Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 142 of 292
Found at i:42181357 original size:26 final size:26
Alignment explanation
Indices: 42181321--42181430 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
42181311 CATGAAATTC
*
42181321 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
42181347 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
42181373 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
42181399 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
42181425 TTATCA
1 TTATCA
42181431 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:42182328 original size:27 final size:27
Alignment explanation
Indices: 42182280--42182438 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
42182270 GCGAGACTGC
* *
42182280 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
42182307 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
42182333 CAAATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
42182360 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
42182387 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
42182414 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
42182439 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 9 0.08
27 101 0.88
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:42182380 original size:54 final size:54
Alignment explanation
Indices: 42182298--42182438 Score: 239
Period size: 54 Copynumber: 2.6 Consensus size: 54
42182288 GTGACGAAGT
*
42182298 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAAATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAAATATATGTGGCAGAGC
* *
42182352 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAAATATATGTGGCAGAGC
42182406 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
42182439 GACGCTTCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 77 0.94
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAAATATATGTGGCAGAGC
Found at i:42184057 original size:26 final size:26
Alignment explanation
Indices: 42184026--42184133 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
42184016 TGAAATGCCC
*
42184026 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
42184052 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
42184078 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
42184104 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
42184130 ATCA
1 ATCA
42184134 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:42184772 original size:24 final size:23
Alignment explanation
Indices: 42184740--42184785 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42184730 CTAAATTATA
* *
42184740 TAGACATTTATAGCACATTCTAAC
1 TAGAAATTTAT-GCAAATTCTAAC
42184764 TAGAAATTTATGCAAATTCTAA
1 TAGAAATTTATGCAAATTCTAA
42184786 GTGCTCATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (23 bp):
TAGAAATTTATGCAAATTCTAAC
Found at i:42193298 original size:46 final size:44
Alignment explanation
Indices: 42193124--42193335 Score: 149
Period size: 46 Copynumber: 4.6 Consensus size: 44
42193114 GTGAGTTAGC
* * * *
42193124 GTAAGACATGTCTGGGACATGCATCAACCACATTATGA-GAGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGACCTC--GA-GACGTGCCAGT
* * * * * * *
42193170 ATAAGACCATGTCTGGGACATGGCATCGTCATTGAGATGAGTGCTAGA
1 GTAAGA-CATGTCTGGGACAT-GCATCGACCTCGAGA--CGTGCCAGT
*
42193218 GTAAGACATGTCTGGGACATGCTTCGACCTCGAGACGTAAGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGACCTCGAGACGT--GCCAGT
* * * *
42193264 GTAAGATATGTCTGGGACATGCATC-AGCTACGAGATGTGTCAGT
1 GTAAGACATGTCTGGGACATGCATCGACCT-CGAGACGTGCCAGT
*
42193308 GTAAGACCATGTCTAGGACATGGCATCG
1 GTAAGA-CATGTCTGGGACAT-GCATCG
42193336 GCACCTGACC
Statistics
Matches: 130, Mismatches: 25, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
44 13 0.10
45 17 0.13
46 56 0.43
47 28 0.22
48 16 0.12
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (44 bp):
GTAAGACATGTCTGGGACATGCATCGACCTCGAGACGTGCCAGT
Found at i:42194330 original size:28 final size:28
Alignment explanation
Indices: 42194298--42194355 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
42194288 CATACAGGCT
42194298 AGGACACGAGCATGT-CATGGCCGTGTGA
1 AGGACACGAGCATGTCCA-GGCCGTGTGA
* *
42194326 AGGACACGGGCGTGTGCCAGGCCGTGTGA
1 AGGACACGAGCATGT-CCAGGCCGTGTGA
42194355 A
1 A
42194356 AACCCCTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 11 0.42
30 2 0.08
ACGTcount: A:0.22, C:0.22, G:0.40, T:0.16
Consensus pattern (28 bp):
AGGACACGAGCATGTCCAGGCCGTGTGA
Found at i:42198771 original size:17 final size:19
Alignment explanation
Indices: 42198751--42198785 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42198741 TATTACTTAA
42198751 AATG-TAAAA-TTATTATC
1 AATGTTAAAACTTATTATC
42198768 AATGTTAAAACTTATTAT
1 AATGTTAAAACTTATTAT
42198786 TAAATAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (19 bp):
AATGTTAAAACTTATTATC
Found at i:42198821 original size:37 final size:38
Alignment explanation
Indices: 42198780--42198853 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 38
42198770 TGTTAAAACT
42198780 TATTATTAAATAAGTTTAATAAAATAA-AAATAATATC
1 TATTATTAAATAAGTTTAATAAAATAACAAATAATATC
42198817 TATTATTAAATAAGTTTAATAAAATAACAAATAATAT
1 TATTATTAAATAAGTTTAATAAAATAACAAATAATAT
42198854 TAATAATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 27 0.75
38 9 0.25
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (38 bp):
TATTATTAAATAAGTTTAATAAAATAACAAATAATATC
Found at i:42199720 original size:27 final size:28
Alignment explanation
Indices: 42199690--42199747 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
42199680 TAAACCAAAC
*
42199690 TTTTCAAAAGCACTTCTT-AAAAGTACTT
1 TTTTCAAAAGCACTT-TTCAAAAGCACTT
*
42199718 TTTTC-ACAGCACTTTTCAAAAGCACTT
1 TTTTCAAAAGCACTTTTCAAAAGCACTT
42199745 TTT
1 TTT
42199748 AAAAACATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 20 0.74
28 5 0.19
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (28 bp):
TTTTCAAAAGCACTTTTCAAAAGCACTT
Found at i:42199735 original size:12 final size:13
Alignment explanation
Indices: 42199688--42199751 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
42199678 TTTAAACCAA
42199688 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
42199701 ACTTCTT-AAAAGT
1 ACTT-TTCAAAAGC
*
42199714 ACTTTTTTC-ACAGC
1 AC--TTTTCAAAAGC
42199728 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
42199741 ACTTTTTAAAA
1 ACTTTTCAAAA
42199752 ACATTGCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 5 0.12
13 25 0.61
14 9 0.22
15 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:42200922 original size:3 final size:3
Alignment explanation
Indices: 42200914--42200952 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
42200904 TGCTTTTTGT
* *
42200914 AGA AGA AGA AGA AGA AGA ATA AGA AAA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
42200953 TGATTATGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:42204045 original size:3 final size:3
Alignment explanation
Indices: 42204037--42204062 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42204027 ATTTAGCTAT
42204037 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
42204063 TCCTTTTTGG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:42212511 original size:19 final size:17
Alignment explanation
Indices: 42212483--42212521 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
42212473 TTATGCTTAA
*
42212483 TTATTTAATATTAATATT
1 TTATTTAATAATAA-ATT
42212501 TTATCTTAATAATAAATT
1 TTAT-TTAATAATAAATT
42212519 TTA
1 TTA
42212522 ACAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTTAATAATAAATT
Found at i:42212532 original size:22 final size:20
Alignment explanation
Indices: 42212507--42212549 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
42212497 TATTTTATCT
42212507 TAATAATAAATTTTAACAATAA
1 TAATAATAAA-TTTAA-AATAA
**
42212529 TAATTCTAAATTTAAAATAA
1 TAATAATAAATTTAAAATAA
42212549 T
1 T
42212550 TTTGTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATAATAAATTTAAAATAA
Found at i:42212571 original size:26 final size:27
Alignment explanation
Indices: 42212542--42212600 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
42212532 TTCTAAATTT
* *
42212542 AAAATAATTT-TGTTAATATATTATTA
1 AAAATAATTTATCTTAATATATTAATA
*
42212568 AAAAT-ATTTATCTTAATATTTTAATA
1 AAAATAATTTATCTTAATATATTAATA
42212594 ATAAATA
1 A-AAATA
42212601 TATATTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 4 0.15
26 19 0.70
27 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAATAATTTATCTTAATATATTAATA
Found at i:42212646 original size:16 final size:15
Alignment explanation
Indices: 42212609--42212658 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
42212599 TATATATTAC
42212609 AATATATAAATATTT
1 AATATATAAATATTT
42212624 AAT-TATAAATATTT
1 AATATATAAATATTT
*
42212638 TATGATATAAA-ATTT
1 AAT-ATATAAATATTT
42212653 GAATAT
1 -AATAT
42212659 TTTTAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 13 0.43
15 9 0.30
16 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (15 bp):
AATATATAAATATTT
Found at i:42213031 original size:20 final size:21
Alignment explanation
Indices: 42213006--42213046 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
42212996 CATCCAAATA
42213006 TAAAAAAAT-ATCAATTTTTC
1 TAAAAAAATAATCAATTTTTC
42213026 TAAAAAAATCAATCAATTTTT
1 TAAAAAAAT-AATCAATTTTT
42213047 GCAAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAAAATAATCAATTTTTC
Found at i:42217269 original size:40 final size:40
Alignment explanation
Indices: 42217214--42217308 Score: 181
Period size: 40 Copynumber: 2.4 Consensus size: 40
42217204 TATGTGCATA
42217214 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
42217254 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
42217294 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
42217309 GTTACATCCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:42225303 original size:40 final size:40
Alignment explanation
Indices: 42225248--42225462 Score: 394
Period size: 40 Copynumber: 5.4 Consensus size: 40
42225238 TATGTGCATA
*
42225248 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCAGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
42225288 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
42225328 GCATTCGTGCGGGTTATTATAACCAGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
42225368 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
42225408 GCATTCGTGTGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
42225448 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
42225463 GTTACATCCG
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 169 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:42235641 original size:20 final size:20
Alignment explanation
Indices: 42235589--42235642 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
42235579 GCTGAAAGTA
*
42235589 AGCTCAGTTGAGCTCAAACG
1 AGCTGAGTTGAGCTCAAACG
* *** *
42235609 AGTTGAAACGAGCTCAAATG
1 AGCTGAGTTGAGCTCAAACG
42235629 AGCTGAGTTGAGCT
1 AGCTGAGTTGAGCT
42235643 GGACGGAGCT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (20 bp):
AGCTGAGTTGAGCTCAAACG
Found at i:42244934 original size:33 final size:34
Alignment explanation
Indices: 42244886--42244962 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
42244876 TGTTTGCATT
* * *
42244886 ACTGTTACTGTTACTGTATTGGGCTA-AGCCC-A
1 ACTGATACTGATACTGTAATGGGCTATAGCCCTA
*
42244918 CACTGATACTGATACTGTAATGGGCTATGGCCCTA
1 -ACTGATACTGATACTGTAATGGGCTATAGCCCTA
42244953 ACTGATACTG
1 ACTGATACTG
42244963 GACTGTCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 23 0.61
34 14 0.37
35 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (34 bp):
ACTGATACTGATACTGTAATGGGCTATAGCCCTA
Found at i:42251218 original size:41 final size:40
Alignment explanation
Indices: 42251040--42251219 Score: 186
Period size: 40 Copynumber: 4.5 Consensus size: 40
42251030 GCTCGATTGT
* * *
42251040 CTTCGGGACATT-GCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAGCCCGGATT-TAGTAACTCGCACAAATGC
* *
42251080 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
42251120 CTTCGGGACTTAACCCAGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
42251160 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
42251201 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
42251220 CACCATTCGA
Statistics
Matches: 115, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.02
40 84 0.73
41 28 0.24
42 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:42259213 original size:80 final size:80
Alignment explanation
Indices: 42259100--42259292 Score: 219
Period size: 80 Copynumber: 2.4 Consensus size: 80
42259090 GGATATAGCG
* * * * * *
42259100 ACTCGCTCGATTGTCTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAAT
1 ACTCGCACGAATGCCTTCGGGAC-TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAAT
*
42259164 T-AGCCCGGATTTAGTA
65 TGA-CCCGGATTTAATA
* * *
42259180 ACTCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATT
1 ACTCGCACGAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATT
*
42259245 GACCCGGATTTAATC
66 GACCCGGATTTAATA
* * *
42259260 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 AC-TCGCACGAATGCCTTCGGGACTTAGCCCGG
42259293 ACACCATTCG
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 2 0.02
80 66 0.69
81 27 0.28
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATT
GACCCGGATTTAATA
Found at i:42259281 original size:41 final size:39
Alignment explanation
Indices: 42259114--42259293 Score: 173
Period size: 40 Copynumber: 4.5 Consensus size: 39
42259104 GCTCGATTGT
* * * *
42259114 CTTCGGGACATTGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGA-ATTACCCGGATT-TAGTAACTCGCACAAATGC
*
42259154 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGAATTA-CCCGGATTTAGTAACTCGCACAAATGC
* * *
42259194 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGAATT-ACCCGGATTTAGTAACTCGCACAAATGC
* * * *
42259234 CTTCGGGAATTGACCCGGATTTAATCACTTAGCACAAAAGC
1 CTTCGGGAATT-ACCCGGATTTAGTAAC-TCGCACAAATGC
*
42259275 CTTCGGGACTTAGCCCGGA
1 CTTCGGGAATTA-CCCGGA
42259294 CACCATTCGA
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
39 3 0.03
40 85 0.73
41 29 0.25
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (39 bp):
CTTCGGGAATTACCCGGATTTAGTAACTCGCACAAATGC
Found at i:42260007 original size:2 final size:2
Alignment explanation
Indices: 42260000--42260027 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42259990 ATGTGCAAAC
42260000 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
42260028 GCTAGAGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42261367 original size:24 final size:24
Alignment explanation
Indices: 42261340--42261426 Score: 131
Period size: 24 Copynumber: 3.6 Consensus size: 24
42261330 CTTATTATGT
*
42261340 TCGCACACATAGTGCCATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
42261364 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42261388 TCGCACACATAGTG-CATTAATAAA
1 TCGCACACATAGTGCCA-TAGTAAA
*
42261412 TTGCACACATAGTGC
1 TCGCACACATAGTGC
42261427 ATTTGAGATA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
23 2 0.03
24 56 0.97
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:42261427 original size:24 final size:24
Alignment explanation
Indices: 42261318--42261429 Score: 122
Period size: 24 Copynumber: 4.7 Consensus size: 24
42261308 ACCGAATGTG
* **
42261318 GCACACATAGTGC-TTATTATGTTC
1 GCACACATAGTGCATTAGTA-AATC
*
42261342 GCACACATAGTGCCA-TAGCAAATC
1 GCACACATAGTG-CATTAGTAAATC
42261366 GCACACATAGTGCCA-TAGTAAATC
1 GCACACATAGTG-CATTAGTAAATC
* *
42261390 GCACACATAGTGCATTAATAAATT
1 GCACACATAGTGCATTAGTAAATC
42261414 GCACACATAGTGCATT
1 GCACACATAGTGCATT
42261430 TGAGATAGCC
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
23 2 0.03
24 72 0.92
25 4 0.05
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (24 bp):
GCACACATAGTGCATTAGTAAATC
Found at i:42267892 original size:24 final size:24
Alignment explanation
Indices: 42267865--42267951 Score: 131
Period size: 24 Copynumber: 3.6 Consensus size: 24
42267855 CTTATTATGT
*
42267865 TCGCACACATAGTGCCATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
42267889 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42267913 TCGCACACATAGTG-CATTAATAAA
1 TCGCACACATAGTGCCA-TAGTAAA
*
42267937 TTGCACACATAGTGC
1 TCGCACACATAGTGC
42267952 ATTTGAGATA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
23 2 0.03
24 56 0.97
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:42267952 original size:24 final size:24
Alignment explanation
Indices: 42267843--42267954 Score: 122
Period size: 24 Copynumber: 4.7 Consensus size: 24
42267833 ACCGAATGTG
* **
42267843 GCACACATAGTGC-TTATTATGTTC
1 GCACACATAGTGCATTAGTA-AATC
*
42267867 GCACACATAGTGCCA-TAGCAAATC
1 GCACACATAGTG-CATTAGTAAATC
42267891 GCACACATAGTGCCA-TAGTAAATC
1 GCACACATAGTG-CATTAGTAAATC
* *
42267915 GCACACATAGTGCATTAATAAATT
1 GCACACATAGTGCATTAGTAAATC
42267939 GCACACATAGTGCATT
1 GCACACATAGTGCATT
42267955 TGAGATAGCC
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
23 2 0.03
24 72 0.92
25 4 0.05
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (24 bp):
GCACACATAGTGCATTAGTAAATC
Found at i:42272149 original size:43 final size:43
Alignment explanation
Indices: 42272011--42272181 Score: 159
Period size: 43 Copynumber: 4.0 Consensus size: 43
42272001 CATAAGGCTC
* * * * *
42272011 ATACAATGCC-ATATCCTAGATATGGTCTTACATGTTACCAC-
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
** * * * * *
42272052 ATATCGGTGCCACTGTCCCAAACAGGGTCTTACATGAAATCA-T
1 ATA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
* *
42272095 ATAACATTGCCAATGTCCCAGACATAGTCTTACATGTAATCACA
1 AT-ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
* *
42272139 ATACAATGCCAATGACCCAGACATGGTCTTACTTGTAATCACA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
42272182 TCTCGATAAC
Statistics
Matches: 102, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 3 0.03
42 5 0.05
43 91 0.89
44 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (43 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
Found at i:42273750 original size:182 final size:183
Alignment explanation
Indices: 42273420--42273795 Score: 481
Period size: 182 Copynumber: 2.1 Consensus size: 183
42273410 GTGACTCAGT
* * *
42273420 CGTGTGTCCCTTGTAGGTCTTATTGCATACAAGTTAGGTAGTAACATGGCCTAACACATGGCCTG
1 CGTGTGTCCCTTGTAGGTCTTATTGCACACAAGTCAGGCAGTAACATGGCCTAACACATGGCCTG
*** ** * * *
42273485 GCTTATGGGCTTGTGGGGTTATTTCAAGAGTTACACAGCCTGGCACACGGGCATGAGACACGGCC
66 GAGCACAGGCGTGTGGGGCTATTTCAAGAGTTACACAGCCTGGCACACGGGCATGAGACACGGAC
* * * *
42273550 GTACAACCCTATTTAGTGAGTTACAC-TGTGAGGACATGGGTTGGGACACGAC
131 GTACAACCCTACTTAGTGAGTTACACGGGTGAGGACACGGGTTGGGACACAAC
* *
42273602 CGTGTGTCCCTTGTAGGTTTTATTGCACACAAGTCAGGCAGTTACATGGCCTAACACATGGCCTG
1 CGTGTGTCCCTTGTAGGTCTTATTGCACACAAGTCAGGCAGTAACATGGCCTAACACATGGCCTG
* * *
42273667 GAGCACAGGCGTGTGGGGCTATTTCGAGAGTTACACAGCCTGGCACATGGGCGAATG-G-CA-TG
66 GAGCACAGGCGTGTGGGGCTATTTCAAGAGTTACACAGCCTGGCACACGGGC--ATGAGACACGG
*** *
42273729 ACGTTGTGACCCTACTTAGTGAGTTACACGGGTGAGGACACGGGTTGGGACACAAT
129 ACG-TACAACCCTACTTAGTGAGTTACACGGGTGAGGACACGGGTTGGGACACAAC
42273785 CGTGTGTCCCT
1 CGTGTGTCCCT
42273796 ATTTTGATTC
Statistics
Matches: 166, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
181 3 0.02
182 126 0.76
183 34 0.20
184 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (183 bp):
CGTGTGTCCCTTGTAGGTCTTATTGCACACAAGTCAGGCAGTAACATGGCCTAACACATGGCCTG
GAGCACAGGCGTGTGGGGCTATTTCAAGAGTTACACAGCCTGGCACACGGGCATGAGACACGGAC
GTACAACCCTACTTAGTGAGTTACACGGGTGAGGACACGGGTTGGGACACAAC
Found at i:42283773 original size:26 final size:26
Alignment explanation
Indices: 42283691--42283781 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 26
42283681 AAAAAATCTA
* * *
42283691 TCATTTTACCTTATCGTGGTATTACAG
1 TCATTTTACCCTATAGGGGTATT-CAG
*
42283718 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTA-TTCAG
* *
42283745 TCATTTTACCCTATGGGGGTCTTCAG
1 TCATTTTACCCTATAGGGGTATTCAG
42283771 TCATTTTACCC
1 TCATTTTACCC
42283782 CGTGAGGGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
26 15 0.27
27 39 0.70
28 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (26 bp):
TCATTTTACCCTATAGGGGTATTCAG
Found at i:42283777 original size:53 final size:54
Alignment explanation
Indices: 42283691--42283805 Score: 144
Period size: 53 Copynumber: 2.1 Consensus size: 54
42283681 AAAAAATCTA
* * *
42283691 TCATTTTACCTTATCGTGGTATTACAGTCATTTTACCCTAT-AGGGGTATTTCGG
1 TCATTTTACCCTATCGGGGTATTACAGTCATTTTACCCCATGA-GGGTATTTCGG
* * * *
42283745 TCATTTTACCCTATGGGGGTCTT-CAGTCATTTTACCCCGTGAGGGTATTTTGG
1 TCATTTTACCCTATCGGGGTATTACAGTCATTTTACCCCATGAGGGTATTTCGG
42283798 TCATTTTA
1 TCATTTTA
42283806 TCATATGAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 33 0.62
54 20 0.38
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (54 bp):
TCATTTTACCCTATCGGGGTATTACAGTCATTTTACCCCATGAGGGTATTTCGG
Found at i:42283830 original size:27 final size:27
Alignment explanation
Indices: 42283797--42283949 Score: 234
Period size: 27 Copynumber: 5.7 Consensus size: 27
42283787 GGGTATTTTG
* *
42283797 GTCATTTTATCATATGAAGGAAAAATC
1 GTCATTTTATCACATGAGGGAAAAATC
* *
42283824 GTTATTTTATCACATGAGGGTAAAATC
1 GTCATTTTATCACATGAGGGAAAAATC
* *
42283851 ATCATTTTATCACATGAGGGCAAAATC
1 GTCATTTTATCACATGAGGGAAAAATC
* *
42283878 ATCATTTTATCACATGAGGGTAAAATC
1 GTCATTTTATCACATGAGGGAAAAATC
42283905 GTCATTTTATCACATGAGGGAAAAATC
1 GTCATTTTATCACATGAGGGAAAAATC
42283932 GTCATTTTATCACATGAG
1 GTCATTTTATCACATGAG
42283950 AGTTCAGGTA
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 116 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (27 bp):
GTCATTTTATCACATGAGGGAAAAATC
Found at i:42286290 original size:27 final size:27
Alignment explanation
Indices: 42286260--42286321 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
42286250 ATTTACTAAA
42286260 ATACCCCTAAGTATG-AAAATTACCACT
1 ATACCCCTAAG-ATGCAAAATTACCACT
* *
42286287 ATACCCCT-AGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCACT
42286313 ATACCCCTA
1 ATACCCCTA
42286322 GGGTTAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 21 0.68
27 8 0.26
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCACT
Found at i:42286472 original size:28 final size:28
Alignment explanation
Indices: 42286426--42286542 Score: 148
Period size: 28 Copynumber: 4.2 Consensus size: 28
42286416 GGAGGAAGCG
* *
42286426 TTCTGGTGGCTATGTCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* *
42286454 TTCTGGTGGTTCTGCCACAAATATCTGA
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
42286482 TTCTGGTGGCACTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
42286510 ATCTGGTGACTCTGTCAC-AATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
42286537 TT-TGGT
1 TTCTGGT
42286543 AGCCAAGTTG
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 4 0.05
27 10 0.13
28 63 0.82
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:42292944 original size:84 final size:84
Alignment explanation
Indices: 42292798--42292971 Score: 330
Period size: 84 Copynumber: 2.1 Consensus size: 84
42292788 GCTTGGGTTT
*
42292798 TTGCGACACACGTGGGGAAGGAGTTGGGGTCTTATCAGGACTCCTGGCAGCATGCTGAAGCATTG
1 TTGCTACACACGTGGGGAAGGAGTTGGGGTCTTATCAGGACTCCTGGCAGCATGCTGAAGCATTG
42292863 CAAGGGGTGGATAAGGATG
66 CAAGGGGTGGATAAGGATG
42292882 TTGCTACACACGTGGGGAAGGAGTTGGGGTCTTATCAGGACTCCTGGCAGCATGCTGAAGCATTG
1 TTGCTACACACGTGGGGAAGGAGTTGGGGTCTTATCAGGACTCCTGGCAGCATGCTGAAGCATTG
42292947 CAAGGGGTGGATAAGGATG
66 CAAGGGGTGGATAAGGATG
*
42292966 CTGCTA
1 TTGCTA
42292972 AATCGTGGAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (84 bp):
TTGCTACACACGTGGGGAAGGAGTTGGGGTCTTATCAGGACTCCTGGCAGCATGCTGAAGCATTG
CAAGGGGTGGATAAGGATG
Found at i:42295046 original size:39 final size:40
Alignment explanation
Indices: 42294922--42295105 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
42294912 GCTACTCGTT
*
42294922 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
42294962 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42295002 C-AATGCCTTCGGG-CTTAGCACGGAATTT-GTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTTAGTAACTCGCA
* * * *
42295040 CAAATGCCTTC-GGATCTTAGTCCAGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
42295081 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42295106 CATCATTCGA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
38 20 0.16
39 29 0.24
40 61 0.50
41 13 0.11
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42295068 original size:78 final size:80
Alignment explanation
Indices: 42294922--42295105 Score: 207
Period size: 78 Copynumber: 2.3 Consensus size: 80
42294912 GCTACTCGTT
* *
42294922 CAAATGCCTTCGGGACATAGCCCGG--TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 CAAA-GCCTTCGGGACTTAGCACGGAATT-T-GTAACTCGCACAAATGCCTTCGGGACTTAACCC
* *
42294985 GGATTTAATAAC-TCGCA
63 AGATTTAATAACTTAGCA
* **
42295002 CAATGCCTTCGGG-CTTAGCACGGAATTTGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCAG
1 CAAAGCCTTCGGGACTTAGCACGGAATTTGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCAG
* *
42295065 ATTTAGTCACTTAGCA
65 ATTTAATAACTTAGCA
*
42295081 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCACGGA
42295106 CATCATTCGA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
77 3 0.03
78 44 0.50
79 26 0.30
80 15 0.17
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCACGGAATTTGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGA
TTTAATAACTTAGCA
Found at i:42297080 original size:29 final size:29
Alignment explanation
Indices: 42297046--42297177 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
42297036 TACTCGATTT
** * *
42297046 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* *** * *
42297075 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
42297104 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
42297133 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42297162 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
42297178 ATCTCGTCAC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 2 0.02
29 85 0.98
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:42304427 original size:29 final size:29
Alignment explanation
Indices: 42304393--42304524 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
42304383 TACTCGATTT
** * *
42304393 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* *** * *
42304422 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
42304451 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
42304480 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42304509 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
42304525 ATCTCGTCAC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 2 0.02
29 85 0.98
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:42308300 original size:28 final size:28
Alignment explanation
Indices: 42308260--42308368 Score: 114
Period size: 28 Copynumber: 3.9 Consensus size: 28
42308250 GGAACCGTTC
*
42308260 TGGTGGCTATGCCACAAATATCTGTTTT
1 TGGTGGCTCTGCCACAAATATCTGTTTT
* * *
42308288 TGGTGGCTTTGCCACAAATATCTGATTC
1 TGGTGGCTCTGCCACAAATATCTGTTTT
* * *
42308316 TGGTGGCACTGTCACAAATAAT-TGTATT
1 TGGTGGCTCTGCCACAAAT-ATCTGTTTT
* *
42308344 TGGTGACTCTGTCAC-AATATCTGTT
1 TGGTGGCTCTGCCACAAATATCTGTT
42308369 CTGGCAGCCA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.03
27 6 0.09
28 57 0.85
29 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (28 bp):
TGGTGGCTCTGCCACAAATATCTGTTTT
Found at i:42308346 original size:56 final size:54
Alignment explanation
Indices: 42308256--42308372 Score: 139
Period size: 56 Copynumber: 2.1 Consensus size: 54
42308246 TGGAGGAACC
* * *
42308256 GTTCTGGTGGCTATGCCACAAATATCTGTTTTTGGTGGCTTTGCCACAAATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGTATTTGGTGACTCTGCCAC-AATATCT
* *
42308311 GATTCTGGTGGC-ACTGTCACAAATAAT-TGTATTTGGTGACTCTGTCACAATATCT
1 G-TTCTGGTGGCTA-TGCCACAAAT-ATCTGTATTTGGTGACTCTGCCACAATATCT
42308366 GTTCTGG
1 GTTCTGG
42308373 CAGCCATGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
54 6 0.11
55 10 0.19
56 36 0.67
57 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGTATTTGGTGACTCTGCCACAATATCT
Found at i:42311670 original size:129 final size:130
Alignment explanation
Indices: 42311435--42311687 Score: 393
Period size: 129 Copynumber: 2.0 Consensus size: 130
42311425 TTTAGAATTC
** *
42311435 AAAGAACATGAGTGAAATTCTAAAGGGATATTCGATCATTTTGAACAAATGGGAAATTGCAACCC
1 AAAGAACATGAGTGAAATTCTAAAGGGATATTCGATCATTTTGAACAAACAGGAAATTACAACCC
* *
42311500 AGCACGATAGGGCACGATTCCCCAAGTTGCCAAACATCGAACATTACCTTCGTTTTAAAATTTTT
66 AGCACGATAGGGCACAATTCCCCAAGTTACCAAACATCGAACATTACCTTCGTTTTAAAATTTTT
* *
42311565 AAAG-ACATGAGTGAAATTCTAAA-GGATTATTCGATTATTTTGAACAAACAGGAAATTACAACT
1 AAAGAACATGAGTGAAATTCTAAAGGGA-TATTCGATCATTTTGAACAAACAGGAAATTACAACC
* * *
42311628 CAGCACGATAGGGCACAATTCCCTAAGTTACCAAACATCGAACGTTGCCTTCGTTTTAAA
65 CAGCACGATAGGGCACAATTCCCCAAGTTACCAAACATCGAACATTACCTTCGTTTTAAA
42311688 GAAAATTTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 3 0.03
129 105 0.94
130 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (130 bp):
AAAGAACATGAGTGAAATTCTAAAGGGATATTCGATCATTTTGAACAAACAGGAAATTACAACCC
AGCACGATAGGGCACAATTCCCCAAGTTACCAAACATCGAACATTACCTTCGTTTTAAAATTTTT
Found at i:42317529 original size:79 final size:79
Alignment explanation
Indices: 42317402--42317603 Score: 273
Period size: 79 Copynumber: 2.5 Consensus size: 79
42317392 CGGAATTTAG
* * *
42317402 CCGGATATAACCACAAGCACAATTGCCTTC-GGTCTTAACCCGGGTATAGCAACTCGCACAAATG
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATG
* *
42317466 CCTTCGGGTCTTAGC
65 CCTTCAGGTCTTAAC
* *
42317481 CCGGATAT-ACAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATT
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATG
42317545 CCTTCAGGTCTTAAC
65 CCTTCAGGTCTTAAC
* * *
42317560 CCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGG
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGG
42317604 GTATCATTCA
Statistics
Matches: 108, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
77 1 0.01
78 16 0.15
79 61 0.56
80 29 0.27
81 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (79 bp):
CCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGC
CTTCAGGTCTTAAC
Found at i:42317549 original size:40 final size:40
Alignment explanation
Indices: 42317418--42317603 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
42317408 ATAACCACAA
* *
42317418 GCACAATTGCCTTC-GGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
*
42317457 GCACAAATGCCTTCGGGTCTTAGCCCGGATATA-CAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
42317496 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * * *
42317536 GCACAAATTCCTTCAGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
42317576 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
42317604 GTATCATTCA
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 51 0.39
40 78 0.60
41 2 0.02
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:42325595 original size:40 final size:40
Alignment explanation
Indices: 42325451--42325618 Score: 108
Period size: 40 Copynumber: 4.2 Consensus size: 40
42325441 CGGAATATAA
*** * *
42325451 CCGGATATAACCATGTGCACAAATACCTTCGGGTCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
* * ***
42325491 CCAGATAGAATGTCTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* * * *
42325531 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
*** * * *
42325571 CCGGATATAATTTCCAGCATAATTGTCTTCAGGAT-TTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTC-GGGTCTTAGC
42325611 CCGGATAT
1 CCGGATAT
42325619 CATTCAATTT
Statistics
Matches: 96, Mismatches: 27, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
39 2 0.02
40 89 0.93
41 5 0.05
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:42329162 original size:56 final size:54
Alignment explanation
Indices: 42329068--42329177 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 54
42329058 TGAAAAAAAA
42329068 AAAGAAAAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCG-AATGTACTAAGG
1 AAAGAAAAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCGAAAT-TACTAAGG
* ***
42329122 AAAGAAAAGAAAAATTTGTTCATCCTT-TCTCATCTTCTTGGCCGAAATTACTAAGG
1 AAAGAAAA-AAAAA-ATGTTCATCCTTCTC-CATAGGCTTGGCCGAAATTACTAAGG
42329178 GAAAAGGGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
54 8 0.17
55 7 0.15
56 30 0.62
57 3 0.06
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (54 bp):
AAAGAAAAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCGAAATTACTAAGG
Found at i:42330439 original size:40 final size:39
Alignment explanation
Indices: 42330368--42330523 Score: 142
Period size: 40 Copynumber: 3.9 Consensus size: 39
42330358 ATGAGAAATT
* * *
42330368 GAATGATATCCGGGCTAAG-CCCGAAGACAATTATGCTG
1 GAATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCTG
*
42330406 GAAATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCT-
1 G-AATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCTG
*
42330445 -AATGGCTATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-G
1 GAAT---TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG
* * *
42330485 AGTTATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 -G-AATTATATCCGGGCTAAGACCCGAAGGCAATTGTGC
42330524 ACGTGACTAT
Statistics
Matches: 97, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
37 3 0.03
38 1 0.01
39 19 0.20
40 70 0.72
41 2 0.02
43 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
GAATTATATCCGGGCTAAGACCCGAAGGCAATTGTGCTG
Found at i:42330537 original size:40 final size:40
Alignment explanation
Indices: 42330411--42330539 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
42330401 TGCTGGAAAT
* * * * *
42330411 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAATGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
* * * *
42330451 TATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
*
42330491 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGAC
42330531 TATATCCGG
1 TATATCCGG
42330540 TTATATTCCG
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
Found at i:42335003 original size:39 final size:39
Alignment explanation
Indices: 42334949--42335139 Score: 310
Period size: 39 Copynumber: 4.9 Consensus size: 39
42334939 AATGTTCGAG
42334949 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
*
42334988 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
42335027 TGATATCCGGGCTAAGCCCAAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
42335066 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
42335105 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
42335140 GGTTACCATA
Statistics
Matches: 143, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 126 0.88
40 17 0.12
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
Found at i:42335197 original size:79 final size:78
Alignment explanation
Indices: 42334947--42335198 Score: 258
Period size: 78 Copynumber: 3.2 Consensus size: 78
42334937 TGAATGTTCG
* * * ** *
42334947 AGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTATGATACCCGGGCTAAGCCCGAAGG
1 AGTGATATCCGGGTTAAGCCCAAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGG
**
42335012 CAATTGTGCGAGCT
66 CAATTGAACGAG-T
* ** *
42335026 A-TGATATCCGGGCTAAGCCCAAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGG
1 AGTGATATCCGGGTTAAGCCCAAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGG
**
42335090 CAATTGTGCGAGT
66 CAATTGAACGAGT
* * * * *
42335103 TGTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAA
1 AGTGATATCCGGGTTAAG-CCCAAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAG-CCCGAA
**
42335168 GGCGTTTGAACGAGT
64 GGCAATTGAACGAGT
42335183 AGCT-ATATCC-GGTTAA
1 AG-TGATATCCGGGTTAA
42335199 ACTCCGAAGG
Statistics
Matches: 152, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
77 1 0.01
78 87 0.57
79 39 0.26
80 24 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (78 bp):
AGTGATATCCGGGTTAAGCCCAAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGG
CAATTGAACGAGT
Found at i:42337310 original size:34 final size:34
Alignment explanation
Indices: 42337268--42337345 Score: 79
Period size: 35 Copynumber: 2.3 Consensus size: 34
42337258 TTGTTTGCAT
* * *
42337268 ACTGTACTGATA-TGTTAACGGGCTTA-GGCCCAG
1 ACTGTACTGATACTG-AAACAGGCTCAGGGCCCAG
*
42337301 ACTGTTACTGTTACTGAAACAGGCTCAGGGCCCAG
1 ACTG-TACTGATACTGAAACAGGCTCAGGGCCCAG
42337336 ACTGCTACTG
1 ACTG-TACTG
42337346 TTAAAGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 4 0.11
34 15 0.41
35 18 0.49
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (34 bp):
ACTGTACTGATACTGAAACAGGCTCAGGGCCCAG
Found at i:42346374 original size:41 final size:41
Alignment explanation
Indices: 42346329--42346410 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
42346319 CGCTCTACAT
42346329 AGATTGTAATATATCCAACATCAGCCTTTATAGAACAACCA
1 AGATTGTAATATATCCAACATCAGCCTTTATAGAACAACCA
42346370 AGATTGTAATATATCCAACATCAGCCTTTATAGAACAACCA
1 AGATTGTAATATATCCAACATCAGCCTTTATAGAACAACCA
42346411 GTTACGGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (41 bp):
AGATTGTAATATATCCAACATCAGCCTTTATAGAACAACCA
Found at i:42350395 original size:40 final size:40
Alignment explanation
Indices: 42350346--42350513 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
42350336 TCTTCGGAAT
* * *
42350346 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* * *** *
42350385 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
42350425 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
42350465 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
42350505 TTAGCCCGG
1 TTAGCCCGG
42350514 GTATCATTCA
Statistics
Matches: 107, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 103 0.96
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
Found at i:42353779 original size:27 final size:28
Alignment explanation
Indices: 42353723--42353791 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
42353713 AAATTTGTAC
*
42353723 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCAAGTTTGATTATAT
*
42353751 AGCACTGAGTGTGCAAG-TTGATTATAT
1 AGCACTAAGTGTGCAAGTTTGATTATAT
42353778 AGCACTAAGTGTGC
1 AGCACTAAGTGTGC
42353792 GGACTCACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCAAGTTTGATTATAT
Found at i:42355841 original size:2 final size:2
Alignment explanation
Indices: 42355788--42355830 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42355778 GTTGTTTTGT
42355788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42355830 T
1 T
42355831 TGAAAATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42369294 original size:27 final size:27
Alignment explanation
Indices: 42369226--42369375 Score: 88
Period size: 27 Copynumber: 5.6 Consensus size: 27
42369216 CGACTTGTAA
*
42369226 AATTACCAAAGTACTCC-CGATTTACAG
1 AATTACCAAAATAC-CCTCGATTTACAG
**** *
42369253 AATTACCGTTTTACCCTCAATTTACAG
1 AATTACCAAAATACCCTCGATTTACAG
* * * *
42369280 AATTACCAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTCGATTTACAG
* * * ** *
42369307 AATCACCAAAATACCCTTGGTTTGTAA
1 AATTACCAAAATACCCTCGATTTACAG
* * * *
42369334 AATTACTAAAATACCCTTTG-TTTATAA
1 AATTACCAAAATACCC-TCGATTTACAG
42369361 AATTACCAAAATACC
1 AATTACCAAAATACC
42369376 AATGGTTTGA
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 2 0.02
27 96 0.95
28 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (27 bp):
AATTACCAAAATACCCTCGATTTACAG
Found at i:42369322 original size:54 final size:54
Alignment explanation
Indices: 42369264--42369375 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
42369254 ATTACCGTTT
*
42369264 TACCCTCAATTTACAGAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
1 TACCCTCAATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
*** ** * * *
42369318 TACCCTTGGTTTGTAAAATTACTAAAATACCCTTTGTTTATAAAATTACCAAAA
1 TACCCTCAATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
42369372 TACC
1 TACC
42369376 AATGGTTTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.32
Consensus pattern (54 bp):
TACCCTCAATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAA
Found at i:42369382 original size:54 final size:54
Alignment explanation
Indices: 42369280--42369403 Score: 194
Period size: 54 Copynumber: 2.3 Consensus size: 54
42369270 CAATTTACAG
* ** *
42369280 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCTTGGTTTGTAA
1 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCAATGGTTTGAAA
* *
42369334 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCAATGGTTTGAAA
1 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCAATGGTTTGAAA
42369388 AATTACTAAAATACCC
1 AATTACTAAAATACCC
42369404 CTGTAGGGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (54 bp):
AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCAATGGTTTGAAA
Found at i:42369383 original size:27 final size:27
Alignment explanation
Indices: 42369280--42369403 Score: 169
Period size: 27 Copynumber: 4.6 Consensus size: 27
42369270 CAATTTACAG
42369280 AATTACCAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
* *
42369307 AATCACCAAAATACCCTTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* *
42369334 AATTACTAAAATACCCTTTGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
**
42369361 AATTACCAAAATACCAATGGTTTGA-AA
1 AATTACCAAAATACCCTTGGTTT-ATAA
*
42369388 AATTACTAAAATACCC
1 AATTACCAAAATACCC
42369404 CTGTAGGGTA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 83 0.99
28 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTATAA
Found at i:42369416 original size:27 final size:27
Alignment explanation
Indices: 42369386--42369447 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
42369376 AATGGTTTGA
42369386 AAAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
* *
42369413 AAAATTACTAAAATACCCTTGTGGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
42369440 AAAATTAC
1 AAAATTAC
42369448 CATTTTGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGTAGGGT
Found at i:42369416 original size:54 final size:54
Alignment explanation
Indices: 42369280--42369429 Score: 160
Period size: 54 Copynumber: 2.8 Consensus size: 54
42369270 CAATTTACAG
* ** * ** *
42369280 AATTACCAAAATACCCT-TGGTTTATAAAATCACCAAAATACCCTTGGTTTGTAA
1 AATTACTAAAATACCCTCT-GTGGATAAAATTACCAAAATACCAATGGTTTGAAA
* **
42369334 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCAATGGTTTGAAA
1 AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCAATGGTTTGAAA
* *
42369388 AATTACTAAAATACCC-CTGTAGGGTAAAATTACTAAAATACC
1 AATTACTAAAATACCCTCTGT-GGATAAAATTACCAAAATACC
42369430 CTTGTGGGGT
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 3 0.04
54 80 0.95
55 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (54 bp):
AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCAATGGTTTGAAA
Found at i:42369432 original size:81 final size:81
Alignment explanation
Indices: 42369280--42369432 Score: 211
Period size: 81 Copynumber: 1.9 Consensus size: 81
42369270 CAATTTACAG
** * **
42369280 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCTTGGTTTGTAAAATTACTAAAA
1 AATTACCAAAATACCAATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
42369345 TACCCTTTGTTTATAA
66 TACCCTTTGTTTATAA
* *
42369361 AATTACCAAAATACCAATGGTTTGA-AAAATTACTAAAATACCCCT-GTAGGGTAAAATTACTAA
1 AATTACCAAAATACCAATGGTTT-ATAAAATCACCAAAATACCCCTGGT-GGGTAAAATTACTAA
42369424 AATACCCTT
64 AATACCCTT
42369433 GTGGGGTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
80 2 0.03
81 60 0.95
82 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (81 bp):
AATTACCAAAATACCAATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
TACCCTTTGTTTATAA
Found at i:42370099 original size:28 final size:28
Alignment explanation
Indices: 42370067--42370135 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
42370057 GCGTAGATCA
42370067 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
42370095 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
42370123 CGATA-TACCCCTA
1 CGAAATTACCCCTA
42370136 GGGTTTTAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:42398940 original size:39 final size:39
Alignment explanation
Indices: 42398893--42399075 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
42398883 AATGTTCGAG
42398893 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42398932 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
42398971 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
42399010 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
42399050 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
42399076 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:42406369 original size:39 final size:39
Alignment explanation
Indices: 42406322--42406504 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
42406312 AATGTTCGAG
42406322 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42406361 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
42406400 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
42406439 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
42406479 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
42406505 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:42416588 original size:44 final size:40
Alignment explanation
Indices: 42416530--42416672 Score: 154
Period size: 38 Copynumber: 3.5 Consensus size: 40
42416520 TATATCCGGA
42416530 TAAGA-CCGACAGGCATTTGTGCGAGTTAGCTATAGTCCGGACGT
1 TAAGACCCGA-AGGCATTTGTGCGAGTTAGCTATA--CCGG--GT
*
42416574 TAAGACCCGAAGGCATTTGTGCGAGTTA-CGTATACCGGGC
1 TAAGACCCGAAGGCATTTGTGCGAGTTAGC-TATACCGGGT
*
42416614 T-AG-CCCGAAGGCATTTGAGCGAG-TATGCTATACCGGGT
1 TAAGACCCGAAGGCATTTGTGCGAGTTA-GCTATACCGGGT
*
42416652 TAA-ACCCGAAGGCAATTGTGC
1 TAAGACCCGAAGGCATTTGTGC
42416673 TTGTGGTTAT
Statistics
Matches: 88, Mismatches: 5, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
37 2 0.02
38 29 0.33
39 19 0.22
40 2 0.02
42 4 0.05
43 1 0.01
44 27 0.31
45 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
TAAGACCCGAAGGCATTTGTGCGAGTTAGCTATACCGGGT
Found at i:42424582 original size:40 final size:40
Alignment explanation
Indices: 42424497--42424647 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
42424487 AATTGAATGA
* * *
42424497 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
42424537 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
42424578 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
42424617 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
42424648 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:42424661 original size:40 final size:40
Alignment explanation
Indices: 42424534--42424663 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
42424524 ATGCTGGAAA
* * * *
42424534 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
42424574 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
42424614 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
42424654 TTATATCCGG
1 TTATATCCGG
42424664 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:42426624 original size:23 final size:22
Alignment explanation
Indices: 42426598--42426642 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
42426588 CATTTCATAT
*
42426598 ACCAAAATCAAACCATAATCACA
1 ACCAAAACCAAACCAT-ATCACA
*
42426621 ACCAAAACCAAGCCATATCACA
1 ACCAAAACCAAACCATATCACA
42426643 TGGCTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.53, C:0.33, G:0.02, T:0.11
Consensus pattern (22 bp):
ACCAAAACCAAACCATATCACA
Found at i:42427268 original size:42 final size:42
Alignment explanation
Indices: 42427179--42427325 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 42
42427169 CCAACTTCCT
* * * * *
42427179 AGATGTGGTCTTACATGTAATCAAATATTGATGCCACTGTCCT
1 AGATATGGTCTTACACGAAATCAAATA-TGATGCCAATGTCCC
* **
42427222 AGATAAGGTCTTACACGAAATCAAATACAATGCCAATGTCCC
1 AGATATGGTCTTACACGAAATCAAATATGATGCCAATGTCCC
* *
42427264 AGATATGGTCTTACATGTAAATCATAAGT-TGATGCCAACGTCCC
1 AGATATGGTCTTACACG-AAATCA-AA-TATGATGCCAATGTCCC
*
42427308 AGACATGGTCTTACACGA
1 AGATATGGTCTTACACGA
42427326 TAACACATAT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
42 26 0.30
43 30 0.35
44 29 0.34
45 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (42 bp):
AGATATGGTCTTACACGAAATCAAATATGATGCCAATGTCCC
Found at i:42427324 original size:86 final size:85
Alignment explanation
Indices: 42427162--42427325 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 85
42427152 AAAAAGCTCG
* * * *
42427162 TACAACGCCAACTTCCTAGATGTGGTCTTACATGTAATCAAATATTGATGCCACTGTCCTAGATA
1 TACAACGCCAACTTCCCAGATATGGTCTTACATGTAATCAAATATTGATGCCACTGTCCCAGACA
42427227 AGGTCTTACACGAAATCAAA
66 AGGTCTTACACGAAATCAAA
* *
42427247 TACAATGCCAA-TGTCCCAGATATGGTCTTACATGTAAATCATAA-GTTGATGCCAAC-GTCCCA
1 TACAACGCCAACT-TCCCAGATATGGTCTTACATGT-AATCA-AATATTGATGCC-ACTGTCCCA
*
42427309 GACATGGTCTTACACGA
62 GACAAGGTCTTACACGA
42427326 TAACACATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
84 1 0.01
85 30 0.44
86 33 0.49
87 4 0.06
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (85 bp):
TACAACGCCAACTTCCCAGATATGGTCTTACATGTAATCAAATATTGATGCCACTGTCCCAGACA
AGGTCTTACACGAAATCAAA
Found at i:42430358 original size:32 final size:33
Alignment explanation
Indices: 42430264--42430426 Score: 179
Period size: 32 Copynumber: 5.0 Consensus size: 33
42430254 TTTCTTTCTG
**
42430264 AGTGGTACACACAAAGTATACCTTTCCTTTTCA
1 AGTGGTACACACAAAGTATACCTAACCTTTTCA
* **
42430297 TA-TGGTATACACAAAGTATACCTTTCCTTTTCA
1 -AGTGGTACACACAAAGTATACCTAACCTTTTCA
* *
42430330 AGT-GTACACACAAAGTGTACATAACCTTTTCA
1 AGTGGTACACACAAAGTATACCTAACCTTTTCA
* *
42430362 AGT-GTACACACAAAGTGTACATAACCTTTTCA
1 AGTGGTACACACAAAGTATACCTAACCTTTTCA
** * *
42430394 TCTGGTATACAGAAAGTATACCTAACCTTTTCA
1 AGTGGTACACACAAAGTATACCTAACCTTTTCA
42430427 CATTCGATAC
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
32 58 0.50
33 56 0.49
34 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.33
Consensus pattern (33 bp):
AGTGGTACACACAAAGTATACCTAACCTTTTCA
Found at i:42430483 original size:30 final size:29
Alignment explanation
Indices: 42430419--42430517 Score: 153
Period size: 29 Copynumber: 3.4 Consensus size: 29
42430409 GTATACCTAA
*
42430419 CCTTTTCACATTCGATACCCAAAGCTATC
1 CCTTTTCACATTCGATAGCCAAAGCTATC
*
42430448 CCTTTTCACATTCGATAGCCGAAGCTATCC
1 CCTTTTCACATTCGATAGCCAAAGCTAT-C
* *
42430478 CCTTTTTACATTCGATAGCAAAAGCTATC
1 CCTTTTCACATTCGATAGCCAAAGCTATC
42430507 CCTTTTCACAT
1 CCTTTTCACAT
42430518 GGAATACACA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 37 0.59
30 26 0.41
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.33
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCAAAGCTATC
Found at i:42435011 original size:16 final size:17
Alignment explanation
Indices: 42434990--42435023 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
42434980 CGAACCCTAG
*
42434990 CTTTCTTTTTTAT-TTT
1 CTTTCTTATTTATGTTT
42435006 CTTTCTTATTTATGTTT
1 CTTTCTTATTTATGTTT
42435023 C
1 C
42435024 GGCAAGAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.74
Consensus pattern (17 bp):
CTTTCTTATTTATGTTT
Found at i:42444406 original size:40 final size:40
Alignment explanation
Indices: 42444317--42444410 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
42444307 GACTATGTTC
*
42444317 GGCACTAAGTGTGCGATTTGAAATAGCTTCGGCTATAAAT
1 GGCACTAAGTGTGCGAATTGAAATAGCTTCGGCTATAAAT
* * * * * **
42444357 AGCATTAAGTGTGCTAATTGGAATAGCTTTGGCTATATGT
1 GGCACTAAGTGTGCGAATTGAAATAGCTTCGGCTATAAAT
42444397 GGCACTAAGTGTGC
1 GGCACTAAGTGTGC
42444411 AATATTGAGA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.32
Consensus pattern (40 bp):
GGCACTAAGTGTGCGAATTGAAATAGCTTCGGCTATAAAT
Found at i:42446335 original size:40 final size:40
Alignment explanation
Indices: 42446252--42446459 Score: 184
Period size: 40 Copynumber: 5.2 Consensus size: 40
42446242 CGGGATTTAA
* * * * * *
42446252 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACCTAGC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
* ** * * *
42446292 CCGGTTATAGTGATTCGCACGATTGCCTTCGGGTCTTAAC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * *
42446332 CCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
*
42446372 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
*** * * *
42446412 CCGGATATAATTACTAGCA-TAATTGCCTTCGGGACTTAGC
1 CCGGATATAGCAACTCGCACGAA-TGCCTTCGGGTCTTAGC
42446452 CCGGATAT
1 CCGGATAT
42446460 CATTCCAATG
Statistics
Matches: 139, Mismatches: 28, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
39 2 0.01
40 137 0.99
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:42446372 original size:80 final size:80
Alignment explanation
Indices: 42446278--42446459 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 80
42446268 GCTCGATTGT
* * *** * * * **
42446278 CTTCGGGACCTAGCCCGGTTATAGTGATTCGCACGATTGCCTTCGGGTCTTAACCCGGATTTGGT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
*
42446343 AACTTGCACAAATGC
66 AACTAGCACAAATGC
* *
42446358 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAAT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
* * *
42446423 TACTAGCATAATTGC
66 AACTAGCACAAATGC
42446438 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
42446460 CATTCCAATG
Statistics
Matches: 85, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
AACTAGCACAAATGC
Found at i:42453828 original size:46 final size:46
Alignment explanation
Indices: 42453778--42453999 Score: 252
Period size: 46 Copynumber: 4.8 Consensus size: 46
42453768 TGGTTGAGCA
* *
42453778 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * * * *
42453824 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATTG-TAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGAT-GCGA-ACG
*
42453871 TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
42453917 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
42453963 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42454000 GCGGGTTACA
Statistics
Matches: 148, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
45 4 0.03
46 109 0.74
47 33 0.22
48 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:42453934 original size:93 final size:93
Alignment explanation
Indices: 42453775--42453945 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
42453765 GGATGGTTGA
* * * *
42453775 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42453840 TGAGTCCGAGTTCGTGAATTGTAACTAG
66 TGAGTCCGAGTTCGTGAATTGTAACTAG
*
42453868 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42453933 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
42453946 ACTTATGGAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATTGTAACTAG
Found at i:42460362 original size:16 final size:15
Alignment explanation
Indices: 42460337--42460370 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
42460327 AAAGTTGATA
*
42460337 ATAATTAATATATATT
1 ATAATAAATATA-ATT
42460353 ATAATAAATATAATT
1 ATAATAAATATAATT
42460368 ATA
1 ATA
42460371 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:42460493 original size:30 final size:30
Alignment explanation
Indices: 42460436--42460494 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
42460426 TGCCTTTGAA
* * *
42460436 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGACACACCAAATTTTT
42460466 AATATTTACAAAAAGATCA-ACCAAATTTT
1 AATATTTACAAAAAGA-CACACCAAATTTT
42460495 GAAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGACACACCAAATTTTT
Found at i:42466490 original size:40 final size:40
Alignment explanation
Indices: 42466409--42466626 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
42466399 CAACTAAGTA
* * *
42466409 CCTTCGGGATTTAG-CCGGACATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
42466448 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42466488 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42466528 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
42466568 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATT
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
42466608 CCGTCGGGGCTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42466627 TTATCATCTG
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
39 15 0.09
40 151 0.91
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42475934 original size:40 final size:40
Alignment explanation
Indices: 42475851--42476058 Score: 175
Period size: 40 Copynumber: 5.2 Consensus size: 40
42475841 CGGGATTTAA
* * * * * *
42475851 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACCTAGC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
* ** * * *
42475891 CCGGTTATAGTGATTCGCACGATTGCCTTCGGGTCTTAAC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * ** *
42475931 CCGGATTTGGTAACTTTCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
*
42475971 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
*** * * *
42476011 CCGGATATAATTACTAGCA-TAATTGCCTTCGGGACTTAGC
1 CCGGATATAGCAACTCGCACGAA-TGCCTTCGGGTCTTAGC
42476051 CCGGATAT
1 CCGGATAT
42476059 CATTCCAATG
Statistics
Matches: 137, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
39 2 0.01
40 135 0.99
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:42476038 original size:80 final size:80
Alignment explanation
Indices: 42475877--42476058 Score: 211
Period size: 80 Copynumber: 2.3 Consensus size: 80
42475867 GCTCGATTGT
* * *** * * * **
42475877 CTTCGGGACCTAGCCCGGTTATAGTGATTCGCACGATTGCCTTCGGGTCTTAACCCGGATTTGGT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
**
42475942 AACTTTCACAAATGC
66 AACTAGCACAAATGC
* *
42475957 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAAT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
* * *
42476022 TACTAGCATAATTGC
66 AACTAGCACAAATGC
42476037 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
42476059 CATTCCAATG
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT
AACTAGCACAAATGC
Found at i:42480559 original size:42 final size:43
Alignment explanation
Indices: 42480478--42480570 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 43
42480468 AGTCAGAATG
* *
42480478 TAATCTCGTATCGATGCCAATAGCCCAGCTATGGTCTTACACA
1 TAATCTCATATCGATGCCAATAGCCCAGATATGGTCTTACACA
* *
42480521 -AAGTCTCATATCGATGCC-ATATCCCGGATATGGTCTTACACA
1 TAA-TCTCATATCGATGCCAATAGCCCAGATATGGTCTTACACA
42480563 TAATCTCA
1 TAATCTCA
42480571 GTAACCCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
42 28 0.64
43 16 0.36
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (43 bp):
TAATCTCATATCGATGCCAATAGCCCAGATATGGTCTTACACA
Found at i:42483326 original size:16 final size:16
Alignment explanation
Indices: 42483307--42483337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42483297 CTTTTTCACT
42483307 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
42483323 TACTTACTTACTTAA
1 TACTCACTTACTTAA
42483338 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:42483343 original size:20 final size:20
Alignment explanation
Indices: 42483304--42483343 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42483294 AAACTTTTTC
* *
42483304 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
42483324 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
42483344 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:42483718 original size:55 final size:53
Alignment explanation
Indices: 42483529--42483780 Score: 214
Period size: 55 Copynumber: 4.8 Consensus size: 53
42483519 CGGTTACCTT
* * *
42483529 ACCATTGCCATGA-CTTGTCATGGTCTTACATGGTATCC-T---TT-TGAAACTT
1 ACCAATGCCAT-ACCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AACTC
* ** **
42483578 ACCATTGCCATGTCTCAACATGGTCTTACATGGTATCCTTGCCTTATGAACTC
1 ACCAATGCCATACCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTC
* * * *
42483631 ACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTT
1 ACCAATGCCATACCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-G-AACTC
* * * *
42483686 ATCAATGCCATATCTTGACATGGTCTTGCATGGTATCCTTGCCTTA-GAAACCTT
1 ACCAATGCCATACCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTC
* *
42483740 ACCAACTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 ACCAA-TGCCATACCTTGACATGGTCTTACATGGTATCCTT
42483781 AAACCCTAAT
Statistics
Matches: 167, Mismatches: 24, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
49 33 0.20
50 1 0.01
52 2 0.01
53 47 0.28
54 10 0.06
55 72 0.43
56 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (53 bp):
ACCAATGCCATACCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTC
Found at i:42491012 original size:16 final size:16
Alignment explanation
Indices: 42490993--42491023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42490983 CTTCTTCACT
42490993 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
42491009 TACTTACTTACTTAA
1 TACTCACTTACTTAA
42491024 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:42491029 original size:20 final size:20
Alignment explanation
Indices: 42490990--42491029 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42490980 AAACTTCTTC
* *
42490990 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
42491010 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
42491030 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:42491401 original size:55 final size:53
Alignment explanation
Indices: 42491270--42491465 Score: 198
Period size: 55 Copynumber: 3.6 Consensus size: 53
42491260 CTTACCATTT
**
42491270 CCATGTCTCAACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAACG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAACG
* * * * * * *
42491323 CCATGCCTTGGCATGGTCGTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-G-AACTCACCAACG
* *
42491378 CCATGTCTTGACATGGACTTACATGGTATCCTTGCCTTA-GAAACCTTACCAACTG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAAC-G
* * *
42491433 CCATGCCTTGGCGTGGTCTTACATGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGTATCCTT
42491466 AAACCCTAAT
Statistics
Matches: 116, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 8 0.07
55 70 0.60
56 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAACG
Found at i:42497877 original size:64 final size:64
Alignment explanation
Indices: 42497796--42497979 Score: 196
Period size: 67 Copynumber: 2.8 Consensus size: 64
42497786 AGACATTATG
* *
42497796 ATGTAGCTAGGTCGCATGGGTGATACAATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACAATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
42497860 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACAA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
42497925 AA
63 AA
* * *
42497927 ACTG--GCTAGGTCACATGGGTGGTACTAA-GTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATAC-AATGTGTACACCATGTAG-ACAAGAGAGC
42497980 CGAACTTTAT
Statistics
Matches: 100, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 18 0.18
67 31 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACAATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:42497913 original size:67 final size:64
Alignment explanation
Indices: 42497772--42497925 Score: 182
Period size: 67 Copynumber: 2.3 Consensus size: 64
42497762 CATCATGTGT
* * * *
42497772 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACAATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGCGTGATACAATGAGGACACCATG
42497837 TAG
62 TAG
* * *
42497840 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGT-GATACAA-TG-AGGACACCATGT
42497905 AG
63 AG
42497907 ACAAGAGAGCTACGAGATA
1 ACAAGAGAGCTACGAGATA
42497926 AACTGGCTAG
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
64 20 0.27
65 8 0.11
66 4 0.05
67 30 0.40
68 13 0.17
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.21
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACAATGAGGACACCATGTAG
Found at i:42499894 original size:8 final size:8
Alignment explanation
Indices: 42499881--42499907 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
42499871 CATCTTATAC
42499881 CAAATGAT
1 CAAATGAT
42499889 CAAATGAT
1 CAAATGAT
42499897 CAAATGAT
1 CAAATGAT
42499905 CAA
1 CAA
42499908 CTTGAACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (8 bp):
CAAATGAT
Found at i:42502082 original size:156 final size:156
Alignment explanation
Indices: 42501798--42502109 Score: 615
Period size: 156 Copynumber: 2.0 Consensus size: 156
42501788 GTTTTTGGCC
42501798 CATCGAGGCTCTTTTTCCGAAATACGTTAAAACGTCACACGAACTTACTTACCACCTTGCGGTGC
1 CATCGAGGCTCTTTTTCCGAAATACGTTAAAACGTCACACGAACTTACTTACCACCTTGCGGTGC
42501863 CAGAACTAACAACTACTCTATGTCTTGAGAGCATTCGCATACTCACAAGCCCATGAAATGCCAGA
66 CAGAACTAACAACTACTCTATGTCTTGAGAGCATTCGCATACTCACAAGCCCATGAAATGCCAGA
42501928 ATTTCGGCATTTCGGCTTTTGCCGAA
131 ATTTCGGCATTTCGGCTTTTGCCGAA
*
42501954 CATCGAGGCTCTTTTTTCGAAATACGTTAAAACGTCACACGAACTTACTTACCACCTTGCGGTGC
1 CATCGAGGCTCTTTTTCCGAAATACGTTAAAACGTCACACGAACTTACTTACCACCTTGCGGTGC
42502019 CAGAACTAACAACTACTCTATGTCTTGAGAGCATTCGCATACTCACAAGCCCATGAAATGCCAGA
66 CAGAACTAACAACTACTCTATGTCTTGAGAGCATTCGCATACTCACAAGCCCATGAAATGCCAGA
42502084 ATTTCGGCATTTCGGCTTTTGCCGAA
131 ATTTCGGCATTTCGGCTTTTGCCGAA
42502110 TTGAACTAAG
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (156 bp):
CATCGAGGCTCTTTTTCCGAAATACGTTAAAACGTCACACGAACTTACTTACCACCTTGCGGTGC
CAGAACTAACAACTACTCTATGTCTTGAGAGCATTCGCATACTCACAAGCCCATGAAATGCCAGA
ATTTCGGCATTTCGGCTTTTGCCGAA
Found at i:42503929 original size:42 final size:43
Alignment explanation
Indices: 42503863--42503982 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
42503853 TCGATTAACG
* * * **
42503863 ATGCAAATGTCCCAGATATGGTCTTACATGTAATC-GTATA-A
1 ATGCCAATGTCCCAGACATCGTCTTACATGTAATCACAATACA
* **
42503904 GATGTCAATGTCCCAGACATCGTCTTACACATAATCACAATACA
1 -ATGCCAATGTCCCAGACATCGTCTTACATGTAATCACAATACA
** *
42503948 ATGCCAATGTCCCAGACATTTTCTTATATGTAATC
1 ATGCCAATGTCCCAGACATCGTCTTACATGTAATC
42503983 TGATCTCGGT
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
42 29 0.47
43 32 0.52
44 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATCGTCTTACATGTAATCACAATACA
Found at i:42504109 original size:5 final size:5
Alignment explanation
Indices: 42504099--42504124 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42504089 ACTATTCAAC
42504099 ATTCA ATTCA ATTCA ATTCA ATTCA A
1 ATTCA ATTCA ATTCA ATTCA ATTCA A
42504125 AAATGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTCA
Found at i:42507712 original size:42 final size:41
Alignment explanation
Indices: 42507613--42507729 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 41
42507603 GTACCAATGT
*
42507613 CATATCCCAGATATGGTCTTA-ATGTAATCTCGTATCGATGC
1 CATAT-CCAGATATGGTCTTACATGTAATCTCATATCGATGC
* *
42507654 CAATAGCACAGCTATGGTCTTACATG-AAGTCTCATATCGATGC
1 C-ATATC-CAGATATGGTCTTACATGTAA-TCTCATATCGATGC
*
42507697 CATATCCTAGATATGGTCTTACACGTAATCTCA
1 CATATCC-AGATATGGTCTTACATGTAATCTCA
42507730 ATAACCCTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
41 3 0.05
42 42 0.66
43 19 0.30
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (41 bp):
CATATCCAGATATGGTCTTACATGTAATCTCATATCGATGC
Found at i:42507925 original size:20 final size:20
Alignment explanation
Indices: 42507897--42507938 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
42507887 TAAGCATTTA
* *
42507897 TACATATATAATTTAATTCT
1 TACACATATAATTTAATGCT
42507917 TACACATATAATTTAATGCT
1 TACACATATAATTTAATGCT
42507937 TA
1 TA
42507939 TTAAACATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (20 bp):
TACACATATAATTTAATGCT
Found at i:42508494 original size:26 final size:25
Alignment explanation
Indices: 42508431--42508538 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 25
42508421 TGATACAAAT
42508431 TGATAATGGTTAGGTAAATG-TTCA
1 TGATAATGGTTAGGTAAATGTTTCA
* * *
42508455 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGG-TTAGGTAAATGTTTCA
42508481 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATGTTTCA
42508507 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATGTTTCA
42508533 TGATAA
1 TGATAA
42508539 GAATTTCATG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
24 8 0.11
25 10 0.14
26 54 0.73
27 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTTCA
Found at i:42513248 original size:21 final size:21
Alignment explanation
Indices: 42513219--42513267 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
42513209 TTTTTTGTTA
42513219 ATGAGATAGTTTGTATACAAGT
1 ATGA-ATAGTTTGTATACAAGT
42513241 ATGAATAGTTTGTATACAAGT
1 ATGAATAGTTTGTATACAAGT
42513262 ATGAAT
1 ATGAAT
42513268 GATGATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (21 bp):
ATGAATAGTTTGTATACAAGT
Found at i:42515661 original size:11 final size:11
Alignment explanation
Indices: 42515636--42515683 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
42515626 CGAATCTGTC
* *
42515636 AAAAATAAATC
1 AAAAATTAATT
42515647 AAAAATTAATT
1 AAAAATTAATT
*
42515658 -AAAATTTATT
1 AAAAATTAATT
42515668 ATAAAATTAATT
1 A-AAAATTAATT
42515680 AAAA
1 AAAA
42515684 TTCAACATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 9 0.29
11 12 0.39
12 10 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAATTAATT
Found at i:42517974 original size:3 final size:3
Alignment explanation
Indices: 42517966--42518016 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
42517956 AAACCTTTCC
42517966 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42518014 AAT
1 AAT
42518017 CTCAAAACTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42521098 original size:18 final size:19
Alignment explanation
Indices: 42521063--42521101 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
42521053 TGCCTAAAAT
42521063 AAGGAAAAAGCAAGAAGAA
1 AAGGAAAAAGCAAGAAGAA
42521082 AAGGAAAAGAG-AA-AAGAA
1 AAGGAAAA-AGCAAGAAGAA
42521100 AA
1 AA
42521102 CACAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 10 0.53
20 2 0.11
ACGTcount: A:0.72, C:0.03, G:0.26, T:0.00
Consensus pattern (19 bp):
AAGGAAAAAGCAAGAAGAA
Found at i:42527603 original size:32 final size:32
Alignment explanation
Indices: 42527561--42527628 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
42527551 TGTGTGGCAC
* ***
42527561 GCCCGTGTGGCCCACATGTCCAACTTAGCCTA
1 GCCCATGTGGCCCACACACCCAACTTAGCCTA
42527593 GCCCATGTGGCCCACACACCCAACTTAGCCTA
1 GCCCATGTGGCCCACACACCCAACTTAGCCTA
42527625 GCCC
1 GCCC
42527629 GTGTAGCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.21, C:0.43, G:0.19, T:0.18
Consensus pattern (32 bp):
GCCCATGTGGCCCACACACCCAACTTAGCCTA
Found at i:42527641 original size:32 final size:32
Alignment explanation
Indices: 42527580--42527641 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
42527570 GCCCACATGT
*
42527580 CCAACTTAGCCTAGCCCATGTGGCCCACACAC
1 CCAACTTAGCCTAGCCCATGTAGCCCACACAC
* *
42527612 CCAACTTAGCCTAGCCCGTGTAGCTCACAC
1 CCAACTTAGCCTAGCCCATGTAGCCCACAC
42527642 GGTTACACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.24, C:0.42, G:0.16, T:0.18
Consensus pattern (32 bp):
CCAACTTAGCCTAGCCCATGTAGCCCACACAC
Found at i:42532347 original size:100 final size:100
Alignment explanation
Indices: 42532216--42532403 Score: 322
Period size: 100 Copynumber: 1.9 Consensus size: 100
42532206 GATGGTTAGG
*
42532216 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGCCACATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCACATGTGTAGTACT
*
42532281 AAGTGCAGGCTACTATGCATACCCGAAAACTGTGA
66 AAGTACAGGCTACTATGCATACCCGAAAACTGTGA
* * * *
42532316 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCACATGTGTAGTACT
42532381 AAGTACAGGCTACTATGCATACC
66 AAGTACAGGCTACTATGCATACC
42532404 AGATAGCTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCACATGTGTAGTACT
AAGTACAGGCTACTATGCATACCCGAAAACTGTGA
Found at i:42532404 original size:49 final size:49
Alignment explanation
Indices: 42532113--42532408 Score: 306
Period size: 49 Copynumber: 5.9 Consensus size: 49
42532103 TCTATTATGA
* *
42532113 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCA-AAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTA-CCAGATAA-T-T
* * * * **
42532164 GATCACTTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * *
42532213 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * * * *
42532263 GGCCACATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-T-T
* * * * *
42532314 GATCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * * *
42532363 GGTCGCATGTGTAGTACTAAGTACAGGCTACTATGCATACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
42532409 GCTTCGGCTA
Statistics
Matches: 201, Mismatches: 40, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
49 79 0.39
50 48 0.24
51 74 0.37
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:42535753 original size:37 final size:37
Alignment explanation
Indices: 42535694--42535839 Score: 231
Period size: 37 Copynumber: 3.9 Consensus size: 37
42535684 AGCTCAGACG
* *
42535694 AAATCTCCACACGA-AGTTATCGGGTCTTACCCTGACA
1 AAATCTCCACAC-ATAGTCATCGGGTCTTACCCGGACA
42535731 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
* *
42535768 AAATCTCCACACGTAGTCATTGGGTCTTACCCGGACA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
*
42535805 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACATAGTCATCGGGTCTTACCCGGA
42535840 ATATATTTCC
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
36 1 0.01
37 102 0.99
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACATAGTCATCGGGTCTTACCCGGACA
Found at i:42535955 original size:48 final size:48
Alignment explanation
Indices: 42535884--42536077 Score: 316
Period size: 48 Copynumber: 4.0 Consensus size: 48
42535874 TGTTACAACA
* * * * *
42535884 TTCACATTAGCCATTCGGCTTTACCACATATTCGTATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
42535932 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
42535980 TTCACATTAGCCCTTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
42536028 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
42536076 TT
1 TT
42536078 ATTTATCTTG
Statistics
Matches: 136, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 136 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:42546376 original size:34 final size:34
Alignment explanation
Indices: 42546302--42546415 Score: 83
Period size: 30 Copynumber: 3.4 Consensus size: 34
42546292 ATGTTGCTAC
* * * * **
42546302 TATTTTATTGTTATTATTTAGATATTATATAAAACT
1 TATTTTATTGTTA--ATTTTGTTATTATTTTAAAGG
42546338 TATTTTATTGTTAATTTTGTTATTATTTTAAAGG
1 TATTTTATTGTTAATTTTGTTATTATTTTAAAGG
* *
42546372 TA---T-TTGTTAATTTTGTTATTAATTTAGAGG
1 TATTTTATTGTTAATTTTGTTATTATTTTAAAGG
* **
42546402 CATTTGCTTGTTAA
1 TATTTTATTGTTAA
42546416 GTTATATTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
30 26 0.41
31 1 0.02
34 24 0.38
36 13 0.20
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (34 bp):
TATTTTATTGTTAATTTTGTTATTATTTTAAAGG
Found at i:42546379 original size:30 final size:30
Alignment explanation
Indices: 42546345--42546407 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
42546335 ACTTATTTTA
* *
42546345 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTGTTATTAATTTAAAGGCAT
*
42546375 TTGTTAATTTTGTTATTAATTTAGAGGCAT
1 TTGTTAATTTTGTTATTAATTTAAAGGCAT
42546405 TTG
1 TTG
42546408 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTAATTTAAAGGCAT
Found at i:42546545 original size:11 final size:11
Alignment explanation
Indices: 42546529--42546559 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42546519 TATATATATG
42546529 TAAAAATTATA
1 TAAAAATTATA
*
42546540 TAAAAATAATA
1 TAAAAATTATA
42546551 TAAAAATTA
1 TAAAAATTA
42546560 ATATGAGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:42546556 original size:12 final size:11
Alignment explanation
Indices: 42546529--42546563 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
42546519 TATATATATG
*
42546529 TAAAAATTATA
1 TAAAAATAATA
42546540 TAAAAATAATA
1 TAAAAATAATA
42546551 TAAAAATTAATA
1 TAAAAA-TAATA
42546563 T
1 T
42546564 GAGCGAGCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:42552081 original size:35 final size:35
Alignment explanation
Indices: 42552042--42552111 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
42552032 CTTTGAATTT
42552042 GACCCAGAACTCATGGGTAGCTTCAGATTTTTTTA
1 GACCCAGAACTCATGGGTAGCTTCAGATTTTTTTA
42552077 GACCCAGAACTCATGGGTAGCTTCAGATTTTTTTA
1 GACCCAGAACTCATGGGTAGCTTCAGATTTTTTTA
42552112 TTTCCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (35 bp):
GACCCAGAACTCATGGGTAGCTTCAGATTTTTTTA
Found at i:42559005 original size:60 final size:60
Alignment explanation
Indices: 42558941--42559085 Score: 238
Period size: 60 Copynumber: 2.4 Consensus size: 60
42558931 GGGCTTTGTC
42558941 GGATTACCAGTCCAGACTAAATCCTTTATATGACAAAGAACTCCTTAGAGAGTCAAATCT
1 GGATTACCAGTCCAGACTAAATCCTTTATATGACAAAGAACTCCTTAGAGAGTCAAATCT
* *
42559001 GGATTACCAGTCCA-AGCTAAATCCTTTATATGACAAAGAACTCTTTATAGAGTCAAATCT
1 GGATTACCAGTCCAGA-CTAAATCCTTTATATGACAAAGAACTCCTTAGAGAGTCAAATCT
* *
42559061 GGATTACCAATCCAGGCTAAATCCT
1 GGATTACCAGTCCAGACTAAATCCT
42559086 AATCGAAACA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
59 1 0.01
60 78 0.99
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (60 bp):
GGATTACCAGTCCAGACTAAATCCTTTATATGACAAAGAACTCCTTAGAGAGTCAAATCT
Found at i:42563596 original size:27 final size:27
Alignment explanation
Indices: 42563015--42563595 Score: 726
Period size: 27 Copynumber: 21.6 Consensus size: 27
42563005 AAAGTACTCC
*
42563015 CGATTTACATAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
42563042 C-AGGTTATAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
42563069 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
42563096 CAATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42563123 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42563150 CGATTTACAGAAATACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
42563177 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
42563204 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42563231 C-AGTTTACAGAATTATTGTTTTACCAT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
42563258 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42563285 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42563312 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
42563339 CGATTTACA-AATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
42563365 C-AGTTTACA-AATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
42563391 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
42563417 CTAATTTACATAATTACCATTTTACCCC
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
42563445 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
42563472 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42563499 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
42563526 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
42563553 TGATTCACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
42563580 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
42563596 TAAAATACCC
Statistics
Matches: 482, Mismatches: 61, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
25 1 0.00
26 49 0.10
27 428 0.89
28 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Done.