Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 79 of 199
Found at i:28374093 original size:88 final size:88
Alignment explanation
Indices: 28374001--28374171 Score: 263
Period size: 88 Copynumber: 1.9 Consensus size: 88
28373991 CCCATAAAAA
*
28374001 CTAACCCCTAAACCTTATTGAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCT
1 CTAACCCCTAAACCTTATTGAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCT
*
28374066 AACCCTAAC-CCGACTCCAAATCC
66 AA-CCTAACACCGAATCCAAATCC
* * * **
28374089 CTAACCCCTAAACTTTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAATTCT
1 CTAACCCCTAAACCTTATTGAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCT
28374154 AACCTAACACCGAATCCA
66 AACCTAACACCGAATCCA
28374172 TAAACCTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
87 6 0.08
88 69 0.92
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (88 bp):
CTAACCCCTAAACCTTATTGAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCT
AACCTAACACCGAATCCAAATCC
Found at i:28374239 original size:21 final size:22
Alignment explanation
Indices: 28374172--28374239 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 22
28374162 ACCGAATCCA
*
28374172 TAAACCTTAAATCCCTAACTCT
1 TAAACCTTAAATCCCTAACCCT
* * *
28374194 T-AACCTTTAACCCCTAACCCA
1 TAAACCTTAAATCCCTAACCCT
*
28374215 TAAACCTTAAATCAC-AACCCT
1 TAAACCTTAAATCCCTAACCCT
28374236 TAAA
1 TAAA
28374240 TCAGAATCCC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 26 0.70
22 11 0.30
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAACCTTAAATCCCTAACCCT
Found at i:28374725 original size:41 final size:41
Alignment explanation
Indices: 28374680--28374955 Score: 338
Period size: 41 Copynumber: 6.7 Consensus size: 41
28374670 AAATGTTTTT
* ** *
28374680 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
28374721 GCGGCACTTTTCCAAAAACGCCGCTAAAGATTTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
** * *
28374762 GCGATGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCATTC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
28374803 GTGGCGCTATTTT-AAAAACGCCGCTAAAGATTTGAGCATTC
1 GCGGCGCT-TTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
28374844 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGGGCATTC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
28374885 GCGACGCTTTTTCAAAAATGCTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
28374926 GCGACGCTTTTTTAAAGAACGCCGCTAAAG
1 GCGGCGCTTTTTCAAA-AACGCCGCTAAAG
28374956 CCCCAAAAGG
Statistics
Matches: 202, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
40 4 0.02
41 183 0.91
42 15 0.07
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:28374901 original size:123 final size:122
Alignment explanation
Indices: 28374680--28374955 Score: 381
Period size: 123 Copynumber: 2.2 Consensus size: 122
28374670 AAATGTTTTT
*
28374680 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCACTTTTCCAAAAACGCCGC
1 GCGGCGCTTTTT-AAAAACGCCGCTAAAGACCCGAGCATTAGCGGCACTTTTCCAAAAACGCCGC
* * *
28374745 TAAAGATTTGAGCATTAGCGATGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCATTC
65 TAAAGATCTGAGCATTAGCGACGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCATTA
* *** * * *
28374803 GTGGCGCTATTTTAAAAACGCCGCTAAAGATTTGAGCATTCGCGGCGCTTTTTCAAAAACGCCGC
1 GCGGCGCT-TTTTAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCACTTTTCCAAAAACGCCGC
* * *
28374868 TAAAGATCTGGGCATTCGCGACGCTTTTTCAAAAATGCTGCTAAAGATCTGAGCATTA
65 TAAAGATCTGAGCATTAGCGACGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCATTA
*
28374926 GCGACGCTTTTTTAAAGAACGCCGCTAAAG
1 GCGGCGC-TTTTTAAA-AACGCCGCTAAAG
28374956 CCCCAAAAGG
Statistics
Matches: 134, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
123 116 0.87
124 18 0.13
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (122 bp):
GCGGCGCTTTTTAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCACTTTTCCAAAAACGCCGCT
AAAGATCTGAGCATTAGCGACGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCATTA
Found at i:28375467 original size:19 final size:20
Alignment explanation
Indices: 28375430--28375466 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
28375420 ACTATTATGT
28375430 TCTTTCGAGCTTTTTTTTTG
1 TCTTTCGAGCTTTTTTTTTG
28375450 TCTTT-GAG-TTTTTTTTT
1 TCTTTCGAGCTTTTTTTTT
28375467 TATTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.05, C:0.11, G:0.14, T:0.70
Consensus pattern (20 bp):
TCTTTCGAGCTTTTTTTTTG
Found at i:28381682 original size:16 final size:17
Alignment explanation
Indices: 28381661--28381704 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
28381651 TTTGGTTCGC
*
28381661 TGTAAT-GTAATATAGG
1 TGTAATAGTAATAGAGG
28381677 TGTAATAG-AATAGAGG
1 TGTAATAGTAATAGAGG
*
28381693 CGTAATAGTAAT
1 TGTAATAGTAAT
28381705 TCAATTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.32
Consensus pattern (17 bp):
TGTAATAGTAATAGAGG
Found at i:28382417 original size:10 final size:11
Alignment explanation
Indices: 28382402--28382431 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
28382392 ATATATATAT
28382402 TTTTATTTTC-
1 TTTTATTTTCA
28382412 TTTTATTTTCA
1 TTTTATTTTCA
28382423 TTTTATTTT
1 TTTTATTTT
28382432 TCCTAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:28383034 original size:3 final size:3
Alignment explanation
Indices: 28383026--28383084 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
28383016 TGTTTTTAAA
* *
28383026 ATT ATT ATT ATT ATT ATC ATTT ATT ATC ATT ATT ATT A-T ATT ATAT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT-T
*
28383072 ATT ATC ATT ATT A
1 ATT ATT ATT ATT A
28383085 CTGTTACTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:28383079 original size:24 final size:25
Alignment explanation
Indices: 28383029--28383084 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
28383019 TTTTAAAATT
*
28383029 ATTATTATTATTATCATTTATTATC
1 ATTATTATTATTATCATATATTATC
*
28383054 ATTATTATTA-TATTATATATTATC
1 ATTATTATTATTATCATATATTATC
28383078 ATTATTA
1 ATTATTA
28383085 CTGTTACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTATTATTATCATATATTATC
Found at i:28385333 original size:19 final size:20
Alignment explanation
Indices: 28385289--28385333 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
28385279 AACGTCTCTT
*
28385289 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
28385308 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
28385327 TATGCAT
1 TATGCAT
28385334 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:28387990 original size:51 final size:49
Alignment explanation
Indices: 28387878--28387971 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
28387868 TAAAAGGTGG
* * * *
28387878 GACCAATGTGAAAGCTTACAAAGGGCGCTTTGAGTAAAAAAAAAAAAGA
1 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAGA
28387927 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAAAA
1 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAAAA
28387972 TGGAGAGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (49 bp):
GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAAAAAAGA
Found at i:28388000 original size:51 final size:49
Alignment explanation
Indices: 28387878--28388008 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 49
28387868 TAAAAGGTGG
* * * *
28387878 GACCAATGTGAAAGCTTACAAAGGGCGCTTTGAGTAAAAAAAAAAAAGA
1 GACCAAGGTGAAAACCTACAAAGGGCGCCTTGAGTAAAAAAAAAAAAGA
* * *
28387927 GACCAAGGTGAAAGCCTACAAAGGGAGCCTTGAGTAAAAAAAAAATGGAGA
1 GACCAAGGTGAAAACCTACAAAGGGCGCCTTGAGTAAAAAAAAAA--AAGA
* * *
28387978 GGCTAAGGTGAAAA-CTCGCAAAGGGCGCCTT
1 GACCAAGGTGAAAACCT-ACAAAGGGCGCCTT
28388009 AGACCAAAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 41 0.59
50 2 0.03
51 26 0.38
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.15
Consensus pattern (49 bp):
GACCAAGGTGAAAACCTACAAAGGGCGCCTTGAGTAAAAAAAAAAAAGA
Found at i:28389378 original size:89 final size:88
Alignment explanation
Indices: 28389273--28389996 Score: 539
Period size: 89 Copynumber: 8.1 Consensus size: 88
28389263 ATCGAAGACC
* * *
28389273 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATC
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
28389338 GGCGTGAAGTAGATCAAAGTCAAA
66 GGCGTGAAGTAGATCAAAGT-AAA
* * * *
28389362 AAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-AA-AAATGGCAAATCTTATATTCATGTA
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAA--GCAGATCTTGTCTTCATGTA
* * **
28389425 TTGGCGTGAAGTAGATCAGAGATACT
64 TCGGCGTGAAGTAGATCAAAG-TAAA
* * *
28389451 AGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTA-C
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
* **
28389515 TGGCGTGAAGTAGATCAGAGATACT
66 -GGCGTGAAGTAGATCAAAG-TAAA
*** * * * * * ***
28389540 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATA-C
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
* * *
28389603 TGGTGGTGGAGTAGATCGAAG-AAA
66 -GG-CGTGAAGTAGATCAAAGTAAA
*** * * * * *
28389627 GTAGATCTTGTCTTCATGTA-TCGG-CGTGAAGTAGATCAAAGTCAA-CAAATCTTGCCTTCCCA
1 --AGATCTTGTCTTCCCATACT-GGTGGTGAAGTAGATCGAAG-AAAGCAGATCTTGTCTT--CA
* * *
28389689 TACTAGT-GGC--GAAGTAGATCGAAGAAAA
60 T-GTA-TCGGCGTGAAGTAGATCAAAGTAAA
*** * * *
28389717 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AGAGATA-CTAGATCTAGTCTTCATGT
1 -AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGA-AGAAAGC-AGATCTTGTCTTCATGT
**
28389779 A-CTGGCGTGAAGTAGATCAAAGATACC
63 ATC-GGCGTGAAGTAGATCAAAG-TAAA
* * *
28389806 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATC
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
28389871 GGCGTGAAGTAGATCAAAGTCAACA
66 GGCGTGAAGTAGATCAAAGT-AA-A
* * * *
28389896 A-ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCATGTAT
1 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAA-AGCAGATCTTGTCTTCATGTAT
* * ** *
28389959 TGGTGTGAAGTAGATTGAAGAAAA
65 CGGCGTGAAGTAGATCAAAGTAAA
28389983 CAGATCTTGTCTTC
1 -AGATCTTGTCTTC
28389997 ATGTATTGGC
Statistics
Matches: 519, Mismatches: 82, Indels: 68
0.78 0.12 0.10
Matches are distributed among these distances:
86 5 0.01
87 8 0.02
88 78 0.15
89 409 0.79
90 11 0.02
91 4 0.01
92 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (88 bp):
AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATC
GGCGTGAAGTAGATCAAAGTAAA
Found at i:28389687 original size:222 final size:222
Alignment explanation
Indices: 28389317--28390020 Score: 1021
Period size: 222 Copynumber: 3.2 Consensus size: 222
28389307 TCGAAGAAAG
** * *
28389317 TAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAAG-TCAAAAAATCTTGTCTTCCCATA
1 TAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAGAT-ACCAGATCTTGTCTCCCCATA
* * * * * *
28389380 CTGGTGGTGAAGTAGATC-AA-AAATGGCAAATCTTATATTCATGTATTGGCGTGAAGTAGATCA
64 CTGGTGGTGGAGTAGATCGAAGAAA--GTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCA
* *
28389443 GAG--ATACTAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTC
127 AAGTCA-AC-AAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTC
28389506 TTCATGTACTGGCGTGAAGTAGATCAGAGATAC
190 TTCATGTACTGGCGTGAAGTAGATCAGAGATAC
28389539 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
1 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
28389604 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
66 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
*
28389669 CAACAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATG
131 CAACAAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATG
28389734 TACTGGCGTGAAGTAGATCAGAGATAC
196 TACTGGCGTGAAGTAGATCAGAGATAC
*
28389761 TAGATCTAGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
1 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
28389826 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
66 GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
* * ** * * *
28389891 CAACAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCAT
131 CAACAAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA-AACAGATCTTGTCTTCAT
* * * *
28389955 GTATTGGTGTGAAGTAGAT-TGAAGAAAAC
195 GTACTGGCGTGAAGTAGATCAG-AG-ATAC
* *
28389984 -AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAA
1 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
28390021 GAACGGTAGA
Statistics
Matches: 444, Mismatches: 29, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
221 3 0.01
222 428 0.96
223 9 0.02
224 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (222 bp):
TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACT
GGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGT
CAACAAATCTTGCCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATG
TACTGGCGTGAAGTAGATCAGAGATAC
Found at i:28389840 original size:311 final size:310
Alignment explanation
Indices: 28389270--28389973 Score: 952
Period size: 311 Copynumber: 2.3 Consensus size: 310
28389260 TGGATCGAAG
28389270 ACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
1 ACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
* * *
28389335 ATCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAA
66 ATCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATCAA
* * * *
28389400 AAATGGCAAATCTTATATTCATGTATTGGCGTGAAGTAGATCAGAGATACTAGATCTTGCCTTCC
131 AAA-GACAAATCTTATATTCATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGCCTTCA
* * * **
28389465 CATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGAT
195 CATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTCCACATACTGGCGTGAAGTAGAT
*
28389530 C-AGAGATACTAGATCTTGTCTTCATGTA-CTGGCGTGAAGTAGATCAAAGAT-
260 CGA-AGAAACTAGATCTTGTCTTCATGTATC-GGCGTGAAGTAGATCAAAG-TC
28389581 ACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
1 ACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
*
28389646 ATCGGCGTGAAGTAGATCAAAGTCAACAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATCGA
66 ATCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATC-A
* * * *
28389711 AGAAA-ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGTCTTC
130 A-AAAGACAAATCTTATATTCATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGCCTTC
** * * * * * *
28389775 ATGTACTGG-CGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAG
194 ACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTCCACATACTGG-CGTGAAGTAG
*
28389839 ATCGAAGAAAGTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGTC
258 ATCGAAGAAACTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGTC
* * * * * * * * *
28389892 AACAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AATGGCAAATCTTATATTCATG
1 ACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAA-AGTAGATCTTGTCTTCATG
* *
28389956 TATTGGTGTGAAGTAGAT
65 TATCGGCGTGAAGTAGAT
28389974 TGAAGAAAAC
Statistics
Matches: 348, Mismatches: 38, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
310 38 0.11
311 303 0.87
312 4 0.01
313 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (310 bp):
ACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGT
ATCGGCGTGAAGTAGATCAAAGTCAAAAAATCTTGCCTTCCCATACTAGTGGCGAAGTAGATCAA
AAAGACAAATCTTATATTCATGTACTGGCGTGAAGTAGATCAGAGATACTAGATCTAGCCTTCAC
ATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTCCACATACTGGCGTGAAGTAGATC
GAAGAAACTAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAAGTC
Found at i:28389997 original size:133 final size:131
Alignment explanation
Indices: 28389289--28390020 Score: 584
Period size: 133 Copynumber: 5.5 Consensus size: 131
28389279 TGTCTCCCCA
* **
28389289 TACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATC
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATC
* *** * ** * *
28389353 AAAGTCAAA-AAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAAATGGCAAATCTTATA
65 AAAG--AAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAATAACAAATCTTGTC
28389417 TTCATG
126 TTCATG
* * * * *** * *
28389423 TATTGG-CGTGAAGTAGATC--AGAGATACTAGATCTTGCCTTCCCATACTGGTGGCGAAGTAGA
1 TACTGGTGGTGAAGTAGATCGAAGA-AAAC-AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGA
* * *
28389485 TCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGAT-ACTAGATCTTGT
63 TCAAAG-AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA-AAATAAC-AAATCTTGT
28389549 CTTCATG
125 CTTCATG
* * * * * *** * *
28389556 TACTGG-CGTGAAGTAGATCAAAGATACCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
* * * *
28389620 GAAGAAAGTAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAAGTCAACAAATCTTGCCT
65 AAAGAAA-CAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAAT-AACAAATCTTGTCT
***
28389684 TCCCA
127 TCATG
* *
28389689 TACTAGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
* * * * * *
28389754 GAGATACTAGATCTAGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTCC
66 AAGAAAC-AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA-ATAACAAATCTTGTCTTC
***
28389819 CCA
129 ATG
* **
28389822 TACTGGTGGTGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATC
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATC
* * *** * ** * *
28389886 AAAGTCAACAAATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAAATGGCAAATCTTATAT
65 AAAG-AAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAATAACAAATCTTGTCT
28389951 TCATG
127 TCATG
* * * *
28389956 TATTGGT-GTGAAGTAGATTGAAGAAAACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCA
1 TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
28390020 A
66 A
28390021 GAACGGTAGA
Statistics
Matches: 485, Mismatches: 91, Indels: 45
0.78 0.15 0.07
Matches are distributed among these distances:
131 3 0.01
132 10 0.02
133 355 0.73
134 111 0.23
135 6 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (131 bp):
TACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
AAGAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAATAACAAATCTTGTCTTCAT
G
Found at i:28390971 original size:10 final size:11
Alignment explanation
Indices: 28390956--28390985 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
28390946 TATATATATT
28390956 TTTTATTTTC-
1 TTTTATTTTCA
28390966 TTTTATTTTCA
1 TTTTATTTTCA
28390977 TTTTATTTT
1 TTTTATTTT
28390986 TCCTAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:28391585 original size:3 final size:3
Alignment explanation
Indices: 28391579--28391635 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
28391569 TTTTTTTTAA
* *
28391579 ATT ATT ATT ATT ATT ATT ATT ATC ATTT ATT ATC ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT AT-T ATT
*
28391626 ATC ATT ATT A
1 ATT ATT ATT A
28391636 CTGTTACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 41 0.89
4 5 0.11
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:28391610 original size:16 final size:16
Alignment explanation
Indices: 28391582--28391635 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
28391572 TTTTTAAATT
*
28391582 ATTATTA-TTATTATT
1 ATTATTATTTATTATC
*
28391597 ATTATCATTTATTATC
1 ATTATTATTTATTATC
*
28391613 ATTATTATATATTATC
1 ATTATTATTTATTATC
28391629 ATTATTA
1 ATTATTA
28391636 CTGTTACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 6 0.18
16 28 0.82
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTATTTATTATC
Found at i:28391610 original size:19 final size:19
Alignment explanation
Indices: 28391579--28391635 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
28391569 TTTTTTTTAA
28391579 ATTAT-TATTATTATTATT
1 ATTATATATTATTATTATT
*
28391597 ATTATCAT-TTATTATCATT
1 ATTAT-ATATTATTATTATT
*
28391616 ATTATATATTATCATTATT
1 ATTATATATTATTATTATT
28391635 A
1 A
28391636 CTGTTACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 7 0.21
19 25 0.76
20 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATATTATTATTATT
Found at i:28391792 original size:22 final size:21
Alignment explanation
Indices: 28391745--28391787 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
28391735 CAAACATATA
*
28391745 TATATACATTTTTTTGAATTAT
1 TATAAACATTTTTTT-AATTAT
28391767 TATAAACATTTTTTT-ATTAT
1 TATAAACATTTTTTTAATTAT
28391787 T
1 T
28391788 CTATATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
TATAAACATTTTTTTAATTAT
Found at i:28392843 original size:18 final size:18
Alignment explanation
Indices: 28392820--28392857 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28392810 TTATTATTAA
*
28392820 ATATAATTTAATCAAAAT
1 ATATAATTTAATAAAAAT
28392838 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
28392856 AT
1 AT
28392858 TCTTATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:28392957 original size:18 final size:18
Alignment explanation
Indices: 28392928--28392973 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
28392918 TTATTATTAA
28392928 ATATAA-TTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
28392945 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
28392963 AT-TAATATTAA
1 ATATAAT-TTAA
28392974 ATATTCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:28393121 original size:121 final size:121
Alignment explanation
Indices: 28392852--28393503 Score: 1200
Period size: 121 Copynumber: 5.4 Consensus size: 121
28392842 AATTTAATAA
28392852 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
*
28392917 ATTATTATTAAATATAA-TTAATAAAAATATATAATTTAATAAAATTATTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
28392972 AAATATTCTTATATGAATTTATTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
28393037 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
28393093 AAATATTATGATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
* *
28393158 TTTACTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
28393214 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATGCTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
28393279 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
28393335 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATGCTATAAAATATAA-TTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
* *
28393399 ATTATTATTAAATATAATTTAATAAAAATATATAATTTTATAAAATTCTTAAAATT
66 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
28393455 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAA
28393504 GATAATGTAT
Statistics
Matches: 516, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
120 192 0.37
121 324 0.63
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (121 bp):
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
Found at i:28393399 original size:362 final size:362
Alignment explanation
Indices: 28392852--28393503 Score: 1216
Period size: 362 Copynumber: 1.8 Consensus size: 362
28392842 AATTTAATAA
28392852 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
28392917 ATTATTATTAAATATAATTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTCTT
66 ATTATTATTAAATATAATTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTCTT
*
28392982 ATATGAATTTATTAAAATCATAATATATAATACTATAAAATATAATTTTAACATAATTATTATTA
131 ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATAATTATTATTA
*
28393047 AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTATGATATGAATT
196 AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATTAAATATTATGATATGAATT
28393112 TACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATATTTACTATTAAATATAATT
261 TACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATATTTACTATTAAATATAATT
28393177 TAATAAAAATATATAATTTAATAAAATTCTTAATATT
326 TAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
28393214 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATGCTATAAAATATAATTTTAACATA
1 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
*
28393279 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCT
66 ATTATTATTAAATATAA-TTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTCT
*
28393344 TATATGAATTTACTAAAATCATAATATATAATGCTATAAAATATAA-TTTAACATAATTATTATT
130 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATAATTATTATT
* * *
28393408 AAATATAATTTAATAAAAATATATAATTTTATAAAATTCTTAAAATTAAATATTCTTATATGAAT
195 AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATTAAATATTATGATATGAAT
28393473 TTACTAAAATCATAATATATAATACTATAAA
260 TTACTAAAATCATAATATATAATACTATAAA
28393504 GATAATGTAT
Statistics
Matches: 281, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
362 191 0.68
363 90 0.32
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (362 bp):
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATA
ATTATTATTAAATATAATTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTCTT
ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATAATTATTATTA
AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATTAAATATTATGATATGAATT
TACTAAAATCATAATATATAATACTATAAAATATAATTTTAACATATTTACTATTAAATATAATT
TAATAAAAATATATAATTTAATAAAATTCTTAATATT
Found at i:28403125 original size:26 final size:27
Alignment explanation
Indices: 28403073--28403125 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
28403063 CCATTTACAA
* *
28403073 AAATATACAGGCCCAAATACATTACCC
1 AAATATACAAGCCCAAATACATAACCC
28403100 AAAT-TACAAGCCCAAACTAC-TAACCC
1 AAATATACAAGCCCAAA-TACATAACCC
28403126 TAGTCCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.45, C:0.32, G:0.06, T:0.17
Consensus pattern (27 bp):
AAATATACAAGCCCAAATACATAACCC
Found at i:28415801 original size:94 final size:90
Alignment explanation
Indices: 28415640--28415969 Score: 300
Period size: 88 Copynumber: 3.7 Consensus size: 90
28415630 TAAAATCACT
* * * * *
28415640 ATAGCGAATCTCATCTCCCTGAAGTTGCAGT-GAGGCAGATTTAAGCTACAGATCTTA-CACCCT
1 ATAGCGAATCTTATCTCCTTGAAGTTGCAGTGGA-GCAGATTAAAGCTACAAATCTTATCTCCC-
* *
28415703 TGAAGTCGCAATGG-GACGGATTGAATCTACC
64 TGAAGTCGCAATGGAG-CAGATT-AA---AAC
* * * *
28415734 ATAGCGAATCTTATCTTCTTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTCATCTTCCTG
1 ATAGCGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTG
* * *
28415799 AAGTTGTAGTGGAGCAGATTAAAAC
66 AAGTCGCAATGGAGCAGATTAAAAC
*
28415824 -TA-CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAA-CTACAAATCTTATCTCCCT
1 ATAGCGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAATCTTATCTCCCT
* ** * *
28415886 AAAGTTACAGTGGAGCAGATTAAAGC
65 GAAGTCGCAATGGAGCAGATTAAAAC
* * * *
28415912 -TA-CAAATCTTATCTTCC-TGAAGTTGTAGTAGAGCAGATTGAAGCTACAAATCTTATCT
1 ATAGCGAATCTTATC-TCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
28415970 TGTTGAAGTT
Statistics
Matches: 204, Mismatches: 26, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
87 2 0.01
88 121 0.59
89 8 0.04
90 2 0.01
93 2 0.01
94 63 0.31
95 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (90 bp):
ATAGCGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTG
AAGTCGCAATGGAGCAGATTAAAAC
Found at i:28415803 original size:44 final size:44
Alignment explanation
Indices: 28415740--28416219 Score: 384
Period size: 44 Copynumber: 10.6 Consensus size: 44
28415730 TACCATAGCG
* *
28415740 AATCTTATCTTCTTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
28415784 AATCTCATCTTCCTGAAGTTGTAGTGGAGCAGATTAAAACTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
28415828 AATCTTATC-TCCTTGAAGTTGCAGTGGAGCAGATTGAAA-CTACA
1 AATCTTATCTTCC-TGAAGTTGCAGTGGAGCAGATT-AAAGCTACA
* * *
28415872 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
28415916 AATCTTATCTTCCTGAAGTTGTAGTAGAGCAGATTGAAGCTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
** * *
28415960 AATCTTATCTTGTTGAAGTTGCAGTGGAGAAGATTGAAG-TGACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCT-ACA
* * *
28416004 AATCTTATGCCT-CTGAAGTTACAGTGG-GTC-GAATTAAATCTACCA
1 AATCTTAT-CTTCCTGAAGTTGCAGTGGAG-CAG-ATTAAAGCTA-CA
* * * *
28416049 TAGCGAGTTTTAT-TTCCCTGAAGTTGCAGTGGAATAGATTAAATCTACAAGTTACA
1 -A---A-TCTTATCTT-CCTGAAGTTGCAGTGG---AG--CAGAT-TA-AAGCTACA
* * *
28416105 AATCTTATCTCCCTGAACTTGCAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * ** * **
28416149 AGTCCTATCACCCTAAAGTTGCAGTGGAATAGATTGAAA-CTACA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTACA
* * *
28416193 ATTCCTATAC-CCCTGAAGTTGCAGTGG
1 AATCTTAT-CTTCCTGAAGTTGCAGTGG
28416220 GTTAGAATGA
Statistics
Matches: 357, Mismatches: 51, Indels: 56
0.77 0.11 0.12
Matches are distributed among these distances:
43 9 0.03
44 272 0.76
45 14 0.04
46 4 0.01
48 3 0.01
49 1 0.00
50 19 0.05
51 20 0.06
52 2 0.01
54 1 0.00
55 4 0.01
56 4 0.01
57 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
Found at i:28415930 original size:132 final size:132
Alignment explanation
Indices: 28415740--28416219 Score: 452
Period size: 132 Copynumber: 3.5 Consensus size: 132
28415730 TACCATAGCG
* * * *
28415740 AATCTTATCTTCTTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTTCCTGAAGTTG
*
28415805 TAGTGGAGCAGATTAAAACTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTA
66 CAGTGGAGCAGATTAAAACTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTA
28415870 CA
131 CA
28415872 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTTCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTTCCTGAAGTTG
* * * * ** * *
28415937 TAGTAGAGCAGATTGAAGCTACAAATCTTATCTTGTTGAAGTTGCAGTGGAGAAGATTG-AAGTG
66 CAGTGGAGCAGATTAAAACTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACT-
28416001 ACA
130 ACA
* * * *
28416004 AATCTTATGC-CTCTGAAGTTACAGTGG-GTC-GAATTAAATCTACCATAGCGAGTTTTAT-TTC
1 AATCTTAT-CTCCCTAAAGTTACAGTGGAG-CAG-ATTAAAGCTA-CA-A---A-TCTTATCTT-
** * *
28416065 CCTGAAGTTGCAGTGGAATAGATTAAATCTACAAGTTACAAATCTTATCTCCCTGAACTTGCAGT
56 CCTGAAGTTGCAGTGGAGCAGATTAAA---AC----TACAAATCTTATCTCCTTGAAGTTGCAGT
*
28416130 GGAGCAGATTGAAGCTACA
114 GGAGCAGATTGAAACTACA
* * * * ** * * *
28416149 AGTCCTATCACCCTAAAGTTGCAGTGGAATAGATTGAAA-CTACAATTCCTATAC-CCCTGAAGT
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATT-AAAGCTACAAATCTTAT-CTTCCTGAAGT
28416212 TGCAGTGG
64 TGCAGTGG
28416220 GTTAGAATGA
Statistics
Matches: 284, Mismatches: 39, Indels: 43
0.78 0.11 0.12
Matches are distributed among these distances:
131 5 0.02
132 150 0.53
133 3 0.01
134 1 0.00
137 3 0.01
138 27 0.10
139 20 0.07
141 1 0.00
143 1 0.00
144 3 0.01
145 64 0.23
146 6 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (132 bp):
AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTTCCTGAAGTTG
CAGTGGAGCAGATTAAAACTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTA
CA
Found at i:28416235 original size:44 final size:44
Alignment explanation
Indices: 28416123--28416235 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 44
28416113 CTCCCTGAAC
** * *
28416123 TTGCAGTGGAGCAGATTGAAGCTACAAGTCCTATCACCCTAAAG
1 TTGCAGTGGAATAGAATGAAACTACAAGTCCTATCACCCTAAAG
* * *
28416167 TTGCAGTGGAATAGATTGAAACTACAATTCCTAT-ACCCCTGAAG
1 TTGCAGTGGAATAGAATGAAACTACAAGTCCTATCA-CCCTAAAG
** *
28416211 TTGCAGTGGGTTAGAATGAGACTAC
1 TTGCAGTGGAATAGAATGAAACTAC
28416236 TTTAGAAAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 58 0.98
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
TTGCAGTGGAATAGAATGAAACTACAAGTCCTATCACCCTAAAG
Found at i:28417692 original size:24 final size:24
Alignment explanation
Indices: 28417660--28417711 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
28417650 TTACAATTCT
* *
28417660 TTTTATTTATACGTTTTATT-TTA
1 TTTTATTTATACCTATTATTATTA
*
28417683 TTTTATTTTATCCCTATTATTATTA
1 TTTTA-TTTATACCTATTATTATTA
28417708 TTTT
1 TTTT
28417712 TATTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 12 0.50
25 7 0.29
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTATTTATACCTATTATTATTA
Found at i:28417875 original size:3 final size:3
Alignment explanation
Indices: 28417859--28417901 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
28417849 TTGTTGCCCC
* *
28417859 TAT TAT TAC CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28417902 TATTTTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28422075 original size:33 final size:33
Alignment explanation
Indices: 28422033--28422095 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
28422023 GGAAAGATAC
28422033 AAAGAATTATTATGGAAGCGCCCTCATCACAGA
1 AAAGAATTATTATGGAAGCGCCCTCATCACAGA
* *
28422066 AAAGAATTATTATGGAAGTGCCCTTATCAC
1 AAAGAATTATTATGGAAGCGCCCTCATCAC
28422096 GGAATCCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (33 bp):
AAAGAATTATTATGGAAGCGCCCTCATCACAGA
Found at i:28425113 original size:44 final size:42
Alignment explanation
Indices: 28424997--28425123 Score: 102
Period size: 44 Copynumber: 2.9 Consensus size: 42
28424987 AAGGCTTGTA
* *
28424997 CAATGCCAACGTCCCAGACATGGTCTTAC-CTGTAATCACATAT
1 CAATGCCAACGTCCTAGAC-TGGTCTTACAC-GTAATCACAAAT
*
28425040 CAATGCC-ACTGTCCTCA-A-TAGAGTTTTACACGTAAATCACAAAT
1 CAATGCCAAC-GTCCT-AGACT-G-GTCTTACACGT-AATCACAAAT
*
28425084 CGATGCCAACGTCCTAGACGTGGTCTTACACGATAA-CACA
1 CAATGCCAACGTCCTAGAC-TGGTCTTACACG-TAATCACA
28425124 CAATAGAATC
Statistics
Matches: 68, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 25 0.37
44 34 0.50
45 4 0.06
46 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (42 bp):
CAATGCCAACGTCCTAGACTGGTCTTACACGTAATCACAAAT
Found at i:28426350 original size:22 final size:23
Alignment explanation
Indices: 28426317--28426360 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
28426307 GAACATGTTG
28426317 AATTTTACTTAATTTT-ATAATA
1 AATTTTACTTAATTTTGATAATA
28426339 AATTTTGA-TTAATTTTGATAAT
1 AATTTT-ACTTAATTTTGATAAT
28426361 TTTCAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
AATTTTACTTAATTTTGATAATA
Found at i:28430094 original size:21 final size:21
Alignment explanation
Indices: 28430056--28430095 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28430046 CTAAAGTTTG
**
28430056 GTTTCTTGCAAATTAAGTCAA
1 GTTTCTTGCAAAACAAGTCAA
28430077 GTTTCTTGCAAAACAAGTC
1 GTTTCTTGCAAAACAAGTC
28430096 GCTTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
GTTTCTTGCAAAACAAGTCAA
Found at i:28436765 original size:17 final size:16
Alignment explanation
Indices: 28436731--28436761 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28436721 AATTAATTTA
*
28436731 AATTAACTAATTTTTC
1 AATTAAATAATTTTTC
28436747 AATTAAATAATTTTT
1 AATTAAATAATTTTT
28436762 TCAACCCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAAATAATTTTTC
Found at i:28436900 original size:4 final size:4
Alignment explanation
Indices: 28436891--28436927 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
28436881 TATTCAAACT
28436891 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA -TAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
28436928 TAAAAAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:28440605 original size:33 final size:34
Alignment explanation
Indices: 28440568--28440639 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 34
28440558 TTTAGTCTAA
*
28440568 TTATTTATT-TTA-ATATTGTGTATATT-TTATATG
1 TTATTTATTATTACATATTAT-TAT-TTATTATATG
*
28440601 TTA-TTATTATTACATTTTATTATTTATTATATG
1 TTATTTATTATTACATATTATTATTTATTATATG
28440634 TTATTT
1 TTATTT
28440640 TTAAATACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
32 7 0.21
33 19 0.58
34 7 0.21
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (34 bp):
TTATTTATTATTACATATTATTATTTATTATATG
Found at i:28440629 original size:17 final size:17
Alignment explanation
Indices: 28440598--28440642 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
28440588 TATATTTTAT
28440598 ATGTTATTA-TTATTAC
1 ATGTTATTATTTATTAC
* *
28440614 ATTTTATTATTTATTAT
1 ATGTTATTATTTATTAC
28440631 ATGTTATT-TTTA
1 ATGTTATTATTTA
28440643 AATACAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (17 bp):
ATGTTATTATTTATTAC
Found at i:28442606 original size:2 final size:2
Alignment explanation
Indices: 28442599--28442641 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28442589 TAATCTAACA
28442599 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28442641 T
1 T
28442642 AACCTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28451864 original size:31 final size:32
Alignment explanation
Indices: 28451816--28451884 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
28451806 CAACCCAATT
*
28451816 TTTATTTTTATTATTATTTT-TTTT-TCTTTAC
1 TTTATTTTTACTATTATTTTATTTTAT-TTTAC
28451847 TTTATTTATTACT-TTATTTTATTTTATTTTAC
1 TTTATTT-TTACTATTATTTTATTTTATTTTAC
28451879 -TTATTT
1 TTTATTT
28451885 GGATATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
31 20 0.59
32 13 0.38
33 1 0.03
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (32 bp):
TTTATTTTTACTATTATTTTATTTTATTTTAC
Found at i:28451867 original size:17 final size:16
Alignment explanation
Indices: 28451815--28451871 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
28451805 GCAACCCAAT
*
28451815 TTTTATTTTTATTATTA
1 TTTTATTTTTACT-TTA
28451832 TTTT-TTTTT-CTTTA
1 TTTTATTTTTACTTTA
*
28451846 CTTTATTTATTACTTTA
1 TTTTATTT-TTACTTTA
28451863 TTTTATTTT
1 TTTTATTTT
28451872 ATTTTACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 6 0.18
15 4 0.12
16 8 0.24
17 16 0.47
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTTTACTTTA
Found at i:28452912 original size:17 final size:17
Alignment explanation
Indices: 28452890--28452926 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28452880 CCTAAAGCAT
28452890 TAAAAAAAGAAAAAAAA
1 TAAAAAAAGAAAAAAAA
*
28452907 TAAAAAAAGGAAAAAAA
1 TAAAAAAAGAAAAAAAA
28452924 TAA
1 TAA
28452927 TTTGGGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (17 bp):
TAAAAAAAGAAAAAAAA
Found at i:28459626 original size:42 final size:42
Alignment explanation
Indices: 28459595--28459689 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
28459585 GGCCAGGAAT
28459595 ATGGGCATGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
1 ATGGGCATGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
* * ** * *
28459637 ATGGGCGTGTGCCCAAGCCCTGTGAGTTACACGGGCAAAGAC
1 ATGGGCATGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
28459679 ATGGGCATGTG
1 ATGGGCATGTG
28459690 TCCAGGTCGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.16
Consensus pattern (42 bp):
ATGGGCATGTGCCCAAGCCATGTGAGCCACACGAGCAAGGAC
Found at i:28461378 original size:813 final size:813
Alignment explanation
Indices: 28459812--28461444 Score: 3221
Period size: 813 Copynumber: 2.0 Consensus size: 813
28459802 GAATAGGATC
28459812 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
1 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
28459877 TTATCTGAATTTGATCGTAAGAGGACTATATAATGCTTTAAGACTGATATATGGATGATATATGC
66 TTATCTGAATTTGATCGTAAGAGGACTATATAATGCTTTAAGACTGATATATGGATGATATATGC
28459942 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
131 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
*
28460007 AACCTAAGTGAGTAGGACCTGTTAGAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
196 AACCTAAGTGAGTAGGACCTGTCAGAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
28460072 ACGATATGTATTCTATTAAGTTTGTTGGTACACCTCTGCATTGCTTTGTTAATGAAGAATATGTG
261 ACGATATGTATTCTATTAAGTTTGTTGGTACACCTCTGCATTGCTTTGTTAATGAAGAATATGTG
28460137 AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
326 AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
28460202 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
391 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
*
28460267 TGTTATTTAGAGATGGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
456 TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
28460332 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
521 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
28460397 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
586 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
28460462 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
651 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
28460527 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
716 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
28460592 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
781 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
28460625 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
1 TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
*
28460690 TTATCTGAATTTGATCGTAAGAGGACTATATGATGCTTTAAGACTGATATATGGATGATATATGC
66 TTATCTGAATTTGATCGTAAGAGGACTATATAATGCTTTAAGACTGATATATGGATGATATATGC
28460755 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
131 GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
28460820 AACCTAAGTGAGTAGGACCTGTCAGAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
196 AACCTAAGTGAGTAGGACCTGTCAGAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
28460885 ACGATATGTATTCTATTAAGTTTGTTGGTACACCTCTGCATTGCTTTGTTAATGAAGAATATGTG
261 ACGATATGTATTCTATTAAGTTTGTTGGTACACCTCTGCATTGCTTTGTTAATGAAGAATATGTG
*
28460950 AACATATTAGACTGATTATTATTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
326 AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
28461015 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
391 GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
28461080 TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
456 TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
28461145 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
521 CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
28461210 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
586 CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
28461275 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
651 TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
28461340 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
716 CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
28461405 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
781 ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
*
28461438 TGCATCT
1 TGAATCT
28461445 GCATAAACAT
Statistics
Matches: 815, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
813 815 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (813 bp):
TGAATCTTATTTTTTTAGGTTGTGAGTTTTTCCCAACACGTGCACTGACCTCCACAATGTATTTA
TTATCTGAATTTGATCGTAAGAGGACTATATAATGCTTTAAGACTGATATATGGATGATATATGC
GATATCTAAATGTCTTAGACTGATGATGAACAACTTGTGATCTATACGTATATCTATTATGTTTG
AACCTAAGTGAGTAGGACCTGTCAGAATGTAATGTCCTATTGTCTATGTGTGCAAATTATCAGGT
ACGATATGTATTCTATTAAGTTTGTTGGTACACCTCTGCATTGCTTTGTTAATGAAGAATATGTG
AACATATTAGACTGATTATTACTGATTCTAATTTATAACCCTGTATGTGACTTAATGGCAAATCT
GATTTGGTCCGTTGAGGTTTGATAAGTCTGTTTTACAAAACATGGACTCCCATACTTACTTATTC
TGTTATTTAGAGATAGCATGACTTACATGTTCATTACTCTGATTCTGCATAAGCATACCATGGCA
CACTACATAAGACTTGGGTTGATGTAAAAGGAGGAAGTTTCTGGCAGTTTAATGATATGCATTAT
CTAGTGGTTTATCCACACTTCTGTTCTGACAATTCAACTGTACTATAATGGCTTGACCACATATA
TTCGATCTGGGAGTTTTAACTGCAAAATACTGGTGGCACTATCCACAGTTATCTGTTGGTGTGAT
CTGGCTGGACGAGTTCTGGGGGAACTCTATTTCGGTGTATAGCGAAGTTGGGTAGGATGTTTTTG
ATGAATTTGCATTCTGATCTGTTTGAAAAATAT
Found at i:28463266 original size:5 final size:5
Alignment explanation
Indices: 28463256--28463288 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
28463246 TAATAAGAAG
28463256 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28463289 CATGTTGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28465096 original size:44 final size:44
Alignment explanation
Indices: 28465023--28465381 Score: 242
Period size: 44 Copynumber: 8.0 Consensus size: 44
28465013 ACTCTCTGTG
* *
28465023 GTAGATTTAATCTGAC-CCACTGCAACTTCAGAGG-TATAGGATTT
1 GTAGCTTTAATCT-ACTCCACTGCAACTTCAG-GGATATAAGATTT
* * * * *
28465067 GTCGCTTTAATCTACTCCATTGCAGCTTCAGCGAGATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGATATAAGATTT
* * * *
28465111 GTAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATTAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGATATAAGATTT
* *
28465155 GTAGCTTTAATATGCTCCACTGCAACTTCAGGGATATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGATATAAGATTT
* * * *
28465199 GTAGCTTTAA-CTTGCTCCACTACAACTTCAAGGAAATAAGATTCGCCAT
1 GTAGCTTTAATC-TACTCCACTGCAACTTCAGGGATATAAGATT-----T
* * * *
28465248 GGTAACTTTAATCCGACT-CACTGCAACTTTAGGG-TATAGGATATT
1 -GTAGCTTTAAT-CTACTCCACTGCAACTTCAGGGATATAAGAT-TT
* * * ** * * * * *
28465293 TTAGCTTCAATTTGTTCTACTACAACTTCAAGAAGATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGATATAAGATTT
* * * ** * *
28465337 GTGGCTTTAATCTGCTCTACTATAGCTTCAGGGAGATAAGATTT
1 GTAGCTTTAATCTACTCCACTGCAACTTCAGGGATATAAGATTT
28465381 G
1 G
28465382 CCTTGGTAAC
Statistics
Matches: 248, Mismatches: 53, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
43 4 0.02
44 204 0.82
45 7 0.03
49 7 0.03
50 23 0.09
51 2 0.01
52 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (44 bp):
GTAGCTTTAATCTACTCCACTGCAACTTCAGGGATATAAGATTT
Found at i:28465241 original size:88 final size:87
Alignment explanation
Indices: 28465039--28465381 Score: 280
Period size: 88 Copynumber: 3.8 Consensus size: 87
28465029 TTAATCTGAC
* * * * * * * *
28465039 CCACTGCAACTTCAGAGG-TATAGGATTTGTCGCTTTAATCTACTCCATTGCAGCTTCAGCGAGA
1 CCACTACAACTTCA-AGGAAATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGA
*
28465103 TAAGATTTGTAGTTTTAATCTGCT
65 TAAGATTTGTAGCTTTAAT-TGCT
* * * * * *
28465127 CCACTGCAACTTCAGGGAGATTAGATTTGTAGCTTTAATATGCTCCACTGCAACTTCAGGGATAT
1 CCACTACAACTTCAAGGAAATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
28465192 AAGATTTGTAGCTTTAACTTGCT
66 AAGATTTGTAGCTTTAA-TTGCT
* * *
28465215 CCACTACAACTTCAAGGAAATAAGATTCGCCATGGTAACTTTAATCCGACT-CACTGCAACTTTA
1 CCACTACAACTTCAAGGAAATAAGATT-----T-GTAGCTTTAATCTG-CTCCACTGCAACTTCA
* * * * *
28465279 GGG-TATAGGATATTTTAGCTTCAATTTGTT
59 GGGAGATAAGAT-TTGTAGCTTTAA-TTGCT
* * * ** *
28465309 CTACTACAACTTCAA-GAAGATAAGATTTGTGGCTTTAATCTGCTCTACTATAGCTTCAGGGAGA
1 CCACTACAACTTCAAGGAA-ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGA
28465373 TAAGATTTG
65 TAAGATTTG
28465382 CCTTGGTAAC
Statistics
Matches: 205, Mismatches: 37, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
87 4 0.02
88 118 0.58
89 8 0.04
93 11 0.05
94 62 0.30
95 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (87 bp):
CCACTACAACTTCAAGGAAATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
AAGATTTGTAGCTTTAATTGCT
Found at i:28466773 original size:41 final size:41
Alignment explanation
Indices: 28466723--28466980 Score: 408
Period size: 41 Copynumber: 6.3 Consensus size: 41
28466713 AATTCATCAT
* *
28466723 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28466764 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28466805 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28466846 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28466887 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
28466928 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
28466969 ATTCATATCACC
1 ATTCAGATCACC
28466981 AATTCCAAAC
Statistics
Matches: 197, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 197 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:28466866 original size:82 final size:82
Alignment explanation
Indices: 28466729--28466980 Score: 495
Period size: 82 Copynumber: 3.1 Consensus size: 82
28466719 TCATATTCGG
28466729 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
28466794 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
28466811 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
28466876 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
*
28466893 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
28466958 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
28466975 ATCACC
1 ATCACC
28466981 AATTCCAAAC
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 169 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:28467216 original size:19 final size:19
Alignment explanation
Indices: 28467192--28467228 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28467182 TTGTTCGATC
*
28467192 CACACATATATATATATTA
1 CACACATATACATATATTA
28467211 CACACATATACATATATT
1 CACACATATACATATATT
28467229 CGCACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (19 bp):
CACACATATACATATATTA
Found at i:28474485 original size:41 final size:41
Alignment explanation
Indices: 28474435--28474692 Score: 408
Period size: 41 Copynumber: 6.3 Consensus size: 41
28474425 AATTCATCAT
* *
28474435 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28474476 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28474517 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28474558 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
28474599 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
28474640 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
28474681 ATTCATATCACC
1 ATTCAGATCACC
28474693 AATTCCAAAC
Statistics
Matches: 197, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 197 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:28474578 original size:82 final size:82
Alignment explanation
Indices: 28474441--28474692 Score: 495
Period size: 82 Copynumber: 3.1 Consensus size: 82
28474431 TCATATTCGG
28474441 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
28474506 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
28474523 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
28474588 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
*
28474605 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
28474670 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
28474687 ATCACC
1 ATCACC
28474693 AATTCCAAAC
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 169 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:28474928 original size:19 final size:19
Alignment explanation
Indices: 28474904--28474940 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28474894 TTGTTCGATC
*
28474904 CACACATATATATATATTA
1 CACACATATACATATATTA
28474923 CACACATATACATATATT
1 CACACATATACATATATT
28474941 CGCACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (19 bp):
CACACATATACATATATTA
Found at i:28489840 original size:6 final size:6
Alignment explanation
Indices: 28489831--28489860 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28489821 TAATAATGAC
28489831 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
28489861 CCTATCGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:28490039 original size:2 final size:2
Alignment explanation
Indices: 28490034--28490062 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28490024 TGATTCTTGG
28490034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28490063 AGTCAACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28491373 original size:21 final size:23
Alignment explanation
Indices: 28491345--28491402 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
28491335 TTAACTTTAA
28491345 TTATAATTATTTATTAAA-AAAC
1 TTATAATTATTTATTAAATAAAC
*
28491367 TT-TAATTA-TAATTAAATAAAC
1 TTATAATTATTTATTAAATAAAC
28491388 TTATCAA-TATTTATT
1 TTAT-AATTATTTATT
28491403 TATAAATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 5 0.17
23 6 0.20
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATAATTATTTATTAAATAAAC
Found at i:28499205 original size:21 final size:21
Alignment explanation
Indices: 28499166--28499205 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28499156 ACGTTATCGA
* **
28499166 TTTTTAATTTAATTGATTAAT
1 TTTTTAATTAAATAAATTAAT
28499187 TTTTTAATTAAATAAATTA
1 TTTTTAATTAAATAAATTA
28499206 CTAAAAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTTAATTAAATAAATTAAT
Found at i:28502024 original size:16 final size:15
Alignment explanation
Indices: 28502003--28502032 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28501993 AATTAAATAC
28502003 AACAACATTCATTAAT
1 AACAACATT-ATTAAT
28502019 AACAACATTATTAA
1 AACAACATTATTAA
28502033 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
AACAACATTATTAAT
Found at i:28508361 original size:8 final size:8
Alignment explanation
Indices: 28508337--28508371 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
28508327 AAATATTGTA
28508337 TTTATTAT
1 TTTATTAT
28508345 CTCTTATTAT
1 -T-TTATTAT
28508355 TTTATTAT
1 TTTATTAT
28508363 TTTATTAT
1 TTTATTAT
28508371 T
1 T
28508372 ACGAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 16 0.64
9 2 0.08
10 7 0.28
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTATTAT
Found at i:28512769 original size:4 final size:4
Alignment explanation
Indices: 28512760--28512787 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
28512750 ATAAATACAG
28512760 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
28512788 TCAGTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:28514863 original size:21 final size:21
Alignment explanation
Indices: 28514839--28514880 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28514829 ATTTTCAAAT
*
28514839 TAATTGCACATTGATTTGTAA
1 TAATTGCACATTAATTTGTAA
*
28514860 TAATTGCATATTAATTTGTAA
1 TAATTGCACATTAATTTGTAA
28514881 ATTTTTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (21 bp):
TAATTGCACATTAATTTGTAA
Found at i:28516356 original size:32 final size:32
Alignment explanation
Indices: 28516320--28516390 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
28516310 TTGTTGGATT
*
28516320 TTGAAATTATTATGTTTTAAATTTGTTAGACA
1 TTGAAATTATTATGTTTTAAACTTGTTAGACA
* * *
28516352 TTGAATTTATTATGTTTTAAACTTGTTGGATA
1 TTGAAATTATTATGTTTTAAACTTGTTAGACA
28516384 TTGAAAT
1 TTGAAAT
28516391 GATTGAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (32 bp):
TTGAAATTATTATGTTTTAAACTTGTTAGACA
Found at i:28519283 original size:19 final size:19
Alignment explanation
Indices: 28519247--28519294 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
28519237 TTAGTAAAAT
*
28519247 ATTTAATATTACAATTTAA
1 ATTTAATAATACAATTTAA
*
28519266 TTTTAATAATA-AATTTTAA
1 ATTTAATAATACAA-TTTAA
*
28519285 AATTAATAAT
1 ATTTAATAAT
28519295 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAATAATACAATTTAA
Found at i:28529341 original size:23 final size:24
Alignment explanation
Indices: 28529292--28529349 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
28529282 ATAAAATATT
28529292 TAAAATATTTTAATATAATTTTAATA
1 TAAAATA--TTAATATAATTTTAATA
*
28529318 TAAAATATTAATTTAA-TTTAATA
1 TAAAATATTAATATAATTTTAATA
28529341 TAAAATATT
1 TAAAATATT
28529350 TTATTTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 16 0.52
24 8 0.26
26 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATATTAATATAATTTTAATA
Found at i:28529355 original size:24 final size:24
Alignment explanation
Indices: 28529292--28529429 Score: 93
Period size: 24 Copynumber: 5.3 Consensus size: 24
28529282 ATAAAATATT
*
28529292 TAAAATATTTTAATATAATTTTAATA
1 TAAAATATTTT-ATTTAA-TTTAATA
*
28529318 TAAAATA-TTAATTTAATTTAATA
1 TAAAATATTTTATTTAATTTAATA
*
28529341 TAAAATATTTTATTTCAAAATATAATTTGAAA
1 TAAAATATTTTATTT---AATTTAA--T---A
*
28529373 TAAAATATTTTATATAATTTAATA
1 TAAAATATTTTATTTAATTTAATA
*
28529397 TAAAA-ATAATTATATT-ATTTAATAA
1 TAAAATAT-TTTAT-TTAATTTAAT-A
28529422 TAAAATAT
1 TAAAATAT
28529430 GATTAAATTA
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
23 16 0.18
24 28 0.31
25 9 0.10
26 9 0.10
27 7 0.08
29 7 0.08
32 15 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
TAAAATATTTTATTTAATTTAATA
Found at i:28529441 original size:26 final size:25
Alignment explanation
Indices: 28529371--28529443 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 25
28529361 TATAATTTGA
* *
28529371 AATAAAATATTTTATATAATTTAAT
1 AATAAAATATATTATATTATTTAAT
28529396 -ATAAAA-ATAATTATATTATTTAAT
1 AATAAAATAT-ATTATATTATTTAAT
*
28529420 AATAAAATATGATTAAATTATTTA
1 AATAAAATAT-ATTATATTATTTA
28529444 TTTTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.05
24 19 0.46
25 6 0.15
26 14 0.34
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (25 bp):
AATAAAATATATTATATTATTTAAT
Found at i:28530462 original size:32 final size:32
Alignment explanation
Indices: 28530426--28530490 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28530416 CACCCAAGTA
28530426 AGATTTATTTAAATTAGATTGTATATCCACAC
1 AGATTTATTTAAATTAGATTGTATATCCACAC
28530458 AGATTTATTTAAATTAGATTGTATATCCACAC
1 AGATTTATTTAAATTAGATTGTATATCCACAC
28530490 A
1 A
28530491 ACATTGATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (32 bp):
AGATTTATTTAAATTAGATTGTATATCCACAC
Found at i:28532240 original size:13 final size:13
Alignment explanation
Indices: 28532222--28532246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28532212 TGTCAAATAA
28532222 TAAAAAATATTTT
1 TAAAAAATATTTT
28532235 TAAAAAATATTT
1 TAAAAAATATTT
28532247 CAAGCAATAC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAAAATATTTT
Found at i:28532291 original size:20 final size:20
Alignment explanation
Indices: 28532266--28532313 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
28532256 CAATATATAT
28532266 ATCAATTTTTTTTTCAAAA-A
1 ATCAATTTTTTTTT-AAAAGA
**
28532286 ATCAATTCATTTTTAAAAGA
1 ATCAATTTTTTTTTAAAAGA
28532306 ATC-ATTTT
1 ATCAATTTT
28532314 CCGAATAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (20 bp):
ATCAATTTTTTTTTAAAAGA
Found at i:28534683 original size:20 final size:20
Alignment explanation
Indices: 28534654--28534707 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
28534644 CGTATATCCT
* *
28534654 AATTTTATTTGATTCTAATC
1 AATTTCATTTAATTCTAATC
*
28534674 AATTTCATTTAATTTTAATC
1 AATTTCATTTAATTCTAATC
28534694 AAATTT-ATTTAATT
1 -AATTTCATTTAATT
28534708 GCTCCTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 25 0.83
21 5 0.17
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (20 bp):
AATTTCATTTAATTCTAATC
Found at i:28535137 original size:18 final size:18
Alignment explanation
Indices: 28535110--28535147 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28535100 TTTATTTTAT
28535110 TTTATATATAAATATTTG
1 TTTATATATAAATATTTG
* *
28535128 TTTATTTATATATATTTG
1 TTTATATATAAATATTTG
28535146 TT
1 TT
28535148 CGCTAATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTATATATAAATATTTG
Found at i:28543212 original size:5 final size:5
Alignment explanation
Indices: 28543202--28543260 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
28543192 TATTAACATG
* * *
28543202 AAAAT AAAAT AAAAT AAAAT AAAGT AATAT ATAAT AAAAT AATAA- ATAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT
28543253 -AAAT AAAA
1 AAAAT AAAA
28543261 ATTGGGTTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.09
5 37 0.84
6 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:28549776 original size:17 final size:17
Alignment explanation
Indices: 28549754--28549787 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28549744 TAAGTTCACG
*
28549754 CTTTTTGCCTCCAATTT
1 CTTTTTACCTCCAATTT
*
28549771 CTTTTTACCTTCAATTT
1 CTTTTTACCTCCAATTT
28549788 AGTCCCTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (17 bp):
CTTTTTACCTCCAATTT
Found at i:28566145 original size:33 final size:33
Alignment explanation
Indices: 28566100--28566168 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
28566090 GAAACACCAT
*
28566100 CACCACCTACAAATACTGAACCACAT-ATTGAAC
1 CACCACCCACAAATACTGAACCACATGA-TGAAC
28566133 CACCACCCACAAATACTGAACCACATGATGAAC
1 CACCACCCACAAATACTGAACCACATGATGAAC
28566166 CAC
1 CAC
28566169 ATATTGAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.42, C:0.36, G:0.07, T:0.14
Consensus pattern (33 bp):
CACCACCCACAAATACTGAACCACATGATGAAC
Found at i:28573152 original size:15 final size:15
Alignment explanation
Indices: 28573132--28573163 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28573122 ATAAACTAGA
*
28573132 TTCAACATTTAATTT
1 TTCAACACTTAATTT
28573147 TTCAACACTTAATTT
1 TTCAACACTTAATTT
28573162 TT
1 TT
28573164 TAGTTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:28573948 original size:18 final size:18
Alignment explanation
Indices: 28573910--28573945 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28573900 TTATTATTTT
*
28573910 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
28573928 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
28573946 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:28578561 original size:27 final size:26
Alignment explanation
Indices: 28578531--28578645 Score: 124
Period size: 27 Copynumber: 4.3 Consensus size: 26
28578521 CATCCTGGCG
28578531 GACTACTCCATGTTTAATGTCCCATCA
1 GACTA-TCCATGTTTAATGTCCCATCA
* ** * *
28578558 GACTATCCTGTGTTTAACATCCCGTCG
1 GACTATCC-ATGTTTAATGTCCCATCA
28578585 GACTATCC-TGTGTTAAATGTCCCATCA
1 GACTATCCATGT-TT-AATGTCCCATCA
28578612 GACTATCCCATGTTTAATGTCCCATCA
1 GACTAT-CCATGTTTAATGTCCCATCA
*
28578639 CACTATC
1 GACTATC
28578646 TTCGATTTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
25 3 0.04
26 6 0.08
27 57 0.78
28 4 0.05
29 3 0.04
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (26 bp):
GACTATCCATGTTTAATGTCCCATCA
Found at i:28578589 original size:54 final size:54
Alignment explanation
Indices: 28578510--28578628 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 54
28578500 TCTTAATATC
* *
28578510 CCCATGTTTATCATCCTGGCGGACTACTCCATGT-TT-AATGTCCCATCAGACTAT
1 CCCATGTTTAACATCCCGGCGGACTA-TCC-TGTGTTAAATGTCCCATCAGACTAT
** *
28578564 CCTGTGTTTAACATCCCGTCGGACTATCCTGTGTTAAATGTCCCATCAGACTAT
1 CCCATGTTTAACATCCCGGCGGACTATCCTGTGTTAAATGTCCCATCAGACTAT
28578618 CCCATGTTTAA
1 CCCATGTTTAA
28578629 TGTCCCATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
52 3 0.05
53 5 0.09
54 48 0.86
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.34
Consensus pattern (54 bp):
CCCATGTTTAACATCCCGGCGGACTATCCTGTGTTAAATGTCCCATCAGACTAT
Found at i:28578644 original size:54 final size:54
Alignment explanation
Indices: 28578541--28578645 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
28578531 GACTACTCCA
* ** * **
28578541 TGTTTAATGTCCCATCAGACTATCCTGTGTTTAACATCCCGTCGGACTATCCTG
1 TGTTAAATGTCCCATCAGACTATCCCATGTTTAACATCCCATCACACTATCCTG
**
28578595 TGTTAAATGTCCCATCAGACTATCCCATGTTTAATGTCCCATCACACTATC
1 TGTTAAATGTCCCATCAGACTATCCCATGTTTAACATCCCATCACACTATC
28578646 TTCGATTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (54 bp):
TGTTAAATGTCCCATCAGACTATCCCATGTTTAACATCCCATCACACTATCCTG
Found at i:28585190 original size:22 final size:22
Alignment explanation
Indices: 28585160--28585202 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28585150 ACAGCAGAAC
* *
28585160 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
28585182 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
28585203 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:28585479 original size:42 final size:42
Alignment explanation
Indices: 28585274--28585628 Score: 473
Period size: 42 Copynumber: 8.4 Consensus size: 42
28585264 ACGTCACTAA
*
28585274 CTTTTGCGGCGCTTACGTAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-G-AAAAAAACGCCGCTAAAGATCATGTT
*
28585318 CTTTAGCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTT
* * *
28585361 CTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTT
* *
28585404 CTTTAGCGGCGCTTAG--AAAAACGCCCCTAAAGATCATGAT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
28585444 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
28585486 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
28585528 CTTTAGCGGCGCTTAGGAAAAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* ** * *
28585570 CTTTTAGCGGCGCTTTGGAAGGAAACGCCTCTAAA-ACTAATGTT
1 C-TTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
*
28585614 CTATAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
28585629 TTTCACAAAC
Statistics
Matches: 284, Mismatches: 21, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
40 35 0.12
41 2 0.01
42 110 0.39
43 101 0.36
44 36 0.13
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:28586113 original size:21 final size:21
Alignment explanation
Indices: 28586072--28586129 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
28586062 GCTTCTCTCG
*
28586072 CTACTTCTCTCGCTGCGGCCT
1 CTACTTCTCTCGCTGCAGCCT
*
28586093 CTACTTCTCTCGCTGTAGCCT
1 CTACTTCTCTCGCTGCAGCCT
* * *
28586114 TTGCTTCCCTCGCTGC
1 CTACTTCTCTCGCTGC
28586130 CGTCTCTGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.05, C:0.41, G:0.17, T:0.36
Consensus pattern (21 bp):
CTACTTCTCTCGCTGCAGCCT
Found at i:28591611 original size:16 final size:17
Alignment explanation
Indices: 28591590--28591688 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 17
28591580 GATTTAGGAA
28591590 TAAGTTATGTA-TTATG
1 TAAGTTATGTAGTTATG
*
28591606 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
* *
28591624 TAAGTTGTGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
* *
28591642 T-A-TTATGAAACTTATG
1 TAAGTTATG-TAGTTATG
* *
28591658 TACGTTATGT-CTTATG
1 TAAGTTATGTAGTTATG
28591674 TAAGTTATGTA-TTAT
1 TAAGTTATGTAGTTAT
28591689 TATGTAAGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
16 39 0.57
17 2 0.03
18 27 0.40
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.47
Consensus pattern (17 bp):
TAAGTTATGTAGTTATG
Found at i:28591615 original size:9 final size:9
Alignment explanation
Indices: 28591590--28591697 Score: 86
Period size: 9 Copynumber: 12.6 Consensus size: 9
28591580 GATTTAGGAA
28591590 TAAGTTATG
1 TAAGTTATG
28591599 T-A-TTATG
1 TAAGTTATG
28591606 TAAGTTATG
1 TAAGTTATG
*
28591615 TAAGTTGTG
1 TAAGTTATG
*
28591624 TAAGTTGTG
1 TAAGTTATG
*
28591633 TAAGTTGTG
1 TAAGTTATG
28591642 T-A-TTATG
1 TAAGTTATG
* *
28591649 AAACTTATG
1 TAAGTTATG
*
28591658 TACGTTATG
1 TAAGTTATG
*
28591667 T--CTTATG
1 TAAGTTATG
28591674 TAAGTTATG
1 TAAGTTATG
28591683 TATTA-TTATG
1 TA--AGTTATG
28591693 TAAGT
1 TAAGT
28591698 AGGGATGTAG
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
7 16 0.20
8 5 0.06
9 53 0.65
10 7 0.09
11 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28591779 original size:10 final size:11
Alignment explanation
Indices: 28591764--28591825 Score: 74
Period size: 12 Copynumber: 5.5 Consensus size: 11
28591754 TTTATGGATG
28591764 TTATGTA-TTA
1 TTATGTAGTTA
28591774 TTATGTA-TTA
1 TTATGTAGTTA
28591784 TTATGTAAGTTA
1 TTATGT-AGTTA
28591796 TTATGTAGGTTA
1 TTATGTA-GTTA
*
28591808 TTATGTAAGTCA
1 TTATGT-AGTTA
28591820 TTATGT
1 TTATGT
28591826 TGGTTATGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
10 16 0.34
11 2 0.04
12 28 0.60
13 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (11 bp):
TTATGTAGTTA
Found at i:28591798 original size:12 final size:12
Alignment explanation
Indices: 28591771--28591825 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
28591761 ATGTTATGTA
28591771 TTATTATGT-A-
1 TTATTATGTAAG
28591781 TTATTATGTAAG
1 TTATTATGTAAG
*
28591793 TTATTATGTAGG
1 TTATTATGTAAG
28591805 TTATTATGTAAG
1 TTATTATGTAAG
*
28591817 TCATTATGT
1 TTATTATGT
28591826 TGGTTATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 9 0.22
11 1 0.03
12 30 0.75
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:28591813 original size:24 final size:24
Alignment explanation
Indices: 28591764--28591832 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
28591754 TTTATGGATG
28591764 TTATGT-A-TTATTATGTA--TTA
1 TTATGTAAGTTATTATGTAGGTTA
28591784 TTATGTAAGTTATTATGTAGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
* *
28591808 TTATGTAAGTCATTATGTTGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
28591832 T
1 T
28591833 GTAAGTTGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.14
21 1 0.02
22 10 0.23
24 26 0.60
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.54
Consensus pattern (24 bp):
TTATGTAAGTTATTATGTAGGTTA
Found at i:28591834 original size:21 final size:22
Alignment explanation
Indices: 28591784--28591838 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
28591774 TTATGTATTA
*
28591784 TTATGTAAGTTATTATGTAGGTT
1 TTATGTAAGTCATTATGTAGG-T
*
28591807 ATTATGTAAGTCATTATGTTGG-
1 -TTATGTAAGTCATTATGTAGGT
28591829 TTATGTAAGT
1 TTATGTAAGT
28591839 TGTGATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
24 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTATGTAAGTCATTATGTAGGT
Found at i:28592016 original size:21 final size:21
Alignment explanation
Indices: 28591969--28592016 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
28591959 CAATTTTTAA
* *
28591969 AAATATATATAAATTTTAAAT
1 AAATATATATAAACTATAAAT
* *
28591990 ATATATATATAAACTATATAT
1 AAATATATATAAACTATAAAT
28592011 AAATAT
1 AAATAT
28592017 TAATAAGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATATATAAACTATAAAT
Found at i:28592034 original size:9 final size:9
Alignment explanation
Indices: 28592020--28592095 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 9
28592010 TAAATATTAA
28592020 TAAGTTATG
1 TAAGTTATG
28592029 TAAGTTATG
1 TAAGTTATG
* *
28592038 TATTA-TAAATT
1 TA--AGT-TATG
*
28592049 TAAGTTGTG
1 TAAGTTATG
28592058 TAAGTTATG
1 TAAGTTATG
28592067 -AA-TTATG
1 TAAGTTATG
*
28592074 TAAGATATG
1 TAAGTTATG
* *
28592083 TAAATTACG
1 TAAGTTATG
28592092 TAAG
1 TAAG
28592096 AAATGAAATT
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
7 5 0.10
8 4 0.08
9 34 0.68
10 2 0.04
11 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.42
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28592094 original size:18 final size:17
Alignment explanation
Indices: 28592067--28592105 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
28592057 GTAAGTTATG
* *
28592067 AATTATGTAAGATATGTA
1 AATTACGTAAGAAATG-A
28592085 AATTACGTAAGAAATGA
1 AATTACGTAAGAAATGA
28592102 AATT
1 AATT
28592106 TGAACTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (17 bp):
AATTACGTAAGAAATGA
Found at i:28593867 original size:45 final size:44
Alignment explanation
Indices: 28593802--28593901 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 44
28593792 CTGGAAGGAG
* * *
28593802 GAAGGAGGCGATTTAGGGATTTCGGATTTCAAGAAATTAGGCAA
1 GAAGGAGGCAATTTACGGATTTCGGAATTCAAGAAATTAGGCAA
* * *
28593846 GAAAGGAGGCAATTTTCGGATTTGGGAATTCAAGAAATTGGGCAA
1 G-AAGGAGGCAATTTACGGATTTCGGAATTCAAGAAATTAGGCAA
*
28593891 GAAGGACGCAA
1 GAAGGAGGCAA
28593902 CAATTTCACA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 10 0.21
45 38 0.79
ACGTcount: A:0.36, C:0.10, G:0.32, T:0.22
Consensus pattern (44 bp):
GAAGGAGGCAATTTACGGATTTCGGAATTCAAGAAATTAGGCAA
Found at i:28595132 original size:7 final size:7
Alignment explanation
Indices: 28595075--28595140 Score: 53
Period size: 7 Copynumber: 9.3 Consensus size: 7
28595065 TAAATTAAGT
28595075 ACCCTAA
1 ACCCTAA
*
28595082 ACCCCAA
1 ACCCTAA
*
28595089 ACCTTAA
1 ACCCTAA
*
28595096 ACCTTAA
1 ACCCTAA
**
28595103 ACTTTAA
1 ACCCTAA
28595110 ATCCC-AA
1 A-CCCTAA
28595117 ACTCCTAA
1 AC-CCTAA
28595125 ACCCTAA
1 ACCCTAA
*
28595132 ACCCAAA
1 ACCCTAA
28595139 AC
1 AC
28595141 ACCATAATCG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
6 1 0.02
7 43 0.88
8 5 0.10
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (7 bp):
ACCCTAA
Found at i:28595133 original size:29 final size:28
Alignment explanation
Indices: 28595079--28595133 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
28595069 TTAAGTACCC
* *
28595079 TAAACCCCAAACCTTAAACCTTAAACTT
1 TAAACCCCAAACCCTAAACCCTAAACTT
*
28595107 TAAATCCCAAACTCCTAAACCCTAAAC
1 TAAACCCCAAAC-CCTAAACCCTAAAC
28595134 CCAAAACACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.22
Consensus pattern (28 bp):
TAAACCCCAAACCCTAAACCCTAAACTT
Found at i:28595690 original size:114 final size:114
Alignment explanation
Indices: 28595549--28595903 Score: 480
Period size: 114 Copynumber: 3.1 Consensus size: 114
28595539 TTCTCGTGAA
*
28595549 CGCCACTAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCAGCGC
1 CGCCACTAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
* * * *
28595614 TTATAAGAAAGCGCCGCTAATAGTATACTTTTGCGTCGTTTACGGAAAG
66 TTCTAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCGTTTCCAGAAAG
* ** * * *
28595663 CGCCACTAATTCAAGTATATGTCAAGATCTAAACGCAGCGTTTAGGTTAATATATCTTGCGGCGC
1 CGCCACTAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
* * * * *
28595728 TTCTAATAAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTG-AA-
66 TTCTAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCG--TT-TCCAGAAAG
* * *
28595778 TGCCACTAACTCCAGTATACATCAAGATTTAAACGCAGCGTTTCCGTTAATATATATTGCGGCGC
1 CGCCACTAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
* *
28595843 TTCTAAGAAAGCGACGCTAATAGTATACTTTTGCGGCGTTTCCATAAAG
66 TTCTAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCGTTTCCAGAAAG
28595892 CGCCACTAATTC
1 CGCCACTAATTC
28595904 TAATATACCT
Statistics
Matches: 203, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
112 3 0.01
113 4 0.02
114 100 0.49
115 89 0.44
116 4 0.02
117 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (114 bp):
CGCCACTAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGC
TTCTAAGAAAGCGCCGCTAATAGTATACTTTTGCGGCGTTTCCAGAAAG
Found at i:28595819 original size:115 final size:114
Alignment explanation
Indices: 28595507--28595903 Score: 485
Period size: 115 Copynumber: 3.5 Consensus size: 114
28595497 GCTAACAAAT
* * *
28595507 AAGCGCCGCTAATAATATGATTTAGCGGTGATTTCTCGTGAACGCCACTAATTCCAGTATACATC
1 AAGCGCCGCTAATAATATAATTTAGCGGCG-TTTCTCCTGAACGCCACTAATTCCAGTATACATC
* *
28595572 AAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCAGCGCTTATAAGA
65 AAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
* * * * * * * **
28595622 AAGCGCCGCTAATAGTATACTTTTGCGTCG-TT-TACGGAAAGCGCCACTAATTCAAGTATATGT
1 AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTG-AA-CGCCACTAATTCCAGTATACAT
* * * *
28595685 CAAGATCTAAACGCAGCGTTTAGGTTAATATATCTTGCGGCGCTTCTAATA
64 CAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
* *
28595736 AAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAATGCCACTAACTCCAGTATACATC
1 AAGCGCCGCTAATAATATAATTTAGCGGCG-TTTCTCCTGAACGCCACTAATTCCAGTATACATC
*
28595801 AAGATTTAAACGCAGCGTTTCCGTTAATATATATTGCGGCGCTTCTAAGA
65 AAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
* * * * * *
28595851 AAGCGACGCTAATAGTATACTTTTGCGGCGTTTC-CATAAAGCGCCACTAATTC
1 AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTGAA-CGCCACTAATTC
28595904 TAATATACCT
Statistics
Matches: 234, Mismatches: 42, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
112 2 0.01
113 8 0.03
114 104 0.44
115 113 0.48
116 4 0.02
117 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (114 bp):
AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTGAACGCCACTAATTCCAGTATACATCA
AGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
Found at i:28595894 original size:229 final size:229
Alignment explanation
Indices: 28595490--28595903 Score: 677
Period size: 229 Copynumber: 1.8 Consensus size: 229
28595480 TGAAGATCTT
* * *
28595490 TTGCGGCGCTAACAAATAAGCGCCGCTAATAATATGATTTAGCGGTGATTTCTCGTGAACGCCAC
1 TTGCGGCGCTAACAAATAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCAC
* *
28595555 TAATTCCAGTATACATCAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCAGCGCTTATAA
66 TAACTCCAGTATACATCAAGATTTAAACGCAGCGTTTCCGTTAATATATATTGCAGCGCTTATAA
* * *
28595620 GAAAGCGCCGCTAATAGTATACTTTTGCGTCGTTTACGGAAAGCGCCACTAATTCAAGTATATGT
131 GAAAGCGACGCTAATAGTATACTTTTGCGGCGTTTACAGAAAGCGCCACTAATTCAAGTATATGT
28595685 CAAGATCTAAACGCAGCGTTTAGGTTAATATATC
196 CAAGATCTAAACGCAGCGTTTAGGTTAATATATC
* * *
28595719 TTGCGGCGCT-TCTAATAAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAATGCCA
1 TTGCGGCGCTAACAAAT-AAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCA
* *
28595783 CTAACTCCAGTATACATCAAGATTTAAACGCAGCGTTTCCGTTAATATATATTGCGGCGCTTCTA
65 CTAACTCCAGTATACATCAAGATTTAAACGCAGCGTTTCCGTTAATATATATTGCAGCGCTTATA
* *
28595848 AGAAAGCGACGCTAATAGTATACTTTTGCGGCGTTTCCATAAAGCGCCACTAATTC
130 AGAAAGCGACGCTAATAGTATACTTTTGCGGCGTTTACAGAAAGCGCCACTAATTC
28595904 TAATATACCT
Statistics
Matches: 169, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
228 4 0.02
229 165 0.98
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (229 bp):
TTGCGGCGCTAACAAATAAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCAC
TAACTCCAGTATACATCAAGATTTAAACGCAGCGTTTCCGTTAATATATATTGCAGCGCTTATAA
GAAAGCGACGCTAATAGTATACTTTTGCGGCGTTTACAGAAAGCGCCACTAATTCAAGTATATGT
CAAGATCTAAACGCAGCGTTTAGGTTAATATATC
Found at i:28598360 original size:6 final size:6
Alignment explanation
Indices: 28598346--28598378 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
28598336 GAAAGCAGCG
*
28598346 AAAAGT AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
28598379 TGGCTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:28602242 original size:30 final size:30
Alignment explanation
Indices: 28602197--28602276 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
28602187 CATATTTATG
28602197 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAATCAAAGATATGGGTATCAAATAATA
* * *
28602227 GAAAGTCAAATATATGGGTATCAAATATTA
1 GAAAATCAAAGATATGGGTATCAAATAATA
*
28602257 GAAATTCAAAGATATGGGTA
1 GAAAATCAAAGATATGGGTA
28602277 CCGAGATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (30 bp):
GAAAATCAAAGATATGGGTATCAAATAATA
Found at i:28602250 original size:15 final size:15
Alignment explanation
Indices: 28602201--28602254 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28602191 TTTATGGAAA
*
28602201 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
28602216 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
28602230 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
28602246 ATCAAATAT
1 ATCAAATAT
28602255 TAGAAATTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:28612541 original size:571 final size:573
Alignment explanation
Indices: 28611438--28612590 Score: 1748
Period size: 571 Copynumber: 2.0 Consensus size: 573
28611428 ACGTATAGAG
* *
28611438 AAACATTAGGAAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTTTCATAT
1 AAACGTTAAGAAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTTTCATAT
* *
28611503 CAAAAATAAAATAATAATAATAATAAGAAAAAACTAAAAAATAGAATCCAACGTTTTAAAACCAG
66 CAAAAATAAAATAATAATAATAATAAGAAAAAAATAAAAAATAG-ATCCAACCTTTTAAAACCAG
* *
28611568 AACAAAGCTAAATCAAAATAATTCCCTTAAAGCACACCTGAGGACTCGAACTCCAAACCCCCAAG
130 AACAAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAGGACTCAAACTCCAAACCCCCAAG
* * * *
28611633 CTAAACTAGCACACAACCAACCACCAAAGCAGTAGACCCATTCTGACACTTGAATGAAAAAAGAT
195 CTAAACTAGAAAACAACCAACCACAAAAGCAGCAGACCCATTCTGACACTTGAATGAAAAAAGAT
* * * *
28611698 ACACAACAGTCCGATTTAGCCACTGCCCCCTTCCTACAACTCACAAAACTTCCAACCTAAGAATC
260 ACACAACAATCCGATTTAGCCACTGCCCCCTTCCCACAACTCACAAAACTTCCAACCCAAGAACC
* *
28611763 GGGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCCAAAATTTCCAACTAACAAATAGC
325 GGGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCCAAAAATACCAACTAACAAATAGC
* *
28611828 CGCTCTGAACACAAAAATCACCACTATGCTCCAGATGCACACTTTGATCCCAAAACACTACCGTA
390 CACTCTGAACACAAAAATCACCACTATGCTCCAGATGCACACTTTGATCCCAAAACACTACCATA
* *
28611893 CTAAACTTTAAAATCCCAGACTCACATTCCAAGAAAGGGGCTTAGACCAAAAACCTCAAACACAC
455 CTAAACTTTAAAATCCCAGACTCACATTCCAAGAAAGAGACTTAGACCAAAAACCTCAAACACAC
* * * *
28611958 ATCTAGAACACTTAGCCACTGAAGCAGATAGTCAATTATATATATCGCACACAC
520 ATCCAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACAC
*
28612012 AAACGTTAAGAAACCCAAAACGTGAAAGAAAACTCTTGTTTTCTTTTT-CCCCTTTTTTCTCATA
1 AAACGTTAAGAAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTT-TCATA
* *
28612076 TCAAAAATAAAA-AAT-AT-A-AATAAGCAAAACAAATAAAAAA-AG-TCTAACCTTTTAAAACT
65 TCAAAAATAAAATAATAATAATAATAAG-AAAA-AAATAAAAAATAGATCCAACCTTTTAAAACC
**
28612135 AGAACAAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAGGACTCAAAAC-CTGAACCCCC
128 AGAACAAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAGGACTC-AAACTCCAAACCCCC
* * *
28612199 AGGCTAAACTAAGAAAACAACCAACCA-AAAGAGCAGCAGGCCCATTCTGACACTTGAATGCAAA
192 AAGCTAAACT-AGAAAACAACCAACCACAAA-AGCAGCAGACCCATTCTGACACTTGAATGAAAA
* * *
28612263 AATATACACAACAATCCGATTTAGCTACTGCCCCTTTCCCACAACTCACAAAACTTCCAACCCCA
255 AAGATACACAACAATCCGATTTAGCCACTGCCCCCTTCCCACAACTCACAAAACTTCCAA-CCCA
*
28612328 AGAACCGGGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCTAAAAATACCAACTAACA
319 AGAACCGGGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCCAAAAATACCAACTAACA
* * * * * * *
28612393 GATAGCCACTCTGAACACAAAACTCACCATTATGCTCCAGCTGCGCACTTTGATCCCGAAACATT
384 AATAGCCACTCTGAACACAAAAATCACCACTATGCTCCAGATGCACACTTTGATCCCAAAACACT
* * * *
28612458 ACCATACTAAACTTTAAAATCCTAGACTCGCATTCCAAGAATGAGACTTAGACCTAAAACCTCAA
449 ACCATACTAAACTTTAAAATCCCAGACTCACATTCCAAGAAAGAGACTTAGACCAAAAACCTCAA
28612523 ACACACATCCAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACAC
514 ACACACATCCAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACAC
28612583 AAACGTTA
1 AAACGTTA
28612591 CAATTCTAAA
Statistics
Matches: 525, Mismatches: 47, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
569 81 0.15
570 108 0.21
571 250 0.48
572 11 0.02
573 13 0.02
574 62 0.12
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (573 bp):
AAACGTTAAGAAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTTTCATAT
CAAAAATAAAATAATAATAATAATAAGAAAAAAATAAAAAATAGATCCAACCTTTTAAAACCAGA
ACAAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAGGACTCAAACTCCAAACCCCCAAGC
TAAACTAGAAAACAACCAACCACAAAAGCAGCAGACCCATTCTGACACTTGAATGAAAAAAGATA
CACAACAATCCGATTTAGCCACTGCCCCCTTCCCACAACTCACAAAACTTCCAACCCAAGAACCG
GGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCCAAAAATACCAACTAACAAATAGCC
ACTCTGAACACAAAAATCACCACTATGCTCCAGATGCACACTTTGATCCCAAAACACTACCATAC
TAAACTTTAAAATCCCAGACTCACATTCCAAGAAAGAGACTTAGACCAAAAACCTCAAACACACA
TCCAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACAC
Found at i:28615093 original size:14 final size:14
Alignment explanation
Indices: 28615074--28615123 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
28615064 TTTTTATTTC
28615074 AAAAATAAAAATAA
1 AAAAATAAAAATAA
28615088 AAAAATAAAAATAA
1 AAAAATAAAAATAA
** *
28615102 GCAAA-ACAAAT-A
1 AAAAATAAAAATAA
28615114 AAAAATAAAA
1 AAAAATAAAA
28615124 TCTAACCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 4 0.14
13 8 0.28
14 17 0.59
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:28615099 original size:20 final size:20
Alignment explanation
Indices: 28615074--28615123 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28615064 TTTTTATTTC
28615074 AAAAATAAAAATAAAAAAAT-
1 AAAAATAAAAA-AAAAAAATA
** *
28615094 AAAAATAAGCAAAACAAATA
1 AAAAATAAAAAAAAAAAATA
28615114 AAAAATAAAA
1 AAAAATAAAA
28615124 TCTAACCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAAATAAAAAAAAAAAATA
Found at i:28616521 original size:26 final size:26
Alignment explanation
Indices: 28616485--28616536 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
28616475 CACCACTGAA
* *
28616485 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
28616511 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
28616537 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:28616610 original size:70 final size:71
Alignment explanation
Indices: 28616497--28616646 Score: 248
Period size: 70 Copynumber: 2.1 Consensus size: 71
28616487 GGGGAATCAT
* *
28616497 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
28616561 ATATCG
66 ATATCG
***
28616567 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
28616632 ATATCG
66 ATATCG
28616638 CACTTAGCA
1 CACTTAGCA
28616647 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 44 0.59
71 30 0.41
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
ATATCG
Found at i:28616750 original size:104 final size:103
Alignment explanation
Indices: 28616566--28616788 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
28616556 AATGGATATC
28616566 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
28616631 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
28616669 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
28616734 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
28616773 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
28616789 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:28623774 original size:26 final size:26
Alignment explanation
Indices: 28623744--28623794 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
28623734 ACCAATGAAC
*
28623744 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
28623770 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
28623795 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:28623834 original size:103 final size:104
Alignment explanation
Indices: 28623650--28623872 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 104
28623640 AATGGATATC
28623650 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
28623715 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATATCGCACATAGCACCACCAATAAACCGGGGAATCA
28623754 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
28623818 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
28623857 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
28623873 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 94 0.84
104 18 0.16
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:28625232 original size:13 final size:13
Alignment explanation
Indices: 28625198--28625274 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
28625188 TAAATCAAAC
*
28625198 TTTTCAAAAGTACT
1 TTTTCAAAAGCA-T
*
28625212 TATT-AAAAGCAT
1 TTTTCAAAAGCAT
*
28625224 TTCTCAAAAGCAT
1 TTTTCAAAAGCAT
*
28625237 TTTTCCACAA-CACT
1 TTTT-CAAAAGCA-T
28625251 TTTT-AAAAGCAT
1 TTTTCAAAAGCAT
28625263 TTTTCAAAAGCA
1 TTTTCAAAAGCA
28625275 ATGTTAAACT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
12 11 0.22
13 28 0.55
14 12 0.24
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:28627971 original size:26 final size:26
Alignment explanation
Indices: 28627933--28627986 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
28627923 TTAAATTTAG
28627933 AAAGCACGATAGTTAG-AACTTTCTGA
1 AAAGCACGATAGTTAGTAA-TTTCTGA
28627959 AAAGCAC-AGTAGTTAGTAATTTCTGA
1 AAAGCACGA-TAGTTAGTAATTTCTGA
28627985 AA
1 AA
28627987 CTATATTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 1 0.04
26 23 0.88
27 2 0.08
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (26 bp):
AAAGCACGATAGTTAGTAATTTCTGA
Found at i:28635312 original size:42 final size:42
Alignment explanation
Indices: 28635258--28635347 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
28635248 AACATGTTTG
28635258 GATC-ATATTGCATGTAATTTCCATACCATACATCCATACAT
1 GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
28635299 GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
1 GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
28635341 GATCTAT
1 GATCTAT
28635348 GTCATTTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (42 bp):
GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
Found at i:28638462 original size:20 final size:20
Alignment explanation
Indices: 28638437--28638484 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
28638427 TACAATATAT
28638437 ATCAATTTTTTTTTCAAAA-A
1 ATCAATTTTTTTTT-AAAAGA
**
28638457 ATCAATTCATTTTTAAAAGA
1 ATCAATTTTTTTTTAAAAGA
28638477 ATC-ATTTT
1 ATCAATTTT
28638485 CCGACAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (20 bp):
ATCAATTTTTTTTTAAAAGA
Found at i:28639571 original size:28 final size:29
Alignment explanation
Indices: 28639531--28639598 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 29
28639521 CTTTTTTTTT
*
28639531 TTTACAATTTTTTAAGAA-TAACCAAATA
1 TTTAGAATTTTTTAAGAATTAACCAAATA
28639559 TTTAGAATTTTTTTAAGAATTAACCAAATA
1 TTTAGAA-TTTTTTAAGAATTAACCAAATA
28639589 TTTAGAATTT
1 TTTAGAATTT
28639599 CATCAAATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 6 0.16
29 14 0.38
30 17 0.46
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (29 bp):
TTTAGAATTTTTTAAGAATTAACCAAATA
Found at i:28639578 original size:29 final size:30
Alignment explanation
Indices: 28639538--28639598 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28639528 TTTTTTACAA
28639538 TTTTTTAAGAA-TAACCAAATATTTAGAAT
1 TTTTTTAAGAATTAACCAAATATTTAGAAT
28639567 TTTTTTAAGAATTAACCAAATATTTAGAAT
1 TTTTTTAAGAATTAACCAAATATTTAGAAT
28639597 TT
1 TT
28639599 CATCAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (30 bp):
TTTTTTAAGAATTAACCAAATATTTAGAAT
Found at i:28642056 original size:26 final size:26
Alignment explanation
Indices: 28642027--28642133 Score: 153
Period size: 26 Copynumber: 4.1 Consensus size: 26
28642017 AACACACCAA
* * *
28642027 TATCGCAGCAAAACTGCCAGTAATAG
1 TATCACAGCAAAGCTGCCAGTAACAG
*
28642053 TATCACAACAAAGCTGCCAGTAACAG
1 TATCACAGCAAAGCTGCCAGTAACAG
28642079 TATCACAGCAAAGCTGCCAGTAACAG
1 TATCACAGCAAAGCTGCCAGTAACAG
*
28642105 TATCGA-AGCAAAGCTGCTAGTAACAG
1 TATC-ACAGCAAAGCTGCCAGTAACAG
28642131 TAT
1 TAT
28642134 ACTTCCTCCA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
26 73 0.99
27 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (26 bp):
TATCACAGCAAAGCTGCCAGTAACAG
Found at i:28644758 original size:65 final size:65
Alignment explanation
Indices: 28644665--28644801 Score: 172
Period size: 65 Copynumber: 2.1 Consensus size: 65
28644655 TCCTCCACTC
* * * * * *
28644665 GTGTGATCC-TAT-TTTGTAAATAGCGAGGTATATGGCCTGGACACACGCTCGTGTCCTTGGCCC
1 GTGTGAACCTTATATTTGTAAATAGCGAGGTACACGGCATGGACACACACCCGTGTCCTTGG-CC
28644728 T
65 T
* *
28644729 -TGTGAACCTTATATTTGTAAATAGTGAGGTACACGGTATGGACACACACCCGTGTCCTTGGCCT
1 GTGTGAACCTTATATTTGTAAATAGCGAGGTACACGGCATGGACACACACCCGTGTCCTTGGCCT
28644793 GTGTGAACC
1 GTGTGAACC
28644802 CTACACTAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
63 7 0.11
64 6 0.10
65 49 0.79
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGTGAACCTTATATTTGTAAATAGCGAGGTACACGGCATGGACACACACCCGTGTCCTTGGCCT
Found at i:28645443 original size:6 final size:6
Alignment explanation
Indices: 28645433--28645477 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
28645423 GAAGAAGAAT
28645433 AAAAATG AAAAAG -AAAAG AAAAAG AAAAAG --AAAG AAAAATG AAAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAA
28645478 GAGGCAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.12
5 5 0.15
6 15 0.44
7 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:28645446 original size:16 final size:16
Alignment explanation
Indices: 28645427--28645477 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
28645417 GGAATAGAAG
*
28645427 AAGAATAAAAATGAAA
1 AAGAAAAAAAATGAAA
*
28645443 AAGAAAAGAAAAAGAAA
1 AAGAAAA-AAAATGAAA
28645460 AAGAAAGAAAAATGAAA
1 AAGAAA-AAAAATGAAA
28645477 A
1 A
28645478 GAGGCAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.20
17 23 0.77
18 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AAGAAAAAAAATGAAA
Done.