Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 156 of 344
Found at i:51965606 original size:6 final size:6
Alignment explanation
Indices: 51965580--51965628 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
51965570 TTCTTAAGCA
* *
51965580 AAAAAG AAAAA- AGAGAA- AAAAAG AAAAAG AAAAAG AAAAA- CAAAAG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
51965626 AAA
1 AAA
51965629 TGCATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:51965607 original size:23 final size:23
Alignment explanation
Indices: 51965580--51965628 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
51965570 TTCTTAAGCA
*
51965580 AAAAAGAAAAAAGAGAAA-AAAAG
1 AAAAAG-AAAAAGAAAAACAAAAG
51965603 AAAAAGAAAAAGAAAAACAAAAG
1 AAAAAGAAAAAGAAAAACAAAAG
51965626 AAA
1 AAA
51965629 TGCATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAGAAAAACAAAAG
Found at i:51965612 original size:11 final size:10
Alignment explanation
Indices: 51965579--51965628 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
51965569 ATTCTTAAGC
51965579 AAAAAAG-AA
1 AAAAAAGAAA
*
51965588 AAAAGAGAAA
1 AAAAAAGAAA
51965598 AAAAGAA-AAA
1 AAAA-AAGAAA
*
51965608 GAAAAAGAAA
1 AAAAAAGAAA
51965618 AACAAAAGAAA
1 AA-AAAAGAAA
51965629 TGCATTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.24
10 16 0.48
11 9 0.27
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:51965618 original size:17 final size:16
Alignment explanation
Indices: 51965579--51965628 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
51965569 ATTCTTAAGC
*
51965579 AAAAAAGAAAAAAGAGA
1 AAAAAAG-AAAAAGAAA
51965596 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
51965612 AAGAAAA-ACAAAAGAAA
1 AA-AAAAGA-AAAAGAAA
51965629 TGCATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:51966275 original size:10 final size:10
Alignment explanation
Indices: 51966251--51966309 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
51966241 AATTTTAGCT
*
51966251 TTTATCTTCA
1 TTTATCTTTA
51966261 TTTATCTTTA
1 TTTATCTTTA
* *
51966271 ATTATATTTA
1 TTTATCTTTA
* *
51966281 ATCATCTTTA
1 TTTATCTTTA
51966291 TTTAT-TTGTA
1 TTTATCTT-TA
51966301 TTTATCTTT
1 TTTATCTTT
51966310 TAAAATTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 2 0.05
10 36 0.90
11 2 0.05
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:51968307 original size:3 final size:3
Alignment explanation
Indices: 51968299--51968333 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
51968289 CCATTTCCTA
51968299 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
51968334 AAGTAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:51971054 original size:23 final size:22
Alignment explanation
Indices: 51971011--51971054 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
51971001 AAATAAAATC
*
51971011 TAATCCCTATAAACCTGCTATG
1 TAATCCCTATAAACCTACTATG
* *
51971033 TAATCTCCTCTAAATCTACTAT
1 TAATC-CCTATAAACCTACTAT
51971055 ACAAATATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (22 bp):
TAATCCCTATAAACCTACTATG
Found at i:51971251 original size:1 final size:1
Alignment explanation
Indices: 51971245--51971272 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
51971235 CTGTATTGGC
51971245 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
51971273 GAAGGATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:51973150 original size:33 final size:33
Alignment explanation
Indices: 51973106--51973173 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
51973096 TGATACATGT
*
51973106 CCTATATCAGTGTCTTCATCA-TTAGATCCAACC
1 CCTATACCAGTGTCTTCATCATTTA-ATCCAACC
*
51973139 CCTATACCAGTGTCTTCGTCATTTAATCCAACC
1 CCTATACCAGTGTCTTCATCATTTAATCCAACC
51973172 CC
1 CC
51973174 AATTAACCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.25, C:0.34, G:0.09, T:0.32
Consensus pattern (33 bp):
CCTATACCAGTGTCTTCATCATTTAATCCAACC
Found at i:51975486 original size:19 final size:19
Alignment explanation
Indices: 51975462--51975502 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
51975452 TATTTTAAAG
51975462 TTATTTAGATAGATAAATC
1 TTATTTAGATAGATAAATC
*
51975481 TTATTTAGGTAGATAAATC
1 TTATTTAGATAGATAAATC
51975500 TTA
1 TTA
51975503 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (19 bp):
TTATTTAGATAGATAAATC
Found at i:51982919 original size:13 final size:13
Alignment explanation
Indices: 51982883--51982919 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
51982873 TTTTTTAAAA
51982883 TTTATATTATTT-T
1 TTTATATT-TTTAT
51982896 TTTAT-TTTTTAT
1 TTTATATTTTTAT
51982908 TTTATATTTTTA
1 TTTATATTTTTA
51982920 AATTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 8 0.36
13 11 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATATTTTTAT
Found at i:52001984 original size:47 final size:47
Alignment explanation
Indices: 52001932--52002337 Score: 623
Period size: 47 Copynumber: 8.6 Consensus size: 47
52001922 GATAATTGTG
* * *
52001932 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATATGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
52001979 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
52002026 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
52002075 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
52002122 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
52002171 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
52002218 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
52002265 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
52002312 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
52002338 TCCCGAAGGG
Statistics
Matches: 330, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
47 240 0.73
49 90 0.27
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:52002039 original size:96 final size:96
Alignment explanation
Indices: 52001932--52002337 Score: 680
Period size: 96 Copynumber: 4.3 Consensus size: 96
52001922 GATAATTGTG
*
52001932 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATATGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
52001995 ATGTGATAAGGCCGAATGGCCAATGTGATGA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
52002026 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
52002091 ATGTGATAAGGCCGAATGGCCAATGTGATGA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
52002122 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * *
52002187 ATGTGATAAGGCCTAATAGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
*
52002218 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * *
52002281 ATGTGACAGGGCCGAGTGGCCAACGTGATGG
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
52002312 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
52002338 TCCCGAAGGG
Statistics
Matches: 294, Mismatches: 14, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
94 99 0.34
95 3 0.01
96 192 0.65
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:52002079 original size:143 final size:143
Alignment explanation
Indices: 52001932--52002337 Score: 640
Period size: 143 Copynumber: 2.9 Consensus size: 143
52001922 GATAATTGTG
* * *
52001932 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATATGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
*
52001997 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
66 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATA
52002062 GCCGATGTGATGA
131 GCCGATGTGATGA
* *
52002075 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT
* *
52002140 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAA
64 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAA
52002203 TAGCCGATGTGATGA
129 TAGCCGATGTGATGA
*
52002218 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* * * * *
52002283 GTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
66 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
52002338 TCCCGAAGGG
Statistics
Matches: 241, Mismatches: 18, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
141 50 0.21
142 1 0.00
143 145 0.60
145 45 0.19
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (143 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATA
GCCGATGTGATGA
Found at i:52007490 original size:4 final size:4
Alignment explanation
Indices: 52007483--52007507 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
52007473 GCTAGTGCTA
52007483 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
52007508 TAAAGGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:52011014 original size:40 final size:40
Alignment explanation
Indices: 52010970--52011225 Score: 363
Period size: 40 Copynumber: 6.4 Consensus size: 40
52010960 GATGACAACG
* * * *
52010970 GGGCTAAGTCCCGAAGGCATTTGTGCTAATGACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* **
52011010 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTTT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
52011050 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
52011090 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
**
52011130 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
52011170 GGGCTAAGTCCCGAAGGCATTTGAGTGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* *
52011210 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
52011226 TACTTGGTTT
Statistics
Matches: 198, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 16 0.08
40 182 0.92
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:52019634 original size:12 final size:12
Alignment explanation
Indices: 52019606--52019647 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
52019596 ACACACACAC
*
52019606 CCGTGTGGCTAGC
1 CCGTGT-GCTAGG
52019619 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
52019631 CCGTATGCTAGG
1 CCGTGTGCTAGG
52019643 CCGTG
1 CCGTG
52019648 CCAATCCTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.24
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:52021435 original size:54 final size:55
Alignment explanation
Indices: 52021332--52021440 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 55
52021322 CTAGCCAAAT
* *
52021332 TTCAATTAGGTCTCTAATAGCCCATATATTTAATTGATTTCATAGTTTAACCATG
1 TTCAATTAGGTCTCTAATAGCCCATATATTTAATTGATTTCACAATTTAACCATG
* * *
52021387 TTCAATTAGGTCTCTAGTAG-CCATATTTTTCACTT-ATTTCACAATTTAACCATG
1 TTCAATTAGGTCTCTAATAGCCCATATATTT-AATTGATTTCACAATTTAACCATG
52021441 AATTTTACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
54 26 0.54
55 22 0.46
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.42
Consensus pattern (55 bp):
TTCAATTAGGTCTCTAATAGCCCATATATTTAATTGATTTCACAATTTAACCATG
Found at i:52021479 original size:29 final size:29
Alignment explanation
Indices: 52021421--52021479 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
52021411 ATTTTTCACT
* **
52021421 TATTTCACAATTTAACCATGAATTTTACA
1 TATTTCACAAATTAACCATGAATTGGACA
*
52021450 TATTTCACAAATTAATCC-TTAATTGGACA
1 TATTTCACAAATTAA-CCATGAATTGGACA
52021479 T
1 T
52021480 TTACTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (29 bp):
TATTTCACAAATTAACCATGAATTGGACA
Found at i:52024606 original size:14 final size:14
Alignment explanation
Indices: 52024580--52024609 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
52024570 GTATTTGGCC
52024580 AAGGGAAGAAAAAT
1 AAGGGAAGAAAAAT
52024594 AAGGAGAAGAAAAAT
1 AAGG-GAAGAAAAAT
52024609 A
1 A
52024610 TTTTTTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (14 bp):
AAGGGAAGAAAAAT
Found at i:52034079 original size:29 final size:29
Alignment explanation
Indices: 52034045--52034119 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
52034035 CCATTAATTC
52034045 ATATGGCCCATTAGGCCCAAATCA-ACTGT
1 ATATGGCCCATTAGGCCCAAATCACA-TGT
*
52034074 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATGT
*
52034103 ATATGGCCCGTTAGGCC
1 ATATGGCCCATTAGGCC
52034120 TAGTCACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 42 0.98
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATGT
Found at i:52035758 original size:46 final size:46
Alignment explanation
Indices: 52035615--52035823 Score: 181
Period size: 46 Copynumber: 4.4 Consensus size: 46
52035605 TTTGTACGCC
* * *
52035615 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA-TATCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGT-GCT
* * *** * * *
52035661 AGTGTAAGACCATGTCTGGGACACGGCATCGGCGTTGA-GACGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCAGC-CACATTATGAGTGCT
*
52035709 AGTGTAAGACATGTCTTGGACATGCATCAGCCACATTATGAGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGTGCT
* * *
52035755 AGTGTAAGACATGTCTGGAACATGCATCAG-CACGTATATACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC--AT-TATGAGTGCT
*
52035803 AGTGTAATACCATGTCTGGGA
1 AGTGTAAGA-CATGTCTGGGA
52035824 TATGGCGTCG
Statistics
Matches: 130, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
45 4 0.03
46 51 0.39
47 27 0.21
48 37 0.28
49 11 0.08
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGTGCT
Found at i:52035798 original size:94 final size:94
Alignment explanation
Indices: 52035615--52035823 Score: 255
Period size: 94 Copynumber: 2.2 Consensus size: 94
52035605 TTTGTACGCC
* *
52035615 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGATATCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGATAGCCAGTGTAAGACCATGTCTGG
* * *
52035680 GACACGGCATCGGCGTTGAGACGAGGGCT
66 AACACGGCATCGACGTTGAGACGAGAGCT
* *
52035709 AGTGTAAGACATGTCTTGGACATGCATCAGCCACATTATGAGT-GCTAGTGTAAGA-CATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGA-TAGCCAGTGTAAGACCATGTCTG
* *
52035772 GAACA-TGCATCAGCACGTAT-ATACGAGAGCT
65 GAACACGGCATC-G-ACGT-TGAGACGAGAGCT
*
52035803 AGTGTAATACCATGTCTGGGA
1 AGTGTAAGA-CATGTCTGGGA
52035824 TATGGCGTCG
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
92 5 0.05
93 13 0.13
94 69 0.70
95 12 0.12
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGATAGCCAGTGTAAGACCATGTCTGG
AACACGGCATCGACGTTGAGACGAGAGCT
Found at i:52039344 original size:46 final size:46
Alignment explanation
Indices: 52039271--52039539 Score: 257
Period size: 46 Copynumber: 5.8 Consensus size: 46
52039261 TATTTGGGAA
*
52039271 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
52039317 TCTGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
52039362 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
52039410 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
52039455 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
52039503 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52039540 GCGGGTTACA
Statistics
Matches: 179, Mismatches: 26, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
42 4 0.02
43 9 0.05
45 6 0.03
46 88 0.49
47 54 0.30
48 6 0.03
50 8 0.04
51 4 0.02
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52039384 original size:47 final size:47
Alignment explanation
Indices: 52039320--52039485 Score: 216
Period size: 47 Copynumber: 3.6 Consensus size: 47
52039310 GCGAATGTCT
52039320 GAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
* * * *
52039367 GAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAAC---GC--CC
1 GAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
52039413 GAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
*
52039460 GAGCTCGTTGAGTTGAGTCTGAGTTC
1 GAGCTCGTTGAGTTGAGTCCGAGTTC
52039486 ACTTATGGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 4 0.04
46 27 0.27
47 52 0.51
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (47 bp):
GAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
Found at i:52039429 original size:93 final size:93
Alignment explanation
Indices: 52039270--52039532 Score: 499
Period size: 93 Copynumber: 2.8 Consensus size: 93
52039260 ATATTTGGGA
* * *
52039270 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCTGAGCTCGTTGAGTTG
1 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
52039335 AGTCCGAGTTCGTGAGATGTAACTAGGC
66 AGTCCGAGTTCGTGAGATGTAACTAGGC
52039363 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
1 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
52039428 AGTCCGAGTTCGTGAGATGTAACTAGGC
66 AGTCCGAGTTCGTGAGATGTAACTAGGC
52039456 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
1 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
52039521 AGTCCGAGTTCG
66 AGTCCGAGTTCG
52039533 CTTATGGGCG
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 167 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (93 bp):
ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
AGTCCGAGTTCGTGAGATGTAACTAGGC
Found at i:52039900 original size:38 final size:38
Alignment explanation
Indices: 52039849--52039924 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
52039839 AAGTTATTTG
52039849 TTATTTGCACGTGGACTTACTAAGCATCTATGCTTACT
1 TTATTTGCACGTGGACTTACTAAGCATCTATGCTTACT
52039887 TTATTTGCACGTGGACTTACTAAGCATCTATGCTTACT
1 TTATTTGCACGTGGACTTACTAAGCATCTATGCTTACT
52039925 CCCTTCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (38 bp):
TTATTTGCACGTGGACTTACTAAGCATCTATGCTTACT
Found at i:52041914 original size:16 final size:16
Alignment explanation
Indices: 52041890--52041920 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52041880 AAATTCAAGC
*
52041890 TTTCGGGATTTTTGGA
1 TTTCAGGATTTTTGGA
52041906 TTTCAGGATTTTTGG
1 TTTCAGGATTTTTGG
52041921 GGCGTTACAC
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:0.13, C:0.06, G:0.29, T:0.52
Consensus pattern (16 bp):
TTTCAGGATTTTTGGA
Found at i:52045182 original size:27 final size:26
Alignment explanation
Indices: 52045107--52045221 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 26
52045097 TGGAGTAAGC
* *
52045107 GTTCTGGTGGCTATGCCACAAATATTT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
*
52045134 GTTTCTGGTGGCTAC-GCTACAAATATCT
1 G-TTCTGGTGGCT-CTGCCAC-AATATCT
52045162 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * * *
52045188 ATATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
52045215 GTTCTGG
1 GTTCTGG
52045222 AAGCCATGCT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
26 13 0.18
27 38 0.51
28 23 0.31
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:52052862 original size:28 final size:28
Alignment explanation
Indices: 52052818--52052907 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
52052808 GGAGGAAGCG
* *
52052818 TTCTGATGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTACGCCACAAATATCTGT
52052846 TTCTGGTGGCTACGCCACAAATATCTGT
1 TTCTGGTGGCTACGCCACAAATATCTGT
52052874 TT-TGGTGGC-ACTGCCAC-AATATCTGT
1 TTCTGGTGGCTAC-GCCACAAATATCTGT
*
52052900 ATCTGGTG
1 TTCTGGTG
52052908 ACTCTGTCTC
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
26 12 0.21
27 17 0.30
28 28 0.49
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (28 bp):
TTCTGGTGGCTACGCCACAAATATCTGT
Found at i:52052889 original size:27 final size:29
Alignment explanation
Indices: 52052818--52052931 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 29
52052808 GGAGGAAGCG
*
52052818 TTCTGATGGCTA-TGCCACAAATATCTGT
1 TTCTGGTGGCTACTGCCACAAATATCTGT
52052846 TTCTGGTGGCTAC-GCCACAAATATCTGT
1 TTCTGGTGGCTACTGCCACAAATATCTGT
52052874 TT-TGGTGGC-ACTGCCAC-AATATCTGT
1 TTCTGGTGGCTACTGCCACAAATATCTGT
* * * *
52052900 ATCTGGTGACT-CTGTCTC-AATATCTG-
1 TTCTGGTGGCTACTGCCACAAATATCTGT
52052926 TTCTGG
1 TTCTGG
52052932 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
26 17 0.22
27 31 0.41
28 28 0.37
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (29 bp):
TTCTGGTGGCTACTGCCACAAATATCTGT
Found at i:52056446 original size:12 final size:13
Alignment explanation
Indices: 52056429--52056461 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52056419 GTTTCGCACG
52056429 TTTAAATAGTT-T
1 TTTAAATAGTTGT
*
52056441 TTTAAATTGTTGT
1 TTTAAATAGTTGT
52056454 TTTAAATA
1 TTTAAATA
52056462 CTATCATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (13 bp):
TTTAAATAGTTGT
Found at i:52058442 original size:63 final size:63
Alignment explanation
Indices: 52058341--52058460 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
52058331 TTACCTATCT
*
52058341 GGGCTAAATCCTTAATGCACACATATTCATCAAAAGGCTCGATTACTCAAGGAACACCCATTC
1 GGGCTAAATCCTTAATGCACACATATTCATCAAAAGGCTCGATCACTCAAGGAACACCCATTC
* * *
52058404 GGGCTAGAA-CCTTAATGCACACATATTCTTCGAGAGGCTCGATCACTCAAGGAACAC
1 GGGCTA-AATCCTTAATGCACACATATTCATCAAAAGGCTCGATCACTCAAGGAACAC
52058461 TCGTCTGAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 50 0.96
64 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (63 bp):
GGGCTAAATCCTTAATGCACACATATTCATCAAAAGGCTCGATCACTCAAGGAACACCCATTC
Found at i:52059802 original size:29 final size:29
Alignment explanation
Indices: 52059768--52059967 Score: 172
Period size: 29 Copynumber: 6.9 Consensus size: 29
52059758 TGCCATCAAG
*
52059768 TATGAAAATGGATGGTTTCGACCATCGAC
1 TATGAAAAGGGATGGTTTCGACCATCGAC
* * * *
52059797 TATGAAAAGGGATAGTTTTGACCATTGAT
1 TATGAAAAGGGATGGTTTCGACCATCGAC
* * * * *
52059826 TATGAAAAGGGTTAGTTTTGACTATTGAC
1 TATGAAAAGGGATGGTTTCGACCATCGAC
** *
52059855 TATG-AAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTTTCGACCATCGAC
* * *
52059883 TATGAAAAGGGATGATGAT-GACCATCAACC
1 TATGAAAAGGGATGGT-TTCGACCATCGA-C
* * * *
52059913 AATGAAAATGGATGGTTCCGACCATCGAA
1 TATGAAAAGGGATGGTTTCGACCATCGAC
*
52059942 TATGAAAAGGGAT-GTTACGACCATCG
1 TATGAAAAGGGATGGTTTCGACCATCG
52059968 TTTAGCACAC
Statistics
Matches: 138, Mismatches: 29, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
28 32 0.23
29 84 0.61
30 22 0.16
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (29 bp):
TATGAAAAGGGATGGTTTCGACCATCGAC
Found at i:52066825 original size:44 final size:42
Alignment explanation
Indices: 52066753--52066910 Score: 108
Period size: 43 Copynumber: 3.7 Consensus size: 42
52066743 ATGTGTTTTC
* * * *
52066753 GTGTAAGACCACGTCTAGGACGTTGGCATCG-ACTTATGATTTAT
1 GTGTAAGACCACATCTAGGACATAGGCATAGTAC-T-TGA-TTAT
* *
52066797 GTGTAAGAGCACATCTGGGACATAGGCATAGTACTTGATTAT
1 GTGTAAGACCACATCTAGGACATAGGCATAGTACTTGATTAT
* * * *
52066839 GTGTAAGACC-CTGTCTAGGACAGT-GGCATCGATAATTGATTAC
1 GTGTAAGACCAC-ATCTAGGACA-TAGGCATAG-TACTTGATTAT
* * *
52066882 CTGTAAGACCACGAT-TGGGACATTGGCAT
1 GTGTAAGACCAC-ATCTAGGACATAGGCAT
52066911 TATACGAGCT
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.01
42 28 0.30
43 33 0.36
44 28 0.30
45 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCACATCTAGGACATAGGCATAGTACTTGATTAT
Found at i:52066860 original size:42 final size:40
Alignment explanation
Indices: 52066753--52066891 Score: 109
Period size: 42 Copynumber: 3.2 Consensus size: 40
52066743 ATGTGTTTTC
*
52066753 GTGTAAGACCACGTCTAGGACGTTGGCATCG-ACTTATGATTTAT
1 GTGTAAGACC-CGTCTAGGAC-ATGGCATCGTAC-T-TGA-TTAT
* * * *
52066797 GTGTAAGAGCACATCTGGGACATAGGCATAGTACTTGATTAT
1 GTGTAAGA-CCCGTCTAGGACAT-GGCATCGTACTTGATTAT
* *
52066839 GTGTAAGACCCTGTCTAGGACAGTGGCATCGATAATTGATTAC
1 GTGTAAGACCC-GTCTAGGACA-TGGCATCG-TACTTGATTAT
*
52066882 CTGTAAGACC
1 GTGTAAGACC
52066892 ACGATTGGGA
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
41 2 0.03
42 26 0.34
43 23 0.30
44 23 0.30
45 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (40 bp):
GTGTAAGACCCGTCTAGGACATGGCATCGTACTTGATTAT
Found at i:52069450 original size:27 final size:27
Alignment explanation
Indices: 52069392--52069501 Score: 143
Period size: 27 Copynumber: 4.1 Consensus size: 27
52069382 AGCATGACTG
* *
52069392 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
52069418 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
**
52069445 TTAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
52069472 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
52069499 CCA
1 CCA
52069502 AGACGCTTCC
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.21
27 56 0.77
28 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:52069474 original size:54 final size:53
Alignment explanation
Indices: 52069394--52069498 Score: 165
Period size: 54 Copynumber: 2.0 Consensus size: 53
52069384 CATGACTGCC
*
52069394 AGAACAGATAATGTGACAGAGTCACCAGAACAGATAATTGTGGCAGAGCCATT
1 AGAACAGATAATGTGACAGAGCCACCAGAACAGATAATTGTGGCAGAGCCATT
* * *
52069447 AGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 AGAACAGATA-ATGTGACAGAGCCACCAGAACAGATAATTGTGGCAGAGCCA
52069499 CCAAGACGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 10 0.21
54 37 0.79
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (53 bp):
AGAACAGATAATGTGACAGAGCCACCAGAACAGATAATTGTGGCAGAGCCATT
Found at i:52070935 original size:24 final size:24
Alignment explanation
Indices: 52070900--52070999 Score: 155
Period size: 24 Copynumber: 4.2 Consensus size: 24
52070890 CCAACACTGT
* *
52070900 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52070924 TCTCCCTTATCAACTCCTGAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52070948 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52070972 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
52070996 TCTC
1 TCTC
52071000 ATGACAGACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.25, C:0.40, G:0.02, T:0.33
Consensus pattern (24 bp):
TCTCCCTTATCAACTCCTAAATCC
Found at i:52072202 original size:26 final size:27
Alignment explanation
Indices: 52072173--52072223 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
52072163 TCAACCTTAA
*
52072173 CCCTAGGGGTATATCAGT-AATTTTGC
1 CCCTAGGGGTAAATCAGTAAATTTTGC
*
52072199 CCCTAGGGGTAAATCTGTAAATTTT
1 CCCTAGGGGTAAATCAGTAAATTTT
52072224 CCACCTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (27 bp):
CCCTAGGGGTAAATCAGTAAATTTTGC
Found at i:52076689 original size:46 final size:46
Alignment explanation
Indices: 52076598--52076723 Score: 139
Period size: 46 Copynumber: 2.7 Consensus size: 46
52076588 TAGTTCATGA
* * * *
52076598 ATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGAAGCTGATG-C
1 ATGTCCCAGACATGTCTTACACTAGCCT-CATCTCGAAACCGATGCC
52076644 ATGTCCCAGACATGTCTTACACTAGCACTCATCTC-AATACCGATGCC
1 ATGTCCCAGACATGTCTTACACTAGC-CTCATCTCGAA-ACCGATGCC
* *
52076691 ATGTCTCAGACATGGTCTTACACTGGCTCTCAT
1 ATGTCCCAGACAT-GTCTTACACTAGC-CTCAT
52076724 AATGTGGCTG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 2 0.03
46 36 0.52
47 14 0.20
48 17 0.25
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.29
Consensus pattern (46 bp):
ATGTCCCAGACATGTCTTACACTAGCCTCATCTCGAAACCGATGCC
Found at i:52083852 original size:40 final size:40
Alignment explanation
Indices: 52083796--52083936 Score: 237
Period size: 40 Copynumber: 3.5 Consensus size: 40
52083786 TATGTGCATA
52083796 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
52083836 GCATTCGTGCGAGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
52083876 GCATTCGTGCGGGTTATTATAACCGGATTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* * *
52083916 GCATTCATGCTGGTTGTTATA
1 GCATTCGTGCGGGTTATTATA
52083937 TCCGAGCCAA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:52083954 original size:80 final size:80
Alignment explanation
Indices: 52083796--52083954 Score: 221
Period size: 80 Copynumber: 2.0 Consensus size: 80
52083786 TATGTGCATA
* *
52083796 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTATAACCG
1 GCATTCGTGCGGGTTATTATAACCGGATTAAGTCCCGAAGGCATTCATGCGAGTTATTATAACCG
* ** *
52083861 GGTTAAGTCCCGAAG
66 AGCCAAATCCCGAAG
* *
52083876 GCATTCGTGCGGGTTATTATAACCGGATTAAGTCCCGAAGGCATTCATGCTG-GTTGTTATATCC
1 GCATTCGTGCGGGTTATTATAACCGGATTAAGTCCCGAAGGCATTCATGC-GAGTTATTATAACC
*
52083940 GAGCCAAATTCCGAA
65 GAGCCAAATCCCGAA
52083955 AGTATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 68 0.99
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (80 bp):
GCATTCGTGCGGGTTATTATAACCGGATTAAGTCCCGAAGGCATTCATGCGAGTTATTATAACCG
AGCCAAATCCCGAAG
Found at i:52092101 original size:40 final size:40
Alignment explanation
Indices: 52091968--52092083 Score: 214
Period size: 40 Copynumber: 2.9 Consensus size: 40
52091958 GGGTTATATC
52091968 GGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
52092008 GGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
* *
52092048 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATA
1 GGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATA
52092084 TCCGAGCCAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (40 bp):
GGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
Found at i:52100294 original size:40 final size:40
Alignment explanation
Indices: 52100096--52100276 Score: 308
Period size: 40 Copynumber: 4.5 Consensus size: 40
52100086 TATGTGCATA
*
52100096 GCATTCGTGCGGGTTATTATAATCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
52100136 GCATTCGTGCGGGTTATTATAATCGGGTTAAGTCTCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
52100176 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
52100216 GCATTCGTACGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
52100256 GCATTCGTGCTGGTTGTTATA
1 GCATTCGTGCGGGTTATTATA
52100277 TCCGAGCCAA
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 134 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:52105562 original size:80 final size:79
Alignment explanation
Indices: 52105425--52105649 Score: 256
Period size: 80 Copynumber: 2.8 Consensus size: 79
52105415 TTGAATGCTG
* * * * * * * * *
52105425 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
52105489 TGTGCGAGA-TGTTAAA
64 TGTGCGA-ATTGTTAAA
** *
52105505 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
52105570 GTGCGAATTGTTAAA
65 GTGCGAATTGTTAAA
* * * *
52105585 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
52105650 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
79 37 0.30
80 83 0.67
81 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
TGCGAATTGTTAAA
Found at i:52105635 original size:39 final size:40
Alignment explanation
Indices: 52105464--52105647 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
52105454 AAGTGAATAT
* * * *
52105464 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATGTTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
52105504 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
*
52105544 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
52105584 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* *
52105623 ATCCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
52105648 TGAACGAGGA
Statistics
Matches: 132, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 35 0.27
40 97 0.73
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:52105667 original size:79 final size:80
Alignment explanation
Indices: 52105501--52105682 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 80
52105491 TGCGAGATGT
** *
52105501 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGC
** ** *
52105566 ATTCGTGCGAATTGT
66 ATTCGAACGAAGAGC
* * *
52105581 TAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGC
* *
52105645 ATTTGAACGAGGAGC
66 ATTCGAACGAAGAGC
* *
52105660 TATATCC-GGTTAAATCCCGAAGG
1 TAAATCCGGGTTAAGTCCCGAAGG
52105683 TACGTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGC
ATTCGAACGAAGAGC
Found at i:52119031 original size:20 final size:21
Alignment explanation
Indices: 52118992--52119031 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52118982 TAATTAATGG
52118992 CTACACGAGCGTGTTGCCCTT
1 CTACACGAGCGTGTTGCCCTT
*
52119013 CTACACGGGCGTG-TGCCCT
1 CTACACGAGCGTGTTGCCCT
52119032 GTTCCAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (21 bp):
CTACACGAGCGTGTTGCCCTT
Found at i:52119938 original size:21 final size:21
Alignment explanation
Indices: 52119900--52119939 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52119890 AACCAGAACA
* *
52119900 TTTTAGAAATCCATTTTTTAT
1 TTTTAGAAAACCACTTTTTAT
*
52119921 TTTTAGAAAACCCCTTTTT
1 TTTTAGAAAACCACTTTTT
52119940 GACATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTAGAAAACCACTTTTTAT
Found at i:52127485 original size:39 final size:40
Alignment explanation
Indices: 52127440--52127607 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
52127430 CGGGGTTTAG
* * *
52127440 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
52127479 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
52127519 CCGGATATAGTCGCTAGCACAAACGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
52127559 CCGGATGTAGTCGCGTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
52127600 CCGGATAT
1 CCGGATAT
52127608 CATTCGAGTA
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 18 0.17
40 60 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:52127590 original size:41 final size:40
Alignment explanation
Indices: 52127463--52127607 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
52127453 CTCGCACAAG
* * * * * *
52127463 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAA
*
52127503 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAC
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAA
* *
52127543 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCGTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAA
52127584 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
52127608 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 58 0.64
41 27 0.30
42 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAA
Found at i:52134539 original size:39 final size:40
Alignment explanation
Indices: 52134494--52134702 Score: 125
Period size: 41 Copynumber: 5.2 Consensus size: 40
52134484 CGGGGTTTAG
* * *
52134494 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
52134533 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
52134573 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
52134613 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
** * * * *
52134654 CCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
52134695 CCGGATAT
1 CCGGATAT
52134703 CATTCGAGTA
Statistics
Matches: 150, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
39 18 0.12
40 61 0.41
41 68 0.45
42 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:52134644 original size:41 final size:41
Alignment explanation
Indices: 52134517--52134702 Score: 261
Period size: 41 Copynumber: 4.6 Consensus size: 41
52134507 CTCGCACAAG
* * * * * *
52134517 GCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
*
52134557 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
* *
52134597 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAA
52134638 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
52134679 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
52134703 CATTCGAGTA
Statistics
Matches: 133, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 3 0.02
40 59 0.44
41 68 0.51
42 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
Found at i:52134651 original size:81 final size:82
Alignment explanation
Indices: 52134517--52134700 Score: 257
Period size: 81 Copynumber: 2.3 Consensus size: 82
52134507 CTCGCACAAG
* * * * * * *
52134517 GCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
*
52134581 AGTCGC-TAGCACAAAT
66 AGTCGCTTAGCACAAAA
*
52134597 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATA
1 GCCTTCGGGA-CTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATA
52134661 TAGTCGCTTAGCACAAAA
65 TAGTCGCTTAGCACAAAA
52134679 GCCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGACTTAGCCCGGAT
52134701 ATCATTCGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
79 2 0.02
80 21 0.23
81 38 0.42
82 26 0.29
83 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (82 bp):
GCCTTCGGGACTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
AGTCGCTTAGCACAAAA
Found at i:52142462 original size:40 final size:40
Alignment explanation
Indices: 52142404--52142572 Score: 227
Period size: 40 Copynumber: 4.2 Consensus size: 40
52142394 ATAATGCTAA
* * * *
52142404 CCCGGATATGGTCAC-TAGCATAAATGCCTTCGGGACTTAG
1 CCCGGATATAGTCGCTTAGCACAAAAGCCTTC-GGACTTAG
*
52142444 CCCGGATATAGTCGC-TAGCAC-AATGCCTTCGGATCTTAG
1 CCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGA-CTTAG
* *
52142483 TCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGACTTAG
1 CCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGACTTAG
52142523 CCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTAG
1 CCCGGATATAGTCGCTTAGCACAAAAGCCTTC-GGACTTAG
52142564 CCCGGATAT
1 CCCGGATAT
52142573 CATTCGAGTA
Statistics
Matches: 117, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
38 3 0.03
39 27 0.23
40 59 0.50
41 28 0.24
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGACTTAG
Found at i:52154301 original size:27 final size:27
Alignment explanation
Indices: 52154271--52154394 Score: 194
Period size: 27 Copynumber: 4.6 Consensus size: 27
52154261 TTATTAAGTC
* * *
52154271 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
52154298 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
52154325 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* *
52154353 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
52154380 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52154395 GCACAATTTA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 65 0.71
28 26 0.29
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:52154363 original size:55 final size:54
Alignment explanation
Indices: 52154271--52154394 Score: 194
Period size: 55 Copynumber: 2.3 Consensus size: 54
52154261 TTATTAAGTC
* *
52154271 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAGTCAACT
* * *
52154325 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAGTCAACT
52154380 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52154395 GCACAATTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
54 20 0.31
55 44 0.69
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAGTCAACT
Found at i:52162296 original size:28 final size:27
Alignment explanation
Indices: 52162232--52162383 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
52162222 TTATTAAGTC
* *
52162232 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
52162259 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
52162287 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
52162314 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
52162342 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
52162369 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52162384 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:52162316 original size:55 final size:55
Alignment explanation
Indices: 52162232--52162408 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
52162222 TTATTAAGTC
* * *
52162232 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
52162287 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
52162342 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
52162398 CGCACACTTAG
1 CGCACACTTAG
52162409 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:52172784 original size:49 final size:49
Alignment explanation
Indices: 52172712--52172905 Score: 194
Period size: 49 Copynumber: 3.9 Consensus size: 49
52172702 GCCGAAGCTA
**
52172712 TCTGGTATGCGTAGTAGCCTACACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGCGACCAACAG
* *
52172761 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTCACCA-
1 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGCGA-C-CAACAG
** * * * * *
52172811 TCTAATACACGTTGTAGCCTTCACTTAGTACTACACACGTGATC-ACAG
1 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGCGACCAACAG
* * * *
52172859 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGCGACC
52172906 TCACAATAGA
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 39 0.33
50 38 0.32
51 38 0.32
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (49 bp):
TCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGCGACCAACAG
Found at i:52172841 original size:50 final size:49
Alignment explanation
Indices: 52172721--52172905 Score: 176
Period size: 50 Copynumber: 3.7 Consensus size: 49
52172711 ATCTGGTATG
* **
52172721 CGTAGTAGCCTACACTTAGTACTACACATGCGACCAACAGTCTGGTACA
1 CGTAGTAGCCTACACTTAGTACTACACATGTGACCAACAGTCTAATACA
*
52172770 CGTAGTAGCCTACACTTAGTACTACACATGTGACCTCACCA-TCTAATACA
1 CGTAGTAGCCTACACTTAGTACTACACATGTGA-C-CAACAGTCTAATACA
* * * * *** *
52172820 CGTTGTAGCCTTCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACG
1 CGTAGTAGCCTACACTTAGTACTACACATGTGACCAACAG---TCTAATACA
* * *
52172871 CATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 CGTAGTAGCCTACACTTAGTACTACACATGTGACC
52172906 TCACAATAGA
Statistics
Matches: 111, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 32 0.29
50 38 0.34
51 38 0.34
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (49 bp):
CGTAGTAGCCTACACTTAGTACTACACATGTGACCAACAGTCTAATACA
Found at i:52172898 original size:101 final size:99
Alignment explanation
Indices: 52172725--52172909 Score: 255
Period size: 101 Copynumber: 1.8 Consensus size: 99
52172715 GGTATGCGTA
* * *
52172725 GTAGCCTACACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGCCTACACTTAGT
1 GTAGCCTACACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTACACTTAGT
*
52172790 ACTACACATGTGACCTCACCATCTAATACACGTT
66 ACTACACATGCGACCTCACCATCTAATACACGTT
* * * * *
52172824 GTAGCCTTCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCACTT
1 GTAGCCTACACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTACACTT
52172888 AGTACTACACATGCGACCTCAC
63 AGTACTACACATGCGACCTCAC
52172910 AATAGATCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
98 4 0.05
99 27 0.36
101 43 0.58
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (99 bp):
GTAGCCTACACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTACACTTAGT
ACTACACATGCGACCTCACCATCTAATACACGTT
Found at i:52175179 original size:47 final size:46
Alignment explanation
Indices: 52175105--52175370 Score: 243
Period size: 47 Copynumber: 5.7 Consensus size: 46
52175095 TGGGTAAGGT
*
52175105 GCCGATGCCATGTCCCAGACACAGTCTTACACTGGCTCACATCTCAA
1 GCCGATGCCATGTCCCAGACA-TGTCTTACACTGGCTCACATCTCAA
** *
52175152 GTTGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCATA
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCA-CATCTCA-A
* * * * *
52175200 GCCGATG-TATGTCCCAAACATGTCTTACACTGGCTTACTTCTCGAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTC-AA
* * * * * *
52175246 GCCGATG-CATGTGCTAGACATGTCTTACATTAGCCCTCATCTCAA
1 GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAA
* * * ***
52175291 TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 -GCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCACAT-CTCAA
52175340 GCCGATG-CATGTCCCAGACATGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGTCTTACACT
52175371 AGCTTACCCA
Statistics
Matches: 177, Mismatches: 33, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
45 1 0.01
46 68 0.38
47 79 0.45
48 28 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAA
Found at i:52178062 original size:34 final size:34
Alignment explanation
Indices: 52178018--52178082 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
52178008 CAGTAACAGT
*
52178018 TCAATTTCAGT-TAGGGCCATAGCCCATTACAATA
1 TCAATATCAGTGT-GGGCCATAGCCCATTACAATA
*
52178052 TCAATATCAGTGTGGGCCTTAGCCCATTACA
1 TCAATATCAGTGTGGGCCATAGCCCATTACA
52178083 GCGACAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (34 bp):
TCAATATCAGTGTGGGCCATAGCCCATTACAATA
Found at i:52180816 original size:25 final size:24
Alignment explanation
Indices: 52180795--52180869 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 24
52180785 ACTAGCTGTG
*
52180795 AATCGGTATGCTCACTCGAGCTAT
1 AATCGGTATGCTCACACGAGCTAT
* *
52180819 AGATTGGTATGCTCTCACGAGCTAT
1 A-ATCGGTATGCTCACACGAGCTAT
52180844 AAATCGGTATGCTCACACGAGCTAT
1 -AATCGGTATGCTCACACGAGCTAT
52180869 A
1 A
52180870 GGTCGAAACG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
24 2 0.05
25 41 0.93
26 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (24 bp):
AATCGGTATGCTCACACGAGCTAT
Found at i:52187809 original size:28 final size:28
Alignment explanation
Indices: 52187746--52187805 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
52187736 TTTTTAACGA
* *
52187746 TCTATAAAATTAAGATAAAAAAAAAACT
1 TCTATCAACTTAAGATAAAAAAAAAACT
*
52187774 TCTATCAACTTAAGAT-AAAAAAAACCT
1 TCTATCAACTTAAGATAAAAAAAAAACT
52187801 TCTAT
1 TCTAT
52187806 TCAATCCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.28
Consensus pattern (28 bp):
TCTATCAACTTAAGATAAAAAAAAAACT
Found at i:52193408 original size:47 final size:45
Alignment explanation
Indices: 52193333--52193649 Score: 203
Period size: 47 Copynumber: 6.7 Consensus size: 45
52193323 GATTTCTTGT
*
52193333 GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGA
1 GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACA-GATGA
* * *
52193379 GTGCCAGTGTAAGACCATGTCTAGGACATGGCATCAGCGTAGAGATGA
1 GTGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGC-CACAGATGA
* * *
52193427 GTGCCAGTGTAAGACATGTGTGGGACATGCATCGGCCTCGACGATGA
1 GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCAC-A-GATGA
* * * * *
52193474 -TAGCCAGTGTAAGACGTGTCTGGGACATGCATCGACTA-AGA-GTT
1 GT-GCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACAGATG-A
* * * * * *
52193518 GTGCTAGTGTAAGATATGTCTGGGACAAGCATCAG-CACGTATATACGA
1 GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCAC--AGAT--GA
* * * * *
52193566 GAGCTAGTATAAGATCATGTCTGGGACATGGCATCGGCCTC-GATGA
1 GTGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCACAGATGA
* *
52193612 TGATAGCCAATGTAAGACCATGTCTGGGACATGGCATC
1 -G-T-GCCAGTGTAAGA-CATGTCTAGGACAT-GCATC
52193650 AGCAACTTAT
Statistics
Matches: 214, Mismatches: 37, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
43 2 0.01
44 29 0.14
45 2 0.01
46 27 0.13
47 63 0.29
48 39 0.18
49 44 0.21
50 6 0.03
51 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACAGATGA
Found at i:52193494 original size:94 final size:93
Alignment explanation
Indices: 52193333--52193506 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 93
52193323 GATTTCTTGT
**
52193333 GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGAGTGCCAGTGTAAGACCATG
1 GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACACGATGAGTGCCAGTGTAAGACCATG
52193398 TCTAGGACATGGCATCAGCGTAGAGATGA
66 TCTAGGACAT-GCATCAGCGTAGAGATGA
* * * *
52193427 GTGCCAGTGTAAGACATGTGTGGGACATGCATCGGCCTCGACGATGA-TAGCCAGTGTAAGA-CG
1 GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ACGATGAGT-GCCAGTGTAAGACCA
*
52193490 TGTCTGGGACATGCATC
64 TGTCTAGGACATGCATC
52193507 GACTAAGAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
93 5 0.07
94 49 0.69
95 17 0.24
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (93 bp):
GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCACACGATGAGTGCCAGTGTAAGACCATG
TCTAGGACATGCATCAGCGTAGAGATGA
Found at i:52201624 original size:93 final size:93
Alignment explanation
Indices: 52201499--52201667 Score: 293
Period size: 93 Copynumber: 1.8 Consensus size: 93
52201489 CATAAGTGAC
* *
52201499 CTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
1 CTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
52201564 GTTCGGATGCCTAGTTACATTTCACGAA
66 GTTCGGATGCCTAGTTACATTTCACGAA
* * *
52201592 CTCGGACTCAACTCATCGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
1 CTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
52201657 GTTCGGATGCC
66 GTTCGGATGCC
52201668 CAAACATCCT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
CTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
GTTCGGATGCCTAGTTACATTTCACGAA
Found at i:52201663 original size:46 final size:46
Alignment explanation
Indices: 52201488--52201663 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
52201478 TGTAACCCGC
* * * * *
52201488 CCATAAGTGACCTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
52201534 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * * *
52201584 --TTCA-CGAACTCGGACTCAACTCATCGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
52201627 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52201664 TGCCCAAACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:52202122 original size:30 final size:30
Alignment explanation
Indices: 52202088--52202148 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
52202078 CATTTAATAC
*
52202088 AAACTTTGGAAAAATTACACTTTTGCGCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
52202118 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
52202148 A
1 A
52202149 GGCTCAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:52213731 original size:44 final size:45
Alignment explanation
Indices: 52213618--52213743 Score: 148
Period size: 44 Copynumber: 2.7 Consensus size: 45
52213608 CACATTATGA
* *
52213618 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACGAT
1 GTGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTAGACGAT
* *
52213665 GATAGCCAGTGTAAGACGTGTCTAGGACATGCATCGG-CTAAGA-GTT
1 G-T-GCCAGTGTAAGACATGTCTAGGACATGCATCGGCCT-AGACGAT
*
52213711 GTGCTAGTGTAAGACATGTCTAGGACATGCATC
1 GTGCCAGTGTAAGACATGTCTAGGACATGCATC
52213744 AGCACGTGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
44 29 0.41
45 1 0.01
46 5 0.07
47 10 0.14
48 13 0.19
49 12 0.17
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (45 bp):
GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTAGACGAT
Found at i:52223022 original size:21 final size:22
Alignment explanation
Indices: 52222993--52223043 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
52222983 ATTTTGTTTG
52222993 TTTTACTTTTTGAAAAA-TAATA
1 TTTT-CTTTTTGAAAAATTAATA
52223015 TTTTC-TTTTGAAAAATTAATA
1 TTTTCTTTTTGAAAAATTAATA
52223036 TTTT-TTTT
1 TTTTCTTTT
52223044 ATATTTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTTCTTTTTGAAAAATTAATA
Found at i:52223025 original size:20 final size:20
Alignment explanation
Indices: 52222999--52223043 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
52222989 TTTGTTTTAC
52222999 TTTTTGAAAAA-TAATATTT
1 TTTTTGAAAAATTAATATTT
52223018 TCTTTTGAAAAATTAATATTT
1 T-TTTTGAAAAATTAATATTT
52223039 TTTTT
1 TTTTT
52223044 ATATTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 14 0.58
21 9 0.38
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTTGAAAAATTAATATTT
Found at i:52223756 original size:30 final size:29
Alignment explanation
Indices: 52223722--52223789 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
52223712 ATTGGACTCG
* *
52223722 ATTTTCAAATCTAAAAAGTAAAGGGACTAA
1 ATTTTCAAATAT-AAAAGTAAAGAGACTAA
* *
52223752 ATTTTTGAAA-ATAAAAGTATAGAGACTAA
1 A-TTTTCAAATATAAAAGTAAAGAGACTAA
52223781 A-TTTCAAAT
1 ATTTTCAAAT
52223790 TTGTGAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 6 0.19
29 16 0.52
30 2 0.06
31 7 0.23
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (29 bp):
ATTTTCAAATATAAAAGTAAAGAGACTAA
Found at i:52224051 original size:44 final size:44
Alignment explanation
Indices: 52223967--52224061 Score: 172
Period size: 44 Copynumber: 2.1 Consensus size: 44
52223957 TTACTAAAAC
52223967 AAAATTGAAATATTAAATAATTTATTAAAATAATAATTTATATT
1 AAAATTGAAATATTAAATAATTTATTAAAATAATAATTTATATT
*
52224011 AAAATTGAAATATTAAATAATTTATTAAGATAATAATTTATATT
1 AAAATTGAAATATTAAATAATTTATTAAAATAATAATTTATATT
52224055 AATAATT
1 AA-AATT
52224062 TATTATATGA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 45 0.92
45 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (44 bp):
AAAATTGAAATATTAAATAATTTATTAAAATAATAATTTATATT
Found at i:52224057 original size:13 final size:13
Alignment explanation
Indices: 52223997--52224064 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 13
52223987 TTTATTAAAA
52223997 TAATAATTTATAT
1 TAATAATTTATAT
*
52224010 TAA-AATTGAAATAT
1 TAATAATT--TATAT
*
52224024 TAAATAATTTATTAAGA
1 T-AATAATTTA-T-A-T
52224041 TAATAATTTATAT
1 TAATAATTTATAT
52224054 TAATAATTTAT
1 TAATAATTTAT
52224065 TATATGATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
12 4 0.09
13 14 0.32
14 7 0.16
15 4 0.09
16 14 0.32
17 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TAATAATTTATAT
Found at i:52224067 original size:16 final size:16
Alignment explanation
Indices: 52223976--52224069 Score: 53
Period size: 16 Copynumber: 6.2 Consensus size: 16
52223966 CAAAATTGAA
52223976 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
* *
52223993 AAAATAATAA--T-TT
1 ATATTAATAATTTATT
* *
52224006 ATATTAA-AATTGA-A
1 ATATTAATAATTTATT
52224020 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
*
52224037 A-AGATAATAA--T-TT
1 ATA-TTAATAATTTATT
52224050 ATATTAATAATTTATT
1 ATATTAATAATTTATT
52224066 ATAT
1 ATAT
52224070 GATAAGATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 23
0.63 0.11 0.26
Matches are distributed among these distances:
12 2 0.04
13 16 0.29
14 8 0.14
15 3 0.05
16 22 0.39
17 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:52224143 original size:36 final size:35
Alignment explanation
Indices: 52224099--52224169 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 35
52224089 AATATTTATG
* * *
52224099 TTTAATATTATTGAAAATTATAATATT-TTATTAAT
1 TTTAATATTATTAAAAATAAAAAT-TTATTATTAAT
*
52224134 TTTAGATATTTTTAAAAATAAAAATTTATTATTAAT
1 TTTA-ATATTATTAAAAATAAAAATTTATTATTAAT
52224170 ATAATAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
TTTAATATTATTAAAAATAAAAATTTATTATTAAT
Found at i:52226543 original size:50 final size:50
Alignment explanation
Indices: 52226422--52226663 Score: 247
Period size: 50 Copynumber: 4.8 Consensus size: 50
52226412 AGTCGAAGCT
* * * * *
52226422 ATCTGATACGCATAGTAGCCTACACTTAGTACTACACATGCGACC-AATA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATC
* * * *
52226471 ATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATC
* * * *
52226521 ATCTGATACACGTAGTAGCCTGCACTTAGTAATACACACGTGATCGAAGTC
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-TC
* * * * *
52226572 AT-TAAGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTTAA-C
1 ATCTGA-TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATC
* * *
52226621 AGTATGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 A-TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTG
52226664 TACTCACAAT
Statistics
Matches: 156, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
49 41 0.26
50 77 0.49
51 38 0.24
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATC
Found at i:52226632 original size:101 final size:101
Alignment explanation
Indices: 52226476--52226663 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 101
52226466 CAATAATCCG
* * *
52226476 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCATCTGATACACGTAGTAGCC
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACATATGATACACGTAGTAGCC
52226541 TGCACTTAGTAATACACACGTGATCGAAGTCATTAA
66 TGCACTTAGTAATACACACGTGATCGAAGTCATTAA
* * * *
52226577 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CTTAACAGTATGGTACACGTAGTAGC
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACA-TATGATACACGTAGTAGC
*
52226641 CTGCACTTAGTACTACACACGTG
65 CTGCACTTAGTAATACACACGTG
52226664 TACTCACAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 5 0.06
101 73 0.94
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (101 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACATATGATACACGTAGTAGCC
TGCACTTAGTAATACACACGTGATCGAAGTCATTAA
Found at i:52228505 original size:30 final size:31
Alignment explanation
Indices: 52228471--52228533 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
52228461 GATGCAAAAT
* *
52228471 TAAAATATAAACTAAT-TAAATTAATTAACC
1 TAAAAAATAAACTAATGGAAATTAATTAACC
* *
52228501 TAAAAAATAACCTAATGGAATTTAATTAACC
1 TAAAAAATAAACTAATGGAAATTAATTAACC
52228532 TA
1 TA
52228534 GGATAACCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (31 bp):
TAAAAAATAAACTAATGGAAATTAATTAACC
Found at i:52231739 original size:39 final size:39
Alignment explanation
Indices: 52231691--52231822 Score: 210
Period size: 39 Copynumber: 3.4 Consensus size: 39
52231681 GGCGAACCCG
* *
52231691 AAGTTCGAATATGATTCCCGCATATAGCCTACGGACCTT
1 AAGTCCGAATATAATTCCCGCATATAGCCTACGGACCTT
* *
52231730 AAGTCCGAATATAATTTCTGCATATAGCCTACGGACCTT
1 AAGTCCGAATATAATTCCCGCATATAGCCTACGGACCTT
*
52231769 AAGTCCGGATATAATTCCCGCATATAGCCTACGGACCTT
1 AAGTCCGAATATAATTCCCGCATATAGCCTACGGACCTT
*
52231808 AAGTCCGGATATAAT
1 AAGTCCGAATATAAT
52231823 CGCCATATAT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (39 bp):
AAGTCCGAATATAATTCCCGCATATAGCCTACGGACCTT
Found at i:52237820 original size:3 final size:3
Alignment explanation
Indices: 52237814--52237845 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52237804 TAATAATGCG
52237814 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52237846 TCATTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:52244029 original size:20 final size:20
Alignment explanation
Indices: 52244004--52244041 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
52243994 ACATAGAGTT
52244004 CTAAATATAATATTCATCTC
1 CTAAATATAATATTCATCTC
52244024 CTAAATATAATATTCATC
1 CTAAATATAATATTCATC
52244042 ACTCAGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (20 bp):
CTAAATATAATATTCATCTC
Found at i:52245077 original size:19 final size:19
Alignment explanation
Indices: 52245053--52245089 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
52245043 TTTTATTTTA
52245053 TTTTTCATATTATTATTGT
1 TTTTTCATATTATTATTGT
52245072 TTTTTCATATTATTATTG
1 TTTTTCATATTATTATTG
52245090 CTGAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTCATATTATTATTGT
Found at i:52247507 original size:30 final size:30
Alignment explanation
Indices: 52247471--52247530 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
52247461 TTCCCGAGCC
*
52247471 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
52247501 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
52247531 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:52248708 original size:37 final size:37
Alignment explanation
Indices: 52248649--52248755 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
52248639 AGCTCAGACG
* * *
52248649 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
52248686 AAATCTCCACACGTAGTCATCGGGTCTTACTCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
52248723 TAATCTTCACACGTAGTCATCGGGTCTTACCCG
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCG
52248756 TAATATATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:52249040 original size:47 final size:47
Alignment explanation
Indices: 52248961--52249154 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
52248951 TATATATATT
* * * * *
52248961 TCACATTGACCGTTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
52249008 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
52249055 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
52249102 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
52249149 TCACAT
1 TCACAT
52249155 AAAATCCTAA
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:52249081 original size:22 final size:22
Alignment explanation
Indices: 52249054--52249125 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
52249044 GCTCACATTC
52249054 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
52249076 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
52249100 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52249123 ATC
1 ATC
52249126 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52254102 original size:40 final size:40
Alignment explanation
Indices: 52254051--52254242 Score: 212
Period size: 40 Copynumber: 4.8 Consensus size: 40
52254041 GGATATAGCT
* * *
52254051 ACTCGCTCAAATGCCTTTGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
52254091 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
* * *
52254131 ACTCGCACCAATGCCTTCGAG-CTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* * *
52254170 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTA
* *
52254210 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGG
52254243 ATATCATTCG
Statistics
Matches: 128, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 31 0.24
40 67 0.52
41 26 0.20
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:52254169 original size:79 final size:81
Alignment explanation
Indices: 52254086--52254243 Score: 214
Period size: 79 Copynumber: 2.0 Consensus size: 81
52254076 AGCCCGGTTA
* * * *
52254086 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTC
1 TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCACAAAAGCCTTC
52254149 GAG-CTTAGCCCGGAAT
65 GAGACTTAGCCCGGAAT
** *
52254165 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAAGCCTTCG
*
52254230 GGACTTAGCCCGGA
66 AGACTTAGCCCGGA
52254244 TATCATTCGA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 3 0.04
79 39 0.57
80 15 0.22
81 11 0.16
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (81 bp):
TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAAGCCTTCG
AGACTTAGCCCGGAAT
Found at i:52262359 original size:79 final size:79
Alignment explanation
Indices: 52262215--52262433 Score: 257
Period size: 79 Copynumber: 2.7 Consensus size: 79
52262205 GAATCACATA
* * * * *
52262215 CCTTCGGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAG
52262279 TAACTCGCACAAATG
65 TAACTCGCACAAATG
* *
52262294 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATA
52262357 GTAACTCGCACAAATG
64 GTAACTCGCACAAATG
* * *
52262373 CCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
52262434 TATCATTCGA
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.03
79 61 0.51
80 45 0.38
81 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAGT
AACTCGCACAAATG
Found at i:52262362 original size:39 final size:41
Alignment explanation
Indices: 52262229--52262433 Score: 237
Period size: 40 Copynumber: 5.1 Consensus size: 41
52262219 CGGAATTTAA
* *
52262229 CCGG-ATATAGCT-ACTCGCTCAAATGCCTTCGGGACATAGC
1 CCGGAATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52262269 CCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52262309 CCGG-ATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52262348 CCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
52262388 CCGG-ATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGAATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
52262429 CCGGA
1 CCGGA
52262434 TATCATTCGA
Statistics
Matches: 143, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.24
40 81 0.57
41 23 0.16
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52267795 original size:40 final size:40
Alignment explanation
Indices: 52267681--52267796 Score: 196
Period size: 40 Copynumber: 2.9 Consensus size: 40
52267671 TATTCGGATG
*
52267681 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52267721 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52267761 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
52267797 AGCTATATCG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52279090 original size:26 final size:26
Alignment explanation
Indices: 52279054--52279106 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52279044 CTATAAGAAG
52279054 TACAATTTATACTTATGATGTTTCGA
1 TACAATTTATACTTATGATGTTTCGA
52279080 TACAATTTATACTTATGATGTTTCGA
1 TACAATTTATACTTATGATGTTTCGA
52279106 T
1 T
52279107 GATGAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (26 bp):
TACAATTTATACTTATGATGTTTCGA
Found at i:52281325 original size:25 final size:25
Alignment explanation
Indices: 52281286--52281342 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
52281276 GTAAGGAGGG
*
52281286 GATAA-GGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAAGAGCT
52281310 GATAAGGGGAGAAGATTTAAGAGCT
1 GATAAGGGGAGAAGATTTAAGAGCT
52281335 GATCAAGG
1 GAT-AAGG
52281343 AGCAAGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 5 0.17
25 21 0.70
26 4 0.13
ACGTcount: A:0.39, C:0.05, G:0.37, T:0.19
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAAGAGCT
Found at i:52282828 original size:27 final size:27
Alignment explanation
Indices: 52282769--52282834 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
52282759 AACTAACTGA
*
52282769 TCTGGTGGCTCTGCCACATATATATTT
1 TCTGGTGGCTCTACCACATATATATTT
*
52282796 TTTGGTGGCTCTACCACA-AT-TATCTAT
1 TCTGGTGGCTCTACCACATATATAT-T-T
*
52282823 TCTGGTGACTCT
1 TCTGGTGGCTCT
52282835 GTCACATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 3 0.09
26 3 0.09
27 27 0.82
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (27 bp):
TCTGGTGGCTCTACCACATATATATTT
Found at i:52289168 original size:25 final size:25
Alignment explanation
Indices: 52289127--52289183 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
52289117 GTAAGGAGGG
52289127 GATAA-GGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
*
52289151 GATAAGGGGAGAATATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
52289176 GATCAAGG
1 GAT-AAGG
52289184 AGCAAGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 5 0.17
25 21 0.70
26 4 0.13
ACGTcount: A:0.37, C:0.05, G:0.37, T:0.21
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAGGAGCT
Found at i:52290670 original size:54 final size:53
Alignment explanation
Indices: 52290586--52290696 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 53
52290576 AGGAAGCGTC
*
52290586 CTGGTGGCTATGCCACAACTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCACAACTATCTGATCTGGTGACTCTGCCACAT-TATCTATT
* * * * *
52290640 CTGGTGGCTCTGCCACAATTATCTGTTCTGGTGACTCTGTCACATTATCTTTT
1 CTGGTGGCTATGCCACAACTATCTGATCTGGTGACTCTGCCACATTATCTATT
52290693 CTGG
1 CTGG
52290697 CAGCCGTGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 11 0.22
54 40 0.78
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAACTATCTGATCTGGTGACTCTGCCACATTATCTATT
Found at i:52290694 original size:26 final size:26
Alignment explanation
Indices: 52290586--52290696 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
52290576 AGGAAGCGTC
* *
52290586 CTGGTGGCTATGCCACAACTATCTGA-T
1 CTGGTGGCTCTGCCAC-ATTATCT-ATT
52290613 CTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTCTGCCACAT-TATCTATT
*
52290640 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTATT
* * *
52290667 CTGGTGACTCTGTCACATTATCTTTT
1 CTGGTGGCTCTGCCACATTATCTATT
52290693 CTGG
1 CTGG
52290697 CAGCCGTGCT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 15 0.20
27 58 0.77
28 2 0.03
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTATT
Found at i:52293008 original size:29 final size:29
Alignment explanation
Indices: 52292945--52293052 Score: 121
Period size: 29 Copynumber: 3.8 Consensus size: 29
52292935 TTAACATACC
* ** *
52292945 TGTATTTGGCCCATTAATCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
52292973 TTTATATGGCCCATT-GGACCCAAATCACC
1 TGTATATGGCCCATTAGG-CCCAAATCACA
*
52293002 TGTATATGGCCCATTAGGCCCAAATTACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
*
52293031 TTTATATGGCCCATTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
52293053 GTCACATTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.24
29 49 0.73
30 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:52298350 original size:51 final size:51
Alignment explanation
Indices: 52298295--52298394 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
52298285 CCACCACATA
* *
52298295 ACATGTAA-CACATCCATAATGAACTCGGACCTCTCTATAAGCTCGGATGTT
1 ACATG-AATCACATCCATAATGAACTCGGACCTCTCAACAAGCTCGGATGTT
* * * *
52298346 ACATGAATCCCATCCATTATGAACTGGGACCTCTCAACGAGCTCGGATG
1 ACATGAATCACATCCATAATGAACTCGGACCTCTCAACAAGCTCGGATG
52298395 CCACATATCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
ACATGAATCACATCCATAATGAACTCGGACCTCTCAACAAGCTCGGATGTT
Found at i:52303251 original size:63 final size:63
Alignment explanation
Indices: 52303160--52303281 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
52303150 TTACCCATCT
* *
52303160 GGGCTAAATTCTTAATGCACCCATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACC
1 GGGCTAAATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACC
*
52303223 GGGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCC
1 GGGCTAAATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCC
52303282 GTCCAGGCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (63 bp):
GGGCTAAATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACC
Found at i:52303296 original size:63 final size:63
Alignment explanation
Indices: 52303161--52303298 Score: 213
Period size: 63 Copynumber: 2.2 Consensus size: 63
52303151 TACCCATCTG
* * * *
52303161 GGCTAAATTCTTAATGCACCCATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCG
1 GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCA
**
52303224 GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCGTCCA
1 GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCA
*
52303287 GGCTTGATCCTT
1 GGCTAGATCCTT
52303299 TCTATATTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.22
Consensus pattern (63 bp):
GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCA
Found at i:52304690 original size:29 final size:29
Alignment explanation
Indices: 52304644--52304750 Score: 119
Period size: 29 Copynumber: 3.7 Consensus size: 29
52304634 TTCGACTTTG
52304644 AAAGGGATGGTGACGACCATCAACTATGA
1 AAAGGGATGGTGACGACCATCAACTATGA
* * *
52304673 AAAGGGATGATGATGACCATCAACTAATCA
1 AAAGGGATGGTGACGACCATCAACT-ATGA
* **
52304703 AAACGGATGGTTCCGACCATCGAA-TATGA
1 AAAGGGATGGTGACGACCATC-AACTATGA
*
52304732 AAAGGGAT-GTTACGACCAT
1 AAAGGGATGGTGACGACCAT
52304751 ATTTAACACA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 10 0.15
29 33 0.51
30 20 0.31
31 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (29 bp):
AAAGGGATGGTGACGACCATCAACTATGA
Found at i:52306631 original size:25 final size:25
Alignment explanation
Indices: 52306597--52306646 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
52306587 TTAAATTACT
52306597 GAAGTGGCTCAATTTTATCTCACAA
1 GAAGTGGCTCAATTTTATCTCACAA
52306622 GAAGTGGCTCAATTTTATCTCACAA
1 GAAGTGGCTCAATTTTATCTCACAA
52306647 TCTCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (25 bp):
GAAGTGGCTCAATTTTATCTCACAA
Found at i:52308749 original size:27 final size:27
Alignment explanation
Indices: 52308719--52308772 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
52308709 TTAGACATAG
52308719 TCAACTATGCAACATACCTTTAAATTA
1 TCAACTATGCAACATACCTTTAAATTA
52308746 TCAACTATGCAACATACCTTTAAATTA
1 TCAACTATGCAACATACCTTTAAATTA
52308773 ATCTAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (27 bp):
TCAACTATGCAACATACCTTTAAATTA
Found at i:52327756 original size:17 final size:18
Alignment explanation
Indices: 52327728--52327762 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
52327718 TCCTTCAAGA
52327728 GTTTTGGGTTTTCTTTAT
1 GTTTTGGGTTTTCTTTAT
52327746 GTTTT-GGTTTTCTTTAT
1 GTTTTGGGTTTTCTTTAT
52327763 TCTTCTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.69
Consensus pattern (18 bp):
GTTTTGGGTTTTCTTTAT
Found at i:52339789 original size:34 final size:34
Alignment explanation
Indices: 52339735--52339803 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
52339725 GCACAGTTAA
* *
52339735 AACAGTCTTGGGCCCAAGCCCTTTTCAGTATCAGT
1 AACAGTCTTGGGCCCAAGCCCATCTCAGTA-CAGT
**
52339770 AACAGT-TTGGGCCTTAGCCCATCTCAGTACAGT
1 AACAGTCTTGGGCCCAAGCCCATCTCAGTACAGT
52339803 A
1 A
52339804 TCGAATATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.63
35 6 0.20
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (34 bp):
AACAGTCTTGGGCCCAAGCCCATCTCAGTACAGT
Found at i:52341006 original size:24 final size:24
Alignment explanation
Indices: 52340961--52341006 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
52340951 CGTCAAAGAG
* * *
52340961 TTTTTGAGAAAGAAAAGAACCAAA
1 TTTTTGAAAAAAAAAACAACCAAA
*
52340985 TTTTTGAAAAAAAAAACTACCA
1 TTTTTGAAAAAAAAAACAACCA
52341007 GATATTCCCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (24 bp):
TTTTTGAAAAAAAAAACAACCAAA
Found at i:52342674 original size:16 final size:18
Alignment explanation
Indices: 52342641--52342674 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52342631 TCAGGCTATA
52342641 TCAGAACAGAAGCTTGAG
1 TCAGAACAGAAGCTTGAG
52342659 TCAGAACA-AA-CTTGAG
1 TCAGAACAGAAGCTTGAG
52342675 CTTCTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (18 bp):
TCAGAACAGAAGCTTGAG
Found at i:52345887 original size:29 final size:29
Alignment explanation
Indices: 52345823--52345951 Score: 119
Period size: 29 Copynumber: 4.6 Consensus size: 29
52345813 TACATCCATG
52345823 CATATGG-CCA-CTAGGCCCAATCTCA-TT
1 CATATGGCCCATCT-GGCCCAATCTCACTT
* *
52345850 TATATGGCCTATCTGGCCCAAT-TCACGTT
1 CATATGGCCCATCTGGCCCAATCTCAC-TT
* *
52345879 CATATGGCCCATCAGGACCAAT-TCACATT
1 CATATGGCCCATCTGGCCCAATCTCAC-TT
*
52345908 CCTATGGCCCAT-TAGGCCCAATCTC-CTT
1 CATATGGCCCATCT-GGCCCAATCTCACTT
*
52345936 TATATGGCCCATCTGG
1 CATATGGCCCATCTGG
52345952 AACAAATCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
27 9 0.11
28 24 0.29
29 48 0.58
30 2 0.02
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (29 bp):
CATATGGCCCATCTGGCCCAATCTCACTT
Found at i:52346067 original size:19 final size:19
Alignment explanation
Indices: 52346043--52346080 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52346033 AGCAGCCCAT
* *
52346043 CGGCCCATTTAGCCCATTC
1 CGGCCCATTAAGCCAATTC
52346062 CGGCCCATTAAGCCAATTC
1 CGGCCCATTAAGCCAATTC
52346081 ACAGCCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.39, G:0.16, T:0.24
Consensus pattern (19 bp):
CGGCCCATTAAGCCAATTC
Found at i:52353624 original size:28 final size:28
Alignment explanation
Indices: 52353591--52353725 Score: 130
Period size: 28 Copynumber: 4.8 Consensus size: 28
52353581 CTCATCCATG
*
52353591 CATATGACCCATTAGGCCCAATCTCATT
1 CATATGGCCCATTAGGCCCAATCTCATT
* *
52353619 TATATGGCCCATTCGGCCCAAT-TCACGTT
1 CATATGGCCCATTAGGCCCAATCTCA--TT
* * *
52353648 CATATGGCCTATTAGGACCAATTCACATT
1 CATATGGCCCATTAGGCCCAA-TCTCATT
* * *
52353677 CCTACGGCCCATTAGGCCCAATCTCCTT
1 CATATGGCCCATTAGGCCCAATCTCATT
*
52353705 TATATGGCCCATCT-GGCCCAA
1 CATATGGCCCAT-TAGGCCCAA
52353726 ATCACATTAT
Statistics
Matches: 85, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
27 3 0.04
28 40 0.47
29 39 0.46
30 1 0.01
31 2 0.02
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.28
Consensus pattern (28 bp):
CATATGGCCCATTAGGCCCAATCTCATT
Found at i:52353668 original size:29 final size:29
Alignment explanation
Indices: 52353591--52353737 Score: 142
Period size: 29 Copynumber: 5.2 Consensus size: 29
52353581 CTCATCCATG
* *
52353591 CATATGACCCATTAGGCCCAA-TCTCATT
1 CATATGGCCCATTAGGCCCAATTCACATT
* * *
52353619 TATATGGCCCATTCGGCCCAATTCACGTT
1 CATATGGCCCATTAGGCCCAATTCACATT
* *
52353648 CATATGGCCTATTAGGACCAATTCACATT
1 CATATGGCCCATTAGGCCCAATTCACATT
* *
52353677 CCTACGGCCCATTAGGCCCAATCTC-C-TT
1 CATATGGCCCATTAGGCCCAAT-TCACATT
* *
52353705 TATATGGCCCATCT-GGCCCAAATCACATT
1 CATATGGCCCAT-TAGGCCCAATTCACATT
52353734 -ATAT
1 CATAT
52353738 TCATGCTCAC
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
27 2 0.02
28 41 0.43
29 51 0.53
30 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAATTCACATT
Found at i:52353838 original size:19 final size:19
Alignment explanation
Indices: 52353804--52353850 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
52353794 TATGGCCCAA
*
52353804 TAGCCCA-TCGGGCCCATT
1 TAGCCCATTCCGGCCCATT
52353822 TAGCCCATTCCGGCCCATT
1 TAGCCCATTCCGGCCCATT
* *
52353841 AAGCCAATTC
1 TAGCCCATTC
52353851 ACAACCCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCCCATTCCGGCCCATT
Found at i:52357463 original size:20 final size:21
Alignment explanation
Indices: 52357424--52357463 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
52357414 TAATTAATGG
52357424 CTACACGGGCGTGTTGCCCTT
1 CTACACGGGCGTGTTGCCCTT
52357445 CTACACGGGCGTG-TGCCCT
1 CTACACGGGCGTGTTGCCCT
52357464 GTTCCAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.10, C:0.35, G:0.30, T:0.25
Consensus pattern (21 bp):
CTACACGGGCGTGTTGCCCTT
Found at i:52365877 original size:49 final size:49
Alignment explanation
Indices: 52365814--52365996 Score: 185
Period size: 49 Copynumber: 3.8 Consensus size: 49
52365804 ACATTAAAGT
*
52365814 CGATGCCATGTCCCAGACAGGTCTTACACT-GACTTTCATATATTGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAG-CTCTCATATATTGAGGC
* * * * ** *
52365863 CGATGCCGTATCCCAAACAGGTCTTACACTAGCTCTCATCTATTGCTGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATTGAGGC
* * * *
52365912 CGATGACATGTTCCAGACAGGTCTTACACTAGCT-T-GTATATCTCGAGAC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATAT-T-GAGGC
* *
52365961 TGATG-CATGTCCCAGACATGTCTTACACTAGCTCTC
1 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTC
52365997 GTCTCAAAGC
Statistics
Matches: 107, Mismatches: 22, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
47 4 0.04
48 28 0.26
49 74 0.69
50 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATTGAGGC
Done.