Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 27 of 97
Found at i:11425762 original size:17 final size:18
Alignment explanation
Indices: 11425730--11425763 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11425720 TATTAATTAT
*
11425730 TTTTATTTACTTTTTAAC
1 TTTTATATACTTTTTAAC
11425748 TTTTATATA-TTTTTAA
1 TTTTATATACTTTTTAA
11425764 TATAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATATACTTTTTAAC
Found at i:11426495 original size:20 final size:21
Alignment explanation
Indices: 11426472--11426510 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11426462 TAAAATTAAA
11426472 TAAATTTAT-ATTTTTTAATG
1 TAAATTTATAATTTTTTAATG
*
11426492 TAAATTTTTAATTTTTTAA
1 TAAATTTATAATTTTTTAA
11426511 ATTTTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TAAATTTATAATTTTTTAATG
Found at i:11426637 original size:28 final size:29
Alignment explanation
Indices: 11426585--11426644 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
11426575 ATTTAGATAT
11426585 TAAAATATATAAAATTATTTTTTTTAAAA
1 TAAAATATATAAAATTATTTTTTTTAAAA
* *
11426614 TAAAAT-TATTAAA-TATTTATTTTTATAA
1 TAAAATATATAAAATTATTT-TTTTTAAAA
11426642 TAA
1 TAA
11426645 TGCTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.18
28 17 0.61
29 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAAATATATAAAATTATTTTTTTTAAAA
Found at i:11431927 original size:28 final size:28
Alignment explanation
Indices: 11431895--11431960 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
11431885 GCCTATAACC
* * *
11431895 AAGAAGAAAAGAGAAATGAGAGGAAAGA
1 AAGAAGAAAAGAGAAAGGAAAGGAAAAA
11431923 AAGAAGAAAAGAGAAAGGAAAGGAAAAA
1 AAGAAGAAAAGAGAAAGGAAAGGAAAAA
11431951 AAGAGAGAAA
1 AAGA-AGAAA
11431961 TGAGGGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (28 bp):
AAGAAGAAAAGAGAAAGGAAAGGAAAAA
Found at i:11431938 original size:18 final size:20
Alignment explanation
Indices: 11431917--11431956 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11431907 GAAATGAGAG
*
11431917 GAAA-GAAA-GAAGAAAAGA
1 GAAAGGAAAGGAAAAAAAGA
11431935 GAAAGGAAAGGAAAAAAAGA
1 GAAAGGAAAGGAAAAAAAGA
11431955 GA
1 GA
11431957 GAAATGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAAGGAAAGGAAAAAAAGA
Found at i:11433264 original size:34 final size:35
Alignment explanation
Indices: 11433198--11433265 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
11433188 AACCACTTTG
* *
11433198 GGTTTTAGTTGAGCCTTTGAAAAACTAGTGTAAAA
1 GGTTTTAGCTGAGCCTTTGAAAAACCAGTGTAAAA
* * *
11433233 GGTTTTGGCTGAGCC-TTGAAAAGCCATTGTAAA
1 GGTTTTAGCTGAGCCTTTGAAAAACCAGTGTAAA
11433266 GCTTGGTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (35 bp):
GGTTTTAGCTGAGCCTTTGAAAAACCAGTGTAAAA
Found at i:11434690 original size:27 final size:26
Alignment explanation
Indices: 11434644--11434704 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
11434634 CTATTAGACA
* *
11434644 TGGCTAGGGCCATGGTTTGTGGTATATG
1 TGGCTAAGGCCATGGGTTGT--TATATG
11434672 TGG-TAAGGCCATGGGTTGTTATATG
1 TGGCTAAGGCCATGGGTTGTTATATG
11434697 TGGCTAAG
1 TGGCTAAG
11434705 CCACATGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.30
26 4 0.13
27 14 0.47
28 3 0.10
ACGTcount: A:0.18, C:0.10, G:0.38, T:0.34
Consensus pattern (26 bp):
TGGCTAAGGCCATGGGTTGTTATATG
Found at i:11457406 original size:876 final size:871
Alignment explanation
Indices: 11455708--11457428 Score: 1870
Period size: 876 Copynumber: 2.0 Consensus size: 871
11455698 ACTGAGTATG
* *
11455708 AGAATGATTTTGGCACGAGCCAAAATTTTTGAAAATCATAAGCCTCGTTGTTTATTTTGGTGAAA
1 AGAATGATTTTGGCACGAGCCAAAATTTTAGAAAATCATAAGCCTCGTTGATTATTTTGGTGAAA
* * *** *
11455773 TGAATCTATTTTATCTTATTAAAATGAGTTCGAAATATTGAGAATCATTTTTATGCTAATCTATT
66 TAAATCTATTTTATCTTATTAAAATGAGTTCGAAACATTGAGAATCATTAGAATGATAATCTATT
* * *
11455838 TTATCTGTCTCCATTTACTCAACTTTAGATATTTTAGATGATATTTGTTTATTCTTCTGGAATTA
131 TTATCTGTCTCCATTTACTCAACTTTAGATATTTTAGATGATATTTGTTTACTCATCTAGAATTA
* ** * * * * * *
11455903 TATAATCTCACCACCCTTCTTTCCACCCATTTTAGGCTCAGGATAGTCGGTAGATAGCTCACTTT
196 TATAAACTCACCACCCTTCTTTCCACCCATTCCAAGATCAGGATAGTCGGAAAATAGCTCAATTC
* * ** * *
11455968 GTTGAGGTCTACAGTTGGACTTGCATCCTCAAAAACTGTAGGTTTACTGCTTTTGATACTTTTAG
261 GTCGAGGTCTACAGTTGGACTCGCATCCTCAAAAACTGTAGGTCCACTGCCTTTGATACCTTTAG
* * ** ** * *
11456033 TCGTTCGTGGGCCCACGTGTCACTGTAAATTAAATTTTATAGTTTGGTTATCTGTATTACAGTAT
326 TCATTCGAGGGCCCACACGTCACTGTAAATTAAATTACATACTCTGGTTATCTGTATTACAGTAT
*
11456098 GTATGAATTTATTTAGTTTTTACGCTACAAAAATTATTTACAGGTAACTCTATAAATATTGTTTT
391 GTATGAATTTATTTAGCTTTTACGCTACAAAAATTATTTACAGGT-A-TCTATAAATATTGTTTT
* * * * **
11456163 ATAAGAAAATAGAATATTTTATTAAATATTTTTATTATATTCAAATAGTTATAATTTCACTTTAA
454 ATAAGAAAATAGAATATTTCATTAAATATTTTTATTATATTCAAATAGCTACAAGTTCACCCT-A
* * ** * * * *
11456228 ATGAATGTTTTAGATATCTAAACTTATTTTTTATTATGAAATATGTGTTTTCCACTTGCATACTA
518 A-GAATGTTTAAGACATAAAAACTTAGTTTTAATTATGAAATATGTATTTTCCACTTACATACTA
* ** * *
11456293 CATTTTTAGCTGGTTTCAAAATTTTTGGGGAAAAATGACCAAAATGCCCCTGTGAGACAGAAATC
582 CATTTTCAGCAAGTTTCAAAATTTTTGAGGAAAAATGACCAAAATACCCCTGTGAGACAGAAATC
** ** * * *
11456358 ATTTTTTTTATTGATTTAAGTTGGAAATAGCTTAAAATCTTTTAGAACATGATATTTGGCAACGG
647 ATTTTTTTTATTGATTTAAGTTAAAAATAGCTTAAAATCCCTTAAAACATGATATTTAGCAACGA
** * *
11456423 TTACTCATAGGGAAAATGAGAAACTCATATTAAAGCCTTGCGGGGTTTCGGTTGACATTCCAAGT
712 TTACTCATAGGGAAAATGAGAAACTCATAGCAAAGCCTTACGAGGTTTCGGTTGACATTCCAAGT
* * * *
11456488 AATGAGTGTCGATCGAGACACCTCGGCGGTTATCATGGGCTCGAGGGGAGTACCGAGTCGTGACA
777 AATGAATGTCGATCGAGACACCACGGCGGATATCATGGGCTCGAAGGGAGTACCGAGTCGTGACA
11456553 CGGTTGGATGTCCCGGCCAAGGTATCCCCA
842 CGGTTGGATGTCCCGGCCAAGGTATCCCCA
* *
11456583 AGAATGAGTTTTGGCATGAGCCAAAATTTTAAGAAATTCATAAGCCAT-GTTGATTA-TTTGAGT
1 AGAATGA-TTTTGGCACGAGCCAAAATTTT-AGAAAATCATAAGCC-TCGTTGATTATTTTG-GT
* * *
11456646 GAAATAAAAT-TATTTTAT-TTAGTTGAAATGAGTTTGAAACGTT-ATGAATCA-TAGAATGATG
62 GAAAT-AAATCTATTTTATCTTA-TTAAAATGAGTTCGAAACATTGA-GAATCATTAGAATGAT-
*
11456707 AA-CTATTTTAAGT-TGTCTCCATTTACTCGACTTTAGATATTTTAGATGATATTTGTTTACTCA
123 AATCTATTTT-A-TCTGTCTCCATTTACTCAACTTTAGATATTTTAGATGATATTTGTTTACTC-
* * * *
11456770 AT-TAG-TTTATATAAACTCACCACCTTTCTTTTCACTCATTCCAAGATCAGGATAGTTC-GAAA
185 ATCTAGAATTATATAAACTCACCACCCTTCTTTCCACCCATTCCAAGATCAGGATAG-TCGGAAA
* * * *
11456832 ATAGCT-AATTACGTCGAGGGT-TATTA-TTGGACTCGCCTCCTCAGAAATTGTAGGTCCA-TAG
249 ATAGCTCAATT-CGTCGA-GGTCTA-CAGTTGGACTCGCATCCTCAAAAACTGTAGGTCCACT-G
* * *
11456893 CCTTTGTTACCTTTGGTCATTCGAGGGCCCACACGTCATTGTAAATTAAATTACATACTCTGGTT
310 CCTTTGATACCTTTAGTCATTCGAGGGCCCACACGTCACTGTAAATTAAATTACATACTCTGGTT
* * * *
11456958 ATCTGTGTTACTGTATGTATGAATTTATTTTGCTTTTACGTTACAAAAATTATTTACGCAGAGT-
375 ATCTGTATTACAGTATGTATGAATTTATTTAGCTTTTACGCTACAAAAATTATTTA--CAG-GTA
* * * *
11457022 TCTATAAATATTGTTTTATAAGAAAATAGAATATTTCATTTAATATTTTTATTTTATTCTATTAG
437 TCTATAAATATTGTTTTATAAGAAAATAGAATATTTCATTAAATATTTTTATTATATTCAAATAG
*
11457087 CTACAAGTTCACCCT-A-AATGTTTAAGACATAAAAACTT-GTTTTAATTATGAAATGTGTATTT
502 CTACAAGTTCACCCTAAGAATGTTTAAGACATAAAAACTTAGTTTTAATTATGAAATATGTATTT
* * * * *
11457149 TCC-CTTATATATTATATTTTCAGCAAGTTTCAAAATTTTTGAGTAAAAATGACCAAAATACCCT
567 TCCACTTACATACTACATTTTCAGCAAGTTTCAAAATTTTTGAGGAAAAATGACCAAAATACCCC
* * * * * * * * ***
11457213 TGTGTGATAGAAATTATTTTTTTGTTTTTGTTTGTTTTGATTTAAAAATAGTTTATGTTCCCTTA
632 TGTGAGACAGAAATCA----TTT-TTTTT-ATTGATTTAAGTTAAAAATAGCTTAAAATCCCTTA
* * * * *
11457278 AAACATGATATTTAGTAACTATTGCTCATATGGG-AGATGTA-AAACTGAT-GCAAGAGCCTTAC
691 AAACATGATATTTAGCAACGATTACTCATA-GGGAAAATG-AGAAACTCATAGCAA-AGCCTTAC
* ** * * *
11457340 GAGGTTTCGGTTGACATTTCGGGTAATGAATGTCTG-TCGAGACATCACGGCTGATGTCATGGGC
753 GAGGTTTCGGTTGACATTCCAAGTAATGAATGTC-GATCGAGACACCACGGCGGATATCATGGGC
*
11457404 TCGAAGGGAGTACCGGGTCGTGACA
817 TCGAAGGGAGTACCGAGTCGTGACA
11457429 AATTGATTAT
Statistics
Matches: 694, Mismatches: 123, Indels: 57
0.79 0.14 0.07
Matches are distributed among these distances:
870 63 0.09
871 23 0.03
872 18 0.03
874 4 0.01
875 18 0.03
876 436 0.63
877 121 0.17
878 9 0.01
879 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (871 bp):
AGAATGATTTTGGCACGAGCCAAAATTTTAGAAAATCATAAGCCTCGTTGATTATTTTGGTGAAA
TAAATCTATTTTATCTTATTAAAATGAGTTCGAAACATTGAGAATCATTAGAATGATAATCTATT
TTATCTGTCTCCATTTACTCAACTTTAGATATTTTAGATGATATTTGTTTACTCATCTAGAATTA
TATAAACTCACCACCCTTCTTTCCACCCATTCCAAGATCAGGATAGTCGGAAAATAGCTCAATTC
GTCGAGGTCTACAGTTGGACTCGCATCCTCAAAAACTGTAGGTCCACTGCCTTTGATACCTTTAG
TCATTCGAGGGCCCACACGTCACTGTAAATTAAATTACATACTCTGGTTATCTGTATTACAGTAT
GTATGAATTTATTTAGCTTTTACGCTACAAAAATTATTTACAGGTATCTATAAATATTGTTTTAT
AAGAAAATAGAATATTTCATTAAATATTTTTATTATATTCAAATAGCTACAAGTTCACCCTAAGA
ATGTTTAAGACATAAAAACTTAGTTTTAATTATGAAATATGTATTTTCCACTTACATACTACATT
TTCAGCAAGTTTCAAAATTTTTGAGGAAAAATGACCAAAATACCCCTGTGAGACAGAAATCATTT
TTTTTATTGATTTAAGTTAAAAATAGCTTAAAATCCCTTAAAACATGATATTTAGCAACGATTAC
TCATAGGGAAAATGAGAAACTCATAGCAAAGCCTTACGAGGTTTCGGTTGACATTCCAAGTAATG
AATGTCGATCGAGACACCACGGCGGATATCATGGGCTCGAAGGGAGTACCGAGTCGTGACACGGT
TGGATGTCCCGGCCAAGGTATCCCCA
Found at i:11486506 original size:17 final size:17
Alignment explanation
Indices: 11486480--11486515 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11486470 AAGTAAAATA
11486480 AGCACACACTAAGGGGG
1 AGCACACACTAAGGGGG
* *
11486497 AGCACTCACTTAGGGGG
1 AGCACACACTAAGGGGG
11486514 AG
1 AG
11486516 AAATCCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.36, T:0.11
Consensus pattern (17 bp):
AGCACACACTAAGGGGG
Found at i:11487060 original size:73 final size:71
Alignment explanation
Indices: 11486865--11487061 Score: 193
Period size: 73 Copynumber: 2.7 Consensus size: 71
11486855 AACAGAAAAG
** * *
11486865 ACTTAGTCGACCAAGAAATGGGTTAGTCGACTAAGAGTCTACTGCCAGAAATCTGGACTTCAAGA
1 ACTTAGTCGACCAAG-AATAAGTTAGTCGACTAAGAG-CTACTGCCAGAAATCTGGACTACAAAA
11486930 CAGAACCA
64 CAGAACCA
* * * *
11486938 ACTTAATCGACCAAGAAGTAAGTTAGTCGACTAAGTGCTCACTGTCAGAAA-CTGGAAAC-AGAA
1 ACTTAGTCGACCAAGAA-TAAGTTAGTCGACTAAGAGCT-ACTGCCAGAAATCTGG--ACTACAA
11487001 AACAGAGA-CA
62 AACAGA-ACCA
* * *
11487011 ACTTAGTCGACTAAGACATATGTTAGTCGACTAAGAGCATTCTGCCAGAAA
1 ACTTAGTCGACCAAGA-ATAAGTTAGTCGACTAAGAGC-TACTGCCAGAAA
11487062 ATTTGAATTA
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
72 8 0.08
73 90 0.87
74 5 0.05
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (71 bp):
ACTTAGTCGACCAAGAATAAGTTAGTCGACTAAGAGCTACTGCCAGAAATCTGGACTACAAAACA
GAACCA
Found at i:11488416 original size:23 final size:24
Alignment explanation
Indices: 11488369--11488416 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
11488359 AAATTTAATA
11488369 TTTAAAAAGATGAAATTATAAATTT
1 TTTAAAAAGATGAAA-TATAAATTT
11488394 TTTAAAAA-ATGAAGA-ATAAATTT
1 TTTAAAAAGATGAA-ATATAAATTT
11488417 ATAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.36
24 5 0.23
25 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (24 bp):
TTTAAAAAGATGAAATATAAATTT
Found at i:11497693 original size:23 final size:23
Alignment explanation
Indices: 11497671--11497788 Score: 80
Period size: 23 Copynumber: 5.2 Consensus size: 23
11497661 TCAAGCAATA
* *
11497671 CCTAATAAACCAGTCACGTAATA
1 CCTAACAAACCAGTCACGTAATG
* * * *
11497694 CCTAACAAATCAATTACTTAATG
1 CCTAACAAACCAGTCACGTAATG
* * *
11497717 CCTAACAAACCATTCATGCAATG
1 CCTAACAAACCAGTCACGTAATG
* * **
11497740 CCTAA-AAATCAGTCCCGTAACC
1 CCTAACAAACCAGTCACGTAATG
*
11497762 CCT-A-TAACCTAGTCACGTAATG
1 CCTAACAAACC-AGTCACGTAATG
11497784 CCTAA
1 CCTAA
11497789 AAATCAACCC
Statistics
Matches: 69, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
21 4 0.06
22 25 0.36
23 40 0.58
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24
Consensus pattern (23 bp):
CCTAACAAACCAGTCACGTAATG
Found at i:11497854 original size:22 final size:22
Alignment explanation
Indices: 11497829--11497890 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
11497819 TACATCTCAC
*
11497829 AATGCCTAAAAACCAATCACGT
1 AATGCTTAAAAACCAATCACGT
* *
11497851 AATGCTTACAACCCAATCACGT
1 AATGCTTAAAAACCAATCACGT
*
11497873 AATGCTTAAAATCCAATC
1 AATGCTTAAAAACCAATC
11497891 TCACAATGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (22 bp):
AATGCTTAAAAACCAATCACGT
Found at i:11497898 original size:22 final size:22
Alignment explanation
Indices: 11497826--11497899 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 22
11497816 GCCTACATCT
*
11497826 CACAATGCCTAAAAACCAATCA
1 CACAATGCTTAAAAACCAATCA
** * *
11497848 CGTAATGCTTACAACCCAATCA
1 CACAATGCTTAAAAACCAATCA
** * *
11497870 CGTAATGCTTAAAATCCAATCT
1 CACAATGCTTAAAAACCAATCA
11497892 CACAATGC
1 CACAATGC
11497900 CTCAATCACG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.41, C:0.30, G:0.08, T:0.22
Consensus pattern (22 bp):
CACAATGCTTAAAAACCAATCA
Found at i:11497955 original size:60 final size:60
Alignment explanation
Indices: 11497842--11497961 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
11497832 GCCTAAAAAC
* * **
11497842 CAATCACGTAATGCTTACAACCCAATCACGTAATGCTTAAAATCCAATCTCACAATGCCT
1 CAATCACGCAATGCCTACAACCCAATCACACAATGCTTAAAATCCAATCTCACAATGCCT
* * * * *
11497902 CAATCACGCAATGCCTACAATCCAATCACACAATCTCTTAAAA-CTAGTTTCACAATGCCT
1 CAATCACGCAATGCCTACAACCCAATCACACAAT-GCTTAAAATCCAATCTCACAATGCCT
11497962 ACAAACTAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 43 0.86
61 7 0.14
ACGTcount: A:0.37, C:0.31, G:0.07, T:0.25
Consensus pattern (60 bp):
CAATCACGCAATGCCTACAACCCAATCACACAATGCTTAAAATCCAATCTCACAATGCCT
Found at i:11498881 original size:19 final size:19
Alignment explanation
Indices: 11498826--11498881 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
11498816 TCGCCCTTAC
*
11498826 AAAAATTTTAAAATTTTTTTA
1 AAAAATTTTATAA--TTTTTA
* * *
11498847 ACATATTTT-TATTTTTTA
1 AAAAATTTTATAATTTTTA
11498865 AAAAATTTTATAATTTT
1 AAAAATTTTATAATTTT
11498882 ACCCTCATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
18 13 0.48
19 6 0.22
20 1 0.04
21 7 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AAAAATTTTATAATTTTTA
Found at i:11500232 original size:21 final size:21
Alignment explanation
Indices: 11500207--11500289 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 21
11500197 AAATAAAATT
11500207 ATATTACTATTTTAATAATAA
1 ATATTACTATTTTAATAATAA
* *
11500228 ATATTAATATTAATGTAATAAAAA
1 ATATTACTATT--T-TAATAATAA
*
11500252 TACTTTTATTATTATTTTAATAATAA
1 -A----TATTACTATTTTAATAATAA
11500278 ATATTACTATTT
1 ATATTACTATTT
11500290 ACTCTTAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
21 20 0.41
23 1 0.02
24 8 0.16
25 2 0.04
26 8 0.16
27 1 0.02
29 9 0.18
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (21 bp):
ATATTACTATTTTAATAATAA
Found at i:11500247 original size:50 final size:50
Alignment explanation
Indices: 11500193--11500288 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
11500183 AATAGTTCAA
11500193 TAATAAATAA-AATTATATTACTATTTTAATAATAAATATTAATATTAATG
1 TAATAAA-AATAATTATATTACTATTTTAATAATAAATATTAATATTAATG
* * * *
11500243 TAATAAAAATACTTTTATTATTATTTTAATAATAAATATTACTATT
1 TAATAAAAATAATTATATTACTATTTTAATAATAAATATTAATATT
11500289 TACTCTTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 2 0.05
50 39 0.95
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (50 bp):
TAATAAAAATAATTATATTACTATTTTAATAATAAATATTAATATTAATG
Found at i:11504315 original size:108 final size:108
Alignment explanation
Indices: 11504201--11504407 Score: 342
Period size: 108 Copynumber: 1.9 Consensus size: 108
11504191 TATAAGAAAT
*
11504201 TTTGAGTAAATTTAAATAAAACGTAAATTGGGTAAGAGTTAAATAATTGCAAAAGAATGTGTATT
1 TTTGAGTAAATTTAAATAAAACGTAAATTGGATAAGAGTTAAATAATTGCAAAAGAATGTGTATT
*
11504266 TATAAGTTGTGAAAGTTATAACTAAATCAACATATTTTGCTAA
66 TATAAATTGTGAAAGTTATAACTAAATCAACATATTTTGCTAA
* * * *
11504309 TTTGAGTAAATTTAAATAAAATGTTAATTGGATAAGAGTTGAATAATTTCAAAAGAATGTGTATT
1 TTTGAGTAAATTTAAATAAAACGTAAATTGGATAAGAGTTAAATAATTGCAAAAGAATGTGTATT
* *
11504374 TGTAAATTGTGAAAGTTGTAACTAAATCAACATA
66 TATAAATTGTGAAAGTTATAACTAAATCAACATA
11504408 ATTAGTCATT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 91 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAACGTAAATTGGATAAGAGTTAAATAATTGCAAAAGAATGTGTATT
TATAAATTGTGAAAGTTATAACTAAATCAACATATTTTGCTAA
Found at i:11504613 original size:17 final size:16
Alignment explanation
Indices: 11504588--11504626 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
11504578 AAAATATTTA
*
11504588 TATATATTTTTTAACAC
1 TATAAATTTTTT-ACAC
11504605 TATAAATTTTTTACAC
1 TATAAATTTTTTACAC
11504621 T-TAAAT
1 TATAAAT
11504627 ATTTAGCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAAATTTTTTACAC
Found at i:11504630 original size:17 final size:18
Alignment explanation
Indices: 11504586--11504630 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
11504576 AGAAAATATT
11504586 TATATATATTTTTTAACAC
1 TATA-ATATTTTTTAACAC
11504605 TATAA-ATTTTTT-ACAC
1 TATAATATTTTTTAACAC
11504621 T-TAAATATTT
1 TAT-AATATTT
11504631 AGCTTATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 7 0.29
17 11 0.46
18 1 0.04
19 4 0.17
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAATATTTTTTAACAC
Found at i:11507532 original size:42 final size:42
Alignment explanation
Indices: 11507398--11507539 Score: 230
Period size: 42 Copynumber: 3.4 Consensus size: 42
11507388 ACGGCTTATG
*
11507398 CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
* * * *
11507440 CACACATAACCAGGTCAGCAACGGCTTATGTGCACTCCTACG
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
*
11507482 CGCACATAGCCGGGTTAGCAACGGCTTATGTGCACTCCTACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
11507524 CGCACATAGCCGGGTC
1 CGCACATAGCCGGGTC
11507540 CAAATCAACA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (42 bp):
CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
Found at i:11508804 original size:28 final size:27
Alignment explanation
Indices: 11508751--11508804 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
11508741 ACAAGTGCTG
* *
11508751 GGGAGAAAAATTTACCGATTTGCCCTC
1 GGGAGAAAAAATTACCGATTTACCCTC
11508778 GGGATGAAAAAATTACC-ATTTTACCCT
1 GGGA-GAAAAAATTACCGA-TTTACCCT
11508805 TATGGTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (27 bp):
GGGAGAAAAAATTACCGATTTACCCTC
Found at i:11513087 original size:20 final size:20
Alignment explanation
Indices: 11513037--11513091 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
11513027 TTATAATTGT
11513037 ATTAATTAATT-AA-TTTAA
1 ATTAATTAATTCAATTTTAA
*
11513055 ATGAATTATATTCAATTTTAA
1 ATTAATTA-ATTCAATTTTAA
*
11513076 ATTAACTAATTCAATT
1 ATTAATTAATTCAATT
11513092 CCATAGATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 10 0.32
21 11 0.35
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTAATTAATTCAATTTTAA
Found at i:11532895 original size:14 final size:16
Alignment explanation
Indices: 11532865--11532896 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11532855 TGGAGAGAAG
11532865 AAAGAGAAGATGGAAA
1 AAAGAGAAGATGGAAA
11532881 AAAGAGAA-A-GGAAA
1 AAAGAGAAGATGGAAA
11532895 AA
1 AA
11532897 TAAGAAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (16 bp):
AAAGAGAAGATGGAAA
Found at i:11538159 original size:19 final size:19
Alignment explanation
Indices: 11538135--11538172 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11538125 CCATTTAACT
*
11538135 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
11538154 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
11538173 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:11539621 original size:13 final size:13
Alignment explanation
Indices: 11539603--11539627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11539593 AGAGAAATTG
11539603 TGATTTTATAAAA
1 TGATTTTATAAAA
11539616 TGATTTTATAAA
1 TGATTTTATAAA
11539628 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:11549715 original size:23 final size:22
Alignment explanation
Indices: 11549680--11549726 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
11549670 ACGATCAATG
11549680 AAAGAAAAGAAAAAAAGAGATAA
1 AAAGAAAAGAAAAAAAGAGA-AA
11549703 AAAGTAAAA-AAAAAAAGAGAAA
1 AAAG-AAAAGAAAAAAAGAGAAA
11549725 AA
1 AA
11549727 TGAGCTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (22 bp):
AAAGAAAAGAAAAAAAGAGAAA
Found at i:11551044 original size:31 final size:31
Alignment explanation
Indices: 11550951--11552152 Score: 449
Period size: 31 Copynumber: 39.2 Consensus size: 31
11550941 TTTGAGTCTC
** *
11550951 AAGCCCAATTTACCTGGCATCCAAGATGTAT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * * *
11550982 AAGTCC-AGTTACATTGGCA-CAAAGGA-ATTT
1 AAGCCCAATTTA-GTTGGCATCCAA-GATGTTT
*
11551012 AAGCCCAATTTAGTTAGCATCCAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * *
11551043 AAGCCCAGTTATA-TTGGCAT-AAAGACGATT
1 AAGCCCAATT-TAGTTGGCATCCAAGATGTTT
* *
11551073 AAGCCCAATTTAGCTAGCA-CCAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* ** * *
11551103 AAG-CCTAGCTATGTTAGCAT-AAAGA-GATTT
1 AAGCCCAATTTA-GTTGGCATCCAAGATG-TTT
* * *
11551133 AAGCCCAATTCAATTGGCATCCAAGATGTAT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * *
11551164 AAGTCCAA-TTACATTGGCA-CAAAGGA-ATTT
1 AAGCCCAATTTA-GTTGGCATCCAA-GATGTTT
* *
11551194 AAGCCCAATTTAGCTGGCATTCAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * * *
11551225 AAACCCAGTTATA-TTGGCA-CAAAGACGATT
1 AAGCCCAATT-TAGTTGGCATCCAAGATGTTT
*
11551255 AAGCCATAATTTAGTTGGCATCCAAGATGTTT
1 AAGCC-CAATTTAGTTGGCATCCAAGATGTTT
* ** * * * *
11551287 AAG-CCTAGCTACATTGGCGT--AAAAAGATTT
1 AAGCCCAATTTA-GTTGGCATCCAAGATG-TTT
** * *
11551317 AAGCCCAATTTAACTGGCATCTAAGATGTAT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * *
11551348 AAGTCC-AGTTACATTGGCA-CAAAGA-GATTT
1 AAGCCCAATTTA-GTTGGCATCCAAGATG-TTT
* *
11551378 AAGCCCAA-TTAGACTGGCATCCAAGATGTAT
1 AAGCCCAATTTAG-TTGGCATCCAAGATGTTT
* * * *
11551409 AAG-TCTAGTTACGTTGGCA-CAAAGA-GATTT
1 AAGCCCAATTTA-GTTGGCATCCAAGATG-TTT
** * *
11551439 AAGCCCAATTTAACTGGCATCCAAAATGTAT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * *
11551470 AAGTCCAA-TTACATTGGCA-CAAAGGA-ATTT
1 AAGCCCAATTTA-GTTGGCATCCAA-GATGTTT
* * *
11551500 AAGCCCAATTTAGCTGGCAGCCAGGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * *
11551531 AAGCCCAGTTATA-TTGGCA-CAAAGAAGATT
1 AAGCCCAATT-TAGTTGGCATCCAAGATGTTT
* * *
11551561 AAGCCAAATTTAGCTAGCATCCAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* ** *
11551592 AAG-CCTAGCTACGTTGGCA-CAAAAAGATGTTT
1 AAGCCCAATTTA-GTTGGCATC--CAAGATGTTT
* ** *
11551624 AAGCCTAATTTAACTGGCATCCAAGATGATT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
*
11551655 AAGCCCAATTATA-TTGGCAT-AAAGATGTTT
1 AAGCCCAATT-TAGTTGGCATCCAAGATGTTT
**
11551685 AAGCCCAATTTAAACTGGCATCCAAGATGTTT
1 AAGCCCAATTT-AGTTGGCATCCAAGATGTTT
* * * *
11551717 AAGCCCAGTTATA-TTGGCA-CAAAGAAGATT
1 AAGCCCAATT-TAGTTGGCATCCAAGATGTTT
* * *
11551747 AAGCCAAATTTAGCTAGCATCCAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* ** *
11551778 AAG-CCTAGCTACGTTGGCA-CAAAAAGATGTTT
1 AAGCCCAATTTA-GTTGGCATC--CAAGATGTTT
* ** *
11551810 AAGCCTAATTTAACTGGCATCCAAGATGTAT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * *
11551841 AAG-TCTAGTTACGTTGGCA-CAAAAAGA-GTTT
1 AAGCCCAATTTA-GTTGGCATC--CAAGATGTTT
* ** * *
11551872 AAGCCTAATTTAACTGGTATCCAAGATGTAT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * **
11551903 AAG-TCTAGTTACGTTGGCATAAAAAGA-GTTT
1 AAGCCCAATTTA-GTTGGCAT-CCAAGATGTTT
* *
11551934 AAACCCAATTTAGCTGGCATCCAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* *
11551965 AAGCCCAGTTATA-TTGGCA-CAAAGA-GATTT
1 AAGCCCAATT-TAGTTGGCATCCAAGATG-TTT
* * *
11551995 AAGTCCAATTTAATTGGCATCTAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
* * * * *
11552026 AAGTCC-AGTTACATTGTCA--AAAGA-GTTT
1 AAGCCCAATTTA-GTTGGCATCCAAGATGTTT
** * *
11552054 -AGACCCAATTTACCTGGCAACCAAGTATGTAT
1 AAG-CCCAATTTAGTTGGCATCCAAG-ATGTTT
* * *
11552086 AAGTCCAA-TTACGTTGCCA-CAAAAGGA-GTTT
1 AAGCCCAATTTA-GTTGGCATC-CAA-GATGTTT
* *
11552117 AAGCCCAATTTAGCTAGCATCCAAGATGTTT
1 AAGCCCAATTTAGTTGGCATCCAAGATGTTT
11552148 AAGCC
1 AAGCC
11552153 TAGCTATGGT
Statistics
Matches: 842, Mismatches: 235, Indels: 188
0.67 0.19 0.15
Matches are distributed among these distances:
27 2 0.00
28 10 0.01
29 30 0.04
30 301 0.36
31 366 0.43
32 119 0.14
33 14 0.02
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
AAGCCCAATTTAGTTGGCATCCAAGATGTTT
Found at i:11551051 original size:61 final size:60
Alignment explanation
Indices: 11550951--11552244 Score: 1164
Period size: 61 Copynumber: 21.1 Consensus size: 60
11550941 TTTGAGTCTC
* * *
11550951 AAGCCCAATTTACCTGGCATCCAAGATGTATAAGTCCAGTTACATTGGCACAAAGGAATTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAA-GAATTT
* * * *
11551012 AAGCCCAATTTAGTTAGCATCCAAGATGTTTAAGCCCAGTTATATTGGCATAAAGACGA-TT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGA--ATTT
* * * ** * *
11551073 AAGCCCAATTTAGCTAGCA-CCAAGATGTTTAAGCCTAGCTATGTTAGCATAAAGAGATTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGA-ATTT
* ** * * *
11551133 AAGCCCAATTCAATTGGCATCCAAGATGTATAAGTCCAATTACATTGGCACAAAGGAATTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAA-GAATTT
* * *
11551194 AAGCCCAATTTAGCTGGCATTCAAGATGTTTAAACCCAGTTATATTGGCACAAAGACGA-TT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGA--ATTT
* * * * *
11551255 AAGCCATAATTTAGTTGGCATCCAAGATGTTTAAGCCTAGCTACATTGGCGTAAAAAG-ATTT
1 AAGCC-CAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGC--ACAAAGAATTT
* * * *
11551317 AAGCCCAATTTAACTGGCATCTAAGATGTATAAGTCCAGTTACATTGGCACAAAGAGATTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGA-ATTT
* * * *
11551378 AAGCCCAA-TTAGACTGGCATCCAAGATGTATAAGTCTAGTTACGTTGGCACAAAGAGATTT
1 AAGCCCAATTTAG-CTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGA-ATTT
* * * * *
11551439 AAGCCCAATTTAACTGGCATCCAAAATGTATAAGTCCAATTACATTGGCACAAAGGAATTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAA-GAATTT
* * * *
11551500 AAGCCCAATTTAGCTGGCAGCCAGGATGTTTAAGCCCAGTTATATTGGCACAAAGAAGATT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGAA-TTT
* * * * * *
11551561 AAGCCAAATTTAGCTAGCATCCAAGATGTTTAAGCCTAGCTACGTTGGCACAAAAAGATGTTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCAC--AAAGA-ATTT
* * * * * * *
11551624 AAGCCTAATTTAACTGGCATCCAAGATGATTAAGCCCAATTATATTGGCATAAAGATGTTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGA-ATTT
* * *
11551685 AAGCCCAATTTAAACTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAAGATT
1 AAGCCCAATTT-AGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGAA-TTT
* * * * * *
11551747 AAGCCAAATTTAGCTAGCATCCAAGATGTTTAAGCCTAGCTACGTTGGCACAAAAAGATGTTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCAC--AAAGA-ATTT
* * * * * * *
11551810 AAGCCTAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACGTTGGCACAAAAAGAGTTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCAC--AAAGAATTT
* * * * * * * * *
11551872 AAGCCTAATTTAACTGGTATCCAAGATGTATAAGTCTAGTTACGTTGGCATAAAAAGAGTTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGC--ACAAAGAATTT
* *
11551934 AAACCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGATTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGA-ATTT
* ** * * * *
11551995 AAGTCCAATTTAATTGGCATCTAAGATGTTTAAGTCCAGTTACATTGTCA-AAAGAGTTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGAATTT
* * * * * * * *
11552054 -AGACCCAATTTACCTGGCAACCAAGTATGTATAAGTCCAATTACGTTGCCACAAAAGGAGTTT
1 AAG-CCCAATTTAGCTGGCATCCAAG-ATGTTTAAGCCCAGTTACATTGGCAC-AAA-GAATTT
* * * ** *
11552117 AAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGCCTAGCTATGGTTGGCACAAAAAGATGTTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTA-CATTGGCAC--AAAGA-ATTT
* * * ** * *
11552181 AAGCCCAATTGAGCTAGAATCCAAGACATCTAAGCCCAGTTATC-TTGGCACGAGAGAATTT
1 AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTA-CATTGGCAC-AAAGAATTT
11552242 AAG
1 AAG
11552245 TTACGTAGCC
Statistics
Matches: 1034, Mismatches: 162, Indels: 74
0.81 0.13 0.06
Matches are distributed among these distances:
58 2 0.00
59 27 0.03
60 91 0.09
61 487 0.47
62 227 0.22
63 148 0.14
64 52 0.05
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (60 bp):
AAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTACATTGGCACAAAGAATTT
Found at i:11551077 original size:30 final size:30
Alignment explanation
Indices: 11551010--11551756 Score: 217
Period size: 30 Copynumber: 24.4 Consensus size: 30
11551000 ACAAAGGAAT
* * *
11551010 TTAAGCCCAATT-TAGTTAGCATCCAAGATGT
1 TTAAGCCCAATTATA-TTGGCAT-AAAGATGA
* *
11551041 TTAAGCCCAGTTATATTGGCATAAAGACGA
1 TTAAGCCCAATTATATTGGCATAAAGATGA
* * ** *
11551071 TTAAGCCCAATT-TAGCTAGCACCAAGATGT
1 TTAAGCCCAATTATA-TTGGCATAAAGATGA
* ** * *
11551101 TTAAGCCTAGCTATGTTAGCATAAAGA-GA
1 TTAAGCCCAATTATATTGGCATAAAGATGA
*
11551130 TTTAAGCCCAATTCA-ATTGGCATCCAAGATG-
1 -TTAAGCCCAATT-ATATTGGCAT-AAAGATGA
* * *
11551161 TATAAGTCCAATTACATTGGCACAAAG--GAA
1 T-TAAGCCCAATTATATTGGCATAAAGATG-A
* * *
11551191 TTTAAGCCCAATT-TAGCTGGCATTCAAGATGT
1 -TTAAGCCCAATTATA-TTGGCA-TAAAGATGA
* * * *
11551223 TTAAACCCAGTTATATTGGCACAAAGACGA
1 TTAAGCCCAATTATATTGGCATAAAGATGA
* * *
11551253 TTAAGCCATAATT-TAGTTGGCATCCAAGATGT
1 TTAAGCC-CAATTATA-TTGGCAT-AAAGATGA
* ** * * *
11551285 TTAAGCCTAGCTACATTGGCGTAAA-AAGA
1 TTAAGCCCAATTATATTGGCATAAAGATGA
* *
11551314 TTTAAGCCCAATT-TAACTGGCATCTAAGATG-
1 -TTAAGCCCAATTAT-ATTGGCAT-AAAGATGA
* * * *
11551345 TATAAGTCCAGTTACATTGGCACAAAGA-GA
1 T-TAAGCCCAATTATATTGGCATAAAGATGA
* * *
11551375 TTTAAGCCCAATTAGACTGGCATCCAAGATG-
1 -TTAAGCCCAATTATATTGGCAT-AAAGATGA
* * * ** *
11551406 TATAAGTCTAGTTACGTTGGCACAAAGA-GA
1 T-TAAGCCCAATTATATTGGCATAAAGATGA
*
11551436 TTTAAGCCCAATT-TAACTGGCATCCAAA-ATG-
1 -TTAAGCCCAATTAT-ATTGGCAT--AAAGATGA
* * *
11551467 TATAAGTCCAATTACATTGGCACAAAG--GAA
1 T-TAAGCCCAATTATATTGGCATAAAGATG-A
* ** * *
11551497 TTTAAGCCCAATT-TAGCTGGCAGCCAGGATGT
1 -TTAAGCCCAATTATA-TTGGCA-TAAAGATGA
* * *
11551529 TTAAGCCCAGTTATATTGGCACAAAGAAGA
1 TTAAGCCCAATTATATTGGCATAAAGATGA
* * * * *
11551559 TTAAGCCAAATT-TAGCTAGCATCCAAGATGT
1 TTAAGCCCAATTATA-TTGGCAT-AAAGATGA
* ** ** * *
11551590 TTAAGCCTAGCTACGTTGGCACAAAAAGATGT
1 TTAAGCCCAATTATATTGG--CATAAAGATGA
* * *
11551622 TTAAGCCTAATT-TAACTGGCATCCAAGATGA
1 TTAAGCCCAATTAT-ATTGGCAT-AAAGATGA
*
11551653 TTAAGCCCAATTATATTGGCATAAAGATGT
1 TTAAGCCCAATTATATTGGCATAAAGATGA
* * * *
11551683 TTAAGCCCAATTTAAACTGGCATCCAAGATGT
1 TTAAGCCCAA-TTATATTGGCAT-AAAGATGA
* * *
11551715 TTAAGCCCAGTTATATTGGCACAAAGAAGA
1 TTAAGCCCAATTATATTGGCATAAAGATGA
*
11551745 TTAAGCCAAATT
1 TTAAGCCCAATT
11551757 TAGCTAGCAT
Statistics
Matches: 509, Mismatches: 148, Indels: 119
0.66 0.19 0.15
Matches are distributed among these distances:
28 2 0.00
29 14 0.03
30 215 0.42
31 210 0.41
32 64 0.13
33 4 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (30 bp):
TTAAGCCCAATTATATTGGCATAAAGATGA
Found at i:11552215 original size:64 final size:63
Alignment explanation
Indices: 11552098--11552216 Score: 166
Period size: 64 Copynumber: 1.9 Consensus size: 63
11552088 GTCCAATTAC
* * * ** *
11552098 GTTGCCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGCCTAGCTATG
1 GTTGCCACAAAAAGAGTTTAAGCCCAATTGAGCTAGAATCCAAGACATCTAAGCCTAGCTATG
*
11552161 GTTGGCACAAAAAGATGTTTAAGCCCAATTGAGCTAGAATCCAAGACATCTAAGCC
1 GTTGCCACAAAAAGA-GTTTAAGCCCAATTGAGCTAGAATCCAAGACATCTAAGCC
11552217 CAGTTATCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 13 0.27
64 35 0.73
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (63 bp):
GTTGCCACAAAAAGAGTTTAAGCCCAATTGAGCTAGAATCCAAGACATCTAAGCCTAGCTATG
Found at i:11552677 original size:29 final size:27
Alignment explanation
Indices: 11552617--11552707 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 27
11552607 ACACCTATTT
*
11552617 TAAA-AAAAAAATCAAAAAAATAATAA
1 TAAATAAAAAAATAAAAAAAATAATAA
*
11552643 TGAAATAAAAAAACTAAAAAAAATGATAAA
1 T-AAATAAAAAAA-TAAAAAAAATAAT-AA
** *
11552673 TAAAT-TTAAAATAATAAAAA-AATAA
1 TAAATAAAAAAATAAAAAAAATAATAA
11552698 -AAATAAAAAA
1 TAAATAAAAAA
11552708 GAGGGTAAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
24 4 0.08
25 5 0.10
26 3 0.06
27 11 0.21
28 11 0.21
29 15 0.29
30 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (27 bp):
TAAATAAAAAAATAAAAAAAATAATAA
Found at i:11552707 original size:8 final size:8
Alignment explanation
Indices: 11552621--11552700 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
11552611 CTATTTTAAA
11552621 AAAAAAAT
1 AAAAAAAT
11552629 CAAAAAAAT
1 -AAAAAAAT
11552638 AATAATGAAAT
1 AA-AA--AAAT
11552649 AAAAAAACT
1 AAAAAAA-T
11552658 AAAAAAAAT
1 -AAAAAAAT
11552667 GATAAATAAATTT
1 -A-AAA-AAA--T
*
11552680 AAAATAAT
1 AAAAAAAT
11552688 AAAAAAAT
1 AAAAAAAT
11552696 AAAAA
1 AAAAA
11552701 TAAAAAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
8 18 0.31
9 13 0.22
10 14 0.24
11 12 0.20
12 1 0.02
13 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (8 bp):
AAAAAAAT
Found at i:11555585 original size:4 final size:4
Alignment explanation
Indices: 11555576--11555620 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
11555566 ATTCATTTTG
**
11555576 AAAT AAAT AAAT AAAT AAAT AAAT -GTT AAAT AAA- AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
11555621 AAGGAAGCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 4 0.11
4 31 0.89
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:11555616 original size:11 final size:11
Alignment explanation
Indices: 11555576--11555622 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
11555566 ATTCATTTTG
11555576 AAATAAATAAA
1 AAATAAATAAA
11555587 TAAATAAATAAA
1 -AAATAAATAAA
***
11555599 TGTTAAATAAA
1 AAATAAATAAA
11555610 AAATAAATAAA
1 AAATAAATAAA
11555621 AA
1 AA
11555623 GGAAGCAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:11556621 original size:15 final size:16
Alignment explanation
Indices: 11556590--11556623 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11556580 TAGTTTTTTT
*
11556590 AAATAATATATATAAA
1 AAATAATATAAATAAA
11556606 AAATAATA-AAATAAA
1 AAATAATATAAATAAA
11556621 AAA
1 AAA
11556624 ATATATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATATAAATAAA
Found at i:11556626 original size:16 final size:16
Alignment explanation
Indices: 11556590--11556623 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11556580 TAGTTTTTTT
*
11556590 AAATAATATATATAAA
1 AAATAATAAATATAAA
11556606 AAATAATAAA-ATAAA
1 AAATAATAAATATAAA
11556621 AAA
1 AAA
11556624 ATATATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATAAATATAAA
Found at i:11564078 original size:30 final size:30
Alignment explanation
Indices: 11564034--11564113 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
11564024 TAAGAGATGA
*
11564034 TCTATCTTAACCTTGAAAAGATAGTG-ATAT
1 TCTATCTTAACCTTGAAAAGATAG-GAAAAT
* * *
11564064 TCTATATTAGCCTTGAAAGGATAGGAAAAT
1 TCTATCTTAACCTTGAAAAGATAGGAAAAT
11564094 TCTATCTTAACCTTGAAAAG
1 TCTATCTTAACCTTGAAAAG
11564114 GTATTCGTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.98
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (30 bp):
TCTATCTTAACCTTGAAAAGATAGGAAAAT
Found at i:11564868 original size:45 final size:45
Alignment explanation
Indices: 11564799--11564892 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
11564789 ATTAAATTTA
* *
11564799 AATAATACTTAATAATATTCTTTATTACATTTATTATATTCAAAT
1 AATAATACTTAATAATATTCTTTATAACATTTATTATAGTCAAAT
* *
11564844 AATAATA-TTAAGTAATATGT-TTTATAATATTTATTATAGTGAAAT
1 AATAATACTTAA-TAATAT-TCTTTATAACATTTATTATAGTCAAAT
11564889 AATA
1 AATA
11564893 TTAATATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 4 0.09
45 38 0.88
46 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (45 bp):
AATAATACTTAATAATATTCTTTATAACATTTATTATAGTCAAAT
Found at i:11575061 original size:17 final size:18
Alignment explanation
Indices: 11575041--11575075 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
11575031 AAAAGAACGG
11575041 TTAAACAG-AAAGAGACA
1 TTAAACAGTAAAGAGACA
11575058 TTAAACAGTTAAAGAGAC
1 TTAAACAG-TAAAGAGAC
11575076 CTTTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (18 bp):
TTAAACAGTAAAGAGACA
Found at i:11575627 original size:145 final size:144
Alignment explanation
Indices: 11575446--11575736 Score: 573
Period size: 145 Copynumber: 2.0 Consensus size: 144
11575436 ATTTAATATT
11575446 AAAACTTAATGGATTTGGATTAGTAAACTTACTTTTTTTAAAAAATTTTGATAGGCTTAACATAT
1 AAAACTTAATGGATTTGGATTAGTAAACTTACTTTTTTTAAAAAATTTTGATAGGCTTAACATAT
11575511 TAATTTAGAATTTATTTGTTGGGCTTAACTAGCAATATGCTAACCATAATAACTCTAATTTTATC
66 TAATTTAGAATTTATTTGTTGGGCTTAACTAGCAATATGCTAACCATAATAACTCTAATTTTATC
11575576 AAAATAGTTTGAAG
131 AAAATAGTTTGAAG
11575590 AANAACTTAATGGATTTGGATTAGTAAACTTACTTTTTTTAAAAAATTTTGATAGGCTTAACATA
1 AA-AACTTAATGGATTTGGATTAGTAAACTTACTTTTTTTAAAAAATTTTGATAGGCTTAACATA
11575655 TTAATTTAGAATTTATTTGTTGGGCTTAACTAGCAATATGCTAACCATAATAACTCTAATTTTAT
65 TTAATTTAGAATTTATTTGTTGGGCTTAACTAGCAATATGCTAACCATAATAACTCTAATTTTAT
11575720 CAAAATAGTTTGAAG
130 CAAAATAGTTTGAAG
11575735 AA
1 AA
11575737 TAAAACTAAT
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
144 2 0.01
145 144 0.99
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (144 bp):
AAAACTTAATGGATTTGGATTAGTAAACTTACTTTTTTTAAAAAATTTTGATAGGCTTAACATAT
TAATTTAGAATTTATTTGTTGGGCTTAACTAGCAATATGCTAACCATAATAACTCTAATTTTATC
AAAATAGTTTGAAG
Found at i:11582405 original size:21 final size:21
Alignment explanation
Indices: 11582379--11582436 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
11582369 CTAGTTTTTA
11582379 GATATTGCGTGACTAACTTTG
1 GATATTGCGTGACTAACTTTG
*
11582400 GATATTGCGTGACTGACTTTG
1 GATATTGCGTGACTAACTTTG
* *
11582421 GGTATTACGTGACTAA
1 GATATTGCGTGACTAA
11582437 TTTTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (21 bp):
GATATTGCGTGACTAACTTTG
Found at i:11582454 original size:47 final size:47
Alignment explanation
Indices: 11582403--11582603 Score: 178
Period size: 47 Copynumber: 4.3 Consensus size: 47
11582393 AACTTTGGAT
* * *
11582403 ATTGCGTGACTGACTTTGGGTATTACGTGACTAATTTTTTATAAGGC
1 ATTGCGTGACTAACTTTGGGCATTACGTGACTAATTTTTGATAAGGC
* * * * *
11582450 ATTGCGTGATTAACTTTAGGCATTGCGTGACTAGTTTTTGATAAGGT
1 ATTGCGTGACTAACTTTGGGCATTACGTGACTAATTTTTGATAAGGC
** * ** *
11582497 ATTGCGTGACTAGTTTCTGATAAGGCATTACATGA-T--TAGTT-AT-AGAC
1 ATTGCGTGACTAACTT-TG----GGCATTACGTGACTAATTTTTGATAAGGC
*
11582544 ATTGCGTGACTAACTTTGAGCATTACGTGACTAATTTTTGATAAGGC
1 ATTGCGTGACTAACTTTGGGCATTACGTGACTAATTTTTGATAAGGC
*
11582591 ATTACGTGACTAA
1 ATTGCGTGACTAA
11582604 TTTTTGATAA
Statistics
Matches: 118, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
42 10 0.08
43 1 0.01
45 3 0.03
46 4 0.03
47 83 0.70
48 3 0.03
49 3 0.03
51 1 0.01
52 10 0.08
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (47 bp):
ATTGCGTGACTAACTTTGGGCATTACGTGACTAATTTTTGATAAGGC
Found at i:11582536 original size:26 final size:26
Alignment explanation
Indices: 11582467--11582627 Score: 117
Period size: 26 Copynumber: 6.6 Consensus size: 26
11582457 GATTAACTTT
*
11582467 AGGCATTGCGTGACTAGTTTTTGATA
1 AGGCATTGCGTGACTAGTTTCTGATA
*
11582493 AGGTATTGCGTGACTAGTTTCTGATA
1 AGGCATTGCGTGACTAGTTTCTGATA
* * *
11582519 AGGCATTACATGATTAG--T-T-AT-
1 AGGCATTGCGTGACTAGTTTCTGATA
* **
11582540 AGACATTGCGTGACTAACTT-TG---
1 AGGCATTGCGTGACTAGTTTCTGATA
* * *
11582562 A-GCATTACGTGACTAATTTTTGATA
1 AGGCATTGCGTGACTAGTTTCTGATA
* * *
11582587 AGGCATTACGTGACTAATTTTTGATA
1 AGGCATTGCGTGACTAGTTTCTGATA
*
11582613 AGGCATTGCATGACT
1 AGGCATTGCGTGACT
11582628 TAGGCATTAC
Statistics
Matches: 111, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
21 27 0.24
22 5 0.05
23 3 0.03
24 1 0.01
25 1 0.01
26 74 0.67
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (26 bp):
AGGCATTGCGTGACTAGTTTCTGATA
Found at i:11582547 original size:94 final size:95
Alignment explanation
Indices: 11582449--11582630 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 95
11582439 TTTTATAAGG
* * * * * *
11582449 CATTGCGTGATTAACTTT-AGGCATTGCGTGACTAGTTTTTGATAAGGTATTGCGTGACTAGTTT
1 CATTGCGTGACTAACTTTGA-GCATTACGTGACTAATTTTTGATAAGGCATTACGTGACTAATTT
11582513 CTGATAAGGCATTACATGA-TTAGTTATAGA
65 CTGATAAGGCATTACATGACTTAGTTATAGA
*
11582543 CATTGCGTGACTAACTTTGAGCATTACGTGACTAATTTTTGATAAGGCATTACGTGACTAATTTT
1 CATTGCGTGACTAACTTTGAGCATTACGTGACTAATTTTTGATAAGGCATTACGTGACTAATTTC
*
11582608 TGATAAGGCATTGCATGACTTAG
66 TGATAAGGCATTACATGACTTAG
11582631 GCATTACTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 73 0.94
95 5 0.06
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (95 bp):
CATTGCGTGACTAACTTTGAGCATTACGTGACTAATTTTTGATAAGGCATTACGTGACTAATTTC
TGATAAGGCATTACATGACTTAGTTATAGA
Found at i:11582673 original size:22 final size:22
Alignment explanation
Indices: 11582639--11582717 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
11582629 AGGCATTACT
* *
11582639 TAAAAATCT-GTCACGCAATGCC
1 TAAAAA-CTAGTCACGTAATGAC
*
11582661 TAAAAACTAGTCACGTAATGTC
1 TAAAAACTAGTCACGTAATGAC
* * *
11582683 T-AAAACCAATCACGTAATAAC
1 TAAAAACTAGTCACGTAATGAC
11582704 TAAAAACTAGTCAC
1 TAAAAACTAGTCAC
11582718 ACGGTGATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 19 0.40
22 28 0.60
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (22 bp):
TAAAAACTAGTCACGTAATGAC
Found at i:11585325 original size:29 final size:29
Alignment explanation
Indices: 11585283--11585340 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
11585273 GATATAAGAC
11585283 AGTCTTATTTGTCACCCTGTAATCGAGGT
1 AGTCTTATTTGTCACCCTGTAATCGAGGT
11585312 AGTCTTATTTGTCACCCTGTAATCGAGGT
1 AGTCTTATTTGTCACCCTGTAATCGAGGT
11585341 TATTTCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (29 bp):
AGTCTTATTTGTCACCCTGTAATCGAGGT
Found at i:11589267 original size:2 final size:2
Alignment explanation
Indices: 11589256--11589284 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11589246 AAAGAAAATT
11589256 TA TA -A 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
11589285 ACAATTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11594522 original size:21 final size:22
Alignment explanation
Indices: 11594482--11594527 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11594472 GGCATGATAG
*
11594482 TTAAAAAAAGTCTTTCAATTAT
1 TTAAAAAAAGTCATTCAATTAT
* *
11594504 TTAAAATAAGTCATT-AATTTT
1 TTAAAAAAAGTCATTCAATTAT
11594525 TTA
1 TTA
11594528 TTACATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (22 bp):
TTAAAAAAAGTCATTCAATTAT
Found at i:11595744 original size:22 final size:21
Alignment explanation
Indices: 11595716--11595762 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11595706 TATTTTAATT
*
11595716 AAATATTTAATAGATAAATTTA
1 AAATATTGAATA-ATAAATTTA
* *
11595738 AAATATTGAGTAATAATTTTA
1 AAATATTGAATAATAAATTTA
11595759 AAAT
1 AAAT
11595763 TGAATCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
AAATATTGAATAATAAATTTA
Found at i:11597056 original size:13 final size:13
Alignment explanation
Indices: 11597038--11597071 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11597028 GTCTACCAAA
11597038 AGTTCAGGAGTTC
1 AGTTCAGGAGTTC
* *
11597051 AGTTCAAGAGTTG
1 AGTTCAGGAGTTC
11597064 AGTTCAGG
1 AGTTCAGG
11597072 TCTTAAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (13 bp):
AGTTCAGGAGTTC
Found at i:11600081 original size:18 final size:17
Alignment explanation
Indices: 11600015--11600111 Score: 69
Period size: 17 Copynumber: 5.7 Consensus size: 17
11600005 ATCCCTAATA
11600015 AAAAAT-AAATAAAATT
1 AAAAATAAAATAAAATT
* *
11600031 GAGACAAATATAATCAAATT
1 -A-A-AAATAAAATAAAATT
11600051 -AAAAT-AAAT-AAA-T
1 AAAAATAAAATAAAATT
11600064 AAATAATAAAACTAAAATT
1 AAA-AATAAAA-TAAAATT
*
11600083 AAAAATAAAATAAAAAT
1 AAAAATAAAATAAAATT
* *
11600100 AATAAGAAAATA
1 AAAAATAAAATA
11600112 TAAAAATAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
13 1 0.02
14 5 0.08
15 6 0.09
16 7 0.11
17 19 0.29
18 11 0.17
19 8 0.12
20 8 0.12
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAATAAAATAAAATT
Found at i:11600089 original size:29 final size:29
Alignment explanation
Indices: 11600056--11600119 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
11600046 AAATTAAAAT
*
11600056 AAATAAATAAATAATAA-AACTAAAAT-TAA
1 AAATAAATAAA-AATAATAA-GAAAATATAA
11600085 AAATAAAATAAAAATAATAAGAAAATATAA
1 AAAT-AAATAAAAATAATAAGAAAATATAA
11600115 AAATA
1 AAATA
11600120 GTGTCTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (29 bp):
AAATAAATAAAAATAATAAGAAAATATAA
Found at i:11600095 original size:26 final size:26
Alignment explanation
Indices: 11600040--11600091 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
11600030 TGAGACAAAT
* *
11600040 ATAATCAAATTAAAATAAATAAATAA
1 ATAATAAAACTAAAATAAATAAATAA
*
11600066 ATAATAAAACTAAAATTAA-AAATAA
1 ATAATAAAACTAAAATAAATAAATAA
11600091 A
1 A
11600092 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (26 bp):
ATAATAAAACTAAAATAAATAAATAA
Found at i:11600098 original size:11 final size:11
Alignment explanation
Indices: 11600046--11600116 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
11600036 AAATATAATC
*
11600046 AAATTAAAAT-
1 AAATAAAAATA
11600056 AAATAAATAA-A
1 AAATAAA-AATA
* *
11600067 TAATAAAACTA
1 AAATAAAAATA
11600078 AAATTAAAAATA
1 AAA-TAAAAATA
11600090 AAATAAAAATA
1 AAATAAAAATA
*
11600101 ATAAGAAAATATA
1 A-AATAAAA-ATA
11600114 AAA
1 AAA
11600117 ATAGTGTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
10 7 0.14
11 20 0.41
12 18 0.37
13 4 0.08
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:11600100 original size:6 final size:6
Alignment explanation
Indices: 11600046--11600119 Score: 60
Period size: 6 Copynumber: 11.8 Consensus size: 6
11600036 AAATATAATC
* * *
11600046 AAATTA AAATAAA TAAATAA ATAATAA AACTAA AATTAA AAAT-A AAATAA
1 AAATAA AAAT-AA -AAATAA A-AATAA AAATAA AAATAA AAATAA AAATAA
* *
11600096 AAATAA TAAGAA AATATAA AAATA
1 AAATAA AAATAA AA-ATAA AAATA
11600120 GTGTCTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
5 5 0.09
6 32 0.58
7 14 0.25
8 4 0.07
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (6 bp):
AAATAA
Found at i:11601205 original size:14 final size:14
Alignment explanation
Indices: 11601186--11601213 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11601176 GGTAAATGCA
11601186 AACAATATTGAGTT
1 AACAATATTGAGTT
11601200 AACAATATTGAGTT
1 AACAATATTGAGTT
11601214 TTTCCTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
AACAATATTGAGTT
Found at i:11601864 original size:21 final size:21
Alignment explanation
Indices: 11601819--11601862 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
11601809 AGTATTTAAT
*
11601819 AAACCATGCTATTTTAGTTTG
1 AAACCATGCAATTTTAGTTTG
11601840 AAACCATGCAATTTTA-TTTG
1 AAACCATGCAATTTTAGTTTG
11601860 AAA
1 AAA
11601863 ACATAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (21 bp):
AAACCATGCAATTTTAGTTTG
Found at i:11603915 original size:26 final size:27
Alignment explanation
Indices: 11603819--11603919 Score: 177
Period size: 27 Copynumber: 3.8 Consensus size: 27
11603809 TTTCTTACAA
11603819 ATTTTACTTTCATCAAAATAATACATT
1 ATTTTACTTTCATCAAAATAATACATT
11603846 ATTTTACTTTCATCAAAATAATACATT
1 ATTTTACTTTCATCAAAATAATACATT
*
11603873 ATTTTACTTTCATCAAAATAATATATT
1 ATTTTACTTTCATCAAAATAATACATT
*
11603900 GTTTT-CTTTCATCAAAATAA
1 ATTTTACTTTCATCAAAATAA
11603920 AATAATATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
26 15 0.21
27 57 0.79
ACGTcount: A:0.40, C:0.14, G:0.01, T:0.46
Consensus pattern (27 bp):
ATTTTACTTTCATCAAAATAATACATT
Found at i:11604460 original size:25 final size:25
Alignment explanation
Indices: 11604425--11604478 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
11604415 GAGCTTTTCC
*
11604425 TGTTCAGCTTTTCT-TCTATGATCTT
1 TGTTCAACTTTTCTCT-TATGATCTT
11604450 TGTTCAACTTTTCTCTTATGATCTT
1 TGTTCAACTTTTCTCTTATGATCTT
11604475 TGTT
1 TGTT
11604479 TCATCCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.13, C:0.19, G:0.11, T:0.57
Consensus pattern (25 bp):
TGTTCAACTTTTCTCTTATGATCTT
Found at i:11623861 original size:28 final size:28
Alignment explanation
Indices: 11623806--11623859 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
11623796 TTGGAGTATA
*
11623806 AGGGCGAAATGATAATTTTGTCACCCCG
1 AGGGCGAAATGATAAATTTGTCACCCCG
11623834 AGGGC-AAATCGATAAATTT-TCACCCC
1 AGGGCGAAAT-GATAAATTTGTCACCCC
11623860 CGGCACTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (28 bp):
AGGGCGAAATGATAAATTTGTCACCCCG
Found at i:11637333 original size:19 final size:18
Alignment explanation
Indices: 11637309--11637345 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
11637299 GACTTAGTAG
11637309 AGTATGATTTGAGTATTTA
1 AGTATGATTTGAG-ATTTA
11637328 AGTATGATTTGAGATTTA
1 AGTATGATTTGAGATTTA
11637346 GAAGTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (18 bp):
AGTATGATTTGAGATTTA
Found at i:11645687 original size:16 final size:16
Alignment explanation
Indices: 11645666--11645697 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11645656 TTATTCTGTG
11645666 GGAATAGAATAAAATA
1 GGAATAGAATAAAATA
*
11645682 GGAATAGAATAGAATA
1 GGAATAGAATAAAATA
11645698 ATTATTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (16 bp):
GGAATAGAATAAAATA
Found at i:11658508 original size:19 final size:22
Alignment explanation
Indices: 11658484--11658529 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
11658474 ACATGCTTGG
11658484 TTTAAAG-AA-ATGATATTTT-
1 TTTAAAGTAATATGATATTTTA
*
11658503 TTTAAAGTAATATGATTTTTTA
1 TTTAAAGTAATATGATATTTTA
11658525 TTTAA
1 TTTAA
11658530 TATATCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 9 0.39
22 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTAAAGTAATATGATATTTTA
Found at i:11659026 original size:11 final size:11
Alignment explanation
Indices: 11659010--11659036 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11659000 TTTTATCACC
11659010 TATTCCTTTCT
1 TATTCCTTTCT
11659021 TATTCCTTTCT
1 TATTCCTTTCT
11659032 TATTC
1 TATTC
11659037 TAATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTCCTTTCT
Found at i:11675719 original size:2 final size:2
Alignment explanation
Indices: 11675712--11675740 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11675702 TTGAAGGATA
11675712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11675741 AGAAAACCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11683273 original size:20 final size:19
Alignment explanation
Indices: 11683250--11683292 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
11683240 GTTACTATAC
11683250 TTTTATCTTTCT-GCAATTT
1 TTTTAT-TTTCTAGCAATTT
*
11683269 GTTTTCTTTTCTAGCAATTT
1 -TTTTATTTTCTAGCAATTT
11683289 TTTT
1 TTTT
11683293 CTAAGCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTATTTTCTAGCAATTT
Found at i:11683292 original size:19 final size:19
Alignment explanation
Indices: 11683257--11683294 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
11683247 TACTTTTATC
11683257 TTTCTGCAATTTGTTTTCT
1 TTTCTGCAATTTGTTTTCT
11683276 TTTCTAGCAATTT-TTTTCT
1 TTTCT-GCAATTTGTTTTCT
11683295 AAGCAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.13, C:0.16, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTCTGCAATTTGTTTTCT
Found at i:11690636 original size:58 final size:58
Alignment explanation
Indices: 11690546--11690718 Score: 296
Period size: 58 Copynumber: 3.0 Consensus size: 58
11690536 ATAGTGGATA
**
11690546 GGTGGAGACACAACCTCCAGTAACATGAAATAGAAAACTACCACTAACAATAAAATAG
1 GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
11690604 GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
1 GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
* *
11690662 GGTGGAG--ACAACCTCCAACAACATGAAATGGAAAACTACCACTAACACTAAAATAG
1 GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
11690718 G
1 G
11690719 AACCACAATG
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
56 48 0.43
58 63 0.57
ACGTcount: A:0.48, C:0.22, G:0.16, T:0.14
Consensus pattern (58 bp):
GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
Found at i:11695440 original size:58 final size:58
Alignment explanation
Indices: 11695370--11695483 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
11695360 AAAGTGGAAA
* *
11695370 GGTGGAGACACAACCTCTAATAACATGAAATAAAAAACTACCACTAACAATAAAATGG
1 GGTGGAGACACAACCTCCAACAACATGAAATAAAAAACTACCACTAACAATAAAATGG
* *
11695428 GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACACTAAAAT
1 GGTGGAGACACAACCTCCAACAACATGAAATAAAAAACTACCACTAACAATAAAAT
11695484 AGGAACCACA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.49, C:0.22, G:0.13, T:0.16
Consensus pattern (58 bp):
GGTGGAGACACAACCTCCAACAACATGAAATAAAAAACTACCACTAACAATAAAATGG
Found at i:11696754 original size:14 final size:14
Alignment explanation
Indices: 11696735--11696763 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11696725 TGACTAAGGT
11696735 TTATCCTTATGAAC
1 TTATCCTTATGAAC
11696749 TTATCCTTATGAAC
1 TTATCCTTATGAAC
11696763 T
1 T
11696764 AAGTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (14 bp):
TTATCCTTATGAAC
Found at i:11705815 original size:65 final size:65
Alignment explanation
Indices: 11705710--11705841 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
11705700 CTTGATTAGG
*
11705710 CTATTTATCTAAGTTTAGTTAGCTGCATCATAGGTGTAGTAACCAATGGATTAATTTCAACTTTC
1 CTATTTATCTAAGTTTAGTTAGCTGCATCATAGGTCTAGTAACCAATGGATTAATTTCAACTTTC
11705775 CTATTTATCTAAGTTTAGTTAGCTGCATCATAGGTCTAGTAACCAATGGATTAATTTCAACTTTC
1 CTATTTATCTAAGTTTAGTTAGCTGCATCATAGGTCTAGTAACCAATGGATTAATTTCAACTTTC
11705840 CT
1 CT
11705842 CTCTATTAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (65 bp):
CTATTTATCTAAGTTTAGTTAGCTGCATCATAGGTCTAGTAACCAATGGATTAATTTCAACTTTC
Found at i:11705952 original size:20 final size:21
Alignment explanation
Indices: 11705927--11705966 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11705917 ACAGCTGCAT
*
11705927 TTATTG-TTGTATTTTGTGGG
1 TTATTGATTGTATTCTGTGGG
*
11705947 TTATTGATTTTATTCTGTGG
1 TTATTGATTGTATTCTGTGG
11705967 CATTTCAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.03, G:0.25, T:0.60
Consensus pattern (21 bp):
TTATTGATTGTATTCTGTGGG
Found at i:11719828 original size:2 final size:2
Alignment explanation
Indices: 11719821--11719851 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11719811 TTATAAGGAA
11719821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11719852 CACACACACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11726980 original size:31 final size:32
Alignment explanation
Indices: 11726944--11727026 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 32
11726934 TCATAGGAAT
* * *
11726944 TAAATTCAACAAAATTATAA-AATAGATGAAC
1 TAAATTAAATAAAATTATAAGAATAGAAGAAC
*
11726975 TAAATTAAATAAAATT-TAAGAATATAAGAAC
1 TAAATTAAATAAAATTATAAGAATAGAAGAAC
*
11727006 TAAATTGAATAAAATTCATAA
1 TAAATTAAATAAAATT-ATAA
11727027 TTACCCGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
30 3 0.07
31 38 0.86
33 3 0.07
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (32 bp):
TAAATTAAATAAAATTATAAGAATAGAAGAAC
Found at i:11736182 original size:30 final size:29
Alignment explanation
Indices: 11736122--11736194 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
11736112 AAACAATTCC
**
11736122 GTTGGAAATTATTTTCCAACTGAATTTTAT
1 GTTGGAAATT-TTTTCCAACTGAAAATTAT
11736152 GTTGGAAATTTCTTTCCAAC-GAAAAATTAT
1 GTTGGAAATTT-TTTCCAACTG-AAAATTAT
*
11736182 GTTGAAAATTTTT
1 GTTGGAAATTTTT
11736195 CCGTTGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (29 bp):
GTTGGAAATTTTTTCCAACTGAAAATTAT
Found at i:11736268 original size:30 final size:30
Alignment explanation
Indices: 11736232--11736288 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11736222 AACTAATTAA
*
11736232 ATTTCCAAC-GAAATTTTCTGTTGGAAAAAC
1 ATTTCCAACGGAAAATTTC-GTTGGAAAAAC
11736262 ATTTCCAACGGAAAATTTCGTTGGAAA
1 ATTTCCAACGGAAAATTTCGTTGGAAA
11736289 TTTAATTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (30 bp):
ATTTCCAACGGAAAATTTCGTTGGAAAAAC
Found at i:11737960 original size:19 final size:22
Alignment explanation
Indices: 11737938--11737986 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
11737928 AAAAAATTAT
11737938 ATATTAA-AATTT-A-TAACAA
1 ATATTAACAATTTCATTAACAA
11737957 ATA-TAACAATTTCATTAACAA
1 ATATTAACAATTTCATTAACAA
11737978 ATA-TAACAA
1 ATATTAACAA
11737987 ACATAACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 8 0.30
20 1 0.04
21 15 0.56
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATTAACAATTTCATTAACAA
Found at i:11744664 original size:13 final size:14
Alignment explanation
Indices: 11744646--11744683 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
11744636 TATGTGTGTG
11744646 TAATAATATA-ATA
1 TAATAATATATATA
11744659 TAATAATATATATA
1 TAATAATATATATA
11744673 T-A-AATATATAT
1 TAATAATATATAT
11744684 TAACTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.38
13 11 0.46
14 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATAATATATATA
Found at i:11747042 original size:21 final size:22
Alignment explanation
Indices: 11746989--11747043 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
11746979 TAATCACCGT
*
11746989 GTGACTAGTTTTGAGTCATTAC
1 GTGACTAGTTTTGAGACATTAC
* *
11747011 GTGATTGGTTTT-AGACATTAC
1 GTGACTAGTTTTGAGACATTAC
11747032 GTGACTAGTTTT
1 GTGACTAGTTTT
11747044 TATACATTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.44
Consensus pattern (22 bp):
GTGACTAGTTTTGAGACATTAC
Found at i:11747050 original size:22 final size:22
Alignment explanation
Indices: 11746989--11747051 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
11746979 TAATCACCGT
*
11746989 GTGACTAGTTTTGAGT-CATTAC
1 GTGACTAGTTTTTA-TACATTAC
* * *
11747011 GTGA-TTGGTTTTAGACATTAC
1 GTGACTAGTTTTTATACATTAC
11747032 GTGACTAGTTTTTATACATT
1 GTGACTAGTTTTTATACATT
11747052 GCATGACTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (22 bp):
GTGACTAGTTTTTATACATTAC
Found at i:11747058 original size:22 final size:22
Alignment explanation
Indices: 11747019--11747067 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
11747009 ACGTGATTGG
*
11747019 TTTTAGACATTACGTGACT-AGT
1 TTTTAGACATTACATGACTGA-T
* *
11747041 TTTTATACATTGCATGACTGAT
1 TTTTAGACATTACATGACTGAT
11747063 TTTTA
1 TTTTA
11747068 AACAATGCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (22 bp):
TTTTAGACATTACATGACTGAT
Found at i:11747112 original size:23 final size:24
Alignment explanation
Indices: 11747079--11747183 Score: 92
Period size: 23 Copynumber: 4.5 Consensus size: 24
11747069 ACAATGCCTA
*
11747079 AGTCACACAATACCTTA-CGAACT
1 AGTCACGCAATACCTTATCGAACT
* * *
11747102 AGTCACGCAATGCCTTAT-TAACA
1 AGTCACGCAATACCTTATCGAACT
11747125 AGTCACGCAATA-CTTATC-AACT
1 AGTCACGCAATACCTTATCGAACT
* * * *
11747147 TGTCATGCAATGCCTTATTAGAAACT
1 AGTCACGCAATACCTTA-TCG-AACT
11747173 AGTCACGCAAT
1 AGTCACGCAAT
11747184 GTCTTATAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
22 17 0.27
23 33 0.52
24 1 0.02
26 13 0.20
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (24 bp):
AGTCACGCAATACCTTATCGAACT
Found at i:11747165 original size:45 final size:46
Alignment explanation
Indices: 11747078--11747166 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 46
11747068 AACAATGCCT
11747078 AAGTCACACAATACCTTACGAACTAGTCACGCAATGCCTTATTAAC
1 AAGTCACACAATACCTTACGAACTAGTCACGCAATGCCTTATTAAC
* * *
11747124 AAGTCACGCAATA-CTTATC-AACTTGTCATGCAATGCCTTATTA
1 AAGTCACACAATACCTTA-CGAACTAGTCACGCAATGCCTTATTA
11747167 GAAACTAGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 26 0.67
46 13 0.33
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (46 bp):
AAGTCACACAATACCTTACGAACTAGTCACGCAATGCCTTATTAAC
Found at i:11747177 original size:26 final size:26
Alignment explanation
Indices: 11747143--11747277 Score: 127
Period size: 26 Copynumber: 5.4 Consensus size: 26
11747133 AATACTTATC
* * * *
11747143 AACTTGTCATGCAATGCCTTATTAGA
1 AACTAGTCACGCAATGCCTTATAAAA
*
11747169 AACTAGTCACGCAATGTCTTATAAAA
1 AACTAGTCACGCAATGCCTTATAAAA
*
11747195 AACTAGTCACGCAATGCC----CAAA
1 AACTAGTCACGCAATGCCTTATAAAA
** *
11747217 GTC-AGTCACGTAATGCCTTATAAAA
1 AACTAGTCACGCAATGCCTTATAAAA
* *
11747242 AACTAGTCACGTAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATAAAA
*
11747268 AATTAGTCAC
1 AACTAGTCAC
11747278 ATAATACCCA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
21 13 0.15
22 4 0.04
25 4 0.04
26 68 0.76
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (26 bp):
AACTAGTCACGCAATGCCTTATAAAA
Found at i:11747251 original size:73 final size:73
Alignment explanation
Indices: 11747155--11747299 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
11747145 CTTGTCATGC
* * * * *
11747155 AATGCCTTATTAGAAACTAGTCACGCAATGTCTTATAAAAAACTAGTCACGCAATGCCCAAAGTC
1 AATGCCTTATAAAAAACTAGTCACGCAATGCCTTATAAAAAACTAGTCACACAATACCCAAAGTC
*
11747220 AGTCACGT
66 AATCACGT
* * * *
11747228 AATGCCTTATAAAAAACTAGTCACGTAATGCCTTATCAAAAATTAGTCACATAATACCCAAAGTC
1 AATGCCTTATAAAAAACTAGTCACGCAATGCCTTATAAAAAACTAGTCACACAATACCCAAAGTC
11747293 AATCACG
66 AATCACG
11747300 CAATACTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (73 bp):
AATGCCTTATAAAAAACTAGTCACGCAATGCCTTATAAAAAACTAGTCACACAATACCCAAAGTC
AATCACGT
Found at i:11749512 original size:2 final size:2
Alignment explanation
Indices: 11749505--11749541 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11749495 ATATCATTTA
*
11749505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11749542 CCATTTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11752591 original size:51 final size:48
Alignment explanation
Indices: 11752499--11752597 Score: 164
Period size: 47 Copynumber: 2.1 Consensus size: 48
11752489 GTTCTCTGTT
* *
11752499 TTTTTATTCAGTTTTCATGACATCAAGCAGTACCTTTCTTTCTTCCTC
1 TTTTTATTCAATTTTCATGACATCAAGCAGCACCTTTCTTTCTTCCTC
*
11752547 TTTTT-TTCAATTTTCATGACATCAAGCAGCACCTTTCTTTCTTTCTC
1 TTTTTATTCAATTTTCATGACATCAAGCAGCACCTTTCTTTCTTCCTC
11752594 TTTT
1 TTTT
11752598 CCAAACATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 43 0.90
48 5 0.10
ACGTcount: A:0.18, C:0.24, G:0.07, T:0.51
Consensus pattern (48 bp):
TTTTTATTCAATTTTCATGACATCAAGCAGCACCTTTCTTTCTTCCTC
Found at i:11757023 original size:14 final size:15
Alignment explanation
Indices: 11757004--11757033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11756994 ACTCTTATAC
11757004 TAAACTT-ATGAATA
1 TAAACTTGATGAATA
11757018 TAAACTTGATGAATA
1 TAAACTTGATGAATA
11757033 T
1 T
11757034 TAATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (15 bp):
TAAACTTGATGAATA
Found at i:11757079 original size:15 final size:15
Alignment explanation
Indices: 11757037--11757118 Score: 53
Period size: 15 Copynumber: 5.5 Consensus size: 15
11757027 TGAATATTAA
11757037 TATTTAATTTAAAA-
1 TATTTAATTTAAAAT
* **
11757051 TATTAAAAAATAAAAT
1 TATT-TAATTTAAAAT
*
11757067 TATTTAATTT-AAAC
1 TATTTAATTTAAAAT
* *
11757081 TATTTTAACTTAAAAA
1 TA-TTTAATTTAAAAT
*
11757097 TA-TTAATATTTAAAT
1 TATTTAAT-TTAAAAT
11757112 TATTTAA
1 TATTTAA
11757119 CATAATTAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
14 13 0.26
15 24 0.48
16 13 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTTAATTTAAAAT
Found at i:11757095 original size:30 final size:30
Alignment explanation
Indices: 11757035--11757118 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
11757025 GATGAATATT
*
11757035 AATATTTAATTTAAAATATTAAAAAATAAA
1 AATATTTAATTTAAAATATTTAAAAATAAA
* * * **
11757065 ATTATTTAATTTAAACTATTTTAACTTAAA
1 AATATTTAATTTAAAATATTTAAAAATAAA
* *
11757095 AATATTAATATTTAAATTATTTAA
1 AATATTTA-ATTTAAAATATTTAA
11757119 CATAATTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
30 30 0.70
31 13 0.30
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
AATATTTAATTTAAAATATTTAAAAATAAA
Found at i:11760609 original size:3 final size:3
Alignment explanation
Indices: 11760590--11760623 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
11760580 ATAATTTAAA
11760590 ATT ATTT ATT AATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT -ATT ATT ATT ATT ATT ATT ATT AT
11760624 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11765985 original size:27 final size:28
Alignment explanation
Indices: 11765949--11766007 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
11765939 ACCTGTCATT
11765949 TTATATCTAACCTTTACTAGG-CAAACA
1 TTATATCTAACCTTTACTAGGCCAAACA
11765976 TTATATCTAACCTTTACTAGGCCAAACA
1 TTATATCTAACCTTTACTAGGCCAAACA
11766004 TTAT
1 TTAT
11766008 TTATGCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (28 bp):
TTATATCTAACCTTTACTAGGCCAAACA
Found at i:11772201 original size:20 final size:20
Alignment explanation
Indices: 11772176--11772228 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
11772166 GAACAAATAA
*
11772176 TTTTATTA-ATTATTTTTTAT
1 TTTTATTATA-TATTTTTAAT
11772196 TTTTA-TATATATTTTTAAT
1 TTTTATTATATATTTTTAAT
11772215 TTTTA-TATAT-TTTT
1 TTTTATTATATATTTT
11772229 AATATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.13
19 21 0.68
20 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTATATATTTTTAAT
Found at i:11772208 original size:19 final size:19
Alignment explanation
Indices: 11772186--11772228 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
11772176 TTTTATTAAT
*
11772186 TATTTTTTATTTTTATATA
1 TATTTTTAATTTTTATATA
11772205 TATTTTTAATTTTTATATA
1 TATTTTTAATTTTTATATA
11772224 T-TTTT
1 TATTTT
11772229 AATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTAATTTTTATATA
Found at i:11772221 original size:17 final size:18
Alignment explanation
Indices: 11772189--11772231 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
11772179 TATTAATTAT
*
11772189 TTTTTATTTTTATATATA
1 TTTTTAATTTTATATATA
11772207 TTTTTAATTTT-TATATA
1 TTTTTAATTTTATATATA
11772224 TTTTTAAT
1 TTTTTAAT
11772232 ATAATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTAATTTTATATATA
Found at i:11803815 original size:72 final size:69
Alignment explanation
Indices: 11803737--11803870 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 69
11803727 TATATATAGG
*
11803737 AAAAAATAGTTATTGGAGATCATTAAATACATATTACTGTTAGTTGATCGAAAATAGGAGAAATA
1 AAAAAATAGTTATT--AGA-CATTAAATACATATTACTATTAGTTGATCGAAAATAGGAGAAATA
11803802 GATGAGA
63 GATGAGA
* * *
11803809 AAAAAATAGTTGTTAGAGATTAAATACATATTACTATTAGTTGATTGAAAATAGGAGAAATA
1 AAAAAATAGTTATTAGACATTAAATACATATTACTATTAGTTGATCGAAAATAGGAGAAATA
11803871 ATTAAGAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
69 42 0.72
70 3 0.05
72 13 0.22
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (69 bp):
AAAAAATAGTTATTAGACATTAAATACATATTACTATTAGTTGATCGAAAATAGGAGAAATAGAT
GAGA
Found at i:11805062 original size:18 final size:20
Alignment explanation
Indices: 11805041--11805081 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
11805031 TGTACTATTA
11805041 TTTTT-ATTTATATT-TGTT
1 TTTTTAATTTATATTATGTT
*
11805059 TTTTTAATTTCTATTATGTT
1 TTTTTAATTTATATTATGTT
11805079 TTT
1 TTT
11805082 CACATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 8 0.40
20 7 0.35
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTTAATTTATATTATGTT
Found at i:11805345 original size:61 final size:61
Alignment explanation
Indices: 11805269--11805392 Score: 232
Period size: 61 Copynumber: 2.0 Consensus size: 61
11805259 TGTGGTTCTC
11805269 AAATATAAGTTGTAATGTTACACTGTTATTTAAAATTTCATCAATTTATCA-TTTTTTATT
1 AAATATAAGTTGTAATGTTACACTGTTATTTAAAATTTCATCAATTTATCATTTTTTTATT
11805329 ANAATATAAGTTGTAATGTTACACTGTTATTTAAAATTTCATCAATTTATCATTTTTTTATT
1 A-AATATAAGTTGTAATGTTACACTGTTATTTAAAATTTCATCAATTTATCATTTTTTTATT
11805391 AA
1 AA
11805393 TCCTAATTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
60 1 0.02
61 51 0.82
62 10 0.16
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.49
Consensus pattern (61 bp):
AAATATAAGTTGTAATGTTACACTGTTATTTAAAATTTCATCAATTTATCATTTTTTTATT
Found at i:11805591 original size:20 final size:22
Alignment explanation
Indices: 11805546--11805590 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
11805536 TATTTAACTA
*
11805546 TTTATATTTTATGTATTAGAGT
1 TTTATATTTTATGTATTAAAGT
11805568 TTTATA-TTTA-GTATTATAAGT
1 TTTATATTTTATGTATTA-AAGT
11805589 TT
1 TT
11805591 AAATAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 9 0.43
22 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (22 bp):
TTTATATTTTATGTATTAAAGT
Found at i:11806940 original size:11 final size:11
Alignment explanation
Indices: 11806924--11806949 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11806914 ATAATATAAT
11806924 AAAAATTAAAA
1 AAAAATTAAAA
11806935 AAAAATTAAAA
1 AAAAATTAAAA
11806946 AAAA
1 AAAA
11806950 GAGAGAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATTAAAA
Found at i:11807334 original size:12 final size:12
Alignment explanation
Indices: 11807317--11807370 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
11807307 GACGCCGACC
11807317 AAGGAAAGAGAG
1 AAGGAAAGAGAG
*
11807329 AAGGAAAGAAAG
1 AAGGAAAGAGAG
*
11807341 AAAGAAA-A-A-
1 AAGGAAAGAGAG
* *
11807350 AAGGAGAGAGGG
1 AAGGAAAGAGAG
11807362 AAGGAAAGA
1 AAGGAAAGA
11807371 AAAAAACGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
9 5 0.15
10 2 0.06
11 1 0.03
12 25 0.76
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (12 bp):
AAGGAAAGAGAG
Found at i:11807391 original size:33 final size:31
Alignment explanation
Indices: 11807320--11807410 Score: 87
Period size: 33 Copynumber: 2.9 Consensus size: 31
11807310 GCCGACCAAG
*
11807320 GAAAGAGA-GAAGGAAAGAAAGAAA-GAAAA
1 GAAAGAGAGGAAGGAAAGAAAAAAACGAAAA
*
11807349 AAAGGAGAGAGGGAAGGAAAGAAAAAAACGAAGAA
1 GAA--AGAGA-GGAAGGAAAGAAAAAAACGAA-AA
* * *
11807384 GAAAGAGAGGTAGAAAAGAAGAAAACG
1 GAAAGAGAGGAAGGAAAGAAAAAAACG
11807411 CTGGCTAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.04
31 5 0.10
32 16 0.32
33 20 0.40
34 3 0.06
35 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.01
Consensus pattern (31 bp):
GAAAGAGAGGAAGGAAAGAAAAAAACGAAAA
Found at i:11807524 original size:13 final size:13
Alignment explanation
Indices: 11807508--11807544 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
11807498 AAGAGAGAGA
11807508 AAAAAAAGGAAAG
1 AAAAAAAGGAAAG
*
11807521 AAAAAAATGAAAAG
1 AAAAAAA-GGAAAG
11807535 AAAAAAAGGA
1 AAAAAAAGGA
11807545 GAAGTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAAAAAGGAAAG
Found at i:11807532 original size:23 final size:23
Alignment explanation
Indices: 11807479--11807538 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
11807469 AAAAATGAGG
*
11807479 AAAAGAAAGAAAAGGAAAGAAGA
1 AAAAGAAAAAAAAGGAAAGAAGA
* *
11807502 GAGAGAAAAAAAAGGAAAGAA-A
1 AAAAGAAAAAAAAGGAAAGAAGA
11807524 AAAATGAAAAGAAAA
1 AAAA-GAAAA-AAAA
11807539 AAAGGAGAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 3 0.10
23 23 0.77
24 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAAAAAGGAAAGAAGA
Found at i:11811475 original size:2 final size:2
Alignment explanation
Indices: 11811468--11811508 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
11811458 GGACATGTAA
*
11811468 AG AG AG AG AG AG AG AG AG GG AG -G AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11811509 TGAGTGAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11812047 original size:2 final size:2
Alignment explanation
Indices: 11812040--11812082 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11812030 ATGTGTNATG
11812040 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
11812082 T
1 T
11812083 GTTGTGCATT
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:11812183 original size:38 final size:39
Alignment explanation
Indices: 11812128--11812230 Score: 118
Period size: 38 Copynumber: 2.6 Consensus size: 39
11812118 TAACCGTGCG
* * * * * *
11812128 TGTGCACAATGTAGGGGGATGTACAGGATGGCTCTGAC-
1 TGTGCACGATGTGGGGGGATGCACACGATGACTCCGACA
*
11812166 TGTGCACGATGTGGGGGGATGCACACGATGACTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACGATGACTCCGAC-A
*
11812206 TGTGCATGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
11812231 TGAGCTAGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 31 0.56
40 24 0.44
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.22
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACTCCGACA
Found at i:11822671 original size:22 final size:20
Alignment explanation
Indices: 11822642--11822683 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
11822632 ATATTATGCT
11822642 TAAAAAAACATAACAAGAAAAAA
1 TAAAAAAA-ATAA-AA-AAAAAA
11822665 TAAAAAAAATAAAAAAAAA
1 TAAAAAAAATAAAAAAAAA
11822684 TGGAATGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 4 0.21
23 8 0.42
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (20 bp):
TAAAAAAAATAAAAAAAAAA
Found at i:11823756 original size:58 final size:59
Alignment explanation
Indices: 11823613--11824326 Score: 579
Period size: 58 Copynumber: 11.9 Consensus size: 59
11823603 CATTAGAGAA
* * * * * *
11823613 TTAAATCGAACCTATTGTGAGATAGGTCAAGCCCAGATTAAGTCTAGG-ATTTCAATTT
1 TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* **
11823671 TT-AATCGAA-TCTGTTCTGATATTGGTCGAATCTAGATTAAGTCTAGGAATTTCAATTT
1 TTAAATCGAACT-TGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * * * *
11823729 TTAAATCAAACTTGTTTTG-TATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTT
1 TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA-TTT
* * *
11823788 TTAAATCGAA-TCCGCTCTGATATAGGTTGAGCCTAGATTAAGTCTAGGAATTTCAA-TT
1 TTAAATCGAACT-TGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * ** ** ** * **
11823846 TTAAATCAAACCTATTGAAT-TGAACTTATTCTGTATAGGTCGAACCTAGATTAAGTCTAAAAAT
1 TTAAATCGAA-C--TTG-TTCTG-A--TA-TAGGTCGA-G-CCTA--GA--TTAAGTCTAGGAAT
11823910 TTCAATTTT
52 TTCAA-TTT
* * * * * * *
11823919 TTAAATCAAACCTGTTTTGATATAGGTCAAGTCTAAATTAAGTATAGGAATTTCAA-TT
1 TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* ** * * * ** *
11823977 TTAAATCGAACTTGTTGTGCGATAGTTTGAGCCTAGATTAAGTTTAAAAATTTTAATTT
1 TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* *
11824036 TTAAATCGAACCTATTCTG-TATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTT
1 TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA-TTT
* * *
11824095 TTAAATCGAACATGTTCTGATATAGGTCAAGCCTAGATTAAGTGTAGGAATTTCAA-TT
1 TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * ** * *
11824153 TTAAATCAAACTTGTTGTGAGGTAGGTCAAGCCTAGATTAAGTCTAAGAATTTCAATTT
1 TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * * * *
11824212 TTCAAATCAAACATGTTCTGATATAGGTTGAGCCTAGATCAAGTCTAGGAATTTTAATTT
1 TT-AAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
* * *
11824272 TTAAATCGAATCTAT-TT-TGAGATAGGTCGAGCCTAGATCAAGTCTAGAAATTTCA
1 TTAAATCGAA-CT-TGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCA
11824327 TTGAACTTAT
Statistics
Matches: 524, Mismatches: 100, Indels: 63
0.76 0.15 0.09
Matches are distributed among these distances:
57 35 0.07
58 180 0.34
59 111 0.21
60 136 0.26
61 4 0.01
62 4 0.01
64 3 0.01
65 5 0.01
66 5 0.01
67 4 0.01
69 3 0.01
70 4 0.01
71 17 0.03
72 1 0.00
73 12 0.02
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (59 bp):
TTAAATCGAACTTGTTCTGATATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTT
Found at i:11823824 original size:118 final size:118
Alignment explanation
Indices: 11823634--11824326 Score: 650
Period size: 118 Copynumber: 5.8 Consensus size: 118
11823624 CTATTGTGAG
* * * *
11823634 ATAGGTCAAGCCCAGATTAAGTCTAGG-ATTTCAATTTTT-AATCGAATCTGTTCTGATATTGGT
1 ATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCGAATCCGTTCTGATATAGGT
** *
11823697 CGAATCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCAAACTTGTTTTG-T
66 CGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCAAACTTGTTCTGAT
* * * *
11823749 ATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTTTAAATCGAATCCGCTCTGATATAGG
1 ATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA-TTTTTAAATCGAATCCGTTCTGATATAGG
* *
11823814 TTGAGCCTAGATTAAGTCTAGGAATTTCAA-TTTTAAATCAAACCTATTGAATTGAACTTATTCT
65 TCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCAAA-C--TTG--TT---CTGA----
11823878 GT
118 -T
* ** * *
11823880 ATAGGTCGAACCTAGATTAAGTCTAAAAATTTCAATTTTTTAAATC-AAACCTGTTTTGATATAG
1 ATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA-TTTTTAAATCGAATCC-GTTCTGATATAG
* * * * * * **
11823944 GTCAAGTCTAAATTAAGTATAGGAATTTCAA-TTTTAAATCGAACTTGTTGTGCG
64 GTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCAAACTTGTTCTGAT
* * * ** * *
11823998 ATAGTTTGAGCCTAGATTAAGTTTAAAAATTTTAATTTTTAAATCGAA-CCTATTCTG-TATAGG
1 ATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCGAATCC-GTTCTGATATAGG
* *
11824061 TCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTTAAATCGAACATGTTCTGAT
65 TCGAGCCTAGATTAAGTCTAGGAATTTCAA-TTTTTAAATCAAACTTGTTCTGAT
* * * * * **
11824116 ATAGGTCAAGCCTAGATTAAGTGTAGGAATTTCAA-TTTTAAATC-AAACTTGTTGTGAGGTAGG
1 ATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCGAATC-CGTTCTGATATAGG
* * *
11824179 TCAAGCCTAGATTAAGTCTAAGAATTTCAATTTTTCAAATCAAACATGTTCTGAT
65 TCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTT-AAATCAAACTTGTTCTGAT
* * * ** * *
11824234 ATAGGTTGAGCCTAGATCAAGTCTAGGAATTTTAATTTTTAAATCGAATCTATTTTGAGATAGGT
1 ATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCGAATCCGTTCTGATATAGGT
* *
11824299 CGAGCCTAGATCAAGTCTAGAAATTTCA
66 CGAGCCTAGATTAAGTCTAGGAATTTCA
11824327 TTGAACTTAT
Statistics
Matches: 476, Mismatches: 75, Indels: 50
0.79 0.12 0.08
Matches are distributed among these distances:
115 23 0.05
116 40 0.08
117 53 0.11
118 207 0.43
119 45 0.09
120 6 0.01
122 2 0.00
123 1 0.00
125 1 0.00
126 2 0.00
128 3 0.01
130 5 0.01
131 88 0.18
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (118 bp):
ATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCGAATCCGTTCTGATATAGGT
CGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTAAATCAAACTTGTTCTGAT
Found at i:11823971 original size:131 final size:131
Alignment explanation
Indices: 11823737--11823983 Score: 334
Period size: 131 Copynumber: 1.9 Consensus size: 131
11823727 TTTTAAATCA
* * * * ** * *
11823737 AACTTGTTTTGTATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTTTAAATCGAATCCG
1 AACTTATTCTGTATAGGTCGAACCTAAATTAAGTCTAAAAATTTCAATTTTTTAAATCGAAACCG
** * *
11823802 CTCTGATATAGGTTGAGCCTAGATTAAGTCTAGGAATTTCAATTTTAAATCAAACCTATTGAATT
66 CTCTGATATAGGTCAAGCCTAAATTAAGTATAGGAATTTCAATTTTAAATCAAACCTATTGAATT
11823867 G
131 G
*
11823868 AACTTATTCTGTATAGGTCGAACCTAGATTAAGTCTAAAAATTTCAATTTTTTAAATC-AAACCT
1 AACTTATTCTGTATAGGTCGAACCTAAATTAAGTCTAAAAATTTCAATTTTTTAAATCGAAACC-
* * *
11823932 GTTTTGATATAGGTCAAGTCTAAATTAAGTATAGGAATTTCAATTTTAAATC
65 GCTCTGATATAGGTCAAGCCTAAATTAAGTATAGGAATTTCAATTTTAAATC
11823984 GAACTTGTTG
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
130 4 0.04
131 95 0.96
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (131 bp):
AACTTATTCTGTATAGGTCGAACCTAAATTAAGTCTAAAAATTTCAATTTTTTAAATCGAAACCG
CTCTGATATAGGTCAAGCCTAAATTAAGTATAGGAATTTCAATTTTAAATCAAACCTATTGAATT
G
Found at i:11824167 original size:176 final size:176
Alignment explanation
Indices: 11823867--11824326 Score: 593
Period size: 176 Copynumber: 2.6 Consensus size: 176
11823857 CTATTGAATT
* * ** * *
11823867 GAACTTATTCTGTATAGGTCGAACCTAGATTAAGTCTAAAAATTTCAATTTTTTAAATCAAACCT
1 GAACATATTCTGTATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTTAAATCGAACAT
* * * *
11823932 GTTTTGATATAGGTCAAGTCTAAATTAAGTATAGGAATTTCAATTTTAAATCGAACTTGTTGTGC
66 G-TTTGATATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAATTTTAAATCAAACTTGTTGTGA
* ** * *
11823997 GATAGTTTGAGCCTAGATTAAGTTTAAAAATTTTAATTTTT-AAATC
130 GATAGGTCAAGCCTAGATTAAGTCTAAAAATTTCAATTTTTCAAATC
*
11824043 GAACCTATTCTGTATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTTAAATCGAACAT
1 GAACATATTCTGTATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTTAAATCGAACAT
*
11824108 GTTCTGATATAGGTCAAGCCTAGATTAAGTGTAGGAATTTCAATTTTAAATCAAACTTGTTGTGA
66 GTT-TGATATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAATTTTAAATCAAACTTGTTGTGA
* *
11824173 GGTAGGTCAAGCCTAGATTAAGTCTAAGAATTTCAATTTTTCAAATC
130 GATAGGTCAAGCCTAGATTAAGTCTAAAAATTTCAATTTTTCAAATC
* * * * *
11824220 AAACATGTTCTGATATAGGTTGAGCCTAGATCAAGTCTAGGAATTTTAA-TTTTTAAATCGAATC
1 GAACATATTCTG-TATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTTAAATCGAA-C
* * * * *
11824284 TAT-TTTGAGATAGGTCGAGCCTAGATCAAGTCTAGAAATTTCA
64 -ATGTTTGATATAGGTCAAGCCTAGATTAAGTATAGGAATTTCA
11824327 TTGAACTTAT
Statistics
Matches: 250, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
175 2 0.01
176 150 0.60
177 60 0.24
178 36 0.14
179 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (176 bp):
GAACATATTCTGTATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTTTAAATCGAACAT
GTTTGATATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAATTTTAAATCAAACTTGTTGTGAG
ATAGGTCAAGCCTAGATTAAGTCTAAAAATTTCAATTTTTCAAATC
Found at i:11824338 original size:50 final size:50
Alignment explanation
Indices: 11824284--11824378 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
11824274 AAATCGAATC
*
11824284 TATTTTGAGATAGGTCGAGCCTAGATCAAG-TCTAGAAATTTCATTGAACT
1 TATTTTGAGATAGGTCGAGCCTAAATCAAGCTC-AGAAATTTCATTGAACT
*
11824334 TATTTTGAGATAGGTCGTGCCTAAATCAAGCTCAGAAATTTCATT
1 TATTTTGAGATAGGTCGAGCCTAAATCAAGCTCAGAAATTTCATT
11824379 TTTTCAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (50 bp):
TATTTTGAGATAGGTCGAGCCTAAATCAAGCTCAGAAATTTCATTGAACT
Found at i:11824593 original size:16 final size:16
Alignment explanation
Indices: 11824572--11824605 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11824562 ACCTATTCTT
*
11824572 TAAAAATCAATAAAAA
1 TAAAAATAAATAAAAA
*
11824588 TAAAAATAAATAATAA
1 TAAAAATAAATAAAAA
11824604 TA
1 TA
11824606 TAATATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAATAAATAAAAA
Found at i:11825206 original size:17 final size:17
Alignment explanation
Indices: 11825163--11825206 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
11825153 ACCGACCAAG
*
11825163 GAAAGAGATAAGGAAAGA
1 GAAAGAGA-AAGAAAAGA
* *
11825181 AAAAAAGAAAGAAAAGA
1 GAAAGAGAAAGAAAAGA
11825198 GAAAGAGAA
1 GAAAGAGAA
11825207 GGAGGGAGGA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.02
Consensus pattern (17 bp):
GAAAGAGAAAGAAAAGA
Found at i:11831664 original size:23 final size:23
Alignment explanation
Indices: 11831613--11831666 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
11831603 GTTTAGAGTT
* * *
11831613 TGTGAAACGGCATGATGGGCATG
1 TGTGACACGACATGATGGGAATG
*
11831636 TGTGACACGACATGGTGGGAATG
1 TGTGACACGACATGATGGGAATG
11831659 TGTGACAC
1 TGTGACAC
11831667 AACTGTGACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (23 bp):
TGTGACACGACATGATGGGAATG
Found at i:11831710 original size:24 final size:24
Alignment explanation
Indices: 11831681--11831747 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
11831671 GTGACATGGT
11831681 AGGGTTTAGGGTTTGTGACACGAC
1 AGGGTTTAGGGTTTGTGACACGAC
* * * *
11831705 ATGG-TT-GGAATGTGTGACACGGC
1 AGGGTTTAGG-GTTTGTGACACGAC
*
11831728 AGGGTTTAGAGTTTGTGACA
1 AGGGTTTAGGGTTTGTGACA
11831748 TGCCATGAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 2 0.06
23 16 0.50
24 13 0.41
25 1 0.03
ACGTcount: A:0.22, C:0.10, G:0.37, T:0.30
Consensus pattern (24 bp):
AGGGTTTAGGGTTTGTGACACGAC
Found at i:11831762 original size:47 final size:46
Alignment explanation
Indices: 11831669--11831892 Score: 148
Period size: 47 Copynumber: 4.8 Consensus size: 46
11831659 TGTGACACAA
* * * * *
11831669 CTGTGACATGGTAGGGTTTAGGGTTTGTGACACGACATG-GTTGGAAT
1 CTGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGAG--GGAAT
* * *
11831716 GTGTGACACGGCAGGGTTTAGAGTTTGTGACATGCCATGAAGGGAAT
1 CTGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATG-AGGGAAT
* * * ** * *
11831763 TTGTGACATGCCAGCATTCAGAGTTGGTGACACGCCATTGAGAGAAT
1 CTGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCA-TGAGGGAAT
* * * * * * *
11831810 CTATGACACGGTAGGGTTCAAAGTTTGTCAAACTCCATG-GAG-AT
1 CTGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGAGGGAAT
* * * * *
11831854 CCGTGACACGGTAGGGTTTAGAGTGTGTGACACGACATG
1 CTGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATG
11831893 GCAATTTATG
Statistics
Matches: 138, Mismatches: 36, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
44 32 0.23
45 3 0.02
46 2 0.01
47 98 0.71
48 2 0.01
49 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (46 bp):
CTGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGAGGGAAT
Done.