Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 101 of 213
Found at i:28553084 original size:17 final size:18
Alignment explanation
Indices: 28553062--28553102 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
28553052 TTTTCCTGGG
28553062 CCCAAAACCAAT-ACAAA
1 CCCAAAACCAATAACAAA
* *
28553079 CCC-AAACTATTAACAAA
1 CCCAAAACCAATAACAAA
28553096 CCCAAAA
1 CCCAAAA
28553103 TAAATTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.30
17 11 0.55
18 3 0.15
ACGTcount: A:0.56, C:0.34, G:0.00, T:0.10
Consensus pattern (18 bp):
CCCAAAACCAATAACAAA
Found at i:28554525 original size:3 final size:3
Alignment explanation
Indices: 28554519--28554548 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28554509 ATTATTCTAT
28554519 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28554549 TATTAGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:28558580 original size:9 final size:9
Alignment explanation
Indices: 28558566--28558594 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28558556 TTCAGACTCA
28558566 AAAAAAATC
1 AAAAAAATC
28558575 -AAAAAATC
1 AAAAAAATC
28558583 AAAAAAATC
1 AAAAAAATC
28558592 AAA
1 AAA
28558595 GTCAAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:28558621 original size:6 final size:6
Alignment explanation
Indices: 28558598--28558656 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
28558588 AATCAAAGTC
* * *
28558598 AAAATAG AAAAA- AAAAAG AAAAAG GAAAA- AAGAAG AAAAAG TAAAAG
1 AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
28558645 TAAAAG TAAAAG
1 AAAAAG AAAAAG
28558657 GAGAGGTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.18
6 33 0.73
7 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:28558628 original size:17 final size:17
Alignment explanation
Indices: 28558606--28558658 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
28558596 TCAAAATAGA
28558606 AAAAAAAAAGAAAAAGG
1 AAAAAAAAAGAAAAAGG
* *
28558623 AAAAAAGAAGAAAAAGT
1 AAAAAAAAAGAAAAAGG
* *
28558640 AAAAGTAAAAGTAAAAGG
1 AAAA-AAAAAGAAAAAGG
28558658 A
1 A
28558659 GAGGTCAAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAGG
Found at i:28561302 original size:50 final size:50
Alignment explanation
Indices: 28561240--28562266 Score: 1194
Period size: 50 Copynumber: 20.5 Consensus size: 50
28561230 ACAGTTAAAA
*
28561240 AGATTGAAGCTACAACAGTGGATCTTACTTTCTTAGCATTGCAATGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * * ** *
28561290 AGATTGAAGCTACAGCAGCGGATCTTACTTCCCT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* * *
28561340 AGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * * ** *
28561390 AGATTGAAGCTACAACAGCGAATCTTACTTCCAT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* *
28561440 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * ** * *
28561490 AGATTGAAGCCACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAAT
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * * *
28561540 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAAT-TAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAA-C
* *
28561590 AGATTGAAGCTACAACAGCAGATCTTACTTTCTTAGCGTTGCAATGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * ** *
28561640 AGATTGAAGCTACAACAGCGTATCTTACTTTCCT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* *
28561690 AGATTGAAGCTACAACAGCGGATTTTACTTT-TCTAGCATTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCT-TAGCATTGCAATGGAAC
* * ** *
28561740 AGATTGAAGCTACAATAGCGGATCTTACTTCTCTGA-CATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTT-TCTTAGCATTGCAATGGAAC
* *
28561790 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * ** *
28561840 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* *
28561890 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * ** *
28561940 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* *
28561990 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * * ** *
28562040 AGATTGAAGCTACAACAGCAGATCTTACTTCCCT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* * *
28562090 AGATTGAAGCTACAACAGCGAATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
* * * ** *
28562140 AGATTGAAACTACAACAGCGGATCTTACTTCCAT-GACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CATTGCAATGGAAC
* *
28562190 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
*
28562240 AGATTGAAGCCACAACAGCGGATCTTA
1 AGATTGAAGCTACAACAGCGGATCTTA
28562267 GTGGAACAGA
Statistics
Matches: 816, Mismatches: 139, Indels: 44
0.82 0.14 0.04
Matches are distributed among these distances:
49 14 0.02
50 789 0.97
51 12 0.01
52 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAAC
Found at i:28561373 original size:100 final size:100
Alignment explanation
Indices: 28561240--28562266 Score: 1449
Period size: 100 Copynumber: 10.3 Consensus size: 100
28561230 ACAGTTAAAA
* * ** *
28561240 AGATTGAAGCTACAACAGTGGATCTTACTTT-CTTAGCATTGCAATGGAACAGATTGAAGCTACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGA-CATTGCAATTAAAAAGATTGAAGCTACA
* * * * * ** *
28561304 GCAGCGGATCTTACTTCCCT-GACATTGCAATTAAAA
65 ACAGCGGATCTTACTTTCTTAG-CGTTGCAGTGGAAC
* * * * ** *
28561340 AGATTGAAGCTACAACAGCGAATCTTACTTT-CTTAGCGTTGCAGTGGAACAGATTGAAGCTACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGA-CATTGCAATTAAAAAGATTGAAGCTACA
* * * * * ** *
28561404 ACAGCGAATCTTACTTCCAT-GACATTGCAATTAAAA
65 ACAGCGGATCTTACTTTCTTAG-CGTTGCAGTGGAAC
* * * ** * *
28561440 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTTAGCGTTGCAGTGGAACAGATTGAAGCCACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGA-CATTGCAATTAAAAAGATTGAAGCTACA
* * *
28561504 ACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAAT
65 ACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
* *
28561540 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
* *
28561605 CAGCAGATCTTACTTTCTTAGCGTTGCAATGGAAC
66 CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
*
28561640 AGATTGAAGCTACAACAGCGTATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
* *
28561705 CAGCGGATTTTACTTT-TCTAGCATTGCAGTGGAAC
66 CAGCGGATCTTACTTTCT-TAGCGTTGCAGTGGAAC
*
28561740 AGATTGAAGCTACAATAGCGGATCTTAC-TTCTCTGACATTGCAATTAAAAAGATTGAAGCTACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTC-CTGACATTGCAATTAAAAAGATTGAAGCTACA
28561804 ACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
65 ACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
*
28561840 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
28561905 CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
66 CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
*
28561940 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
28562005 CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
66 CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
* *
28562040 AGATTGAAGCTACAACAGCAGATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
*
28562105 CAGCGAATCTTACTTTCTTAGCGTTGCAGTGGAAC
66 CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
*
28562140 AGATTGAAACTACAACAGCGGATCTTAC-TTCCATGACATTGCAATTAAAAAGATTGAAGCTACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCC-TGACATTGCAATTAAAAAGATTGAAGCTACA
28562204 ACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
65 ACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
*
28562240 AGATTGAAGCCACAACAGCGGATCTTA
1 AGATTGAAGCTACAACAGCGGATCTTA
28562267 GTGGAACAGA
Statistics
Matches: 867, Mismatches: 53, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
99 7 0.01
100 853 0.98
101 7 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (100 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAAC
Found at i:28561476 original size:200 final size:199
Alignment explanation
Indices: 28561240--28562574 Score: 1549
Period size: 200 Copynumber: 6.8 Consensus size: 199
28561230 ACAGTTAAAA
* * ** *
28561240 AGATTGAAGCTACAACAGTGGATCTTACTTT-CTTAGCATTGCAATGGAACAGATTGAAGCTACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGA-CATTGCAATTAAAAAGATTGAAGCTACA
* * * * ** * *
28561304 GCAGCGGATCTTACTTCCCT-GACATTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTAC
65 ACAGCGGATCTTACTT-TCTAG-CGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTAC
* * * * ** * * * * *
28561368 TT-TCTTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCAT-GACATTG
128 TTCCCTGA-CATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CGTTG
* ** *
28561431 CAATTAAAA
191 CAGTGGAAC
* * * ** * *
28561440 AGATTGAAGCTACAACAGCGGATCTTACTTT-CTTAGCGTTGCAGTGGAACAGATTGAAGCCACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGA-CATTGCAATTAAAAAGATTGAAGCTACA
* *
28561504 ACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAATAGATTGAAGCTACAACAGCGGATCTTACT
65 ACAGCGGATCTTACTTT-CTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACT
* * *
28561569 TCCCTGACATTGCAATTAAGAAGATTGAAGCTACAACAGCAGATCTTACTTTCTTAGCGTTGCAA
129 TCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAG
28561634 TGGAAC
194 TGGAAC
*
28561640 AGATTGAAGCTACAACAGCGTATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
* * *
28561705 CAGCGGATTTTACTTTTCTAGCATTGCAGTGGAACAGATTGAAGCTACAATAGCGGATCTTACTT
66 CAGCGGATCTTAC-TTTCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
*
28561770 CTCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGT
130 CCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGT
28561835 GGAAC
195 GGAAC
*
28561840 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
28561905 CAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
66 CAGCGGATCTTACTTTC-TAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
28561970 CCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGT
130 CCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGT
28562035 GGAAC
195 GGAAC
* *
28562040 AGATTGAAGCTACAACAGCAGATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
* *
28562105 CAGCGAATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAACTACAACAGCGGATCTTACTT
66 CAGCGGATCTTACTTTC-TAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
*
28562170 CCATGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGT
130 CCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGT
28562235 GGAAC
195 GGAAC
* * * *
28562240 AGATTGAAGCCACAACAGCGGATCTTA-------G----TG-----GAACAGATTGAAGCCACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
* * *
28562289 CAGAGGATCTTACTTTCTTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGCTT
66 CAGCGGATCTTACTTTC-TAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
* * * * *
28562354 CCC---C--GGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTC-CAGGCGGTGCAG
130 CCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA-GCGTTGCAG
*
28562413 TGGAAT
194 TGGAAC
* * ***
28562419 AGATTAAAGCTACAACGGTAAATCTT-CTTTCCCTGACATTGCAATTAAAAAGATTGAAG-TCAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTT-CCTGACATTGCAATTAAAAAGATTGAAGCT-AC
** * * * * * * * * * * *
28562482 AATGGCGAATCTTACTTCCCAGAAGATGTAATGGAATAGATTGAAGCTACGACGGCGAATCTTAC
64 AACAGCGGATCTTACTTTCTAG-CGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTAC
** * * *
28562547 TTCCCCAACATTGTAGTTAAACAGATTG
128 TTCCCTGACATTGCAATTAAAAAGATTG
28562575 GAGATGGCAG
Statistics
Matches: 1002, Mismatches: 101, Indels: 64
0.86 0.09 0.05
Matches are distributed among these distances:
178 1 0.00
179 73 0.07
181 1 0.00
184 78 0.08
186 1 0.00
189 2 0.00
190 2 0.00
193 1 0.00
194 2 0.00
195 65 0.06
198 1 0.00
199 4 0.00
200 760 0.76
201 11 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (199 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAA
CAGCGGATCTTACTTTCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTC
CCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTG
GAAC
Found at i:28562270 original size:34 final size:34
Alignment explanation
Indices: 28562232--28562300 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
28562222 TTAGCGTTGC
*
28562232 AGTGGAACAGATTGAAGCCACAACAGCGGATCTT
1 AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
28562266 AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
1 AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
28562300 A
1 A
28562301 CTTTCTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (34 bp):
AGTGGAACAGATTGAAGCCACAACAGAGGATCTT
Found at i:28562301 original size:84 final size:84
Alignment explanation
Indices: 28562190--28562349 Score: 284
Period size: 84 Copynumber: 1.9 Consensus size: 84
28562180 GCAATTAAAA
* *
28562190 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
1 AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
28562255 CAGCGGATCTTAGTGGAAC
66 CAGCGGATCTTAGTGGAAC
* *
28562274 AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
28562339 CAGCGGATCTT
66 CAGCGGATCTT
28562350 GCTTCCCCGG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (84 bp):
AGATTGAAGCCACAACAGAGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCCACAA
CAGCGGATCTTAGTGGAAC
Found at i:28562429 original size:50 final size:50
Alignment explanation
Indices: 28562369--28562548 Score: 177
Period size: 50 Copynumber: 3.6 Consensus size: 50
28562359 GCAATTAAAA
* * *
28562369 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGTGGAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGACGATGCAATGGAAT
* ** * ** *
28562419 AGATTAAAGCTACAACGGTAAATCTT-CTTTCCCTGAC-ATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTT-CCAGACGA-TGCAATGGAAT
* * * *
28562469 AGATTGAAG-TCACAATGGCGAATCTTACTTCCCAGAAGATGTAATGGAAT
1 AGATTGAAGCT-ACAACGGCGAATCTTACTTTCCAGACGATGCAATGGAAT
*
28562519 AGATTGAAGCTACGACGGCGAATCTTACTT
1 AGATTGAAGCTACAACGGCGAATCTTACTT
28562549 CCCCAACATT
Statistics
Matches: 101, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
49 5 0.05
50 91 0.90
51 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTTCCAGACGATGCAATGGAAT
Found at i:28562444 original size:95 final size:95
Alignment explanation
Indices: 28562313--28562553 Score: 261
Period size: 100 Copynumber: 2.5 Consensus size: 95
28562303 TTCTTAGTGT
* * *
28562313 TGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGCTTCCCC-GGCAATTAAAAAGATTGAA
1 TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTT-CTTCCCCAGGCAATTAAAAAGATTGAA
* ** *
28562377 G-CTACAACGGCGAATCTTACTTTCCAGGCGG
65 GTC-ACAACGGCGAATCTTACTTCCCAGAAGA
* ** *
28562408 TGCAGTGGAATAGATTAAAGCTACAACGGTAAATCTTCTTTCCCTGACATTGCAATTAAAAAGAT
1 TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTC-TTCCC---CA-GGCAATTAAAAAGAT
*
28562473 TGAAGTCACAATGGCGAATCTTACTTCCCAGAAGA
61 TGAAGTCACAACGGCGAATCTTACTTCCCAGAAGA
* * *
28562508 TGTAATGGAATAGATTGAAGCTACGACGGCGAATCTTACTTCCCCA
1 TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTT-CTTCCCCA
28562554 ACATTGTAGT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
94 1 0.01
95 36 0.30
97 2 0.02
98 1 0.01
100 78 0.65
101 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (95 bp):
TGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTCTTCCCCAGGCAATTAAAAAGATTGAAG
TCACAACGGCGAATCTTACTTCCCAGAAGA
Found at i:28562573 original size:50 final size:50
Alignment explanation
Indices: 28562359--28562574 Score: 152
Period size: 50 Copynumber: 4.3 Consensus size: 50
28562349 TGCTTCCCCG
* * **
28562359 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTT-TCCAGGCGGT
1 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCA-ACATT
* ** * * ** **
28562409 GCAGTGGAATAGATTAAAGCTACAACGGTAAATCTT-CTTTCCCTGACATT
1 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCCAACATT
* * *
28562459 GCAATTAAAAAGATTGAAG-TCACAATGGCGAATCTTACTTCCCAGAAGA-T
1 GCAATTAAAAAGATTGAAGCT-ACAACGGCGAATCTTACTTCCC-CAACATT
* ** * *
28562509 GTAATGGAATAGATTGAAGCTACGACGGCGAATCTTACTTCCCCAACATT
1 GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATT
* * *
28562559 GTAGTTAAACAGATTG
1 GCAATTAAAAAGATTG
28562575 GAGATGGCAG
Statistics
Matches: 123, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
49 5 0.04
50 113 0.92
51 5 0.04
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (50 bp):
GCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATT
Found at i:28562648 original size:18 final size:18
Alignment explanation
Indices: 28562625--28562659 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28562615 GATCGCATCT
*
28562625 AGTCCTATCTCCCTAAGC
1 AGTCCTATCACCCTAAGC
28562643 AGTCCTATCACCCTAAG
1 AGTCCTATCACCCTAAG
28562660 TAGTAGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (18 bp):
AGTCCTATCACCCTAAGC
Found at i:28562890 original size:132 final size:132
Alignment explanation
Indices: 28562643--28563274 Score: 976
Period size: 132 Copynumber: 4.8 Consensus size: 132
28562633 CTCCCTAAGC
* * *
28562643 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTGTCATCCTAAGCAGT
1 AGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * * *
28562708 AGTGGAGCAGATCGAAAATGGTGAATCTTATCTTCGCAATACAGTAGAGAAGCAGATTTAAGTCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
28562773 TT
131 TT
* * * *
28562775 TGTCCTATCACCCTAAGTAGTAGTGGAGTAGATTGAATATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
28562840 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATATAGTGGAGAAGCAAATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
28562905 TT
131 TT
* * * ** * *
28562907 AGTCTTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGCAGATTCTGTCACCTTAAACAGT
1 AGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
*
28562972 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAACAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
28563037 TT
131 TT
* * * * *
28563039 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCGAAGATTACAGATTCTGTCACCCTAAGTAGT
1 AGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * * *
28563104 AGTGGAGCAGATCGAATATGGTGAATCTTATCTTTCCAATACAGTGGAGAAGTAGATTTAAGCCG
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
28563169 TT
131 TT
* *
28563171 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGT
1 AGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
28563236 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
28563275 GTGGAATGAA
Statistics
Matches: 455, Mismatches: 45, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 455 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (132 bp):
AGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
TT
Found at i:28563478 original size:17 final size:18
Alignment explanation
Indices: 28563456--28563497 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
28563446 TTTTCCTGGG
28563456 CCCAAAACCAAT-ACAAA
1 CCCAAAACCAATAACAAA
* *
28563473 CCC-AAACTATTAACAAA
1 CCCAAAACCAATAACAAA
28563490 CCCAAAAC
1 CCCAAAAC
28563498 AAATTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.55, C:0.36, G:0.00, T:0.10
Consensus pattern (18 bp):
CCCAAAACCAATAACAAA
Found at i:28565596 original size:2 final size:2
Alignment explanation
Indices: 28565589--28565625 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28565579 CTGTGTATGA
28565589 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
28565626 ATCGATCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:28569936 original size:6 final size:6
Alignment explanation
Indices: 28569927--28569958 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
28569917 CACGCCTTTG
28569927 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CC
1 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CC
28569959 CATTGCTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.53, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTTCA
Found at i:28572726 original size:29 final size:30
Alignment explanation
Indices: 28572689--28572745 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28572679 TCCGAGCCTT
*
28572689 GGGGAAAAAT-GTAATTATGTAAAAGTTTA
1 GGGGAAAAATCGTAATTATGAAAAAGTTTA
* *
28572718 GGGGCAAAATCGTAATTTTGAAAAAGTT
1 GGGGAAAAATCGTAATTATGAAAAAGTT
28572746 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.30
Consensus pattern (30 bp):
GGGGAAAAATCGTAATTATGAAAAAGTTTA
Found at i:28573154 original size:50 final size:50
Alignment explanation
Indices: 28573079--28573377 Score: 402
Period size: 50 Copynumber: 5.9 Consensus size: 50
28573069 CATTTGGGTA
* *
28573079 GAGAGGTCTCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
28573129 GAGAGGTCCCATGTAAGGCCATGTCTGGGACATGGCGTTGGCATTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC----G--TTGGCACCGAGAT
* * **
28573185 GAGAGGTCCCATATAAGACCATGTCTGAGACATGGCACTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
28573235 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * *
28573285 GTGAGGTCCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
** *
28573334 GAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
28573378 TGTTATGATC
Statistics
Matches: 222, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
49 38 0.17
50 107 0.48
51 30 0.14
54 1 0.00
56 46 0.21
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:28573264 original size:106 final size:104
Alignment explanation
Indices: 28573079--28573378 Score: 414
Period size: 106 Copynumber: 2.9 Consensus size: 104
28573069 CATTTGGGTA
* * *
28573079 GAGAGGTCTCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTA
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-ATGGCACCGAGATGAGAGGTCCCATGTA
*
28573144 AGGCCATGTCTGGGACATGGCGTTGGCATTGGCACCGAGAT
65 AGACCATGTCTGGGACATGGC-TTGGCATTGGCACCGAGAT
* *
28573185 GAGAGGTCCCATATAAGACCATGTCTGAGACATGGCACTGGCACCGAGATGAGAGGTCCCATGTA
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TGGCACCGAGATGAGAGGTCCCATGTA
28573250 AGACCATGTCTGGGACATGGC---G--TTGGCACCGAGAT
65 AGACCATGTCTGGGACATGGCTTGGCATTGGCACCGAGAT
* * **
28573285 GTGAGGTCCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT-GGCACCGAGATGAG-AGGTCCCATGT
28573349 AAGACCATGTCTGGGACATGGCTTTGGCAT
64 AAGACCATGTCTGGGACATGGC-TTGGCAT
28573379 GTTATGATCA
Statistics
Matches: 173, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
98 1 0.01
99 37 0.21
100 53 0.31
102 1 0.01
104 1 0.01
106 80 0.46
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.21
Consensus pattern (104 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGAGATGAGAGGTCCCATGTAA
GACCATGTCTGGGACATGGCTTGGCATTGGCACCGAGAT
Found at i:28573377 original size:156 final size:151
Alignment explanation
Indices: 28573079--28573370 Score: 426
Period size: 156 Copynumber: 1.9 Consensus size: 151
28573069 CATTTGGGTA
* *
28573079 GAGAGGTCTCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTA
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTA
* * **
28573144 AGGCCATGTCTGGGACATGGCGTTGGCATTGGCACCGAGATGAGAGGTCCCATATAAGACCATGT
66 AGACCATGTCTGGGACA----G-TGGCATGGGCACCGAGATGAGACATCCCATATAAGACCATGT
28573209 CTGAGACATGGCACTGGCACCGAGAT
126 CTGAGACATGGCACTGGCACCGAGAT
*
28573235 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGTGAGGTCCC-TGTA
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTA
* * *
28573299 AGACCATGTCTGGGACA-TGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGG
66 AGACCATGTCTGGGACAGTGGCATGGGCACCGAGATGAG-ACATCCCATATAAGACCATGTCTGA
28573363 GACATGGC
130 GACATGGC
28573371 TTTGGCATGT
Statistics
Matches: 125, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
149 19 0.15
150 29 0.23
155 20 0.16
156 57 0.46
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.21
Consensus pattern (151 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTA
AGACCATGTCTGGGACAGTGGCATGGGCACCGAGATGAGACATCCCATATAAGACCATGTCTGAG
ACATGGCACTGGCACCGAGAT
Found at i:28595982 original size:26 final size:27
Alignment explanation
Indices: 28595938--28595991 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28595928 TGGATCCGTA
*
28595938 TGTTACTTGTTTTTGTTAATTTTAATT
1 TGTTACTTGTTTTTGTTAATTTCAATT
* *
28595965 TGTTTCTT-TTTTTTTTAATTTCAATT
1 TGTTACTTGTTTTTGTTAATTTCAATT
28595991 T
1 T
28595992 ACTAAGCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.17, C:0.06, G:0.07, T:0.70
Consensus pattern (27 bp):
TGTTACTTGTTTTTGTTAATTTCAATT
Found at i:28602149 original size:19 final size:20
Alignment explanation
Indices: 28602127--28602171 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
28602117 AAAAAATACA
28602127 AAAAAATTA-AAATATTT-AT
1 AAAAAATTACAAAT-TTTCAT
28602146 AAAAAATTACAAATTTTCAT
1 AAAAAATTACAAATTTTCAT
28602166 AAAAAA
1 AAAAAA
28602172 AATTTCACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATTACAAATTTTCAT
Found at i:28604522 original size:22 final size:21
Alignment explanation
Indices: 28604497--28604544 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
28604487 ACTTATGTTT
28604497 TAAAA-TTCAAAAAATAAATGAA
1 TAAAATTTCAAAAAATAAA--AA
*
28604519 TAAAATTTCTAAAAATAAAAA
1 TAAAATTTCAAAAAATAAAAA
28604540 TAAAA
1 TAAAA
28604545 GTTTGGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 12 0.50
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAAATTTCAAAAAATAAAAA
Found at i:28605262 original size:9 final size:9
Alignment explanation
Indices: 28605248--28605275 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28605238 TTATTGTTAG
28605248 TGTGAATAT
1 TGTGAATAT
28605257 TGTGAATAT
1 TGTGAATAT
28605266 TGTGAATAT
1 TGTGAATAT
28605275 T
1 T
28605276 ATTTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (9 bp):
TGTGAATAT
Found at i:28606775 original size:19 final size:19
Alignment explanation
Indices: 28606742--28606789 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
28606732 TAAACAATTC
28606742 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
28606759 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
28606778 AATAATATAAAT
1 AATAATATAAAT
28606790 AGTAGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:28606929 original size:17 final size:16
Alignment explanation
Indices: 28606879--28606941 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 16
28606869 GGGTAAGAAG
28606879 TAAAAGTTTAGGGGAAAAA
1 TAAAAGTTTA-GGG--AAA
*
28606898 TAAAAAGTTTTGGGAAA
1 T-AAAAGTTTAGGGAAA
28606915 TAAAAGTTTGAGGGAAA
1 TAAAAGTTT-AGGGAAA
28606932 GTAAATAGTT
1 -TAAA-AGTT
28606942 GGAGTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 8 0.21
17 10 0.26
18 4 0.11
19 8 0.21
20 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (16 bp):
TAAAAGTTTAGGGAAA
Found at i:28608305 original size:7 final size:8
Alignment explanation
Indices: 28608288--28608312 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28608278 ATGAAATTAT
28608288 AAAAATAA
1 AAAAATAA
28608296 AAAAATAA
1 AAAAATAA
28608304 AAAAATAA
1 AAAAATAA
28608312 A
1 A
28608313 TTATGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:28608641 original size:19 final size:19
Alignment explanation
Indices: 28608617--28608656 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28608607 ACTAATTACA
28608617 AAGCTTAAATCATCTCCCT
1 AAGCTTAAATCATCTCCCT
28608636 AAGCTTAAATCATCTCCCT
1 AAGCTTAAATCATCTCCCT
28608655 AA
1 AA
28608657 CGGGTAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (19 bp):
AAGCTTAAATCATCTCCCT
Found at i:28611373 original size:43 final size:43
Alignment explanation
Indices: 28611325--28611411 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
28611315 ATAATGTCAT
*
28611325 TAGTTAGTCTAAATATTTAATATTATTAACTATTTCAATAAAA
1 TAGTTAGTCTAAATATTTAATACTATTAACTATTTCAATAAAA
* *
28611368 TAGTTAGTCTAAATATTTAATACTGTTAACTGTTTCAATAAAA
1 TAGTTAGTCTAAATATTTAATACTATTAACTATTTCAATAAAA
28611411 T
1 T
28611412 TGTTTATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (43 bp):
TAGTTAGTCTAAATATTTAATACTATTAACTATTTCAATAAAA
Found at i:28612337 original size:43 final size:44
Alignment explanation
Indices: 28612234--28612469 Score: 219
Period size: 44 Copynumber: 5.4 Consensus size: 44
28612224 GGGTCTCCAA
* * ** *
28612234 TCCC-ATCTTATGTGTATGCGATATGTGAATTTTATCCCGTTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* *
28612277 TCCCCATCTTATATGTATGCTATGTGTGGGTTTT-TCCAGTTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* * *
28612320 TCCCTATCTTGTGTGTATG-TCATGTATGGGTTTTATCCAATTCT
1 TCCCTATCTTATGTGTATGCT-ATGTGTGGGTTTTATCCAGTTCT
* * * * * *
28612364 TTCCTAT-TTGTGTATATACTATGTGTGGATTTTATCTAGTTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* * * * * *
28612407 TCCCTATCTTGTGTGTACGCCATGTATGAGTTTTATCCAATTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* *
28612451 TCTCTCTCTTATGTGTATG
1 TCCCTATCTTATGTGTATG
28612470 TCCGTTGTGC
Statistics
Matches: 156, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.01
43 74 0.47
44 81 0.52
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (44 bp):
TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
Found at i:28612442 original size:44 final size:44
Alignment explanation
Indices: 28612263--28612469 Score: 211
Period size: 43 Copynumber: 4.8 Consensus size: 44
28612253 GATATGTGAA
* * * * * *
28612263 TTTTATCCCGTTCTTCCCCATCTTATATGTATGCTATGTGTGGG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
*
28612307 TTTT-TCCAGTTCTTCCCTATCTTGTGTGTATGTCATGTATGGG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
* * * * * * *
28612350 TTTTATCCAATTCTTTCCTAT-TTGTGTATATACTATGTGTGGA
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
* * *
28612393 TTTTATCTAGTTCTTCCCTATCTTGTGTGTACGCCATGTATGAG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
* * * *
28612437 TTTTATCCAATTCTTCTCTCTCTTATGTGTATG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATG
28612470 TCCGTTGTGC
Statistics
Matches: 130, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
43 70 0.54
44 60 0.46
ACGTcount: A:0.15, C:0.19, G:0.16, T:0.49
Consensus pattern (44 bp):
TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
Found at i:28617426 original size:19 final size:18
Alignment explanation
Indices: 28617386--28617426 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
28617376 TTGAGCTTGG
*
28617386 ATTTCACCATATTAAGCC
1 ATTTCACCATATTAAGCA
*
28617404 ATTTCACCATTATTGAGCA
1 ATTTCACCA-TATTAAGCA
28617423 ATTT
1 ATTT
28617427 TTTGTCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (18 bp):
ATTTCACCATATTAAGCA
Found at i:28617666 original size:79 final size:79
Alignment explanation
Indices: 28617535--28617701 Score: 300
Period size: 79 Copynumber: 2.1 Consensus size: 79
28617525 CAAAACAATT
28617535 TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAA-TTTTGAAAGGATTAA
1 TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTG-AAGGATTAA
*
28617599 ATCGAATTTTTATAA
65 ATAGAATTTTTATAA
*
28617614 TTTTAGGGGCGGATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTGAAGGATTAAA
1 TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTGAAGGATTAAA
28617679 TAGAATTTTTATAA
66 TAGAATTTTTATAA
28617693 TTTTAGGGG
1 TTTTAGGGG
28617702 GCTAAAGTGT
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
79 80 0.94
80 5 0.06
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (79 bp):
TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTGAAGGATTAAA
TAGAATTTTTATAA
Found at i:28619342 original size:26 final size:27
Alignment explanation
Indices: 28619309--28619368 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
28619299 AAAAATAATT
28619309 AAAATATTAT-AATTTTTTTATTTATC
1 AAAATATTATAAATTTTTTTATTTATC
28619335 AAAATATTATAAATTTTTTTATTTATC
1 AAAATATTATAAATTTTTTTATTTATC
28619362 AAAATAT
1 AAAATAT
28619369 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
AAAATATTATAAATTTTTTTATTTATC
Found at i:28619683 original size:18 final size:18
Alignment explanation
Indices: 28619662--28619696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28619652 GTAATAACTC
*
28619662 TATTTTAATTTAATAAAT
1 TATTCTAATTTAATAAAT
*
28619680 TATTCTCATTTAATAAA
1 TATTCTAATTTAATAAA
28619697 CTCTAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTCTAATTTAATAAAT
Found at i:28619707 original size:15 final size:15
Alignment explanation
Indices: 28619687--28619716 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28619677 AATTATTCTC
28619687 ATTTAATAAACTCTA
1 ATTTAATAAACTCTA
28619702 ATTTAATAAACTCTA
1 ATTTAATAAACTCTA
28619717 TTTTGGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAATAAACTCTA
Found at i:28619786 original size:45 final size:45
Alignment explanation
Indices: 28619722--28619810 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
28619712 CTCTATTTTG
28619722 GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTAA
1 GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTAA
*
28619767 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
1 GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTA
28619811 CTTATTAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (45 bp):
GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTAA
Found at i:28620516 original size:26 final size:27
Alignment explanation
Indices: 28620465--28620524 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
28620455 TGTTTTTGGT
** *
28620465 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTAATAAATAAAAAAAGTTATA
28620492 ATATTTTAATAAAT-AAAAAAGTTATA
1 ATATTTTAATAAATAAAAAAAGTTATA
28620518 ATATTTT
1 ATATTTT
28620525 GTTATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (27 bp):
ATATTTTAATAAATAAAAAAAGTTATA
Found at i:28620966 original size:23 final size:23
Alignment explanation
Indices: 28620940--28621011 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 23
28620930 ATTGTTATTA
*
28620940 ATTTTGAAAAATTTGAAATATAT
1 ATTTTGAAAAATTTTAAATATAT
**
28620963 A-TTTGAAATGTTTTATAATATAT
1 ATTTTGAAAAATTTTA-AATATAT
*
28620986 ATTTT-TAAAATTTTAAATAT-T
1 ATTTTGAAAAATTTTAAATATAT
28621007 ATTTT
1 ATTTT
28621012 TAAATTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.15
22 16 0.39
23 16 0.39
24 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (23 bp):
ATTTTGAAAAATTTTAAATATAT
Found at i:28620996 original size:25 final size:22
Alignment explanation
Indices: 28620947--28621069 Score: 79
Period size: 23 Copynumber: 5.1 Consensus size: 22
28620937 TTAATTTTGA
* *
28620947 AAAATTTGAAATATATA-TTTG
1 AAAATTTTAAATATATATTTTT
*
28620968 AAATGTTTTATAATATATATTTTT
1 AAA-ATTTTA-AATATATATTTTT
28620992 AAAATTTTAAATAT-TATTTTT
1 AAAATTTTAAATATATATTTTT
28621013 AAATTATTTTTTAAATTTTGAATATTATGTTTT
1 AAA--A--TTTTAAA---T--ATA-TAT-TTTT
*
28621046 AAAATATTAAATATATATTTTT
1 AAAATTTTAAATATATATTTTT
28621068 AA
1 AA
28621070 TAATATAAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 29
0.71 0.04 0.25
Matches are distributed among these distances:
21 13 0.16
22 15 0.18
23 17 0.21
24 9 0.11
25 7 0.09
26 1 0.01
28 1 0.01
29 6 0.07
30 2 0.02
31 1 0.01
32 3 0.04
33 7 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
AAAATTTTAAATATATATTTTT
Found at i:28621021 original size:32 final size:33
Alignment explanation
Indices: 28620984--28621053 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
28620974 TTTATAATAT
28620984 ATATTTTTAAAATTTTAAATATTAT-TTTTAAA
1 ATATTTTTAAAATTTTAAATATTATGTTTTAAA
* * *
28621016 TTATTTTTTAAATTTTGAATATTATGTTTTAAA
1 ATATTTTTAAAATTTTAAATATTATGTTTTAAA
28621049 ATATT
1 ATATT
28621054 AAATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (33 bp):
ATATTTTTAAAATTTTAAATATTATGTTTTAAA
Found at i:28621022 original size:23 final size:23
Alignment explanation
Indices: 28620947--28621015 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 23
28620937 TTAATTTTGA
* *
28620947 AAAATTTGA-AATATATA-TTTG
1 AAAATTTTATAATATATATTTTT
*
28620968 AAATGTTTTATAATATATATTTTT
1 AAA-ATTTTATAATATATATTTTT
28620992 AAAATTTTA-AATAT-TATTTTT
1 AAAATTTTATAATATATATTTTT
28621013 AAA
1 AAA
28621016 TTATTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 13 0.32
22 9 0.22
23 13 0.32
24 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
AAAATTTTATAATATATATTTTT
Found at i:28621026 original size:33 final size:33
Alignment explanation
Indices: 28620970--28621053 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
28620960 TATATTTGAA
28620970 ATGTTTTATAATATATATTTTTAAAATTTTAAATATT
1 ATGTTTTA-AAT-TAT-TTTTT-AAATTTTAAATATT
*
28621007 AT-TTTTAAATTATTTTTTAAATTTTGAATATT
1 ATGTTTTAAATTATTTTTTAAATTTTAAATATT
*
28621039 ATGTTTTAAAATATT
1 ATGTTTTAAATTATT
28621054 AAATATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 15 0.34
33 16 0.36
34 3 0.07
35 3 0.07
36 5 0.11
37 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (33 bp):
ATGTTTTAAATTATTTTTTAAATTTTAAATATT
Found at i:28621050 original size:22 final size:21
Alignment explanation
Indices: 28621007--28621083 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
28620997 TTTAAATATT
* *
28621007 ATTTTTAA-ATTATTTTTTAA
1 ATTTTAAATATTATTTTTAAA
*
28621027 ATTTTGAATATTATGTTTTAAA
1 ATTTTAAATATTAT-TTTTAAA
*
28621049 ATATTAAATATATATTTTTAATA
1 ATTTTAAATAT-TATTTTTAA-A
* *
28621072 ATATAAAATATT
1 ATTTTAAATATT
28621084 TAAATATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 7 0.15
21 5 0.10
22 22 0.46
23 14 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTTAAATATTATTTTTAAA
Found at i:28621080 original size:23 final size:22
Alignment explanation
Indices: 28621033--28621083 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
28621023 TTAAATTTTG
*
28621033 AATATTATGTTTTAAAATATTA
1 AATATTATGTTTTAAAATATAA
28621055 AATATATAT-TTTTAATAATATAA
1 AATAT-TATGTTTTAA-AATATAA
28621078 AATATT
1 AATATT
28621084 TAAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AATATTATGTTTTAAAATATAA
Found at i:28621152 original size:19 final size:21
Alignment explanation
Indices: 28621128--28621176 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28621118 TATTAGTTTT
28621128 TTTAA-TATTTT-TAATATTA
1 TTTAATTATTTTATAATATTA
28621147 TTTAATTTATTTTATAATATT-
1 TTTAA-TTATTTTATAATATTA
*
28621168 TTAAATTAT
1 TTTAATTAT
28621177 GATTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 10 0.38
22 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAATTATTTTATAATATTA
Found at i:28621170 original size:10 final size:9
Alignment explanation
Indices: 28621126--28621169 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 9
28621116 ATTATTAGTT
28621126 TTTTTAATA
1 TTTTTAATA
28621135 TTTTTAATA
1 TTTTTAATA
28621144 TTATTTAATTTA
1 TT-TTTAA--TA
28621156 TTTTATAATA
1 TTTT-TAATA
28621166 TTTT
1 TTTT
28621170 AAATTATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 11 0.35
10 11 0.35
11 2 0.06
12 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAATA
Found at i:28621170 original size:20 final size:21
Alignment explanation
Indices: 28621133--28621176 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28621123 GTTTTTTTAA
*
28621133 TATTTTTAATATTATTTAATT
1 TATTTTTAATATTATTTAAAT
28621154 TATTTTATAATA-T-TTTAAAT
1 TATTTT-TAATATTATTTAAAT
28621174 TAT
1 TAT
28621177 GATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTTAATATTATTTAAAT
Found at i:28621753 original size:13 final size:13
Alignment explanation
Indices: 28621735--28621760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28621725 TATAGTGAAA
28621735 ACATTTCAAATAT
1 ACATTTCAAATAT
28621748 ACATTTCAAATAT
1 ACATTTCAAATAT
28621761 GCGCCATTTA
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTCAAATAT
Found at i:28622649 original size:7 final size:7
Alignment explanation
Indices: 28622637--28622661 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28622627 TGTTAGAGTT
28622637 TAAAGTA
1 TAAAGTA
28622644 TAAAGTA
1 TAAAGTA
28622651 TAAAGTA
1 TAAAGTA
28622658 TAAA
1 TAAA
28622662 TATTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
TAAAGTA
Found at i:28629322 original size:7 final size:7
Alignment explanation
Indices: 28629306--28629383 Score: 54
Period size: 7 Copynumber: 10.9 Consensus size: 7
28629296 TTAATATCCA
*
28629306 AATAAGT
1 AATAAAT
28629313 AATAAAT
1 AATAAAT
28629320 AAT-AA-
1 AATAAAT
28629325 AATAAAGT
1 AATAAA-T
28629333 AATAAAT
1 AATAAAT
*
28629340 AAAGTAAAGA
1 -AA-TAAA-T
*
28629350 AAAATAAT
1 AATA-AAT
28629358 AATAAAT
1 AATAAAT
*
28629365 AATAAAA
1 AATAAAT
28629372 AATAAA-
1 AATAAAT
28629378 AATAAA
1 AATAAA
28629384 AATTGGGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
5 3 0.05
6 10 0.17
7 25 0.43
8 12 0.21
9 8 0.14
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (7 bp):
AATAAAT
Found at i:28629334 original size:20 final size:20
Alignment explanation
Indices: 28629305--28629383 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 20
28629295 ATTAATATCC
28629305 AAAT-AAGTAATAAATAATA
1 AAATAAAGTAATAAATAATA
28629324 AAATAAAGTAAT--A-AATA
1 AAATAAAGTAATAAATAATA
*
28629341 AAGTAAAG-AA-AAATAAT-
1 AAATAAAGTAATAAATAATA
*
28629358 -AATAAA-TAATAAAAAATAA
1 AAATAAAGTAATAAATAAT-A
28629377 AAATAAA
1 AAATAAA
28629384 AATTGGGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
16 9 0.19
17 18 0.38
18 4 0.08
19 4 0.08
20 13 0.27
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (20 bp):
AAATAAAGTAATAAATAATA
Found at i:28629381 original size:13 final size:14
Alignment explanation
Indices: 28629317--28629385 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 14
28629307 ATAAGTAATA
28629317 AATAATAAAATAAAG
1 AATAA-AAAATAAAG
28629332 TAATAAATAAAGTAAAG
1 -AATAAA-AAA-TAAAG
* *
28629349 AAAAATAATAATAAAT
1 AATAA-AA-AATAAAG
28629365 AATAAAAAATAAA-
1 AATAAAAAATAAAG
28629378 AATAAAAA
1 AATAAAAA
28629386 TTGGGTTGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
13 8 0.17
14 6 0.13
15 3 0.07
16 21 0.46
17 8 0.17
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
AATAAAAAATAAAG
Found at i:28635281 original size:32 final size:32
Alignment explanation
Indices: 28635240--28635312 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
28635230 CTAGCTAACA
*
28635240 ATCGCTTCTGTGGGATCGTCTTATGCTAGATC
1 ATCGCTTCTGTGGGATCATCTTATGCTAGATC
28635272 ATCGCTTCTGTGGGATCATCTTATGCTAGATC
1 ATCGCTTCTGTGGGATCATCTTATGCTAGATC
*
28635304 AACGCTTCT
1 ATCGCTTCT
28635313 CAATGGCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (32 bp):
ATCGCTTCTGTGGGATCATCTTATGCTAGATC
Found at i:28651454 original size:86 final size:86
Alignment explanation
Indices: 28651309--28651477 Score: 302
Period size: 86 Copynumber: 2.0 Consensus size: 86
28651299 ACATGTTTTA
* * *
28651309 TATCGATGGTAGATGTTTCCTATAAAATGGAGATGATATGGAAAGATTTTTTGGAGTTAAGATAA
1 TATCGATGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
28651374 CCTTTGTGGAGAAAATTTACT
66 CCTTTGTGGAGAAAATTTACT
*
28651395 TATCGGTGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
1 TATCGATGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
28651460 CCTTTGTGGAGAAAATTT
66 CCTTTGTGGAGAAAATTT
28651478 TCATGTTGAG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.35
Consensus pattern (86 bp):
TATCGATGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
CCTTTGTGGAGAAAATTTACT
Found at i:28658109 original size:29 final size:29
Alignment explanation
Indices: 28658062--28658137 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
28658052 AATGGTACAT
* * * *
28658062 AGTACTTGATAAATATAACACCGGCATAG
1 AGTACTTGATAACTGTAACAACGGCATAA
* *
28658091 AGT-GTCTGATAACTGTAACAACGGTATAA
1 AGTACT-TGATAACTGTAACAACGGCATAA
28658120 AGTACTTGATAACTGTAA
1 AGTACTTGATAACTGTAA
28658138 TCACTGGCTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.03
29 36 0.95
30 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (29 bp):
AGTACTTGATAACTGTAACAACGGCATAA
Found at i:28668867 original size:19 final size:19
Alignment explanation
Indices: 28668834--28668878 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28668824 TGCATTCATT
* *
28668834 TTTCAGTCATCAGCATTACA
1 TTTCA-TCATAAGCATTAAA
28668854 TTTCATCATAAGCATTAAA
1 TTTCATCATAAGCATTAAA
28668873 TTTCAT
1 TTTCAT
28668879 AAAAAATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (19 bp):
TTTCATCATAAGCATTAAA
Found at i:28671195 original size:9 final size:9
Alignment explanation
Indices: 28671181--28671217 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28671171 GAGGCTAAGG
28671181 AATTCTTGA
1 AATTCTTGA
*
28671190 AATTCTCGA
1 AATTCTTGA
28671199 AATTCTTGA
1 AATTCTTGA
28671208 AATTCTTGA
1 AATTCTTGA
28671217 A
1 A
28671218 GCATAGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (9 bp):
AATTCTTGA
Found at i:28677085 original size:44 final size:44
Alignment explanation
Indices: 28677016--28677405 Score: 354
Period size: 44 Copynumber: 8.6 Consensus size: 44
28677006 TTTAATATAG
* *
28677016 CAAATCTTATCTCCCTGAAGATGCAGTGGAGAAAGA-TGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCTA
* * * * * *
28677060 CAAATCCTATATCCCTAAAGTTGCAGTGGATCGGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
28677104 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * *
28677148 CAAATCTTATCTCCTTGAAGTTGCAGTAGTGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
28677192 CAAATCTTATCTCGCTAAATTTACAGTGGAGCAGATTGAAGCGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
28677236 CAAATCCTATACT-TCTGAAGTTGCAGTGG-GTCGGATTAAATCTA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCTA
* * * * *
28677280 CCATAGCGAGTCTTATTTCCCTAAAGTTGCAGTGGAACAAATTAAAGCTACAAACTA
1 -CA-A---A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G----AAGCTA
* *
28677337 CAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
*
28677381 CGAATCTTATCTCCCTGAAGTTGCA
1 CAAATCTTATCTCCCTGAAGTTGCA
28677406 ACGAAGTAGA
Statistics
Matches: 276, Mismatches: 52, Indels: 36
0.76 0.14 0.10
Matches are distributed among these distances:
43 3 0.01
44 206 0.75
45 4 0.01
46 1 0.00
48 1 0.00
49 2 0.01
50 23 0.08
51 27 0.10
52 1 0.00
55 1 0.00
56 2 0.01
57 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
Found at i:28677144 original size:88 final size:88
Alignment explanation
Indices: 28677016--28677453 Score: 371
Period size: 88 Copynumber: 4.8 Consensus size: 88
28677006 TTTAATATAG
* * *
28677016 CAAATCTTATCTCCCTGAAGATGCAGTGGAGAAAGA-TGAAGCTACAAATCCTATATCCCTAAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCTACAAATCCTATATCCCTGAAG
*
28677080 TTGCAGTGGATCGGATTAAAGCTA
65 TTGCAGTGGATCAGATTAAAGCTA
* * *
28677104 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCTTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCCTATATCCCTGAAGT
* *
28677169 TGCAGTAG-TGCAGATTGAAGCTA
66 TGCAGTGGAT-CAGATTAAAGCTA
* * * * * *
28677192 CAAATCTTATCTCGCTAAATTTACAGTGGAGCAGATTGAAGCGACAAATCCTATA-CTTCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCCTATATC-CCTGAAG
* * *
28677256 TTGCAGTGGGTCGGATTAAATCTA
65 TTGCAGTGGATCAGATTAAAGCTA
* * * * *
28677280 CCATAGCGAGTCTTATTTCCCTAAAGTTGCAGTGGAACAAATTAAAGCTACAAACTACAAATCT-
1 -CA-A---A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAA-T-C----CTA
* * *
28677344 TATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCTA
54 TATC-CC-TGAAGTTGCAGTGGATCAGATTAAAGCTA
* ** * * * * * *
28677381 CGAATCTTATCTCCCTGAAGTTGCAACGAAGTAGATTGAAACTACAATTCCTATACCCCTAAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCCTATATCCCTGAAGT
*
28677446 TGTAGTGG
66 TGCAGTGG
28677454 GTTAGAATGA
Statistics
Matches: 278, Mismatches: 53, Indels: 38
0.75 0.14 0.10
Matches are distributed among these distances:
87 5 0.02
88 155 0.56
89 7 0.03
90 4 0.01
93 2 0.01
94 37 0.13
95 34 0.12
96 2 0.01
99 3 0.01
100 6 0.02
101 23 0.08
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (88 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCCTATATCCCTGAAGT
TGCAGTGGATCAGATTAAAGCTA
Found at i:28677417 original size:44 final size:44
Alignment explanation
Indices: 28677331--28677427 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
28677321 TTAAAGCTAC
*
28677331 AAACTACAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTG
* * *
28677375 AAGCTACGAATCTTATCTCCCTGAAGTTGCA--ACGAAGTAGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTA-G-AGCAGATTG
28677419 AAACTACAA
1 AAACTACAA
28677428 TTCCTATACC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.02
43 1 0.02
44 43 0.96
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (44 bp):
AAACTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTG
Found at i:28679385 original size:31 final size:31
Alignment explanation
Indices: 28679337--28679403 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
28679327 AATCGTGTTT
28679337 AAATATACTTATCTATTTTTGTACTACGCCC
1 AAATATACTTATCTATTTTTGTACTACGCCC
* * *
28679368 AAATGTACTTATTTATTTTTGTACTATGCCC
1 AAATATACTTATCTATTTTTGTACTACGCCC
28679399 AAATA
1 AAATA
28679404 AGTTAAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.43
Consensus pattern (31 bp):
AAATATACTTATCTATTTTTGTACTACGCCC
Found at i:28680922 original size:30 final size:31
Alignment explanation
Indices: 28680883--28680942 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28680873 GGAGGTGGGA
*
28680883 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
28680914 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
28680943 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:28681169 original size:9 final size:9
Alignment explanation
Indices: 28681155--28681191 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28681145 TATAGTTTGA
28681155 TATTCGAAT
1 TATTCGAAT
28681164 TATTCGAAT
1 TATTCGAAT
*
28681173 TATTCGAGT
1 TATTCGAAT
28681182 TATTCGAAT
1 TATTCGAAT
28681191 T
1 T
28681192 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28694006 original size:266 final size:266
Alignment explanation
Indices: 28693493--28694022 Score: 745
Period size: 266 Copynumber: 2.0 Consensus size: 266
28693483 CTTAAAGGAT
* * * * * * * *
28693493 CTTTCCTGAAAGAAAGTATGTATTTATATTTTTAAAGAGGGAATTTGCCATAATAGTCTGTTAGT
1 CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAATAGCCTATCAAT
* * * * *
28693558 TTAGGATATTGGCTTATTCGAAGTTATGAAAAGTATAAGAGTTTATTGGTCTGAGTTGGTCTACG
66 ATAGGATATGGGCATATTCGAAGTTATGAAAAGTATAAGAGTTCATTGGTCTGAGTTGGTCTACA
* * *
28693623 CTATGTAAGGATAAAATCTGAGTTATCTGGCATTCACCATATTTGAATAGTTTTATGTCTAGTTT
131 CTATGTAAGGATAAAACCTGAGTTATCTGGCATCCACCATATTTGAATAGTTTCATGTCTAGTTT
* * * * * * *
28693688 TGAAGTTATCTGAAATTTGAGTCGTTTGTCAATTTAGGCGTTCTTTTGTTATGTAATATAGACGA
196 TGAAGTTATCTAAAATCTAAGCCATTTGTCAATTTAGGCGTTATTGTGTTATGTAATATAGACGA
28693753 TTGGGC
261 TTGGGC
*
28693759 CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAGTAGCCTATCAAT
1 CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAATAGCCTATCAAT
* *
28693824 ATAGGATATGGGCATATTTGAAGTTATGAAAAGTATAAGAGTTCGTTGGTCTGAGTTGGTCTACA
66 ATAGGATATGGGCATATTCGAAGTTATGAAAAGTATAAGAGTTCATTGGTCTGAGTTGGTCTACA
* * * *
28693889 CTATGTAATGATGAAACCTGAGTTATCTGGCATCCGCCATATTTGAATAGTTTCATGTCTCGTTT
131 CTATGTAAGGATAAAACCTGAGTTATCTGGCATCCACCATATTTGAATAGTTTCATGTCTAGTTT
* * * * *
28693954 TGAGGTTATCTAAAATCTAAGCCATTTGTTAATTTGGGTGTTATTGTGTTATGTAATATAGACGC
196 TGAAGTTATCTAAAATCTAAGCCATTTGTCAATTTAGGCGTTATTGTGTTATGTAATATAGACGA
28694019 TTGG
261 TTGG
28694023 AATTCTTCAA
Statistics
Matches: 229, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
266 229 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.39
Consensus pattern (266 bp):
CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAATAGCCTATCAAT
ATAGGATATGGGCATATTCGAAGTTATGAAAAGTATAAGAGTTCATTGGTCTGAGTTGGTCTACA
CTATGTAAGGATAAAACCTGAGTTATCTGGCATCCACCATATTTGAATAGTTTCATGTCTAGTTT
TGAAGTTATCTAAAATCTAAGCCATTTGTCAATTTAGGCGTTATTGTGTTATGTAATATAGACGA
TTGGGC
Found at i:28695384 original size:22 final size:22
Alignment explanation
Indices: 28695330--28695384 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
28695320 TGCCAGTAGT
*
28695330 CAGAATGGCTAAGAGCCGTAAA
1 CAGAATGGCTAAGAGCCATAAA
* * *
28695352 CAGGATAGCTATA-AGCTATAAA
1 CAGAATGGCTA-AGAGCCATAAA
28695374 CAGAATGGCTA
1 CAGAATGGCTA
28695385 CAAGTCATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTAAGAGCCATAAA
Found at i:28695471 original size:32 final size:32
Alignment explanation
Indices: 28695400--28695590 Score: 238
Period size: 32 Copynumber: 6.0 Consensus size: 32
28695390 CATAAGTATA
* * * * *
28695400 GTAATATAATTGGCACAAAGCTATCAGTAGCA
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* * * *
28695432 GTGATATGATCGGCACACAGCCATCAATAATG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
**
28695464 GTAATATGATCGGCACAAAGCCATCAGTAATA
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* *
28695496 GTAATATAATCGGTACAAAGCCATCAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
*
28695528 GTAATATGATCGGTACAAAGCCATCAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* *
28695560 ATAATATGATCGGCACAAAGCCATTAGTAAC
1 GTAATATGATCGGCACAAAGCCATCAGTAAC
28695591 ATCGCAGCAA
Statistics
Matches: 138, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 138 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (32 bp):
GTAATATGATCGGCACAAAGCCATCAGTAACG
Found at i:28695565 original size:96 final size:96
Alignment explanation
Indices: 28695397--28695589 Score: 278
Period size: 96 Copynumber: 2.0 Consensus size: 96
28695387 AGTCATAAGT
* * * * *
28695397 ATAGTAATATAATTGGCACAAAGCTATCAGTAGCAGTGATATGATCGGCACACAGCCATCAATAA
1 ATAGTAATATAATCGGCACAAAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAATAA
* *
28695462 TGGTAATATGATCGGCACAAAGCCATCAGTA
66 CGATAATATGATCGGCACAAAGCCATCAGTA
* * * *
28695493 ATAGTAATATAATCGGTACAAAGCCATCAGTAACGGTAATATGATCGGTACAAAGCCATCAGTAA
1 ATAGTAATATAATCGGCACAAAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAATAA
*
28695558 CGATAATATGATCGGCACAAAGCCATTAGTA
66 CGATAATATGATCGGCACAAAGCCATCAGTA
28695589 A
1 A
28695590 CATCGCAGCA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (96 bp):
ATAGTAATATAATCGGCACAAAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAATAA
CGATAATATGATCGGCACAAAGCCATCAGTA
Found at i:28695653 original size:26 final size:27
Alignment explanation
Indices: 28695591--28695656 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
28695581 CATTAGTAAC
*
28695591 ATCGCAGCAAA-TTTTCCAGCAACAGT
1 ATCGCAGCAAAGCTTTCCAGCAACAGT
* *
28695617 ATCACAACAAAGCTTT-CAGCAACAGT
1 ATCGCAGCAAAGCTTTCCAGCAACAGT
28695643 ATCGCAGCAAAGCT
1 ATCGCAGCAAAGCT
28695657 GCCAGTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 31 0.91
27 3 0.09
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (27 bp):
ATCGCAGCAAAGCTTTCCAGCAACAGT
Found at i:28695688 original size:27 final size:27
Alignment explanation
Indices: 28695658--28695717 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
28695648 AGCAAAGCTG
28695658 CCAGTAATAGT-ATATGTGACCA-AGCCA
1 CCAGTAATAGTGAT-TGTG-CCAGAGCCA
*
28695685 CCAGTAATAGTGATTGTGGCAGAGCCA
1 CCAGTAATAGTGATTGTGCCAGAGCCA
28695712 CCAGTA
1 CCAGTA
28695718 CAGTACTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.07
27 26 0.87
28 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (27 bp):
CCAGTAATAGTGATTGTGCCAGAGCCA
Found at i:28695813 original size:24 final size:24
Alignment explanation
Indices: 28695786--28695838 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
28695776 TCATGCTCGG
28695786 AATCAGTCATACAAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
** *
28695810 AATCAGTCATTTACATCATAGACA
1 AATCAGTCATACAAATCATAGACA
28695834 AATCA
1 AATCA
28695839 AACATTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.25
Consensus pattern (24 bp):
AATCAGTCATACAAATCATAGACA
Found at i:28695844 original size:24 final size:24
Alignment explanation
Indices: 28695800--28695848 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
28695790 AGTCATACAA
**
28695800 ATCATAGACAAATCAGTCATTTAC
1 ATCATAGACAAATCAAACATTTAC
28695824 ATCATAGACAAATCAAACATTTAC
1 ATCATAGACAAATCAAACATTTAC
28695848 A
1 A
28695849 CTCGATGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (24 bp):
ATCATAGACAAATCAAACATTTAC
Found at i:28695915 original size:27 final size:27
Alignment explanation
Indices: 28695885--28695944 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
28695875 CTCTAAAGGC
*
28695885 ATTACGATCATTTTACCCTA-TGAGGGT
1 ATTACGATCATTTTACCCTACAG-GGGT
* *
28695912 ATTATGGTCATTTTACCCTACAGGGGT
1 ATTACGATCATTTTACCCTACAGGGGT
28695939 ATTACG
1 ATTACG
28695945 GATGTAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (27 bp):
ATTACGATCATTTTACCCTACAGGGGT
Found at i:28697011 original size:3 final size:3
Alignment explanation
Indices: 28697005--28697060 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
28696995 TAATAAATTT
* * *
28697005 TTA TTA TTA TCA TTA TAA TTA TTA -TA TTA TTTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
28697050 CTA TTA TTA TT
1 TTA TTA TTA TT
28697061 TCTATATTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28697114 original size:21 final size:21
Alignment explanation
Indices: 28697084--28697125 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28697074 ACATACATGG
28697084 TTTTTATATAATATA-TATGCA
1 TTTTTATAT-ATATAGTATGCA
*
28697105 TTTTTTTATATATAGTATGCA
1 TTTTTATATATATAGTATGCA
28697126 CTAGACCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTTATATATATAGTATGCA
Found at i:28697337 original size:22 final size:24
Alignment explanation
Indices: 28697311--28697354 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28697301 GAAAAATATT
28697311 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
28697333 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
28697355 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:28697465 original size:9 final size:9
Alignment explanation
Indices: 28697451--28697478 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28697441 TTTTGTTACA
28697451 ACAATTAAT
1 ACAATTAAT
28697460 ACAATTAAT
1 ACAATTAAT
28697469 ACAATTAAT
1 ACAATTAAT
28697478 A
1 A
28697479 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:28697494 original size:68 final size:68
Alignment explanation
Indices: 28697421--28697630 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
28697411 TCAAGTTTGT
*
28697421 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
28697486 AAA
66 AAA
28697489 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
28697554 AAA
66 AAA
28697557 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
28697620 AAT
66 AAA
28697623 TTTACTAA
1 TTTACTAA
28697631 CAATTAAATT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 112 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:28697531 original size:9 final size:9
Alignment explanation
Indices: 28697519--28697546 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28697509 TTTTATTACA
28697519 ACAATTAAT
1 ACAATTAAT
28697528 ACAATTAAT
1 ACAATTAAT
28697537 ACAATTAAT
1 ACAATTAAT
28697546 A
1 A
28697547 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:28697658 original size:16 final size:16
Alignment explanation
Indices: 28697619--28697660 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28697609 AATAATTTGA
*
28697619 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
*
28697635 TAAATTTAATAACAAT
1 TAATTTTAATAACAAT
*
28697651 TAGTTTTAAT
1 TAATTTTAAT
28697661 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:28700272 original size:12 final size:12
Alignment explanation
Indices: 28700257--28700282 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28700247 AAAATTAAGC
28700257 AAAAAATGATGG
1 AAAAAATGATGG
28700269 AAAAAATGATGG
1 AAAAAATGATGG
28700281 AA
1 AA
28700283 CCTCAAGGGA
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:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAATGATGG
Found at i:28701644 original size:186 final size:186
Alignment explanation
Indices: 28701330--28701702 Score: 728
Period size: 186 Copynumber: 2.0 Consensus size: 186
28701320 ATCAAGACAA
28701330 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
1 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
*
28701395 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTTAAGCCTCCACAGCCTC
66 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
*
28701460 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
131 CGTATCCCAAATGGTACGACGTAAGTACACAATGCGATTATCATGCGGGAATTACG
28701516 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
1 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
28701581 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
66 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
28701646 CGTATCCCAAATGGTACGACGTAAGTACACAATGCGATTATCATGCGGGAATTACG
131 CGTATCCCAAATGGTACGACGTAAGTACACAATGCGATTATCATGCGGGAATTACG
28701702 G
1 G
28701703 GACACTCAAT
Statistics
Matches: 185, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 185 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (186 bp):
GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
CGTATCCCAAATGGTACGACGTAAGTACACAATGCGATTATCATGCGGGAATTACG
Found at i:28704484 original size:44 final size:44
Alignment explanation
Indices: 28704348--28704579 Score: 125
Period size: 44 Copynumber: 5.3 Consensus size: 44
28704338 GATAGCAGAT
* *
28704348 CTTGCCTTCCTGCACCGATAGCGAAGTAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
* **** * * ** * * *
28704392 CTTGCCTCCCTGGGTTG-CAGC-AGAGCAGGTTAAAAATTA-CAGAT
1 CTTGCCTTCCTGCACCGATAGCGA-AGCAGATCGAAGA-CACCAG-C
28704436 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
** * * ** * * * *
28704480 CTTGCC-TCCTTG-AGTTG-TAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCC-TGCA-CCGATAGCGAAGCAGATCGAAGACACCAG-C
* *
28704524 CTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
*
28704568 CTTGCCTCCCTG
1 CTTGCCTTCCTG
28704580 GGTTGCAGCG
Statistics
Matches: 127, Mismatches: 49, Indels: 24
0.63 0.25 0.12
Matches are distributed among these distances:
42 1 0.01
43 35 0.28
44 55 0.43
45 35 0.28
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.22
Consensus pattern (44 bp):
CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
Found at i:28704668 original size:88 final size:88
Alignment explanation
Indices: 28704339--28704645 Score: 472
Period size: 88 Copynumber: 3.5 Consensus size: 88
28704329 ATCAATGAAG
* * *
28704339 ATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGTAGATCGAAGACACTAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
28704404 GGTTGCAGCAGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* *
28704427 ATTA-CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCTT
1 A-TAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
* *
28704491 GAGTTGTAGCGGAGCAGGTTAAAA
65 GGGTTGCAGCGGAGCAGGTTAAAA
*
28704515 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
28704580 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * * **
28704603 ATAGTAGATCTTACCTTCCTACACCGACAATGAAGCAGATCGA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
28704646 TGACCCTAGC
Statistics
Matches: 200, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
87 2 0.01
88 196 0.98
89 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGTTAAAA
Found at i:28704686 original size:88 final size:88
Alignment explanation
Indices: 28704339--28704686 Score: 288
Period size: 88 Copynumber: 4.0 Consensus size: 88
28704329 ATCAATGAAG
* * * * * * * *
28704339 ATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGTAGATCGAAGACACTAGCCTTGCCTCCCTG
1 ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCTG
*** * *
28704404 GGTTGCAGCAGAGCAGGTTAAAA
66 GACAGCAGCGGAACAGGTTAAAA
* * * * * *
28704427 ATTA-CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCT-CCT
1 A-TAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCT
* ** * *
28704490 TGAGTTGTAGCGGAGCAGGTTAAAA
65 GGA-CAGCAGCGGAACAGGTTAAAA
* * * * * *
28704515 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCTG
*** *
28704580 GGTTGCAGCGGAGCAGGTTAAAA
66 GACAGCAGCGGAACAGGTTAAAA
* * * *
28704603 ATAGTAGATCTTACCTTCCTACACCGACAATGAAGCAGATCGATGAC-CCTAGCCCTATCTCCCT
1 ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACC-AGCCCTACCTCCCT
* *
28704667 GGACAGCAGTGGAATAGGTT
65 GGACAGCAGCGGAACAGGTT
28704687 GAAGATTGTA
Statistics
Matches: 228, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
87 8 0.04
88 214 0.94
89 6 0.03
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (88 bp):
ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCTG
GACAGCAGCGGAACAGGTTAAAA
Found at i:28704722 original size:44 final size:43
Alignment explanation
Indices: 28704656--28704777 Score: 174
Period size: 44 Copynumber: 2.8 Consensus size: 43
28704646 TGACCCTAGC
*
28704656 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCTGG-CAGTAGTGGAATAGGTTGAAGATTGTGAA-T
28704700 CCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGG-CAGTAGTGGAATAGGTTGAAGATTGTGAAT
* *
28704744 CCTATCTCCCTGAGCAATAGTGGAGTAGGTTGAA
1 CCTATCTCCCTG-GCAGTAGTGGAATAGGTTGAA
28704778 AATAACAGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
44 69 0.96
45 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
CCTATCTCCCTGGCAGTAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:28704886 original size:50 final size:51
Alignment explanation
Indices: 28704831--28704943 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 51
28704821 AAGACATCAG
* * *
28704831 TCTTATCGT-CTTGACATTGCAATGGAAAAGATTGAAGCCACAACTGCGAA
1 TCTTATCGTCCCTGACATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
* * * ** *
28704881 TCTTAT-TTCCCTGACATTGTAGCGGAGCAGATTGAAGCCACGACGGCGAA
1 TCTTATCGTCCCTGACATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
28704931 TCTTATC-TCCCTG
1 TCTTATCGTCCCTG
28704944 GTGTTAAGGC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 1 0.02
50 51 0.98
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (51 bp):
TCTTATCGTCCCTGACATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
Found at i:28705503 original size:217 final size:218
Alignment explanation
Indices: 28705128--28705643 Score: 698
Period size: 217 Copynumber: 2.4 Consensus size: 218
28705118 AATTTAAAAT
* * * *
28705128 ACTGAAGATGGCGATTTTTATCTCCCTGAAGTTGCAGTGGAGTAAATTAAAGCCAATAATCCTAT
1 ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCAAATAATCCTAT
* * *
28705193 CTCCCTGAAGTCGTAGTGGAGCGGATTAAAATCACGGATCTTATCTCTCTGAAGTTGCAGAGAGC
66 CTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
* * *
28705258 ATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGTAAGCAAGCCTTATC
131 ATATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAGCCTTATC
*
28705322 -CTCCTGAAGTTGTAGT-GAGGCAA
196 TC-CCTGAAGTTGCAGTGGA-GCAA
*
28705345 ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTAATAATCCTAT
1 ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCAAATAATCCTAT
*
28705410 CTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
66 CTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
* * * *
28705475 ATATCGCATCGGGTCTTATCTCCCTGAAGTTTCAGTGGAGCAGACCCAAGAAAGCGAGTCTTATC
131 ATATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAGCCTTATC
*
28705540 TCCCTGAAGTTGCAGTGGAGCAG
196 TCCCTGAAGTTGCAGTGGAGCAA
* *** * * * * * ** *
28705563 ACTCAAGAAATC-AAGTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAAAAAATCCTA
1 ACTGAAGATGGCGAA-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCAAATAATCCTA
*
28705627 TCTCCCTAAAGTTGCAG
65 TCTCCCTGAAGTTGCAG
28705644 CAGATCAAGT
Statistics
Matches: 264, Mismatches: 31, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
217 165 0.62
218 96 0.36
219 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (218 bp):
ACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCAAATAATCCTAT
CTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGC
ATATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAGCCTTATC
TCCCTGAAGTTGCAGTGGAGCAA
Found at i:28705610 original size:45 final size:45
Alignment explanation
Indices: 28705269--28705643 Score: 258
Period size: 45 Copynumber: 8.5 Consensus size: 45
28705259 TATCGCATCT
*
28705269 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * **
28705313 AGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAAACTGAAGATGGCGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGAAAGC-A
* * * * *
28705359 A-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTAA-TA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAAGCA
* ** * *
28705403 A-TCCTATCTCCCTGAAGTTGCAGTGGAGTGGA-T-TA-AAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * * *
28705444 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCATA-TC--G-CATCG
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * *
28705486 GGTCTTATCTCCCTGAAGTTTCAGTGGAGCAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
*
28705531 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * * *
28705576 AGTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAA-AA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * *
28705620 AATCCTATCTCCCTAAAGTTGCAG
1 AGTCTTATCTCCCTGAAGTTGCAG
28705644 CAGATCAAGT
Statistics
Matches: 260, Mismatches: 53, Indels: 36
0.74 0.15 0.10
Matches are distributed among these distances:
40 22 0.08
41 8 0.03
42 6 0.02
43 9 0.03
44 99 0.38
45 111 0.43
46 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
Found at i:28706815 original size:3 final size:3
Alignment explanation
Indices: 28706809--28706864 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
28706799 TAATAAATTG
* * * *
28706809 TTA TTA TTA TCA TTC TAA TTA TTA -TA TTA TTTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
28706854 CTA TTA TTA TT
1 TTA TTA TTA TT
28706865 TCTATATTCA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28716870 original size:26 final size:26
Alignment explanation
Indices: 28716815--28716872 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
28716805 TTTTATAACT
**
28716815 TTTTAATTTTCTATAATTTTCAAGTT
1 TTTTAATTTTCTATAATTTTCAAGAG
* *
28716841 TTTTAATTTTTTTATAATTTT-ATGAG
1 TTTTAA-TTTTCTATAATTTTCAAGAG
28716867 TTTTAA
1 TTTTAA
28716873 GATTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (26 bp):
TTTTAATTTTCTATAATTTTCAAGAG
Found at i:28716870 original size:27 final size:25
Alignment explanation
Indices: 28716805--28716870 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
28716795 AATTTTGTGT
*
28716805 TTTTATAACTTTTTAATTTTCTATAA
1 TTTTAT-AGTTTTTAATTTTCTATAA
*
28716831 TTTTCA-AGTTTTTTAATTTTTTTATAA
1 TTTT-ATAG-TTTTTAA-TTTTCTATAA
28716858 TTTTATGAGTTTT
1 TTTTAT-AGTTTT
28716871 AAGATTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
25 1 0.03
26 12 0.36
27 18 0.55
28 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (25 bp):
TTTTATAGTTTTTAATTTTCTATAA
Found at i:28717208 original size:22 final size:22
Alignment explanation
Indices: 28717180--28717226 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
28717170 ACAAATCCTA
28717180 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
28717202 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
28717224 TCT
1 TCT
28717227 TAAACTCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:28717258 original size:52 final size:52
Alignment explanation
Indices: 28717180--28717278 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
28717170 ACAAATCCTA
* *
28717180 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
*
28717232 TCTCAATTTCCTTTCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
28717279 CAAATCCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
Found at i:28717259 original size:22 final size:22
Alignment explanation
Indices: 28717231--28717281 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
28717221 TTCTCTTAAA
* *
28717231 CTCTCAATTTCCTTTC-AAAAT
1 CTCTCAATTTCATTCCAAAAAT
28717252 CCTCTCAATTTCATTCCAAAAAT
1 -CTCTCAATTTCATTCCAAAAAT
28717275 CTCTCAA
1 CTCTCAA
28717282 ATCCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCAATTTCATTCCAAAAAT
Found at i:28717350 original size:31 final size:31
Alignment explanation
Indices: 28717315--28717381 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
28717305 CTTCAATTTC
28717315 ATTTTTT-AAAATAATTTCAAATTTTTTTTAT
1 ATTTTTTAAAAATAATTT-AAATTTTTTTTAT
*
28717346 ATTTTTTAAAAATAATTTTAATTTTTTTTAT
1 ATTTTTTAAAAATAATTTAAATTTTTTTTAT
28717377 ATTTT
1 ATTTT
28717382 CATCAATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (31 bp):
ATTTTTTAAAAATAATTTAAATTTTTTTTAT
Found at i:28720233 original size:68 final size:68
Alignment explanation
Indices: 28720154--28720363 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
28720144 TCAAGTTTGT
* *
28720154 TTTACTAATCAAATGTTAGATTTTGTTACAACAAGTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
28720219 AAA
66 AAA
28720222 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
28720287 AAA
66 AAA
28720290 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
28720353 AAT
66 AAA
28720356 TTTACTAA
1 TTTACTAA
28720364 CAATTAGTTT
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 111 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:28720264 original size:9 final size:9
Alignment explanation
Indices: 28720252--28720279 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28720242 TTTTATTACA
28720252 ACAATTAAT
1 ACAATTAAT
28720261 ACAATTAAT
1 ACAATTAAT
28720270 ACAATTAAT
1 ACAATTAAT
28720279 A
1 A
28720280 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:28720377 original size:22 final size:23
Alignment explanation
Indices: 28720342--28720404 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
28720332 ATTAACAATT
*
28720342 AATAATTTGATAATTTTACT-AACA
1 AATAATTT--TAATTTTACTAAAAA
* * *
28720366 ATTAGTTTTAATTTTATTAAAAA
1 AATAATTTTAATTTTACTAAAAA
28720389 AATAATTTTAATTTTA
1 AATAATTTTAATTTTA
28720405 ATTAAAAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 9 0.28
23 17 0.53
24 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
AATAATTTTAATTTTACTAAAAA
Found at i:28723526 original size:19 final size:19
Alignment explanation
Indices: 28723502--28723546 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28723492 GATGAGAAGG
*
28723502 GATATAGAACTTTCGATTA
1 GATATAGAACTTTCGAATA
*
28723521 GATATAAAACTTTCGAATA
1 GATATAGAACTTTCGAATA
28723540 G-TATAGA
1 GATATAGA
28723547 TAGTACAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (19 bp):
GATATAGAACTTTCGAATA
Found at i:28723631 original size:21 final size:21
Alignment explanation
Indices: 28723607--28723648 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28723597 TAAATAAAAT
28723607 TTTTA-AATAATTTAATAATTA
1 TTTTATAATAATTTAA-AATTA
*
28723628 TTTTATAATATTTTAAAATTA
1 TTTTATAATAATTTAAAATTA
28723649 ACAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAATAATTTAAAATTA
Found at i:28727589 original size:9 final size:9
Alignment explanation
Indices: 28727575--28727611 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28727565 TATAGTTTGA
28727575 TATTCGAAT
1 TATTCGAAT
28727584 TATTCGAAT
1 TATTCGAAT
*
28727593 TATTCGAGT
1 TATTCGAAT
28727602 TATTCGAAT
1 TATTCGAAT
28727611 T
1 T
28727612 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28727681 original size:9 final size:9
Alignment explanation
Indices: 28727664--28727694 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28727654 TCGAGTTGAT
28727664 TCGAATAAC
1 TCGAATAAC
*
28727673 TCGATTAAC
1 TCGAATAAC
28727682 TCGAATAAC
1 TCGAATAAC
28727691 TCGA
1 TCGA
28727695 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:28729099 original size:4 final size:4
Alignment explanation
Indices: 28729090--28729127 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
28729080 GAGAAGTTGT
*
28729090 TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
28729128 GTTGTGTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:28730801 original size:23 final size:23
Alignment explanation
Indices: 28730766--28730810 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28730756 TGGAGTATAA
* *
28730766 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
28730789 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
28730811 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:28731437 original size:42 final size:42
Alignment explanation
Indices: 28731390--28731616 Score: 282
Period size: 42 Copynumber: 5.5 Consensus size: 42
28731380 CAGTGCCTAT
28731390 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
28731432 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
28731474 TAGGCTTAATGTCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
28731516 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * * * * *
28731557 CAGGCTAAATGCCAGTG-TACTGA-ATCAGGCTTTAAGTCTAG
1 CAGGCTTAATGCCGGTGAAAC-AATATCAGACTTTACGTCTAG
*
28731598 CAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAA-TGCCGGTGAA
28731617 TCTGTTTAAA
Statistics
Matches: 161, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.02
41 59 0.37
42 98 0.61
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:28737544 original size:1 final size:1
Alignment explanation
Indices: 28737403--28737535 Score: 176
Period size: 1 Copynumber: 133.0 Consensus size: 1
28737393 AATTGGTTCG
* * * * *** * * *
28737403 TTTTTGTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTGTTATAAATGTTTATTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28737468 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28737533 TTT
1 TTT
28737536 ATGATTTTTA
Statistics
Matches: 116, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 116 1.00
ACGTcount: A:0.04, C:0.01, G:0.03, T:0.92
Consensus pattern (1 bp):
T
Found at i:28737863 original size:16 final size:17
Alignment explanation
Indices: 28737828--28737877 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
28737818 TGAAATATAA
28737828 GTATATGTTATAATAAGTAT
1 GTATATGTTAT-AT--GTAT
28737848 G-ATATGTTATATGTAT
1 GTATATGTTATATGTAT
28737864 GTATATG-TATATGT
1 GTATATGTTATATGT
28737878 TTATATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.41
17 5 0.17
18 2 0.07
19 9 0.31
20 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (17 bp):
GTATATGTTATATGTAT
Found at i:28738459 original size:41 final size:42
Alignment explanation
Indices: 28738359--28738537 Score: 283
Period size: 41 Copynumber: 4.3 Consensus size: 42
28738349 CAGTGCCTAT
28738359 CAGGCTTAATGCCGGTGAAACAATATT-AGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAAT-TTCAGACTTTACGTCTAG
*
28738401 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
*
28738443 -AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
* *
28738484 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
*
28738525 CAGGCTAAATGCC
1 CAGGCTTAATGCC
28738538 AGTGTACTGA
Statistics
Matches: 128, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
41 70 0.55
42 58 0.45
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
Found at i:28738499 original size:83 final size:83
Alignment explanation
Indices: 28738359--28738584 Score: 298
Period size: 83 Copynumber: 2.7 Consensus size: 83
28738349 CAGTGCCTAT
*
28738359 CAGGCTTAATGCCGGTGAAACAATATTAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA-AA
*
28738424 TTTCAGACTTTACGTCTAG
65 TTTCAGACTATACGTCTAG
*
28738443 -AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAT
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAAT
*
28738507 TTCAGACTATATGTCTAG
66 TTCAGACTATACGTCTAG
* * * * * * *
28738525 CAGGCTAAATGCCAGTG-TACTGA-ATCAGGCTTTAAGTCTAGCAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAATGCCGGTGAAAC-AATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAA
28738585 TCTGTTTAAA
Statistics
Matches: 128, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
81 3 0.02
82 50 0.39
83 75 0.59
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (83 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAAT
TTCAGACTATACGTCTAG
Found at i:28739584 original size:1 final size:1
Alignment explanation
Indices: 28739514--28739567 Score: 108
Period size: 1 Copynumber: 54.0 Consensus size: 1
28739504 TCTAAGTTTC
28739514 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28739568 CTTTCTTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28746956 original size:539 final size:539
Alignment explanation
Indices: 28745939--28747004 Score: 1623
Period size: 539 Copynumber: 2.0 Consensus size: 539
28745929 TTGACCTAAT
* * *
28745939 CATCAGTAATAACTTTTGTACCTACAGAAGTGTTAACCTGAACATCTCCTATTCCCTTGGCTTCA
1 CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCCCCTATTCCCTTGGCTTCA
* * *
28746004 ATGATCTGGCCATTTCAAACTCTGATTCTCGAACTGAATAATCTATCAATCTCCTTGAACATGCT
66 ATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGCT
* * *
28746069 TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACTAGTTTTTCTTGTCTTGGTTGT
131 TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTAGTTGT
*
28746134 TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGCTTGATTTTCTTCAGCACTTGAG
196 TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTGAG
* * *
28746199 CCTAATTAGACTACTATTGTTGTTACTGCACTTTGTTTTTATAAATTCTAAAATCGTGGCCGAAT
261 CCTAATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAAAT
* *** * * *
28746264 TGCTTACAGTTTTTACACTGTGCACCAATTTTTATCCAACAAAACTTTTATGAATGACCCATCTT
326 TGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATCTT
* * * *
28746329 TTTGCAATTCGATCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTTCCCTTTCTCTTGCTT
391 TTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTACCCTTTCTCTTGCTT
* * * * * *
28746394 GATTCCTTTTCTTCTTGCCTTTGTTTCTTGAAGAGCATGGAGTTTCCTTGTTTCTCGCTTGGTAA
456 GATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGTAA
28746459 GCACCTTCTACGTGAAAGA
521 GCACCTTCTACGTGAAAGA
* *
28746478 CATCAGTAATAACTTTTGTACCTATAGAAGTGCTAACCTAAACGTCCCC-ATTTCCCTTGGCTTC
1 CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCCCCTA-TTCCCTTGGCTTC
* * * *
28746542 AATGATCTGGCCATTTCCAAGTCTGATTCTCAAACTGAAGGATATGTCAATCTCCTTGAACATGC
65 AATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGC
* * *
28746607 TTTCATCTGAAACCATATGGTTTGTACAACCTCTGTCAATCAACCATTTTTTCTTATCTTAGTTG
130 TTTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTAGTTG
* * * *
28746672 TTGATTTTGAAGCATGAAGTAGTGAAT-TCGAGCTCCTCCTGAGATTGATTTTCTTCAGCACTTG
195 TTGACTGTGAAGCATGAAGCAGTGAATGT-GAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTG
* * * *
28746736 AGCCTGATTAGACTGCTATTGTTGCTGCTGCACTTTGTTTTTACAAATTCTAAAATTGTGGCCAA
259 AGCCTAATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAA
* * * *
28746801 ATTGCTTACAATTTTTACACTACACACCAGGTCTTGTCCAGCAAAACTTTTCTAAATGACCCATC
324 ATTGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATC
* *
28746866 TTTTTGCAATCCAAGCATGGTGGATACTTTTTCTTTTCACCATCTCTTTTTAGCCTTTCTCTTGC
389 TTTTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTACCCTTTCTCTTGC
28746931 TTGATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGT
454 TTGATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGT
28746996 AAGCACCTT
519 AAGCACCTT
28747005 TTGTGTGCCC
Statistics
Matches: 472, Mismatches: 53, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
538 2 0.00
539 470 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (539 bp):
CATCAGTAATAACTTTTGTACCTACAGAAGTGCTAACCTAAACATCCCCTATTCCCTTGGCTTCA
ATGATCTGGCCATTTCAAACTCTGATTCTCAAACTGAAGAATATATCAATCTCCTTGAACATGCT
TTCATCTGAAACCATATGGTTTGTACAACCACTATCAATCAACCAGTTTTTCTTATCTTAGTTGT
TGACTGTGAAGCATGAAGCAGTGAATGTGAGCTCCTCCTAAGATTGATTTTCTTCAGCACTTGAG
CCTAATTAGACTACTATTGTTGCTACTGCACTTTGTTTTTACAAATTCTAAAATCGTGGCCAAAT
TGCTTACAATTTTTACACTACACACCAAGTCTTATCCAACAAAACTTTTATAAATGACCCATCTT
TTTGCAATCCAAGCATGGTGGATACTTTTTCTTTCCACCATCTCTTTTTACCCTTTCTCTTGCTT
GATGCCATTTCTTCTTGCCTTTGTTGCTTGAAAAGCATAGAGTTTCCTTGTTTCTCACTTGGTAA
GCACCTTCTACGTGAAAGA
Found at i:28776924 original size:23 final size:23
Alignment explanation
Indices: 28776889--28776933 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28776879 TGGAGTATAA
* *
28776889 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
28776912 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
28776934 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:28777657 original size:84 final size:83
Alignment explanation
Indices: 28777515--28777741 Score: 298
Period size: 84 Copynumber: 2.7 Consensus size: 83
28777505 CAGTGCCTAT
*
28777515 CAGGCTTAATGCCGGTGAAACAATATTAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA-AA
*
28777580 TTTCAGACTTTACGTCTAG
65 TTTCAGACTATACGTCTAG
* *
28777599 TAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAT
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAAT
*
28777664 TTCAGACTATATGTCTAG
66 TTCAGACTATACGTCTAG
* * * * * * *
28777682 CAGGCTAAATGCCAGTG-TACTGA-ATCAGGCTTTAAGTCTAGCAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAATGCCGGTGAAAC-AATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAA
28777742 TCTGTTTAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
81 3 0.02
82 32 0.25
83 33 0.26
84 60 0.47
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (83 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAAT
TTCAGACTATACGTCTAG
Found at i:28777681 original size:41 final size:42
Alignment explanation
Indices: 28777515--28777694 Score: 283
Period size: 42 Copynumber: 4.3 Consensus size: 42
28777505 CAGTGCCTAT
28777515 CAGGCTTAATGCCGGTGAAACAATATT-AGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAAT-TTCAGACTTTACGTCTAG
*
28777557 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
* *
28777599 TAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
* *
28777641 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
*
28777682 CAGGCTAAATGCC
1 CAGGCTTAATGCC
28777695 AGTGTACTGA
Statistics
Matches: 128, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
41 31 0.24
42 97 0.76
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
Found at i:28779006 original size:25 final size:25
Alignment explanation
Indices: 28778978--28779189 Score: 180
Period size: 25 Copynumber: 8.5 Consensus size: 25
28778968 TATAAGAAAT
28778978 GCCTTTGTGGCTAGTTATCTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * * *
28779003 GCCTCTATGACAAGTTATCTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * *
28779028 GCCTTTATGACATA-TTATCAT-AAAA
1 GCCTTTGTGGC-TAGTTATC-TGTAAA
* * *
28779053 GCCTTTATGACTAGTTATTTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * * *
28779078 GCATTTGTGGCGAATTATCAT-AAAA
1 GCCTTTGTGGCTAGTTATC-TGTAAA
*
28779103 GCTTTTGTGG-TGAGTTATCTGTAAA
1 GCCTTTGTGGCT-AGTTATCTGTAAA
*
28779128 GCCTTTGTGGCGAGTTATCTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * *
28779153 GCCTTTGTGGCGAATTATCTGAAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
*
28779178 GTCTTTGTGGCT
1 GCCTTTGTGGCT
28779190 TGTTGTATGG
Statistics
Matches: 153, Mismatches: 26, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
24 4 0.03
25 146 0.95
26 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (25 bp):
GCCTTTGTGGCTAGTTATCTGTAAA
Found at i:28779096 original size:75 final size:75
Alignment explanation
Indices: 28778951--28779183 Score: 217
Period size: 75 Copynumber: 3.1 Consensus size: 75
28778941 GAATCAAACC
* * * * * *
28778951 AAGCCTTTATGGAGA-ATTATAAGAAATGCCTTTGTGGCTAGTTATCTGTAAAGCCTCTATGAC-
1 AAGCCTTTAT-GAGATATTATCATAAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGGCG
*
28779014 AAGTTATCTGTA
65 AA-TTATCTGAA
* * * * *
28779026 AAGCCTTTATGACATATTATCATAAAAGCCTTTATGACTAGTTATTTGTAAAGCATTTGTGGCGA
1 AAGCCTTTATGAGATATTATCATAAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGGCGA
28779091 ATTATCAT-AA
66 ATTATC-TGAA
* * * *
28779101 AAG-CTTT-TGTGGTGAGTTATC-TGTAAAGCCTTTGTGGCGAGTTATCTGTAAAGCCTTTGTGG
1 AAGCCTTTATGAGAT-A-TTATCAT-AAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGG
28779163 CGAATTATCTGAA
63 CGAATTATCTGAA
*
28779176 AAGTCTTT
1 AAGCCTTT
28779184 GTGGCTTGTT
Statistics
Matches: 129, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
73 3 0.02
74 10 0.08
75 109 0.84
76 7 0.05
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (75 bp):
AAGCCTTTATGAGATATTATCATAAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGGCGA
ATTATCTGAA
Found at i:28781638 original size:27 final size:28
Alignment explanation
Indices: 28781592--28781654 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
28781582 AATACTCTTT
* ** *
28781592 TGGCAAACTCCCTAGTTCGTTGAAGCAC
1 TGGCGAACTCCCTAGTTCGTCAAAACAC
28781620 TGGCGAACT-CCTAGTTCGTCAAAACAC
1 TGGCGAACTCCCTAGTTCGTCAAAACAC
28781647 TGGCGAAC
1 TGGCGAAC
28781655 CCTTACTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (28 bp):
TGGCGAACTCCCTAGTTCGTCAAAACAC
Done.