GTTGGAGTATCCCCGATTAT-AGAAAATT--AATGTTTT-GAAAGTAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTAT-TTTTGGAAA-TAAAATCGGA
* *
2090543 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
2090561 GTGGAGAATT
Statistics
Matches: 298, Mismatches: 60, Indels: 57
0.72 0.14 0.14
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 5 0.02
51 80 0.27
52 81 0.27
53 60 0.20
54 35 0.12
55 17 0.06
56 3 0.01
57 3 0.01
58 5 0.02
59 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:2090255 original size:104 final size:104
Alignment explanation
Indices: 2090124--2090563 Score: 426
Period size: 104 Copynumber: 4.2 Consensus size: 104
2090114 AATAACGAGG
* *
2090124 TTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
* *
2090189 GATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
66 GATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
*
2090228 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
* * *
2090293 GATTAAAGGAGAAATTGGTGTTGTGAAAATGAAACCGGGG
66 GATTAAAGGA-AAATTGGTGTTTTGAAAATAAAACCGGGA
* * * * * *
2090333 TTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTAT-CCC
* * ** * ** ** * *
2090397 TCAGAAATAACGG--GGTTGGAGTATCCCCGATGAT-TAA-CGGGG
65 -C-G-ATTAAAGGAAAATTGGTGT-T--TTGAAAATAAAACCGGGA
* *
2090439 TTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 TTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
* ** * *
2090504 CCGATTATA-GAAAATTAATGTTTTGAAAGTAAAATC-GGA
64 CCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
* *
2090543 GTTGGAATATCCTCGATTGTG
1 -TTGGAGTATCCCCGATTGTG
2090564 GAGAATTGAG
Statistics
Matches: 269, Mismatches: 51, Indels: 31
0.77 0.15 0.09
Matches are distributed among these distances:
103 3 0.01
104 102 0.38
105 83 0.31
106 32 0.12
107 10 0.04
108 13 0.05
109 26 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (104 bp):
TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
GATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
Found at i:2090442 original size:27 final size:28
Alignment explanation
Indices: 2090379--2090454 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2090369 AAAATAAAGT
*
2090379 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2090407 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2090434 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2090455 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2092935 original size:13 final size:13
Alignment explanation
Indices: 2092917--2092942 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2092907 TACAAGATCC
2092917 ATGTATCGATACA
1 ATGTATCGATACA
2092930 ATGTATCGATACA
1 ATGTATCGATACA
2092943 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2092959 original size:33 final size:32
Alignment explanation
Indices: 2092897--2092962 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
2092887 AAAATTTCCA
***
2092897 AATGTATCGATACAAGATCCATGTATCGATAC
1 AATGTATCGATACAAGAAAAATGTATCGATAC
2092929 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACA-AGAAAAATGTATCGATAC
2092962 A
1 A
2092963 TTTTCCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (32 bp):
AATGTATCGATACAAGAAAAATGTATCGATAC
Found at i:2093007 original size:19 final size:18
Alignment explanation
Indices: 2092983--2093049 Score: 90
Period size: 18 Copynumber: 3.9 Consensus size: 18
2092973 CAGTAGCTAA
2092983 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2093002 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2093017 -T-TGTATCGATACAAAC
1 TTATGTATCGATACAAAC
2093033 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2093050 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 14 0.33
19 14 0.33
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2093023 original size:13 final size:13
Alignment explanation
Indices: 2093005--2093029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2092995 ACAATACTTA
2093005 TGTATCGATACAT
1 TGTATCGATACAT
2093018 TGTATCGATACA
1 TGTATCGATACA
2093030 AACTTATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2093038 original size:31 final size:32
Alignment explanation
Indices: 2092986--2093047 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 32
2092976 TAGCTAATTA
2092986 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
2093018 TGTATCGATACAA-ACTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
2093048 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:2093128 original size:21 final size:21
Alignment explanation
Indices: 2093104--2093160 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2093094 CATTTGTAGG
2093104 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2093125 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2093146 ATGTATCGATACATT
1 ATGTATCGATACATT
2093161 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2093171 original size:1 final size:1
Alignment explanation
Indices: 2093165--2093224 Score: 93
Period size: 1 Copynumber: 60.0 Consensus size: 1
2093155 TACATTTAAA
***
2093165 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2093225 CAAAACACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.03, C:0.02, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Done.