Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 72 of 121
Found at i:12424349 original size:5 final size:4
Alignment explanation
Indices: 12424292--12424347 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
12424282 AAGTATTTAA
* * * *
12424292 AAAT AAAT AAAC AAAT AAAT AAAT AAAT ACAT AAGT AAAT AAAAT AGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
12424341 AAAT AAA
1 AAAT AAA
12424348 ATTAGCATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
4 39 0.91
5 4 0.09
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:12426520 original size:12 final size:12
Alignment explanation
Indices: 12426503--12426536 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12426493 TTTCTTTAAA
12426503 ATTATTATTACT
1 ATTATTATTACT
*
12426515 ATTATTATTGCT
1 ATTATTATTACT
12426527 ATTATTATTA
1 ATTATTATTA
12426537 ATATGCATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (12 bp):
ATTATTATTACT
Found at i:12429605 original size:35 final size:36
Alignment explanation
Indices: 12429552--12429621 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
12429542 ATTAAAATGA
* * *
12429552 TTATCAAAATAATTTCTCCATCTTTTGTTAATCTCC
1 TTATCAAAATAATCTCTCCATCTCTTATTAATCTCC
12429588 TTAT-AAAATAATCTCTCCATCTCTTATTAATCTC
1 TTATCAAAATAATCTCTCCATCTCTTATTAATCTC
12429622 ATCATACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.30, C:0.23, G:0.01, T:0.46
Consensus pattern (36 bp):
TTATCAAAATAATCTCTCCATCTCTTATTAATCTCC
Found at i:12430298 original size:20 final size:20
Alignment explanation
Indices: 12430273--12430319 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12430263 TTAAAAGTAT
*
12430273 ATTTATTAATCTAT-TAAAAA
1 ATTTATT-ATCTATCCAAAAA
*
12430293 ATTTATTTTCTATCCAAAAA
1 ATTTATTATCTATCCAAAAA
12430313 ATTTATT
1 ATTTATT
12430320 TGAATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATTATCTATCCAAAAA
Found at i:12430765 original size:29 final size:30
Alignment explanation
Indices: 12430732--12430799 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 30
12430722 TTGCATTATA
*
12430732 ATTAAAAAATATA-AAAATATTATTTTAAAT
1 ATTAAAAAATATATAAAATA-TATTTGAAAT
* * *
12430762 -TT-AATAGTTTATAAAATATATTTGAAAT
1 ATTAAAAAATATATAAAATATATTTGAAAT
12430790 ATTAAAAAAT
1 ATTAAAAAAT
12430800 TCAAGATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
28 15 0.52
29 10 0.34
30 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
ATTAAAAAATATATAAAATATATTTGAAAT
Found at i:12434170 original size:20 final size:20
Alignment explanation
Indices: 12434145--12434186 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
12434135 ATGATAATAT
*
12434145 TTGCATGATATTATTGTATA
1 TTGCATGATATAATTGTATA
*
12434165 TTGCATGATATAATTTTATA
1 TTGCATGATATAATTGTATA
12434185 TT
1 TT
12434187 TATTGCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
TTGCATGATATAATTGTATA
Found at i:12437217 original size:29 final size:27
Alignment explanation
Indices: 12437183--12437251 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 27
12437173 TGAAATGTGC
*
12437183 AAAAAAAAAAAAAGTGAAATGAA-AAGAA
1 AAAAAAAAAAAAAGGGAAA--AACAAGAA
* *
12437211 AAGAAAAGAAAAAAGGGAAAAACAAGCA
1 AA-AAAAAAAAAAAGGGAAAAACAAGAA
12437239 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
12437252 TTGATGGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.34
28 8 0.23
29 15 0.43
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAAAAAGGGAAAAACAAGAA
Found at i:12437230 original size:24 final size:24
Alignment explanation
Indices: 12437203--12437248 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12437193 AAAGTGAAAT
*
12437203 GAAAAGAAAAG-AAAAGAAAAAAGG
1 GAAAA-AAAAGCAAAAAAAAAAAGG
*
12437227 GAAAAACAAGCAAAAAAAAAAA
1 GAAAAAAAAGCAAAAAAAAAAA
12437249 AAATTGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.00
Consensus pattern (24 bp):
GAAAAAAAAGCAAAAAAAAAAAGG
Found at i:12437587 original size:18 final size:19
Alignment explanation
Indices: 12437548--12437611 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 19
12437538 AATAAATAAA
*
12437548 AAAAGTAAAAAAAA-AAACAT
1 AAAA-TAAAAAAAATAGA-AT
*
12437568 AAAATAAGAAAAAT-GAAT
1 AAAATAAAAAAAATAGAAT
**
12437586 AAAGCAAAAAAAATAGAA-
1 AAAATAAAAAAAATAGAAT
12437604 AAAATAAA
1 AAAATAAA
12437612 GACTTAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 19 0.54
19 12 0.34
20 4 0.11
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (19 bp):
AAAATAAAAAAAATAGAAT
Found at i:12438351 original size:27 final size:28
Alignment explanation
Indices: 12438299--12438351 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
12438289 TAGTTCTCAA
* *
12438299 AAAAATGAAGAAGAACATGATGGAAACT
1 AAAAAGGAAGAAGAACATGATAGAAACT
12438327 AAAAAGGAGAGAA-AACATGA-AGAAA
1 AAAAAGGA-AGAAGAACATGATAGAAA
12438352 AGCCTTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 4 0.18
28 14 0.64
29 4 0.18
ACGTcount: A:0.62, C:0.06, G:0.23, T:0.09
Consensus pattern (28 bp):
AAAAAGGAAGAAGAACATGATAGAAACT
Found at i:12438625 original size:13 final size:13
Alignment explanation
Indices: 12438607--12438645 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
12438597 AAAACCTTTT
12438607 CATTCATTGCATA
1 CATTCATTGCATA
*
12438620 CATTCATTGCATG
1 CATTCATTGCATA
* *
12438633 TATTCAATGCATA
1 CATTCATTGCATA
12438646 TGTTTGGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (13 bp):
CATTCATTGCATA
Found at i:12438817 original size:48 final size:48
Alignment explanation
Indices: 12438756--12439005 Score: 285
Period size: 48 Copynumber: 5.2 Consensus size: 48
12438746 TTTGAGGTAA
* *
12438756 GAATTTTAAAGTTTCAAACCTTCGTTAAAAAGGAGCCTTT-TTGGTCAT
1 GAATTTTAAAGTTTCAAACCTTTGTTGAAAAGGAG-CTTTCTTGGTCAT
* * * * *
12438804 GAAATTTAAAGTTTC-AAGCTTTCATTGAAAATGAGCTTTCTTGGACAT
1 GAATTTTAAAGTTTCAAACCTTT-GTTGAAAAGGAGCTTTCTTGGTCAT
* * * *
12438852 GAATTTTAAAGTTTCAATCCTTTGTTGAGAAGGAACTTTCTTGGACATT
1 GAATTTTAAAGTTTCAAACCTTTGTTGAAAAGGAGCTTTCTTGGTCA-T
*
12438901 GAATTTTAAAATTTCAAACCTTTGTT-AAGAAGGAGCTTTCTTGGAT-AT
1 GAATTTTAAAGTTTCAAACCTTTGTTGAA-AAGGAGCTTTCTTGG-TCAT
* *
12438949 GAATTTTAAAGTTTCAAGCCTTTGTTGAAAA-GAGCTTTCCTGGTCAT
1 GAATTTTAAAGTTTCAAACCTTTGTTGAAAAGGAGCTTTCTTGGTCAT
*
12438996 GATTTTTAAA
1 GAATTTTAAA
12439006 ATTTTAAGCT
Statistics
Matches: 171, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
46 1 0.01
47 31 0.18
48 92 0.54
49 47 0.27
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (48 bp):
GAATTTTAAAGTTTCAAACCTTTGTTGAAAAGGAGCTTTCTTGGTCAT
Found at i:12438951 original size:97 final size:95
Alignment explanation
Indices: 12438756--12439009 Score: 289
Period size: 97 Copynumber: 2.6 Consensus size: 95
12438746 TTTGAGGTAA
* * * * *
12438756 GAATTTTAAAGTTTCAAACCTTCGTTAAAAAGGAGCCTTT-TTGGTCATGAAATTTAAAGTTTCA
1 GAATTTTAAAGTTTCAAACCTTTGTT-GAAAGGA-ACTTTCTTGGTCATGAATTTTAAAATTTCA
* *
12438820 AGCTTTCATTGAAAATGAGCTTTCTTGGACAT
64 ACCTTTCATTGAAAAGGAGCTTTCTTGGACAT
* *
12438852 GAATTTTAAAGTTTCAATCCTTTGTTGAGAAGGAACTTTCTTGGACATTGAATTTTAAAATTTCA
1 GAATTTTAAAGTTTCAAACCTTTGTTGA-AAGGAACTTTCTTGGTCA-TGAATTTTAAAATTTC-
* *
12438917 AACCTTT-GTT-AAGAAGGAGCTTTCTTGGATAT
63 AACCTTTCATTGAA-AAGGAGCTTTCTTGGACAT
* * * * *
12438949 GAATTTTAAAGTTTCAAGCCTTTGTTGAAAAGAGCTTTCCTGGTCATGATTTTTAAAATTT
1 GAATTTTAAAGTTTCAAACCTTTGTTGAAAGGAACTTTCTTGGTCATGAATTTTAAAATTT
12439010 TAAGCTTCAA
Statistics
Matches: 136, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
95 19 0.14
96 51 0.38
97 60 0.44
98 6 0.04
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (95 bp):
GAATTTTAAAGTTTCAAACCTTTGTTGAAAGGAACTTTCTTGGTCATGAATTTTAAAATTTCAAC
CTTTCATTGAAAAGGAGCTTTCTTGGACAT
Found at i:12439116 original size:22 final size:24
Alignment explanation
Indices: 12439059--12439117 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 24
12439049 GCCTTGGTGG
*
12439059 AGTATTTTATTTTTCAAAGTTGAAACA
1 AGTACTTTATTTTTCAAAGTTG--A-A
*
12439086 AGTATTTTATTTTTCAAAGTTG-A
1 AGTACTTTATTTTTCAAAGTTGAA
12439109 AGT-CTTTAT
1 AGTACTTTAT
12439118 GGAGGAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 5 0.16
23 4 0.13
27 22 0.71
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (24 bp):
AGTACTTTATTTTTCAAAGTTGAA
Found at i:12439136 original size:37 final size:37
Alignment explanation
Indices: 12439086--12439208 Score: 98
Period size: 37 Copynumber: 3.4 Consensus size: 37
12439076 AGTTGAAACA
*
12439086 AGTATTTTATTTTTCAAAGTTGAAGTCTTTATGGAGG
1 AGTATATTATTTTTCAAAGTTGAAGTCTTTATGGAGG
* ** *
12439123 AGTATATTATTTTTC----TTGAAATCTTGGTGAAGG
1 AGTATATTATTTTTCAAAGTTGAAGTCTTTATGGAGG
* * *
12439156 AGTAT-TATATTTTTTAAAGTTGAAGCCTTTATTGAGG
1 AGTATAT-TATTTTTCAAAGTTGAAGTCTTTATGGAGG
12439193 -G-ATACTTTATTTTTCA
1 AGTATA--TTATTTTTCA
12439209 CAAAAAAAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
32 1 0.02
33 26 0.40
35 2 0.03
36 1 0.02
37 34 0.52
38 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.47
Consensus pattern (37 bp):
AGTATATTATTTTTCAAAGTTGAAGTCTTTATGGAGG
Found at i:12439794 original size:18 final size:18
Alignment explanation
Indices: 12439771--12439809 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12439761 GTTCGAAAAC
12439771 TTAATTGTAACTTTGATT
1 TTAATTGTAACTTTGATT
* *
12439789 TTAATTTTAATTTTGATT
1 TTAATTGTAACTTTGATT
12439807 TTA
1 TTA
12439810 TTTGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (18 bp):
TTAATTGTAACTTTGATT
Found at i:12440962 original size:27 final size:28
Alignment explanation
Indices: 12440922--12440974 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
12440912 ATCAATTTAG
* * *
12440922 ATTTTTTATTAAAAATTTTA-TTAAATT
1 ATTTTTAATAAAAAACTTTACTTAAATT
12440949 ATTTTTAATAAAAAACTTTACTTAAA
1 ATTTTTAATAAAAAACTTTACTTAAA
12440975 AAACTTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTTTAATAAAAAACTTTACTTAAATT
Found at i:12450969 original size:34 final size:36
Alignment explanation
Indices: 12450912--12450978 Score: 111
Period size: 34 Copynumber: 1.9 Consensus size: 36
12450902 GTCATGCTCA
*
12450912 CAAAAAATAAAAGAAAGTTCAAACTTTATACAAAAG
1 CAAAAAATAAAAGAAAATTCAAACTTTATACAAAAG
12450948 CAAAAAA-AAAA-AAAATTCAAACTTTATACAA
1 CAAAAAATAAAAGAAAATTCAAACTTTATACAA
12450979 TTAATGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 19 0.63
35 4 0.13
36 7 0.23
ACGTcount: A:0.64, C:0.12, G:0.04, T:0.19
Consensus pattern (36 bp):
CAAAAAATAAAAGAAAATTCAAACTTTATACAAAAG
Found at i:12463103 original size:19 final size:17
Alignment explanation
Indices: 12463079--12463134 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
12463069 AGTTGGATCT
12463079 TCCACTTTGATTAGGAAA
1 TCCACTTTGATTA-GAAA
*
12463097 TCTCACTTTGACTTAGAAT
1 TC-CACTTTGA-TTAGAAA
*
12463116 TCCTACTTTGATTACAAA
1 TCC-ACTTTGATTAGAAA
12463134 T
1 T
12463135 AATAGTTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.28
19 20 0.62
20 3 0.09
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (17 bp):
TCCACTTTGATTAGAAA
Found at i:12464327 original size:32 final size:32
Alignment explanation
Indices: 12464285--12464387 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 32
12464275 TTTGTTGACA
* * **
12464285 TCAACTCAGTCTAGGTCATTTTATTTTCAACT
1 TCAATTCAGTCTAAGTCATTGCATTTTCAACT
*
12464317 TCAATTCAGTCCAAGTCATTGCATTTTCCAACT
1 TCAATTCAGTCTAAGTCATTGCATTTT-CAACT
* * *
12464350 TCAAGTCAATCTAAATCATTGCATTTTCAACT
1 TCAATTCAGTCTAAGTCATTGCATTTTCAACT
*
12464382 TAAATT
1 TCAATT
12464388 TAATTCAAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 31 0.53
33 28 0.47
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (32 bp):
TCAATTCAGTCTAAGTCATTGCATTTTCAACT
Found at i:12464369 original size:33 final size:32
Alignment explanation
Indices: 12464307--12464382 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 32
12464297 AGGTCATTTT
* * *
12464307 ATTTTCAACTTCAATTCAGTCCAAGTCATTGC
1 ATTTTCAACTTCAAGTCAATCCAAATCATTGC
*
12464339 ATTTTCCAACTTCAAGTCAATCTAAATCATTGC
1 ATTTT-CAACTTCAAGTCAATCCAAATCATTGC
12464372 ATTTTCAACTT
1 ATTTTCAACTT
12464383 AAATTTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (32 bp):
ATTTTCAACTTCAAGTCAATCCAAATCATTGC
Found at i:12464436 original size:33 final size:33
Alignment explanation
Indices: 12464393--12464474 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
12464383 AAATTTAATT
* *
12464393 CAAGTTATTTCAATTTTGAACTTTGGCTCAGTT
1 CAAGTCATTTCAATTTTGAACTTTGGCTCAGTA
* * ** *
12464426 TAAGTCATTTCATTTTTTTATTTTGGCTCAGTA
1 CAAGTCATTTCAATTTTGAACTTTGGCTCAGTA
*
12464459 CAGGTCATTTC-ATTTT
1 CAAGTCATTTCAATTTT
12464475 CAAATTTTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 4 0.10
33 35 0.90
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (33 bp):
CAAGTCATTTCAATTTTGAACTTTGGCTCAGTA
Found at i:12464482 original size:33 final size:33
Alignment explanation
Indices: 12464414--12464482 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
12464404 AATTTTGAAC
** ***
12464414 TTTGGCTCAGTTTAAGTCATTTCATTTTTTTAT
1 TTTGGCTCAGTACAAGTCATTTCATTTTCAAAT
*
12464447 TTTGGCTCAGTACAGGTCATTTCATTTTCAAAT
1 TTTGGCTCAGTACAAGTCATTTCATTTTCAAAT
12464480 TTT
1 TTT
12464483 AGCTTAGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.20, C:0.14, G:0.13, T:0.52
Consensus pattern (33 bp):
TTTGGCTCAGTACAAGTCATTTCATTTTCAAAT
Found at i:12464594 original size:43 final size:43
Alignment explanation
Indices: 12464547--12464753 Score: 144
Period size: 43 Copynumber: 5.0 Consensus size: 43
12464537 TTGCCTCTGA
* **
12464547 TTAGAATAGCTTTTCCTAATTTTAAAAGTTTTATTACCTCTAG
1 TTAGAATAGCTTTTCCAAATTTTAAAAGTTACATTACCTCTAG
* **
12464590 TTAG-ATAAGCCTTTT--AAGATTTTAATAGTTACATTGTCTCT--
1 TTAGAAT-AG-CTTTTCCAA-ATTTTAAAAGTTACATTACCTCTAG
** * * **
12464631 TT-GAGGAGCTTTTCTAAATTTT-AAAGTTACATCACCTAAAG
1 TTAGAATAGCTTTTCCAAATTTTAAAAGTTACATTACCTCTAG
** * *
12464672 TGGGAATAGCTTTTCCAAATTTTAAAAGTTTCACTACCTCTAG
1 TTAGAATAGCTTTTCCAAATTTTAAAAGTTACATTACCTCTAG
* * * *
12464715 TTTGAAGAG-TTTTCCAAATTTT-AAAGTTATATTGCCTCT
1 TTAGAATAGCTTTTCCAAATTTTAAAAGTTACATTACCTCT
12464754 GTTTAGATTC
Statistics
Matches: 124, Mismatches: 30, Indels: 22
0.70 0.17 0.12
Matches are distributed among these distances:
39 16 0.13
40 8 0.06
41 18 0.15
42 33 0.27
43 44 0.35
44 5 0.04
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (43 bp):
TTAGAATAGCTTTTCCAAATTTTAAAAGTTACATTACCTCTAG
Found at i:12471355 original size:2 final size:2
Alignment explanation
Indices: 12471348--12471377 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12471338 TCAAATTTTC
12471348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12471378 ACAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12474900 original size:216 final size:216
Alignment explanation
Indices: 12474526--12474964 Score: 824
Period size: 216 Copynumber: 2.0 Consensus size: 216
12474516 AAGGCAAAGG
12474526 CAAAAATTCGTAGGCTAAGTCAAAGAGGCGAGGTGCAGAAGTATGTTCGAGAATTTTTAGAACTA
1 CAAAAATTCGTAGGCTAAGTCAAAGAGGCGAGGTGCAGAAGTATGTTCGAGAATTTTTAGAACTA
*
12474591 ATGCTCCAAATTTCAAACCTTAGAAAAGAAGAAGGTCTTTTTTGTTTTATGAATGAACTCAAAAC
66 ATGCTCCAAATTTCAAACCTTAGAAAAGAAGAAGGTCTTTTTGGTTTTATGAATGAACTCAAAAC
*
12474656 GTAGGCCAAAAATGAGTTACAATAAAAGGATGTCAAAGATCTGGCCAAAACCATGACAGTTATTG
131 GTAGGCCAAAAATGAGTTACAATAAAAGGATGTCAAAGATCTGGCCAAAACCATGACAGCTATTG
12474721 AATCTTTGATGGAGATTTGAC
196 AATCTTTGATGGAGATTTGAC
12474742 CAAAAATTCGTAGGCTAAGTCAAAGAGGCGAGGTGCAGAAGTATGTTCGAGAATTTTTAGAACTA
1 CAAAAATTCGTAGGCTAAGTCAAAGAGGCGAGGTGCAGAAGTATGTTCGAGAATTTTTAGAACTA
12474807 ATGCTCCAAATTTCAAACCTTAGAAAAGAAGAAGGTCTTTTTGGTTTTATGAATGAACTCAAAAC
66 ATGCTCCAAATTTCAAACCTTAGAAAAGAAGAAGGTCTTTTTGGTTTTATGAATGAACTCAAAAC
* * *
12474872 GTAGGCCAAGAATGAGTTACAATAAAAGGATGTCAAAGATCTGGCCAAAATCGTGACAGCTATTG
131 GTAGGCCAAAAATGAGTTACAATAAAAGGATGTCAAAGATCTGGCCAAAACCATGACAGCTATTG
12474937 AATCTTTGATGGAGATTTGAC
196 AATCTTTGATGGAGATTTGAC
12474958 CATAAAA
1 CA-AAAA
12474965 AAAGTTTGAG
Statistics
Matches: 217, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
216 213 0.98
217 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (216 bp):
CAAAAATTCGTAGGCTAAGTCAAAGAGGCGAGGTGCAGAAGTATGTTCGAGAATTTTTAGAACTA
ATGCTCCAAATTTCAAACCTTAGAAAAGAAGAAGGTCTTTTTGGTTTTATGAATGAACTCAAAAC
GTAGGCCAAAAATGAGTTACAATAAAAGGATGTCAAAGATCTGGCCAAAACCATGACAGCTATTG
AATCTTTGATGGAGATTTGAC
Found at i:12478180 original size:64 final size:63
Alignment explanation
Indices: 12478099--12478324 Score: 187
Period size: 62 Copynumber: 3.6 Consensus size: 63
12478089 TTCAAGAGCA
* * * *
12478099 AAAAATGCTTTAAATAATCTCATCAATAAATATTTATAAGGGATTATTAAAGGTGTTTTTGATC
1 AAAAATACTTTAAATAATCTCTTC-ATAAATATTTATAAGGGATTATTGAAGGTATTTTTGATC
* * * *
12478163 AAAAATACCTTT-AATAATCCCTTC-TAAAT-TTTTTCAGAGGATTATTGAAGGTATTTTTTA-C
1 AAAAATA-CTTTAAATAATCTCTTCATAAATATTTATAAG-GGATTATTGAAGGTATTTTTGATC
* * ** *
12478224 AAAAAATACTTTCAATAATC-CTTTCAATAAATATTTATGATAGATTATTGAAGGTATTTTTTGG
1 -AAAAATACTTTAAATAATCTC-TTC-ATAAATATTTATAAGGGATTATTGAAGGTA-TTTTTGA
*
12478288 TA
62 TC
* *
12478290 AAAAAT-GTCTTCAATAATCTC-TCATAAATATTTAT
1 AAAAATACT-TTAAATAATCTCTTCATAAATATTTAT
12478325 TGAATGAATT
Statistics
Matches: 134, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
61 12 0.09
62 41 0.31
63 12 0.09
64 38 0.28
65 30 0.22
66 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (63 bp):
AAAAATACTTTAAATAATCTCTTCATAAATATTTATAAGGGATTATTGAAGGTATTTTTGATC
Found at i:12478338 original size:65 final size:64
Alignment explanation
Indices: 12478097--12478324 Score: 188
Period size: 64 Copynumber: 3.6 Consensus size: 64
12478087 TTTTCAAGAG
* * * ** * * *
12478097 CAAAAAATGCTTTAAATAAT-CTCATCAATAAATATTTATAAGGGATTATTAAAGGTGTTTTTGA
1 CAAAAAATACTTTCAATAATCCTC-TCAATAAATATTTATGATAGATTATTGAAGGTATTTTTTA
* * *
12478161 TC-AAAAATACCTTT-AATAATCC-CTTC--TAAAT-TTTTTCAGAGGATTATTGAAGGTATTTT
1 -CAAAAAATA-CTTTCAATAATCCTC-TCAATAAATATTTATGATA-GATTATTGAAGGTATTTT
12478220 TTA
62 TTA
* *
12478223 CAAAAAATACTTTCAATAATCCTTTCAATAAATATTTATGATAGATTATTGAAGGTATTTTTTGG
1 CAAAAAATACTTTCAATAATCCTCTCAATAAATATTTATGATAGATTATTGAAGGTATTTTTT-A
* *
12478288 TAAAAAAT-GTCTTCAATAAT-CTCTC-ATAAATATTTAT
1 CAAAAAATACT-TTCAATAATCCTCTCAATAAATATTTAT
12478325 TGAATGAATT
Statistics
Matches: 136, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
61 11 0.08
62 40 0.29
63 12 0.09
64 45 0.33
65 28 0.21
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.41
Consensus pattern (64 bp):
CAAAAAATACTTTCAATAATCCTCTCAATAAATATTTATGATAGATTATTGAAGGTATTTTTTA
Found at i:12478360 original size:25 final size:25
Alignment explanation
Indices: 12478332--12478399 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
12478322 TATTGAATGA
*
12478332 ATTATTGCAGGCATTTTTATGAGAG
1 ATTATTGAAGGCATTTTTATGAGAG
*
12478357 ATTATTGAAGGCATTTTTATGAGGG
1 ATTATTGAAGGCATTTTTATGAGAG
* *
12478382 ATTAATGAAGGTATTTTT
1 ATTATTGAAGGCATTTTT
12478400 TGTTAAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (25 bp):
ATTATTGAAGGCATTTTTATGAGAG
Found at i:12478447 original size:62 final size:63
Alignment explanation
Indices: 12478381--12478499 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
12478371 TTTTATGAGG
** * * *
12478381 GATTAATGAAGGT-ATTTTTTGTTAAAAACACCTTCAATAATCCCTTCTAAATTTTTTCAAGA
1 GATTAATGAAAATGATTTTTGGCTAAAAACACCTTCAATAATCCCTTATAAATTTTTTCAAGA
* * *
12478443 GATTATTGAAAATGCTTTTTGGCTAAAAACACTTTCAATAATCCCTTATAAATTTTT
1 GATTAATGAAAATGATTTTTGGCTAAAAACACCTTCAATAATCCCTTATAAATTTTT
12478500 ATTAGGGATT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
62 10 0.21
63 38 0.79
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (63 bp):
GATTAATGAAAATGATTTTTGGCTAAAAACACCTTCAATAATCCCTTATAAATTTTTTCAAGA
Found at i:12478472 original size:63 final size:64
Alignment explanation
Indices: 12478403--12478596 Score: 204
Period size: 63 Copynumber: 3.1 Consensus size: 64
12478393 TATTTTTTGT
* * *
12478403 TAAAAACACCTTCAATAATCCCTTCTAAATTTTTTCAAGAGATTATTGAAAATGC-TTTTTGGC
1 TAAAAACACTTTCAATAATCCCTTCTAAATTTTTTCAAGAGATTATTGAAAAGGCGTTTTTGAC
* * * *
12478466 TAAAAACACTTTCAATAATCCCTTATAAATTTTTAT-TAGGGATTATT--AAAGGCGTTTTTGAT
1 TAAAAACACTTTCAATAATCCCTTCTAAATTTTT-TCAAGAGATTATTGAAAAGGCGTTTTTGAC
* * **
12478528 TAAAAA-ATGCTTTCAATAATCTCTTCCAAAAATTTTCAAGAGATTATTG--AAGGCGTTTTTGA
1 TAAAAACA--CTTTCAATAATCCCTTCTAAATTTTTTCAAGAGATTATTGAAAAGGCGTTTTTGA
12478590 C
64 C
*
12478591 AAAAAA
1 TAAAAA
12478597 AAAAAAAACC
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
61 6 0.06
62 13 0.12
63 89 0.82
64 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (64 bp):
TAAAAACACTTTCAATAATCCCTTCTAAATTTTTTCAAGAGATTATTGAAAAGGCGTTTTTGAC
Found at i:12480022 original size:17 final size:18
Alignment explanation
Indices: 12480000--12480039 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12479990 TAATAGAATA
*
12480000 AATTTAATT-GAATAATT
1 AATTTAATTAAAATAATT
*
12480017 AATTTAATTAAAATTATT
1 AATTTAATTAAAATAATT
12480035 AATTT
1 AATTT
12480040 GATACAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTTAATTAAAATAATT
Found at i:12482660 original size:31 final size:30
Alignment explanation
Indices: 12482613--12482671 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
12482603 GTCATTTAAA
12482613 AAAATAAAATTTATCAATCAATTATCTTTT
1 AAAATAAAATTTATCAATCAATTATCTTTT
*
12482643 AAAATATAATATTATCAATCAATTATCTT
1 AAAATAAAAT-TTATCAATCAATTATCTT
12482672 ACTTTGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (30 bp):
AAAATAAAATTTATCAATCAATTATCTTTT
Found at i:12484178 original size:2 final size:2
Alignment explanation
Indices: 12484171--12484199 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12484161 TTTTCAAACT
12484171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12484200 CATTAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12486509 original size:12 final size:12
Alignment explanation
Indices: 12486472--12486510 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
12486462 GATTTATATT
*
12486472 TTAAATATTACA
1 TTAAATATTATA
12486484 TTAAATATTATA
1 TTAAATATTATA
*
12486496 TTAAATATTTTA
1 TTAAATATTATA
12486508 TTA
1 TTA
12486511 TAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:12487760 original size:20 final size:20
Alignment explanation
Indices: 12487722--12487767 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
12487712 AATTAAGTTC
*
12487722 AAAATTTTAAAATCCTTTTA
1 AAAATTTTAAAATCATTTTA
* * *
12487742 AAAATTTTTATATCATTTTG
1 AAAATTTTAAAATCATTTTA
12487762 AAAATT
1 AAAATT
12487768 AAGTAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATTTTAAAATCATTTTA
Found at i:12487775 original size:31 final size:33
Alignment explanation
Indices: 12487740--12487808 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
12487730 AAAATCCTTT
* ** *
12487740 TAAAAATTTT-TATATC-ATTTTGAAAATTAAG
1 TAAAAATTTTCAATATCAATTTAAAAAATTAAA
12487771 T-AAAATTTTCAATATCAATTTAAAAAATTAAA
1 TAAAAATTTTCAATATCAATTTAAAAAATTAAA
12487803 TAAAAA
1 TAAAAA
12487809 ATACATATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 8 0.26
31 6 0.19
32 13 0.42
33 4 0.13
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (33 bp):
TAAAAATTTTCAATATCAATTTAAAAAATTAAA
Found at i:12487940 original size:29 final size:29
Alignment explanation
Indices: 12487885--12487940 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
12487875 ATTCAAAAAT
*
12487885 CTATTTTCTCTAAACAATCTATTTTTACG
1 CTATTTTCTCTAAACAATCTATATTTACG
* *
12487914 CTATTTTCTATTAAA-AATTTATATTTA
1 CTATTTTCT-CTAAACAATCTATATTTA
12487941 AATAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (29 bp):
CTATTTTCTCTAAACAATCTATATTTACG
Found at i:12489259 original size:20 final size:20
Alignment explanation
Indices: 12489234--12489271 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12489224 GTTCTTTCTT
* *
12489234 ATTTATTCTTTTTTTATTAA
1 ATTTATTATTTATTTATTAA
12489254 ATTTATTATTTATTTATT
1 ATTTATTATTTATTTATT
12489272 TATTTATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTATTATTTATTTATTAA
Found at i:12496461 original size:18 final size:17
Alignment explanation
Indices: 12496438--12496476 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12496428 TCATACATAA
*
12496438 ATGTTTTGCTGTTGGATT
1 ATGTTTTGCTCTTGGA-T
*
12496456 ATGTTTTGGTCTTGGAT
1 ATGTTTTGCTCTTGGAT
12496473 ATGT
1 ATGT
12496477 GATAGATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.13, C:0.05, G:0.28, T:0.54
Consensus pattern (17 bp):
ATGTTTTGCTCTTGGAT
Found at i:12498021 original size:20 final size:20
Alignment explanation
Indices: 12497996--12498035 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12497986 TGACAATTAT
12497996 TTTTAATAATCT-TTGTTTTC
1 TTTTAAT-ATCTATTGTTTTC
*
12498016 TTTTAATGTCTATTGTTTTC
1 TTTTAATATCTATTGTTTTC
12498036 CTTGATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAATATCTATTGTTTTC
Found at i:12501167 original size:44 final size:41
Alignment explanation
Indices: 12501100--12501180 Score: 94
Period size: 44 Copynumber: 1.9 Consensus size: 41
12501090 ATCATTTTGA
12501100 TGTTTAAATAAATTATAAATATTTAATT-TTTAAATAATTTT
1 TGTTTAAATAAATTATAAATATTT-ATTGTTTAAATAATTTT
*
12501141 TGTTTAAATATTAATT-TAAATTTATTTTTTGTTTAAATAA
1 TGTTTAAATA--AATTATAAA--TATTTATTGTTTAAATAA
12501181 ATGGATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
41 10 0.29
42 4 0.12
43 6 0.18
44 14 0.41
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (41 bp):
TGTTTAAATAAATTATAAATATTTATTGTTTAAATAATTTT
Found at i:12501233 original size:19 final size:19
Alignment explanation
Indices: 12501193--12501307 Score: 55
Period size: 19 Copynumber: 6.2 Consensus size: 19
12501183 GGATTAATCG
* *
12501193 TATATAATCGTGTT-TTTCA
1 TATATAATCATGTTAATT-A
12501212 TATATAATCATGTTAATTA
1 TATATAATCATGTTAATTA
*
12501231 TAT-TATATCATATTATATTA
1 TATATA-ATCATGTTA-ATTA
* *
12501251 T-T-T-A-CATAATTAATTG
1 TATATAATCAT-GTTAATTA
* *
12501267 TGTCTAATCATGTT-ATTCA
1 TATATAATCATGTTAATT-A
* *
12501286 TATATAATTATGTTAATCA
1 TATATAATCATGTTAATTA
12501305 TAT
1 TAT
12501308 CGTGTTATGT
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
16 7 0.09
17 6 0.08
18 6 0.08
19 45 0.59
20 12 0.16
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (19 bp):
TATATAATCATGTTAATTA
Found at i:12501413 original size:15 final size:15
Alignment explanation
Indices: 12501393--12501441 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
12501383 ATGTGTTATG
12501393 TTTATATTTAAATTA
1 TTTATATTTAAATTA
*
12501408 TTTATATTTATATTA
1 TTTATATTTAAATTA
12501423 TGTT-TATGTTAAAATTA
1 T-TTATAT-TT-AAATTA
12501440 TT
1 TT
12501442 CATGTCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 18 0.62
16 5 0.17
17 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (15 bp):
TTTATATTTAAATTA
Found at i:12503942 original size:6 final size:6
Alignment explanation
Indices: 12503931--12503960 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12503921 AAAATTCGCC
*
12503931 CCATCA CCATCA CCATCG CCATCA CCATCA
1 CCATCA CCATCA CCATCA CCATCA CCATCA
12503961 TCTGGACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.50, G:0.03, T:0.17
Consensus pattern (6 bp):
CCATCA
Found at i:12507914 original size:20 final size:18
Alignment explanation
Indices: 12507891--12507999 Score: 75
Period size: 20 Copynumber: 5.9 Consensus size: 18
12507881 TCTCAACACT
*
12507891 CCACCACACCTAATCCCTTC
1 CCACCACACCCAATCCC--C
*
12507911 CCA-CAC-CGCCAA-CACC
1 CCACCACAC-CCAATCCCC
12507927 CCACCACACCCAATCCCTCC
1 CCACCACACCCAAT-CC-CC
*
12507947 CCACCACACCCTATCCCTC
1 CCACCACACCCAATCCC-C
* *
12507966 CCTACCCCA-CCAA-CACC
1 CC-ACCACACCCAATCCCC
12507983 CCACCACACCCAATCCC
1 CCACCACACCCAATCCC
12508000 TCCCCACATG
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
16 9 0.13
17 14 0.20
18 9 0.13
19 15 0.21
20 23 0.33
ACGTcount: A:0.27, C:0.62, G:0.01, T:0.10
Consensus pattern (18 bp):
CCACCACACCCAATCCCC
Found at i:12507963 original size:56 final size:56
Alignment explanation
Indices: 12507891--12508006 Score: 182
Period size: 56 Copynumber: 2.1 Consensus size: 56
12507881 TCTCAACACT
*
12507891 CCACCACACCTAATCCCTTCCC-ACACCGCCAACACCCCACCACACCCAATCCCTCC
1 CCACCACACCTAATCCC-TCCCTACACCACCAACACCCCACCACACCCAATCCCTCC
*
12507947 CCACCACACCCT-ATCCCTCCCTACCCCACCAACACCCCACCACACCCAATCCCTCC
1 CCACCACA-CCTAATCCCTCCCTACACCACCAACACCCCACCACACCCAATCCCTCC
12508003 CCAC
1 CCAC
12508007 ATGTCTGCCC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
55 4 0.07
56 49 0.88
57 3 0.05
ACGTcount: A:0.26, C:0.63, G:0.01, T:0.10
Consensus pattern (56 bp):
CCACCACACCTAATCCCTCCCTACACCACCAACACCCCACCACACCCAATCCCTCC
Found at i:12508004 original size:20 final size:20
Alignment explanation
Indices: 12507925--12508006 Score: 100
Period size: 20 Copynumber: 4.3 Consensus size: 20
12507915 ACCGCCAACA
12507925 CCCCACCACACCCAATCCCT
1 CCCCACCACACCCAATCCCT
*
12507945 CCCCACCACACCCTATCCCT
1 CCCCACCACACCCAATCCCT
* * *
12507965 CCCTACCCCA-CCAA---CA
1 CCCCACCACACCCAATCCCT
12507981 CCCCACCACACCCAATCCCT
1 CCCCACCACACCCAATCCCT
12508001 CCCCAC
1 CCCCAC
12508007 ATGTCTGCCC
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
16 9 0.18
17 4 0.08
19 3 0.06
20 34 0.68
ACGTcount: A:0.24, C:0.66, G:0.00, T:0.10
Consensus pattern (20 bp):
CCCCACCACACCCAATCCCT
Found at i:12510442 original size:18 final size:18
Alignment explanation
Indices: 12510353--12510453 Score: 75
Period size: 18 Copynumber: 5.8 Consensus size: 18
12510343 CCTTTGTTCT
*
12510353 TGATACATTTGAGGTGGA
1 TGATACATTTGAAGTGGA
* *
12510371 GGATATATTTG-A--GGA
1 TGATACATTTGAAGTGGA
* *
12510386 TGATACATTT-ATGGTGGG
1 TGATACATTTGA-AGTGGA
* ** **
12510404 GGATACATTTGTGGTAAA
1 TGATACATTTGAAGTGGA
12510422 TGATACATTTGAAGTGGA
1 TGATACATTTGAAGTGGA
12510440 TGATACATTTGAAG
1 TGATACATTTGAAG
12510454 GAGGTGGAGA
Statistics
Matches: 61, Mismatches: 17, Indels: 10
0.69 0.19 0.11
Matches are distributed among these distances:
15 11 0.18
18 50 0.82
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.35
Consensus pattern (18 bp):
TGATACATTTGAAGTGGA
Found at i:12516894 original size:27 final size:27
Alignment explanation
Indices: 12516864--12516915 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
12516854 TGTGGTGGTG
* *
12516864 GTTATTAGTAATTTGGTAAGTTTGACA
1 GTTATTAGCAATTTGGTAAGCTTGACA
12516891 GTTATTAGCAATTTGGTAAGCTTGA
1 GTTATTAGCAATTTGGTAAGCTTGA
12516916 TAGCTTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (27 bp):
GTTATTAGCAATTTGGTAAGCTTGACA
Found at i:12517461 original size:2 final size:2
Alignment explanation
Indices: 12517454--12517478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12517444 TGCCCTGAGG
12517454 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12517479 TAATATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12517789 original size:67 final size:67
Alignment explanation
Indices: 12517659--12517793 Score: 164
Period size: 67 Copynumber: 2.0 Consensus size: 67
12517649 TGGAAGATAA
* * * * *
12517659 TAAAGTGGTTATTATCATACTTGTTAGTTTTTACTGTTATTTTTTTATCAGTAGAGAACCATGTT
1 TAAAGTGGTTATTATCATACATATTAGTTTTTACTATTATCTTTTGATCAGTAGAGAACCATGTT
12517724 TC
66 TC
* * ** *
12517726 TAAAGTGGTTATTATCATACATATTAATTTTTTCCTATTATCTTTTGATTGGTAGAG-ATCATGT
1 TAAAGTGGTTATTATCATACATATT-AGTTTTTACTATTATCTTTTGATCAGTAGAGAACCATGT
12517790 TTC
65 TTC
12517793 T
1 T
12517794 TGTTTAGTTG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 33 0.58
68 24 0.42
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (67 bp):
TAAAGTGGTTATTATCATACATATTAGTTTTTACTATTATCTTTTGATCAGTAGAGAACCATGTT
TC
Found at i:12518409 original size:77 final size:77
Alignment explanation
Indices: 12518314--12518494 Score: 299
Period size: 77 Copynumber: 2.4 Consensus size: 77
12518304 ATTTGGGATA
* * * *
12518314 TTTGAGTTTTGCTATATACAGTGAAATTTTTGAGTTCACTGTTGTTTGAAAATATTGGTGAATTG
1 TTTGAGTTTTGTTATATACAATGAAATTTTTGAGTTCACTGTTGTTTGAAAATATTGATGAATTA
12518379 CTTTTAGTGTTG
66 CTTTTAGTGTTG
*
12518391 TTTGAGTTTTGTTATATACAATGAATTTTTTGAGTTCACTGTTGTTTGAAAATATTGATGAATTA
1 TTTGAGTTTTGTTATATACAATGAAATTTTTGAGTTCACTGTTGTTTGAAAATATTGATGAATTA
*
12518456 TTTTTAGTGTTG
66 CTTTTAGTGTTG
*
12518468 TTTGAGTTTTGTTATATATAATGAAAT
1 TTTGAGTTTTGTTATATACAATGAAAT
12518495 CAAGTTTAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 96 1.00
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.50
Consensus pattern (77 bp):
TTTGAGTTTTGTTATATACAATGAAATTTTTGAGTTCACTGTTGTTTGAAAATATTGATGAATTA
CTTTTAGTGTTG
Found at i:12521661 original size:27 final size:27
Alignment explanation
Indices: 12521631--12521682 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
12521621 TGTGGTGGTG
*
12521631 GTTATTAGTAATTTGGTAAGTTTGACA
1 GTTATTAGCAATTTGGTAAGTTTGACA
12521658 GTTATTAGCAATTTGGTAAGTTTGA
1 GTTATTAGCAATTTGGTAAGTTTGA
12521683 TAGCTTCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.44
Consensus pattern (27 bp):
GTTATTAGCAATTTGGTAAGTTTGACA
Found at i:12522513 original size:68 final size:67
Alignment explanation
Indices: 12522390--12522525 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 67
12522380 TGGAAGATAA
* * *
12522390 TAAAGTGGTTATTATCATACTTATTAGTTTTTTACTGTTATTTTTTTATCAGTAGAGAACCATGT
1 TAAAGTGGTTATTATCATACTTATTAGTTTTTTACTATTATCTTTTGATCAGTAGAG-ACCATGT
12522455 TTC
65 TTC
* ** *
12522458 TAAAGTGGTTATTATCATACTTATTAGTTTTTTCCTATTATCTTTTGATTGGTAGAGATCATGTT
1 TAAAGTGGTTATTATCATACTTATTAGTTTTTTACTATTATCTTTTGATCAGTAGAGACCATGTT
12522523 TC
66 TC
12522525 T
1 T
12522526 TGTTTAGTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
67 10 0.16
68 51 0.84
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (67 bp):
TAAAGTGGTTATTATCATACTTATTAGTTTTTTACTATTATCTTTTGATCAGTAGAGACCATGTT
TC
Found at i:12528956 original size:24 final size:24
Alignment explanation
Indices: 12528929--12528975 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12528919 AATTTTAGAT
*
12528929 TTTGTTA-GATTACATTTCTACAAG
1 TTTGTTATG-TTACATCTCTACAAG
12528953 TTTGTTATGTTACATCTCTACAA
1 TTTGTTATGTTACATCTCTACAA
12528976 TATTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (24 bp):
TTTGTTATGTTACATCTCTACAAG
Found at i:12535237 original size:25 final size:21
Alignment explanation
Indices: 12535185--12535227 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12535175 TTGACCTTGC
12535185 TGATTAAATATAACAAGGTTT
1 TGATTAAATATAACAAGGTTT
*
12535206 TGATTAACTATAACAAGGTTT
1 TGATTAAATATAACAAGGTTT
12535227 T
1 T
12535228 TATTGATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (21 bp):
TGATTAAATATAACAAGGTTT
Found at i:12537121 original size:14 final size:14
Alignment explanation
Indices: 12537055--12537121 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
12537045 TAAAAATTAA
*
12537055 AAAATCTAAACCCT
1 AAAATCAAAACCCT
* ** *
12537069 AAAACCCTAACCTT
1 AAAATCAAAACCCT
*
12537083 AAAATTGAAAACCCT
1 AAAA-TCAAAACCCT
*
12537098 -AAACCAAAACCCT
1 AAAATCAAAACCCT
12537111 AAAATCAAAAC
1 AAAATCAAAAC
12537122 TCAAAACTTC
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
13 8 0.21
14 26 0.67
15 5 0.13
ACGTcount: A:0.54, C:0.28, G:0.01, T:0.16
Consensus pattern (14 bp):
AAAATCAAAACCCT
Found at i:12537146 original size:13 final size:14
Alignment explanation
Indices: 12537104--12537162 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
12537094 CCCTAAACCA
* *
12537104 AAACCCTAAAATCA
1 AAACTCTAAAATCC
12537118 AAACTC-AAAACTTCC
1 AAACTCTAAAA--TCC
*
12537133 AAAC-CTTAAATCC
1 AAACTCTAAAATCC
12537146 AAAACTCTAAAATCC
1 -AAACTCTAAAATCC
12537161 AA
1 AA
12537163 CCCCCAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 7 0.19
14 12 0.33
15 17 0.47
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACTCTAAAATCC
Found at i:12537245 original size:8 final size:8
Alignment explanation
Indices: 12537220--12537290 Score: 62
Period size: 8 Copynumber: 9.4 Consensus size: 8
12537210 TCAAAACCAT
12537220 AAACCCTA
1 AAACCCTA
*
12537228 AAA-TCTA
1 AAACCCTA
12537235 AAACCCTA
1 AAACCCTA
*
12537243 AAACCCCA
1 AAACCCTA
*
12537251 AAA-CCTT
1 AAACCCTA
12537258 AAACCCTA
1 AAACCCTA
12537266 AAA---TA
1 AAACCCTA
*
12537271 AAACCCTTT
1 AAACCC-TA
12537280 AAACCCTA
1 AAACCCTA
12537288 AAA
1 AAA
12537291 ATAAAACCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
5 5 0.10
7 11 0.22
8 26 0.53
9 7 0.14
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (8 bp):
AAACCCTA
Found at i:12537246 original size:30 final size:29
Alignment explanation
Indices: 12537212--12537423 Score: 104
Period size: 30 Copynumber: 7.2 Consensus size: 29
12537202 TCCAAAAATC
12537212 AAAACCATAAACCCTAAAATCTAAAACCCT
1 AAAACCATAAACCCTAAAATCTAAAA-CCT
* **
12537242 AAAACCCCA-AAACCTTAAACCCTAAAA--T
1 AAAA--CCATAAACCCTAAAATCTAAAACCT
* *
12537270 AAAACCCTTTAAACCCTAAAA-ATAAAACCT
1 AAAA-CC-ATAAACCCTAAAATCTAAAACCT
* * * *
12537300 TAAACTCTTTAAACCCTAAAAACAAAAACCT
1 AAAAC-C-ATAAACCCTAAAATCTAAAACCT
*
12537331 -AAACCTTATAAACCCTAAAAT-TAAAAATCT
1 AAAACC--ATAAACCCTAAAATCT-AAAACCT
* *
12537361 -AAACCTTCCAAATCCTAAAATC-AAAACCCT
1 AAAACCAT--AAACCCTAAAATCTAAAA-CCT
*
12537391 -AAACC-TCAAATCCTAAAAT-TAAAACCT
1 AAAACCAT-AAACCCTAAAATCTAAAACCT
12537418 AAAACC
1 AAAACC
12537424 CTCCAAATCC
Statistics
Matches: 149, Mismatches: 17, Indels: 34
0.75 0.09 0.17
Matches are distributed among these distances:
27 6 0.04
28 33 0.22
29 16 0.11
30 69 0.46
31 22 0.15
32 3 0.02
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (29 bp):
AAAACCATAAACCCTAAAATCTAAAACCT
Found at i:12537284 original size:22 final size:23
Alignment explanation
Indices: 12537256--12537298 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
12537246 CCCCAAAACC
12537256 TTAAACCCT-AAAATAAAACCCT
1 TTAAACCCTAAAAATAAAACCCT
12537278 TTAAACCCTAAAAATAAAACC
1 TTAAACCCTAAAAATAAAACC
12537299 TTAAACTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (23 bp):
TTAAACCCTAAAAATAAAACCCT
Found at i:12537304 original size:21 final size:20
Alignment explanation
Indices: 12537250--12537304 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 20
12537240 CTAAAACCCC
12537250 AAAACCTTAAACCCTAAAAT
1 AAAACCTTAAACCCTAAAAT
12537270 AAAACCCTTTAAACCCTAAAAAT
1 AAAA-CC-TTAAACCCT-AAAAT
12537293 AAAACCTTAAAC
1 AAAACCTTAAAC
12537305 TCTTTAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.12
21 8 0.25
22 11 0.34
23 9 0.28
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAACCTTAAACCCTAAAAT
Found at i:12537335 original size:60 final size:59
Alignment explanation
Indices: 12537275--12537438 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 59
12537265 AAAATAAAAC
* *
12537275 CCTTTAAACCCTAAAAATAAAACCTTAAACTCTT-TAAACCCTAAAAACAAAAACCTAAA
1 CCTTTAAACCCTAAAATTAAAACCTTAAAC-CTTCCAAACCCTAAAAACAAAAACCTAAA
* * * *
12537334 CCTTATAAACCCTAAAATTAAAA-ATCTAAACCTTCCAAATCCTAAAATCAAAACCCTAAA
1 CCTT-TAAACCCTAAAATTAAAACCT-TAAACCTTCCAAACCCTAAAAACAAAAACCTAAA
* * * * *
12537394 CC-TCAAATCCTAAAATTAAAACCTAAAACCCTCCAAATCCTAAAA
1 CCTTTAAACCCTAAAATTAAAACCTTAAACCTTCCAAACCCTAAAA
12537439 TCCAAGCCCT
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
58 35 0.39
59 10 0.11
60 45 0.50
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (59 bp):
CCTTTAAACCCTAAAATTAAAACCTTAAACCTTCCAAACCCTAAAAACAAAAACCTAAA
Found at i:12537381 original size:8 final size:8
Alignment explanation
Indices: 12537370--12537441 Score: 50
Period size: 8 Copynumber: 9.8 Consensus size: 8
12537360 TAAACCTTCC
12537370 AAATCCTA
1 AAATCCTA
12537378 AAAT-C-A
1 AAATCCTA
*
12537384 AAACCCT-
1 AAATCCTA
*
12537391 AAA-CCTC
1 AAATCCTA
12537398 AAATCCTA
1 AAATCCTA
12537406 AAAT--TA
1 AAATCCTA
12537412 AAA-CCTA
1 AAATCCTA
* *
12537419 AAACCCTCC
1 AAATCCT-A
12537428 AAATCCTA
1 AAATCCTA
12537436 AAATCC
1 AAATCC
12537442 AAGCCCTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 12 0.24
7 13 0.25
8 20 0.39
9 6 0.12
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (8 bp):
AAATCCTA
Found at i:12537429 original size:58 final size:59
Alignment explanation
Indices: 12537280--12537451 Score: 186
Period size: 58 Copynumber: 2.9 Consensus size: 59
12537270 AAAACCCTTT
* * ** * * * *
12537280 AAACCCTAAAAATAAAACCTTAAACTCTTTAAACCCTAAAAACAAAAACCTAAACCTTAT
1 AAACCCTAAAATTAAAACC-TAAACCCTCCAAATCCTAAAATCAAAACCCTAAACCTTAC
* *
12537340 AAACCCTAAAATTAAAAATCTAAACCTTCCAAATCCTAAAATCAAAACCCTAAACC-T-C
1 AAACCCTAAAATT-AAAACCTAAACCCTCCAAATCCTAAAATCAAAACCCTAAACCTTAC
* * *
12537398 AAATCCTAAAATTAAAACCTAAAACCCTCCAAATCCTAAAATCCAAGCCCTAAA
1 AAACCCTAAAATTAAAACCT-AAACCCTCCAAATCCTAAAATCAAAACCCTAAA
12537452 ACCCTTTAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
57 6 0.06
58 42 0.44
59 1 0.01
60 41 0.43
61 5 0.05
ACGTcount: A:0.51, C:0.28, G:0.01, T:0.20
Consensus pattern (59 bp):
AAACCCTAAAATTAAAACCTAAACCCTCCAAATCCTAAAATCAAAACCCTAAACCTTAC
Found at i:12537433 original size:30 final size:29
Alignment explanation
Indices: 12537324--12537439 Score: 128
Period size: 30 Copynumber: 4.0 Consensus size: 29
12537314 CCTAAAAACA
* ** *
12537324 AAAACCTAAACCTTATAAACCCTAAAATT
1 AAAACCTAAACCCTCCAAATCCTAAAATT
* * *
12537353 AAAAATCTAAACCTTCCAAATCCTAAAATC
1 -AAAACCTAAACCCTCCAAATCCTAAAATT
12537383 AAAACCCTAAA-CCT-CAAATCCTAAAATT
1 AAAA-CCTAAACCCTCCAAATCCTAAAATT
12537411 AAAACCTAAAACCCTCCAAATCCTAAAAT
1 AAAACCT-AAACCCTCCAAATCCTAAAAT
12537440 CCAAGCCCTA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.04
28 20 0.27
29 9 0.12
30 42 0.57
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.22
Consensus pattern (29 bp):
AAAACCTAAACCCTCCAAATCCTAAAATT
Found at i:12537437 original size:17 final size:17
Alignment explanation
Indices: 12537415--12537490 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
12537405 AAAATTAAAA
12537415 CCTAAAACCCTCCAAAT
1 CCTAAAACCCTCCAAAT
**
12537432 CCTAAAA---TCCAAGC
1 CCTAAAACCCTCCAAAT
**
12537446 CCTAAAACCCTTTAAAT
1 CCTAAAACCCTCCAAAT
* *
12537463 TCTAAAACCCTCTAAAT
1 CCTAAAACCCTCCAAAT
*
12537480 TCTAAAACCCT
1 CCTAAAACCCT
12537491 TAGAACTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.25
17 36 0.75
ACGTcount: A:0.41, C:0.34, G:0.01, T:0.24
Consensus pattern (17 bp):
CCTAAAACCCTCCAAAT
Found at i:12546230 original size:37 final size:37
Alignment explanation
Indices: 12546189--12546297 Score: 159
Period size: 37 Copynumber: 2.9 Consensus size: 37
12546179 TTCGACTTAC
*
12546189 GGTATTG-TCCCGATCAATTCTTTATTTTTCAACTCGT
1 GGTATTGTTCCAG-TCAATTCTTTATTTTTCAACTCGT
* *
12546226 GGTATTATTTCAGTCAA-TCTTTTATTTTTCAACTCGT
1 GGTATTGTTCCAGTCAATTC-TTTATTTTTCAACTCGT
12546263 GGTATTGTTCCAGTCAATTCTTTATTTTTCAACTC
1 GGTATTGTTCCAGTCAATTCTTTATTTTTCAACTC
12546298 ACAGTGTTGT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
36 2 0.03
37 57 0.89
38 5 0.08
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (37 bp):
GGTATTGTTCCAGTCAATTCTTTATTTTTCAACTCGT
Found at i:12546233 original size:20 final size:20
Alignment explanation
Indices: 12546210--12546268 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
12546200 GATCAATTCT
12546210 TTATTTTTCAACTCGTGGTA
1 TTATTTTTCAACTCGTGGTA
*
12546230 TTATTTCAGTCAA-TC-T--T-
1 TTATTT--TTCAACTCGTGGTA
12546247 TTATTTTTCAACTCGTGGTA
1 TTATTTTTCAACTCGTGGTA
12546267 TT
1 TT
12546269 GTTCCAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
15 4 0.13
16 2 0.07
17 7 0.23
18 1 0.03
19 1 0.03
20 9 0.30
21 2 0.07
22 4 0.13
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (20 bp):
TTATTTTTCAACTCGTGGTA
Found at i:12546492 original size:22 final size:22
Alignment explanation
Indices: 12546464--12546525 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
12546454 TACAATTTTC
12546464 AAGACCTCTGGGCATAATCTCT
1 AAGACCTCTGGGCATAATCTCT
*
12546486 AAGACCTCTGGGCATAATTTCT
1 AAGACCTCTGGGCATAATCTCT
** *
12546508 AAGATTTCTAGGCATAAT
1 AAGACCTCTGGGCATAAT
12546526 TTCAACTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (22 bp):
AAGACCTCTGGGCATAATCTCT
Found at i:12546526 original size:22 final size:22
Alignment explanation
Indices: 12546460--12546528 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
12546450 ATTTTACAAT
*
12546460 TTTC-AAGACCTCTGGGCATAA
1 TTTCTAAGACCTCTAGGCATAA
* *
12546481 TCTCTAAGACCTCTGGGCATAA
1 TTTCTAAGACCTCTAGGCATAA
**
12546503 TTTCTAAGATTTCTAGGCATAA
1 TTTCTAAGACCTCTAGGCATAA
12546525 TTTC
1 TTTC
12546529 AACTTGTAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 3 0.07
22 39 0.93
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (22 bp):
TTTCTAAGACCTCTAGGCATAA
Found at i:12546762 original size:22 final size:21
Alignment explanation
Indices: 12546702--12546789 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
12546692 TAGTCGATTC
12546702 TTTAAGACCTCAAAGCATAAT
1 TTTAAGACCTCAAAGCATAAT
** *
12546723 TTTAAGACCTTTAGGCATAAT
1 TTTAAGACCTCAAAGCATAAT
** **
12546744 TTCTAAGACCTCCGAGCATTACC
1 TT-TAAGACCTCAAAGCA-TAAT
*
12546767 TTTAAGACCTCAAGGCATAAT
1 TTTAAGACCTCAAAGCATAAT
12546788 TT
1 TT
12546790 AGACTCATGG
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
21 24 0.47
22 23 0.45
23 4 0.08
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (21 bp):
TTTAAGACCTCAAAGCATAAT
Found at i:12547028 original size:132 final size:132
Alignment explanation
Indices: 12546782--12547031 Score: 333
Period size: 132 Copynumber: 1.9 Consensus size: 132
12546772 GACCTCAAGG
*
12546782 CATAATTTAGACTCATGGTGTGGTCTCGATCGATTCTTTATTATTTGACTCGCGGTGTTATCCCG
1 CATAATTTAGACTCATGGTGTGGTCTCGATCGATTCTTTATTATTTGACTCGCGATGTTATCCCG
* * * *
12546847 ATCAATTCTATAAGACCTTCAAGCATAATTTTTAAGACTTCCGGACATAATTTCTAAAATCTTTA
66 ATCAATTCTATAAAACCTTCAAGCATAATTTCTAAGACCTCCAGACATAATTTCTAAAATCTTTA
12546912 AA
131 AA
* * * * *
12546914 CATAATTTCGACTCGTGGTGTTGTC-CAGGTCGATTCTTTATTATTTGACTTGCGATGTTATCCC
1 CATAATTTAGACTCATGGTGTGGTCTC-GATCGATTCTTTATTATTTGACTCGCGATGTTATCCC
* * ** *
12546978 GATCGATTCTGTAAAACCTTCGGGCATAATTTCTCAGACCTCCA-AGCATAATTT
65 GATCAATTCTATAAAACCTTCAAGCATAATTTCTAAGACCTCCAGA-CATAATTT
12547032 TCAAGCGTTC
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
131 2 0.02
132 99 0.98
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (132 bp):
CATAATTTAGACTCATGGTGTGGTCTCGATCGATTCTTTATTATTTGACTCGCGATGTTATCCCG
ATCAATTCTATAAAACCTTCAAGCATAATTTCTAAGACCTCCAGACATAATTTCTAAAATCTTTA
AA
Found at i:12547202 original size:38 final size:37
Alignment explanation
Indices: 12547122--12547215 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 37
12547112 ATCCTAATCG
* * * *
12547122 ATTCTTTATTTCTCGACTTGCGGTGTTGTTTTGATCA
1 ATTCTTTATTTCTCGACTTGCAGTGTTATTTCGACCA
12547159 ATTCTTTACTTTCT-GACTTGCAGTGTTATTTCGACCA
1 ATTCTTTA-TTTCTCGACTTGCAGTGTTATTTCGACCA
*
12547196 TTTTCTTTATTAT-TCGACTT
1 -ATTCTTTATT-TCTCGACTT
12547216 ATGGTGATTG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
37 30 0.62
38 18 0.38
ACGTcount: A:0.16, C:0.18, G:0.14, T:0.52
Consensus pattern (37 bp):
ATTCTTTATTTCTCGACTTGCAGTGTTATTTCGACCA
Found at i:12549099 original size:37 final size:36
Alignment explanation
Indices: 12549052--12549122 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
12549042 AAAAAATTCT
*
12549052 AAATAAATTAACAATAATAATAAATTTTCTAAAAAAG
1 AAATAAATTAAAAATAATAATAAATTTTC-AAAAAAG
* ** *
12549089 AAATATATTAAAAATTTTAATTAATTTTCAAAAA
1 AAATAAATTAAAAATAATAATAAATTTTCAAAAA
12549123 TCATAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 5 0.17
37 24 0.83
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (36 bp):
AAATAAATTAAAAATAATAATAAATTTTCAAAAAAG
Found at i:12549248 original size:28 final size:28
Alignment explanation
Indices: 12549202--12549268 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
12549192 TAAAAGTTAA
* ** *
12549202 AAAATCTAAACCCCAAAACCCTAGCACT
1 AAAATCAAAACCCCAAAACCAAAACACT
** *
12549230 AAAATCAAAACCCTTAAACCAAAACCCT
1 AAAATCAAAACCCCAAAACCAAAACACT
12549258 AAAATCAAAAC
1 AAAATCAAAAC
12549269 TCAAAACTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.54, C:0.31, G:0.01, T:0.13
Consensus pattern (28 bp):
AAAATCAAAACCCCAAAACCAAAACACT
Found at i:12549298 original size:15 final size:15
Alignment explanation
Indices: 12549229--12549311 Score: 61
Period size: 15 Copynumber: 5.7 Consensus size: 15
12549219 ACCCTAGCAC
12549229 TAAAAT-CAAAACCCT
1 TAAAATCCAAAA-CCT
*
12549244 T-AAA-CCAAAACCC
1 TAAAATCCAAAACCT
12549257 TAAAAT-CAAAA-CT
1 TAAAATCCAAAACCT
*
12549270 CAAAACTTCC-AAACCT
1 TAAAA--TCCAAAACCT
* *
12549286 TTAAATTCAAAACCT
1 TAAAATCCAAAACCT
12549301 TAAAATCCAAA
1 TAAAATCCAAA
12549312 CCTCAAAACC
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
13 8 0.15
14 18 0.35
15 20 0.38
16 6 0.12
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAAATCCAAAACCT
Found at i:12549303 original size:14 final size:14
Alignment explanation
Indices: 12549229--12549319 Score: 69
Period size: 14 Copynumber: 6.4 Consensus size: 14
12549219 ACCCTAGCAC
12549229 TAAAATCAAAACCCT
1 TAAAATCAAAA-CCT
* *
12549244 T-AAACCAAAACCC
1 TAAAATCAAAACCT
12549257 TAAAATCAAAA-CT
1 TAAAATCAAAACCT
* *
12549270 CAAAACTTCCAAACCTT
1 TAAAA--TCAAAACC-T
*
12549287 TAAATTCAAAACCT
1 TAAAATCAAAACCT
*
12549301 TAAAATCCAAACCT
1 TAAAATCAAAACCT
*
12549315 CAAAA
1 TAAAA
12549320 CCTTCAAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
13 8 0.14
14 33 0.56
15 13 0.22
16 1 0.02
17 4 0.07
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAATCAAAACCT
Found at i:12549320 original size:22 final size:23
Alignment explanation
Indices: 12549292--12549340 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
12549282 ACCTTTAAAT
12549292 TCAAAACCTT-AAAATCC-AAACC
1 TCAAAACCTTCAAAA-CCTAAACC
12549314 TCAAAACCTTCAAAACCTAAACC
1 TCAAAACCTTCAAAACCTAAACC
12549337 -CAAA
1 TCAAA
12549341 GTTTGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (23 bp):
TCAAAACCTTCAAAACCTAAACC
Found at i:12549386 original size:15 final size:15
Alignment explanation
Indices: 12549368--12549410 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
12549358 TCAAAACCAT
12549368 AAACCCTAAAATCTA
1 AAACCCTAAAATCTA
* * *
12549383 AAACCCCAAAACCTT
1 AAACCCTAAAATCTA
*
12549398 AAACCTTAAAATC
1 AAACCCTAAAATC
12549411 AAACCCTTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (15 bp):
AAACCCTAAAATCTA
Found at i:12549483 original size:30 final size:30
Alignment explanation
Indices: 12549415--12549609 Score: 118
Period size: 30 Copynumber: 6.6 Consensus size: 30
12549405 AAAATCAAAC
* * *
12549415 CCTT-TAAACCCCAAAAATAAAA-CCTTAA
1 CCTTCTAAACCCTAAAAACAAAACCCTAAA
* * *
12549443 CATTTTTAAACCCTAAAAACAAAATCCTAAA
1 C-CTTCTAAACCCTAAAAACAAAACCCTAAA
**
12549474 CCTTCTAAACCCTAAAATA-AAAAATCTAAA
1 CCTTCTAAACCCTAAAA-ACAAAACCCTAAA
* *
12549504 CCTT-TCAAATCCTAAAATCAAAACCCTAAA
1 CCTTCT-AAACCCTAAAAACAAAACCCTAAA
* **
12549534 CC-TC-AAACCGTAAAATTAAAACCCTAAA
1 CCTTCTAAACCCTAAAAACAAAACCCTAAA
* * * *
12549562 CCCTTC-AAATCCTAAAATCCAAACCTTAAAA
1 -CCTTCTAAACCCTAAAAACAAAACCCT-AAA
*
12549593 CCCTTC-AAATCCTAAAA
1 -CCTTCTAAACCCTAAAA
12549610 CTCTTAAAAC
Statistics
Matches: 137, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
28 22 0.16
29 6 0.04
30 82 0.60
31 27 0.20
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.23
Consensus pattern (30 bp):
CCTTCTAAACCCTAAAAACAAAACCCTAAA
Found at i:12549484 original size:60 final size:59
Alignment explanation
Indices: 12549415--12549578 Score: 152
Period size: 60 Copynumber: 2.8 Consensus size: 59
12549405 AAAATCAAAC
* * * * *
12549415 CCTTTAAACCCCAAAA-ATAAAACCTTAACATTTTTAAACCCTAAAAACAAAATCCTAAA
1 CCTTTAAACCCCAAAATAAAAAACCTAAAC-CTTTCAAACCCTAAAAACAAAACCCTAAA
* * * *
12549474 CCTTCTAAACCCTAAAATAAAAAATCTAAACCTTTCAAATCCTAAAATCAAAACCCTAAA
1 CCTT-TAAACCCCAAAATAAAAAACCTAAACCTTTCAAACCCTAAAAACAAAACCCTAAA
* ** * * * *
12549534 CC-TCAAACCGTAAAATTAAAACCCTAAACCCTTCAAATCCTAAAA
1 CCTTTAAACCCCAAAATAAAAAACCTAAACCTTTCAAACCCTAAAA
12549579 TCCAAACCTT
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 36 0.41
59 5 0.06
60 37 0.42
61 10 0.11
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (59 bp):
CCTTTAAACCCCAAAATAAAAAACCTAAACCTTTCAAACCCTAAAAACAAAACCCTAAA
Found at i:12549493 original size:59 final size:60
Alignment explanation
Indices: 12549415--12549609 Score: 161
Period size: 58 Copynumber: 3.3 Consensus size: 60
12549405 AAAATCAAAC
* * * *
12549415 CCTT-TAAACCCCAAAAATAAAACCT-T-AACATTTTTAAACCCTAAAAACAAAATCCTAAA
1 CCTTCTAAA-CCCTAAAATAAAACCTCTAAAC-CTTTCAAACCCTAAAAACAAAACCCTAAA
** * *
12549474 CCTTCTAAACCCTAAAATAAAAAATCTAAACCTTTCAAATCCTAAAATCAAAACCCTAAA
1 CCTTCTAAACCCTAAAATAAAACCTCTAAACCTTTCAAACCCTAAAAACAAAACCCTAAA
* * * * * *
12549534 CC-TC-AAACCGTAAAATTAAAACC-CTAAACCCTTCAAATCCTAAAATCCAAACCTTAAAA
1 CCTTCTAAACCCTAAAA-TAAAACCTCTAAACCTTTCAAACCCTAAAAACAAAACCCT-AAA
*
12549593 CCCTTC-AAATCCTAAAA
1 -CCTTCTAAACCCTAAAA
12549610 CTCTTAAAAC
Statistics
Matches: 113, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
58 39 0.35
59 27 0.24
60 33 0.29
61 14 0.12
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.23
Consensus pattern (60 bp):
CCTTCTAAACCCTAAAATAAAACCTCTAAACCTTTCAAACCCTAAAAACAAAACCCTAAA
Found at i:12549533 original size:14 final size:14
Alignment explanation
Indices: 12549514--12549561 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
12549504 CCTTTCAAAT
12549514 CCTAAAATCAAAAC
1 CCTAAAATCAAAAC
*
12549528 CCTAAACCTC-AAAC
1 CCTAAA-ATCAAAAC
* *
12549542 CGTAAAATTAAAAC
1 CCTAAAATCAAAAC
12549556 CCTAAA
1 CCTAAA
12549562 CCCTTCAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.89
15 2 0.07
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.17
Consensus pattern (14 bp):
CCTAAAATCAAAAC
Found at i:12549569 original size:58 final size:60
Alignment explanation
Indices: 12549454--12549609 Score: 183
Period size: 58 Copynumber: 2.6 Consensus size: 60
12549444 ATTTTTAAAC
* * * *
12549454 CCTAAAAACAAAATCCTAAACCTTCTAAACCCTAAAATAAAAAATCTAAACCTTTCAAAT
1 CCTAAAATCAAAACCCTAAACCTTCTAAACCCTAAAATAAAAAACCTAAACCCTTCAAAT
* * *
12549514 CCTAAAATCAAAACCCTAAACC-TC-AAACCGTAAAATTAAAACCCTAAACCCTTCAAAT
1 CCTAAAATCAAAACCCTAAACCTTCTAAACCCTAAAATAAAAAACCTAAACCCTTCAAAT
* * *
12549572 CCTAAAATCCAAACCTTAAAACCCTTC-AAATCCTAAAA
1 CCTAAAATCAAAACCCT-AAA-CCTTCTAAACCCTAAAA
12549610 CTCTTAAAAC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 44 0.54
59 5 0.06
60 22 0.27
61 11 0.13
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (60 bp):
CCTAAAATCAAAACCCTAAACCTTCTAAACCCTAAAATAAAAAACCTAAACCCTTCAAAT
Found at i:12549661 original size:15 final size:15
Alignment explanation
Indices: 12549643--12549675 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12549633 CTTAAAATTC
12549643 AAAATCTGAAACCCT
1 AAAATCTGAAACCCT
*
12549658 AAAATCTTAAACCCT
1 AAAATCTGAAACCCT
12549673 AAA
1 AAA
12549676 TTTGGCACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAATCTGAAACCCT
Found at i:12551534 original size:19 final size:19
Alignment explanation
Indices: 12551506--12551552 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
12551496 CACCATGTGG
12551506 TTTTCTTTTTCTTTT-TTT
1 TTTTCTTTTTCTTTTGTTT
*
12551524 TTTTGCTTTTTGTTTTGTTT
1 TTTT-CTTTTTCTTTTGTTT
12551544 TTTT-TTTTT
1 TTTTCTTTTT
12551553 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 9 0.35
19 10 0.38
20 7 0.27
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (19 bp):
TTTTCTTTTTCTTTTGTTT
Found at i:12552254 original size:20 final size:18
Alignment explanation
Indices: 12552212--12552254 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
12552202 TTCTATTCAC
*
12552212 TTTTTTTATATTTAATAAA
1 TTTTTTTATATTTAA-CAA
*
12552231 TTTTTTGATATTTTAACAA
1 TTTTTTTATA-TTTAACAA
12552250 TTTTT
1 TTTTT
12552255 AAAATGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTTTATATTTAACAA
Found at i:12552864 original size:17 final size:18
Alignment explanation
Indices: 12552839--12552872 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12552829 AAGTCATTCA
*
12552839 ATTTTCTTTT-CTTTTTG
1 ATTTACTTTTCCTTTTTG
12552856 ATTTACTTTTCCTTTTT
1 ATTTACTTTTCCTTTTT
12552873 CCTTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTACTTTTCCTTTTTG
Found at i:12553120 original size:27 final size:27
Alignment explanation
Indices: 12553090--12553142 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
12553080 TTTAAATCTA
*
12553090 TAATACAAATATATGT-TTTTATTAATT
1 TAAT-CAAATATATGTATTATATTAATT
* *
12553117 TAATTATATATATGTATTATATTAAT
1 TAATCAAATATATGTATTATATTAAT
12553143 AAAATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
TAATCAAATATATGTATTATATTAATT
Found at i:12553148 original size:27 final size:26
Alignment explanation
Indices: 12553098--12553150 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
12553088 TATAATACAA
* **
12553098 ATATATGTTTTTATTAATTTAATTAT
1 ATATATGTTTATATTAATAAAATTAT
12553124 ATATATGTATTATATTAATAAAATTAT
1 ATATATGT-TTATATTAATAAAATTAT
12553151 TATTTAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
ATATATGTTTATATTAATAAAATTAT
Found at i:12553366 original size:18 final size:18
Alignment explanation
Indices: 12553331--12553366 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12553321 CTTATTTATA
*
12553331 AATTATTTTTTAATATTT
1 AATTATTTTTTAACATTT
*
12553349 AATTATTTTTTTACATTT
1 AATTATTTTTTAACATTT
12553367 TAAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
AATTATTTTTTAACATTT
Found at i:12553627 original size:13 final size:13
Alignment explanation
Indices: 12553605--12553638 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12553595 CATATATAAA
*
12553605 TATATATTTTTAT
1 TATATATTTTAAT
*
12553618 TATTTATTTTAAT
1 TATATATTTTAAT
12553631 TATATATT
1 TATATATT
12553639 ATATTAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTTAAT
Found at i:12554090 original size:29 final size:29
Alignment explanation
Indices: 12554033--12554091 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
12554023 ATGTATTATC
* *
12554033 TTAATAAAATTATTATTTAATATCTTAAT
1 TTAATAAAAATATTATTTAATATCATAAT
*
12554062 TTAATAAAAATATTATATTTATA-CATAAT
1 TTAATAAAAATATTAT-TTAATATCATAAT
12554091 T
1 T
12554092 AAGATGTAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAATAAAAATATTATTTAATATCATAAT
Found at i:12555706 original size:8 final size:8
Alignment explanation
Indices: 12555693--12555737 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
12555683 TTTTTTTAAT
12555693 AAAAAATA
1 AAAAAATA
12555701 AAAAAATA
1 AAAAAATA
*
12555709 AAAAAGCTGA
1 AAAAA-AT-A
12555719 AAAAAATGA
1 AAAAAAT-A
12555728 AAAAAATA
1 AAAAAATA
12555736 AA
1 AA
12555738 TAGTTGAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 16 0.48
9 11 0.33
10 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:12561477 original size:59 final size:59
Alignment explanation
Indices: 12561383--12561494 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
12561373 ACATAATGTG
* *
12561383 GATCAAAGGACAGAATTTATTCTGAAATGATTAGTGCT-AAGAAGCTTGTGAATACTATA
1 GATCAAAGGACAAAATTTATTCTGAAATGACTAGTGCTGAA-AAGCTTGTGAATACTATA
*
12561442 GATCAATA-GACAAAATTTGTTCTAGAAATG-CTAGTGCTGAAAAGCTTGTGAAT
1 GATCAA-AGGACAAAATTTATTCT-GAAATGACTAGTGCTGAAAAGCTTGTGAAT
12561495 TACGGTCAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
59 38 0.81
60 9 0.19
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (59 bp):
GATCAAAGGACAAAATTTATTCTGAAATGACTAGTGCTGAAAAGCTTGTGAATACTATA
Found at i:12561965 original size:30 final size:30
Alignment explanation
Indices: 12561924--12562019 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 30
12561914 CCTTAAAAGA
* *
12561924 GAATCTTTGAGTTTTCAAATGAGAATCTTT
1 GAATTTTTGAGTTTTCAAATGAGAGTCTTT
12561954 GAATTTTTGAGTTTTCAAATGAGAGTCTTT
1 GAATTTTTGAGTTTTCAAATGAGAGTCTTT
12561984 GAATTTTTGAGTTTTCAAATGAGAGTCTTT
1 GAATTTTTGAGTTTTCAAATGAGAGTCTTT
*
12562014 AAATTT
1 GAATTT
12562020 CAAATGAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (30 bp):
GAATTTTTGAGTTTTCAAATGAGAGTCTTT
Found at i:12562224 original size:23 final size:24
Alignment explanation
Indices: 12562197--12562242 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
12562187 TTTGGATGAG
*
12562197 AATCTCACAAATGTGAA-TCTTGA
1 AATCTCACAAATCTGAATTCTTGA
**
12562220 AATCTTGCAAATCTGAATTCTTG
1 AATCTCACAAATCTGAATTCTTG
12562243 CATATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (24 bp):
AATCTCACAAATCTGAATTCTTGA
Found at i:12562241 original size:16 final size:17
Alignment explanation
Indices: 12562212--12562244 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12562202 CACAAATGTG
12562212 AATCTTGAAATCTTGCA
1 AATCTTGAAATCTTGCA
*
12562229 AATC-TGAATTCTTGCA
1 AATCTTGAAATCTTGCA
12562245 TATATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (17 bp):
AATCTTGAAATCTTGCA
Found at i:12562308 original size:31 final size:31
Alignment explanation
Indices: 12562249--12562308 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
12562239 CTTGCATATA
* * *
12562249 TAAAATTTTGCGAATCAAATTCGTATGAAAC
1 TAAAATTTTGAGAAGCAAATTCGAATGAAAC
12562280 TAAAATTTTGAGAAGCAAATTTC-AATGAA
1 TAAAATTTTGAGAAGCAAA-TTCGAATGAA
12562309 TTCTTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (31 bp):
TAAAATTTTGAGAAGCAAATTCGAATGAAAC
Found at i:12562605 original size:82 final size:83
Alignment explanation
Indices: 12562443--12563216 Score: 590
Period size: 84 Copynumber: 9.1 Consensus size: 83
12562433 TTGATAAGCT
* * ** *
12562443 TTTATTTTTTAAAGTTGTTGTGTCTCTATTTAAAGGAG-CTTTTATTTTTTCAAAAGTTGTTGTG
1 TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGTCTTTTA-TTTTTC-AAAGTTGTTGTG
* **
12562507 CCTTTGTTTAGAAGAGCCT-
64 CCTCTACTTAGAAGAGCCTA
** *
12562526 TTTATTTTTCAAAGTTGTTGTGCCTCTATTTAGAGGAGTCTTTTATTTTTCAAAGTTATTGTGCC
1 TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGTCTTTTATTTTTCAAAGTTGTTGTGCC
* *
12562591 TCTATTTAGAAGAGCTTAA
66 TCTACTTAGAAGAGCCT-A
* * * *
12562610 TTTATTTTTCAAAGTTGTTTTGCCTCTGCTTAAAAGAGTTTTATTCATTTTT-AAAGTTGTTGTG
1 TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGTCTT-TT-ATTTTTCAAAGTTGTTGTG
*
12562674 CCTCTATTTAGAAGAGCC--
64 CCTCTACTTAGAAGAGCCTA
* * * * *
12562692 TTTATTTTTCAAAGTTATTGTACCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTTGTTGA
1 TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAG-TCT-TTTA-TTTTTCAAAGTTGTTGT
12562757 GCCTCTACTTA-AAGGAGCC--
63 GCCTCTACTTAGAA-GAGCCTA
* * * * *
12562776 TTTA-TTTT-AAAATTGTTGAGCCTCTACTTAGAAGAGCTTTATTTTTTTATTTTTCAAAGTTG-
1 TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAG-AG-G----AGTCTTTTATTTTTCAAAGTTGT
* * *
12562838 TGTAGCCTCTACTTGGAGGAGCTTTA
60 TGT-GCCTCTACTTAGAAGAGC-CTA
* * * * *
12562864 TTTATTTTTCAAAGTTGTTGTACCTCTGTTTATAGGA-ACCTTTATTTTTCAAAGTTGTTGTGCC
1 TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGTCTTTTATTTTTCAAAGTTGTTGTGCC
* * *
12562928 TCTACTTAGAGGAACTTTA
66 TCTACTTAGAAGAGC-CTA
* * * *
12562947 TTTATTTTTTCAAAGTTATTGAGCCTCTGCTTAGAAGAG-CTTTTA-TTTT-AAAGTTGTTGAGC
1 TTTA-TTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGTCTTTTATTTTTCAAAGTTGTTGTGC
* * * *
12563009 CTTTGCTTAGAGGAGCTTTATTTA
65 CTCTACTTAGAAGAGC-----CTA
* * * *
12563033 TTTATTTTTCAAAGTTGTTGAGCCTCTGCTTGGAGGAGTTTTATTTATTTTTTCAAAGTTGTTGA
1 TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAG-TCT-TTTA-TTTTTCAAAGTTGTTGT
* *
12563098 GCATCTACTTAGAGGAGCCTTA
63 GCCTCTACTTAGAAGAGCC-TA
* * * * *
12563120 TTTATTTTTTTCAAAGTTGTTGAGCCTCTACTTAGAAGAGCCTTATTTATTTTTCAAAGTTATTG
1 TTTA--TTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGTC-T-TTTATTTTTCAAAGTTGTTG
* *
12563185 AGCCTCTGA-TTAGAAGAGCTTAA
62 TGCCTCT-ACTTAGAAGAGCCT-A
12563208 TTTATTTTT
1 TTTATTTTT
12563217 TTCCAAAGTC
Statistics
Matches: 576, Mismatches: 73, Indels: 81
0.79 0.10 0.11
Matches are distributed among these distances:
82 102 0.18
83 104 0.18
84 111 0.19
85 88 0.15
86 24 0.04
87 11 0.02
88 45 0.08
89 44 0.08
90 21 0.04
91 26 0.05
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (83 bp):
TTTATTTTTCAAAGTTGTTGTGCCTCTGCTTAGAGGAGTCTTTTATTTTTCAAAGTTGTTGTGCC
TCTACTTAGAAGAGCCTA
Found at i:12562750 original size:44 final size:44
Alignment explanation
Indices: 12562443--12563272 Score: 641
Period size: 43 Copynumber: 19.4 Consensus size: 44
12562433 TTGATAAGCT
* * * *
12562443 TTTATTTTTTAAAGTTGTTGT-GTCTCTATTTAAAGGAGCTTT-
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* * ** * *
12562485 TAT-TTTTTCAAAAGTTGTTGT-GCCTTTGTTTAGAAGAGC-CT-
1 TTTATTTTTC-AAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* *
12562526 TTTATTTTTCAAAGTTGTTGT-GCCTCTATTTAGAGGAG-TCT-
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* * * *
12562567 TTTATTTTTCAAAGTTATTGT-GCCTCTATTTAGAAGAGCTTAA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* * * * *
12562610 TTTATTTTTCAAAGTTGTT-TTGCCTCTGCTTAAAAGAGTTTTA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* * * *
12562653 TTCATTTTT-AAAGTTGTTGT-GCCTCTATTTAGAAGAGC---C
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* **
12562692 TTTATTTTTCAAAGTTATTGTA-CCTCTGTTTAGAGGAGCTTTA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* *
12562735 TTTATTTTTTCAAAGTTGTTG-AGCCTCTACTTAAAGGAGC---C
1 TTTA-TTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* *
12562776 TTTA-TTTT-AAAATTGTTG-AGCCTCTACTTAGAAGAGCTTTA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
*
12562817 TTTTTTTATTTTTCAAAGTTG-TGTAGCCTCTACTTGGAGGAGCTTTA
1 ----TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
** * * *
12562864 TTTATTTTTCAAAGTTGTTGTA-CCTCTGTTTATAGGAAC---C
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
*
12562904 TTTATTTTTCAAAGTTGTTGT-GCCTCTACTTAGAGGAACTTTA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* * *
12562947 TTTATTTTTTCAAAGTTATTG-AGCCTCTGCTTAGAAGAGC--T-
1 TTTA-TTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* *
12562988 TTTA-TTTT-AAAGTTGTTG-AGCCTTTGCTTAGAGGAGCTTTATTTA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGC----TTTA
* * *
12563033 TTTATTTTTCAAAGTTGTTG-AGCCTCTGCTTGGAGGAGTTTTA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* *
12563076 TTTATTTTTTCAAAGTTGTTG-AGCATCTACTTAGAGGAGCCTTA
1 TTTA-TTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* *
12563120 TTTATTTTTTTCAAAGTTGTTG-AGCCTCTACTTAGAAGAGCCTTA
1 TTTA--TTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
* * *
12563165 TTTATTTTTCAAAGTTATTG-AGCCTCTGA-TTAGAAGAGCTTAA
1 TTTATTTTTCAAAGTTGTTGTAGCCTCT-ACTTAGAGGAGCTTTA
** ** *
12563208 TTTATTTTTTTCCAAAGTCATTG-AGCCTCTTTTTAGAGGA-CTTTTG
1 TTTA--TTTTT-CAAAGTTGTTGTAGCCTCTACTTAGAGGAGC-TTTA
12563254 TTTACTTTTTCAAAGTTGT
1 TTTA-TTTTTCAAAGTTGT
12563273 GGAGTCTCTG
Statistics
Matches: 657, Mismatches: 83, Indels: 94
0.79 0.10 0.11
Matches are distributed among these distances:
38 52 0.08
39 16 0.02
40 60 0.09
41 79 0.12
42 58 0.09
43 128 0.19
44 110 0.17
45 61 0.09
46 40 0.06
47 53 0.08
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (44 bp):
TTTATTTTTCAAAGTTGTTGTAGCCTCTACTTAGAGGAGCTTTA
Found at i:12562801 original size:38 final size:38
Alignment explanation
Indices: 12562489--12562820 Score: 148
Period size: 41 Copynumber: 8.1 Consensus size: 38
12562479 AGCTTTTATT
* * **
12562489 TTTTCAAAAGTTGTTGTGCCTTTGTTTAGAAGAGCCTTTTA
1 TTTTCAAAA-TTGTTGAGCCTCTACTTAGAAGAG-C-TTTA
* * * *
12562530 TTTTTCAAAGTTGTTGTGCCTCTATTTAGAGGAGTCTTTTA
1 -TTTTCAAAATTGTTGAGCCTCTACTTAGAAGAG-C-TTTA
* * * *
12562571 TTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCTTAATTTA
1 -TTTTCAAAATTGTTGAGCCTCTACTTAGAAGAGC----TTTA
* ** * * *
12562614 TTTTTCAAAGTTGTTTTGCCTCTGCTTAAAAGAGTTTTATTCA
1 -TTTTCAAAATTGTTGAGCCTCTACTTAGAAGAG--CT-TT-A
* * * *
12562657 TTTTTAAAGTTGTTGTGCCTCTATTTAGAAGAGCCTTTA
1 TTTTCAAAATTGTTGAGCCTCTACTTAGAAGAG-CTTTA
* * ** *
12562696 TTTTTCAAAGTTATTGTA-CCTCTGTTTAGAGGAGCTTTATTTA
1 -TTTTCAAAATTGTTG-AGCCTCTACTTAGAAGAGC----TTTA
*
12562739 TTTTTTCAAAGTTGTTGAGCCTCTACTTA-AAGGAGCCTTTA
1 --TTTTCAAAATTGTTGAGCCTCTACTTAGAA-GAG-CTTTA
12562780 TTTT-AAAATTGTTGAGCCTCTACTTAGAAGAGCTTTA
1 TTTTCAAAATTGTTGAGCCTCTACTTAGAAGAGCTTTA
12562817 TTTT
1 TTTT
12562821 TTTATTTTTC
Statistics
Matches: 241, Mismatches: 31, Indels: 41
0.77 0.10 0.13
Matches are distributed among these distances:
37 9 0.04
38 24 0.10
39 8 0.03
40 30 0.12
41 65 0.27
42 38 0.16
43 40 0.17
44 26 0.11
45 1 0.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.47
Consensus pattern (38 bp):
TTTTCAAAATTGTTGAGCCTCTACTTAGAAGAGCTTTA
Found at i:12562917 original size:212 final size:211
Alignment explanation
Indices: 12562443--12563191 Score: 838
Period size: 212 Copynumber: 3.5 Consensus size: 211
12562433 TTGATAAGCT
* ** * * *
12562443 TTTATTTTTTAAAGTTGTTGTGTCTCTATTTAAAGGAGCTTTTATTTTTTCAAAAGTTGTTGTGC
1 TTTATTTTTCAAAGTTGTTGTACCTCTATTTAGAGGAGCCTTTATTTTTTC-AAAGTTGTTGTAC
* ** * * * * *
12562508 CTTTGTTTAGAAGAGC-CT-TTTATTTTTCAAAGTTGTTGTGCCTCTATTTAGAGGAGTCTTTTA
65 CTCTACTTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGAGCCTCTACTTAAAGGAG-CTTTTA
* * * *
12562571 TTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGC-TTA---ATTTATTTTTCAAAGTTGTTTTG
129 -TTTT-AAAGTTGTTGAGCCTCTACTTAGAAGAGCTTTATTTATTTATTTTTCAAAGTTG-TTAG
** *
12562632 CCTCTGCTTAAAAGAGTTTTA
191 CCTCTGCTTGGAGGAGTTTTA
* * * *
12562653 TTCATTTTT-AAAGTTGTTGTGCCTCTATTTAGAAGAGCCTTTA-TTTTTCAAAGTTATTGTACC
1 TTTATTTTTCAAAGTTGTTGTACCTCTATTTAGAGGAGCCTTTATTTTTTCAAAGTTGTTGTACC
** * * *
12562716 TCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTCTACTTAAAGGAGCCTTTAT
66 TCTACTTAGAAGAGCTTTATTTA-TTTTTCAAAGTTATTGAGCCTCTACTTAAAGGAGCTTTTAT
* *
12562781 TTTAAAATTGTTGAGCCTCTACTTAGAAGAGCTTTATTTTTTTATTTTTCAAAGTTGTGTAGCCT
130 TTTAAAGTTGTTGAGCCTCTACTTAGAAGAGCTTTATTTATTTATTTTTCAAAGTTGT-TAGCCT
* *
12562846 CTACTTGGAGGAGCTTTA
194 CTGCTTGGAGGAGTTTTA
* * * *
12562864 TTTATTTTTCAAAGTTGTTGTACCTCTGTTTATAGGAACCTTTA-TTTTTCAAAGTTGTTGTGCC
1 TTTATTTTTCAAAGTTGTTGTACCTCTATTTAGAGGAGCCTTTATTTTTTCAAAGTTGTTGTACC
* * *
12562928 TCTACTTAGAGGAACTTTATTTATTTTTTCAAAGTTATTGAGCCTCTGCTTAGAA-GAGCTTTTA
66 TCTACTTAGAAGAGCTTTATTTA-TTTTTCAAAGTTATTGAGCCTCTACTTA-AAGGAGCTTTTA
* * *
12562992 TTTTAAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTATTTATTTATTTTTCAAAGTTGTTGAGCC
129 TTTTAAAGTTGTTGAGCCTCTACTTAGAAGAGCTTTATTTATTTATTTTTCAAAGTTGTT-AGCC
12563057 TCTGCTTGGAGGAGTTTTA
193 TCTGCTTGGAGGAGTTTTA
* *
12563076 TTTATTTTTTCAAAGTTGTTG-AGCATCTACTTAGAGGAGCCTTATTTATTTTTTTCAAAGTTGT
1 TTTA-TTTTTCAAAGTTGTTGTA-CCTCTATTTAGAGGAGCC---TTTA-TTTTTTCAAAGTTGT
*
12563140 TG-AGCCTCTACTTAGAAGAGCCTTATTTATTTTTCAAAGTTATTGAGCCTCT
60 TGTA-CCTCTACTTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGAGCCTCT
12563192 GATTAGAAGA
Statistics
Matches: 465, Mismatches: 55, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
207 50 0.11
208 14 0.03
209 39 0.08
210 40 0.09
211 44 0.09
212 182 0.39
213 31 0.07
216 4 0.01
217 23 0.05
218 38 0.08
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (211 bp):
TTTATTTTTCAAAGTTGTTGTACCTCTATTTAGAGGAGCCTTTATTTTTTCAAAGTTGTTGTACC
TCTACTTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGAGCCTCTACTTAAAGGAGCTTTTATT
TTAAAGTTGTTGAGCCTCTACTTAGAAGAGCTTTATTTATTTATTTTTCAAAGTTGTTAGCCTCT
GCTTGGAGGAGTTTTA
Found at i:12563287 original size:44 final size:44
Alignment explanation
Indices: 12562443--12563298 Score: 638
Period size: 44 Copynumber: 20.0 Consensus size: 44
12562433 TTGATAAGCT
* * ** *
12562443 TTTATTTTTT-AAAGTTGTTGTGTCTCTATTTAAAGGAGC--T-
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * * * *
12562483 TTTATTTTTTCAAAAGTTGTTGTGCCTTTGTTTAGAAGAGC-CT-
1 TTTATTTTTTC-AAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* ** *
12562526 TTTA-TTTTTCAAAGTTGTTGTGCCTCTATTTAGAGGAG-TCT-
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * ** * *
12562567 TTTA-TTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCTTAA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
** * * *
12562610 TTTA-TTTTTCAAAGTTGTTTTGCCTCTGCTTAAAAGAGTTTTA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * ** * *
12562653 TTCA-TTTTT-AAAGTTGTTGTGCCTCTATTTAGAAGAGC---C
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* *
12562692 TTTA-TTTTTCAAAGTTATTGTA-CCTCTGTTTAGAGGAGCTTTA
1 TTTATTTTTTCAAAGTTGTTG-AGCCTCTGCTTAGAGGAGCTTTA
* * *
12562735 TTTATTTTTTCAAAGTTGTTGAGCCTCTACTTAAAGGAGC---C
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * *
12562776 TTTA--TTTT-AAAATTGTTGAGCCTCTACTTAGAAGAGCTTTA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * *
12562817 TTTTTTTATTTTTCAAAGTTG-TGTAGCCTCTACTTGGAGGAGCTTTA
1 --TTTAT-TTTTTCAAAGTTGTTG-AGCCTCTGCTTAGAGGAGCTTTA
* * * *
12562864 TTTA-TTTTTCAAAGTTGTTGTA-CCTCTGTTTATAGGAAC---C
1 TTTATTTTTTCAAAGTTGTTG-AGCCTCTGCTTAGAGGAGCTTTA
* * *
12562904 TTTA-TTTTTCAAAGTTGTTGTGCCTCTACTTAGAGGAACTTTA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* *
12562947 TTTATTTTTTCAAAGTTATTGAGCCTCTGCTTAGAAGAGC--T-
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
*
12562988 TTTA--TTTT-AAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* *
12563029 TTTATTTATTTTTCAAAGTTGTTGAGCCTCTGCTTGGAGGAGTTTTA
1 TTTA--T-TTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * *
12563076 TTTATTTTTTCAAAGTTGTTGAGCATCTACTTAGAGGAGCCTTA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * *
12563120 TTTATTTTTTTCAAAGTTGTTGAGCCTCTACTTAGAAGAGCCTTA
1 TTTA-TTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
* * * *
12563165 TTTA-TTTTTCAAAGTTATTGAGCCTCTGATTAGAAGAGCTTAA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
** ** *
12563208 TTTATTTTTTTCCAAAGTCATTGAGCCTCTTTTTAGAGGA-CTTTTG
1 TTTA-TTTTTT-CAAAGTTGTTGAGCCTCTGCTTAGAGGAGC-TTTA
* * * * * *
12563254 TTTACTTTTTCAAAGTTGTGGAGTCTCTGTTTAGATGAGTTTTA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
12563298 T
1 T
12563299 GTTGTTCAAG
Statistics
Matches: 677, Mismatches: 95, Indels: 84
0.79 0.11 0.10
Matches are distributed among these distances:
38 52 0.08
39 16 0.02
40 69 0.10
41 75 0.11
42 56 0.08
43 124 0.18
44 127 0.19
45 57 0.08
46 40 0.06
47 61 0.09
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (44 bp):
TTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTA
Found at i:12589372 original size:21 final size:21
Alignment explanation
Indices: 12589346--12589385 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12589336 AATGTCAACC
*
12589346 TCAAGTATCTCAATTCCAATA
1 TCAAGTACCTCAATTCCAATA
*
12589367 TCAAGTGCCTCAATTCCAA
1 TCAAGTACCTCAATTCCAA
12589386 CCACCCCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (21 bp):
TCAAGTACCTCAATTCCAATA
Found at i:12598613 original size:14 final size:14
Alignment explanation
Indices: 12598574--12598619 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
12598564 TTTAATTTAA
12598574 ATATAAAATTAAAT
1 ATATAAAATTAAAT
*
12598588 ATATATAA--AAAT
1 ATATAAAATTAAAT
12598600 ATATAAAATTAAAT
1 ATATAAAATTAAAT
*
12598614 AAATAA
1 ATATAA
12598620 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAAAATTAAAT
Found at i:12598638 original size:14 final size:14
Alignment explanation
Indices: 12598608--12598636 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12598598 ATATATAAAA
12598608 TTAAATAAATAATT
1 TTAAATAAATAATT
12598622 TTAAA-AAATAATT
1 TTAAATAAATAATT
12598635 TT
1 TT
12598637 TATATATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAATAAATAATT
Found at i:12605499 original size:19 final size:20
Alignment explanation
Indices: 12605466--12605504 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
12605456 TACATACTCC
12605466 TTTTTAACAAAAAAAAATTA
1 TTTTTAACAAAAAAAAATTA
*
12605486 TTTTTAA-AATAAAAAATTA
1 TTTTTAACAAAAAAAAATTA
12605505 AAAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTTAACAAAAAAAAATTA
Found at i:12607983 original size:13 final size:14
Alignment explanation
Indices: 12607965--12607993 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12607955 TAACATAATC
12607965 AAGAT-ATATCAAT
1 AAGATAATATCAAT
12607978 AAGATAATATCAAT
1 AAGATAATATCAAT
12607992 AA
1 AA
12607994 CAATTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
AAGATAATATCAAT
Found at i:12614701 original size:20 final size:21
Alignment explanation
Indices: 12614676--12614728 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
12614666 GAAATTTTTA
12614676 AATATTTATATTT-AAAAAAT
1 AATATTTATATTTAAAAAAAT
12614696 AATATTTTATATTTAAAAAAAT
1 AATA-TTTATATTTAAAAAAAT
12614718 AATATTT-TATT
1 AATATTTATATT
12614729 AATTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.26
21 12 0.39
22 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTATATTTAAAAAAAT
Found at i:12614703 original size:30 final size:30
Alignment explanation
Indices: 12614647--12614703 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
12614637 ATTTTTATTT
* *
12614647 ATATATATATTTATATAATGAAATTTTTAA
1 ATATATATATTTAAAAAATGAAATTTTTAA
*
12614677 ATATTTATATTTAAAAAAT-AATATTTT
1 ATATATATATTTAAAAAATGAA-ATTTT
12614704 ATATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATATATATATTTAAAAAATGAAATTTTTAA
Found at i:12614706 original size:21 final size:22
Alignment explanation
Indices: 12614676--12614727 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12614666 GAAATTTTTA
12614676 AATA-TTTATATTT-AAAAAAT
1 AATATTTTATATTTAAAAAAAT
12614696 AATATTTTATATTTAAAAAAAT
1 AATATTTTATATTTAAAAAAAT
12614718 AATATTTTAT
1 AATATTTTAT
12614728 TAATTCGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
22 17 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:12620288 original size:19 final size:19
Alignment explanation
Indices: 12620262--12620305 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
12620252 GATTTACCTT
*
12620262 AACT-TTAAAAATAATATA
1 AACTCTTAAAAATAAAATA
*
12620280 AACTCTTAAAGATAAAATA
1 AACTCTTAAAAATAAAATA
12620299 AACTCTT
1 AACTCTT
12620306 TTATTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (19 bp):
AACTCTTAAAAATAAAATA
Found at i:12626449 original size:27 final size:29
Alignment explanation
Indices: 12626419--12626472 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
12626409 ATTAATTTAA
12626419 ATTTTAAATCATATTATT-T-TTATATAT
1 ATTTTAAATCATATTATTATATTATATAT
* *
12626446 ATTTTATATTATATTATTATATTATAT
1 ATTTTAAATCATATTATTATATTATAT
12626473 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 1 0.04
29 6 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTTAAATCATATTATTATATTATATAT
Found at i:12626467 original size:13 final size:12
Alignment explanation
Indices: 12626429--12626474 Score: 69
Period size: 13 Copynumber: 3.9 Consensus size: 12
12626419 ATTTTAAATC
12626429 ATATTAT-TTTT
1 ATATTATATTTT
12626440 ATA-TATATTTT
1 ATATTATATTTT
12626451 ATATTATATTATT
1 ATATTATATT-TT
12626464 ATATTATATTT
1 ATATTATATTT
12626475 AAAAATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.09
11 10 0.31
12 7 0.22
13 12 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:12630968 original size:22 final size:22
Alignment explanation
Indices: 12630921--12630973 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
12630911 AATTTAAACG
*
12630921 AAAATTTTTCTCTAAACACTCT
1 AAAATTTTTCTCTAAACACTCC
12630943 AAAATTTTTCT-TGAATAC-CTCC
1 AAAATTTTTCTCT-AA-ACACTCC
12630965 AAAATTTTT
1 AAAATTTTT
12630974 TTCTGCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 1 0.04
22 25 0.89
23 2 0.07
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATTTTTCTCTAAACACTCC
Found at i:12632087 original size:142 final size:141
Alignment explanation
Indices: 12631929--12632208 Score: 357
Period size: 142 Copynumber: 2.0 Consensus size: 141
12631919 TTTTTAAAAA
* * * * *
12631929 AAAAACTCAGATCATGTTTAAATATTACTTT-ATGAGTTTTAATGCTTTGAAAATTTTGATTGCA
1 AAAAACTCAGATCATGTTTAAATATTA-TTTCATAAATTTTAATACATTGAAAATCTTGATTGCA
* *
12631993 CATTACAAA-AAGTGAAATTACTAAAATATCATTTAAGGGTATTTTCATAATTTGATCTTTTCGA
65 CATTA-AAATAAGTGAAATTACTAAAATACCATTTAAGGGTATTTTCATAATTTGACCTTTTCGA
12632057 AGTTATTTTTCAC
129 AGTTATTTTTCAC
*
12632070 AAAAACTACAGATCATGTTTAAATATTATTTCATAAATTTTGATACATTGAAAATCTTGATTGCA
1 AAAAACT-CAGATCATGTTTAAATATTATTTCATAAATTTTAATACATTGAAAATCTTGATTGCA
* * * * ** * * *
12632135 CCTTAAAATGAGTGAAATTACTAAAATGCCTTTTATTGGTATTTTCGTAATTTGGCCTTTTCGAG
65 CATTAAAATAAGTGAAATTACTAAAATACCATTTAAGGGTATTTTCATAATTTGACCTTTTCGAA
*
12632200 GTTGTTTTT
130 GTTATTTTT
12632209 TTATGAAAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
141 13 0.11
142 105 0.89
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (141 bp):
AAAAACTCAGATCATGTTTAAATATTATTTCATAAATTTTAATACATTGAAAATCTTGATTGCAC
ATTAAAATAAGTGAAATTACTAAAATACCATTTAAGGGTATTTTCATAATTTGACCTTTTCGAAG
TTATTTTTCAC
Found at i:12633072 original size:2 final size:2
Alignment explanation
Indices: 12633065--12633096 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12633055 GTGCTTGTCA
*
12633065 AT AT AT AT AC 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
12633097 TTGAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.