Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 85 of 136
Found at i:28047773 original size:23 final size:23
Alignment explanation
Indices: 28047656--28047773 Score: 82
Period size: 23 Copynumber: 5.2 Consensus size: 23
28047646 GAAGGGACTT
*
28047656 ACACTTCAATTTGCAGCACTTTA
1 ACACTTCAATTTGCAGCACTTAA
** * * *
28047679 ACA-TATCAATTAACAACATTTAT
1 ACACT-TCAATTTGCAGCACTTAA
* * *
28047702 ACACATCAA-TTACAGCGA-TAAA
1 ACACTTCAATTTGCAGC-ACTTAA
* *
28047724 ACA-TCTCACTTTGTAGCACTTAA
1 ACACT-TCAATTTGCAGCACTTAA
28047747 ACACTTCAATTTGCAGCACTTAA
1 ACACTTCAATTTGCAGCACTTAA
28047770 ACAC
1 ACAC
28047774 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
22 15 0.21
23 54 0.77
24 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (23 bp):
ACACTTCAATTTGCAGCACTTAA
Found at i:28048250 original size:46 final size:46
Alignment explanation
Indices: 28048179--28048267 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
28048169 TAAATACTTC
* *
28048179 AATTTGTAGCACTTAAACACTTCAATTTACAACATTTAGACACTAA
1 AATTTGCAGCACTTAAACACTTCAATTAACAACATTTAGACACTAA
* *
28048225 AATTTGCATCACTTAAACA-TATCAATTAACAACATTTATACAC
1 AATTTGCAGCACTTAAACACT-TCAATTAACAACATTTAGACAC
28048268 CTCAATTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (46 bp):
AATTTGCAGCACTTAAACACTTCAATTAACAACATTTAGACACTAA
Found at i:28048348 original size:23 final size:23
Alignment explanation
Indices: 28048169--28048351 Score: 106
Period size: 23 Copynumber: 8.0 Consensus size: 23
28048159 NNNNNNNNAC
* **
28048169 TAAATACTTCAATTTGTAGCACT
1 TAAACACTTCAATTTACAGCACT
* *
28048192 TAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTACAGCACT
* ** * *
28048215 TAGACACTAAAATTTGCATCACT
1 TAAACACTTCAATTTACAGCACT
* * *
28048238 TAAACA-TATCAATTAACAACATT
1 TAAACACT-TCAATTTACAGCACT
* * *
28048261 TATACACCTCAA-TTACAGTGA-T
1 TAAACACTTCAATTTACAG-CACT
* *
28048283 AAAACA-TCTCAATTTCCAGCAAC-
1 TAAACACT-TCAATTTACAGC-ACT
* *
28048306 TAAATACTTCAATTTCCAGCACT
1 TAAACACTTCAATTTACAGCACT
*
28048329 TAAACACTTCAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCACT
28048352 ATCAAACTTC
Statistics
Matches: 119, Mismatches: 32, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
22 16 0.13
23 102 0.86
24 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (23 bp):
TAAACACTTCAATTTACAGCACT
Found at i:28048770 original size:41 final size:39
Alignment explanation
Indices: 28048687--28048770 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
28048677 GCACAATACA
**
28048687 ATATAAAAAGAATATATAAATATATGAATGTAGAGGCAT
1 ATATAAAAAGAATATATAAATATATGAATGTAGAGAAAT
* * *
28048726 ATATAAAAAGCATATATAAATATATGTATGTCATAGAAACT
1 ATATAAAAAGAATATATAAATATATGAATGT-AGAGAAA-T
28048767 ATAT
1 ATAT
28048771 TCATTTATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 29 0.76
40 4 0.11
41 5 0.13
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (39 bp):
ATATAAAAAGAATATATAAATATATGAATGTAGAGAAAT
Found at i:28050272 original size:39 final size:39
Alignment explanation
Indices: 28050222--28050345 Score: 108
Period size: 40 Copynumber: 3.1 Consensus size: 39
28050212 TGGGCTTAGG
*
28050222 TTTTTTTCGGTGTTTTTGGAAAAACGCCGCTAATGCT-AA
1 TTTTTTGCGGTGTTTTTGG-AAAACGCCGCTAATGCTCAA
* * *
28050261 TTTTTTGCGGTGCTTTCTTGG-AAACACCGTTAATGCTCGA
1 TTTTTTGCGGTG-TTT-TTGGAAAACGCCGCTAATGCTCAA
* * * * * *
28050301 TCTTTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTCAA
1 TTTTTTGCGGTGTTTT-TGGAAAACGCCGCTAATGCTCAA
28050341 TTTTT
1 TTTTT
28050346 AAAAAACGCC
Statistics
Matches: 66, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
38 1 0.02
39 29 0.44
40 32 0.48
41 4 0.06
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (39 bp):
TTTTTTGCGGTGTTTTTGGAAAACGCCGCTAATGCTCAA
Found at i:28055183 original size:12 final size:12
Alignment explanation
Indices: 28055166--28055191 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28055156 TCAATAAAAA
28055166 AATAAAAAAATC
1 AATAAAAAAATC
28055178 AATAAAAAAATC
1 AATAAAAAAATC
28055190 AA
1 AA
28055192 AATGAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AATAAAAAAATC
Found at i:28055225 original size:8 final size:7
Alignment explanation
Indices: 28055207--28055246 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
28055197 AAATGATAAC
28055207 AAAAGAGA
1 AAAAGA-A
*
28055215 AAAAGGA
1 AAAAGAA
28055222 AAAAGAA
1 AAAAGAA
28055229 AAAAGAAA
1 AAAAG-AA
28055237 AAAAGAA
1 AAAAGAA
28055244 AAA
1 AAA
28055247 GGAGAGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 17 0.59
8 12 0.41
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:28055227 original size:15 final size:15
Alignment explanation
Indices: 28055207--28055249 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
28055197 AAATGATAAC
28055207 AAAAGAGAAAAAGGA
1 AAAAGAGAAAAAGGA
28055222 AAAAGA-AAAAA-GA
1 AAAAGAGAAAAAGGA
*
28055235 AAAAAAGAAAAAGGA
1 AAAAGAGAAAAAGGA
28055250 GAGGCCAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
15 8 0.32
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAAAGGA
Found at i:28057509 original size:45 final size:45
Alignment explanation
Indices: 28057446--28058037 Score: 270
Period size: 43 Copynumber: 13.5 Consensus size: 45
28057436 GTAAGCTTGG
* *
28057446 TCTCCCTGAGCAGCAGTGGAGTAAGTTGAAAAATTACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
* * * * *** * *
28057491 TTTCCCTAAGTAGTAGTGGAGT-AGATCG-AAGACCCCAG-CCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAAG-TTGAAAAATTACAGATCTTA
* * * *
28057534 TCTCCCTAAGCAGCAGTGGAGTAGGTTAAAAAATTACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
* ** * * * *** * *
28057579 TCTCCCTAAGCAATAGTGGA-CCAGATCAAAGACCCCAG-CCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
* *
28057622 TCTCCCTGAGCAGTAGTGGAGTACGTTGAAAAATTACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
* * * *** * *
28057667 TCTCCCTAAGCAGTAGTGGAG-CAGATCG-AAGACCCCAG-CCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAAG-TTGAAAAATTACAGATCTTA
* * ** *
28057710 TCTCACTGAGCACCAGTGGAGTAGGTTGAAAAATTACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
* * * *** * *
28057755 TCTCCCTAAGCAGTAGTGGAG-CAGATCG-AAGACCCCAG-CCTTT
1 TCTCCCTAAGCAGTAGTGGAGTAAG-TTGAAAAATTACAGATCTTA
* * * * * * *
28057798 TGTCCCTGAGCAGCAATAGAGTAGGTTG-AAAATTACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
* * * * ** * *
28057842 TCTCCCTAAGCAATAGTGGAG-CAGATCG-AAGA-CCCTAG-CCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAAG-TTGAAAAATTAC-AGATCTTA
* * * *
28057885 TCTCCCTGAGCAGCAGTGGAATAGGTTG-AAAATTACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
* * * * * ** *
28057929 TCTCCCTAAGCAATAGTGGAG-CAGATTG-AAGACT-CCGGCCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAAG-TTGAAAAATTACAGATCTTA
* * * *
28057972 TCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
28058017 TCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAG
28058038 CAGATCGAAA
Statistics
Matches: 369, Mismatches: 156, Indels: 44
0.65 0.27 0.08
Matches are distributed among these distances:
43 147 0.40
44 111 0.30
45 111 0.30
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (45 bp):
TCTCCCTAAGCAGTAGTGGAGTAAGTTGAAAAATTACAGATCTTA
Found at i:28057596 original size:88 final size:88
Alignment explanation
Indices: 28057445--28058090 Score: 1017
Period size: 88 Copynumber: 7.4 Consensus size: 88
28057435 TGTAAGCTTG
* * *
28057445 GTCTCCCTGAGCAGCAGTGGAGTAAGTTGAAAAATTACAGATCTTATTTCCCTAAGTAGTAGTGG
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
*
28057510 AGTAGATCGAAGACCCCAGCCTT
66 AGCAGATCGAAGACCCCAGCCTT
* * * *
28057533 GTCTCCCTAAGCAGCAGTGGAGTAGGTTAAAAAATTACAAATCTTATCTCCCTAAGCAATAGTGG
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* *
28057598 ACCAGATCAAAGACCCCAGCCTT
66 AGCAGATCGAAGACCCCAGCCTT
* *
28057621 GTCTCCCTGAGCAGTAGTGGAGTACGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
28057686 AGCAGATCGAAGACCCCAGCCTT
66 AGCAGATCGAAGACCCCAGCCTT
* *
28057709 GTCTCACTGAGCACCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
28057774 AGCAGATCGAAGACCCCAGCCTT
66 AGCAGATCGAAGACCCCAGCCTT
* * * * * *
28057797 TTGTCCCTGAGCAGCAATAGAGTAGGTTG-AAAATTACAAATCTTATCTCCCTAAGCAATAGTGG
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
*
28057861 AGCAGATCGAAGACCCTAGCCTT
66 AGCAGATCGAAGACCCCAGCCTT
* *
28057884 GTCTCCCTGAGCAGCAGTGGAATAGGTTG-AAAATTACAGATCTTATCTCCCTAAGCAATAGTGG
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
28057948 AGCAGATTGAAGACTCCGGCCTT
66 AGCAGATCGAAGACCCCAGCCTT
*
28057971 GTCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* *
28058036 AGCAGATCGAAAACCTCAGCCTT
66 AGCAGATCGAAGACCCCAGCCTT
28058059 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAA
1 GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAA
28058091 GCAGAGTAGA
Statistics
Matches: 507, Mismatches: 50, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
87 159 0.31
88 348 0.69
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (88 bp):
GTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACCCCAGCCTT
Found at i:28058250 original size:89 final size:88
Alignment explanation
Indices: 28058090--28058423 Score: 371
Period size: 89 Copynumber: 3.8 Consensus size: 88
28058080 GTAGGTTGAA
* * * * ** *
28058090 AGCAGAGTAGACTGAAGATAGCAGATCTTGCCTTTCTGTACCAACAGCGAAGTAGATCGAAGACA
1 AGCAGAGCAGACTGAAGACAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACA
* *
28058155 CTAGCCTTGCCTCCCTGGGTTTCC
66 CCAGCCTTGCCTCCCTGGG-TTAC
* * * * * *
28058179 AGTAGAGCAGACTGAAGACAGCAAATCTTGTCTTCCTGTACTGACAGCAAAGCAGATCAAAGACA
1 AGCAGAGCAGACTGAAGACAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACA
** *
28058244 CCAGCCTTGCCTCATTGGGCTGAC
66 CCAGCCTTGCCTCCCTGGG-TTAC
* * * * *
28058268 AGCGGAGCAGATTGAAGATAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATTGAAGATA
1 AGCAGAGCAGACTGAAGACAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACA
* *
28058333 CCAACCTTGCCTCCCTGGGTTGC
66 CCAGCCTTGCCTCCCTGGGTTAC
* * * * * *
28058356 AGCAGAGCAGACTGAAAACACCAGATATTGCCTTCCTATATTGGCAGCGAAGCAGATCGAATACA
1 AGCAGAGCAGACTGAAGACAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACA
28058421 CCA
66 CCA
28058424 ACTTCATTTC
Statistics
Matches: 201, Mismatches: 44, Indels: 1
0.82 0.18 0.00
Matches are distributed among these distances:
88 59 0.29
89 142 0.71
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (88 bp):
AGCAGAGCAGACTGAAGACAGCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACA
CCAGCCTTGCCTCCCTGGGTTAC
Found at i:28058313 original size:45 final size:45
Alignment explanation
Indices: 28058184--28058412 Score: 146
Period size: 45 Copynumber: 5.2 Consensus size: 45
28058174 TTTCCAGTAG
* * * * * * *
28058184 AGCAGACTGAAGACAGCAAATCTTGTCTTCCTGTACTGACAGCAA
1 AGCAGATTGAAGATACCAGATCTTGCCTTCCTATACTGACAGCGA
** * * * * *
28058229 AGCAGATCAAAGACACCAG-CCTTGCC-TCAT-TGGGCTGACAGCGG
1 AGCAGATTGAAGATACCAGATCTTGCCTTCCTAT--ACTGACAGCGA
*
28058273 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTATACTGACAGCGA
1 AGCAGATTGAAGATACCAGATCTTGCCTTCCTATACTGACAGCGA
* * ****
28058318 AGCAGATTGAAGATACCA-ACCTTGCCTCCCTGGGTTG-CAGC-A
1 AGCAGATTGAAGATACCAGATCTTGCCTTCCTATACTGACAGCGA
* * * * * *
28058360 GAGCAGACTGAAAACACCAGATATTGCCTTCCTATATTGGCAGCGA
1 -AGCAGATTGAAGATACCAGATCTTGCCTTCCTATACTGACAGCGA
28058406 AGCAGAT
1 AGCAGAT
28058413 CGAATACACC
Statistics
Matches: 139, Mismatches: 36, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
42 2 0.01
43 22 0.16
44 54 0.39
45 56 0.40
46 4 0.03
47 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (45 bp):
AGCAGATTGAAGATACCAGATCTTGCCTTCCTATACTGACAGCGA
Found at i:28058422 original size:45 final size:45
Alignment explanation
Indices: 28058289--28058423 Score: 116
Period size: 44 Copynumber: 3.0 Consensus size: 45
28058279 TTGAAGATAG
* * * * *
28058289 CAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATTGAAGATAC
1 CAGATCTTGCCTTCCTATATTGGCAGCGAAGCAGATCGAAAACAC
* * ***
28058334 CA-ACCTTGCCTCCCTGGGTT-GCAGC-AGAGCAGA-CTGAAAACAC
1 CAGATCTTGCCTTCCTATATTGGCAGCGA-AGCAGATC-GAAAACAC
* *
28058377 CAGATATTGCCTTCCTATATTGGCAGCGAAGCAGATCGAATACAC
1 CAGATCTTGCCTTCCTATATTGGCAGCGAAGCAGATCGAAAACAC
28058422 CA
1 CA
28058424 ACTTCATTTC
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
42 1 0.01
43 18 0.27
44 24 0.36
45 22 0.33
46 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (45 bp):
CAGATCTTGCCTTCCTATATTGGCAGCGAAGCAGATCGAAAACAC
Found at i:28058664 original size:50 final size:50
Alignment explanation
Indices: 28058557--28058697 Score: 120
Period size: 50 Copynumber: 2.8 Consensus size: 50
28058547 ATCTCTTTAG
* * * * *
28058557 CATTACAGTGGAATAGATTTAAGCTACAACAGTGAATCTTACTTCCCAGG
1 CATTGCAGTGGAACAGATTGAAGCCACAACAGTGAATCTTACTTCCCAGA
** ** * *
28058607 CGGTGCAGTGGAACAGATTGAAGCCACAATGGTGAATCTTGCTTCCCTGA
1 CATTGCAGTGGAACAGATTGAAGCCACAACAGTGAATCTTACTTCCCAGA
** * * * **
28058657 CATTGCAGTTAAAAAGATTAAAGCTACAACAACGAATCTTA
1 CATTGCAGTGGAACAGATTGAAGCCACAACAGTGAATCTTA
28058698 TCTCCTTGAG
Statistics
Matches: 68, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (50 bp):
CATTGCAGTGGAACAGATTGAAGCCACAACAGTGAATCTTACTTCCCAGA
Found at i:28058771 original size:44 final size:44
Alignment explanation
Indices: 28058740--28059070 Score: 128
Period size: 44 Copynumber: 7.7 Consensus size: 44
28058730 AAATCAATCC
*
28058740 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACCACAGATCA
1 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACAACAGATCA
* * *** * *
28058784 TATCTCTCTAAAGTTGCAGTAGAGCAGATCGCATC--CAG-TCT
1 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACAACAGATCA
* * * * * * *
28058825 TATCTCACTGAAGTTGCAGTGGAGCAGA-CAGGAGAA-ACCA-ATCC
1 TATCTCCCTAAAGTTGCAGTAGAGCGGATTA--A-AACAACAGATCA
* * * * *
28058869 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
1 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACAACAGATCA
* * ** ** ** *
28058913 TATCTCTCTGAAGTTGTGGTAGAGAAGA-T--CGCATACA-ATCT
1 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACA-ACAGATCA
* * * * * * *
28058954 TATCTTCCTAAAGTTGCAGTGGAACAGA--AAGAAGAAACAAATCC
1 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAA-AA-CAACAGATCA
* * * * * *
28058998 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGATCT
1 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACAACAGATCA
* *
28059042 TATCTCTCTAAAGTTGCAGTAGAGTGGAT
1 TATCTCCCTAAAGTTGCAGTAGAGCGGAT
28059071 CGCATCCTAT
Statistics
Matches: 217, Mismatches: 53, Indels: 34
0.71 0.17 0.11
Matches are distributed among these distances:
40 1 0.00
41 52 0.24
42 8 0.04
43 8 0.04
44 143 0.66
45 3 0.01
46 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (44 bp):
TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACAACAGATCA
Found at i:28058927 original size:129 final size:129
Alignment explanation
Indices: 28058693--28059721 Score: 1368
Period size: 129 Copynumber: 8.0 Consensus size: 129
28058683 CAACAACGAA
* * * * * *
28058693 TCTTATCTCCTTGAGGTTACAGTGGAGCACATTA-AAGAAATC-AATCCTATCTCCCTAAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAGAAA-CAAATCCTATCTCCCTGAAGTTG
* * * *
28058756 CAGTAGAGCGGATTAAAACCACAGATCATATCTCTCTAAAGTTGCAGTAGAGCAGATCGCATCCA
64 CAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA
28058821 G
129 G
* * *
28058822 TCTTATCTCACTGAAGTTGCAGTGGAGCAGACAGGAGAAACCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
** * * *
28058887 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGTGGTAGAGAAGATCGCATACAA
66 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
* * * * *
28058951 TCTTATCTTCCTAAAGTTGCAGTGGAACAGAAAGAAGAAACAAATCCTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
* **
28059016 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGTGGATCGCATCCTA-
66 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCC-AG
* * * *
28059080 TCTTATCTCCCTGAAGTTGCAATAGAGCAAACAGAAGAAATC-AATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAA-CAAATCCTATCTCCCTGAAGTTGC
* * * * *
28059144 AGTGGAG-TGAATTAAAACCACAAATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCGCATCCA
65 AGTGGAGCAG-ATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA
28059208 G
129 G
* **
28059209 TCTTATCTCCCTGAAGTTGCGGTAAAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
* * * * * * * *
28059274 GTGGAACGGATTCAAACCATAGATCTTATCGCTCTGAAGTTGCAGTAGAGTAGATAGCATCTAG
66 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
* **
28059338 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTATA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
* * *
28059403 GTAGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAG
66 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
* *
28059467 TATTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
* * * * * * *
28059532 GTGGAG-TGAATTGAAACCACAAATCTTATCTCTCTAAAGTTGCAGTAAAGCAAATCACATCCAG
66 GTGGAGCAG-ATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
* *
28059596 TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
* * *
28059661 GTGCAGCAGATTAAAACCACAGATCTCATATCTCTGAAGTTGCAGTAGAGCAGATCGCATC
66 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATC
28059722 AGAATTATCT
Statistics
Matches: 790, Mismatches: 100, Indels: 20
0.87 0.11 0.02
Matches are distributed among these distances:
128 6 0.01
129 780 0.99
130 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACAAATCCTATCTCCCTGAAGTTGCA
GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
Found at i:28059175 original size:44 final size:44
Alignment explanation
Indices: 28058990--28059710 Score: 189
Period size: 44 Copynumber: 16.7 Consensus size: 44
28058980 GAAAGAAGAA
* * * * *
28058990 ACAAATCCTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAAAACC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG-TGACATAAAACC
* * * * *** *
28059034 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGTG-GATCGCATC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACATAAAACC
* * ** *
28059077 -C-TATCTTATCTCCCTGAAGTTGCAATAGAGCAAACAGAAGAA--
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG-TGACATAA-AACC
* * *
28059119 ATC-AATCCTATCTCCCTGAAGTTACAGTGGAGTGA-ATTAAAACC
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACA-TAAAACC
** * * *** *
28059163 ACAAATCTTATCTTTCTGAAGTTACAGTAGAGT-AGATCGCATC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACATAAAACC
* * * * *
28059206 -C-AGTCTTATCTCCCTGAAGTTGCGGTAAAGCAGACAGAAGAA--
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG-TGACATAA-AACC
* * * *
28059248 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAACG-GA-TTCAAACC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAG-A-GTGACATAAAACC
* * * * * *
28059292 ATAGATCTTATCGCTCTGAAGTTGCAGTAGAGT-AGAT---AGC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACATAAAACC
* * * * *
28059332 ATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA--
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTAGAG-TGACATAA-AACC
* * ** * *
28059377 ACCAATCCTATCTCCCTGAAGTTATAGTAGAGCGGA-TTAAAACC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG-TGACATAAAACC
* * * * * * *
28059421 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAG-CAGATCACATC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACATAAAACC
* * * * * *
28059464 -C-AGTATTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAA--
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG-TGACATAA-AACC
* * *
28059506 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGA-ATTGAAACC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACA-TAAAACC
* * * * * * * *
28059550 ACAAATCTTATCTCTCTAAAGTTGCAGTAAAG-CAAATCACATC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACATAAAACC
* * * * * *
28059593 -C-AGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACAGAAGAA--
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG-TGACATAA-AACC
* * *
28059635 ACAAATCCTATCTCCCTGAAGTTGCAGT-GCAGCAGA-TTAAAACC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAG-AG-TGACATAAAACC
* * * *
28059679 ACAGATCTCATATCTCTGAAGTTGCAGTAGAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAG
28059711 CAGATCGCAT
Statistics
Matches: 482, Mismatches: 145, Indels: 100
0.66 0.20 0.14
Matches are distributed among these distances:
40 3 0.01
41 119 0.25
42 19 0.04
43 46 0.10
44 290 0.60
45 3 0.01
46 1 0.00
47 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTGACATAAAACC
Found at i:28065631 original size:21 final size:21
Alignment explanation
Indices: 28065557--28065633 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
28065547 TGCTAGTACA
*
28065557 GTGTAAATAAACCACTAATCG
1 GTGTAGATAAACCACTAATCG
* * ** * *
28065578 ATGCAGATAAAAACTGCTAGTACA
1 GTGTAGAT--AAACCACTAAT-CG
*
28065602 GTGTGGATAAACCACTAATCG
1 GTGTAGATAAACCACTAATCG
28065623 GTGTAGATAAA
1 GTGTAGATAAA
28065634 TTGCTCAGAC
Statistics
Matches: 38, Mismatches: 15, Indels: 6
0.64 0.25 0.10
Matches are distributed among these distances:
21 16 0.42
22 8 0.21
23 8 0.21
24 6 0.16
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (21 bp):
GTGTAGATAAACCACTAATCG
Found at i:28065631 original size:45 final size:45
Alignment explanation
Indices: 28065512--28065633 Score: 154
Period size: 45 Copynumber: 2.7 Consensus size: 45
28065502 TACTAGTATG
* * * * **
28065512 GTGTGGATAAACCACTCATTGGTACAAATAAAAGTTGCTAGTACA
1 GTGTGGATAAACCACTAATCGGTGCAGATAAAAACTGCTAGTACA
** *
28065557 GTGTAAATAAACCACTAATCGATGCAGATAAAAACTGCTAGTACA
1 GTGTGGATAAACCACTAATCGGTGCAGATAAAAACTGCTAGTACA
*
28065602 GTGTGGATAAACCACTAATCGGTGTAGATAAA
1 GTGTGGATAAACCACTAATCGGTGCAGATAAA
28065634 TTGCTCAGAC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (45 bp):
GTGTGGATAAACCACTAATCGGTGCAGATAAAAACTGCTAGTACA
Found at i:28065748 original size:34 final size:34
Alignment explanation
Indices: 28065685--28065749 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
28065675 ATGCAATATG
**
28065685 ACATGCTTATAACAGACCAAGACGGTAGCAAGGA
1 ACATGCTTATAACAGACCAAGACAATAGCAAGGA
* * *
28065719 ACATGCTTATAACAGATCAATATAATAGCAA
1 ACATGCTTATAACAGACCAAGACAATAGCAA
28065750 TATATATGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (34 bp):
ACATGCTTATAACAGACCAAGACAATAGCAAGGA
Found at i:28076045 original size:21 final size:21
Alignment explanation
Indices: 28076019--28076081 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
28076009 TTGGTATTTG
28076019 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
28076040 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
28076061 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
28076082 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:28077196 original size:30 final size:30
Alignment explanation
Indices: 28077138--28077196 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28077128 TTGAAAATGT
* *
28077138 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
28077168 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
28077197 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:28081358 original size:21 final size:21
Alignment explanation
Indices: 28081318--28081358 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28081308 TCACACTTCA
*
28081318 ATCACATACTCATATTTGTTT
1 ATCACATACTCATATCTGTTT
28081339 ATCA-ATACTCATATCCTGTT
1 ATCACATACTCATAT-CTGTT
28081359 GAACACGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
ATCACATACTCATATCTGTTT
Found at i:28081561 original size:51 final size:51
Alignment explanation
Indices: 28081431--28081618 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 51
28081421 TATCATTAGA
* * * * *
28081431 TACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAACT-TTTCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAATCTTCCAG
* * *
28081481 TTCACGTGGTAGCCTGCACATAGTACTACACACGTGACCAAAATCTTCCAG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAATCTTCCAG
* * ** *
28081532 TACACATAGTAGCATGCACATAGTACTACACATGTGACCATTATCTATCGA-
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAATCT-TCCAG
* *
28081583 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTG
28081619 TTTATAGGCA
Statistics
Matches: 116, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
50 38 0.33
51 75 0.65
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAATCTTCCAG
Found at i:28089206 original size:51 final size:51
Alignment explanation
Indices: 28089076--28089264 Score: 220
Period size: 51 Copynumber: 3.7 Consensus size: 51
28089066 ATTATCATTC
* * * *
28089076 GTACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAACTTTCCA
1 GTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCG
* *
28089126 GTTCACGTGGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCG
1 GTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCG
* * ** *
28089177 GTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTAT-CG
1 GTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCT-TCCG
* * * *
28089228 ATACACGTAGTAGCCTACACTTAGCACTACACACGTG
1 GTACACGTAGTAGCCTGCACATAGTACTACACACGTG
28089265 TTTATAAGCA
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 36 0.31
51 81 0.69
52 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (51 bp):
GTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCG
Found at i:28098719 original size:21 final size:18
Alignment explanation
Indices: 28098666--28098710 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
28098656 CAGTGGAATA
*
28098666 AAATAATTT-AAACAAAAC
1 AAATTATTTGAAA-AAAAC
28098684 AAATTATTTGAAAAAAAC
1 AAATTATTTGAAAAAAAC
28098702 AAATTATTT
1 AAATTATTT
28098711 TTTGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTATTTGAAAAAAAC
Found at i:28101676 original size:101 final size:101
Alignment explanation
Indices: 28101387--28101792 Score: 620
Period size: 101 Copynumber: 4.0 Consensus size: 101
28101377 TTCTCGAATT
*
28101387 TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTGGCTATTTGGTCGA
1 TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGA
*
28101452 ACGAGAAATCGAAACCTAGTACCTTAGGGCACGTTCCTC
66 ACGAGAAATCGAAACCCAGTACCTTAGGGCACG-T--TC
* * *
28101491 GAATTTCCAAACGCAAAATATTGCCTTA-TTTTGAAAA-TTTTTGAAAAGGATAATAAG-TCATT
1 -----TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTT-AAAAGGATATTTAGCT-ATT
* *
28101553 TGGTGGAACGAGAAATCCAAACCCAGTACCTTAGGGCACGTTC
59 TGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
28101596 TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGA
1 TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGA
*
28101661 ACTAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
66 ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
28101697 TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGA
1 TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGA
*
28101762 ACTAGAAATCGAAACCCAGTACCTTAGGGCA
66 ACGAGAAATCGAAACCCAGTACCTTAGGGCA
28101793 TGTTTTCTCG
Statistics
Matches: 279, Mismatches: 13, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
100 22 0.08
101 160 0.57
102 6 0.02
105 2 0.01
107 7 0.03
108 60 0.22
109 22 0.08
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (101 bp):
TCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGA
ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
Found at i:28104683 original size:51 final size:50
Alignment explanation
Indices: 28104628--28104728 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 50
28104618 TATTACAGCC
28104628 CCTCTCTTTTCTTTAATCCCTTGTCCTCTCTTTTTTTTTAATCCCTTGTGT
1 CCTCTCTTTTCTTTAATCCCTTGTCCTCTC-TTTTTTTTAATCCCTTGTGT
*
28104679 CCTCTCTTTTCTTTAATCTCTTGTCCTCTCTTTTTTTTAATCCCTTGTGT
1 CCTCTCTTTTCTTTAATCCCTTGTCCTCTCTTTTTTTTAATCCCTTGTGT
28104729 TAGGTATTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 20 0.41
51 29 0.59
ACGTcount: A:0.08, C:0.29, G:0.06, T:0.57
Consensus pattern (50 bp):
CCTCTCTTTTCTTTAATCCCTTGTCCTCTCTTTTTTTTAATCCCTTGTGT
Found at i:28104688 original size:26 final size:24
Alignment explanation
Indices: 28104628--28104726 Score: 144
Period size: 24 Copynumber: 4.0 Consensus size: 24
28104618 TATTACAGCC
28104628 CCTCTCTTTTCTTTAATCCCTTGT
1 CCTCTCTTTTCTTTAATCCCTTGT
*
28104652 CCTCTCTTTTTTTTTAATCCCTTGTGT
1 CCTCTC-TTTTCTTTAATCCC-T-TGT
*
28104679 CCTCTCTTTTCTTTAATCTCTTGT
1 CCTCTCTTTTCTTTAATCCCTTGT
*
28104703 CCTCTCTTTTTTTTAATCCCTTGT
1 CCTCTCTTTTCTTTAATCCCTTGT
28104727 GTTAGGTATT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
24 31 0.46
25 14 0.21
26 13 0.19
27 9 0.13
ACGTcount: A:0.08, C:0.29, G:0.05, T:0.58
Consensus pattern (24 bp):
CCTCTCTTTTCTTTAATCCCTTGT
Found at i:28111883 original size:26 final size:26
Alignment explanation
Indices: 28111851--28111962 Score: 152
Period size: 26 Copynumber: 4.3 Consensus size: 26
28111841 TTTACCCTAG
* * * *
28111851 TAAAATTTTAATAATTTTACTCCCGG
1 TAAAATTTTGATGATTTTACCCCCGA
*
28111877 TAAAATTTTGATGATTTTACCCCCAA
1 TAAAATTTTGATGATTTTACCCCCGA
*
28111903 TAAAATTTTGACGATTTTACCCCCGA
1 TAAAATTTTGATGATTTTACCCCCGA
* *
28111929 TAAAATTTTGACGATTTTATCCCCGA
1 TAAAATTTTGATGATTTTACCCCCGA
28111955 TAAAATTT
1 TAAAATTT
28111963 CGAGAAAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (26 bp):
TAAAATTTTGATGATTTTACCCCCGA
Found at i:28115132 original size:7 final size:7
Alignment explanation
Indices: 28115120--28115145 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28115110 TGTCGTTTAA
28115120 AGTCTAG
1 AGTCTAG
28115127 AGTCTAG
1 AGTCTAG
28115134 AGTCTAG
1 AGTCTAG
28115141 AGTCT
1 AGTCT
28115146 TCCAAACGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (7 bp):
AGTCTAG
Found at i:28116393 original size:26 final size:26
Alignment explanation
Indices: 28116363--28116415 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
28116353 ATGGAGTTGG
28116363 TGGATTATAGGGTTCTGCAAACATGA
1 TGGATTATAGGGTTCTGCAAACATGA
*
28116389 TGGATTATAGGGTTGTGCAAACATGA
1 TGGATTATAGGGTTCTGCAAACATGA
28116415 T
1 T
28116416 AACATCTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.32
Consensus pattern (26 bp):
TGGATTATAGGGTTCTGCAAACATGA
Found at i:28124216 original size:25 final size:27
Alignment explanation
Indices: 28124188--28124256 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
28124178 AGCCTGGATA
*
28124188 AGCTTCCCGTTATTTGGCTC-ACA-TG
1 AGCTTCCCGTTATTTGGCTCGACAGAG
* * *
28124213 AGCTTCCTGTTATATGGCTCGAGAGAG
1 AGCTTCCCGTTATTTGGCTCGACAGAG
28124240 AGCTTCCCGATTATTTG
1 AGCTTCCCG-TTATTTG
28124257 CTTTAATGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
25 18 0.51
26 2 0.06
27 9 0.26
28 6 0.17
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (27 bp):
AGCTTCCCGTTATTTGGCTCGACAGAG
Found at i:28129455 original size:21 final size:21
Alignment explanation
Indices: 28129430--28129470 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
28129420 TTGGATGACA
28129430 AAAAACATAAATTTAAAAAAAT
1 AAAAACA-AAATTTAAAAAAAT
28129452 AAAAACAAAATTTAAAAAA
1 AAAAACAAAATTTAAAAAA
28129471 GGAAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAACAAAATTTAAAAAAAT
Found at i:28138075 original size:26 final size:26
Alignment explanation
Indices: 28138061--28138113 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
28138051 ACCAAAAATT
*
28138061 TATTTTAAAAATAAAAAATAAAAAAAG
1 TATTTTAAAAAT-AAAAACAAAAAAAG
*
28138088 TATTTTAAAAATAAAAAAATAAAAAA
1 TATTTTAAAAATAAAAACA-AAAAAA
28138114 TAAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
TATTTTAAAAATAAAAACAAAAAAAG
Found at i:28138098 original size:28 final size:28
Alignment explanation
Indices: 28138061--28138113 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
28138051 ACCAAAAATT
28138061 TATTTTAAAAAT-AAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAG
28138088 TATTTTAAAAATAAAAAAATAAAAAA
1 TATTTTAAAAATAAAAAAATAAAAAA
28138114 TAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (28 bp):
TATTTTAAAAATAAAAAAATAAAAAAAG
Found at i:28142340 original size:3 final size:3
Alignment explanation
Indices: 28142332--28142356 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28142322 AATTTTAAGG
28142332 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
28142357 GCTACCTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28147484 original size:24 final size:24
Alignment explanation
Indices: 28147452--28147499 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28147442 GCAAAAAAAG
28147452 ATAGGCAGTGGATTTGGTTAGCTT
1 ATAGGCAGTGGATTTGGTTAGCTT
28147476 ATAGGCAGTGGATTTGGTTAGCTT
1 ATAGGCAGTGGATTTGGTTAGCTT
28147500 GAAAACCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.33, T:0.38
Consensus pattern (24 bp):
ATAGGCAGTGGATTTGGTTAGCTT
Found at i:28162692 original size:31 final size:31
Alignment explanation
Indices: 28162624--28162692 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
28162614 ATATTAGAAT
*
28162624 TAAAATTTCAAAATTTGAAAAGTAGATAAAC
1 TAAAATTTCAAAATTTGAAAAGTAAATAAAC
*
28162655 TAAAATTT-AACAATTTG-AAAGATAAATGAAC
1 TAAAATTTCAA-AATTTGAAAAG-TAAATAAAC
*
28162686 TCAAATT
1 TAAAATT
28162693 GATTAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (31 bp):
TAAAATTTCAAAATTTGAAAAGTAAATAAAC
Found at i:28167797 original size:46 final size:44
Alignment explanation
Indices: 28167715--28167803 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 44
28167705 ACCTCTATTA
* * *
28167715 CATTCAACCAAATACAAGAATACCATTACGGCTCTATTCCATTC
1 CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTC
*
28167759 CATTCAACCAAACAAAAGATTTACCTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGA-ATACC-ATTACGCCTCTATTCCATT
28167804 ACGCATCTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 17 0.44
45 4 0.10
46 18 0.46
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (44 bp):
CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTC
Found at i:28167806 original size:16 final size:16
Alignment explanation
Indices: 28167785--28167837 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
28167775 AGATTTACCT
*
28167785 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
*
28167801 ATTACGCATCTATTTC
1 ATTACGCATCTATTCC
* *
28167817 ATTACACATCTGTTCC
1 ATTACGCATCTATTCC
28167833 ATTAC
1 ATTAC
28167838 AGCGAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:28169426 original size:398 final size:394
Alignment explanation
Indices: 28168682--28169852 Score: 1961
Period size: 398 Copynumber: 3.0 Consensus size: 394
28168672 TACCACCGAT
28168682 CGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGT
1 CGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGT
* * * *
28168747 CGGGTTCAAACTCCTGAAACGGTCGGATCTATTTTTTTTCCTCTTCAGATATGGCCGATCTGGGT
66 CGGGTTCAAAATCCTGATACAGTCGGATCTTTTTTTTTTCCTCTTC-GATATGGCCGATCTGGGT
28168812 TAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGAG
130 TAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGAG
* * *
28168877 GTGGGTGAGGAAGTAAAGACTGTGATTCCTGATTCACTGTTGAAGAAGATTAAGGGGAATGAAGA
195 GTGGGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAGA
* *
28168942 ATGGGAGCTTGCTAAAAAGCAGGAACGCGAAGCTGCAGAGAGGAAGAAAGTCGAGAACCGCAAGC
260 ATGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCAAGC
* * * *
28169007 ACATTTACTGAAGAGCTATGCAGTGTGCAAAAGAGTGTGAGACTCAGGTATATTTAAAGGTGAAA
325 TCATTTACTCAAGAGCTATGCAGTATGCAAAAGAGTGTGAGGCTCAGGTATATTTAAAGGTGAAA
*
28169072 TCTAA
390 ACTAA
28169077 CGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGT
1 CGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGT
* *
28169142 CGGGTTCAAAATCCTGATACAGTCGGTTCTTTTTTTTTTTTGCCTCTTCGTATATGGCCGATCTC
66 CGGGTTCAAAATCCTGATACAGTCGGATC--TTTTTTTTTT-CCTCTTCG-ATATGGCCGATCTG
*
28169207 GGCTAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTA
127 GGTTAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTA
** *
28169272 GAGGTGGGTGAGGAAGTTAAGACTGTGATTCCTGATTCAAAGTTGAAGAAGAATGAGAGGAATGA
192 GAGGTGGGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGA
* * *
28169337 AAAATGGGAGCTTGCTAAAAAGCAGGAATTCGAAGCTGCAAAGAGGAAGAATGTCGAGAACCGCA
257 AGAATGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCA
* * * * *
28169402 AGCTCATTTACTCAAGAACTATGCAGTATGCGAAAGAGAGTGAGGGTCAGGTATATTTGAAGGTG
322 AGCTCATTTACTCAAGAGCTATGCAGTATGCAAAAGAGTGTGAGGCTCAGGTATATTTAAAGGTG
28169467 AAAACTAA
387 AAAACTAA
*
28169475 TGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGT
1 CGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGT
*
28169540 CGGGTTCAAAATCCTG-TAGCAGTCGGATC-TATTTTTTTCCTCTTCGGATATGGCCGATCTGGG
66 CGGGTTCAAAATCCTGATA-CAGTCGGATCTTTTTTTTTTCCTCTTC-GATATGGCCGATCTGGG
* *
28169603 TTAAACTCGACCCAAGTCGTTCCTGCAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGA
129 TTAAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGA
28169668 GGTGGGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAG
194 GGTGGGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAG
28169733 AA-GGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCAAG
259 AATGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCAAG
*
28169797 CTCATTTACTCAAGAGCTATGCAGTATGCAAAAGAGTATGAGGCTCAGGTATATTT
324 CTCATTTACTCAAGAGCTATGCAGTATGCAAAAGAGTGTGAGGCTCAGGTATATTT
28169853 GCTGGTCTTC
Statistics
Matches: 724, Mismatches: 46, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
393 111 0.15
394 147 0.20
395 99 0.14
397 12 0.02
398 355 0.49
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (394 bp):
CGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCGATTCACGT
CGGGTTCAAAATCCTGATACAGTCGGATCTTTTTTTTTTCCTCTTCGATATGGCCGATCTGGGTT
AAACTCGACCCGAGTCGTTCCTGAAAGAATAAGGGAATCCCTGCCTGCCGTCCGTTGATTAGAGG
TGGGTGAGGAAGTTAAGACTGTGATTCCTGATTCACTGTTGAAGAAGAATAAGAGGAATGAAGAA
TGGGAGCTTGCTAAAAAGCAGGAACTCGAAGCTGCAAAGAGGAAGAAAGTCGAGAACCGCAAGCT
CATTTACTCAAGAGCTATGCAGTATGCAAAAGAGTGTGAGGCTCAGGTATATTTAAAGGTGAAAA
CTAA
Found at i:28177304 original size:2 final size:2
Alignment explanation
Indices: 28177297--28177328 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28177287 AACTTTGACC
28177297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28177329 AGAGCTCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28182845 original size:38 final size:38
Alignment explanation
Indices: 28182794--28183623 Score: 1660
Period size: 38 Copynumber: 21.8 Consensus size: 38
28182784 GTAGTTTTTG
28182794 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28182832 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28182870 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28182908 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28182946 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28182984 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183022 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183060 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183098 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183136 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183174 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183212 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183250 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183288 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183326 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183364 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183402 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183440 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183478 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183516 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183554 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
1 TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
28183592 TTGGAATCCCTATAATTAAGGATAGAAATCTG
1 TTGGAATCCCTATAATTAAGGATAGAAATCTG
28183624 TTGTGATCTC
Statistics
Matches: 792, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 792 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (38 bp):
TTGGAATCCCTATAATTAAGGATAGAAATCTGATGGTA
Found at i:28196976 original size:16 final size:16
Alignment explanation
Indices: 28196955--28196986 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28196945 GCAAATAGGT
28196955 CTAGAATATTGATTGG
1 CTAGAATATTGATTGG
*
28196971 CTAGAATTTTGATTGG
1 CTAGAATATTGATTGG
28196987 ACCCGATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (16 bp):
CTAGAATATTGATTGG
Found at i:28198381 original size:25 final size:25
Alignment explanation
Indices: 28198265--28198377 Score: 111
Period size: 25 Copynumber: 4.5 Consensus size: 25
28198255 GACACACCAC
* * *
28198265 AGCTCGTATGAGCTTATTGATTTAT
1 AGCTTGTATGAGCTTACTGATTCAT
* * * **
28198290 AGCTCGTATGAGCTTCCCGATTTGT
1 AGCTTGTATGAGCTTACTGATTCAT
* *
28198315 AGCTTGTATGAGCTTCCTGATTCAC
1 AGCTTGTATGAGCTTACTGATTCAT
*
28198340 AGCTTGTGA-GAGCATACTGATTCAT
1 AGCTTGT-ATGAGCTTACTGATTCAT
28198365 AGCTTGTATGAGC
1 AGCTTGTATGAGC
28198378 ATACATGAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
24 1 0.01
25 72 0.97
26 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (25 bp):
AGCTTGTATGAGCTTACTGATTCAT
Found at i:28202876 original size:13 final size:13
Alignment explanation
Indices: 28202858--28202889 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28202848 AAGAATAGAA
28202858 AAAGAAACAAAAC
1 AAAGAAACAAAAC
28202871 AAAGAAACAAAAC
1 AAAGAAACAAAAC
*
28202884 AGAGAA
1 AAAGAA
28202890 GGAAAGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAC
Found at i:28202877 original size:30 final size:30
Alignment explanation
Indices: 28202841--28202912 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
28202831 TAAATAAATA
*
28202841 AAAGAAAAAGAATAGAAAAAGAAACAAAAC
1 AAAGAAAAAGAACAGAAAAAGAAACAAAAC
* * * **
28202871 AAAGAAACAA-AACAGAGAAGGAAAGAAAGG
1 AAAGAAA-AAGAACAGAAAAAGAAACAAAAC
28202901 AAAGAAAAAGAA
1 AAAGAAAAAGAA
28202913 GAAAAATTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 2 0.06
30 30 0.88
31 2 0.06
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.01
Consensus pattern (30 bp):
AAAGAAAAAGAACAGAAAAAGAAACAAAAC
Found at i:28203912 original size:13 final size:13
Alignment explanation
Indices: 28203894--28203925 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28203884 AAGAATAGAA
28203894 AAAGAAACAAAAC
1 AAAGAAACAAAAC
28203907 AAAGAAACAAAAC
1 AAAGAAACAAAAC
*
28203920 AGAGAA
1 AAAGAA
28203926 GGAAAGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAC
Found at i:28203913 original size:30 final size:30
Alignment explanation
Indices: 28203877--28203948 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
28203867 TAAATAAATA
*
28203877 AAAGAAAAAGAATAGAAAAAGAAACAAAAC
1 AAAGAAAAAGAACAGAAAAAGAAACAAAAC
* * * **
28203907 AAAGAAACAA-AACAGAGAAGGAAAGAAAGG
1 AAAGAAA-AAGAACAGAAAAAGAAACAAAAC
28203937 AAAGAAAAAGAA
1 AAAGAAAAAGAA
28203949 GAAAAATTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 2 0.06
30 30 0.88
31 2 0.06
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.01
Consensus pattern (30 bp):
AAAGAAAAAGAACAGAAAAAGAAACAAAAC
Found at i:28206615 original size:16 final size:16
Alignment explanation
Indices: 28206594--28206630 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28206584 TTGGTTCGCT
28206594 GTAATGAAATAGAGGC
1 GTAATGAAATAGAGGC
*
28206610 GTAATGGAATAGAGGC
1 GTAATGAAATAGAGGC
28206626 GTAAT
1 GTAAT
28206631 AGTAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (16 bp):
GTAATGAAATAGAGGC
Found at i:28206676 original size:45 final size:44
Alignment explanation
Indices: 28206612--28206704 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
28206602 ATAGAGGCGT
* *
28206612 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGTATGG
1 AATGGAATAGAGACGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
28206657 AATGGAATAGA-ACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGAC-GTAATAGTATTCATGTGTTTGGTTGAATGG
28206701 AATG
1 AATG
28206705 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGACGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:28210579 original size:9 final size:9
Alignment explanation
Indices: 28210565--28210617 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
28210555 TTAAAATACT
*
28210565 TTTTTTTTA
1 TTTTTTTAA
28210574 TTTTTTTAA
1 TTTTTTTAA
***
28210583 TTTTAAAATA
1 TTTTTTTA-A
28210593 TTTTTTTAAA
1 TTTTTTT-AA
28210603 TTTTTTTAA
1 TTTTTTTAA
28210612 TTTTTT
1 TTTTTT
28210618 AAAATAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 21 0.60
10 13 0.37
11 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:28210614 original size:19 final size:19
Alignment explanation
Indices: 28210565--28210622 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
28210555 TTAAAATACT
*
28210565 TTTTTTTTATTTTTTT-AA
1 TTTTTTTAATTTTTTTAAA
***
28210583 TTTTAAAATATTTTTTTAAA
1 TTTTTTTA-ATTTTTTTAAA
*
28210603 TTTTTTTAATTTTTTAAAA
1 TTTTTTTAATTTTTTTAAA
28210622 T
1 T
28210623 AAAAATGGGC
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
18 4 0.13
19 19 0.63
20 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTTAATTTTTTTAAA
Found at i:28212338 original size:13 final size:13
Alignment explanation
Indices: 28212320--28212345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28212310 TCCAGATTTG
28212320 AGCAAAAGCAAAA
1 AGCAAAAGCAAAA
28212333 AGCAAAAGCAAAA
1 AGCAAAAGCAAAA
28212346 CAAAATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (13 bp):
AGCAAAAGCAAAA
Found at i:28217938 original size:89 final size:89
Alignment explanation
Indices: 28217838--28218016 Score: 358
Period size: 89 Copynumber: 2.0 Consensus size: 89
28217828 TAAAATAAAA
28217838 ATTAAAAGTGATACGATATGATAAAATGAATAAAGAAGACAATTATGTGAAAAAAAATCAAAGCA
1 ATTAAAAGTGATACGATATGATAAAATGAATAAAGAAGACAATTATGTGAAAAAAAATCAAAGCA
28217903 AATAAAATTATAAGTACCTCAATT
66 AATAAAATTATAAGTACCTCAATT
28217927 ATTAAAAGTGATACGATATGATAAAATGAATAAAGAAGACAATTATGTGAAAAAAAATCAAAGCA
1 ATTAAAAGTGATACGATATGATAAAATGAATAAAGAAGACAATTATGTGAAAAAAAATCAAAGCA
28217992 AATAAAATTATAAGTACCTCAATT
66 AATAAAATTATAAGTACCTCAATT
28218016 A
1 A
28218017 AAATTTTGTT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (89 bp):
ATTAAAAGTGATACGATATGATAAAATGAATAAAGAAGACAATTATGTGAAAAAAAATCAAAGCA
AATAAAATTATAAGTACCTCAATT
Found at i:28219317 original size:29 final size:30
Alignment explanation
Indices: 28219254--28219318 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
28219244 TTACAATACA
* * *
28219254 ATAACGTAAGTGACTAAAATGTAACATTTC
1 ATAACATAAGTGACTAAAATATAACATATC
*
28219284 A-AACATAAGTGAGTAAAATATAACATAT-
1 ATAACATAAGTGACTAAAATATAACATATC
28219312 ATAACAT
1 ATAACAT
28219319 GAGATAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (30 bp):
ATAACATAAGTGACTAAAATATAACATATC
Found at i:28227919 original size:19 final size:18
Alignment explanation
Indices: 28227884--28227935 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
28227874 TAAATTATTA
28227884 TTTAATAATTACAATAT-TT
1 TTTAA-AATTA-AATATGTT
28227903 GTTTAAAATTAATATATGTT
1 -TTTAAAATTAA-ATATGTT
*
28227923 TTTAATATTAAAT
1 TTTAAAATTAAAT
28227936 GAAGAGTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 3 0.10
19 19 0.66
20 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
TTTAAAATTAAATATGTT
Found at i:28232400 original size:21 final size:21
Alignment explanation
Indices: 28232371--28232412 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28232361 ATCGAGGTAA
* *
28232371 CCAACTTAAACTATTACCTTC
1 CCAAATTAAAATATTACCTTC
*
28232392 CCAAATTAAAATATTGCCTTC
1 CCAAATTAAAATATTACCTTC
28232413 AATTTTACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (21 bp):
CCAAATTAAAATATTACCTTC
Found at i:28235656 original size:19 final size:19
Alignment explanation
Indices: 28235627--28235687 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
28235617 AAAAAAAAAC
* *
28235627 ATTTTAATTTTCCTATTATT
1 ATTTTATTTTTACTATT-TT
28235647 A-TTTATTTTTTACTATTTT
1 ATTTTA-TTTTTACTATTTT
*
28235666 ATTTTATTTTCA-T-TTTT
1 ATTTTATTTTTACTATTTT
28235683 ATTTT
1 ATTTT
28235688 TGCAGGAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.25
18 1 0.03
19 12 0.33
20 14 0.39
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTATTTTTACTATTTT
Found at i:28235657 original size:20 final size:20
Alignment explanation
Indices: 28235634--28235675 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28235624 AACATTTTAA
*
28235634 TTTTCCTATTATTA-TTTATT
1 TTTTACTATT-TTATTTTATT
28235654 TTTTACTATTTTATTTTATT
1 TTTTACTATTTTATTTTATT
28235674 TT
1 TT
28235676 CATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTACTATTTTATTTTATT
Found at i:28249679 original size:25 final size:26
Alignment explanation
Indices: 28249651--28249709 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
28249641 TTTTTTTATT
*
28249651 AAAATAATATAA-AAAATTAATTACG
1 AAAATAATATAACAAAATTAATTACA
* * *
28249676 AAAATGATATAACTAAATTAATTATA
1 AAAATAATATAACAAAATTAATTACA
28249702 AAAATAAT
1 AAAATAAT
28249710 CGTTTTCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAATAATATAACAAAATTAATTACA
Found at i:28251175 original size:29 final size:29
Alignment explanation
Indices: 28251125--28251181 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
28251115 AGCCCCGTGA
* *
28251125 CAAGTGGTATCCGAGCTGTTGGTTCGAAC
1 CAAGTGATATCCGAGCTATTGGTTCGAAC
* *
28251154 CAAGTGATATCTGAGTTATTGGTTCGAA
1 CAAGTGATATCCGAGCTATTGGTTCGAA
28251182 GGCACCGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (29 bp):
CAAGTGATATCCGAGCTATTGGTTCGAAC
Found at i:28254458 original size:76 final size:77
Alignment explanation
Indices: 28254332--28254495 Score: 305
Period size: 76 Copynumber: 2.1 Consensus size: 77
28254322 AAGTTTTATG
28254332 TTAATT-TGATAAAAGTTGATTGATAATATTATTAGGTTTGAATTTTTTATGATTTTGTTAATAG
1 TTAATTGTGA-AAAAGTTGATTGATAATATTATTAGGTTTGAATTTTTTATGATTTTGTTAATAG
28254396 AATAAATTTAAT-
65 AATAAATTTAATA
28254408 TTAATTGTGAAAAAGTTGATTGATAATATTATTAGGTTTGAATTTTTTATGATTTTGTTAATAGA
1 TTAATTGTGAAAAAGTTGATTGATAATATTATTAGGTTTGAATTTTTTATGATTTTGTTAATAGA
28254473 ATAAATTTAATA
66 ATAAATTTAATA
28254485 TTAATTGTGAA
1 TTAATTGTGAA
28254496 TTTTTTAATT
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
76 72 0.84
77 14 0.16
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (77 bp):
TTAATTGTGAAAAAGTTGATTGATAATATTATTAGGTTTGAATTTTTTATGATTTTGTTAATAGA
ATAAATTTAATA
Found at i:28260936 original size:26 final size:27
Alignment explanation
Indices: 28260907--28260960 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28260897 TTTTTAATTA
*
28260907 AATTTGACTATCAACCTTTCA-AAAAG
1 AATTTGACCATCAACCTTTCAGAAAAG
* *
28260933 AATTTGACCATCAATCTTTTAGAAAAG
1 AATTTGACCATCAACCTTTCAGAAAAG
28260960 A
1 A
28260961 GTCAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTTGACCATCAACCTTTCAGAAAAG
Found at i:28268791 original size:45 final size:46
Alignment explanation
Indices: 28268718--28268809 Score: 168
Period size: 45 Copynumber: 2.0 Consensus size: 46
28268708 ATACAAAAGC
*
28268718 ATTTAATATGCAATTGAAAAAATGATCTATATTAGTGGCAGTTTAG
1 ATTTAATATGCAATGGAAAAAATGATCTATATTAGTGGCAGTTTAG
28268764 ATTTAATAT-CAATGGAAAAAATGATCTATATTAGTGGCAGTTTAG
1 ATTTAATATGCAATGGAAAAAATGATCTATATTAGTGGCAGTTTAG
28268809 A
1 A
28268810 AGAAGGATTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 36 0.80
46 9 0.20
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (46 bp):
ATTTAATATGCAATGGAAAAAATGATCTATATTAGTGGCAGTTTAG
Found at i:28276638 original size:21 final size:20
Alignment explanation
Indices: 28276600--28276639 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28276590 GAAAGTAGTC
*
28276600 AAAAAAAGAACAGGTGAGAG
1 AAAAAAAGAACAAGTGAGAG
*
28276620 AAAAAAAGAATCAATTGAGA
1 AAAAAAAGAA-CAAGTGAGA
28276640 ATGGGGGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.62, C:0.05, G:0.23, T:0.10
Consensus pattern (20 bp):
AAAAAAAGAACAAGTGAGAG
Found at i:28277898 original size:19 final size:19
Alignment explanation
Indices: 28277856--28277901 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28277846 TAGAACTTTT
*
28277856 TTTTGAAATTTTTATAAATA
1 TTTTGAAA-TTTTAAAAATA
28277876 TTTTGAAA-TTTAAAAATTA
1 TTTTGAAATTTTAAAAA-TA
28277895 TTTTGAA
1 TTTTGAA
28277902 TTATTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 9 0.38
20 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTTGAAATTTTAAAAATA
Found at i:28288991 original size:16 final size:16
Alignment explanation
Indices: 28288970--28289003 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28288960 TACAATCAAG
28288970 ATCATTTAATCTTA-CA
1 ATCATTTAA-CTTATCA
28288986 ATCATTTAACTTATCA
1 ATCATTTAACTTATCA
28289002 AT
1 AT
28289004 TCATGTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (16 bp):
ATCATTTAACTTATCA
Found at i:28292163 original size:25 final size:25
Alignment explanation
Indices: 28292135--28292199 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
28292125 GATATTTGGT
*
28292135 TCTCACGAGCTTCCCAATTAATGGC
1 TCTCACGAACTTCCCAATTAATGGC
** *
28292160 TCTCTTGAACTTCCCAATTTATGGC
1 TCTCACGAACTTCCCAATTAATGGC
*
28292185 TCAT-ATGAACTTCCC
1 TC-TCACGAACTTCCC
28292200 GATATACAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 33 0.97
26 1 0.03
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.34
Consensus pattern (25 bp):
TCTCACGAACTTCCCAATTAATGGC
Found at i:28292211 original size:25 final size:25
Alignment explanation
Indices: 28292165--28292255 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
28292155 ATGGCTCTCT
* * **
28292165 TGAACTTCCCAATTTATGGCTCATA
1 TGAACTTCCCGATATACAGCTCATA
28292190 TGAACTTCCCGATATACAGCTCGAT-
1 TGAACTTCCCGATATACAGCTC-ATA
* * * *
28292215 TGAGCTTCCCGTTATACAACTCACA
1 TGAACTTCCCGATATACAGCTCATA
* *
28292240 TGAGCTTCCCGTTATA
1 TGAACTTCCCGATATA
28292256 TGGCTCAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.02
25 53 0.95
26 2 0.04
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (25 bp):
TGAACTTCCCGATATACAGCTCATA
Found at i:28292248 original size:50 final size:49
Alignment explanation
Indices: 28292184--28292281 Score: 115
Period size: 50 Copynumber: 2.0 Consensus size: 49
28292174 CAATTTATGG
* * **
28292184 CTCATATGAACTTCCCGATATACAGCTCGATTGAGCTTCCCGTTATACAA
1 CTCACATGAACTTCCCGATATACAGCTCAAAAGAGCTTCCCGTT-TACAA
* * **
28292234 CTCACATGAGCTTCCCGTTATATGGCTCAAAAGAGCTTCCCGTTTACA
1 CTCACATGAACTTCCCGATATACAGCTCAAAAGAGCTTCCCGTTTACA
28292282 TGCTCGTATG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 4 0.10
50 36 0.90
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (49 bp):
CTCACATGAACTTCCCGATATACAGCTCAAAAGAGCTTCCCGTTTACAA
Found at i:28292262 original size:25 final size:24
Alignment explanation
Indices: 28292183--28292286 Score: 93
Period size: 25 Copynumber: 4.2 Consensus size: 24
28292173 CCAATTTATG
* *
28292183 GCTCATATGAACTTCCCGATATACA
1 GCTCA-ATGAGCTTCCCGTTATACA
*
28292208 GCTCGATTGAGCTTCCCGTTATACA
1 GCTC-AATGAGCTTCCCGTTATACA
* **
28292233 ACTCACATGAGCTTCCCGTTATATG
1 GCTCA-ATGAGCTTCCCGTTATACA
*
28292258 GCTCAAAAGAGCTTCCCGTT-TACA
1 GCTC-AATGAGCTTCCCGTTATACA
28292282 TGCTC
1 -GCTC
28292287 GTATGAGCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.05
25 59 0.92
26 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (24 bp):
GCTCAATGAGCTTCCCGTTATACA
Found at i:28292294 original size:25 final size:24
Alignment explanation
Indices: 28292183--28292299 Score: 92
Period size: 25 Copynumber: 4.7 Consensus size: 24
28292173 CCAATTTATG
* *
28292183 GCTCATATGAACTTCCCGATATACA
1 GCTCATATGAGCTTCCCG-TTTACA
28292208 GCTCGAT-TGAGCTTCCCGTTATACA
1 GCTC-ATATGAGCTTCCCGTT-TACA
* * **
28292233 ACTCACATGAGCTTCCCGTTATATG
1 GCTCATATGAGCTTCCCGTT-TACA
* *
28292258 GCTCAAAAGAGCTTCCCGTTTACA
1 GCTCATATGAGCTTCCCGTTTACA
*
28292282 TGCTCGTATGAGCATTCC
1 -GCTCATATGAGC-TTCC
28292300 TAAATAGGAA
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
24 4 0.05
25 63 0.86
26 6 0.08
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (24 bp):
GCTCATATGAGCTTCCCGTTTACA
Found at i:28295175 original size:18 final size:18
Alignment explanation
Indices: 28295154--28295189 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28295144 TAAAAATTTG
*
28295154 TTTTCATTTAATTGAATT
1 TTTTAATTTAATTGAATT
*
28295172 TTTTAATTTAATTTAATT
1 TTTTAATTTAATTGAATT
28295190 AAAATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTAATTTAATTGAATT
Found at i:28302947 original size:21 final size:20
Alignment explanation
Indices: 28302918--28302981 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
28302908 GGCTTTGCCG
28302918 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCAC-TTATGTGTCGT
* **
28302939 ATCAAGCACCTCGTGTGTCGT
1 ATCAGGCA-CTTATGTGTCGT
*
28302960 -TACAGGCACTTAAGTGTCGT
1 AT-CAGGCACTTATGTGTCGT
28302980 AT
1 AT
28302982 GCTGATCAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 10 0.30
21 22 0.67
22 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (20 bp):
ATCAGGCACTTATGTGTCGT
Found at i:28310311 original size:34 final size:35
Alignment explanation
Indices: 28310227--28310318 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 35
28310217 AGAGTTTTTT
* *
28310227 TAAAATTAATTAAATTAGGGTTTATGGGTTTTAAA
1 TAAAATAAATTAAATTAGGGTTTATGGATTTTAAA
*
28310262 TAAAAAAAATTAAATTAGGGTTTATGGATTTTAAA
1 TAAAATAAATTAAATTAGGGTTTATGGATTTTAAA
28310297 T-AAATAAATTAAATTAGGGTTT
1 TAAAATAAATTAAATTAGGGTTT
28310319 TTAAAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 20 0.38
35 33 0.62
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (35 bp):
TAAAATAAATTAAATTAGGGTTTATGGATTTTAAA
Found at i:28310638 original size:126 final size:126
Alignment explanation
Indices: 28310413--28310680 Score: 344
Period size: 126 Copynumber: 2.1 Consensus size: 126
28310403 AGAAGGATTT
* * * *
28310413 TTTTTCTACAGTAGTTTTAGAAAAATTAATTTTGAGAAGACAATTCTGAAAAGATAATGTTAAAA
1 TTTTTCTACAGTAGTTCTAGAAAAATTAATTTTGAGAAGACAATTCTAAAAAAATAATGTCAAAA
* * * *
28310478 ACGCTTCAAATAGGATGCATAATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGCCGCTC
66 ACACTTCAAACAAGATGCATAATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
** *
28310539 TTTTTCTACAGTAGTTCCT-GTAAAAA-TAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTCAA
1 TTTTTCTACAGTAGTT-CTAG-AAAAATTAATTTTGAGAAGACAATTCTAAAAAAATAATGTCAA
* * * * *
28310602 AAACATTTCAAGCAAGATGCACT-GTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
64 AAACACTTCAAACAAGATGCA-TAATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
28310665 TTTTTCTACAGTAGTT
1 TTTTTCTACAGTAGTT
28310681 TTAGCTTGGC
Statistics
Matches: 123, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
126 116 0.94
127 7 0.06
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCTAGAAAAATTAATTTTGAGAAGACAATTCTAAAAAAATAATGTCAAAA
ACACTTCAAACAAGATGCATAATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
Found at i:28312326 original size:40 final size:40
Alignment explanation
Indices: 28312282--28312386 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
28312272 GTTTGGACAA
* *
28312282 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTCTCAT
1 AAAACGCCGCTAAAAATCGAGCATTAGCAGCGCTTCTCAT
28312322 AAAACGCCGCTAAAAATCGAGCATTAGCAGCGCTTCTCAT
1 AAAACGCCGCTAAAAATCGAGCATTAGCAGCGCTTCTCAT
*
28312362 AAAACGCCGCTAAAGATCGAGCATT
1 AAAACGCCGCTAAAAATCGAGCATT
28312387 CACTAAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCAGCGCTTCTCAT
Found at i:28312531 original size:41 final size:40
Alignment explanation
Indices: 28312473--28312665 Score: 269
Period size: 41 Copynumber: 4.7 Consensus size: 40
28312463 CCTTTTAGGC
28312473 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGG
1 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGG
*
28312513 CTTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTCAGAG
1 C-TTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAG-G
* *
28312555 CTTTAGCGGCATTTTCAAAAAAGCGCCGCTAATGCTCAGAG
1 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAG-G
* ** * * *
28312596 CTTTAGTGGCGTTTTCCAAGAAGCGCCGCTAATGTTCGGGG
1 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTC-AGG
28312637 CTTTAGCGGCGTTTTTAAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTAAAAAAGCGCCGC
28312666 AAAAACATTT
Statistics
Matches: 138, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
40 1 0.01
41 134 0.97
42 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGG
Found at i:28313005 original size:14 final size:14
Alignment explanation
Indices: 28312986--28313019 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28312976 TATAGTTTAG
*
28312986 GGTTTAATATATAT
1 GGTTTAAGATATAT
*
28313000 GGTTTAAGGTATAT
1 GGTTTAAGATATAT
28313014 GGTTTA
1 GGTTTA
28313020 GGGTATAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (14 bp):
GGTTTAAGATATAT
Found at i:28313024 original size:14 final size:14
Alignment explanation
Indices: 28312995--28313031 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28312985 GGGTTTAATA
28312995 TATATGGTTTAAGG
1 TATATGGTTTAAGG
*
28313009 TATATGGTTTAGGG
1 TATATGGTTTAAGG
*
28313023 TATAGGGTT
1 TATATGGTT
28313032 AATTTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.43
Consensus pattern (14 bp):
TATATGGTTTAAGG
Found at i:28313099 original size:7 final size:7
Alignment explanation
Indices: 28313089--28313119 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28313079 AGATTATGGA
28313089 ATTAGGG
1 ATTAGGG
*
28313096 ATTATGG
1 ATTAGGG
28313103 ATTAGGG
1 ATTAGGG
28313110 ATTAGGG
1 ATTAGGG
28313117 ATT
1 ATT
28313120 CTGGTTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (7 bp):
ATTAGGG
Found at i:28313108 original size:14 final size:14
Alignment explanation
Indices: 28313080--28313119 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
28313070 AAGGTTTATA
28313080 GATTATGGAATTAGG
1 GATTATGG-ATTAGG
28313095 GATTATGGATTAGG
1 GATTATGGATTAGG
*
28313109 GATTAGGGATT
1 GATTATGGATT
28313120 CTGGTTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (14 bp):
GATTATGGATTAGG
Found at i:28317056 original size:27 final size:26
Alignment explanation
Indices: 28317026--28317082 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
28317016 AATTTCGAGG
*
28317026 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
* *
28317052 ATTTACGTTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
28317079 TTTA
1 TTTA
28317083 TTATTTAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:28317372 original size:54 final size:54
Alignment explanation
Indices: 28317268--28317376 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
28317258 GTTAAAAACG
* **
28317268 CCGCTAAAGGTCATGGTCTTTAGCGGTGTTTGTGGGAAAAGCGTCACTAAAGGT
1 CCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGT
* * *
28317322 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAGGT
1 CCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGT
28317376 C
1 C
28317377 TTGGTTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (54 bp):
CCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGT
Found at i:28317387 original size:43 final size:43
Alignment explanation
Indices: 28317322--28317477 Score: 213
Period size: 43 Copynumber: 3.6 Consensus size: 43
28317312 CACTAAAGGT
* *
28317322 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCA
1 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
* * * * *
28317365 CCGCTAAAGGTCTTGGTTTTTAGTGACGTTTGTGAGAAAAGTG
1 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
**
28317408 CCGCTAAAGGTCTCAGTCTTTAGCGGCGTTTGTGGGAAAAGCG
1 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
* *
28317451 TCGTTAAAGGTCTTGGTCTTTAGCGGC
1 CCGCTAAAGGTCTTGGTCTTTAGCGGC
28317478 ATTTTTTTCT
Statistics
Matches: 95, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 95 1.00
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
Found at i:28318964 original size:54 final size:54
Alignment explanation
Indices: 28318860--28318968 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
28318850 GTTAAAAACG
* **
28318860 CCGCTAAAGGTCATGGTCTTTAGCGGTGTTTGTGGGAAAAGCGTCACTAAAGGT
1 CCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGT
* * *
28318914 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAGGT
1 CCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGT
28318968 C
1 C
28318969 TTGGTTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (54 bp):
CCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGT
Found at i:28318979 original size:43 final size:43
Alignment explanation
Indices: 28318914--28319069 Score: 213
Period size: 43 Copynumber: 3.6 Consensus size: 43
28318904 CACTAAAGGT
* *
28318914 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCA
1 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
* * * * *
28318957 CCGCTAAAGGTCTTGGTTTTTAGTGACGTTTGTGAGAAAAGTG
1 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
**
28319000 CCGCTAAAGGTCTCAGTCTTTAGCGGCGTTTGTGGGAAAAGCG
1 CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
* *
28319043 TCGTTAAAGGTCTTGGTCTTTAGCGGC
1 CCGCTAAAGGTCTTGGTCTTTAGCGGC
28319070 ATTTTTTTCT
Statistics
Matches: 95, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 95 1.00
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
CCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCG
Found at i:28320970 original size:21 final size:21
Alignment explanation
Indices: 28320945--28320997 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28320935 AGCTTTCGGC
*
28320945 AGGGTTGTGGTTGCTCCAGTG
1 AGGGTTGTGGTTGCTCCAGCG
*
28320966 AGGGTTGTGGTTGCTCCGGCG
1 AGGGTTGTGGTTGCTCCAGCG
*
28320987 GGGGTTGTGGT
1 AGGGTTGTGGT
28320998 AGTTCTGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.06, C:0.13, G:0.49, T:0.32
Consensus pattern (21 bp):
AGGGTTGTGGTTGCTCCAGCG
Found at i:28321275 original size:18 final size:18
Alignment explanation
Indices: 28321249--28321292 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
28321239 AACTGGGAAA
* *
28321249 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
28321267 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
28321285 AGGATACA
1 AGGATACA
28321293 CACCTGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:28322829 original size:25 final size:24
Alignment explanation
Indices: 28322792--28322843 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
28322782 GCTATTATAA
* *
28322792 AAAATTATAAAATAAAAATTAATT
1 AAAATTAAAAAATAAAAATAAATT
*
28322816 AAAATTAAATAAATGAAAATAAATT
1 AAAATTAAA-AAATAAAAATAAATT
28322841 AAA
1 AAA
28322844 TAATATTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTAAAAAATAAAAATAAATT
Found at i:28323921 original size:27 final size:27
Alignment explanation
Indices: 28323883--28323959 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
28323873 CCCTGGGTGG
28323883 AGGGAAGCAGGTTGGCGGCACCAAACA
1 AGGGAAGCAGGTTGGCGGCACCAAACA
** *
28323910 AGGGAAGCAGGTTGGCGGCACCAGTCG
1 AGGGAAGCAGGTTGGCGGCACCAAACA
* *
28323937 AGTGAACCAGGTTGGCGGCACCA
1 AGGGAAGCAGGTTGGCGGCACCA
28323960 GTCCTGCCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.27, C:0.23, G:0.39, T:0.10
Consensus pattern (27 bp):
AGGGAAGCAGGTTGGCGGCACCAAACA
Found at i:28323978 original size:27 final size:27
Alignment explanation
Indices: 28323921--28323984 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
28323911 GGGAAGCAGG
* ** *
28323921 TTGGCGGCACCAGTCGAGTGAACCAGG
1 TTGGCGGCACCAGTCCAGCCAACCAGA
* *
28323948 TTGGCGGCACCAGTCCTGCCAACTAGA
1 TTGGCGGCACCAGTCCAGCCAACCAGA
28323975 TTGGCGGCAC
1 TTGGCGGCAC
28323985 TACTCGTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (27 bp):
TTGGCGGCACCAGTCCAGCCAACCAGA
Found at i:28324801 original size:18 final size:18
Alignment explanation
Indices: 28324773--28324817 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28324763 TTGATATGGT
* *
28324773 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
28324791 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
28324809 TGGTGGCGA
1 TGGTGGCGA
28324818 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:28326108 original size:10 final size:10
Alignment explanation
Indices: 28326095--28326247 Score: 57
Period size: 10 Copynumber: 16.1 Consensus size: 10
28326085 TCCTTCCCTC
28326095 TTCTTCTTCT
1 TTCTTCTTCT
*
28326105 TTCTT-TTTT
1 TTCTTCTTCT
28326114 TCTCTTCTTCT
1 T-TCTTCTTCT
28326125 TTCCTT-TTCT
1 TT-CTTCTTCT
*
28326135 TTC--CTTAT
1 TTCTTCTTCT
28326143 TT-TTCTTTCT
1 TTCTTC-TTCT
* **
28326153 TTCCTCCCCT
1 TTCTTCTTCT
28326163 TTCCTT-TTCT
1 TT-CTTCTTCT
28326173 TTC--CTTCT
1 TTCTTCTTCT
28326181 TT-TTCTTTCT
1 TTCTTC-TTCT
* **
28326191 TTCCTCACCT
1 TTCTTCTTCT
28326201 TTC--CTT-T
1 TTCTTCTTCT
*
28326208 TCCTTCTT-T
1 TTCTTCTTCT
28326217 TTCTTC--CT
1 TTCTTCTTCT
28326225 TTCTTCCTTTCT
1 TTCTT-C-TTCT
28326237 TTCTTCTTCT
1 TTCTTCTTCT
28326247 T
1 T
28326248 CCACTGTCCT
Statistics
Matches: 105, Mismatches: 17, Indels: 42
0.64 0.10 0.26
Matches are distributed among these distances:
7 3 0.03
8 18 0.17
9 18 0.17
10 45 0.43
11 14 0.13
12 7 0.07
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:28326119 original size:23 final size:24
Alignment explanation
Indices: 28326092--28326247 Score: 73
Period size: 24 Copynumber: 6.6 Consensus size: 24
28326082 CCTTCCTTCC
28326092 CTCTTCTTCTTCTTTCTTTT-TTT
1 CTCTTCTTCTTCTTTCTTTTCTTT
*
28326115 CTCTTCTTC-T-TTCCTTTTCTTT
1 CTCTTCTTCTTCTTTCTTTTCTTT
* *
28326137 C-CTTATTTTTCTTTCTTTCCTCCCCTTT
1 CTCTTCTTCTTCTTTCTTT--T---CTTT
*
28326165 C-CTT-TTCTTTCCTTCTTTTTCTTT
1 CTCTTCTTC-TTCTTTC-TTTTCTTT
* ** *
28326189 CT-TTCCTCACCTTTCCTTTTCCTT
1 CTCTTCTTCTTCTTT-CTTTTCTTT
*
28326213 CT-TT-TTCTTCCTTTC-TTCCTTT
1 CTCTTCTTCTT-CTTTCTTTTCTTT
28326235 CT-TTCTTCTTCTT
1 CTCTTCTTCTTCTT
28326248 CCACTGTCCT
Statistics
Matches: 102, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
21 12 0.12
22 18 0.18
23 23 0.23
24 25 0.25
25 4 0.04
27 3 0.03
28 14 0.14
29 3 0.03
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (24 bp):
CTCTTCTTCTTCTTTCTTTTCTTT
Found at i:28326121 original size:20 final size:19
Alignment explanation
Indices: 28326097--28326195 Score: 87
Period size: 20 Copynumber: 5.1 Consensus size: 19
28326087 CTTCCCTCTT
28326097 CTTCTTCTTTCTTTTTTTC
1 CTTCTTCTTTCTTTTTTTC
28326116 TCTTCTTCTTTCCTTTTCTTTC
1 -CTTCTTCTTT-CTTTT-TTTC
* *
28326138 CTTATT-TTTCTTTCTTTC
1 CTTCTTCTTTCTTTTTTTC
**
28326156 C-TCCCCTTTCCTTTTCTTTC
1 CTTCTTCTTT-CTTTT-TTTC
*
28326176 CTTCTT-TTTCTTTCTTTC
1 CTTCTTCTTTCTTTTTTTC
28326194 CT
1 CT
28326196 CACCTTTCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
17 1 0.02
18 14 0.22
19 12 0.19
20 21 0.33
21 12 0.19
22 4 0.06
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTCTTCTTTCTTTTTTTC
Found at i:28326151 original size:18 final size:18
Alignment explanation
Indices: 28326097--28326241 Score: 93
Period size: 18 Copynumber: 7.9 Consensus size: 18
28326087 CTTCCCTCTT
*
28326097 CTTCTTCTTTCTTTTTTTC
1 CTTCTT-TTTCTTTCTTTC
28326116 TCTTCTTCTTTCCTTTTCTTTC
1 -CTTCTT-TTT-C-TTTCTTTC
*
28326138 CTTATTTTTCTTTCTTTC
1 CTTCTTTTTCTTTCTTTC
* * *
28326156 CTCCCCTTTCCTTTTCTTTC
1 CT-TCTTTTTC-TTTCTTTC
28326176 CTTCTTTTTCTTTCTTTC
1 CTTCTTTTTCTTTCTTTC
** *
28326194 C-TCACCTTTC-CT-TTTC
1 CTTC-TTTTTCTTTCTTTC
*
28326210 CTTCTTTTTCTTCCTTT-
1 CTTCTTTTTCTTTCTTTC
*
28326227 CTTC-CTTTCTTTCTT
1 CTTCTTTTTCTTTCTT
28326242 CTTCTTCCAC
Statistics
Matches: 99, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
16 18 0.18
17 9 0.09
18 26 0.26
19 10 0.10
20 23 0.23
21 6 0.06
22 7 0.07
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
CTTCTTTTTCTTTCTTTC
Found at i:28326229 original size:38 final size:38
Alignment explanation
Indices: 28326123--28326209 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
28326113 TTCTCTTCTT
*
28326123 CTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCC
1 CTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCAC
*
28326161 CTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCAC
1 CTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCAC
28326199 CTTTCCTTTTC
1 CTTTCCTTTTC
28326210 CTTCTTTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (38 bp):
CTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCAC
Found at i:28326405 original size:18 final size:18
Alignment explanation
Indices: 28326377--28326421 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
28326367 CGGTTCAGGT
28326377 TTTTTTCTGTTTTTTATTA
1 TTTTTT-TGTTTTTTATTA
* *
28326396 TTTTTTTGTTTTTTTTTG
1 TTTTTTTGTTTTTTATTA
28326414 TTTTTTTG
1 TTTTTTTG
28326422 ATATATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.84
Consensus pattern (18 bp):
TTTTTTTGTTTTTTATTA
Found at i:28326430 original size:28 final size:28
Alignment explanation
Indices: 28326375--28326431 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28326365 ATCGGTTCAG
* *
28326375 GTTTTTTTCTGTTTTTTATTATTTTTTT
1 GTTTTTTTCTGTTTTTTATGATTATTTT
*
28326403 GTTTTTTTTTGTTTTTT-TGATATATTTT
1 GTTTTTTTCTGTTTTTTATGAT-TATTTT
28326431 G
1 G
28326432 ATAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.09, C:0.02, G:0.11, T:0.79
Consensus pattern (28 bp):
GTTTTTTTCTGTTTTTTATGATTATTTT
Found at i:28326485 original size:28 final size:27
Alignment explanation
Indices: 28326426--28326490 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
28326416 TTTTTGATAT
* *
28326426 ATTTTGATAAATAAAAAAATTATATAT
1 ATTTTGGTAAATAAAAAAATTATATAC
*
28326453 TTTTTGGTAAATAAAAAAAAGTTATA-AC
1 ATTTTGGTAAAT-AAAAAAA-TTATATAC
28326481 ATTTTGGTAA
1 ATTTTGGTAA
28326491 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.31
28 17 0.53
29 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAATTATATAC
Found at i:28326809 original size:22 final size:22
Alignment explanation
Indices: 28326766--28326815 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
28326756 CCTTGTATTC
*
28326766 TTCATAAATTTAGAATTTAATTT
1 TTCA-AAATTTAGAATTAAATTT
28326789 TTCAAAATTTA-AATGTAAATTT
1 TTCAAAATTTAGAAT-TAAATTT
*
28326811 ATCAA
1 TTCAA
28326816 GTTCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 17 0.71
23 4 0.17
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
TTCAAAATTTAGAATTAAATTT
Found at i:28342588 original size:23 final size:25
Alignment explanation
Indices: 28342556--28342601 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
28342546 TGGAATGGAT
28342556 TTTACTTTTTAAAT-TTTTTTACAA
1 TTTACTTTTTAAATATTTTTTACAA
28342580 TTTA-TTTTTAAATATTTTTTAC
1 TTTACTTTTTAAATATTTTTTAC
28342602 TAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTACTTTTTAAATATTTTTTACAA
Found at i:28342694 original size:27 final size:28
Alignment explanation
Indices: 28342659--28342716 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
28342649 TTTATTCTAA
28342659 TTTTGATTC-ATTAT-ATTCATATGGATT
1 TTTTGATTCAATTATAATT-ATATGGATT
*
28342686 TTTTTATTCTAATTATACATTATATGGATT
1 TTTTGATTC-AATTATA-ATTATATGGATT
28342716 T
1 T
28342717 CATTCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 8 0.31
29 5 0.19
30 10 0.38
31 3 0.12
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.57
Consensus pattern (28 bp):
TTTTGATTCAATTATAATTATATGGATT
Found at i:28357096 original size:17 final size:17
Alignment explanation
Indices: 28357063--28357095 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28357053 AAAAAGTATT
*
28357063 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
28357080 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
28357096 AGTATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:28358409 original size:139 final size:139
Alignment explanation
Indices: 28358159--28358439 Score: 445
Period size: 139 Copynumber: 2.0 Consensus size: 139
28358149 CCCAAAATTT
* * * * * * *
28358159 CTTCCATCGTTCTGACGTTTATTCACCCCTTTTCTGCCGAATTTTTATTGTTTCCTCCCTTTTTT
1 CTTCCATCATTCTGACGTTTATTCACCCATTGTCTGCCGAATTTTCATCGATTCCTCCCTCTTTT
*
28358224 CTTTTGATTTCTTTTATGCCTCCATCGTGCTCGACGATTGAACTCGCTCAATTCGGTAAGTATTC
66 CTTTTGATTTCTTTTATGCCTCCATCGTGCTCGACGATTGAACTCGCTCAATTCGATAAGTATTC
28358289 GTTTTGCCA
131 GTTTTGCCA
*
28358298 CTTCCATCATTTTGACGTTTATTCACCCATTGTCTGCCGAATTTTCATCGATTCCTCCCTCTTTT
1 CTTCCATCATTCTGACGTTTATTCACCCATTGTCTGCCGAATTTTCATCGATTCCTCCCTCTTTT
* **
28358363 CTTTTGATTTCTTTTATGCCTCCATCGTGGTCGACGATTGAACTCGCTTGATTCGATAAGTATTC
66 CTTTTGATTTCTTTTATGCCTCCATCGTGCTCGACGATTGAACTCGCTCAATTCGATAAGTATTC
*
28358428 GTTTTGTCA
131 GTTTTGCCA
28358437 CTT
1 CTT
28358440 TCTCTCGTTC
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 129 1.00
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.45
Consensus pattern (139 bp):
CTTCCATCATTCTGACGTTTATTCACCCATTGTCTGCCGAATTTTCATCGATTCCTCCCTCTTTT
CTTTTGATTTCTTTTATGCCTCCATCGTGCTCGACGATTGAACTCGCTCAATTCGATAAGTATTC
GTTTTGCCA
Found at i:28368501 original size:1 final size:1
Alignment explanation
Indices: 28368495--28368529 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
28368485 TGTCGATTAC
28368495 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28368530 CAACAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28373774 original size:20 final size:20
Alignment explanation
Indices: 28373751--28373797 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28373741 CAAAAGAAAA
28373751 AATCGATTCAAAAAATTAGC
1 AATCGATTCAAAAAATTAGC
* *
28373771 AATCGATTCAAAATATTATC
1 AATCGATTCAAAAAATTAGC
28373791 AATCGAT
1 AATCGAT
28373798 ACGAACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (20 bp):
AATCGATTCAAAAAATTAGC
Found at i:28373906 original size:42 final size:42
Alignment explanation
Indices: 28373847--28373969 Score: 176
Period size: 42 Copynumber: 2.9 Consensus size: 42
28373837 ATTTTTGAAC
* *
28373847 ATTAGCTTGCTCACAAACGTGTAGCAAGGAAACATGAAAAAT
1 ATTAGCTTGCTCACAAACGTGCAGCAAGGAAGCATGAAAAAT
* *
28373889 ATTAGCTTGCTAACAAACGTGCAACAAAGG-AGCATGAAAAAT
1 ATTAGCTTGCTCACAAACGTGCAGC-AAGGAAGCATGAAAAAT
* *
28373931 ATCAGCTTACTCACAAACGTGCAGCAAGGAAGCATGAAA
1 ATTAGCTTGCTCACAAACGTGCAGCAAGGAAGCATGAAA
28373970 CAATCTGCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 4 0.06
42 63 0.89
43 4 0.06
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.19
Consensus pattern (42 bp):
ATTAGCTTGCTCACAAACGTGCAGCAAGGAAGCATGAAAAAT
Found at i:28377381 original size:18 final size:19
Alignment explanation
Indices: 28377358--28377395 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28377348 GGAAGCAGGC
*
28377358 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
28377376 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
28377395 A
1 A
28377396 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:28388210 original size:26 final size:26
Alignment explanation
Indices: 28388181--28388232 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
28388171 AAAAAGAAAG
28388181 TTTTT-TATTAATTAAAGA-AAAATAA
1 TTTTTGTATTAATTAAA-ATAAAATAA
*
28388206 TTTTTGTATTATTTAAAATAAAATAA
1 TTTTTGTATTAATTAAAATAAAATAA
28388232 T
1 T
28388233 GATTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
TTTTTGTATTAATTAAAATAAAATAA
Found at i:28418674 original size:46 final size:47
Alignment explanation
Indices: 28418621--28418714 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 47
28418611 TTGAATATAA
28418621 TAGATTATGATAAGAAAAAATTATTTTGTTAGTATT-TATAATTTGT
1 TAGATTATGATAAGAAAAAATTATTTTGTTAGTATTATATAATTTGT
*
28418667 TAGATTATGATAAGAAAAAATTATTTTGTTAGTATTATATAGTTTGT
1 TAGATTATGATAAGAAAAAATTATTTTGTTAGTATTATATAATTTGT
28418714 T
1 T
28418715 TAGTGTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 36 0.78
47 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (47 bp):
TAGATTATGATAAGAAAAAATTATTTTGTTAGTATTATATAATTTGT
Found at i:28420694 original size:43 final size:43
Alignment explanation
Indices: 28420550--28420706 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
28420540 TGTGATTTTG
*
28420550 TGTAAGACCACGTCTGGGAC-GATGGCATCGATT-TGA-GATTTGCA
1 TGTAAGACCACGTCTGGGACAG-TGGCATC-ATTAT-ATGA-TTACA
* * * *
28420594 TGTAAGACCATGTCTGGGACATTGGCATC-GTATATGGTTA-A
1 TGTAAGACCACGTCTGGGACAGTGGCATCATTATATGATTACA
* *
28420635 GTGTAAGACC-CTGTCTGGGACAGTGACATCATTATTTGATTACA
1 -TGTAAGACCAC-GTCTGGGACAGTGGCATCATTATATGATTACA
28420679 TGTAAGACCACGTCTGGGAC-GTTGGCAT
1 TGTAAGACCACGTCTGGGACAG-TGGCAT
28420707 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
41 1 0.01
42 30 0.33
43 33 0.36
44 28 0.30
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCATTATATGATTACA
Found at i:28424741 original size:62 final size:62
Alignment explanation
Indices: 28424665--28424789 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
28424655 CAATGTACCT
*
28424665 AATTTATATTACAAAGGTTGTTCCAATTTTTAATGTTGTAATGTACTTAATTTATATAACAA
1 AATTTATATTACAAAGGTTGTTCCAATTTTTAATATTGTAATGTACTTAATTTATATAACAA
* * * *
28424727 AATTTATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTGTATTACAA
1 AATTTATATTACAAAGGTTGTTCCAATTTTTAATATTGTAATGTACTTAATTTATATAACAA
28424789 A
1 A
28424790 GTTTGTTCCA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (62 bp):
AATTTATATTACAAAGGTTGTTCCAATTTTTAATATTGTAATGTACTTAATTTATATAACAA
Found at i:28427507 original size:20 final size:22
Alignment explanation
Indices: 28427468--28427509 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28427458 AATTTCATTT
*
28427468 ATAATATTTATAAGAACATAAA
1 ATAAAATTTATAAGAACATAAA
28427490 ATAAAATTTA-AA-AACATAAA
1 ATAAAATTTATAAGAACATAAA
28427510 CTCTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
ATAAAATTTATAAGAACATAAA
Found at i:28427636 original size:6 final size:7
Alignment explanation
Indices: 28427620--28427647 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28427610 TACCTACATC
28427620 AAAAATA
1 AAAAATA
28427627 AAAAATA
1 AAAAATA
28427634 AAAAATA
1 AAAAATA
28427641 AAAAATA
1 AAAAATA
28427648 TTAAAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:28432967 original size:21 final size:21
Alignment explanation
Indices: 28432885--28432976 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 21
28432875 TTTTATAAAA
* *
28432885 TTTAAA-AA-TTTATGAAATC
1 TTTAAATAATTTTATGATATT
* *
28432904 TTTATATAATTTTATGATTTT
1 TTTAAATAATTTTATGATATT
* ***
28432925 TTTGAAA-AATGTTA-GGGGTT
1 TTT-AAATAATTTTATGATATT
28432945 TTTAAATAATTTTATGATA-T
1 TTTAAATAATTTTATGATATT
28432965 TTTAAAGTAATT
1 TTTAAA-TAATT
28432977 ATGAGTTTTC
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
19 8 0.15
20 21 0.39
21 23 0.43
22 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (21 bp):
TTTAAATAATTTTATGATATT
Found at i:28443490 original size:14 final size:15
Alignment explanation
Indices: 28443471--28443499 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28443461 GTTTTTCTCG
28443471 ATTTAAATT-TTTTT
1 ATTTAAATTATTTTT
28443485 ATTTAAATTATTTTT
1 ATTTAAATTATTTTT
28443500 TGAAAATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTAAATTATTTTT
Done.