Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 139 of 199
Found at i:42071803 original size:9 final size:9
Alignment explanation
Indices: 42071789--42072231 Score: 141
Period size: 9 Copynumber: 52.3 Consensus size: 9
42071779 TTATGATCAA
42071789 TTATGTAAG
1 TTATGTAAG
42071798 TTATGT-A-
1 TTATGTAAG
* *
42071805 TTATGAAAA
1 TTATGTAAG
42071814 TTATGTAAG
1 TTATGTAAG
* * *
42071823 CTGTGT-AC
1 TTATGTAAG
42071831 TGTA--TAAG
1 T-TATGTAAG
42071839 TTATGTAAG
1 TTATGTAAG
* *
42071848 TTATGAAAA
1 TTATGTAAG
42071857 TTATGTAAG
1 TTATGTAAG
42071866 TTATGTAAG
1 TTATGTAAG
* *
42071875 TT-TTTTA-
1 TTATGTAAG
* *
42071882 TTATGAAAA
1 TTATGTAAG
* *
42071891 TTAAGTAAC
1 TTATGTAAG
42071900 TTATGT-A-
1 TTATGTAAG
* *
42071907 TTATGAAAA
1 TTATGTAAG
42071916 TTATGTAAG
1 TTATGTAAG
*
42071925 TTCA-AT-A-
1 TT-ATGTAAG
42071932 TTATGTAAG
1 TTATGTAAG
42071941 TTATGT-A-
1 TTATGTAAG
* * *
42071948 TTACGAAAA
1 TTATGTAAG
42071957 TTATGTAAG
1 TTATGTAAG
*
42071966 TTCA-AT-A-
1 TT-ATGTAAG
42071973 TTATGTAAG
1 TTATGTAAG
42071982 TTATGT-A-
1 TTATGTAAG
* *
42071989 TTATGAAAA
1 TTATGTAAG
42071998 TTATGTAAG
1 TTATGTAAG
*
42072007 TTGTGT-A-
1 TTATGTAAG
* *
42072014 TTGTATAAG
1 TTATGTAAG
*
42072023 TTATGTAGG
1 TTATGTAAG
* *
42072032 TTATGAAAA
1 TTATGTAAG
42072041 TTATGTAAG
1 TTATGTAAG
42072050 TTATGTAAG
1 TTATGTAAG
**
42072059 TTAT-T-TT
1 TTATGTAAG
42072066 TTATG-AA-
1 TTATGTAAG
*
42072073 -AAT-TAAG
1 TTATGTAAG
42072080 TTATGT-A-
1 TTATGTAAG
* *
42072087 TTATGAAAA
1 TTATGTAAG
42072096 TTATGTAAG
1 TTATGTAAG
*
42072105 TTCA-AT-A-
1 TT-ATGTAAG
42072112 TTATGTAAG
1 TTATGTAAG
42072121 TTATGT-A-
1 TTATGTAAG
* * *
42072128 CTATGAAAA
1 TTATGTAAG
42072137 TTATGTAAG
1 TTATGTAAG
**
42072146 TTATGTTTG
1 TTATGTAAG
* *
42072155 TTGTGT-AT
1 TTATGTAAG
42072163 TATATGTAAG
1 T-TATGTAAG
*
42072173 TTATGTATGTG
1 TTATGTA--AG
*
42072184 TATAATGAAAG
1 T-T-ATGTAAG
42072195 TTATGTAAG
1 TTATGTAAG
*
42072204 TTGTGT-A-
1 TTATGTAAG
*
42072211 TAATGTAAG
1 TTATGTAAG
42072220 TTATGTAAG
1 TTATGTAAG
42072229 TTA
1 TTA
42072232 AGTATAATTA
Statistics
Matches: 311, Mismatches: 77, Indels: 92
0.65 0.16 0.19
Matches are distributed among these distances:
6 7 0.02
7 55 0.18
8 34 0.11
9 200 0.64
10 6 0.02
11 4 0.01
12 1 0.00
13 4 0.01
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42071821 original size:25 final size:25
Alignment explanation
Indices: 42071761--42072106 Score: 215
Period size: 25 Copynumber: 13.5 Consensus size: 25
42071751 GTAAGTTGTG
** * *
42071761 AATTATGTAAGTGCTATATTATGATC
1 AATTATGTAAGTTATGTATTATGA-A
42071787 AATTATGTAAGTTATGTATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
* *
42071812 AATTATGTAAGCTGTGTACTGTAT--A
1 AATTATGTAAGTTATGTA-T-TATGAA
* * *
42071837 AGTTATGTAAGTTATGAAAATTATGTA
1 AATTATGTAAGTTATG--TATTATGAA
* * *
42071864 AGTTATGTAAGTTTTTTATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
* *
42071889 AATTAAGTAACTTATGTATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
* *
42071914 AATTATGTAAGTTCA-ATATTATGTA
1 AATTATGTAAGTT-ATGTATTATGAA
* * *
42071939 AGTTATGTATTACGAAAATTATGTAAGT-TCAA
1 AATTATGTA--A-G----TTATGT-ATTATGAA
*
42071971 TATTATGTAAGTTATGTATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
* *
42071996 AATTATGTAAGTTGTGTATTGT-ATA
1 AATTATGTAAGTTATGTATTATGA-A
* * * *
42072021 AGTTATGTAGGTTATGAAAATTATGTA
1 AATTATGTAAGTTATG--TATTATGAA
* * *
42072048 AGTTATGTAAGTTATTTTTTATG-A
1 AATTATGTAAGTTATGTATTATGAA
42072072 AA--AT-TAAGTTATGTATTATGAA
1 AATTATGTAAGTTATGTATTATGAA
42072094 AATTATGTAAGTT
1 AATTATGTAAGTT
42072107 CAATATTATG
Statistics
Matches: 247, Mismatches: 48, Indels: 51
0.71 0.14 0.15
Matches are distributed among these distances:
21 14 0.06
22 5 0.02
24 7 0.03
25 140 0.57
26 24 0.10
27 39 0.16
28 1 0.00
29 1 0.00
30 1 0.00
31 1 0.00
32 12 0.05
33 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.44
Consensus pattern (25 bp):
AATTATGTAAGTTATGTATTATGAA
Found at i:42071934 original size:16 final size:15
Alignment explanation
Indices: 42071915--42071984 Score: 60
Period size: 16 Copynumber: 4.9 Consensus size: 15
42071905 TATTATGAAA
42071915 ATTATGTAAGTTCAAT
1 ATTATGTAAGTT-AAT
42071931 ATTATGTAAGTT-AT
1 ATTATGTAAGTTAAT
* * *
42071945 -GTAT-TACG--AAA
1 ATTATGTAAGTTAAT
42071956 ATTATGTAAGTTCAAT
1 ATTATGTAAGTT-AAT
42071972 ATTATGTAAGTTA
1 ATTATGTAAGTTA
42071985 TGTATTATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
11 1 0.02
12 6 0.14
13 6 0.14
14 2 0.05
15 1 0.02
16 26 0.62
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (15 bp):
ATTATGTAAGTTAAT
Found at i:42071945 original size:41 final size:41
Alignment explanation
Indices: 42071890--42072051 Score: 234
Period size: 41 Copynumber: 3.9 Consensus size: 41
42071880 TATTATGAAA
* *
42071890 ATTAAGTAACTTATGTATTATGAAAATTATGTAAGTTCAAT
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
*
42071931 ATTATGTAAGTTATGTATTACGAAAATTATGTAAGTTCAAT
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
***
42071972 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
* *
42072013 ATTGTATAAGTTATGTAGGTTATGAAAATTATGTAAGTT
1 ATTATGTAAGTTATGTA--TTATGAAAATTATGTAAGTT
42072052 ATGTAAGTTA
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 90 0.82
43 20 0.18
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (41 bp):
ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
Found at i:42071990 original size:16 final size:16
Alignment explanation
Indices: 42071956--42072226 Score: 88
Period size: 16 Copynumber: 17.1 Consensus size: 16
42071946 TATTACGAAA
*
42071956 ATTATGTAAGTTCA-AT
1 ATTATGTAAGTT-ATGT
42071972 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
42071988 ATTATG-AA---A---
1 ATTATGTAAGTTATGT
*
42071997 ATTATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
* *
42072013 ATTGTATAAGTTATGT
1 ATTATGTAAGTTATGT
* *
42072029 AGGTTATGAAAATTATGT
1 A--TTATGTAAGTTATGT
*
42072047 AAGTTATGTAAGTTATTT
1 -A-TTATGTAAGTTATGT
* * * *
42072065 TTTATGAAAATTAAG-
1 ATTATGTAAGTTATGT
*
42072080 -TTATGT-A-TTATGAAA
1 ATTATGTAAGTTATG--T
*
42072095 ATTATGTAAGTTCA-AT
1 ATTATGTAAGTT-ATGT
42072111 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
* * *
42072127 ACTATGAAAATTATGT
1 ATTATGTAAGTTATGT
** *
42072143 AAGTTATGTTTGTTGTGT
1 -A-TTATGTAAGTTATGT
42072161 ATTATATGTAAGTTATGT
1 A-T-TATGTAAGTTATGT
* * *
42072179 A-TGTGT-A-TAATGAA
1 ATTATGTAAGTTATG-T
*
42072193 AGTTATGTAAGTTGTGT
1 A-TTATGTAAGTTATGT
*
42072210 ATAATGTAAGTTATGT
1 ATTATGTAAGTTATGT
42072226 A
1 A
42072227 AGTTAAGTAT
Statistics
Matches: 184, Mismatches: 44, Indels: 54
0.65 0.16 0.19
Matches are distributed among these distances:
9 6 0.03
10 2 0.01
12 5 0.03
13 5 0.03
14 7 0.04
15 8 0.04
16 93 0.51
17 6 0.03
18 50 0.27
19 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.45
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:42072081 original size:21 final size:21
Alignment explanation
Indices: 42072055--42072098 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
42072045 GTAAGTTATG
* *
42072055 TAAGTTATTTTTTATGAAAAT
1 TAAGTTATGTATTATGAAAAT
42072076 TAAGTTATGTATTATGAAAAT
1 TAAGTTATGTATTATGAAAAT
42072097 TA
1 TA
42072099 TGTAAGTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (21 bp):
TAAGTTATGTATTATGAAAAT
Found at i:42072176 original size:27 final size:24
Alignment explanation
Indices: 42072139--42072225 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 24
42072129 TATGAAAATT
42072139 ATGTAAGTTATGTTTGTTGTGTATTA
1 ATGTAAGTTATG-TTGTTGTGTA-TA
*
42072165 TATGTAAGTTATG-T-ATGTGTATA
1 -ATGTAAGTTATGTTGTTGTGTATA
* *
42072188 ATGAAAGTTATGTAAGTTGTGTATA
1 ATGTAAGTTATGT-TGTTGTGTATA
42072213 ATGTAAGTTATGT
1 ATGTAAGTTATGT
42072226 AAGTTAAGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
22 11 0.21
23 2 0.04
24 6 0.12
25 21 0.40
27 12 0.23
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (24 bp):
ATGTAAGTTATGTTGTTGTGTATA
Found at i:42072226 original size:25 final size:25
Alignment explanation
Indices: 42072180--42072243 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
42072170 AAGTTATGTA
*
42072180 TGTGTATAATGAAAGTTATGTAAGT
1 TGTGTATAATGTAAGTTATGTAAGT
42072205 TGTGTATAATGTAAGTTATGTAAGT
1 TGTGTATAATGTAAGTTATGTAAGT
**
42072230 TAAGTATAAT-TAAG
1 TGTGTATAATGTAAG
42072244 CTATTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 4 0.11
25 32 0.89
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (25 bp):
TGTGTATAATGTAAGTTATGTAAGT
Found at i:42072973 original size:17 final size:17
Alignment explanation
Indices: 42072951--42073012 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
42072941 TCAGATGTTT
42072951 ATATAAATACGCTGAAA
1 ATATAAATACGCTGAAA
** *
42072968 ATATAAATA-AATAATATA
1 ATATAAATACGCTGA-A-A
42072986 ATATTAAATACGCTGAAA
1 ATA-TAAATACGCTGAAA
42073004 ATATAAATA
1 ATATAAATA
42073013 AATAGTCCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
16 2 0.06
17 16 0.46
18 8 0.23
19 7 0.20
20 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
ATATAAATACGCTGAAA
Found at i:42072977 original size:21 final size:21
Alignment explanation
Indices: 42072953--42073016 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
42072943 AGATGTTTAT
42072953 ATAAATACGCTGAAAATATAA
1 ATAAATACGCTGAAAATATAA
* *
42072974 ATAAATA--AT-ATAATAT--
1 ATAAATACGCTGAAAATATAA
42072990 -TAAATACGCTGAAAATATAA
1 ATAAATACGCTGAAAATATAA
42073010 ATAAATA
1 ATAAATA
42073017 GTCCCAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
15 6 0.18
17 1 0.03
18 12 0.36
19 1 0.03
21 13 0.39
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (21 bp):
ATAAATACGCTGAAAATATAA
Found at i:42073458 original size:45 final size:43
Alignment explanation
Indices: 42073404--42073507 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 43
42073394 TGCAGAATCT
*
42073404 CATATGCTTAACATTCAAA-ATGTTTAACATTCAAAACATAGCTTAA
1 CATA-GCTTAACATTCAAACATGCTTAACATTC-AAA-AT-GCTTAA
* *
42073450 CATAGCTTACCATTCAAAGCTATGCTTAACATTCAAAATGTTTAA
1 CATAGCTTAACATTCAAA-C-ATGCTTAACATTCAAAATGCTTAA
42073495 CATAGCTTAACAT
1 CATAGCTTAACAT
42073508 AGTTTTCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
45 30 0.59
46 6 0.12
47 3 0.06
48 12 0.24
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (43 bp):
CATAGCTTAACATTCAAACATGCTTAACATTCAAAATGCTTAA
Found at i:42075122 original size:26 final size:25
Alignment explanation
Indices: 42075088--42075139 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
42075078 AGTGTATAAT
42075088 TTAAATA-TTATCAATATTCAAAATTA
1 TTAAATATTTAT-AATATTC-AAATTA
* *
42075114 TTAATTATTTATAGTATTCAAATTA
1 TTAAATATTTATAATATTCAAATTA
42075139 T
1 T
42075140 GTATTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (25 bp):
TTAAATATTTATAATATTCAAATTA
Found at i:42075553 original size:14 final size:15
Alignment explanation
Indices: 42075536--42075577 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
42075526 CCTAAACCCC
42075536 AAACCCCAAAC-CTT
1 AAACCCCAAACTCTT
*
42075550 AAACCTCAAACTCTT
1 AAACCCCAAACTCTT
*
42075565 AAACCCTAAACTC
1 AAACCCCAAACTC
42075578 AAAACTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (15 bp):
AAACCCCAAACTCTT
Found at i:42076330 original size:114 final size:114
Alignment explanation
Indices: 42076108--42076883 Score: 1216
Period size: 114 Copynumber: 6.8 Consensus size: 114
42076098 TACGGCGCTT
* * *
42076108 TGTGATTTAGCGGCATTTTT-TATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
1 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
*
42076172 ATTTTGGTTAAGATATTTTGCGGCG-TTTTGTATAATGCGCCGCTAATAC
66 GTTTTGGTTAAGATATTTTGCGGCGCTTTT-TATAATGCGCCGCTAATAC
* * *
42076221 TGTGCTTTAGCGGTGTTTTTCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAATGCTGC
1 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
* ** * *
42076286 ATTTTAATGAAGATATTTTGCGGCGCTTTTTATAATGCGTCGCTAATAC
66 GTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATAC
42076335 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
1 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
* * * * *
42076400 ATTTTGGTTAAGATATTTTGCGGCGTTTTTTACAATGCGCTGCTAATAT
66 GTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATAC
42076449 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
1 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
*
42076514 GTTTTGGTTAAGATATTTTGCGGCG-TTTTGTATAATGCGCCGCTAATAT
66 GTTTTGGTTAAGATATTTTGCGGCGCTTTT-TATAATGCGCCGCTAATAC
* * * *
42076563 TGTGCTTTAGCGGCATTTTTCCATAAGCGCCACTAATTCTAAGATACCTCAAGACCAAACTCTGC
1 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
*
42076628 GTTTTGGTTAAGATATTTTGCGGCGCCTTTTATAATGCGCCGCTAATAC
66 GTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATAC
* *
42076677 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACGTTGC
1 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
** *
42076742 GTTTTGGTTAAGATATTTTGCGGCATTTTTTACAATGCGCCGCTAATAC
66 GTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATAC
* * * *
42076791 TATGCTTTAGCGGCGTTCTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCTAATGCTGC
1 TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
*
42076856 GTTTTGGTTAAGATATTTTGTGGCGCTT
66 GTTTTGGTTAAGATATTTTGCGGCGCTT
42076884 GCAAATAAAC
Statistics
Matches: 612, Mismatches: 47, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
113 21 0.03
114 584 0.95
115 7 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (114 bp):
TGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGC
GTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATAC
Found at i:42087351 original size:11 final size:11
Alignment explanation
Indices: 42087335--42087359 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42087325 ATTTGGGAGT
42087335 AAAATGAGTGA
1 AAAATGAGTGA
42087346 AAAATGAGTGA
1 AAAATGAGTGA
42087357 AAA
1 AAA
42087360 TTAAAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (11 bp):
AAAATGAGTGA
Found at i:42088142 original size:13 final size:13
Alignment explanation
Indices: 42088124--42088148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42088114 TTGTTGTGTT
42088124 ATTTAGTTAATTA
1 ATTTAGTTAATTA
42088137 ATTTAGTTAATT
1 ATTTAGTTAATT
42088149 TTAGTTTTAA
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTAGTTAATTA
Found at i:42088421 original size:20 final size:20
Alignment explanation
Indices: 42088385--42088422 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42088375 AGCCCTTTTT
*
42088385 TATTTTTATTTTTATTTTAA
1 TATTTTTATTTTAATTTTAA
42088405 TATTTTT-TGTTTAATTTT
1 TATTTTTAT-TTTAATTTT
42088423 TACATTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (20 bp):
TATTTTTATTTTAATTTTAA
Found at i:42099130 original size:24 final size:23
Alignment explanation
Indices: 42099088--42099132 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
42099078 ATTTTTTTTA
*
42099088 TTTGGAATTTTTGTTGATGTTGT
1 TTTGGAATTTTTGTGGATGTTGT
*
42099111 TTTGGATTTATTTGTGGATGTT
1 TTTGGAATT-TTTGTGGATGTT
42099133 TTTGCATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (23 bp):
TTTGGAATTTTTGTGGATGTTGT
Found at i:42102772 original size:6 final size:6
Alignment explanation
Indices: 42102761--42102793 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
42102751 AATAATTATT
42102761 TATTTA TATTTA TATTTA TATTTA -ATTATA TAT
1 TATTTA TATTTA TATTTA TATTTA TATT-TA TAT
42102794 GTTTGAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 3 0.12
6 20 0.80
7 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:42102789 original size:16 final size:16
Alignment explanation
Indices: 42102743--42102791 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
42102733 TACTTTTTCA
*
42102743 TTATTTATAATAATTAT
1 TTATTTATAATTA-TAT
*
42102760 TTATTTATATTTATAT
1 TTATTTATAATTATAT
42102776 TTATATT-TAATTATAT
1 TTAT-TTATAATTATAT
42102792 ATGTTTGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTTATAATTATAT
Found at i:42103390 original size:45 final size:46
Alignment explanation
Indices: 42103341--42103438 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
42103331 AGATAGAAAC
*
42103341 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
42103386 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
42103432 GAAAATA
1 CAAAATA
42103439 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:42108097 original size:45 final size:46
Alignment explanation
Indices: 42108048--42108145 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
42108038 AAATAGAAAC
*
42108048 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
42108093 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
42108139 GAAAATA
1 CAAAATA
42108146 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:42112744 original size:15 final size:15
Alignment explanation
Indices: 42112720--42112751 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42112710 TATGCATGCA
*
42112720 AAATATAAAAGACAT
1 AAATACAAAAGACAT
42112735 AAATACAAAAGACAT
1 AAATACAAAAGACAT
42112750 AA
1 AA
42112752 TAGTGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:42113804 original size:28 final size:29
Alignment explanation
Indices: 42113768--42113836 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
42113758 GGGATAGGAG
* * *
42113768 GGGAATAAAAGTTAT-AGGGGAAGTGAGA
1 GGGAGTAAAAGTTATAAGGGAAAGTAAGA
*
42113796 GGGAGTAAAAGTTTTAAGGGAAAGTAAGA
1 GGGAGTAAAAGTTATAAGGGAAAGTAAGA
42113825 GGGAGTAAAAGT
1 GGGAGTAAAAGT
42113837 ATTGGGGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.19
Consensus pattern (29 bp):
GGGAGTAAAAGTTATAAGGGAAAGTAAGA
Found at i:42113849 original size:29 final size:28
Alignment explanation
Indices: 42113768--42113851 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 28
42113758 GGGATAGGAG
* *
42113768 GGGAATAAAAGT-TATAGGGGAAGTGAGA
1 GGGAGTAAAAGTAT-TAGGGGAAGTAAGA
* *
42113796 GGGAGTAAAAGTTTTAAGGGAAAGTAAGA
1 GGGAGTAAAAGTATT-AGGGGAAGTAAGA
*
42113825 GGGAGTAAAAGTATTGGGGGCAAGTAA
1 GGGAGTAAAAGTATTAGGGG-AAGTAA
42113852 AAAGGTTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
28 15 0.32
29 32 0.68
ACGTcount: A:0.42, C:0.01, G:0.38, T:0.19
Consensus pattern (28 bp):
GGGAGTAAAAGTATTAGGGGAAGTAAGA
Found at i:42113912 original size:18 final size:18
Alignment explanation
Indices: 42113889--42113925 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42113879 TATAGTTTGG
*
42113889 TATTTGATTTATTCGAAT
1 TATTTGAGTTATTCGAAT
42113907 TATTTGAGTTATTCGAAT
1 TATTTGAGTTATTCGAAT
42113925 T
1 T
42113926 TTAACATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TATTTGAGTTATTCGAAT
Found at i:42119108 original size:15 final size:15
Alignment explanation
Indices: 42119072--42119110 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
42119062 AGAAACTCTC
*
42119072 CCACTACAACGGATT
1 CCACTACGACGGATT
42119087 CCACTACGACGGATTT
1 CCACTACGACGGA-TT
42119103 CC-CTACGA
1 CCACTACGA
42119111 TGTTCATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (15 bp):
CCACTACGACGGATT
Found at i:42123481 original size:20 final size:18
Alignment explanation
Indices: 42123434--42123482 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
42123424 CAAGATAAAC
42123434 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
42123451 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
42123471 ATTAAATTAATA
1 ATTAAATTAATA
42123483 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:42134086 original size:18 final size:18
Alignment explanation
Indices: 42134065--42134109 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
42134055 ACCATTAGTA
*
42134065 GGCCCAATACCATCC-TTC
1 GGCCCAACACCA-CCATTC
42134083 GGCCCAACACCACCATTC
1 GGCCCAACACCACCATTC
*
42134101 AGCCCAACA
1 GGCCCAACA
42134110 GTGCCATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.29, C:0.47, G:0.11, T:0.13
Consensus pattern (18 bp):
GGCCCAACACCACCATTC
Found at i:42134295 original size:18 final size:18
Alignment explanation
Indices: 42134272--42134316 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
42134262 AGCAAGCCAC
* *
42134272 TTTTGACCATAATCATAA
1 TTTTGACCAGAAGCATAA
*
42134290 TTTTGACCAGAGGCATAA
1 TTTTGACCAGAAGCATAA
42134308 TTTTGACCA
1 TTTTGACCA
42134317 CTTTCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (18 bp):
TTTTGACCAGAAGCATAA
Found at i:42136321 original size:91 final size:91
Alignment explanation
Indices: 42136166--42136347 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
42136156 AACTCTTGGC
*
42136166 CTAGCGGTATTGGATGCTGATTCTAAAAACCCATGTCATTTGTTCAAATCGTAGGAGCAATTTTA
1 CTAGCGGTATTGGATGCTGATTCTAAAAACCCATATCATTTGTTCAAATCGTAGGAGCAATTTTA
42136231 TTTATGGTGTTTAAGTTGACAATTAT
66 TTTATGGTGTTTAAGTTGACAATTAT
* * * *
42136257 CTAGCGGTATTAGG-TGTTTATTCTAAAAACCCATATCATTTGTTCAGATCGTAGGAGCGATTTT
1 CTAGCGGTATT-GGATGCTGATTCTAAAAACCCATATCATTTGTTCAAATCGTAGGAGCAATTTT
*
42136321 ATTTATGGTGTTTAAGTTGATAATTAT
65 ATTTATGGTGTTTAAGTTGACAATTAT
42136348 TTGCAACTAT
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 82 0.98
92 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (91 bp):
CTAGCGGTATTGGATGCTGATTCTAAAAACCCATATCATTTGTTCAAATCGTAGGAGCAATTTTA
TTTATGGTGTTTAAGTTGACAATTAT
Found at i:42148454 original size:25 final size:25
Alignment explanation
Indices: 42148420--42148478 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
42148410 ACGTTTCAAG
42148420 AATGAGAGTTACAAAGCTAATAATT
1 AATGAGAGTTACAAAGCTAATAATT
*
42148445 AATGAGAGTTACAAAGCTAATAGTT
1 AATGAGAGTTACAAAGCTAATAATT
42148470 AATGAGAGT
1 AATGAGAGT
42148479 AATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (25 bp):
AATGAGAGTTACAAAGCTAATAATT
Found at i:42150159 original size:3 final size:3
Alignment explanation
Indices: 42150151--42150176 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42150141 TTTAGACAAA
42150151 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
42150177 CAAGTTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42152203 original size:1 final size:1
Alignment explanation
Indices: 42152199--42152227 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
42152189 GCTAAAAACT
42152199 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42152228 GTGATCACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:42154880 original size:36 final size:32
Alignment explanation
Indices: 42154815--42154891 Score: 82
Period size: 36 Copynumber: 2.3 Consensus size: 32
42154805 GTTGTACTTT
* *
42154815 TTACTGTTTTCTTGTTTTTTTTTATTATTTTG
1 TTACTATTTTCTTGTTTTTTTTTACTATTTTG
42154847 TTACTATTTTCTTGTTGTTGTTTTTTCACTATTTTG
1 TTACTATTTTCTTG-T-TT-TTTTTT-ACTATTTTG
* *
42154883 CTACCATTT
1 TTACTATTT
42154892 CACAATTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 13 0.35
33 1 0.03
34 2 0.05
35 6 0.16
36 15 0.41
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.68
Consensus pattern (32 bp):
TTACTATTTTCTTGTTTTTTTTTACTATTTTG
Found at i:42155845 original size:45 final size:45
Alignment explanation
Indices: 42155767--42156313 Score: 444
Period size: 45 Copynumber: 12.3 Consensus size: 45
42155757 ACTGATTTAA
* * * * *
42155767 ATAGCAAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* *
42155812 ATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* * *** * * * *
42155857 ATGGCATATCTTGTCTTCATGTATTGGCA-TGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* * *
42155901 ATAGCAGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* **** * * *
42155946 AAAGCAGATCTTGTCTTTATGTATTGGCA-TGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* ** * * *
42155990 AT-GACAGATCTTGTCTT--CAT-GTATTAGCATGAGGTAGATCAAAA
1 ATAG-CAGATCTTGTCTTCCCATACTGGTAGC--GAAGTAGATCGAAG
** * * *
42156034 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* * ** * *
42156079 ATAACATATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* * ** * * *
42156124 ATAACATATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
* *
42156169 ATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
** ** * * *
42156214 ATAATAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
**
42156259 ATAATAGATCTTGTCTTCCCATACTGGT-GCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
*
42156303 ATA-CAAATCTT
1 ATAGCAGATCTT
42156314 ATCCCCCTGA
Statistics
Matches: 408, Mismatches: 85, Indels: 20
0.80 0.17 0.04
Matches are distributed among these distances:
41 2 0.00
42 1 0.00
43 7 0.02
44 102 0.25
45 292 0.72
46 1 0.00
47 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAG
Found at i:42155931 original size:89 final size:90
Alignment explanation
Indices: 42155767--42156313 Score: 633
Period size: 90 Copynumber: 6.1 Consensus size: 90
42155757 ACTGATTTAA
* * * * * * *
42155767 ATAGCAAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATAGCAGATCTTGTCTTCCC
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
*
42155832 ATACTGGTGGCGAAATAGATCGAAG
66 ATACTGGTGGCGAAGTAGATCGAAG
* * *
42155857 ATGGCATATCTTGTCTTCATGTATTGGCA-TGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
* *
42155921 ATACTAGTGGCGAAGTAGATCAAAG
66 ATACTGGTGGCGAAGTAGATCGAAG
* ** *
42155946 AAAGCAGATCTTGTCTTTATGTATTGGCA-TGAAGTAGATCGAAGAT-GACAGATCTTGTCTT--
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAG-CAGATCTTGTCTTCC
* ** * * * *
42156007 CAT-GTATTAGCATGAGGTAGATCAAAA
65 CATACTGGTGGC--GAAGTAGATCGAAG
* * * *
42156034 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATAACATATCTTGTCTTCCT
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
* ** *
42156099 GTACTGGCAGTGAAGTAGATCGAAG
66 ATACTGGTGGCGAAGTAGATCGAAG
* * *
42156124 ATAACATATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
*
42156189 ATACTGGTGGTGAAGTAGATCGAAG
66 ATACTGGTGGCGAAGTAGATCGAAG
** * **
42156214 ATAATAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCCC
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
42156279 ATACTGGT-GCGAAGTAGATCGAAG
66 ATACTGGTGGCGAAGTAGATCGAAG
*
42156303 ATA-CAAATCTT
1 ATAGCAGATCTT
42156314 ATCCCCCTGA
Statistics
Matches: 395, Mismatches: 54, Indels: 18
0.85 0.12 0.04
Matches are distributed among these distances:
86 5 0.01
87 3 0.01
88 45 0.11
89 155 0.39
90 183 0.46
91 1 0.00
92 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (90 bp):
ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCC
ATACTGGTGGCGAAGTAGATCGAAG
Found at i:42157806 original size:3 final size:3
Alignment explanation
Indices: 42157800--42157846 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
42157790 TATTGTATCC
*
42157800 TTA TTA TTA -TA TTA TCTA TTA -TA TTTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
42157845 TT
1 TT
42157847 TCTATATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 29 0.76
4 5 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:42160335 original size:18 final size:17
Alignment explanation
Indices: 42160314--42160348 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42160304 TTATTATTAA
*
42160314 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42160332 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42160349 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42165756 original size:2 final size:2
Alignment explanation
Indices: 42165746--42165780 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
42165736 CATACCACAC
42165746 AT AT A- 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 AT AT
42165781 CAACTCATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42167083 original size:328 final size:328
Alignment explanation
Indices: 42166484--42167138 Score: 1166
Period size: 328 Copynumber: 2.0 Consensus size: 328
42166474 AAAAAAATAA
**
42166484 TTTCATAACCAGCAAGAAATGAAATGCCGATTTACCAAGAACTGAAACAATCGCATGAAAAACTA
1 TTTCATAACCAGCAAGAAATGAAATGCCGATTTACCAAGAACTGAAACAATCGCACAAAAAACTA
*
42166549 ATCGTATTTAAAAAAAAATTGCAATAACACCCATTAAAAATGCATGCAGAGAGGAAATAAATAGA
66 ATCGTATTTAAAAAAAAATTGCAATAACACCCATTAAAAATGCATGCAGAGAGGAAAGAAATAGA
* * * *
42166614 GATTACTTACAGGCGGAGATAACTCACTTGCCACTTCAATGCGTTCGGAGATCTGAGACCGTGGA
131 GATCACTCACAGGCAGAGATAACTCACTTGCCACTTCAATGCGTCCGGAGATCTGAGACCGTGGA
* * *
42166679 GTCGGTGAAAGATGCAAAGATGAAAGTTGGGAGCGGCTGGAGGTTTGGTTCGTTGGCAGCTTCCG
196 GTCGGCGAAAGATGCAAAGATGAAAGTCGGGAGCGGCTGGAGGTTTGGTTCGCTGGCAGCTTCCG
*
42166744 TTGATGTTGGGAGGGAGAGGGTGGGGTGGAGATCGATTTCGGCAAGGGGAGGGTAAAACAGAGAC
261 TTGACGTTGGGAGGGAGAGGGTGGGGTGGAGATCGATTTCGGCAAGGGGAGGGTAAAACAGAGAC
42166809 CGG
326 CGG
42166812 TTTCATAACCAGCAAGAAATGAAATGCCGATTTACCAAGAACTGAAACAATCGCACAAAAAACTA
1 TTTCATAACCAGCAAGAAATGAAATGCCGATTTACCAAGAACTGAAACAATCGCACAAAAAACTA
* *
42166877 ATCGTATTTATAAAAAAATTGCAATAACACCTATTAAAAATGCATGCAGAGAGGAAAGAAATAGA
66 ATCGTATTTAAAAAAAAATTGCAATAACACCCATTAAAAATGCATGCAGAGAGGAAAGAAATAGA
*
42166942 GATCACTCACAGGCAGAGATAACTCACTTGCCGCTTCAATGCGTCCGGAGATCTGAGACCGTGGA
131 GATCACTCACAGGCAGAGATAACTCACTTGCCACTTCAATGCGTCCGGAGATCTGAGACCGTGGA
*
42167007 GTCGGCGAAAGATGCAAAGATGAAAGTCGGGAGCGGCTGGAGGTTTGGTTCGCTGGCAGCTTCTG
196 GTCGGCGAAAGATGCAAAGATGAAAGTCGGGAGCGGCTGGAGGTTTGGTTCGCTGGCAGCTTCCG
*
42167072 TTGACGTTGGGAGGGAGAGGGTGGGGTGGGGATCGATTTCGGCAAGGGGAGGGTAAAACAGAGAC
261 TTGACGTTGGGAGGGAGAGGGTGGGGTGGAGATCGATTTCGGCAAGGGGAGGGTAAAACAGAGAC
42167137 CG
326 CG
42167139 ATTACCTAAT
Statistics
Matches: 311, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
328 311 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (328 bp):
TTTCATAACCAGCAAGAAATGAAATGCCGATTTACCAAGAACTGAAACAATCGCACAAAAAACTA
ATCGTATTTAAAAAAAAATTGCAATAACACCCATTAAAAATGCATGCAGAGAGGAAAGAAATAGA
GATCACTCACAGGCAGAGATAACTCACTTGCCACTTCAATGCGTCCGGAGATCTGAGACCGTGGA
GTCGGCGAAAGATGCAAAGATGAAAGTCGGGAGCGGCTGGAGGTTTGGTTCGCTGGCAGCTTCCG
TTGACGTTGGGAGGGAGAGGGTGGGGTGGAGATCGATTTCGGCAAGGGGAGGGTAAAACAGAGAC
CGG
Found at i:42167836 original size:41 final size:37
Alignment explanation
Indices: 42167763--42167842 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
42167753 TATTTAATGC
* *
42167763 AATAAAATATTTATTATATTTATTTGTTTTTTAATAT
1 AATAAAACAATTATTATATTTATTTGTTTTTTAATAT
42167800 AATAAAACAATTATTATATTTATTTTAGTGTTTTTTAATAT
1 AATAAAACAATTATTATATTTA--TT--TGTTTTTTAATAT
42167841 AA
1 AA
42167843 ATACTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 20 0.54
39 2 0.05
41 15 0.41
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (37 bp):
AATAAAACAATTATTATATTTATTTGTTTTTTAATAT
Found at i:42170137 original size:156 final size:156
Alignment explanation
Indices: 42169938--42170388 Score: 708
Period size: 156 Copynumber: 2.9 Consensus size: 156
42169928 GTAGGATTGG
* * *
42169938 TTTCAAATGGTTGCAGTTAA-GGGGTTACTTGTACAGGCTCTTGGTTAATGGGCACTACCTACTC
1 TTTCAAATGGTTGAAG-TAAGGGGGTTACTTCTATAGGCTCTTGGTTAATGGGCACTACCTACTC
*
42170002 TAAATATTCATATAGAGGCTCTAATTCAAAGTTTTAAAGTTTATTCAATTCAGTCTAGTTTTCAT
65 TAAATATTCATATAGAGGCTCTAATTCAAAGTTTTAAAGTTTATTCGATTCAGTCTAGTTTTCAT
42170067 GATTTAGTCTAGTTTTAAAATTAAAAT
130 GATTTAGTCTAGTTTTAAAATTAAAAT
42170094 TTTCAAATGGTTGAAGTAAGGGGGTTACTTCTATAGGCTCTTGGTTAATGGGCACTACCTACTCT
1 TTTCAAATGGTTGAAGTAAGGGGGTTACTTCTATAGGCTCTTGGTTAATGGGCACTACCTACTCT
42170159 AAATATTCATATAGAGGCTCTAATTCAAAGTTTTAAAGTTTATTCGATTCAGTCTAGTTTTCATG
66 AAATATTCATATAGAGGCTCTAATTCAAAGTTTTAAAGTTTATTCGATTCAGTCTAGTTTTCATG
42170224 ATTTAGTCTAGTTTTAAAATTAAAAT
131 ATTTAGTCTAGTTTTAAAATTAAAAT
** *
42170250 TTTCAAATGGTTGAAGTAAGGGGGTTACTTCTATAGGCTCTTGGTTAGCGGGCATCT-CATACTC
1 TTTCAAATGGTTGAAGTAAGGGGGTTACTTCTATAGGCTCTTGGTTAATGGGCA-CTACCTACTC
* * ** * * * * * * *
42170314 CAAATTTTCACCTAGAGGCTCCAATTCTAAGTTTTGAAGTTTATTCGATTTAGTCTAATTTTTAC
65 TAAATATTCATATAGAGGCTCTAATTCAAAGTTTTAAAGTTTATTCGATTCAGTCTAGTTTTCAT
42170379 GATTTAGTCT
130 GATTTAGTCT
42170389 CTGTACCAAA
Statistics
Matches: 275, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
155 3 0.01
156 270 0.98
157 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (156 bp):
TTTCAAATGGTTGAAGTAAGGGGGTTACTTCTATAGGCTCTTGGTTAATGGGCACTACCTACTCT
AAATATTCATATAGAGGCTCTAATTCAAAGTTTTAAAGTTTATTCGATTCAGTCTAGTTTTCATG
ATTTAGTCTAGTTTTAAAATTAAAAT
Found at i:42176196 original size:30 final size:30
Alignment explanation
Indices: 42176162--42176222 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
42176152 CATGGACTGG
* *
42176162 CACATGGGCATGTGTCTAGCCTGTGTGGCT
1 CACATGGGCATGTGTCCAGCCCGTGTGGCT
*
42176192 CACATGGGCGTGTGTCCAGCCCGTGTGGCT
1 CACATGGGCATGTGTCCAGCCCGTGTGGCT
42176222 C
1 C
42176223 CTGAAATCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.11, C:0.28, G:0.34, T:0.26
Consensus pattern (30 bp):
CACATGGGCATGTGTCCAGCCCGTGTGGCT
Found at i:42178011 original size:43 final size:44
Alignment explanation
Indices: 42177918--42178015 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 44
42177908 AGTGTTTATT
* * * ** *
42177918 TCCACAAACGCCGCTAAAGGACATGAACTTTAGCGCCGCTTTAC
1 TCCAAAAACGCCGCTAAAGAACATAAACTTTAAAGACGCTTTAC
* *
42177962 -CTAAAAACGCTGCTAAAGAACATAAACTTTAAAGACGCTTT-C
1 TCCAAAAACGCCGCTAAAGAACATAAACTTTAAAGACGCTTTAC
42178004 TCCAAAAACGCC
1 TCCAAAAACGCC
42178016 AATAAAGAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (44 bp):
TCCAAAAACGCCGCTAAAGAACATAAACTTTAAAGACGCTTTAC
Found at i:42188836 original size:44 final size:45
Alignment explanation
Indices: 42188716--42189243 Score: 359
Period size: 44 Copynumber: 12.1 Consensus size: 45
42188706 TGTTATCCTT
* * * * *
42188716 GATCTACTTTCTTCGATCTACTTCG-CAACCAGTATGGGAAGATAA
1 GATCTGCTATCTTCGATCTACTTCGAC-ACCAATATAGGAAGACAA
* * * * *
42188761 GATCTGC-ATCTTCGGTCCACTGCG-CTACCAATGTAGGAAGACAG
1 GATCTGCTATCTTCGATCTACTTCGAC-ACCAATATAGGAAGACAA
* ** * *
42188805 GATTTGCTATCTTCGATCTACTTC-ATTCCAATACAAGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCGACACCAATATAGGAAGACAA
* * * * *
42188849 GATCTGTTTTCTTCAATCTACTTC-ACCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCGA-CACCAATATAGGAAGACAA
* * * *
42188894 GACCTTCATAT-TT-GATCCACTTCG-CTACCAATATAGGAAGACAG
1 GATCTGC-TATCTTCGATCTACTTCGAC-ACCAATATAGGAAGACAA
* * * *
42188938 GATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGAGAA
1 GATCTGCTATCTTCGATCTACTTCGACACCAATATAGGAAGACAA
* * * *
42188982 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCGACACCAATATAGGAAGACAA
* * *
42189027 GATCTAC-ATCTTCGATCTACTTCG-CTACCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCGAC-ACCAATATAGGAAGACAA
* * *
42189071 GATCTGCTATC-T---TC-A---CG---CTAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCGACACCAATATAGGAAGACAA
* * * * * *
42189105 GATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCGACACCAATATAGGAAGACAA
* *
42189150 GATCTGC-ATCTTCGATCCACTTCG-CTACCAATATAGGAAGACAG
1 GATCTGCTATCTTCGATCTACTTCGAC-ACCAATATAGGAAGACAA
* * ** *
42189194 GATCTGTTATCTTCGATCTACTTC-ACGCCAATGCATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCGACACCAATATAGGAAGACAA
42189238 GATCTG
1 GATCTG
42189244 TTGTTTTTTA
Statistics
Matches: 368, Mismatches: 89, Indels: 53
0.72 0.17 0.10
Matches are distributed among these distances:
34 21 0.06
35 1 0.00
37 2 0.01
38 2 0.01
39 1 0.00
40 1 0.00
41 2 0.01
42 2 0.01
43 6 0.02
44 224 0.61
45 104 0.28
46 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
GATCTGCTATCTTCGATCTACTTCGACACCAATATAGGAAGACAA
Found at i:42188954 original size:133 final size:133
Alignment explanation
Indices: 42188716--42189243 Score: 752
Period size: 133 Copynumber: 4.0 Consensus size: 133
42188706 TGTTATCCTT
* * * * *
42188716 GATCTACTTTCTTCGATCTACTTCGCAACCAGTATGGGAAGATAAGATCTGCATCTTCGGTCCAC
1 GATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
* * * ** *
42188781 TGCGCTACCAATGTAGGAAGACAGGATTTGCTATCTTCGATCTACTTCATTCCAATACAAGAAGA
66 TTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
42188846 CAA
131 CAA
* * * * * *
42188849 GATCTGTTTTCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGACCTTCATATTTGATCCAC
1 GATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
42188914 TTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
66 TTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
*
42188979 GAA
131 CAA
* * *
42188982 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACATCTTCGATCTAC
1 GATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
* *
42189047 TTCGCTACCAATATAGGAAGATAGGATCTG----C-T--A--T-CTTCACGCTAATACATGAAGA
66 TTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
42189102 CAA
131 CAA
*
42189105 GATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
1 GATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
* *
42189170 TTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATGCATGAAGA
66 TTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
42189235 CAA
131 CAA
42189238 GATCTG
1 GATCTG
42189244 TTGTTTTTTA
Statistics
Matches: 348, Mismatches: 37, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
123 112 0.32
124 1 0.00
126 1 0.00
127 1 0.00
128 2 0.01
129 1 0.00
130 1 0.00
132 1 0.00
133 228 0.66
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (133 bp):
GATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
TTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
CAA
Found at i:42189129 original size:79 final size:77
Alignment explanation
Indices: 42189019--42189162 Score: 207
Period size: 79 Copynumber: 1.8 Consensus size: 77
42189009 ACCAGTATGG
* * * *
42189019 GAAGACAAGATCTACATCTTCGATCTACTTCGCTACCAATATAGGAAGATAGGATCTGCTATCTT
1 GAAGACAAGATCTACATCTTCAATCTACTTCGCCACCAATATAGGAAGACAAGATCTGC-ATCTT
42189084 CACGCTAATACAT
65 CACGCTAATACAT
* * *
42189097 GAAGACAAGATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTAC-ATCTTCAATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCATCTT
42189162 C
65 C
42189163 GATCCACTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 21 0.36
79 37 0.64
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (77 bp):
GAAGACAAGATCTACATCTTCAATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCATCTTC
ACGCTAATACAT
Found at i:42189132 original size:123 final size:123
Alignment explanation
Indices: 42188958--42189207 Score: 428
Period size: 123 Copynumber: 2.0 Consensus size: 123
42188948 CTTCGATCTA
* * *
42188958 CTTCACGCCAATACATGAAGAGAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAG
1 CTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAG
* *
42189023 ACAAGATCTACATCTTCGATCTACTTCGCTACCAATATAGGAAGATAGGATCTGCTAT
66 ACAAGATCTACATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTAT
*
42189081 CTTCACGCTAATACATGAAGACAAGATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAG
1 CTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAG
* *
42189146 ACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTAT
66 ACAAGATCTACATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTAT
42189204 CTTC
1 CTTC
42189208 GATCTACTTC
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (123 bp):
CTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAG
ACAAGATCTACATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTAT
Found at i:42189188 original size:256 final size:262
Alignment explanation
Indices: 42188716--42189243 Score: 780
Period size: 256 Copynumber: 2.0 Consensus size: 262
42188706 TGTTATCCTT
* * * *
42188716 GATCTACTTTCTTCGATCTACTTCGCAACCAGTATGGGAAGATAAGATCTGCATCTTCGGTCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCAACCAGTATGGGAAGACAAGATCTACATCTTCGATCCAC
* * *
42188781 TGCGCTACCAATGTAGGAAGACAGGATTTGCTATCTTCGATCTACTTCATTCCAATACAAGAAGA
66 TGCGCTACCAATATAGGAAGACAGGATCTGCTATCTT--ATCTACTGCA-T-CAATACAAGAAGA
** * *
42188846 CAAGATCTGTTTTCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGACCTTCATATTTGATC
127 CAAGATCTACTTTCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGACCTGCATATTCGATC
42188911 CACTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGA
192 CACTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGA
*
42188976 AGAGAA
257 AGACAA
* *
42188982 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACATCTTCGATCTAC
1 GATCTGCTTTCTTCGATCTACTTCGCAACCAGTATGGGAAGACAAGATCTACATCTTCGATCCAC
* * *
42189047 TTCGCTACCAATATAGGAAGATAGGATCTGCTATC-T-TC-AC-GC-T-AATACATGAAGACAAG
66 TGCGCTACCAATATAGGAAGACAGGATCTGCTATCTTATCTACTGCATCAATACAAGAAGACAAG
* * *
42189106 ATCTACTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACT
131 ATCTACTTTCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGACCTGCATATTCGATCCACT
* *
42189171 TCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATGCATGAAGAC
196 TCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
42189236 AA
261 AA
42189238 GATCTG
1 GATCTG
42189244 TTGTTTTTTA
Statistics
Matches: 240, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
256 143 0.60
258 1 0.00
260 1 0.00
261 2 0.01
262 2 0.01
265 1 0.00
266 90 0.38
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (262 bp):
GATCTGCTTTCTTCGATCTACTTCGCAACCAGTATGGGAAGACAAGATCTACATCTTCGATCCAC
TGCGCTACCAATATAGGAAGACAGGATCTGCTATCTTATCTACTGCATCAATACAAGAAGACAAG
ATCTACTTTCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGACCTGCATATTCGATCCACT
TCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
AA
Found at i:42189441 original size:3 final size:3
Alignment explanation
Indices: 42189433--42189470 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42189423 TGTAGAATGC
42189433 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42189471 TGTCCTACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42189979 original size:26 final size:27
Alignment explanation
Indices: 42189941--42189993 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
42189931 GCAAGTGTCT
42189941 TGAAAAGAAAAAGATATT-CAAGAACAA
1 TGAAAAGAAAAAG-TATTACAAGAACAA
*
42189968 TGAAAA-ATAAAGTATTACAAGAACAA
1 TGAAAAGAAAAAGTATTACAAGAACAA
42189994 AAAAATTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 14 0.58
27 6 0.25
ACGTcount: A:0.62, C:0.08, G:0.13, T:0.17
Consensus pattern (27 bp):
TGAAAAGAAAAAGTATTACAAGAACAA
Found at i:42189998 original size:25 final size:26
Alignment explanation
Indices: 42189950--42189998 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
42189940 TTGAAAAGAA
*
42189950 AAAGATATTCAAGAACAATGAAAAAT
1 AAAGATATTCAAGAACAATAAAAAAT
42189976 AAAG-TATTACAAGAACAA-AAAAA
1 AAAGATATT-CAAGAACAATAAAAA
42189999 TTCTGTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.16
Consensus pattern (26 bp):
AAAGATATTCAAGAACAATAAAAAAT
Found at i:42206323 original size:11 final size:11
Alignment explanation
Indices: 42206307--42206346 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
42206297 TTGGCTCATT
42206307 AAAAATATATA
1 AAAAATATATA
42206318 AAAAATATATA
1 AAAAATATATA
* *
42206329 AAAATTGAAATA
1 AAAAAT-ATATA
42206341 AAAAAT
1 AAAAAT
42206347 TGGGAAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (11 bp):
AAAAATATATA
Found at i:42208293 original size:10 final size:10
Alignment explanation
Indices: 42208278--42208308 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
42208268 ATTAAAATAG
42208278 TTTTATATTT
1 TTTTATATTT
42208288 TTTTATATTT
1 TTTTATATTT
42208298 TTTTATCATTT
1 TTTTAT-ATTT
42208309 ACATTTTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTATATTT
Found at i:42209762 original size:24 final size:24
Alignment explanation
Indices: 42209724--42209975 Score: 132
Period size: 24 Copynumber: 10.8 Consensus size: 24
42209714 TGAATTGGAT
* *
42209724 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
42209749 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
42209773 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
42209793 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * * *
42209818 AATCCAAAATATTAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
42209842 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
42209863 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** ** *
42209887 AATTTAAAATAATGTTA-ACAATG
1 AATTTAAAATAATAATATATGATA
42209910 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* * * *
42209933 AATTAAAAATAGTAAAACATGATA
1 AATTTAAAATAATAATATATGATA
*
42209957 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
42209976 CAATACACTT
Statistics
Matches: 168, Mismatches: 43, Indels: 33
0.69 0.18 0.14
Matches are distributed among these distances:
20 5 0.03
21 13 0.08
22 15 0.09
23 50 0.30
24 73 0.43
25 12 0.07
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:42209820 original size:69 final size:69
Alignment explanation
Indices: 42209746--42210007 Score: 185
Period size: 69 Copynumber: 3.8 Consensus size: 69
42209736 ATAATATATA
* * *
42209746 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TGA-AATAGAT
*
42209807 CATACGTG
63 -ATACATG
** * * *
42209815 ATAAATCCAAAATATTAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
42209880 CATG
66 CATG
** * * * * **
42209884 ATAAATTTAAAATAATGTTA-ACAATGAATTTAAAATAATAATATTGATAAATTAAAAATAG-TA
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGATAAATTTGAAATAGAT-
*
42209947 AAACATG
63 ATACATG
* * * * * *
42209954 ATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAAATT
1 ATAAATTTAAAATAATAATACATAATAAATTTA-AAAATATTAATGA-TAAATT
42210008 AATAATAATA
Statistics
Matches: 153, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
68 9 0.06
69 66 0.43
70 63 0.41
71 15 0.10
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
CATG
Found at i:42209992 original size:70 final size:68
Alignment explanation
Indices: 42209813--42210018 Score: 184
Period size: 70 Copynumber: 3.0 Consensus size: 68
42209803 TAATCATACG
* * * * * **
42209813 TGATAAATCCAAAATATTAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATA
1 TGATAAATCTAAAATAATAATATACAAT-AATTTAATAATATTAATGATAAATTAAAAATAGATA
*
42209878 TACA
65 AACA
* ** * *
42209882 TGATAAATTTAAAATAATGTTA-ACAATGAATTTAAAATAATAATATTGATAAATTAAAAATAG-
1 TGATAAATCTAAAATAATAATATACAAT-AATTT--AATAATATTAATGATAAATTAAAAATAGA
42209945 TAAAACA
63 T-AAACA
* *
42209952 TGATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAAATTAATAATA-A
1 TGATAAATCTAAAATAATAATATACAATA-ATTTA-ATAATATTAATGA-TAAATTAAAAATAGA
42210016 TAA
63 TAA
42210019 GTATAAACAT
Statistics
Matches: 109, Mismatches: 20, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
68 9 0.08
69 19 0.17
70 60 0.55
71 21 0.19
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (68 bp):
TGATAAATCTAAAATAATAATATACAATAATTTAATAATATTAATGATAAATTAAAAATAGATAA
ACA
Found at i:42210832 original size:22 final size:21
Alignment explanation
Indices: 42210807--42210855 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
42210797 TACAAATTAA
42210807 ATCTATAAGATTACAAAATCTT
1 ATCTATAAGATTAC-AAATCTT
* * *
42210829 ATCTTCTAAGATTGCATATCTT
1 ATC-TATAAGATTACAAATCTT
42210851 ATCTA
1 ATCTA
42210856 AGATTGCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (21 bp):
ATCTATAAGATTACAAATCTT
Found at i:42211553 original size:22 final size:21
Alignment explanation
Indices: 42211530--42211589 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
42211520 TTCCATTCAT
*
42211530 TTTTTTATTTTTTAAATTATA
1 TTTTTTATTTTTTGAATTATA
42211551 TTTTTTATTTTTATGAA-TATA
1 TTTTTTATTTTT-TGAATTATA
*
42211572 ATTTTTATTTTTTGAATT
1 TTTTTTATTTTTTGAATT
42211590 TAAAAATTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 28 0.80
22 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTTATTTTTTGAATTATA
Found at i:42214427 original size:24 final size:25
Alignment explanation
Indices: 42214387--42214444 Score: 91
Period size: 24 Copynumber: 2.3 Consensus size: 25
42214377 CTGTTGTTGA
42214387 ATTTTTCAATTGAAAATGGTTTCTGT
1 ATTTTTC-ATTGAAAATGGTTTCTGT
42214413 ATTTTTC-TTGAAAATGGTTTCTGT
1 ATTTTTCATTGAAAATGGTTTCTGT
*
42214437 AGTTTTCA
1 ATTTTTCA
42214445 ATTTGTGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 23 0.77
26 7 0.23
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.52
Consensus pattern (25 bp):
ATTTTTCATTGAAAATGGTTTCTGT
Found at i:42215503 original size:66 final size:66
Alignment explanation
Indices: 42215397--42215527 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
42215387 CAAAAGGTTT
42215397 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAATATAATTTGAACCCAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAATATAATTTGAACCCAAAT
42215462 G
66 G
* *
42215463 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCGAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAATATAATTTGAACCCAAAT
42215528 CACATTTGAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (66 bp):
TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAATATAATTTGAACCCAAAT
G
Found at i:42215867 original size:26 final size:26
Alignment explanation
Indices: 42215838--42215989 Score: 88
Period size: 26 Copynumber: 6.0 Consensus size: 26
42215828 TATATTTTTA
42215838 TTAAATTATATTTAATAATTATTATT
1 TTAAATTATATTTAATAATTATTATT
*
42215864 TTAAATTATATTT--T-A-TAGTATT
1 TTAAATTATATTTAATAATTATTATT
* * * * *
42215886 ATATATTATGATTTTAGTAAAT-TTATA
1 TTAAATTAT-A-TTTAATAATTATTATT
* * *
42215913 TAAGAATATTTACTATTAAGAATT-TTA--
1 TTA-AAT-TATA-T-TTAATAATTATTATT
*
42215940 TTAAATTATATTTAATAATAATTATT
1 TTAAATTATATTTAATAATTATTATT
*
42215966 TTAAATTATATTTTAT-ATTATTAT
1 TTAAATTATATTTAATAATTATTAT
42215990 ATATTATGAT
Statistics
Matches: 95, Mismatches: 19, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
22 13 0.14
23 9 0.09
24 8 0.08
25 10 0.11
26 32 0.34
27 7 0.07
28 5 0.05
29 11 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (26 bp):
TTAAATTATATTTAATAATTATTATT
Found at i:42215946 original size:102 final size:102
Alignment explanation
Indices: 42215833--42216051 Score: 377
Period size: 102 Copynumber: 2.2 Consensus size: 102
42215823 AATTATATAT
*
42215833 TTTTATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
* *
42215898 TTTAGTAAATTTATATAAGAATATTTACTATTAAGAA
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
42215935 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATATTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
*
42216000 TTTAGTTAATTCATATAAGAATATTTAATATTAAGAA
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
42216037 TTTTA-CAAATTATAT
1 TTTTATTAAATTATAT
42216052 ATTTTTATTA
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 9 0.08
102 102 0.92
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (102 bp):
TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
TTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
Found at i:42217244 original size:14 final size:14
Alignment explanation
Indices: 42217234--42217272 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42217224 TTTTTATTTC
42217234 TTTTATATTATTAA
1 TTTTATATTATTAA
*
42217248 TTTTATTTTATTAA
1 TTTTATATTATTAA
*
42217262 TTAT-TATTATT
1 TTTTATATTATT
42217273 GTTATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATATTATTAA
Found at i:42217245 original size:3 final size:3
Alignment explanation
Indices: 42217239--42217287 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
42217229 ATTTCTTTTA
*
42217239 TAT TAT TAAT T-T TAT T-T TAT TAAT TAT TAT TAT TGT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
42217284 TAT T
1 TAT T
42217288 TCAATGCATG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42221499 original size:729 final size:729
Alignment explanation
Indices: 42220102--42221558 Score: 2761
Period size: 729 Copynumber: 2.0 Consensus size: 729
42220092 GGATGACATC
*
42220102 TCGTAGGAGAAATGGATGATAATTTTTCAGAGTTTGCAAGAGGAGGATATCGAGTGGAGAGCTTC
1 TCGTAGGAGAAATGGATGATAATTTTTCAGAGTTTGCAAGAGGAGGATATCAAGTGGAGAGCTTC
42220167 GTGGTTGCTTCCAGATGAGATCCTATATCGGTGCGGGGATTTTGACTGGGTTCCTTTACTCAAAA
66 GTGGTTGCTTCCAGATGAGATCCTATATCGGTGCGGGGATTTTGACTGGGTTCCTTTACTCAAAA
42220232 TTTGGGGAGCTGTTGGTTATGCCCCATTGCTAGTGTTAAGGCAATACAGGTCAAGGTAGTTTGTG
131 TTTGGGGAGCTGTTGGTTATGCCCCATTGCTAGTGTTAAGGCAATACAGGTCAAGGTAGTTTGTG
42220297 CCTGCAACTCAGGGACTGGCTGAGTGTGAATTCTCGTATAAAGATGATGGTTATAAAAAGAAGGC
196 CCTGCAACTCAGGGACTGGCTGAGTGTGAATTCTCGTATAAAGATGATGGTTATAAAAAGAAGGC
*
42220362 TCGTGAGATGGCCAATTCATGGAATTAGACTCACCGAATGAAGAGATTAGCTGTGGGCCCAATGA
261 TCGTGAGATGGCCAATTCATGGAATCAGACTCACCGAATGAAGAGATTAGCTGTGGGCCCAATGA
*
42220427 CAACTCCCGAGTATAACGAATGGTGGGTTAGAAGGATTAATGACAATACTCCTAGGCCAAATTTA
326 CAACTCCAGAGTATAACGAATGGTGGGTTAGAAGGATTAATGACAATACTCCTAGGCCAAATTTA
*
42220492 GAAAGTAGTCAGTCGATGGAGGAGCATTTGCGAGTCGTCCCTTCTGAGTTGGAAATCATAAAGCA
391 GAAAGTAGTCAGTCGATGGAGAAGCATTTGCGAGTCGTCCCTTCTGAGTTGGAAATCATAAAGCA
42220557 GGACTTTGAAAGAAGAAATGCAGAATTAGAGAAGAAAATAGAGCAAATAGAGGAAGAAAAAGTGA
456 GGACTTTGAAAGAAGAAATGCAGAATTAGAGAAGAAAATAGAGCAAATAGAGGAAGAAAAAGTGA
*
42220622 ATTTGAGACTGGATGTGGATGTTCAGAAGCTCGAGGCTGATAAACTAAGGAAGGGAAAGAATAAG
521 ATTTGAGACTAGATGTGGATGTTCAGAAGCTCGAGGCTGATAAACTAAGGAAGGGAAAGAATAAG
*
42220687 GCCGAAGAGGAATTAGATAGCTTGAAGACGGATTACAAAAAGTTACGTCTGTCAATGAGAACTGC
586 GCCGAAGAGGAATTAGATAGCTTGAAGACGGATTACAAAAAGTTACATCTGTCAATGAGAACTGC
*
42220752 CAGGCTTGGAAAAACCTCAAAACAGTGGCGTGAAGAAATTCGAGAAGAAAGAAACAGGTCAGACC
651 CAGGCTTCGAAAAACCTCAAAACAGTGGCGTGAAGAAATTCGAGAAGAAAGAAACAGGTCAGACC
42220817 GGTGGGAAAGAAAT
716 GGTGGGAAAGAAAT
42220831 TCGTAGGAGAAATGGATGATAATTTTTCAGAGTTTGCAAGAGGAGGATATCAAGTGGAGAGCTTC
1 TCGTAGGAGAAATGGATGATAATTTTTCAGAGTTTGCAAGAGGAGGATATCAAGTGGAGAGCTTC
* * *
42220896 GTGGTTTCTTCCGGATGAGATCCTATATCGGTGCGGGGATTTTGACTGGGTTCCTTTACTCGAAA
66 GTGGTTGCTTCCAGATGAGATCCTATATCGGTGCGGGGATTTTGACTGGGTTCCTTTACTCAAAA
42220961 TTTGGGGAGCTGTTGGTTATGCCCCATTGCTAGTGTTAAGGCAATACAGGTCAAGGTAGTTTGTG
131 TTTGGGGAGCTGTTGGTTATGCCCCATTGCTAGTGTTAAGGCAATACAGGTCAAGGTAGTTTGTG
*
42221026 CCTGCAATTCAGGGACTGGCTGAGTGTGAATTCTCGTATAAAGATGATGGTTATAAAAAGAAGGC
196 CCTGCAACTCAGGGACTGGCTGAGTGTGAATTCTCGTATAAAGATGATGGTTATAAAAAGAAGGC
42221091 TCGTGAGATGGCCAATTCATGGAATCAGACTCACCGAATGAAGAGATTAGCTGTGGGCCCAATGA
261 TCGTGAGATGGCCAATTCATGGAATCAGACTCACCGAATGAAGAGATTAGCTGTGGGCCCAATGA
* *
42221156 CAACTCCAGAGTATAACGAATGGTGGGTTAGGAGGATTAATGACAATACTCCTGGGCCAAATTTA
326 CAACTCCAGAGTATAACGAATGGTGGGTTAGAAGGATTAATGACAATACTCCTAGGCCAAATTTA
42221221 GAAAGTAGTCAGTCGATGGAGAAGCATTTGCGAGTCGTCCCTTCTGAGTTGGAAATCATAAAGCA
391 GAAAGTAGTCAGTCGATGGAGAAGCATTTGCGAGTCGTCCCTTCTGAGTTGGAAATCATAAAGCA
*
42221286 GGACTTTGAAAGAAGAAATGCAGAATTAGAGAAGAAAATAGAGCAAATGGAGGAAGAAAAAGTGA
456 GGACTTTGAAAGAAGAAATGCAGAATTAGAGAAGAAAATAGAGCAAATAGAGGAAGAAAAAGTGA
42221351 ATTTGAGACTAGATGTGGATGTTCAGAAGCTCGAGGCTGATAAACTAAGGAAGGGAAAGAATAAG
521 ATTTGAGACTAGATGTGGATGTTCAGAAGCTCGAGGCTGATAAACTAAGGAAGGGAAAGAATAAG
*
42221416 GCTGAAGAGGAATTAGATAGCTTGAAGACGGATTACAAAAAGTTACATCTGTCAATGAGAACTGC
586 GCCGAAGAGGAATTAGATAGCTTGAAGACGGATTACAAAAAGTTACATCTGTCAATGAGAACTGC
* *
42221481 CGGGCTTCGAAAAACCTCAGAACAGTGGCGTGAAGAAATTCGAGAAGAAAGAAACAGGTCAGACC
651 CAGGCTTCGAAAAACCTCAAAACAGTGGCGTGAAGAAATTCGAGAAGAAAGAAACAGGTCAGACC
42221546 GGTGGGAAAGAAA
716 GGTGGGAAAGAAA
42221559 ATTTCAAGAG
Statistics
Matches: 711, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
729 711 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.24
Consensus pattern (729 bp):
TCGTAGGAGAAATGGATGATAATTTTTCAGAGTTTGCAAGAGGAGGATATCAAGTGGAGAGCTTC
GTGGTTGCTTCCAGATGAGATCCTATATCGGTGCGGGGATTTTGACTGGGTTCCTTTACTCAAAA
TTTGGGGAGCTGTTGGTTATGCCCCATTGCTAGTGTTAAGGCAATACAGGTCAAGGTAGTTTGTG
CCTGCAACTCAGGGACTGGCTGAGTGTGAATTCTCGTATAAAGATGATGGTTATAAAAAGAAGGC
TCGTGAGATGGCCAATTCATGGAATCAGACTCACCGAATGAAGAGATTAGCTGTGGGCCCAATGA
CAACTCCAGAGTATAACGAATGGTGGGTTAGAAGGATTAATGACAATACTCCTAGGCCAAATTTA
GAAAGTAGTCAGTCGATGGAGAAGCATTTGCGAGTCGTCCCTTCTGAGTTGGAAATCATAAAGCA
GGACTTTGAAAGAAGAAATGCAGAATTAGAGAAGAAAATAGAGCAAATAGAGGAAGAAAAAGTGA
ATTTGAGACTAGATGTGGATGTTCAGAAGCTCGAGGCTGATAAACTAAGGAAGGGAAAGAATAAG
GCCGAAGAGGAATTAGATAGCTTGAAGACGGATTACAAAAAGTTACATCTGTCAATGAGAACTGC
CAGGCTTCGAAAAACCTCAAAACAGTGGCGTGAAGAAATTCGAGAAGAAAGAAACAGGTCAGACC
GGTGGGAAAGAAAT
Found at i:42225819 original size:28 final size:27
Alignment explanation
Indices: 42225754--42225819 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
42225744 GCCAGTAGTC
*
42225754 TTTTTCATTCTTTTTTTCGAATAATTAT
1 TTTTTCATTC-TTTTTTCCAATAATTAT
*
42225782 TCTTTT-ATTC-TTTTTCCACATCATTCAT
1 T-TTTTCATTCTTTTTTCCA-ATAATT-AT
42225810 TTTTTCATTC
1 TTTTTCATTC
42225820 ATAATCATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
26 7 0.22
27 9 0.28
28 12 0.38
29 4 0.12
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTCATTCTTTTTTCCAATAATTAT
Found at i:42229328 original size:3 final size:3
Alignment explanation
Indices: 42229320--42229361 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
42229310 ATATTTTTCT
42229320 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42229362 AGAGGAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42230629 original size:44 final size:44
Alignment explanation
Indices: 42230525--42230904 Score: 467
Period size: 44 Copynumber: 8.6 Consensus size: 44
42230515 TCTAGAGAAC
*** * * *
42230525 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
* * *
42230570 AGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
*
42230614 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCATGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
* *** * * *
42230658 AGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGT
*
42230703 AGATCAAAGATAGCAGATCTTTTCTTCATGTATTGGCGTGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
* * * *
42230747 AGATCAAAGACAGCAGATCTTGTCTTTCCA--TACTGGTGGCGAAGT
1 AGATCAAAGATAGCAGATCTTGTC-TT-CATGTATTGG-CGTGAAGT
* *
42230792 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
42230836 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
* *
42230880 AAATCGAAGATAGCAGATCTTGTCT
1 AGATCAAAGATAGCAGATCTTGTCT
42230905 CCCCGTGCTG
Statistics
Matches: 286, Mismatches: 43, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
43 2 0.01
44 183 0.64
45 99 0.35
46 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (44 bp):
AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
Found at i:42230702 original size:89 final size:88
Alignment explanation
Indices: 42230525--42230904 Score: 449
Period size: 89 Copynumber: 4.3 Consensus size: 88
42230515 TCTAGAGAAC
*** * * * *
42230525 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA-AAGCAGATC
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAA-CAGATC
* ** * *
42230589 TTATCTTCATGTATTGGCGTGAAGT
64 TTGTCTTCACATACTGGCGCGAAGT
*
42230614 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAACAGATCTT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCTT
* *
42230679 GTCTTCCCATACTGGTGGCGAAGT
66 GTCTTCACATACTGG-CGCGAAGT
* * *
42230703 AGATCAAAGATAGCAGATCTTTTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAGCAGATCTT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCTT
*
42230768 GTCTTTC-CATACTGGTGGCGAAGT
66 GTC-TTCACATACTGG-CGCGAAGT
* * *
42230792 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTT
1 AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCTT
** * *
42230857 GTCTTCATGTATTGGCGTGAAGT
66 GTCTTCACATACTGGCGCGAAGT
* *
42230880 AAATCGAAGATAGCAGATCTTGTCT
1 AGATCAAAGATAGCAGATCTTGTCT
42230905 CCCCGTGCTG
Statistics
Matches: 257, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
88 64 0.25
89 190 0.74
90 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (88 bp):
AGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCTT
GTCTTCACATACTGGCGCGAAGT
Found at i:42230763 original size:133 final size:133
Alignment explanation
Indices: 42230525--42230936 Score: 544
Period size: 133 Copynumber: 3.1 Consensus size: 133
42230515 TCTAGAGAAC
* * *
42230525 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCT
1 AGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGATCT
* *
42230590 TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTT-CAT-GTATTGGCAT
66 TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCATACTAGTGGC--
42230653 GAAGT
129 GAAGT
42230658 AGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGATCT
1 AGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGATCT
* * *
42230723 TTTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAGCAGATCTTGTCTTTCCATACTGGTGGCG
66 TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTC-TTCCATACTAGTGGCG
42230788 AAGT
130 AAGT
* *** * * *
42230792 AGATCGAAGA-AAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAGCAGATC
1 AGATCAAAGATAA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGATC
* * * * * * *
42230855 TTGTCTTCATGTATTGGCGTGAAGTAAATCGAAGATAGCAGATCTTGTCTCCCCGTGCTGGTGGC
65 TTATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCT-TCCATACTAGTGGC
42230920 GAAGT
129 GAAGT
*
42230925 AGATCGAAGATA
1 AGATCAAAGATA
42230937 CAAGTTTTAT
Statistics
Matches: 251, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
132 1 0.00
133 206 0.82
134 36 0.14
135 3 0.01
136 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (133 bp):
AGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGATCT
TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCATACTAGTGGCGA
AGT
Found at i:42230918 original size:222 final size:222
Alignment explanation
Indices: 42230525--42230936 Score: 725
Period size: 222 Copynumber: 1.9 Consensus size: 222
42230515 TCTAGAGAAC
*
42230525 AGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCT
1 AGATCAAAGACAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCT
42230590 TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCATGA
66 TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCATGA
* *
42230655 AGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGA
131 AGTAAATCAAAGATAACAGATCTTGTCTCCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGA
42230720 TCTTTTCTTCATGTATTGGCGTGAAGT
196 TCTTTTCTTCATGTATTGGCGTGAAGT
*
42230747 AGATCAAAGACAGCAGATCTTGTCTTTCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCT
1 AGATCAAAGACAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCT
* *
42230812 TGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGA
66 TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCATGA
* * * * *
42230877 AGTAAATCGAAGATAGCAGATCTTGTCTCCCCGTGCTGGTGGCGAAGTAGATCGAAGATA
131 AGTAAATCAAAGATAACAGATCTTGTCTCCCCATACTGGTGGCGAAGTAGATCAAAGATA
42230937 CAAGTTTTAT
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
222 179 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (222 bp):
AGATCAAAGACAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCT
TATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTATTGGCATGA
AGTAAATCAAAGATAACAGATCTTGTCTCCCCATACTGGTGGCGAAGTAGATCAAAGATAGCAGA
TCTTTTCTTCATGTATTGGCGTGAAGT
Found at i:42231042 original size:42 final size:42
Alignment explanation
Indices: 42230944--42231064 Score: 156
Period size: 44 Copynumber: 2.9 Consensus size: 42
42230934 ATACAAGTTT
* **
42230944 TATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGAAAATGATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCGGATT-AA-AAAATGATCC
*
42230988 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCA-GATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAA-AATGATCC
*
42231030 TATCTCTTTGAAGTTGCAGT-GAGCGGATTAAAAAA
1 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAAAA
42231065 CCACAAGTCT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
40 1 0.01
41 13 0.19
42 26 0.37
43 3 0.04
44 27 0.39
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (42 bp):
TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAAAATGATCC
Found at i:42232290 original size:14 final size:14
Alignment explanation
Indices: 42232268--42232320 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
42232258 CTAATCTGTT
* *
42232268 TTTTTTATTATTTC
1 TTTTATATTATTTA
42232282 TTTTATATTATTTA
1 TTTTATATTATTTA
* *
42232296 TTTTATTTTATTAA
1 TTTTATATTATTTA
*
42232310 TTAT-TATTATT
1 TTTTATATTATT
42232321 GTTATTATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 6 0.18
14 27 0.82
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATATTATTTA
Found at i:42232293 original size:3 final size:3
Alignment explanation
Indices: 42232287--42232335 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
42232277 ATTTCTTTTA
*
42232287 TAT TATT TAT T-T TAT T-T TAT TAAT TAT TAT TAT TGT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
42232332 TAT T
1 TAT T
42232336 TTAATTCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:42232313 original size:12 final size:11
Alignment explanation
Indices: 42232270--42232338 Score: 58
Period size: 12 Copynumber: 6.5 Consensus size: 11
42232260 AATCTGTTTT
*
42232270 TTTTATTATTTC
1 TTTTATTA-TTA
42232282 TTTTA-TATTA
1 TTTTATTATTA
42232292 -TTTATT-TTA
1 TTTTATTATTA
42232301 TTTTATTA--A
1 TTTTATTATTA
*
42232310 TTATTATTATTG
1 TT-TTATTATTA
42232322 TTATTATTATTA
1 TT-TTATTATTA
42232334 TTTTA
1 TTTTA
42232339 ATTCATTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
9 10 0.21
10 15 0.31
11 5 0.10
12 18 0.38
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:42232673 original size:27 final size:27
Alignment explanation
Indices: 42232635--42232688 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
42232625 TCCGCCTCTA
42232635 TTCCATTACATTCAACCAAACAATTGG
1 TTCCATTACATTCAACCAAACAATTGG
42232662 TTCCATTACATTCAACCAAACAATTGG
1 TTCCATTACATTCAACCAAACAATTGG
42232689 ATTACTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (27 bp):
TTCCATTACATTCAACCAAACAATTGG
Found at i:42232720 original size:16 final size:16
Alignment explanation
Indices: 42232695--42232732 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
42232685 TTGGATTACT
*
42232695 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
42232711 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
42232727 ATTACA
1 ATTACA
42232733 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:42236556 original size:30 final size:29
Alignment explanation
Indices: 42236504--42236560 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
42236494 AATATTTTGG
*
42236504 TCACACAAGCTGATATATATCAAGGTTGC
1 TCACACAAGCTGACATATATCAAGGTTGC
*
42236533 TCACACAAGTTGACATCATATCAAGGTT
1 TCACACAAGCTGACAT-ATATCAAGGTT
42236561 ATCCATCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (29 bp):
TCACACAAGCTGACATATATCAAGGTTGC
Found at i:42238530 original size:42 final size:42
Alignment explanation
Indices: 42238451--42238535 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
42238441 TTAAAGGTTG
*
42238451 AGAAAGATACTATGGTTGAACTTTTGAAGTTATAGGTACCAA
1 AGAAAGATACTATGGTTGAACTTTCGAAGTTATAGGTACCAA
42238493 AGAAAGATACTATGGTTGAACTTTCGAAGTTATAGGTACCAA
1 AGAAAGATACTATGGTTGAACTTTCGAAGTTATAGGTACCAA
42238535 A
1 A
42238536 TTGATAGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (42 bp):
AGAAAGATACTATGGTTGAACTTTCGAAGTTATAGGTACCAA
Found at i:42243740 original size:2 final size:2
Alignment explanation
Indices: 42243733--42243779 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
42243723 TATCAATTGG
42243733 AT AT AT AT AT 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 AT AT AT AT AT
42243775 AT AT A
1 AT AT A
42243780 GTTAGGGCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42244307 original size:17 final size:18
Alignment explanation
Indices: 42244287--42244328 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
42244277 TACATAAATA
* *
42244287 TTTTTTATACATTGTT-G
1 TTTTTTATAAATTATTAG
42244304 TTTTTTA-AAATTATTAG
1 TTTTTTATAAATTATTAG
42244321 TTTTTTAT
1 TTTTTTAT
42244329 TTTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTTTTATAAATTATTAG
Found at i:42245234 original size:31 final size:29
Alignment explanation
Indices: 42245212--42245282 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
42245202 AAATTGTAAC
*
42245212 TTTTACTATTTTTAAAGGATTAAATCAAAA
1 TTTTACTATTTTTAAAGGATTAAAT-ATAA
*
42245242 TTTTA-TCATTTTTAAAGGAATAAAGTATAA
1 TTTTACT-ATTTTTAAAGGATTAAA-TATAA
42245272 TTTTACT-TTTT
1 TTTTACTATTTT
42245283 CTACTTATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
29 5 0.14
30 29 0.81
31 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTTACTATTTTTAAAGGATTAAATATAA
Found at i:42252531 original size:17 final size:17
Alignment explanation
Indices: 42252509--42252542 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42252499 AATCGACCTA
42252509 AAACTTAATCAATCGTC
1 AAACTTAATCAATCGTC
42252526 AAACTTAATCAATCGTC
1 AAACTTAATCAATCGTC
42252543 TTACCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
AAACTTAATCAATCGTC
Found at i:42256684 original size:18 final size:18
Alignment explanation
Indices: 42256608--42256676 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
42256598 AGCTCTCAGG
*
42256608 CATTCTTCTCCTTTCATC
1 CATTCTTCTCCCTTCATC
42256626 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
42256644 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
42256662 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
42256677 CTTCATTCCT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.13, C:0.42, G:0.03, T:0.42
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:42257408 original size:12 final size:12
Alignment explanation
Indices: 42257393--42257417 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42257383 GCCGTTTGTG
42257393 TGTTCGATATAA
1 TGTTCGATATAA
42257405 TGTTCGATATAA
1 TGTTCGATATAA
42257417 T
1 T
42257418 ATTTTCTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGTTCGATATAA
Found at i:42260038 original size:20 final size:20
Alignment explanation
Indices: 42260013--42260052 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42260003 AATATTTTTC
*
42260013 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
42260033 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
42260053 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:42260054 original size:34 final size:35
Alignment explanation
Indices: 42260001--42260067 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
42259991 CAAACACCAA
* *
42260001 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
42260036 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42260068 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42260059 original size:14 final size:14
Alignment explanation
Indices: 42260036--42260075 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42260026 ACAGAAAAGT
*
42260036 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
42260050 AAATCATTTTACGG
1 AAAACATTTTACAG
42260064 AAAACATTTTAC
1 AAAACATTTTAC
42260076 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:42266488 original size:14 final size:14
Alignment explanation
Indices: 42266469--42266498 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42266459 CCAAAACCCT
42266469 TCTAAATGCTGTAA
1 TCTAAATGCTGTAA
42266483 TCTAAATGCTGTAA
1 TCTAAATGCTGTAA
42266497 TC
1 TC
42266499 AAAAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (14 bp):
TCTAAATGCTGTAA
Found at i:42269555 original size:20 final size:20
Alignment explanation
Indices: 42269532--42269637 Score: 81
Period size: 20 Copynumber: 5.3 Consensus size: 20
42269522 GTGCTTCTGA
42269532 TAGCACATTCATGCTCATGT
1 TAGCACATTCATGCTCATGT
* *
42269552 TAGCAC-TACGATGCTCATGA
1 TAGCACATTC-ATGCTCATGT
* * *
42269572 TAGCACATTCGTGCTCCTAT
1 TAGCACATTCATGCTCATGT
* ** *
42269592 TTGCAC-TATGGTGCTCATGA
1 TAGCACAT-TCATGCTCATGT
* *
42269612 TAGCACATTCATGCTCTTCT
1 TAGCACATTCATGCTCATGT
42269632 TAGCAC
1 TAGCAC
42269638 TATGGTACTC
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
19 3 0.05
20 58 0.91
21 3 0.05
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (20 bp):
TAGCACATTCATGCTCATGT
Found at i:42269587 original size:40 final size:40
Alignment explanation
Indices: 42269529--42269672 Score: 180
Period size: 40 Copynumber: 3.6 Consensus size: 40
42269519 CAAGTGCTTC
* * *
42269529 TGATAGCACATTCATGCTCATGTTAGCACTACGATGCTCA
1 TGATAGCACATTCATGCTCATATTAGCACTATGGTGCTCA
* * *
42269569 TGATAGCACATTCGTGCTCCTATTTGCACTATGGTGCTCA
1 TGATAGCACATTCATGCTCATATTAGCACTATGGTGCTCA
* * * *
42269609 TGATAGCACATTCATGCTCTTCTTAGCACTATGGTACTCT
1 TGATAGCACATTCATGCTCATATTAGCACTATGGTGCTCA
* *
42269649 TGATAGCATATTCATGCTCCTATT
1 TGATAGCACATTCATGCTCATATT
42269673 TGAATTACGA
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 89 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (40 bp):
TGATAGCACATTCATGCTCATATTAGCACTATGGTGCTCA
Found at i:42274529 original size:22 final size:21
Alignment explanation
Indices: 42274480--42274530 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
42274470 GTGTAAAAAA
**
42274480 AGGCACACGGTCGTGTGGAAT
1 AGGCACACGCCCGTGTGGAAT
*
42274501 -GGCACACGCCCGTGTTGAAT
1 AGGCACACGCCCGTGTGGAAT
42274521 GAGGCACACG
1 -AGGCACACG
42274531 ACTGTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.68
22 8 0.32
ACGTcount: A:0.24, C:0.25, G:0.35, T:0.16
Consensus pattern (21 bp):
AGGCACACGCCCGTGTGGAAT
Found at i:42278111 original size:15 final size:15
Alignment explanation
Indices: 42278091--42278124 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42278081 CCGATTTTTA
42278091 TAATTTTTAATATTT
1 TAATTTTTAATATTT
* *
42278106 TAATTTTTGATTTTT
1 TAATTTTTAATATTT
42278121 TAAT
1 TAAT
42278125 AATTTATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TAATTTTTAATATTT
Found at i:42283377 original size:21 final size:22
Alignment explanation
Indices: 42283352--42283395 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
42283342 ACGACTGAAC
42283352 AAAAAGATGTCATCCTTATCCAAA
1 AAAAAGATGTCATCCTTATCC--A
42283376 AAAAAGATGTCATCCTTATC
1 AAAAAGATGTCATCCTTATC
42283396 AAGAAACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (22 bp):
AAAAAGATGTCATCCTTATCCA
Found at i:42288250 original size:28 final size:29
Alignment explanation
Indices: 42288199--42288255 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
42288189 CCCACCTCTT
42288199 TATTTTAAAGAAAAAAAGGAAAATGGAAA
1 TATTTTAAAGAAAAAAAGGAAAATGGAAA
42288228 TATTTTAAAG-AAAAAAGGAAAATGGAAA
1 TATTTTAAAGAAAAAAAGGAAAATGGAAA
42288256 GAAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (29 bp):
TATTTTAAAGAAAAAAAGGAAAATGGAAA
Found at i:42297921 original size:33 final size:33
Alignment explanation
Indices: 42297874--42297973 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
42297864 AGTTGAACAA
* *
42297874 AATGATGAAACTGCCCCAATAGATGTTCCAATC
1 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
42297907 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
1 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
* * * *
42297940 ATTGATGAAGTTGCCCTGATAGATGTTTCAATC
1 AATGATGAAGCTGCCCCGATAGATGTTCCAATC
42297973 A
1 A
42297974 CTTATGTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (33 bp):
AATGATGAAGCTGCCCCGATAGATGTTCCAATC
Found at i:42312570 original size:14 final size:15
Alignment explanation
Indices: 42312543--42312573 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42312533 TAAAATACGG
42312543 TGGCCCAAATACAAA
1 TGGCCCAAATACAAA
42312558 TGGCCCAAA-ACAAA
1 TGGCCCAAATACAAA
42312572 TG
1 TG
42312574 AAGAAACCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.45, C:0.26, G:0.16, T:0.13
Consensus pattern (15 bp):
TGGCCCAAATACAAA
Found at i:42313756 original size:19 final size:18
Alignment explanation
Indices: 42313727--42313771 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
42313717 CATATGCGTA
*
42313727 TTTTTTA-ATGTAATTATT
1 TTTTTTATATGTAACT-TT
*
42313745 TTTTTTATATGTAGCTTT
1 TTTTTTATATGTAACTTT
42313763 TTTTTTATA
1 TTTTTTATA
42313772 AACTATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (18 bp):
TTTTTTATATGTAACTTT
Found at i:42316123 original size:27 final size:27
Alignment explanation
Indices: 42316085--42316148 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
42316075 ATAAAAAATA
*
42316085 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
42316112 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
42316139 ACCAAAATAT
1 ACCAAAATAT
42316149 ACCAAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:42318792 original size:16 final size:17
Alignment explanation
Indices: 42318771--42318808 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42318761 TAAAAATAGG
* *
42318771 TAAAAG-TTAATAAAAT
1 TAAAAGCTTAAAAAAAC
42318787 TAAAAGCTTAAAAAAAC
1 TAAAAGCTTAAAAAAAC
42318804 TAAAA
1 TAAAA
42318809 AATCAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (17 bp):
TAAAAGCTTAAAAAAAC
Found at i:42323585 original size:3 final size:3
Alignment explanation
Indices: 42323579--42323613 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
42323569 ATTATTATTA
42323579 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
42323614 TTCTTGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:42326081 original size:25 final size:25
Alignment explanation
Indices: 42326053--42326118 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
42326043 TTATTAACGA
*
42326053 GAAGCTCCGGATAGCCATATATCGG
1 GAAGCTCCGGAGAGCCATATATCGG
* ** *
42326078 GAAGTTCAAGCGAGCC--ATATCGG
1 GAAGCTCCGGAGAGCCATATATCGG
42326101 GAAGCTCCGGAGAGCCAT
1 GAAGCTCCGGAGAGCCAT
42326119 TAATTAGGAA
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 19 0.63
25 11 0.37
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.17
Consensus pattern (25 bp):
GAAGCTCCGGAGAGCCATATATCGG
Found at i:42326147 original size:26 final size:26
Alignment explanation
Indices: 42326111--42326160 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
42326101 GAAGCTCCGG
42326111 AGAGCCATTAAT-TAGGAAGCTCACAA
1 AGAGCCATTAATCT-GGAAGCTCACAA
*
42326137 AGAGCCTTTAATCTGGAAGCTCAC
1 AGAGCCATTAATCTGGAAGCTCAC
42326161 GTAAAGCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (26 bp):
AGAGCCATTAATCTGGAAGCTCACAA
Found at i:42326168 original size:26 final size:26
Alignment explanation
Indices: 42326100--42326170 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
42326090 AGCCATATCG
* *
42326100 GGAAGCTC-CGGAGAGCCATTAATTA
1 GGAAGCTCACGAAAAGCCATTAATTA
*
42326125 GGAAGCTCAC-AAAGAGCCTTTAATCT-
1 GGAAGCTCACGAAA-AGCCATTAAT-TA
*
42326151 GGAAGCTCACGTAAAGCCAT
1 GGAAGCTCACGAAAAGCCAT
42326171 ATATCAGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 9 0.24
26 25 0.68
27 3 0.08
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.20
Consensus pattern (26 bp):
GGAAGCTCACGAAAAGCCATTAATTA
Found at i:42326337 original size:24 final size:24
Alignment explanation
Indices: 42326276--42326337 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
42326266 TAAGAACCAT
*
42326276 ATAACGGGAAGCTCGAGAGGGCTA
1 ATAACGGGAAGCTCGAGAGAGCTA
*
42326300 ATAAC-AGAATGCTC-ATGAGAGCTA
1 ATAACGGGAA-GCTCGA-GAGAGCTA
*
42326324 ATAACGGGACGCTC
1 ATAACGGGAAGCTC
42326338 TTTCGAGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 4 0.13
24 25 0.81
25 2 0.06
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.16
Consensus pattern (24 bp):
ATAACGGGAAGCTCGAGAGAGCTA
Found at i:42326672 original size:32 final size:32
Alignment explanation
Indices: 42326636--42326699 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
42326626 TATTTAGATC
42326636 TATACGAATGAATTTTAACATCAATTCATATT
1 TATACGAATGAATTTTAACATCAATTCATATT
42326668 TATACGAATGAATTTTAACATCAATTCATATT
1 TATACGAATGAATTTTAACATCAATTCATATT
42326700 CAATTCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (32 bp):
TATACGAATGAATTTTAACATCAATTCATATT
Found at i:42326712 original size:10 final size:11
Alignment explanation
Indices: 42326688--42326719 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
42326678 AATTTTAACA
42326688 TCAATTCATAT
1 TCAATTCATAT
42326699 TCAATTCA-AT
1 TCAATTCATAT
42326709 TCAATTCATAT
1 TCAATTCATAT
42326720 CTTTGGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (11 bp):
TCAATTCATAT
Found at i:42327751 original size:18 final size:19
Alignment explanation
Indices: 42327717--42327764 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
42327707 AATAAAAGTT
42327717 ATTAAATTTTAATTAAAAA
1 ATTAAATTTTAATTAAAAA
42327736 ATTAAATTTT-ATTAAAAA
1 ATTAAATTTTAATTAAAAA
*
42327754 AATAGAATTTT
1 ATTA-AATTTT
42327765 TTTTAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTAAATTTTAATTAAAAA
Found at i:42333962 original size:3 final size:3
Alignment explanation
Indices: 42333944--42333986 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
42333934 CATTAAATTA
*
42333944 ATT ATT -TT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42333987 AGTTATGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42338088 original size:12 final size:12
Alignment explanation
Indices: 42338068--42338113 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
42338058 GACAGTGGAG
42338068 GCAAAAAAAAGAA
1 GCAAAAAAAA-AA
42338081 GCAAAAAAAAAA
1 GCAAAAAAAAAA
42338093 G-AAAAACAAAAA
1 GCAAAAA-AAAAA
*
42338105 ACAAAAAAA
1 GCAAAAAAA
42338114 GTAAAAAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.17
12 10 0.33
13 15 0.50
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (12 bp):
GCAAAAAAAAAA
Found at i:42338091 original size:16 final size:15
Alignment explanation
Indices: 42338070--42338121 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
42338060 CAGTGGAGGC
*
42338070 AAAAAAAAGAAGCAAA
1 AAAAAAAAAAAGC-AA
*
42338086 AAAAAAAGAAAAACAA
1 AAAAAAA-AAAAGCAA
*
42338102 AAAACAAAAAAAGTAA
1 AAAA-AAAAAAAGCAA
42338118 AAAA
1 AAAA
42338122 CGAGAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 23 0.77
17 7 0.23
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAAGCAA
Found at i:42338103 original size:15 final size:16
Alignment explanation
Indices: 42338069--42338105 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
42338059 ACAGTGGAGG
*
42338069 CAAAAAAAAGAAGCAA
1 CAAAAAAAAGAAGAAA
42338085 -AAAAAAAAGAA-AAA
1 CAAAAAAAAGAAGAAA
42338099 CAAAAAA
1 CAAAAAA
42338106 CAAAAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAGAAGAAA
Found at i:42338605 original size:18 final size:17
Alignment explanation
Indices: 42338582--42338634 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
42338572 TACTTCACTT
42338582 GAAAAAAGGAAACA-AAAA
1 GAAAAAA-GAAA-AGAAAA
42338600 GAAAAAAGAAAAGAAAA
1 GAAAAAAGAAAAGAAAA
*
42338617 GAAAAACAAAAAAGAAAA
1 GAAAAA-AGAAAAGAAAA
42338635 AGGAGAGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 14 0.44
18 17 0.53
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAAGAAAA
Found at i:42338610 original size:17 final size:18
Alignment explanation
Indices: 42338582--42338622 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
42338572 TACTTCACTT
42338582 GAAAAAAGGAAACA-AAAA
1 GAAAAAAGGAAA-AGAAAA
42338600 GAAAAAA-GAAAAGAAAA
1 GAAAAAAGGAAAAGAAAA
42338617 GAAAAA
1 GAAAAA
42338623 CAAAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.64
18 7 0.32
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
GAAAAAAGGAAAAGAAAA
Found at i:42338611 original size:23 final size:23
Alignment explanation
Indices: 42338585--42338634 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
42338575 TTCACTTGAA
* *
42338585 AAAAGGAAACAAAAAGAAAAAAG
1 AAAAGAAAACAAAAACAAAAAAG
*
42338608 AAAAGAAAAGAAAAACAAAAAAG
1 AAAAGAAAACAAAAACAAAAAAG
42338631 AAAA
1 AAAA
42338635 AGGAGAGGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAGAAAACAAAAACAAAAAAG
Found at i:42338628 original size:17 final size:18
Alignment explanation
Indices: 42338582--42338634 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
42338572 TACTTCACTT
*
42338582 GAAAAAAGGAAACA-AAAA
1 GAAAAAAAGAAA-AGAAAA
42338600 G-AAAAAAGAAAAGAAAA
1 GAAAAAAAGAAAAGAAAA
42338617 GAAAAACAA-AAAAGAAAA
1 GAAAAA-AAGAAAAGAAAA
42338635 AGGAGAGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 1 0.03
17 14 0.45
18 14 0.45
19 2 0.06
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (18 bp):
GAAAAAAAGAAAAGAAAA
Found at i:42339618 original size:44 final size:44
Alignment explanation
Indices: 42339541--42340325 Score: 267
Period size: 44 Copynumber: 17.8 Consensus size: 44
42339531 CATATCAAGC
* * * * * *
42339541 CTTATCTCCCTGAGCAGCAGTAGAGTAGGTCGAAGATTATAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
* ** *
42339585 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGA-CGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAG-AT
* * * ** *
42339629 CTTATCT-TCT-CG-AGATAGTAGGAAGCAGATTTAAG-CCACCAG-T
1 CTTATCTCCCTAAGCAG-TAGT-GG-AGCAGATTGAAGATTA-TAGAT
* ** * *
42339672 CCTATCTCCCTGAA-CAACAGTGGAGTAGGTTGAAGA-TAGTAGAT
1 CTTATCTCCCT-AAGCAGTAGTGGAGCAGATTGAAGATTA-TAGAT
* * *** *
42339716 CTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGGTAAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
* * ** *
42339760 CTTATCTTCCC-GAG-A-TAGTAGGAAGCAGATTTAAG-GCACCAG-T
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTA-TAGAT
* * * * *
42339803 CCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
* * *
42339847 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
* * *
42339891 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGA-CGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAG-AT
* * * ** * *
42339935 CTTATCTTCCC-AAGGTATTAG-GGAAGCAGATTTAAG-CCACCAG-C
1 CTTATC-TCCCTAA-GCAGTAGTGG-AGCAGATTGAAGATTA-TAGAT
* * * * *
42339979 CTTATCTCCTTAAGCTGCAGTGGAGTAGGTTGAAGATTATAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
* * ** *
42340023 CTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGA-CGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAG-AT
* * * * ** * *
42340067 CTTATCTTTCC-AAGGTATTAG-GGAAGCAGATTTAAG-CCACCA-AC
1 CTTATC-TCCCTAA-GCAGTAGTGG-AGCAGATTGAAGATTA-TAGAT
* * * * * *
42340111 CTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
* ****
42340155 CTTATCTCCCTAAGGCAGGTAGTGGAGCAGATCGAAGA-CGGGGAAT
1 CTTATCTCCCTAA-GCA-GTAGTGGAGCAGATTGAAGATTATAG-AT
* * * * ** * *
42340201 CTTATCTTTCC-AAGGTATTAG-GGAAGCAGATTTAAG-CCACCAG-C
1 CTTATC-TCCCTAA-GCAGTAGTGG-AGCAGATTGAAGATTA-TAGAT
* * * * * *
42340245 CTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
* *
42340289 CTTATCTCCCTAAGCCGTAGTGGAGCAGATCGAAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAT
42340326 GGGGAATCTT
Statistics
Matches: 539, Mismatches: 148, Indels: 108
0.68 0.19 0.14
Matches are distributed among these distances:
41 2 0.00
42 13 0.02
43 106 0.20
44 317 0.59
45 66 0.12
46 32 0.06
47 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTATAGAT
Found at i:42339855 original size:175 final size:176
Alignment explanation
Indices: 42339674--42340047 Score: 549
Period size: 175 Copynumber: 2.1 Consensus size: 176
42339664 CCACCAGTCC
42339674 TATCTCCCTGAA-CAACAGTGGAGTAGGTTGAAGA-TAGTAGATCTTATCTCCCTAAGCAGTAGT
1 TATCTCCCT-AAGCAACAGTGGAGTAGGTTGAAGATTA-TAGATCTTATCTCCCTAAGCAGTAGT
** * *
42339737 GAAGCAGATCGAAGACGGTAAATCTTATCTTCCCGAGATAGTA-GGAAGCAGATTTAAGGCACCA
64 GAAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATAGTAGGGAAGCAGATTTAAGCCACCA
*
42339801 GTCC-TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCT
129 G-CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCT
* *
42339849 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAACAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGA
* * * *
42339914 AGCAGATCGAAGATGACGAATCTTATCTTCCCAAGGTATTAGGGAAGCAGATTTAAGCCACCAGC
66 AGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATAGTAGGGAAGCAGATTTAAGCCACCAGC
* *
42339979 CTTATCTCCTTAAGCTGCAGTGGAGTAGGTTGAAGATTATAGATCT
131 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCT
* **
42340025 TATCTCTCTAAGCAGTAGTGGAG
1 TATCTCCCTAAGCAACAGTGGAG
42340048 CAGATCGAAG
Statistics
Matches: 180, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
174 2 0.01
175 93 0.52
176 85 0.47
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (176 bp):
TATCTCCCTAAGCAACAGTGGAGTAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGA
AGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATAGTAGGGAAGCAGATTTAAGCCACCAGC
CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTATAGATCT
Done.