Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 113 of 210
Found at i:38021391 original size:26 final size:26
Alignment explanation
Indices: 38021368--38021422 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
38021358 TTATTTTGTA
38021368 GAAAAAATGTGTTGATTGTGTTTGAT
1 GAAAAAATGTGTTGATTGTGTTTGAT
* *
38021394 GAATACATGTGTTGATTGTGTTTGAT
1 GAAAAAATGTGTTGATTGTGTTTGAT
38021420 GAA
1 GAA
38021423 TTGGATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (26 bp):
GAAAAAATGTGTTGATTGTGTTTGAT
Found at i:38021423 original size:26 final size:26
Alignment explanation
Indices: 38021374--38021423 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
38021364 TGTAGAAAAA
38021374 ATGTGTTGATTGTGTTTGATGAATAC
1 ATGTGTTGATTGTGTTTGATGAATAC
38021400 ATGTGTTGATTGTGTTTGATGAAT
1 ATGTGTTGATTGTGTTTGATGAAT
38021424 TGGATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.48
Consensus pattern (26 bp):
ATGTGTTGATTGTGTTTGATGAATAC
Found at i:38055639 original size:33 final size:33
Alignment explanation
Indices: 38055602--38055696 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 33
38055592 TTATTATTTT
38055602 GTATGAGTCATAAAAGTAAGTTTGTTTGTTATA
1 GTATGAGTCATAAAAGTAAGTTTGTTTGTTATA
* * *
38055635 GTATGAGTAAAAAAAGTAAGTTTATTTG-T-TA
1 GTATGAGTCATAAAAGTAAGTTTGTTTGTTATA
* *
38055666 -TATGAATCATAAAAATAAGTTTGTTTGTTAT
1 GTATGAGTCATAAAAGTAAGTTTGTTTGTTAT
38055697 GTAAAGGGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 22 0.42
31 3 0.06
32 2 0.04
33 25 0.48
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (33 bp):
GTATGAGTCATAAAAGTAAGTTTGTTTGTTATA
Found at i:38057352 original size:45 final size:45
Alignment explanation
Indices: 38057288--38057373 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
38057278 GCATACCCGT
38057288 TTGAGAATGGTAGCCGCGTGATCATCAGGCTCTTCGATCTCTACG
1 TTGAGAATGGTAGCCGCGTGATCATCAGGCTCTTCGATCTCTACG
**
38057333 TTGAGAATGGTAGTTGCGTGATCATCAGGCTCTTCGATCTC
1 TTGAGAATGGTAGCCGCGTGATCATCAGGCTCTTCGATCTC
38057374 CACTTCATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
TTGAGAATGGTAGCCGCGTGATCATCAGGCTCTTCGATCTCTACG
Found at i:38062769 original size:115 final size:113
Alignment explanation
Indices: 38062469--38062797 Score: 392
Period size: 115 Copynumber: 2.9 Consensus size: 113
38062459 AAAATAAGTA
** *
38062469 TTAGCGGCGTTTTCCAGAAAGCGCCG-AAAAAAACCTAAGCCCAACCACGCCGTTTTTC-GAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCC-TTTTTCTGAG-T
* *
38062532 TTTGGGGATTTAGAGGCATTTTTAAGAAAACGCCGCTAATGCTCAAGGCT
64 TTTGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAAGGCT
* * * *
38062582 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCTTTTTCTGAG-T
* * *
38062647 TTTGGGGATTTAGCGGCATTTCTAAGAAAGCGCCGCTAATGCTTAGGGCT
64 TTTGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAAGGCT
* * * * **
38062697 TTCGCGGCTTTTTTGAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGTTTTTTTCTGAGATT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCTTTTTCTGAG-TT
* * * *
38062762 TCGGGGGATTTAGCGGCGTTTTTGAGAAAGTGCCGC
65 T-TGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGC
38062798 AAAAAAACCT
Statistics
Matches: 183, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
113 23 0.13
114 36 0.20
115 124 0.68
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCTTTTTCTGAGTTT
TGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAAGGCT
Found at i:38062844 original size:188 final size:188
Alignment explanation
Indices: 38062581--38062965 Score: 531
Period size: 188 Copynumber: 2.0 Consensus size: 188
38062571 TGCTCAAGGC
* ** *
38062581 TTTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAAAACATAAGCCCAACGACGCCGTTTTGTGAGT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACATAAGCCCAACGACGCCGTTTTCAGAGC
* * * * *
38062646 TTTTGGGGATTTAGCGGCATTTCTAAGAAAGCGCCGCTAATGCTTAGGGCTTTCGCGGCTTTTTT
66 TTTCGGGGATTTAGCGGCATTTCTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTT
* *
38062711 GAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACG-TTTTTTTCTGAGATTTCGGGGGA
131 GAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGCTGTTTTT-TAAGATTTC-GGGGA
* * *
38062770 TTTAGCGGCGTTTTTGAGAAAGTGCCGC-AAAAAAACCTAAGCCCAATGACGCCGTTTTCAGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACATAAGCCCAACGACGCCGTTTTCAGAGC
* * * *
38062834 TTTCGGGGATTTAGCGGCGTTTTTTAGAAAGCGTCGCTAATGCTCAAGGCTTTAGCGGCGTTTTT
66 TTTCGGGGATTTAGCGGCATTTCTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTT
* * * * *
38062899 GAGAAAGCGCTGCAAAAAAATCTAAGCCCAACGGCGCTGTTTTTTAAGCTTTCGGGGA
131 GAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGCTGTTTTTTAAGATTTCGGGGA
38062957 TTTAGCGGC
1 TTTAGCGGC
38062966 CAAAAATCTG
Statistics
Matches: 172, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
187 14 0.08
188 126 0.73
189 32 0.19
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (188 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACATAAGCCCAACGACGCCGTTTTCAGAGC
TTTCGGGGATTTAGCGGCATTTCTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTT
GAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGCTGTTTTTTAAGATTTCGGGGA
Found at i:38062856 original size:73 final size:74
Alignment explanation
Indices: 38062700--38062866 Score: 228
Period size: 74 Copynumber: 2.3 Consensus size: 74
38062690 TAGGGCTTTC
* *** *
38062700 GCGGCTTTTTTGAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGTTTTTTTCTGAGATTTCG
1 GCGGCGTTTTTGAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGCCGTTTTCAGAGATTTCG
38062765 GGGGATTTA
66 GGGGATTTA
* * * * *
38062774 GCGGCGTTTTTGAGAAAGTGCCGCAAAAAAACCTAAGCCCAATGACGCCGTTTTCAGAGCTTTC-
1 GCGGCGTTTTTGAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGCCGTTTTCAGAGATTTCG
38062838 GGGGATTTA
66 GGGGATTTA
*
38062847 GCGGCGTTTTTTAGAAAGCG
1 GCGGCGTTTTTGAGAAAGCG
38062867 TCGCTAATGC
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
73 27 0.33
74 54 0.67
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (74 bp):
GCGGCGTTTTTGAGAAAGCGCAGCAAAAAAACCTAAGCACAACGACGCCGTTTTCAGAGATTTCG
GGGGATTTA
Found at i:38063033 original size:41 final size:41
Alignment explanation
Indices: 38062973--38063052 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
38062963 GGCCAAAAAT
*
38062973 CTGGGAGCTTTGGCAGCGTTTTTGAAAAAGCGCCGCTAATG
1 CTGGGAGCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATG
* * *
38063014 CTGGGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
1 CTGGGAGCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAA
38063053 AAATATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (41 bp):
CTGGGAGCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATG
Found at i:38063573 original size:21 final size:21
Alignment explanation
Indices: 38063533--38063613 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
38063523 TTTTATTTTA
* *
38063533 GGTTAGGATTTAAGGTTTAGG
1 GGTTAGGGTTTAAGGGTTAGG
* *
38063554 GGTTAGGGTTTAGGGGTTAGA
1 GGTTAGGGTTTAAGGGTTAGG
* * * *
38063575 TGTTAGTGATTAAGAGTTAGG
1 GGTTAGGGTTTAAGGGTTAGG
*
38063596 GATTTAGGGTTT-AGGGTT
1 G-GTTAGGGTTTAAGGGTT
38063614 TCAAGGGTCA
Statistics
Matches: 44, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
21 37 0.84
22 7 0.16
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.38
Consensus pattern (21 bp):
GGTTAGGGTTTAAGGGTTAGG
Found at i:38063580 original size:14 final size:14
Alignment explanation
Indices: 38063546--38063573 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38063536 TAGGATTTAA
38063546 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
38063560 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
38063574 ATGTTAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (14 bp):
GGTTTAGGGGTTAG
Found at i:38066149 original size:21 final size:21
Alignment explanation
Indices: 38066123--38066167 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38066113 CTGCAGCTTA
* *
38066123 AAGCAGATGCTGCAGCGAGAG
1 AAGCAGAGGCTACAGCGAGAG
*
38066144 AAGCAGAGGCTACAGCGAGGG
1 AAGCAGAGGCTACAGCGAGAG
38066165 AAG
1 AAG
38066168 AAGAACAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.40, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCTACAGCGAGAG
Found at i:38066568 original size:43 final size:43
Alignment explanation
Indices: 38066507--38066802 Score: 375
Period size: 43 Copynumber: 6.9 Consensus size: 43
38066497 CGATTTTAAA
* *
38066507 AAAAGCACCGCTAAAGGTCATGGTTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* *
38066550 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCAGCG-TTGTTGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* * *
38066592 AAAAGCGCCGCTATATGTCATGGTCTTTTAGCGGAGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTTGTGGG
*
38066636 AAAAGCGCCGCTAAAGGTCCA-GGTCTTTAGCGGCATTTGTGGG
1 AAAAGCGCCGCTAAAGGT-CATGGTCTTTAGCGGCGTTTGTGGG
* *
38066679 AAAAACGCCGCTAAAGGTCCA-GGTCTTTAGCGACGTTTGTGGG
1 AAAAGCGCCGCTAAAGGT-CATGGTCTTTAGCGGCGTTTGTGGG
* *
38066722 AAGAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGTG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG-G
* * * * *
38066766 -AAAGCGCTGCTAAAGGCCTTGGTCTTTAACGACGTTT
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
38066803 ATTTCTAAAA
Statistics
Matches: 222, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
42 30 0.14
43 163 0.73
44 27 0.12
45 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.27
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
Found at i:38070493 original size:42 final size:42
Alignment explanation
Indices: 38070429--38070517 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
38070419 ATGGTCCAAC
* * *
38070429 ACACGACCTGGCACATGTGCGTGTGTGGCAACTTAAAGAGTT
1 ACACGACCTGGCACACGGGCGTGTGGGGCAACTTAAAGAGTT
* **
38070471 ACACGACCTGGCACACGGGCGTGTGGGGCATCTTAGTGAGTT
1 ACACGACCTGGCACACGGGCGTGTGGGGCAACTTAAAGAGTT
38070513 ACACG
1 ACACG
38070518 GGTGAGGACA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (42 bp):
ACACGACCTGGCACACGGGCGTGTGGGGCAACTTAAAGAGTT
Found at i:38076654 original size:26 final size:26
Alignment explanation
Indices: 38076603--38076672 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
38076593 AGTGAGCCAT
* *
38076603 ATCGGGAAGCTC-TAGAGAGACATTA
1 ATCGGGAAGCTCACAAAGAGACATTA
* *
38076628 ATCGGGAAGCTCACAAAGAGCCTTTA
1 ATCGGGAAGCTCACAAAGAGACATTA
* *
38076654 ATTGGGAAGCTCACGAAGA
1 ATCGGGAAGCTCACAAAGA
38076673 ACCATATATC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
25 12 0.32
26 26 0.68
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (26 bp):
ATCGGGAAGCTCACAAAGAGACATTA
Found at i:38076686 original size:26 final size:26
Alignment explanation
Indices: 38076626--38076692 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
38076616 AGAGAGACAT
* *
38076626 TAATCGGGAAGCTCACAAAGAGCCTT
1 TAATCGGGAAGCTCACAAAGAACCTA
* *
38076652 TAATTGGGAAGCTCACGAAGAACC-A
1 TAATCGGGAAGCTCACAAAGAACCTA
*
38076677 TATATCGGGACGCTCA
1 TA-ATCGGGAAGCTCA
38076693 TAAGAGCTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
TAATCGGGAAGCTCACAAAGAACCTA
Found at i:38077185 original size:21 final size:21
Alignment explanation
Indices: 38077161--38077201 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38077151 AGTAAATTTA
38077161 ACTCAATGT-AATACAATTCAT
1 ACTCAAT-TCAATACAATTCAT
*
38077182 ACTCAATTCAATCCAATTCA
1 ACTCAATTCAATACAATTCA
38077202 CATCTTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.32
Consensus pattern (21 bp):
ACTCAATTCAATACAATTCAT
Found at i:38078349 original size:21 final size:21
Alignment explanation
Indices: 38078297--38078338 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38078287 CTACAACTTA
*
38078297 AAGCGAAA-GCAGCAGCGAGGG
1 AAGC-AAAGGCAGCAGCAAGGG
38078318 AAGCAAAGGCAGCAGCAAGGG
1 AAGCAAAGGCAGCAGCAAGGG
38078339 CAGTAGAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.40, C:0.19, G:0.40, T:0.00
Consensus pattern (21 bp):
AAGCAAAGGCAGCAGCAAGGG
Found at i:38078936 original size:17 final size:17
Alignment explanation
Indices: 38078890--38078936 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
38078880 GAATTTAGAA
*
38078890 GAATTTT-TAAATTAGT
1 GAATTTTGTAATTTAGT
* * *
38078906 GAATTCTGTGATTTATT
1 GAATTTTGTAATTTAGT
38078923 GAATTTTGTAATTT
1 GAATTTTGTAATTT
38078937 TAAAAAGAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (17 bp):
GAATTTTGTAATTTAGT
Found at i:38080253 original size:46 final size:46
Alignment explanation
Indices: 38080182--38080506 Score: 517
Period size: 46 Copynumber: 7.1 Consensus size: 46
38080172 TCCATGGCAA
* *
38080182 AGTT-TGAAATGTATGTATGGTATTTCAGTGAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
* *
38080227 AGTTGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
* *
38080273 AGTTGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
* *
38080319 AGTTGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
* *
38080365 AGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACTATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
38080411 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
* * * *
38080457 AGTTGTGAAAATTAGGTATGATATTTCCGTGAAGAAAATCATACTG
1 AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
38080503 AGTT
1 AGTT
38080507 ATAGCAATGT
Statistics
Matches: 265, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
45 4 0.02
46 261 0.98
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.30
Consensus pattern (46 bp):
AGTTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTG
Found at i:38082678 original size:19 final size:19
Alignment explanation
Indices: 38082641--38082678 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38082631 CTAATTAATT
*
38082641 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
38082660 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
38082679 GAAAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:38082922 original size:24 final size:24
Alignment explanation
Indices: 38082890--38082956 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
38082880 ATAAGTTAAA
*
38082890 TAAAGACAAATGTATAGTAATGAT
1 TAAATACAAATGTATAGTAATGAT
38082914 TAAATACAAATGTATAGTAATGAT
1 TAAATACAAATGTATAGTAATGAT
* *
38082938 TTAATACAAGTGTATAGTA
1 TAAATACAAATGTATAGTA
38082957 TAGATGATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (24 bp):
TAAATACAAATGTATAGTAATGAT
Found at i:38083202 original size:9 final size:9
Alignment explanation
Indices: 38083180--38083228 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
38083170 AAAGTAAATA
*
38083180 AAAAGAAAC
1 AAAAGAAAG
*
38083189 TAAAGAAAG
1 AAAAGAAAG
38083198 AAAAGAAAG
1 AAAAGAAAG
38083207 AAAAG-AAG
1 AAAAGAAAG
*
38083215 TAAAAGAAAC
1 -AAAAGAAAG
38083225 AAAA
1 AAAA
38083229 AGAACAGCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 3 0.09
9 29 0.85
10 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:38083203 original size:18 final size:18
Alignment explanation
Indices: 38083180--38083228 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
38083170 AAAGTAAATA
*
38083180 AAAAGAAACTAAAGAAAG-
1 AAAAGAAACAAAAG-AAGT
*
38083198 AAAAGAAAGAAAAGAAGT
1 AAAAGAAACAAAAGAAGT
38083216 AAAAGAAACAAAA
1 AAAAGAAACAAAA
38083229 AGAACAGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (18 bp):
AAAAGAAACAAAAGAAGT
Found at i:38084188 original size:23 final size:23
Alignment explanation
Indices: 38084161--38084248 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
38084151 GCCTTGCCGA
38084161 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
38084184 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* * *
38084207 TCAGGCACATCATATGTCG--TT
1 TCAGGCACTTTATGTGTCGTATT
38084228 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
38084249 ACTGATCAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.14
21 10 0.17
22 1 0.02
23 39 0.67
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:38087581 original size:23 final size:22
Alignment explanation
Indices: 38087529--38087593 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
38087519 CCTGATCAGT
38087529 ATACGACACATAAGTGCCTG-A
1 ATACGACACATAAGTGCCTGAA
*
38087550 A-ACGACACATGAGGTGCCTGAA
1 ATACGACACAT-AAGTGCCTGAA
38087572 ATACGACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA
38087594 TCGGCAAGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 9 0.24
21 9 0.24
22 2 0.05
23 18 0.47
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTGAA
Found at i:38088663 original size:59 final size:60
Alignment explanation
Indices: 38088596--38088716 Score: 235
Period size: 59 Copynumber: 2.0 Consensus size: 60
38088586 TAATAAACCT
38088596 TAATAATTATTAATTAAATATCATGTAATATCTTCAATTCAACCAAC-TATGCCCCCTCA
1 TAATAATTATTAATTAAATATCATGTAATATCTTCAATTCAACCAACTTATGCCCCCTCA
38088655 TAATAATTATTAATTAAATATCATGTAATATCTTCAATTCAACCAACTTATGCCCCCTCA
1 TAATAATTATTAATTAAATATCATGTAATATCTTCAATTCAACCAACTTATGCCCCCTCA
38088715 TA
1 TA
38088717 TTTATGAATT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 47 0.77
60 14 0.23
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (60 bp):
TAATAATTATTAATTAAATATCATGTAATATCTTCAATTCAACCAACTTATGCCCCCTCA
Found at i:38090296 original size:208 final size:209
Alignment explanation
Indices: 38089938--38090354 Score: 827
Period size: 208 Copynumber: 2.0 Consensus size: 209
38089928 ATGGTTGGTG
38089938 CGGTGGTGAATGGTGGTTTCTGGAAAACATGATGAAGGTTCTTCTACAATAAAATGAGGAAGAGA
1 CGGTGGTGAATGGTGGTTTCTGGAAAACATGATGAAGGTTCTTCTACAATAAAATGAGGAAGAGA
38090003 AGGGGAAACATGAGAGAGAGGAGAGGTAAAATAATTTATTAACTGATACAAATTAAATAATTTAT
66 AGGGGAAACATGAGAGAGAGGAGAGGTAAAATAATTTATTAACTGATACAAATTAAATAATTTAT
38090068 TAACTTATATATTTAAAAACTTTGAAGATATGTTTTTATTTTAAAAAATAATTCATAATAAACCA
131 TAACTTATATATTTAAAAACTTTGAAGATATGTTTTTATTTTAAAAAATAATTCATAATAAACCA
38090133 AT-ATAAATTAATA
196 ATAATAAATTAATA
38090146 CGGTGGTGAATGGTGGTTTCTGGAAAACATGATGAAGGTTCTTCTACAATAAAATGAGGAAGAGA
1 CGGTGGTGAATGGTGGTTTCTGGAAAACATGATGAAGGTTCTTCTACAATAAAATGAGGAAGAGA
38090211 AGGGGAAACATGAGAGAGAGGAGAGGTAAAATAATTTATTAACTGATACAAATTAAATAATTTAT
66 AGGGGAAACATGAGAGAGAGGAGAGGTAAAATAATTTATTAACTGATACAAATTAAATAATTTAT
38090276 TAACTTATATATTTAAAAACTTTGAAGATATGTTTTTATTTTAAAAAATAATTCATAATAAACCA
131 TAACTTATATATTTAAAAACTTTGAAGATATGTTTTTATTTTAAAAAATAATTCATAATAAACCA
38090341 ATAATAAATTAATA
196 ATAATAAATTAATA
38090355 GTAATATTAA
Statistics
Matches: 208, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
208 197 0.95
209 11 0.05
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (209 bp):
CGGTGGTGAATGGTGGTTTCTGGAAAACATGATGAAGGTTCTTCTACAATAAAATGAGGAAGAGA
AGGGGAAACATGAGAGAGAGGAGAGGTAAAATAATTTATTAACTGATACAAATTAAATAATTTAT
TAACTTATATATTTAAAAACTTTGAAGATATGTTTTTATTTTAAAAAATAATTCATAATAAACCA
ATAATAAATTAATA
Found at i:38090483 original size:17 final size:18
Alignment explanation
Indices: 38090461--38090495 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
38090451 AAATTAAAAC
*
38090461 AATAAATTCA-ATTTGTA
1 AATAAATTAATATTTGTA
38090478 AATAAATTAATATTTGTA
1 AATAAATTAATATTTGTA
38090496 GCAAGGGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (18 bp):
AATAAATTAATATTTGTA
Found at i:38106651 original size:25 final size:26
Alignment explanation
Indices: 38106625--38106673 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
38106615 AATCTTAGGA
*
38106625 AAAATTTTGA-TTTAAAAA-AAAAAG
1 AAAATTTAGATTTTAAAAACAAAAAG
*
38106649 AAAGTTTAGATTTTAAAAACAAAAA
1 AAAATTTAGATTTTAAAAACAAAAA
38106674 TATGTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (26 bp):
AAAATTTAGATTTTAAAAACAAAAAG
Found at i:38107887 original size:27 final size:27
Alignment explanation
Indices: 38107857--38107917 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
38107847 TAAGTAGGTG
*
38107857 TTACATTTTAATGAAACCATAAGGTTT
1 TTACATTTTAATGAAACCATAAAGTTT
*
38107884 TTACATTTTAATGAAATCATAAAGTTT
1 TTACATTTTAATGAAACCATAAAGTTT
38107911 TTACATT
1 TTACATT
38107918 CGGGTTTAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (27 bp):
TTACATTTTAATGAAACCATAAAGTTT
Found at i:38109988 original size:2 final size:2
Alignment explanation
Indices: 38109981--38110011 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38109971 AAAGGAAGTC
38109981 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
38110012 GGGGGGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38112447 original size:16 final size:16
Alignment explanation
Indices: 38112426--38112457 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38112416 TCAAATTTAA
38112426 CTGAAATATGAGTCAT
1 CTGAAATATGAGTCAT
38112442 CTGAAATATGAGTCAT
1 CTGAAATATGAGTCAT
38112458 ACTCAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
CTGAAATATGAGTCAT
Found at i:38113567 original size:16 final size:17
Alignment explanation
Indices: 38113543--38113577 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38113533 TGAATATATA
*
38113543 TGTGTAAATATGA-AAT
1 TGTGCAAATATGATAAT
38113559 TGTGCAAATATGATAAT
1 TGTGCAAATATGATAAT
38113576 TG
1 TG
38113578 GATTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (17 bp):
TGTGCAAATATGATAAT
Found at i:38128360 original size:56 final size:50
Alignment explanation
Indices: 38128277--38128469 Score: 176
Period size: 50 Copynumber: 3.8 Consensus size: 50
38128267 GGTGATGAGA
* * **
38128277 TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----AGA-TATGAGAAC
* *
38128333 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGATATGAGAAC
* * * ** *
38128383 TCCTATGTAAGACCATGTCTGGGATATGTCATTGG--CAG-TACAAGAAATA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGATATGAG-AA-C
*
38128432 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
38128470 CGANNNNNNN
Statistics
Matches: 115, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
47 4 0.03
48 4 0.03
49 31 0.27
50 38 0.33
51 3 0.03
55 1 0.01
56 34 0.30
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGATATGAGAAC
Found at i:38128399 original size:50 final size:52
Alignment explanation
Indices: 38128333--38128472 Score: 182
Period size: 49 Copynumber: 2.8 Consensus size: 52
38128323 TTATGAGAGG
** *
38128333 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGATATGAG-AA-C
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGATACAAGAAATA
* * * *
38128383 TCCTATGTAAGACCATGTCTGGGATATGTCATTGGCA--G-TACAAGAAATA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGATACAAGAAATA
38128432 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
38128473 NNNNNNNNNN
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
47 4 0.05
48 3 0.04
49 33 0.45
50 33 0.45
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.24
Consensus pattern (52 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGATACAAGAAATA
Found at i:38136966 original size:24 final size:23
Alignment explanation
Indices: 38136899--38136966 Score: 55
Period size: 25 Copynumber: 2.8 Consensus size: 23
38136889 AAAGCGTCCT
* * *
38136899 GTTATTAGCTCTTATGAGTTTCCC
1 GTTAATAGCTCTT-GGAGCTTCCC
* *
38136923 GTTATATGGTTCTTGCGAGCTTCCC
1 GTTA-ATAGCTCTTG-GAGCTTCCC
38136948 GTTAATAGCTCTTCGGAGC
1 GTTAATAGCTCTT-GGAGC
38136967 ATCCGAATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (23 bp):
GTTAATAGCTCTTGGAGCTTCCC
Found at i:38137116 original size:25 final size:24
Alignment explanation
Indices: 38137083--38137157 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 24
38137073 GCTTCCTAAA
*
38137083 ATATGGCTCTCTAGAGCTTCCCGTT
1 ATATAGCTCTC-AGAGCTTCCCGTT
* * *
38137108 ATTTAGCTCACATGAGCTTCTCGTT
1 ATATAGCTCTCA-GAGCTTCCCGTT
* * *
38137133 ATATGGCTCTAAAGAGTTTCCCGTT
1 ATATAGCTCT-CAGAGCTTCCCGTT
38137158 TATGTGCTCG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (24 bp):
ATATAGCTCTCAGAGCTTCCCGTT
Found at i:38137173 original size:50 final size:51
Alignment explanation
Indices: 38137083--38137180 Score: 119
Period size: 50 Copynumber: 1.9 Consensus size: 51
38137073 GCTTCCTAAA
** *
38137083 ATATGGCTCTCTAGAGCTTCCCGTTATTTAGCTCACATGAGC-TTCTCGTT
1 ATATGGCTCTAAAGAGCTTCCCGTTATGTAGCTCACATGAGCATTCTCGTT
* **
38137133 ATATGGCTCTAAAGAGTTTCCCGTTTATGT-GCTCGTATGAGCATTCTC
1 ATATGGCTCTAAAGAGCTTCCCG-TTATGTAGCTCACATGAGCATTCTC
38137181 AAATATGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 30 0.75
51 10 0.25
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (51 bp):
ATATGGCTCTAAAGAGCTTCCCGTTATGTAGCTCACATGAGCATTCTCGTT
Found at i:38138065 original size:20 final size:20
Alignment explanation
Indices: 38138040--38138080 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
38138030 CCTTGTGAGT
38138040 TATTCACGAGTATTGCCGTG
1 TATTCACGAGTATTGCCGTG
38138060 TATTCACGAGTATTGCCGTG
1 TATTCACGAGTATTGCCGTG
38138080 T
1 T
38138081 CAATATTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
TATTCACGAGTATTGCCGTG
Found at i:38141227 original size:13 final size:13
Alignment explanation
Indices: 38141209--38141233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38141199 TTGTTTTATA
38141209 ATATTTTAAATGC
1 ATATTTTAAATGC
38141222 ATATTTTAAATG
1 ATATTTTAAATG
38141234 TTTTATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATATTTTAAATGC
Found at i:38141357 original size:69 final size:69
Alignment explanation
Indices: 38141222--38141367 Score: 201
Period size: 69 Copynumber: 2.1 Consensus size: 69
38141212 TTTTAAATGC
* *
38141222 ATATTTTAAATGTTTTATAATATTTTTCTATTCAAACGTTTTCTTAATTTGTTTATTATTTGTTT
1 ATATTTTAAATGTTTTATAATATTTTTCTATTCAAACATTTTCTTAATTTATTTATTATTTGTTT
*
38141287 TATA
66 TAAA
38141291 ATATTTTAAATGTTTTATAATATTTGTT-TATTCAAACATTTT-TTAATTATATTTAAATT-TTT
1 ATATTTTAAATGTTTTATAATATTT-TTCTATTCAAACATTTTCTTAATT-TATTT--ATTATTT
38141353 -TTTTAAA
62 GTTTTAAA
38141360 ATATTTTA
1 ATATTTTA
38141368 TACCACTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
68 6 0.09
69 56 0.80
70 5 0.07
71 3 0.04
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (69 bp):
ATATTTTAAATGTTTTATAATATTTTTCTATTCAAACATTTTCTTAATTTATTTATTATTTGTTT
TAAA
Found at i:38148012 original size:364 final size:362
Alignment explanation
Indices: 38147250--38148287 Score: 1527
Period size: 364 Copynumber: 2.8 Consensus size: 362
38147240 ACAAAGTATA
* * * *
38147250 CTTTCGACTCAGATTCATGTGTCATTGAGAGACTTATATATACAAATTTAGTCACGCCAAATAGA
1 CTTTCAACTCAGATTCATGTGTCATTGAGAGGCTTATATATATAAATTTGGTCACGCCAAATAGA
38147315 ATGGCTCCACCAAATAAAATATTATTTTTAAAAATTTTAAATATAAAAAAATAAATTAAAAAAGA
66 ATGGCTCCACCAAATAAAATATTATTTTTAAAAATTTTAAATAT-AAAAAATAAATT-AAAAA-A
* *
38147380 ACGCATTGGT-GTCGCCATTTAAAATGGCTCCACCAAAAAAAATACATAAAATATTATAAAACAA
128 AC-TATTGGTGGT-GCCATTTAGAATGGCTCCACCAAAAAAAATACATAAAATATTATAAAACAA
* * * *
38147444 ATAATAAAAAAATAAAGAAAAACAAATAAAAAATAGAAAAATGACAAAAGGTAGCAGAGGCATTG
191 ATAATAAACAAATAAAGAAAAACAAATAAAAAACAGAAAAAAGACAAAAGGTAGCAGAGGCGTTG
* * * *
38147509 GAATTTGGTGGCGCCAAATTATTTGGCTCTACTAGAAAAAGGAATATTTGTTTAAAACTCCCCAT
256 GAATCTGGTGGCGCCAAATTATTTGGCTCCACCAGAAAAAGGAAAATTTGTTTAAAACTCCCCA-
*
38147574 TTTTTCATCCTATTCATCCTCTAACAAAGTATAAGTATTTTTT
320 CTTTTCATCCTATTCATCCTCTAACAAAGTATAAGTATTTTTT
*
38147617 -TTTCAACTCAGATTCATGTGTCATTGAGAGGCTTATATATATAAATTTGGTCATGCCAAATAGA
1 CTTTCAACTCAGATTCATGTGTCATTGAGAGGCTTATATATATAAATTTGGTCACGCCAAATAGA
*
38147681 ATGGCTCTACCAAATAAAATATTATATTTTAAAAATTTTAAATATAAAAAATAAATTAAAAAATA
66 ATGGCTCCACCAAATAAAATATTAT-TTTTAAAAATTTTAAATATAAAAAATAAATTAAAAAA-A
38147746 -TATTGGTGGTGCCATTTAGAATGGCTCCACCCAAAAAAAAAATACATAAAATATTATAAAA-AA
129 CTATTGGTGGTGCCATTTAGAATGGCTCCA-CC--AAAAAAAATACATAAAATATTATAAAACAA
* *
38147809 ATAATAAACAAATAAAGAAAAACAAATAAAAAACAGAAAAAGGAC-AAAGGTAGCAGAGGTGTTG
191 ATAATAAACAAATAAAGAAAAACAAATAAAAAACAGAAAAAAGACAAAAGGTAGCAGAGGCGTTG
* *
38147873 GAATCTGGTGGCGCCAAAGTATTTGGCTCCACCAGAAAAAGGAAAATTTGTTTAAAGC-CCCC-C
256 GAATCTGGTGGCGCCAAATTATTTGGCTCCACCAGAAAAAGGAAAATTTGTTTAAAACTCCCCAC
38147936 TTTTCATCAC-ATTCATCCTCTAACAAAGTA-AAGTAAATTTTTCT
321 TTTTCATC-CTATTCATCCTCTAACAAAGTATAAGT--ATTTTT-T
*
38147980 CTTTCAACTTAGATTCATGTGTCATTGAGAGGCTTATATATATAAATTTGGTCACGCCAAATAGA
1 CTTTCAACTCAGATTCATGTGTCATTGAGAGGCTTATATATATAAATTTGGTCACGCCAAATAGA
38148045 ATGGCTCCACCAAATAAAATATTATTTTTTAAAAATTTTAAATATAAAAAATAAATTTAAAAAAA
66 ATGGCTCCACCAAATAAAATATTA-TTTTTAAAAATTTTAAATATAAAAAATAAA-TTAAAAAAA
** * ** *
38148110 CGTATTGGTGACGCCATTTAGAATGGATCCACCTAAAAAGTATACATAAAACATTATAAAACAAA
129 C-TATTGGTGGTGCCATTTAGAATGGCTCCACC-AAAAAAAATACATAAAATATTATAAAACAAA
* * *
38148175 TAATAAACAAATAAAGAAAAACAAATAAAAAAACAGAAAAAAGACAAAAGATAACAGAGGGGTTG
192 TAATAAACAAATAAAGAAAAACAAAT-AAAAAACAGAAAAAAGACAAAAGGTAGCAGAGGCGTTG
* * *
38148240 GAATCTGGTGGCGGCAAATTATTTAGCTCCACCAGAAAAAGAAAAATT
256 GAATCTGGTGGCGCCAAATTATTTGGCTCCACCAGAAAAAGGAAAATT
38148288 ATACTAGAAA
Statistics
Matches: 615, Mismatches: 38, Indels: 36
0.89 0.06 0.05
Matches are distributed among these distances:
360 4 0.01
361 28 0.05
362 7 0.01
363 29 0.05
364 213 0.35
365 90 0.15
366 165 0.27
367 79 0.13
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.28
Consensus pattern (362 bp):
CTTTCAACTCAGATTCATGTGTCATTGAGAGGCTTATATATATAAATTTGGTCACGCCAAATAGA
ATGGCTCCACCAAATAAAATATTATTTTTAAAAATTTTAAATATAAAAAATAAATTAAAAAAACT
ATTGGTGGTGCCATTTAGAATGGCTCCACCAAAAAAAATACATAAAATATTATAAAACAAATAAT
AAACAAATAAAGAAAAACAAATAAAAAACAGAAAAAAGACAAAAGGTAGCAGAGGCGTTGGAATC
TGGTGGCGCCAAATTATTTGGCTCCACCAGAAAAAGGAAAATTTGTTTAAAACTCCCCACTTTTC
ATCCTATTCATCCTCTAACAAAGTATAAGTATTTTTT
Found at i:38148198 original size:14 final size:13
Alignment explanation
Indices: 38148167--38148207 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
38148157 AAAACATTAT
38148167 AAAACAAAT--AA
1 AAAACAAATAAAA
*
38148178 TAAACAAATAAAGA
1 AAAACAAATAAA-A
38148192 AAAACAAATAAAA
1 AAAACAAATAAAA
38148205 AAA
1 AAA
38148208 CAGAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 8 0.32
13 5 0.20
14 12 0.48
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.10
Consensus pattern (13 bp):
AAAACAAATAAAA
Found at i:38148201 original size:22 final size:20
Alignment explanation
Indices: 38148176--38148215 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38148166 TAAAACAAAT
38148176 AATAAACAAATAAAGAAAAACA
1 AATAAA-AAA-AAAGAAAAACA
*
38148198 AATAAAAAAACAGAAAAA
1 AATAAAAAAAAAGAAAAA
38148216 AGACAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (20 bp):
AATAAAAAAAAAGAAAAACA
Found at i:38148435 original size:32 final size:32
Alignment explanation
Indices: 38148375--38148437 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
38148365 ATAAACAAAG
** * *
38148375 ATTATAAAACATTTAAAATATAAATTTAAAAT
1 ATTATAAAACAAATAAAAAACAAATTTAAAAT
*
38148407 ATTATAAAACAAATAAAAAACAATTTTAAAA
1 ATTATAAAACAAATAAAAAACAAATTTAAAA
38148438 AACAAATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (32 bp):
ATTATAAAACAAATAAAAAACAAATTTAAAAT
Found at i:38148469 original size:25 final size:25
Alignment explanation
Indices: 38148412--38148484 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
38148402 AAAATATTAT
* **
38148412 AAAACAAATAAAAAACAATTTTA-A
1 AAAACAAATAAAAAACAAATAAAGA
*
38148436 AAAACAAATAATAAACAAATAAAGA
1 AAAACAAATAAAAAACAAATAAAGA
*
38148461 AAAACAAATAAAAAACAAAAAAAG
1 AAAACAAATAAAAAACAAATAAAG
38148485 GACAAAAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 19 0.45
25 23 0.55
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.12
Consensus pattern (25 bp):
AAAACAAATAAAAAACAAATAAAGA
Found at i:38148483 original size:10 final size:11
Alignment explanation
Indices: 38148412--38148483 Score: 74
Period size: 11 Copynumber: 6.2 Consensus size: 11
38148402 AAAATATTAT
38148412 AAAACAAATAA
1 AAAACAAATAA
*
38148423 AAAACAATTTTAA
1 AAAACAA--ATAA
38148436 AAAACAAATAA
1 AAAACAAATAA
*
38148447 TAAACAAATAAAGA
1 AAAACAAAT--A-A
38148461 AAAACAAATAA
1 AAAACAAATAA
38148472 AAAACAAA-AA
1 AAAACAAATAA
38148482 AA
1 AA
38148484 GGACAAAAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
10 4 0.08
11 27 0.52
12 1 0.02
13 11 0.21
14 9 0.17
ACGTcount: A:0.78, C:0.08, G:0.01, T:0.12
Consensus pattern (11 bp):
AAAACAAATAA
Found at i:38153049 original size:3 final size:3
Alignment explanation
Indices: 38153041--38153074 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
38153031 ACTTGATACT
38153041 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
38153075 ATTCAAGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:38160911 original size:6 final size:6
Alignment explanation
Indices: 38160900--38160928 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38160890 GAACCATGCA
38160900 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
38160929 CACATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:38177908 original size:22 final size:22
Alignment explanation
Indices: 38177865--38177910 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
38177855 TTTTTTTATT
* *
38177865 ATTTTTTTAAATTCGACCTTTA
1 ATTTTTTTAAATTCCACATTTA
38177887 ATTTATTTTAAATTCCA-ATTTA
1 ATTT-TTTTAAATTCCACATTTA
38177909 AT
1 AT
38177911 CCTTTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTTTTTAAATTCCACATTTA
Found at i:38180599 original size:21 final size:20
Alignment explanation
Indices: 38180575--38180657 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 20
38180565 ACCAAAAATT
38180575 TATTTTAAAAATTAAAAAAAA
1 TATTTT-AAAATTAAAAAAAA
38180596 TATTTTAAAATT--AAAAAA
1 TATTTTAAAATTAAAAAAAA
* ***
38180614 T-TTTAAAAAGTATTTTAAAAA
1 TATTTTAAAA-T-TAAAAAAAA
38180635 TATTTTAAAATTAAAAAATAA
1 TATTTTAAAATTAAAAAA-AA
38180656 TA
1 TA
38180658 AAAAAGTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
17 7 0.14
18 8 0.16
19 1 0.02
20 10 0.20
21 17 0.34
22 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
TATTTTAAAATTAAAAAAAA
Found at i:38180630 original size:12 final size:11
Alignment explanation
Indices: 38180606--38180684 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
38180596 TATTTTAAAA
38180606 TTAAAAA-ATT
1 TTAAAAATATT
38180616 TTAAAAAGTATT
1 TTAAAAA-TATT
38180628 TTAAAAATATT
1 TTAAAAATATT
38180639 TT--AAA-A-T
1 TTAAAAATATT
* *
38180646 TAAAAAATA-A
1 TTAAAAATATT
*
38180656 TAAAAAAGTATT
1 TTAAAAA-TATT
38180668 TTAAAAATATT
1 TTAAAAATATT
38180679 TTAAAA
1 TTAAAA
38180685 TTAAAAAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
7 2 0.03
8 1 0.02
9 6 0.10
10 15 0.26
11 18 0.31
12 16 0.28
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:38180642 original size:39 final size:39
Alignment explanation
Indices: 38180591--38180702 Score: 188
Period size: 40 Copynumber: 2.8 Consensus size: 39
38180581 AAAAATTAAA
38180591 AAAAATATTTTAAAATTAAAAAATTTTAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAATTTTAAAAAGTATTTT
* *
38180630 AAAAATATTTTAAAATTAAAAAATAATAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAT-TTTAAAAAGTATTTT
38180670 AAAAATATTTTAAAATTAAAAAATTTTTAAAAA
1 AAAAATATTTTAAAATTAAAAAA-TTTTAAAAA
38180703 ATAAATATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 24 0.36
40 42 0.63
41 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (39 bp):
AAAAATATTTTAAAATTAAAAAATTTTAAAAAGTATTTT
Found at i:38184647 original size:3 final size:3
Alignment explanation
Indices: 38184641--38184690 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
38184631 AAGAAAAAAA
38184641 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
38184689 AA
1 AA
38184691 AAACTAAAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:38191246 original size:22 final size:22
Alignment explanation
Indices: 38191221--38191290 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
38191211 ATTTAATATA
38191221 ATTTTTTAATTCTTTATATTTC
1 ATTTTTTAATTCTTTATATTTC
*
38191243 ATTTTATT--TTTTTTA-ATATT-
1 ATTTT-TTAATTCTTTATAT-TTC
38191263 ATTTTTTTAATTCTTTATATTTC
1 A-TTTTTTAATTCTTTATATTTC
38191286 ATTTT
1 ATTTT
38191291 ATGATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
20 5 0.13
21 12 0.31
22 17 0.44
23 5 0.13
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTTTAATTCTTTATATTTC
Found at i:38191279 original size:43 final size:42
Alignment explanation
Indices: 38191212--38191292 Score: 144
Period size: 43 Copynumber: 1.9 Consensus size: 42
38191202 TTACTTATTA
38191212 TTTAATATAATTTTTTAATTCTTTATATTTCATTTTATTTTT
1 TTTAATATAATTTTTTAATTCTTTATATTTCATTTTATTTTT
*
38191254 TTTAATATTATTTTTTTAATTCTTTATATTTCATTTTAT
1 TTTAATA-TAATTTTTTAATTCTTTATATTTCATTTTAT
38191293 GATTATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 7 0.19
43 30 0.81
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (42 bp):
TTTAATATAATTTTTTAATTCTTTATATTTCATTTTATTTTT
Found at i:38191282 original size:21 final size:22
Alignment explanation
Indices: 38191222--38191290 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 22
38191212 TTTAATATAA
38191222 TTTTTTAATTCTTTATATTTCAT
1 TTTTTTAATTCTTTATA-TTCAT
38191245 TTTATTT--TT-TTTAATATT-AT
1 TTT-TTTAATTCTTT-ATATTCAT
38191265 TTTTTTAATTCTTTATATTTCAT
1 TTTTTTAATTCTTTATA-TTCAT
38191288 TTT
1 TTT
38191291 ATGATTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
21 10 0.26
22 10 0.26
23 8 0.21
24 3 0.08
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTTAATTCTTTATATTCAT
Found at i:38191531 original size:19 final size:18
Alignment explanation
Indices: 38191503--38191540 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
38191493 ACATAAATTT
38191503 AAAAAAAATTAAAAATGA
1 AAAAAAAATTAAAAATGA
38191521 AAAATAAAATTAAAAATGA
1 AAAA-AAAATTAAAAATGA
38191540 A
1 A
38191541 CTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAAAAAATTAAAAATGA
Found at i:38193932 original size:21 final size:21
Alignment explanation
Indices: 38193850--38193932 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
38193840 GTGCATACGA
* *
38193850 GCGTATGGAGTAACCACACAG
1 GCGTGTGGAGTAACCACACGG
* *
38193871 GCGTGTGGAGTAACCACATGA
1 GCGTGTGGAGTAACCACACGG
*
38193892 GAGTGTGGAGTAACCACACGG
1 GCGTGTGGAGTAACCACACGG
38193913 GCGTGTGGAGTAACCACACG
1 GCGTGTGGAGTAACCACACG
38193933 ACCATGTCCA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.29, C:0.22, G:0.34, T:0.16
Consensus pattern (21 bp):
GCGTGTGGAGTAACCACACGG
Found at i:38195227 original size:36 final size:36
Alignment explanation
Indices: 38195187--38195256 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
38195177 ACAGATTATG
38195187 TATGTGTGATCATACACTTTGATGTAAGTAAAAGCA
1 TATGTGTGATCATACACTTTGATGTAAGTAAAAGCA
38195223 TATGTGTGATCATACACTTTGATGTAAGTAAAAG
1 TATGTGTGATCATACACTTTGATGTAAGTAAAAG
38195257 AATGGGTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (36 bp):
TATGTGTGATCATACACTTTGATGTAAGTAAAAGCA
Found at i:38198082 original size:28 final size:27
Alignment explanation
Indices: 38198046--38198169 Score: 99
Period size: 27 Copynumber: 4.5 Consensus size: 27
38198036 AACATGTCAA
*
38198046 GAAAGAAAAGTCTTTGTGGCGAATCAT
1 GAAAGAAAAGCCTTTGTGGCGAATCAT
*
38198073 GAAATGAAAA-CCTTTGT-GCTGAATCTT
1 GAAA-GAAAAGCCTTTGTGGC-GAATCAT
* * *
38198100 GAAAAGAACAGCCTTCGTGGCGAATTAT
1 G-AAAGAAAAGCCTTTGTGGCGAATCAT
* * *
38198128 GAAAGGAAATACCCTTTGTGGCGGATTAT
1 GAAA-GAAA-AGCCTTTGTGGCGAATCAT
* *
38198157 GAAGGAACAGCCT
1 GAAAGAAAAGCCT
38198170 CTACGGCGGG
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
26 2 0.03
27 28 0.36
28 26 0.34
29 21 0.27
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTGTGGCGAATCAT
Found at i:38198087 original size:27 final size:27
Alignment explanation
Indices: 38198047--38198159 Score: 93
Period size: 28 Copynumber: 4.0 Consensus size: 27
38198037 ACATGTCAAG
*
38198047 AAAGAAAAGTCTTTGTGGCGAATCATGA
1 AAAGAAAA-CCTTTGTGGCGAATCATGA
* *
38198075 AATGAAAACCTTTGT-GCTGAATCTTGA
1 AAAGAAAACCTTTGTGGC-GAATCATGA
* * *
38198102 AAAGAACAGCCTTCGTGGCGAATTATGA
1 AAAGAA-AACCTTTGTGGCGAATCATGA
* * *
38198130 AAGGAAATACCCTTTGTGGCGGATTATGA
1 AAAGAAA-A-CCTTTGTGGCGAATCATGA
38198159 A
1 A
38198160 GGAACAGCCT
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
26 2 0.03
27 20 0.29
28 26 0.38
29 20 0.29
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (27 bp):
AAAGAAAACCTTTGTGGCGAATCATGA
Found at i:38202502 original size:31 final size:31
Alignment explanation
Indices: 38202449--38202556 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
38202439 TTAAAAAACT
* * **
38202449 TTTATTTGAGCACTATAAAAAATGTTTGACC
1 TTTATTTGAGAACTTTTGAAAATGTTTGACC
* *
38202480 TTTATTTGAGCACTTTTGAAAATATTTAGA-C
1 TTTATTTGAGAACTTTTGAAAATGTTT-GACC
* * *
38202511 ATTATTTGATAAC-TTTG-AAATGTTTAACC
1 TTTATTTGAGAACTTTTGAAAATGTTTGACC
*
38202540 TTCATTTGAGAACTTTT
1 TTTATTTGAGAACTTTT
38202557 TTTTATAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
28 1 0.02
29 18 0.29
30 7 0.11
31 34 0.55
32 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (31 bp):
TTTATTTGAGAACTTTTGAAAATGTTTGACC
Found at i:38202546 original size:29 final size:29
Alignment explanation
Indices: 38202467--38202555 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
38202457 AGCACTATAA
* *
38202467 AAAATGTTTGACCTTTATTTGAGCACTTTTG
1 AAAATGTTTAACC-TTATTTGAGAAC-TTTG
* * *
38202498 AAAATATTTAGACATTATTTGATAACTTTG
1 AAAATGTTTA-ACCTTATTTGAGAACTTTG
38202528 -AAATGTTTAACCTTCATTTGAGAACTTT
1 AAAATGTTTAACCTT-ATTTGAGAACTTT
38202556 TTTTTATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 4 0.08
29 20 0.42
30 4 0.08
31 18 0.38
32 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (29 bp):
AAAATGTTTAACCTTATTTGAGAACTTTG
Found at i:38202897 original size:21 final size:21
Alignment explanation
Indices: 38202872--38202932 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
38202862 ATTTTTTAAA
38202872 ATAA-TACAAATATGTTAATAT
1 ATAATTACAAATAT-TTAATAT
38202893 ATAATTACAAATATTTAATGAT
1 ATAATTACAAATATTTAAT-AT
*
38202915 -TATATT-TAAATATTTAAT
1 ATA-ATTACAAATATTTAAT
38202933 GTTAACAGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
ATAATTACAAATATTTAATAT
Found at i:38213196 original size:3 final size:3
Alignment explanation
Indices: 38213188--38213219 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
38213178 ATTCTTAAGG
38213188 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38213220 CCTCTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:38224745 original size:24 final size:24
Alignment explanation
Indices: 38224717--38224762 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
38224707 TGTCTTCTAA
38224717 GGTTTAGTTTAAGCTTTTTTTTAG
1 GGTTTAGTTTAAGCTTTTTTTTAG
38224741 GGTTTAGTTTAAGCTTTTTTTT
1 GGTTTAGTTTAAGCTTTTTTTT
38224763 TTTTTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.04, G:0.20, T:0.61
Consensus pattern (24 bp):
GGTTTAGTTTAAGCTTTTTTTTAG
Found at i:38226603 original size:23 final size:23
Alignment explanation
Indices: 38226576--38226743 Score: 228
Period size: 23 Copynumber: 7.3 Consensus size: 23
38226566 AGTGTTATTA
38226576 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGACTACAT
* * * *
38226599 TTCAGTGGTAGCTACGGCTACCT
1 ATCAGTGGTAGCTTCGACTACAT
38226622 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGACTACAT
* * * *
38226645 TTCAGTGGTAGCTACGGCTACCT
1 ATCAGTGGTAGCTTCGACTACAT
38226668 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGACTACAT
* * *
38226691 TTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGACTACAT
*
38226714 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGACTACAT
38226737 ATCAGTG
1 ATCAGTG
38226744 TGACACTTAT
Statistics
Matches: 122, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 122 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGACTACAT
Found at i:38226643 original size:46 final size:46
Alignment explanation
Indices: 38226576--38226743 Score: 300
Period size: 46 Copynumber: 3.7 Consensus size: 46
38226566 AGTGTTATTA
38226576 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACCT
1 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACCT
38226622 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACCT
1 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACCT
* *
38226668 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGACTACGT
1 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACCT
* *
38226714 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGACTACATTTCAGTG
38226744 TGACACTTAT
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACCT
Found at i:38247601 original size:87 final size:88
Alignment explanation
Indices: 38247455--38247630 Score: 345
Period size: 87 Copynumber: 2.0 Consensus size: 88
38247445 TGACCCAAGT
38247455 TAGAGAGTTACACGGGCACGGACACGAGCTGGGACACGGCCGTGTGTCTCTATTTTGAATGTTAC
1 TAGAGAGTTACACGGGCACGGACACGAGCTGGGACACGGCCGTGTGTCTCTATTTTGAATGTTAC
38247520 ACGGCCTGAGAC-CGGGCATGTG
66 ACGGCCTGAGACACGGGCATGTG
38247542 TAGAGAGTTACACGGGCACGGACACGAGCTGGGACACGGCCGTGTGTCTCTATTTTGAATGTTAC
1 TAGAGAGTTACACGGGCACGGACACGAGCTGGGACACGGCCGTGTGTCTCTATTTTGAATGTTAC
38247607 ACGGCCTGAGACACGGGCATGTG
66 ACGGCCTGAGACACGGGCATGTG
38247630 T
1 T
38247631 CTCAGTCGTG
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 77 0.88
88 11 0.12
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (88 bp):
TAGAGAGTTACACGGGCACGGACACGAGCTGGGACACGGCCGTGTGTCTCTATTTTGAATGTTAC
ACGGCCTGAGACACGGGCATGTG
Found at i:38250501 original size:21 final size:21
Alignment explanation
Indices: 38250468--38250508 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38250458 CAAAAAAAGC
**
38250468 TCTCAAATTTCTCTCTAAATT
1 TCTCAAAACTCTCTCTAAATT
*
38250489 TCTCAAAACTCTCTTTAAAT
1 TCTCAAAACTCTCTCTAAAT
38250509 CACAATTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (21 bp):
TCTCAAAACTCTCTCTAAATT
Found at i:38252215 original size:18 final size:18
Alignment explanation
Indices: 38252192--38252229 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
38252182 TGCCAGGTGC
*
38252192 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
38252210 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
38252228 GT
1 GT
38252230 TTCTTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:38253815 original size:26 final size:26
Alignment explanation
Indices: 38253784--38253854 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
38253774 TCAAAATAGG
*
38253784 TAAAATAACCAAAATACCTCATAGAA
1 TAAAATGACCAAAATACCTCATAGAA
* * **
38253810 TAAAATGATCGAAATACCCTCATAGGG
1 TAAAATGACCAAAATA-CCTCATAGAA
*
38253837 TAAAATGACTAAAATACC
1 TAAAATGACCAAAATACC
38253855 CCCATTGGGT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (26 bp):
TAAAATGACCAAAATACCTCATAGAA
Found at i:38253840 original size:27 final size:26
Alignment explanation
Indices: 38253795--38253955 Score: 146
Period size: 27 Copynumber: 6.0 Consensus size: 26
38253785 AAAATAACCA
* **
38253795 AAATACCTCATAGAATAAAATGA-TCG
1 AAATACCCCATAGGGTAAAATGACT-G
*
38253821 AAATACCCTCATAGGGTAAAATGACTA
1 AAATACCC-CATAGGGTAAAATGACTG
* * * *
38253848 AAATACCCCCATTGGGTAGAATAACCG
1 AAATA-CCCCATAGGGTAAAATGACTG
38253875 AAATACCCCTATAGGGTAAAATGACTG
1 AAATACCCC-ATAGGGTAAAATGACTG
38253902 AAATACTCCCATAGGGTAAAATGACTG
1 AAATAC-CCCATAGGGTAAAATGACTG
** *
38253929 TTATACCCC-TAGGAGATGAAATGACTG
1 AAATACCCCATAGG-G-TAAAATGACTG
38253956 TTATGGCTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 13
0.79 0.11 0.09
Matches are distributed among these distances:
25 4 0.04
26 15 0.13
27 86 0.77
28 7 0.06
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (26 bp):
AAATACCCCATAGGGTAAAATGACTG
Found at i:38253939 original size:54 final size:54
Alignment explanation
Indices: 38253782--38253923 Score: 162
Period size: 54 Copynumber: 2.6 Consensus size: 54
38253772 CCTCAAAATA
* * * ** * *
38253782 GGTAAAATAACCAAAATA-CCTCATAGAATAAAATGATCGAAATA-CCCTCATAG
1 GGTAAAATGACTAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCT-ATAG
* *
38253835 GGTAAAATGACTAAAATACCCCCATTGGGTAGAATAACCGAAATACCCCTATAG
1 GGTAAAATGACTAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCTATAG
* *
38253889 GGTAAAATGACTGAAATACTCCCATAGGGTAAAAT
1 GGTAAAATGACTAAAATACCCCCATAGGGTAAAAT
38253924 GACTGTTATA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
53 16 0.22
54 54 0.73
55 4 0.05
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (54 bp):
GGTAAAATGACTAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCTATAG
Found at i:38255963 original size:17 final size:18
Alignment explanation
Indices: 38255931--38255964 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38255921 TTCCATTCAA
*
38255931 AAACAAATTGAATATTAT
1 AAACAAAATGAATATTAT
38255949 AAACAAAAT-AATATTA
1 AAACAAAATGAATATTA
38255965 GTGGTGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
AAACAAAATGAATATTAT
Found at i:38258094 original size:25 final size:25
Alignment explanation
Indices: 38258065--38258113 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
38258055 CCTCACCTTC
38258065 TTCAATTTATATTATTCTAAACTTT
1 TTCAATTTATATTATTCTAAACTTT
* *
38258090 TTCAATTTCTATTCTTCTAAACTT
1 TTCAATTTATATTATTCTAAACTT
38258114 CTCTAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (25 bp):
TTCAATTTATATTATTCTAAACTTT
Found at i:38258121 original size:25 final size:25
Alignment explanation
Indices: 38258066--38258124 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
38258056 CTCACCTTCT
* *
38258066 TCAATTTATATTATTCTAAACTTTT
1 TCAATTTCTATTATTCTAAACTTTC
*
38258091 TCAATTTCTATTCTTCTAAAC-TTC
1 TCAATTTCTATTATTCTAAACTTTC
38258115 TCTAATTTCT
1 TC-AATTTCT
38258125 CTTGCTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (25 bp):
TCAATTTCTATTATTCTAAACTTTC
Found at i:38258473 original size:125 final size:125
Alignment explanation
Indices: 38258195--38258868 Score: 897
Period size: 126 Copynumber: 5.4 Consensus size: 125
38258185 TAGGATGTAT
* * * * * * * *
38258195 TGTAGAAAAAAAGCTTCTAGGTGGGAGCTTTTTTTAGTATTTTTACTGACAA-TGCATCCCGCTT
1 TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCT-AAAAGTGCATCCTGCTT
* *
38258259 GAAGCATTTTTGACCCTATTTATTT-AGAACCATCTTCTCAAAATTATTTTTTCAAAAACTAC
65 GAAGCATTTTTTACCCTATTT-TTTCAGAACCATCTTCTCAAAATTA-TTTTTCAGAAACTAC
* * *
38258321 TATAGAAAAAGAGAGTCCAGGTGGGAGCTTTTTTTAGTACTTTTGCTAAAAGTGCATCCTGCTTG
1 TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAAAAGTGCATCCTGCTTG
*
38258386 AAGCTTTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAACTAC
66 AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAACTAC
* *
38258446 TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTGTTTG
1 TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAAAAGTGCATCCTGCTTG
* * *
38258511 AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAATTATT-TTTTTCAGAAATTAT
66 AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAA-AATTATTTTTCAGAAACTAC
* * * *
38258571 TGTAGAAAAAGAGTGTCTAGGTGGGAGCTTTTTTCGGTACTTTTGCTGAAAGTGCATCCTGCTTG
1 TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAAAAGTGCATCCTGCTTG
* * *
38258636 AAGCGTTTTTTACCCTATTTTTTCAAAACTATCTTCTCAAAATTATTTTTTCAGAAACTAC
66 AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTA-TTTTTCAGAAACTAC
** * * * * *
38258697 TGTAGAAAAAGAGCACCCAAGTGAGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCTTTCTTG
1 TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAAAAGTGCATCCTGCTTG
*** * *
38258762 AAATGTTTTTTACCTTATTTTTTCAGAATCATCTTCTCAAAATTAATTTTTCAGAAACTAC
66 AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATT-ATTTTTCAGAAACTAC
* *
38258823 TGTAGAAAAATAGCGTCCAGCTGGGAGCTCTTTTT-AGTACTTTTGC
1 TGTAGAAAAAGAGCGTCCAGGTGGGAGCT-TTTTTCAGTACTTTTGC
38258869 ACACTGAAAA
Statistics
Matches: 485, Mismatches: 56, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
124 3 0.01
125 228 0.47
126 248 0.51
127 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (125 bp):
TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAAAAGTGCATCCTGCTTG
AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAACTAC
Found at i:38258667 original size:14 final size:14
Alignment explanation
Indices: 38258650--38258695 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
38258640 GTTTTTTACC
38258650 CTATTTTTTCAAAA
1 CTATTTTTTCAAAA
* *
38258664 CTATCTTCTCAAAA
1 CTATTTTTTCAAAA
*
38258678 TTATTTTTTCAGAAA
1 CTATTTTTTCA-AAA
38258693 CTA
1 CTA
38258696 CTGTAGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (14 bp):
CTATTTTTTCAAAA
Found at i:38258688 original size:251 final size:249
Alignment explanation
Indices: 38258195--38258868 Score: 922
Period size: 251 Copynumber: 2.7 Consensus size: 249
38258185 TAGGATGTAT
* * * * * * * * * *
38258195 TGTAGAAAAAAAGCTTCTAGGTGGGAGCTTTTTTTAGTATTTTTACTGACAATGCATCCCGCTTG
1 TGTAGAAAAAGAGCATCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTGTTTG
* * *
38258260 AAGCATTTTTGACCCTATTTATTT-AGAACCATCTTCTCAAAATTATTTTTTCAAAAACTACTAT
66 AAGCATTTTTTACCCTATTT-TTTCAGAACCATCTTCTC-AAATTATTTTTTCAGAAACTACTGT
38258324 AGAAAAAGAGAGTCCAGGTGGGAGCTTTTTTTAGTACTTTTGCTAAAAGTGCATCCTGCTTGAAG
129 AGAAAAAGAGAGTCCAGGTGGGAGC-TTTTTTAGTACTTTTGCTAAAAGTGCATCCTGCTTGAAG
* *
38258389 CTTTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAACTAC
193 CGTTTTTTACCCTATTTTTTCAAAACCATCTTCTCAAAATTATTTTTCAGAAACTAC
*
38258446 TGTAGAAAAAGAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTGTTTG
1 TGTAGAAAAAGAGCATCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTGTTTG
* *
38258511 AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTC-AATTATTTTTTTCAGAAATTATTGTA
66 AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAATTA-TTTTTTCAGAAACTACTGTA
* * * *
38258575 GAAAAAGAGTGTCTAGGTGGGAGCTTTTTTCGGTACTTTTGCTGAAAGTGCATCCTGCTTGAAGC
130 GAAAAAGAGAGTCCAGGTGGGAGCTTTTTT-AGTACTTTTGCTAAAAGTGCATCCTGCTTGAAGC
*
38258640 GTTTTTTACCCTATTTTTTCAAAACTATCTTCTCAAAATTATTTTTTCAGAAACTAC
194 GTTTTTTACCCTATTTTTTCAAAACCATCTTCTCAAAATTA-TTTTTCAGAAACTAC
* * * *
38258697 TGTAGAAAAAGAGCACCCAAGTGAGAGCTTTTTTCAGTACTTTTGCTAACAGTGCAT-CTTTCTT
1 TGTAGAAAAAGAGCATCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTGT-TT
*** * * *
38258761 GAAATGTTTTTTACCTTATTTTTTCAGAATCATCTTCTCAAAATTAATTTTTCAGAAACTACTGT
65 GAAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTC-AAATTATTTTTTCAGAAACTACTGT
* * *
38258826 AGAAAAATAGCGTCCAGCTGGGAGCTCTTTTTAGTACTTTTGC
129 AGAAAAAGAGAGTCCAGGTGGGAGCT-TTTTTAGTACTTTTGC
38258869 ACACTGAAAA
Statistics
Matches: 375, Mismatches: 40, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
249 11 0.03
250 114 0.30
251 192 0.51
252 48 0.13
253 10 0.03
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (249 bp):
TGTAGAAAAAGAGCATCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTGTTTG
AAGCATTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAATTATTTTTTCAGAAACTACTGTAG
AAAAAGAGAGTCCAGGTGGGAGCTTTTTTAGTACTTTTGCTAAAAGTGCATCCTGCTTGAAGCGT
TTTTTACCCTATTTTTTCAAAACCATCTTCTCAAAATTATTTTTCAGAAACTAC
Found at i:38259034 original size:29 final size:27
Alignment explanation
Indices: 38258965--38259086 Score: 124
Period size: 28 Copynumber: 4.4 Consensus size: 27
38258955 CCTAAACAAA
*
38258965 AATTTA-TTTTTAAAAATATTTAAACCCT
1 AATTTATTTTTTAAAAACA--TAAACCCT
38258993 AATTTATTTTTTAAAATA-A-AAACCCCT
1 AATTTATTTTTTAAAA-ACATAAA-CCCT
38259020 AATTTAATTTATTTAAAAACATAAACCCT
1 AATTT-ATTT-TTTAAAAACATAAACCCT
* *
38259049 AATTTATTTTTTAAAACCCCTAAACCCT
1 AATTTATTTTTTAAAA-ACATAAACCCT
*
38259077 AATTCATTTT
1 AATTTATTTT
38259087 CTCTAAACCC
Statistics
Matches: 83, Mismatches: 3, Indels: 16
0.81 0.03 0.16
Matches are distributed among these distances:
26 3 0.04
27 16 0.19
28 33 0.40
29 27 0.33
30 4 0.05
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTTATTTTTTAAAAACATAAACCCT
Found at i:38259073 original size:28 final size:27
Alignment explanation
Indices: 38258985--38259107 Score: 122
Period size: 29 Copynumber: 4.4 Consensus size: 27
38258975 TAAAAATATT
*
38258985 TAAACCCTAATTTATTTTTTAAAA-TA
1 TAAACCCTAATTTATTTTTTAAAACCA
* *
38259011 AAAACCCCTAATTTAATTTATTTAAAAACA
1 TAAA-CCCTAATTT-ATTT-TTTAAAACCA
*
38259041 TAAACCCTAATTTATTTTTTAAAACCCC
1 TAAACCCTAATTTATTTTTTAAAA-CCA
* * *
38259069 TAAACCCTAATTCATTTTCTCTAAACCCT
1 TAAACCCTAATTTATTTT-T-TAAAACCA
38259098 TAAACCCTAA
1 TAAACCCTAA
38259108 ATAAATAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.04
27 16 0.20
28 26 0.32
29 29 0.35
30 8 0.10
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (27 bp):
TAAACCCTAATTTATTTTTTAAAACCA
Found at i:38259104 original size:29 final size:28
Alignment explanation
Indices: 38258985--38259107 Score: 92
Period size: 28 Copynumber: 4.4 Consensus size: 28
38258975 TAAAAATATT
* **
38258985 TAAACCCTAATTTATTTTTTAAAA--TA
1 TAAACCCTAATTCATTTTTTAAAACCCC
* * * *
38259011 AAAACCCCTAATTTAATTTATTTAAAA-ACA
1 TAAA-CCCTAA-TTCATTT-TTTAAAACCCC
*
38259041 TAAACCCTAATTTATTTTTTAAAACCCC
1 TAAACCCTAATTCATTTTTTAAAACCCC
*
38259069 TAAACCCTAATTCATTTTCTCT-AAACCCT
1 TAAACCCTAATTCATTTT-T-TAAAACCCC
38259098 TAAACCCTAA
1 TAAACCCTAA
38259108 ATAAATAAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
26 3 0.04
27 13 0.16
28 30 0.37
29 30 0.37
30 5 0.06
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (28 bp):
TAAACCCTAATTCATTTTTTAAAACCCC
Found at i:38262789 original size:21 final size:21
Alignment explanation
Indices: 38262751--38262816 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
38262741 ATACTCCAAT
38262751 CAGAAGCTC-AAA-AGCTGAA
1 CAGAAGCTCGAAAGAGCTGAA
*
38262770 TAGAAGCTCGAAAGAGCTGAA
1 CAGAAGCTCGAAAGAGCTGAA
*
38262791 CAGAAGCTCGTAAGA-CTTGAA
1 CAGAAGCTCGAAAGAGC-TGAA
38262812 CAGAA
1 CAGAA
38262817 ACTCATAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 8 0.20
20 4 0.10
21 29 0.71
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (21 bp):
CAGAAGCTCGAAAGAGCTGAA
Found at i:38262825 original size:21 final size:21
Alignment explanation
Indices: 38262787--38262838 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
38262777 TCGAAAGAGC
* *
38262787 TGAACAGAAGCTCGTAAGACT
1 TGAACAGAAACTCATAAGACT
*
38262808 TGAACAGAAACTCATAAGAGT
1 TGAACAGAAACTCATAAGACT
*
38262829 TTAACAGAAA
1 TGAACAGAAA
38262839 ATAAAACACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (21 bp):
TGAACAGAAACTCATAAGACT
Found at i:38264935 original size:2 final size:2
Alignment explanation
Indices: 38264928--38264959 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38264918 TGACATTTAC
38264928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38264960 GTANNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38266989 original size:2 final size:2
Alignment explanation
Indices: 38266982--38267018 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38266972 NNNNNNTTAC
*
38266982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38267019 CATTTCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38267253 original size:132 final size:133
Alignment explanation
Indices: 38267016--38267280 Score: 507
Period size: 132 Copynumber: 2.0 Consensus size: 133
38267006 ATATATATGT
38267016 ATACATTTCTTCACATTGATCACATAGCAACAACTTTCAATAACAATTCATAACTAGAATCACGT
1 ATACATTTCTTCACATTGATCACATAGCAACAACTTTCAATAACAATTCATAACTAGAATCACGT
38267081 TAACATGATTCAAAATAACACACCATTTAGTAAGACTTATAAACATATCAAAACATT-TCAACCA
66 TAACATGATTCAAAATAACACACCATTTAGTAAGACTTATAAACATATCAAAACATTGTCAACCA
38267145 AGA
131 AGA
38267148 ATACATTTCTTCACATTGATCACATAGCAACAACTTTCAAGT-ACAATTCATAACTAGAATCACG
1 ATACATTTCTTCACATTGATCACATAGCAACAACTTTCAA-TAACAATTCATAACTAGAATCACG
38267212 TTAACATGATTCAAAATAACACACCATTTAGTAAGACTTATAAACATATCAAAACATTGTCAACC
65 TTAACATGATTCAAAATAACACACCATTTAGTAAGACTTATAAACATATCAAAACATTGTCAACC
38267277 AAGA
130 AAGA
38267281 TTAAAATTAT
Statistics
Matches: 131, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
132 120 0.92
133 11 0.08
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (133 bp):
ATACATTTCTTCACATTGATCACATAGCAACAACTTTCAATAACAATTCATAACTAGAATCACGT
TAACATGATTCAAAATAACACACCATTTAGTAAGACTTATAAACATATCAAAACATTGTCAACCA
AGA
Found at i:38269731 original size:37 final size:37
Alignment explanation
Indices: 38269668--38269780 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
38269658 ATTTTAAAAA
* *
38269668 TAATATTATTTTAATAGT-TTAATATTAAGTTAA-ATT
1 TAATATTATCTTAATAGTATT-TTATTAAGTTAATATT
*
38269704 TAATACTTATCTTAATAGTATTTTATTAATTTAATATT
1 TAATA-TTATCTTAATAGTATTTTATTAAGTTAATATT
* * * *
38269742 AAAGTGATTATCTTAATATTA-ATT-TTAATTTAATATT
1 TAA-T-ATTATCTTAATAGTATTTTATTAAGTTAATATT
38269779 TA
1 TA
38269781 TCTTGATAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
36 5 0.08
37 36 0.55
38 9 0.14
39 14 0.22
40 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (37 bp):
TAATATTATCTTAATAGTATTTTATTAAGTTAATATT
Found at i:38269761 original size:68 final size:69
Alignment explanation
Indices: 38269686--38269820 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 69
38269676 TTTTAATAGT
* * *
38269686 TTAATATTAAGTTAAATTTAATACTTATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTGAT
1 TTAATATTAAGTTAAATTTAATACTTATCTTAATAACTATTATACTAATTTAATATTAAAGTGAT
38269750 TATC
66 TATC
* * * * *
38269754 TTAATATTAATTTTAATTTAATATTTATCTTGATAACTATTATGCTAATTTAATATTAAAGTGAT
1 TTAATATTAAGTTAAATTTAATACTTATCTTAATAACTATTATACTAATTTAATATTAAAGTGAT
38269819 TA
66 TA
38269821 AGTTTAATCA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 30 0.52
69 28 0.48
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.50
Consensus pattern (69 bp):
TTAATATTAAGTTAAATTTAATACTTATCTTAATAACTATTATACTAATTTAATATTAAAGTGAT
TATC
Found at i:38271874 original size:36 final size:36
Alignment explanation
Indices: 38271834--38271913 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
38271824 GGTCGTGTAA
38271834 TTGGGCGTGATATAGAGTGCAGATTTGGGCCTCCTT
1 TTGGGCGTGATATAGAGTGCAGATTTGGGCCTCCTT
* *
38271870 TTGGGCGTGATATGGAGTGCTGATTTGGGCCTCCTT
1 TTGGGCGTGATATAGAGTGCAGATTTGGGCCTCCTT
38271906 TTGGGCGT
1 TTGGGCGT
38271914 AACTTGGGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.12, C:0.16, G:0.36, T:0.35
Consensus pattern (36 bp):
TTGGGCGTGATATAGAGTGCAGATTTGGGCCTCCTT
Found at i:38282463 original size:62 final size:62
Alignment explanation
Indices: 38282393--38282512 Score: 213
Period size: 62 Copynumber: 1.9 Consensus size: 62
38282383 TAACTCGATT
* * *
38282393 TATGGATTCCACTATTAGATTTGACTCTAATCTGGTAGATTTATGTCGTCCTATTTCTGATC
1 TATGGATTCCACTAATAAATTTGACTCTAATCTGGTAGATTTATATCGTCCTATTTCTGATC
38282455 TATGGATTCCACTAATAAATTTGACTCTAATCTGGTAGATTTATATCGTCCTATTTCT
1 TATGGATTCCACTAATAAATTTGACTCTAATCTGGTAGATTTATATCGTCCTATTTCT
38282513 AGGATTACAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.43
Consensus pattern (62 bp):
TATGGATTCCACTAATAAATTTGACTCTAATCTGGTAGATTTATATCGTCCTATTTCTGATC
Found at i:38283382 original size:163 final size:164
Alignment explanation
Indices: 38283112--38283439 Score: 649
Period size: 163 Copynumber: 2.0 Consensus size: 164
38283102 CTTGAAAACA
38283112 ACTCTATTTGTCTGATTTTGGCTCGTTTTTCACTCCTTTCACTCCTAAATGCTCTCCTGAGTATA
1 ACTCTATTTGTCTGATTTTGGCTCGTTTTTCACTCCTTTCACTCCTAAATGCTCTCCTGAGTATA
38283177 GAAACATGAATTTAAAGGATTAGGAGCATCAAATTCACTAATTTGCATAATTAATCATCCAAAAA
66 GAAACATGAATTTAAAGGATTAGGAGCATCAAATTCACTAATTTGCATAATTAATCATCCAAAAA
38283242 TGCATTAAGAATATGATTAAAAT-TGTTACTTTT
131 TGCATTAAGAATATGATTAAAATATGTTACTTTT
38283275 ACTCTATTTGTCTGATTTTGGCTCGTTTTTCACTCCTTTCACTCCTAAATGCTCTCCTGAGTATA
1 ACTCTATTTGTCTGATTTTGGCTCGTTTTTCACTCCTTTCACTCCTAAATGCTCTCCTGAGTATA
38283340 GAAACATGAATTTAAAGGATTAGGAGCATCAAATTCACTAATTTGCATAATTAATCATCCAAAAA
66 GAAACATGAATTTAAAGGATTAGGAGCATCAAATTCACTAATTTGCATAATTAATCATCCAAAAA
38283405 TGCATTAAGAATATGATTAAAATATGTTACTTTT
131 TGCATTAAGAATATGATTAAAATATGTTACTTTT
38283439 A
1 A
38283440 TAGCTTATCA
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 153 0.93
164 11 0.07
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (164 bp):
ACTCTATTTGTCTGATTTTGGCTCGTTTTTCACTCCTTTCACTCCTAAATGCTCTCCTGAGTATA
GAAACATGAATTTAAAGGATTAGGAGCATCAAATTCACTAATTTGCATAATTAATCATCCAAAAA
TGCATTAAGAATATGATTAAAATATGTTACTTTT
Found at i:38291131 original size:43 final size:43
Alignment explanation
Indices: 38291065--38291193 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 43
38291055 TAAGACCTTT
*
38291065 GATATGTGTTTTTCGTGTAAGACCACGTCTGGGATGTTGGCATC
1 GATATGTG-TTTACGTGTAAGACCACGTCTGGGATGTTGGCATC
* *
38291109 GACT-TGTGTTTACGTGTAAGACCATGTCTGGGACAG-TGGCATC
1 GA-TATGTGTTTACGTGTAAGACCACGTCTGGGA-TGTTGGCATC
* * * *
38291152 GATATGTGATTACATGTAAGACCACGTCTAGGATGTTAGCAT
1 GATATGTGTTTACGTGTAAGACCACGTCTGGGATGTTGGCAT
38291194 TGTATGAGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 62 0.86
44 7 0.10
45 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
GATATGTGTTTACGTGTAAGACCACGTCTGGGATGTTGGCATC
Found at i:38293929 original size:15 final size:15
Alignment explanation
Indices: 38293911--38293939 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38293901 TATTTTATTA
38293911 TTTTTTCTTTTTTTG
1 TTTTTTCTTTTTTTG
38293926 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
38293940 CTATACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (15 bp):
TTTTTTCTTTTTTTG
Found at i:38296338 original size:6 final size:6
Alignment explanation
Indices: 38296329--38296361 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
38296319 CATTAAAATT
38296329 AGCCTC AGCCTC AGCCTC AGCCTC AGCCTC AGC
1 AGCCTC AGCCTC AGCCTC AGCCTC AGCCTC AGC
38296362 ATCATCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.48, G:0.18, T:0.15
Consensus pattern (6 bp):
AGCCTC
Found at i:38301630 original size:21 final size:21
Alignment explanation
Indices: 38301588--38301630 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
38301578 GAATAAGATA
*
38301588 TTTTATGCTTTTTCAAGATAT
1 TTTTATGCTTTTTCAAAATAT
*
38301609 TTTTGTGC-TTTTCAAAAGTAT
1 TTTTATGCTTTTTCAAAA-TAT
38301630 T
1 T
38301631 ACAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTTATGCTTTTTCAAAATAT
Found at i:38308147 original size:17 final size:17
Alignment explanation
Indices: 38308110--38308157 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
38308100 GAATTTAAAA
*
38308110 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
38308126 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
38308143 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
38308158 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:38309460 original size:13 final size:13
Alignment explanation
Indices: 38309442--38309471 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38309432 GTGAAAAGTA
*
38309442 GGTATGGTATTTT
1 GGTATGGTATTTC
38309455 GGTATGGTATTTC
1 GGTATGGTATTTC
38309468 GGTA
1 GGTA
38309472 NNNNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.33, T:0.47
Consensus pattern (13 bp):
GGTATGGTATTTC
Found at i:38320301 original size:60 final size:61
Alignment explanation
Indices: 38320237--38320357 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 61
38320227 GCAGCGTATT
38320237 TGATGTATTATATTTTTTAAATTTATTTTTATATAAAAACAAATTTAATA-GGGTGAGTTG
1 TGATGTATTATATTTTTTAAATTTATTTTTATATAAAAACAAATTTAATACGGGTGAGTTG
38320297 TGATGTATTATATTTTTTAAATTTATTTTTATATAAAAACAAATTTAATACGGGTGAGTTG
1 TGATGTATTATATTTTTTAAATTTATTTTTATATAAAAACAAATTTAATACGGGTGAGTTG
38320358 GGTTAGGCTT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 50 0.83
61 10 0.17
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.48
Consensus pattern (61 bp):
TGATGTATTATATTTTTTAAATTTATTTTTATATAAAAACAAATTTAATACGGGTGAGTTG
Found at i:38329774 original size:40 final size:41
Alignment explanation
Indices: 38329701--38329844 Score: 202
Period size: 41 Copynumber: 3.5 Consensus size: 41
38329691 ACCAAAAATT
38329701 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTTAAAAA
38329745 TATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTA-TTTTAAAAA
* * * *
38329786 -AATTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
38329826 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
38329845 TAAAAATATT
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
40 35 0.38
41 41 0.45
42 3 0.03
43 6 0.07
44 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:38329824 original size:11 final size:11
Alignment explanation
Indices: 38329810--38329835 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38329800 AAAATTTAAA
38329810 AAAAGTATTTT
1 AAAAGTATTTT
38329821 AAAAGTATTTT
1 AAAAGTATTTT
38329832 AAAA
1 AAAA
38329836 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:38329845 original size:41 final size:40
Alignment explanation
Indices: 38329701--38329844 Score: 191
Period size: 40 Copynumber: 3.5 Consensus size: 40
38329691 ACCAAAAATT
38329701 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTT-AAAA
38329745 TATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTTTAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTA-TTTTAAAA
* * * *
38329785 AAATTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAA
38329825 GTATTTTAAAATTAAAAAAA
1 -TATTTTAAAATTAAAAAAA
38329845 TAAAAATATT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
40 39 0.43
41 36 0.40
42 3 0.03
43 6 0.07
44 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAA
Found at i:38341226 original size:35 final size:35
Alignment explanation
Indices: 38341176--38341242 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
38341166 GCTTCAGAAA
* *
38341176 ATACCTATATTTGTAACTTCTTTTCTACCATTGAC
1 ATACCTATATCTGTAACTTCTTTTCCACCATTGAC
38341211 ATACCTATATCTGTAACTTCTTTTCCACCATT
1 ATACCTATATCTGTAACTTCTTTTCCACCATT
38341243 CACACAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.45
Consensus pattern (35 bp):
ATACCTATATCTGTAACTTCTTTTCCACCATTGAC
Found at i:38342536 original size:12 final size:11
Alignment explanation
Indices: 38342478--38342538 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
38342468 ATCCCCTACT
*
38342478 AATTTCTCACA
1 AATTTCTCTCA
38342489 ACA-TTCTCTCA
1 A-ATTTCTCTCA
* *
38342500 AAATTCTTTCA
1 AATTTCTCTCA
38342511 AATTTCTCTCA
1 AATTTCTCTCA
*
38342522 AATTCTCTCTTA
1 AATT-TCTCTCA
38342534 AATTT
1 AATTT
38342539 TTTTACTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
10 1 0.02
11 30 0.71
12 11 0.26
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTCTCTCA
Found at i:38344801 original size:32 final size:32
Alignment explanation
Indices: 38344765--38344830 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
38344755 ATGCATTGAT
*
38344765 TAATTTTATCCTTCTATCGAACATTTATATTG
1 TAATTTTATCCTTCTATCAAACATTTATATTG
38344797 TAATTTTATCCTTCTATCAAACATTTATATTG
1 TAATTTTATCCTTCTATCAAACATTTATATTG
38344829 TA
1 TA
38344831 TCGATGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.50
Consensus pattern (32 bp):
TAATTTTATCCTTCTATCAAACATTTATATTG
Found at i:38344903 original size:32 final size:33
Alignment explanation
Indices: 38344866--38344974 Score: 125
Period size: 32 Copynumber: 3.4 Consensus size: 33
38344856 TAGAGGAATA
*
38344866 TTGTTATCATTTAACAAAATGTTAA-TTGATAT
1 TTGTTATCATTTAACAAAATGTAAAGTTGATAT
*
38344898 TTGTTATCATTTTACAAAAT-TAAAGTT-ATAAT
1 TTGTTATCATTTAACAAAATGTAAAGTTGAT-AT
* * * * *
38344930 TTGTTATAAATTCACAAAATGAAAAGCTGATAT
1 TTGTTATCATTTAACAAAATGTAAAGTTGATAT
38344963 TTGTTATCATTT
1 TTGTTATCATTT
38344975 CATAGAACCA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
31 5 0.08
32 40 0.62
33 17 0.27
34 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (33 bp):
TTGTTATCATTTAACAAAATGTAAAGTTGATAT
Found at i:38349638 original size:35 final size:35
Alignment explanation
Indices: 38349480--38349641 Score: 189
Period size: 35 Copynumber: 4.6 Consensus size: 35
38349470 GTACATCGTC
* * * *
38349480 AGTCCAACCAAAACACACCAGATGCTCACACGAGCC
1 AGTCCAACCGAAACACACCA-ATGCTCATAAGAGCT
* ** * *
38349516 ATTCCCTCCAAAACACAGCAATGCTCATAAGAGCT
1 AGTCCAACCGAAACACACCAATGCTCATAAGAGCT
* * *
38349551 ACTCCAACTGAAACACAACAATGCTCATAAGAGCT
1 AGTCCAACCGAAACACACCAATGCTCATAAGAGCT
38349586 AGTCCAACCGAAACACACCAATGCTCATAAGAGCT
1 AGTCCAACCGAAACACACCAATGCTCATAAGAGCT
**
38349621 AGTCCCTCCGAAACACACCAA
1 AGTCCAACCGAAACACACCAA
38349642 ACAGAGAGTA
Statistics
Matches: 108, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
35 92 0.85
36 16 0.15
ACGTcount: A:0.40, C:0.34, G:0.12, T:0.14
Consensus pattern (35 bp):
AGTCCAACCGAAACACACCAATGCTCATAAGAGCT
Found at i:38352956 original size:20 final size:20
Alignment explanation
Indices: 38352931--38352997 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
38352921 TACATCTGAA
*
38352931 TTGTACGTAAATGCCCCTGT
1 TTGTACATAAATGCCCCTGT
* * * *
38352951 TTGTACTTCAATACCCCTGAA
1 TTGTACATAAATGCCCCTG-T
* *
38352972 TTGCACATACATGCCCCTGT
1 TTGTACATAAATGCCCCTGT
38352992 TTGTAC
1 TTGTAC
38352998 TTCGTACTTC
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.34
Consensus pattern (20 bp):
TTGTACATAAATGCCCCTGT
Found at i:38353027 original size:40 final size:41
Alignment explanation
Indices: 38352894--38353039 Score: 168
Period size: 41 Copynumber: 3.6 Consensus size: 41
38352884 TATGAATTTT
* * * *
38352894 ACATACGTGCCTCTGTTTGTACTTCGGTACATCTGAATTGT
1 ACATACATGCCCCTGTTTGTACTTCAGTACATCTGAATTGC
* * * **
38352935 ACGTAAATGCCCCTGTTTGTACTTCAATACCCCTGAATTGC
1 ACATACATGCCCCTGTTTGTACTTCAGTACATCTGAATTGC
* *
38352976 ACATACATGCCCCTGTTTGTACTTC-GTACTTCTAAATTGC
1 ACATACATGCCCCTGTTTGTACTTCAGTACATCTGAATTGC
* *
38353016 ACATACGTGCCCCTTTTTGTACTT
1 ACATACATGCCCCTGTTTGTACTT
38353040 TGGTGCCCTG
Statistics
Matches: 88, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 33 0.38
41 55 0.62
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (41 bp):
ACATACATGCCCCTGTTTGTACTTCAGTACATCTGAATTGC
Found at i:38355549 original size:46 final size:46
Alignment explanation
Indices: 38355496--38355671 Score: 271
Period size: 46 Copynumber: 3.8 Consensus size: 46
38355486 GTGTGGAACA
* * * *
38355496 TAGGTATGATATTTTAGTAAAGAAACCCATGCTGAGTTGTGAAAAG
1 TAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAG
*
38355542 TAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAAG
1 TAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAG
* *
38355588 TAGGTATGGTATTTTAGTAACGAAAACCATACTGAGTTGTGAAAAG
1 TAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAG
* *
38355634 TAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGTT
1 TAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
38355672 ATAGCATTGT
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (46 bp):
TAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAG
Found at i:38362973 original size:41 final size:40
Alignment explanation
Indices: 38362916--38363070 Score: 229
Period size: 41 Copynumber: 3.8 Consensus size: 40
38362906 TGGATTTTAT
*
38362916 AGACTTTACGTCTAGCAGGCTTGATGCCCGTGAAATGTTTC
1 AGACTTTACGTCTAGCAGGCTT-ATGCCGGTGAAATGTTTC
* *
38362957 AGACTTTACGTCTAGCAAGCTTAATGCTGGTGAAATGTTTC
1 AGACTTTACGTCTAGCAGGCTT-ATGCCGGTGAAATGTTTC
*
38362998 AGACTTTACGTCTAGCAGGCTTATTGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCAGGCTTA-TGCCGGTGAAATGTTTC
*
38363039 AGACTTTACGTCTAGCAGGCTAATTGCCGGTG
1 AGACTTTACGTCTAGCAGGCTTA-TGCCGGTG
38363071 TACTGAATCA
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 104 0.99
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (40 bp):
AGACTTTACGTCTAGCAGGCTTATGCCGGTGAAATGTTTC
Found at i:38363095 original size:82 final size:82
Alignment explanation
Indices: 38362916--38363100 Score: 212
Period size: 82 Copynumber: 2.3 Consensus size: 82
38362906 TGGATTTTAT
* * *
38362916 AGACTTTACGTCTAGCAGGCTTGATGCCCGTGAAATGTTTCAGACTTTACGTCTAGCAAGCTTAA
1 AGACTTTAAGCCTAGCAGGCTTGATGCCCGTGAAATATTTCAGACTTTACGTCTAGCAAGCTTAA
* **
38362981 TGCTGGTGAAATGTTTC
66 TGCCGGTGAAATGAATC
* * * *
38362998 AGACTTTACGTCTAGCAGGCTT-ATTGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGC-TA
1 AGACTTTAAGCCTAGCAGGCTTGA-TGCCCGTGAAATATTTCAGACTTTACGTCTAGCAAGCTTA
* *
38363061 ATTGCCGGTGTACTGAATC
65 A-TGCCGGTGAAATGAATC
**
38363080 AGGTTTTAAGCCTAGCAGGCT
1 AGACTTTAAGCCTAGCAGGCT
38363101 AAGCGCCGGT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 4 0.04
82 85 0.96
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (82 bp):
AGACTTTAAGCCTAGCAGGCTTGATGCCCGTGAAATATTTCAGACTTTACGTCTAGCAAGCTTAA
TGCCGGTGAAATGAATC
Found at i:38366682 original size:25 final size:25
Alignment explanation
Indices: 38366653--38366718 Score: 107
Period size: 25 Copynumber: 2.7 Consensus size: 25
38366643 ACACGGCCTG
*
38366653 ACACGGGCGTGTGACATAGCCTGGC
1 ACACGGGCGTGTGACACAGCCTGGC
38366678 ACACGGGCGTGTGACACAGCCTGGC
1 ACACGGGCGTGTGACACAGCCTGGC
*
38366703 ACACGGGC-TGGGACAC
1 ACACGGGCGTGTGACAC
38366719 GGCTAGGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 7 0.18
25 32 0.82
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (25 bp):
ACACGGGCGTGTGACACAGCCTGGC
Found at i:38371099 original size:13 final size:13
Alignment explanation
Indices: 38371081--38371146 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
38371071 AGTTCTTCAT
38371081 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
38371094 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
38371107 TAC-TATGAAAAAG
1 TGCTTTTG-AAAAG
*
38371120 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
38371133 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
38371146 T
1 T
38371147 TTAGTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.07
13 38 0.86
14 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:38382210 original size:69 final size:69
Alignment explanation
Indices: 38382099--38382239 Score: 237
Period size: 69 Copynumber: 2.0 Consensus size: 69
38382089 TTGTTTCCTA
38382099 TAAGATGTATATATATGCTCAAACAAATTAAGTTGACCTGAGAAAGATCTTTCGCTTAAAGTATG
1 TAAGATGTATATATATGCTCAAACAAATTAAGTTGACCTGAGAAAGATCTTTCGCTTAAAGTATG
38382164 ATGT
66 ATGT
* * * * *
38382168 TAAGATGTATATATATGCTCAAACACATTAATTTGACCTGAGAAAGTTCTTTTGCTTGAAGTATG
1 TAAGATGTATATATATGCTCAAACAAATTAAGTTGACCTGAGAAAGATCTTTCGCTTAAAGTATG
38382233 ATGT
66 ATGT
38382237 TAA
1 TAA
38382240 TATGATACTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (69 bp):
TAAGATGTATATATATGCTCAAACAAATTAAGTTGACCTGAGAAAGATCTTTCGCTTAAAGTATG
ATGT
Found at i:38383297 original size:24 final size:24
Alignment explanation
Indices: 38383260--38383312 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
38383250 ATCCGTAACA
* *
38383260 TTTAAATGTATTAATTA-ATAATAT
1 TTTAAATATATTAA-CAGATAATAT
*
38383284 TTTAAATATGTTAACAGATAATAT
1 TTTAAATATATTAACAGATAATAT
38383308 TTTAA
1 TTTAA
38383313 TTATCCTAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (24 bp):
TTTAAATATATTAACAGATAATAT
Found at i:38386088 original size:20 final size:20
Alignment explanation
Indices: 38386063--38386128 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
38386053 TATGTGCATT
38386063 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * **
38386083 CAGGGGCA-CGTATGTGCATT
1 CAGGGGTACCG-AAGTACAAA
*
38386103 CAGGGATACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
38386123 CAGGGG
1 CAGGGG
38386129 CACGTATGTG
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.14
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:38386096 original size:40 final size:40
Alignment explanation
Indices: 38386047--38386184 Score: 213
Period size: 40 Copynumber: 3.5 Consensus size: 40
38386037 TACAAGCAAT
*
38386047 GGCATGTATGTGCATTCAGGGGTACCGAAGTACAAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAGG
*
38386087 GGCACGTATGTGCATTCAGGGATACCGAAGTACAAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAGG
* * * *
38386127 GGCACGTATGTGCATTTAAGGGTACCAAAGTACAAACGGG
1 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAGG
*
38386167 GGCACGTTTGTGCATTCA
1 GGCACGTATGTGCATTCA
38386185 AAAAACACTT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 89 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (40 bp):
GGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAGG
Done.