Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 62 of 82
Found at i:22242166 original size:23 final size:22
Alignment explanation
Indices: 22242140--22242189 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
22242130 TAGGCATTAC
22242140 ATGACAAGTTAGTAAGGTATTGT
1 ATGACAAGTTAGTAA-GTATTGT
* **
22242163 ATGACTAGTTTTTAAGTATTGT
1 ATGACAAGTTAGTAAGTATTGT
*
22242185 GTGAC
1 ATGAC
22242190 TTAGGTATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (22 bp):
ATGACAAGTTAGTAAGTATTGT
Found at i:22242229 original size:22 final size:22
Alignment explanation
Indices: 22242201--22242252 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
22242191 TAGGTATTGT
22242201 CTAAAAATCAATCACACAATAC
1 CTAAAAATCAATCACACAATAC
* ** *
22242223 CTAAAAACCAATCACTTAATGC
1 CTAAAAATCAATCACACAATAC
22242245 CTAAAAAT
1 CTAAAAAT
22242253 TAGTCTCGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.25, G:0.02, T:0.21
Consensus pattern (22 bp):
CTAAAAATCAATCACACAATAC
Found at i:22242309 original size:22 final size:22
Alignment explanation
Indices: 22242260--22242320 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
22242250 AATTAGTCTC
* **
22242260 GCAATACTTAAAAACCAGTGAT
1 GCAATACTTAAAAACTAGCAAT
**
22242282 ATAATACTTAAAAACTAGCAAT
1 GCAATACTTAAAAACTAGCAAT
* *
22242304 GCAATACCTAATAACTA
1 GCAATACTTAAAAACTA
22242321 ATTGATTTGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (22 bp):
GCAATACTTAAAAACTAGCAAT
Found at i:22245796 original size:66 final size:66
Alignment explanation
Indices: 22245725--22245852 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
22245715 CTTTAAGACT
*
22245725 CCCTTATTCGATCTTTGTGGATATTTATAAATTATACTTTCTATAGGAACATGTGTTTCATGAAT
1 CCCTTATTCGATCTTTGTGGATATTTATAAATTATACTTTCTATAGGAACATGTGTATCATGAAT
22245790 C
66 C
*
22245791 CCCTTATTCGATCTTTGTGGATATTTATGAATTATACTTTCTATAGGAACATGTGTATCATG
1 CCCTTATTCGATCTTTGTGGATATTTATAAATTATACTTTCTATAGGAACATGTGTATCATG
22245853 GGACTCATCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (66 bp):
CCCTTATTCGATCTTTGTGGATATTTATAAATTATACTTTCTATAGGAACATGTGTATCATGAAT
C
Found at i:22245890 original size:33 final size:33
Alignment explanation
Indices: 22245848--22245918 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
22245838 AACATGTGTA
*
22245848 TCATGGGACTCATCAAATGTAAAATTTGGGATT
1 TCATGGGACTCATCAAATATAAAATTTGGGATT
* ***
22245881 TCATGGGACTCATCAGATATTGGATTTGGGATT
1 TCATGGGACTCATCAAATATAAAATTTGGGATT
22245914 TCATG
1 TCATG
22245919 AGGGAGAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (33 bp):
TCATGGGACTCATCAAATATAAAATTTGGGATT
Found at i:22251343 original size:13 final size:13
Alignment explanation
Indices: 22251325--22251349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22251315 GGAAAATGGG
22251325 ATTTTATAAAATA
1 ATTTTATAAAATA
22251338 ATTTTATAAAAT
1 ATTTTATAAAAT
22251350 TTTTAAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:22252603 original size:9 final size:9
Alignment explanation
Indices: 22252585--22252621 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
22252575 CGCCGAATGG
22252585 AAAT-TTTT
1 AAATATTTT
*
22252593 AAACATTTT
1 AAATATTTT
22252602 AAATA-TTT
1 AAATATTTT
22252610 AAATATTTT
1 AAATATTTT
22252619 AAA
1 AAA
22252622 AGCGCCGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 11 0.44
9 14 0.56
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (9 bp):
AAATATTTT
Found at i:22252610 original size:17 final size:17
Alignment explanation
Indices: 22252585--22252621 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
22252575 CGCCGAATGG
*
22252585 AAATTTTTAAACATTTT
1 AAATATTTAAACATTTT
*
22252602 AAATATTTAAATATTTT
1 AAATATTTAAACATTTT
22252619 AAA
1 AAA
22252622 AGCGCCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATTTAAACATTTT
Found at i:22261999 original size:203 final size:205
Alignment explanation
Indices: 22261753--22262159 Score: 483
Period size: 203 Copynumber: 2.0 Consensus size: 205
22261743 AAATAACTAA
* **
22261753 TAAACTTATTAACTATAATCATATAAATAAAGTTTATTATAAGTTATAATAATGTTTATGCACAA
1 TAAACTTATTAACTATAATCATATAAATAAAGTTGATTATAAGTTATAATAATACTTATGCACAA
22261818 ATT-A-ATA-ATATGTATA-TATAATATATTACTTTATTATATATATGAAAT-TAATTACACA-A
66 ATTAATATATATATGTATAGTATAATATATTACTTTATTATATATAT-AAATATAATTACACAGA
* * *
22261877 CTTATATGTTATCATGTTTTAA-TTTTTATA-AAAAGGTTTGTATAAATAATAACTAATTATAAA
130 --TA-A-CTTA-CATATTATAATTTTTTATATAAAA-GTTTGTATAAATAATAACTAATTATAAA
22261940 CAATATGTTATAAAAAT
189 CAATATGTTATAAAAAT
* * * *
22261957 TAAA-TTATTAAGTGTAATCATATAAATAAAGTATGA-TATAAGTTATAATAATACTTATGTATA
1 TAAACTTATTAACTATAATCATATAAATAAAGT-TGATTATAAGTTATAATAATACTTATGCACA
* **
22262020 AATTAAATATATGTATATGTATATGTATAATATATTACTTTATTATATATATATATATAATTATT
65 AATT-AATATA--TATATGTATA-GTATAATATATTACTTTATTATATATATAAATATAATTACA
* * * *
22262085 GAGATAACTTACATATTATAATTTTTTATATCAAAGTTTGTGTAAATAATAACTAATTATAAATA
126 CAGATAACTTACATATTATAATTTTTTATATAAAAGTTTGTATAAATAATAACTAATTATAAACA
22262150 ATATGTTATA
191 ATATGTTATA
22262160 GAAACTAAGG
Statistics
Matches: 173, Mismatches: 17, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
203 53 0.31
204 6 0.03
205 1 0.01
206 3 0.02
207 8 0.05
208 49 0.28
209 13 0.08
210 5 0.03
211 34 0.20
212 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (205 bp):
TAAACTTATTAACTATAATCATATAAATAAAGTTGATTATAAGTTATAATAATACTTATGCACAA
ATTAATATATATATGTATAGTATAATATATTACTTTATTATATATATAAATATAATTACACAGAT
AACTTACATATTATAATTTTTTATATAAAAGTTTGTATAAATAATAACTAATTATAAACAATATG
TTATAAAAAT
Found at i:22262262 original size:19 final size:19
Alignment explanation
Indices: 22262240--22262292 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
22262230 AATATTTATG
22262240 TATAAATTAAATATATGTA
1 TATAAATTAAATATATGTA
* *
22262259 TATAGA-TATAATATATTTA
1 TATAAATTA-AATATATGTA
*
22262278 TAT-AATTATATATAT
1 TATAAATTAAATATAT
22262293 ATTCATAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATAAATTAAATATATGTA
Found at i:22267937 original size:160 final size:160
Alignment explanation
Indices: 22267673--22267993 Score: 624
Period size: 160 Copynumber: 2.0 Consensus size: 160
22267663 CTGGTTTAAT
22267673 ATTACATATCATAATTACATTAACAGTCAATCAGCTCTTCAACTCTGTGGTCTGTCTCTTGCAGA
1 ATTACATATCATAATTACATTAACAGTCAATCAGCTCTTCAACTCTGTGGTCTGTCTCTTGCAGA
22267738 GTGCAAGAATATAGAAGGAAACAAAATGCACATCTTACTCATTTTTAAAACAAGATAAGATAAGC
66 GTGCAAGAATATAGAAGGAAACAAAATGCACATCTTACTCATTTTTAAAACAAGATAAGATAAGC
22267803 ATCAGTTTCTACTATGCAAATACATGCGTG
131 ATCAGTTTCTACTATGCAAATACATGCGTG
*
22267833 ATTACATATCATAATTACATTAACAGTCAATCAGCTCTTCAACTCTGTGGTCTGTCTCTTGCAGT
1 ATTACATATCATAATTACATTAACAGTCAATCAGCTCTTCAACTCTGTGGTCTGTCTCTTGCAGA
22267898 GTGCAAGAATATAGAAGGAAACAAAATGCACATCTTACTCATTTTTAAAACAAGATAAGATAAGC
66 GTGCAAGAATATAGAAGGAAACAAAATGCACATCTTACTCATTTTTAAAACAAGATAAGATAAGC
*
22267963 ATCAGTTTCTACTGTGCAAATACATGCGTG
131 ATCAGTTTCTACTATGCAAATACATGCGTG
22267993 A
1 A
22267994 ACTTTAACAT
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 159 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (160 bp):
ATTACATATCATAATTACATTAACAGTCAATCAGCTCTTCAACTCTGTGGTCTGTCTCTTGCAGA
GTGCAAGAATATAGAAGGAAACAAAATGCACATCTTACTCATTTTTAAAACAAGATAAGATAAGC
ATCAGTTTCTACTATGCAAATACATGCGTG
Found at i:22272964 original size:18 final size:18
Alignment explanation
Indices: 22272941--22272975 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22272931 TTGATAATGC
*
22272941 TGCTGCCACTGTTCCTAA
1 TGCTGCCACTGTCCCTAA
*
22272959 TGCTGCCTCTGTCCCTA
1 TGCTGCCACTGTCCCTA
22272976 CTGCCACCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.37, G:0.17, T:0.34
Consensus pattern (18 bp):
TGCTGCCACTGTCCCTAA
Found at i:22278318 original size:2 final size:2
Alignment explanation
Indices: 22278311--22278338 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22278301 CTCTTTAAGT
22278311 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
22278339 CAATTGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:22281780 original size:18 final size:19
Alignment explanation
Indices: 22281747--22281792 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
22281737 TAATATTTTG
* *
22281747 TAATATAAAATGGTATGAA
1 TAATATATAATGGTATAAA
*
22281766 T-ATATATAATTGTATAAA
1 TAATATATAATGGTATAAA
22281784 TAATATATA
1 TAATATATA
22281793 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (19 bp):
TAATATATAATGGTATAAA
Found at i:22283883 original size:33 final size:33
Alignment explanation
Indices: 22283813--22283883 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
22283803 GTGCTCTCGA
* * * *
22283813 CTCCAGCTACTCTGATTCCCATGATCTCGACTC
1 CTCCAGCTACCCTGACTACCATCATCTCGACTC
* * *
22283846 CTCCAGCTACCCTGACTACCATCTTCTTGACTT
1 CTCCAGCTACCCTGACTACCATCATCTCGACTC
22283879 CTCCA
1 CTCCA
22283884 ACTGCTCTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.18, C:0.41, G:0.10, T:0.31
Consensus pattern (33 bp):
CTCCAGCTACCCTGACTACCATCATCTCGACTC
Found at i:22286865 original size:31 final size:31
Alignment explanation
Indices: 22286827--22286940 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 31
22286817 CTACAGTATA
22286827 AACAAGATCTACAACACTTATTTGGGTCATT
1 AACAAGATCTACAACACTTATTTGGGTCATT
* *** *
22286858 AACAAGATCTATAACGAAGAACTTTGTGGATTAATAT
1 AACAAGATCTACAAC-ACTTA-TTTG-GG--TCAT-T
* **
22286895 AAACCAGATCTACAACACTTATTCAGGTCATT
1 -AACAAGATCTACAACACTTATTTGGGTCATT
*
22286927 TACAAGATCTACAA
1 AACAAGATCTACAA
22286941 AGAACTTTGT
Statistics
Matches: 61, Mismatches: 15, Indels: 14
0.68 0.17 0.16
Matches are distributed among these distances:
31 26 0.43
32 3 0.05
33 7 0.11
34 2 0.03
35 2 0.03
36 5 0.08
37 3 0.05
38 13 0.21
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (31 bp):
AACAAGATCTACAACACTTATTTGGGTCATT
Found at i:22286934 original size:69 final size:66
Alignment explanation
Indices: 22286823--22286957 Score: 198
Period size: 69 Copynumber: 2.0 Consensus size: 66
22286813 AAATCTACAG
** *
22286823 TATAAACAAGATCTACAACACTTATTTGGGTCATTAACAAGATCTATAACGAAGAACTTTGTGGA
1 TATAAACAAGATCTACAACACTTATTCAGGTCATTAACAAGATC--T-ACAAAGAACTTTGTGGA
22286888 TTAA
63 TTAA
* *
22286892 TATAAACCAGATCTACAACACTTATTCAGGTCATTTACAAGATCTACAAAGAACTTTGTGGATTA
1 TATAAACAAGATCTACAACACTTATTCAGGTCATTAACAAGATCTACAAAGAACTTTGTGGATTA
22286957 A
66 A
22286958 AAATGATACC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
66 20 0.33
67 1 0.02
69 40 0.66
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (66 bp):
TATAAACAAGATCTACAACACTTATTCAGGTCATTAACAAGATCTACAAAGAACTTTGTGGATTA
A
Found at i:22310353 original size:30 final size:30
Alignment explanation
Indices: 22310319--22310388 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
22310309 ACAATCAAAT
*
22310319 TTTTGTAATTTT-TGTTTGAGTCAAATAAAC
1 TTTTGTAATTTTAT-TTTAAGTCAAATAAAC
*
22310349 TTTTGTAATTTTATTTTAAGTCAAATAAAT
1 TTTTGTAATTTTATTTTAAGTCAAATAAAC
*
22310379 TTTTATAATT
1 TTTTGTAATT
22310389 AATGATTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (30 bp):
TTTTGTAATTTTATTTTAAGTCAAATAAAC
Found at i:22314629 original size:2 final size:2
Alignment explanation
Indices: 22314624--22314714 Score: 120
Period size: 2 Copynumber: 48.0 Consensus size: 2
22314614 CACACATAAA
22314624 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
22314663 AT -T AG AG AN AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22314703 AT AT AT AT AT AT
1 AT AT AT AT AT AT
22314715 TTTGTATGTA
Statistics
Matches: 81, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
1 5 0.06
2 76 0.94
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:22318617 original size:25 final size:26
Alignment explanation
Indices: 22318579--22318628 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
22318569 TATTATCAAA
22318579 TAATATTTTCATATATATATT-ATTTT
1 TAATATTTTCATATAT-TATTGATTTT
*
22318605 TAAT-TTTTTATATATTATTGATTT
1 TAATATTTTCATATATTATTGATTT
22318629 ATTTGTTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 14 0.64
26 4 0.18
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TAATATTTTCATATATTATTGATTTT
Found at i:22325069 original size:15 final size:17
Alignment explanation
Indices: 22325049--22325102 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
22325039 GAATGATGTT
22325049 ATAATTAAAATA-AT-A
1 ATAATTAAAATATATAA
*
22325064 ATAATTAAAAAATATAA
1 ATAATTAAAATATATAA
*
22325081 ATATATTAAAATTTATAA
1 ATA-ATTAAAATATATAA
22325099 ATAA
1 ATAA
22325103 AAATTTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 11 0.33
16 2 0.06
17 5 0.15
18 15 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATTAAAATATATAA
Found at i:22326058 original size:2 final size:2
Alignment explanation
Indices: 22326051--22326133 Score: 120
Period size: 2 Copynumber: 42.5 Consensus size: 2
22326041 TTGGATTCAC
22326051 AG AG AG AG AG A- AG AG AG AG AG ATG AG AG AG ATG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG A-G AG AG AG AG AG
22326094 AG AG AG -G AG AG AG AG AG AG AG -G AG A- 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
22326133 A
1 A
22326134 AAAAAAAAAC
Statistics
Matches: 75, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.05
2 67 0.89
3 4 0.05
ACGTcount: A:0.49, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:22326098 original size:37 final size:37
Alignment explanation
Indices: 22326051--22326133 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
22326041 TTGGATTCAC
*
22326051 AGAGAGAGAGAAGAGAGAGAGATGAGA-GAGATGAGAG
1 AGAGAGAGAGAAGAGAGAGAGA-GAGAGGAGAAGAGAG
*
22326088 AGAGAGAGAGAGGAGAGAGAGAGAGAGGAGAAGAGAG
1 AGAGAGAGAGAAGAGAGAGAGAGAGAGGAGAAGAGAG
22326125 AGAGAGAGA
1 AGAGAGAGA
22326134 AAAAAAAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 4 0.09
37 39 0.91
ACGTcount: A:0.49, C:0.00, G:0.48, T:0.02
Consensus pattern (37 bp):
AGAGAGAGAGAAGAGAGAGAGAGAGAGGAGAAGAGAG
Found at i:22333304 original size:12 final size:12
Alignment explanation
Indices: 22333287--22333312 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22333277 TTTTAACTAA
22333287 ATATTTTATTAT
1 ATATTTTATTAT
22333299 ATATTTTATTAT
1 ATATTTTATTAT
22333311 AT
1 AT
22333313 TTTATCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:22333381 original size:2 final size:2
Alignment explanation
Indices: 22333374--22333416 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
22333364 TTCATACTTT
22333374 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
22333416 T
1 T
22333417 NNNNNNNNNN
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:22334267 original size:17 final size:19
Alignment explanation
Indices: 22334235--22334269 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
22334225 TTTAGTTTTT
22334235 TTTTGTTTGATTGTGGTTA
1 TTTTGTTTGATTGTGGTTA
22334254 TTTT-TTTG-TTGTGGTT
1 TTTTGTTTGATTGTGGTT
22334270 GGATGCGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.06, C:0.00, G:0.26, T:0.69
Consensus pattern (19 bp):
TTTTGTTTGATTGTGGTTA
Found at i:22334844 original size:12 final size:12
Alignment explanation
Indices: 22334805--22334851 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
22334795 TAACATAACT
*
22334805 ATATAGAATAAA
1 ATATAAAATAAA
*
22334817 ATATAAAA-CAA
1 ATATAAAATAAA
*
22334828 A-ATAAAATGAA
1 ATATAAAATAAA
22334839 ATATAAAATAAA
1 ATATAAAATAAA
22334851 A
1 A
22334852 AACAGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 6 0.21
11 6 0.21
12 17 0.59
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (12 bp):
ATATAAAATAAA
Found at i:22335220 original size:31 final size:31
Alignment explanation
Indices: 22335185--22335244 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
22335175 TCAAAGTCGA
*
22335185 AGTTTAAGTTTCTTTAGTTTTCAAAATCATC
1 AGTTTAAGTTTCTTCAGTTTTCAAAATCATC
* *
22335216 AGTTTAATTTTCTTCAGTTTTCAACATCA
1 AGTTTAAGTTTCTTCAGTTTTCAAAATCA
22335245 CCTCGAGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (31 bp):
AGTTTAAGTTTCTTCAGTTTTCAAAATCATC
Found at i:22335306 original size:71 final size:72
Alignment explanation
Indices: 22335231--22335372 Score: 171
Period size: 72 Copynumber: 2.0 Consensus size: 72
22335221 AATTTTCTTC
* * * *
22335231 AGTTTTCAACATCACCTC-GAGTCGAAGTT-TCAATTTTTTCAAACTTCAAAAAGGATTTTAATG
1 AGTTTTCAACATCACCTCAAAGTCGAAGTTCT-AATTCTTTCAAACTTCAAAAAAGATTTCAATG
22335294 GTTGGTCA
65 GTTGGTCA
* * * * **
22335302 AGTTTTCACCATCATCTCAAAGTTGAAGTTCTAGTTCTTTCAAGTTTCAAAAAAGATTTCAATGG
1 AGTTTTCAACATCACCTCAAAGTCGAAGTTCTAATTCTTTCAAACTTCAAAAAAGATTTCAATGG
22335367 TTGGTC
66 TTGGTC
22335373 TTTAATTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
71 16 0.27
72 42 0.71
73 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (72 bp):
AGTTTTCAACATCACCTCAAAGTCGAAGTTCTAATTCTTTCAAACTTCAAAAAAGATTTCAATGG
TTGGTCA
Found at i:22335598 original size:59 final size:60
Alignment explanation
Indices: 22335495--22335614 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 60
22335485 TTTGTCATTT
* * *
22335495 AATTGGAAAGAGAATTTGCTATTATATTGTATGTATCACATTTTATCCATTGATTTATTA
1 AATTGGAAAGAGAATTTGCTATCATATAGTATGTATCACATTTTATCCATTAATTTATTA
* * * *
22335555 AATTGGAAAGTGAATTT-CTATCATGTAGTATGTATCATATTTTATCCCTTAATTTATTA
1 AATTGGAAAGAGAATTTGCTATCATATAGTATGTATCACATTTTATCCATTAATTTATTA
22335614 A
1 A
22335615 TTTGAATTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 37 0.70
60 16 0.30
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (60 bp):
AATTGGAAAGAGAATTTGCTATCATATAGTATGTATCACATTTTATCCATTAATTTATTA
Found at i:22336834 original size:21 final size:21
Alignment explanation
Indices: 22336793--22336832 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
22336783 TTTTTTTATT
22336793 TTTTTAAAAATATAATAAAAA
1 TTTTTAAAAATATAATAAAAA
22336814 TTTTT-AAAAT-TAATAAAAA
1 TTTTTAAAAATATAATAAAAA
22336833 AAGGACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 5 0.26
21 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTTAAAAATATAATAAAAA
Found at i:22337006 original size:27 final size:27
Alignment explanation
Indices: 22336968--22337108 Score: 133
Period size: 27 Copynumber: 5.2 Consensus size: 27
22336958 TTACCCAAAA
* *
22336968 ATTTAATCACTGAAAATGGATAAATAC
1 ATTTAATCACTGAAAGTGGATAGATAC
* *
22336995 ATTTAATCACTGAAAATGGATAGATAT
1 ATTTAATCACTGAAAGTGGATAGATAC
* * * *
22337022 ATTTAACCACCGAAAGTTGAT-GAATAT
1 ATTTAATCACTGAAAGTGGATAG-ATAC
* * * *
22337049 GTTTAA-CTATTGAAAGTGGATGGATGC
1 ATTTAATC-ACTGAAAGTGGATAGATAC
*
22337076 ATTTAATCACTGAAGGTGGATAGATAC
1 ATTTAATCACTGAAAGTGGATAGATAC
22337103 ATTTAA
1 ATTTAA
22337109 CAATTAGAAG
Statistics
Matches: 93, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
26 2 0.02
27 89 0.96
28 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (27 bp):
ATTTAATCACTGAAAGTGGATAGATAC
Found at i:22337108 original size:54 final size:54
Alignment explanation
Indices: 22336968--22337140 Score: 145
Period size: 54 Copynumber: 3.2 Consensus size: 54
22336958 TTACCCAAAA
* * * * * * *
22336968 ATTTAATCACTGAAAATGGATAAATACATTTAA-TCACTGAAAATGGATAGATAT
1 ATTTAACCACTGAAAGTGGATAGATACATTTAACT-ATTGAAAGTGGATGGATAC
* * ** *
22337022 ATTTAACCACCGAAAGTTGAT-GAATATGTTTAACTATTGAAAGTGGATGGATGC
1 ATTTAACCACTGAAAGTGGATAG-ATACATTTAACTATTGAAAGTGGATGGATAC
* * * **
22337076 ATTTAATCACTGAAGGTGGATAGATACATTTAACAATT-AGAAGTAAATGGATAC
1 ATTTAACCACTGAAAGTGGATAGATACATTTAACTATTGA-AAGTGGATGGATAC
22337130 ATTTAACCACT
1 ATTTAACCACT
22337141 ATAAGTGAAT
Statistics
Matches: 92, Mismatches: 23, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
53 1 0.01
54 89 0.97
55 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (54 bp):
ATTTAACCACTGAAAGTGGATAGATACATTTAACTATTGAAAGTGGATGGATAC
Found at i:22337146 original size:27 final size:27
Alignment explanation
Indices: 22337098--22337151 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
22337088 AAGGTGGATA
*
22337098 GATACATTTAACAATTAGAAGTAAATG
1 GATACATTTAACAACTAGAAGTAAATG
* * *
22337125 GATACATTTAACCACTATAAGTGAATG
1 GATACATTTAACAACTAGAAGTAAATG
22337152 AATAGTGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (27 bp):
GATACATTTAACAACTAGAAGTAAATG
Found at i:22344019 original size:29 final size:28
Alignment explanation
Indices: 22343978--22344068 Score: 82
Period size: 29 Copynumber: 3.3 Consensus size: 28
22343968 CACCTACTTC
*
22343978 AAAAAAA-TAATAAAAAAAGCTTAAAAAT
1 AAAAAAATTAATAAAAAAAG-ATAAAAAT
* *
22344006 AAAAAAATTAATAAGAAACAGATGAAAAT
1 AAAAAAATTAATAA-AAAAAGATAAAAAT
* *
22344035 AATAAAAATAAAT-AAATAA-AT-AAAAT
1 AA-AAAAATTAATAAAAAAAGATAAAAAT
22344061 AAAAAAAT
1 AAAAAAAT
22344069 GATGAATGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 6 0.11
26 7 0.13
27 2 0.04
28 10 0.19
29 15 0.28
30 14 0.26
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (28 bp):
AAAAAAATTAATAAAAAAAGATAAAAAT
Found at i:22344042 original size:9 final size:9
Alignment explanation
Indices: 22343980--22344068 Score: 53
Period size: 9 Copynumber: 9.7 Consensus size: 9
22343970 CCTACTTCAA
22343980 AAAAATAAT
1 AAAAATAAT
22343989 AAAAA-AAGCTT
1 AAAAATAA---T
22344000 AAAAATAA-
1 AAAAATAAT
22344008 AAAAATTAAT
1 AAAAA-TAAT
*
22344018 AAGAAACAGAT
1 AA-AAATA-AT
*
22344029 GAAAATAAT
1 AAAAATAAT
22344038 AAAAATAA-
1 AAAAATAAT
*
22344046 ATAAATAA-
1 AAAAATAAT
22344054 ATAAAATAA-
1 A-AAAATAAT
22344063 AAAAAT
1 AAAAAT
22344069 GATGAATGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
8 20 0.31
9 24 0.37
10 7 0.11
11 12 0.18
12 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:22344049 original size:13 final size:13
Alignment explanation
Indices: 22344001--22344068 Score: 59
Period size: 13 Copynumber: 5.0 Consensus size: 13
22343991 AAAAAGCTTA
22344001 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
22344014 -TAATAAGAAACAGAT
1 AAAATAA-AAA-A-AT
22344029 GAAAATAATAAAAAT
1 -AAAATAA-AAAAAT
*
22344044 -AAATAAATAAAT
1 AAAATAAAAAAAT
22344056 AAAATAAAAAAAT
1 AAAATAAAAAAAT
22344069 GATGAATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
12 10 0.23
13 20 0.45
14 1 0.02
15 4 0.09
16 1 0.02
17 8 0.18
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:22345922 original size:31 final size:31
Alignment explanation
Indices: 22345859--22345931 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
22345849 GATATGGATC
*
22345859 TAAATAAATAATAATAATAATAATAATAAAA
1 TAAATAAATAATAATAATAAAAATAATAAAA
* * *
22345890 TAAATAAATAATCCATAA-AAAAATGATGAAA
1 TAAATAAATAAT-AATAATAAAAATAATAAAA
*
22345921 TAAATATATAA
1 TAAATAAATAA
22345932 ATAAAGTGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (31 bp):
TAAATAAATAATAATAATAAAAATAATAAAA
Found at i:22357818 original size:59 final size:59
Alignment explanation
Indices: 22357738--22358027 Score: 391
Period size: 59 Copynumber: 4.9 Consensus size: 59
22357728 CATTAAAGAA
* * * *
22357738 TTAAATCGAACCTGTTTTGAGATAAGTAGAGCTTAGATAAAGTCTAGAAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTT
*
22357797 TTAAATCGAACTTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTT
* * *
22357856 TTAAATCAAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTCT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATT-T
* * * * *
22357916 TTAAGTTGAACCTGTTGTGAGATAGGTCGAACCTATATCAAGTCTAGAAATTTCAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTT
* * * * * * *
22357975 TTAAGTCGAACATATTTTGAGATAGGTCAAGTCTAGATCAAGTCTAGAAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTT
22358028 TCGTTTTTTA
Statistics
Matches: 206, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
59 154 0.75
60 52 0.25
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (59 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTT
Found at i:22357976 original size:119 final size:118
Alignment explanation
Indices: 22357738--22358027 Score: 400
Period size: 119 Copynumber: 2.4 Consensus size: 118
22357728 CATTAAAGAA
* * *
22357738 TTAAATCGAACCTGTTTTGAGATAAGTAGAGCTTAGATAAAGTCTAGAAATTTCAATTTTTAAAT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTTTTAAAT
* *
22357803 CGAACTTGTTGTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTT
66 CGAACCTGTTGTGAGATAGGTCGAACCTAGATAAAGTCTAGAAATTTCAATTT
* * * * *
22357856 TTAAATCAAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTCTTTAAG
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATT-TTTAAA
* * *
22357921 TTGAACCTGTTGTGAGATAGGTCGAACCTATATCAAGTCTAGAAATTTCAATTT
65 TCGAACCTGTTGTGAGATAGGTCGAACCTAGATAAAGTCTAGAAATTTCAATTT
* * * * * *
22357975 TTAAGTCGAACATATTTTGAGATAGGTCAAGTCTAGATCAAGTCTAGAAATTT
1 TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTT
22358028 TCGTTTTTTA
Statistics
Matches: 149, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
118 51 0.34
119 98 0.66
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (118 bp):
TTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGATAAAGTCTAGAAATTTCAATTTTTAAAT
CGAACCTGTTGTGAGATAGGTCGAACCTAGATAAAGTCTAGAAATTTCAATTT
Found at i:22358357 original size:20 final size:20
Alignment explanation
Indices: 22358283--22358364 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
22358273 CCTACTTCAA
22358283 AAAAAAT-AATAAAAA-AAGCT
1 AAAAAATAAATAAAAATAA--T
* *
22358303 TAAAAATAAA-AAAATTAAT
1 AAAAAATAAATAAAAATAAT
* * * *
22358322 AAGAAACAGATGAAAATAAT
1 AAAAAATAAATAAAAATAAT
22358342 AAAAAATAAATAAAAATAA-
1 AAAAAATAAATAAAAATAAT
22358361 AAAA
1 AAAA
22358365 TAAAAAAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
19 11 0.23
20 32 0.68
21 4 0.09
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (20 bp):
AAAAAATAAATAAAAATAAT
Found at i:22358359 original size:17 final size:16
Alignment explanation
Indices: 22358334--22358374 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
22358324 GAAACAGATG
*
22358334 AAAATAATAAAAAATA
1 AAAAAAATAAAAAATA
22358350 AATAAAAATAAAAAATA
1 AA-AAAAATAAAAAATA
22358367 AAAAAAAT
1 AAAAAAAT
22358375 GATGAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAAATAAAAAATA
Found at i:22359038 original size:35 final size:38
Alignment explanation
Indices: 22358999--22359080 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 38
22358989 TCTGCGGTGG
* *
22358999 TAGAGAAGAGAAGTCGTCGACCGACGA-AAAG-A-AAA
1 TAGAGAAAAGAAGGCGTCGACCGACGAGAAAGAAGAAA
* * *
22359034 TAGAGAAAAGCAGGCGTCGGCCGACGAGAAGGAAGAAA
1 TAGAGAAAAGAAGGCGTCGACCGACGAGAAAGAAGAAA
22359072 TAGAGAAAA
1 TAGAGAAAA
22359081 TGAGGAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 23 0.59
36 3 0.08
37 1 0.03
38 12 0.31
ACGTcount: A:0.48, C:0.13, G:0.32, T:0.07
Consensus pattern (38 bp):
TAGAGAAAAGAAGGCGTCGACCGACGAGAAAGAAGAAA
Found at i:22359565 original size:10 final size:10
Alignment explanation
Indices: 22359552--22359755 Score: 255
Period size: 10 Copynumber: 19.6 Consensus size: 10
22359542 CATATATGTA
22359552 TATGTATATG
1 TATGTATATG
22359562 TATGTATATG
1 TATGTATATG
*
22359572 TATGTATATA
1 TATGTATATG
*
22359582 TATGTTTATG
1 TATGTATATG
22359592 TATGTGTATATG
1 TA--TGTATATG
22359604 TATGTATATG
1 TATGTATATG
*
22359614 TATGTATATA
1 TATGTATATG
*
22359624 TATGTTTATG
1 TATGTATATG
22359634 TATGTGTATATG
1 TA--TGTATATG
22359646 TATGTATATG
1 TATGTATATG
*
22359656 TATGTATATA
1 TATGTATATG
*
22359666 TATGTTTATG
1 TATGTATATG
22359676 TATGTGTATATG
1 TA--TGTATATG
22359688 TATGTATATG
1 TATGTATATG
*
22359698 TATGTATATA
1 TATGTATATG
*
22359708 TATGTTTATG
1 TATGTATATG
22359718 TATGTGTATATG
1 TA--TGTATATG
22359730 TATGTATATG
1 TATGTATATG
*
22359740 TATGTATATA
1 TATGTATATG
22359750 TATGTA
1 TATGTA
22359756 CATATATATA
Statistics
Matches: 169, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
10 133 0.79
12 36 0.21
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (10 bp):
TATGTATATG
Found at i:22359760 original size:10 final size:10
Alignment explanation
Indices: 22359526--22359781 Score: 199
Period size: 10 Copynumber: 24.9 Consensus size: 10
22359516 TAAGAAAAGT
* *
22359526 TATACATATA
1 TATATATATG
* *
22359536 TATATACATA
1 TATATATATG
*
22359546 TATGTATATG
1 TATATATATG
*
22359556 TATATGTATG
1 TATATATATG
*
22359566 TATATGTATG
1 TATATATATG
22359576 TATATATATG
1 TATATATATG
* *
22359586 TTTATGTATGTG
1 --TATATATATG
*
22359598 TATATGTATG
1 TATATATATG
*
22359608 TATATGTATG
1 TATATATATG
22359618 TATATATATG
1 TATATATATG
* *
22359628 TTTATGTATGTG
1 --TATATATATG
*
22359640 TATATGTATG
1 TATATATATG
*
22359650 TATATGTATG
1 TATATATATG
22359660 TATATATATG
1 TATATATATG
* *
22359670 TTTATGTATGTG
1 --TATATATATG
*
22359682 TATATGTATG
1 TATATATATG
*
22359692 TATATGTATG
1 TATATATATG
22359702 TATATATATG
1 TATATATATG
* *
22359712 TTTATGTATGTG
1 --TATATATATG
*
22359724 TATATGTATG
1 TATATATATG
*
22359734 TATATGTATG
1 TATATATATG
22359744 TATATATATG
1 TATATATATG
* *
22359754 TACATATATA
1 TATATATATG
22359764 TATATATAT-
1 TATATATATG
*
22359773 AATATATAT
1 TATATATAT
22359782 ANNNNNNNNN
Statistics
Matches: 202, Mismatches: 36, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
9 8 0.04
10 162 0.80
12 32 0.16
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:22359770 original size:42 final size:42
Alignment explanation
Indices: 22359546--22359754 Score: 409
Period size: 42 Copynumber: 5.0 Consensus size: 42
22359536 TATATACATA
*
22359546 TATGTATATGTATATGTATGTATATGTATGTATATATATGTT
1 TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
22359588 TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
1 TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
22359630 TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
1 TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
22359672 TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
1 TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
22359714 TATGTATGTGTATATGTATGTATATGTATGTATATATATGT
1 TATGTATGTGTATATGTATGTATATGTATGTATATATATGT
22359755 ACATATATAT
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 166 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (42 bp):
TATGTATGTGTATATGTATGTATATGTATGTATATATATGTT
Found at i:22360505 original size:3 final size:3
Alignment explanation
Indices: 22360497--22360538 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
22360487 GATCTAAATA
22360497 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
22360539 CCATAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:22364624 original size:38 final size:40
Alignment explanation
Indices: 22364582--22364682 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 40
22364572 ATAGTGCCCG
* * *
22364582 TGTGCACGATGTGGGGAGATGTACACGAA-GGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGCACAC-AATGGCGACGGATA
* *
22364620 TGTGCACGATGTGGGGGGATGCACACAATGGCGCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACAATGGCGACGGATA
22364660 TGTGCACGATGTGGGGGGATGCA
1 TGTGCACGATGTGGGGGGATGCA
22364683 AATGAGCCGA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 2 0.04
38 27 0.49
39 3 0.05
40 23 0.42
ACGTcount: A:0.22, C:0.18, G:0.41, T:0.20
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACAATGGCGACGGATA
Found at i:22376831 original size:17 final size:15
Alignment explanation
Indices: 22376806--22376855 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
22376796 ATTTTTTGAG
22376806 AAATTTTTTTAAAAA
1 AAATTTTTTTAAAAA
22376821 ATAACTTTTTTTAAGAACA
1 A-AA-TTTTTTTAA-AA-A
22376840 AAA-TTTTTTAAAAA
1 AAATTTTTTTAAAAA
22376854 AA
1 AA
22376856 GAGCTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 3 0.10
16 10 0.32
17 9 0.29
18 4 0.13
19 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (15 bp):
AAATTTTTTTAAAAA
Found at i:22377542 original size:27 final size:27
Alignment explanation
Indices: 22377512--22377575 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
22377502 CACAATTTCT
* * *
22377512 ATCTGTTTCAAATAATCGTTACTGTTG
1 ATCTTTTTCAAACAATCGTTACTATTG
*
22377539 ATCTTTTTC-AACAGTCGTTACTATTG
1 ATCTTTTTCAAACAATCGTTACTATTG
*
22377565 GTCTTTTTCAA
1 ATCTTTTTCAA
22377576 CGGACGTGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (27 bp):
ATCTTTTTCAAACAATCGTTACTATTG
Found at i:22377569 original size:26 final size:26
Alignment explanation
Indices: 22377527--22377576 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
22377517 TTTCAAATAA
*
22377527 TCGTTACTGTTGATCTTTTTCAACAG
1 TCGTTACTATTGATCTTTTTCAACAG
*
22377553 TCGTTACTATTGGTCTTTTTCAAC
1 TCGTTACTATTGATCTTTTTCAAC
22377577 GGACGTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (26 bp):
TCGTTACTATTGATCTTTTTCAACAG
Found at i:22389494 original size:2 final size:2
Alignment explanation
Indices: 22389487--22389515 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22389477 CAACGTTAAC
22389487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22389516 TCCGTCCCTN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22389537 original size:2 final size:2
Alignment explanation
Indices: 22389530--22389558 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22389520 TCCCTNTAAC
22389530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22389559 TCCGCCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22390543 original size:13 final size:13
Alignment explanation
Indices: 22390517--22390550 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
22390507 TTCATCAGAA
22390517 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
*
22390530 TTTTCCTTT-TTT
1 TTTTCTTTTCTTT
22390542 TTTTCTTTT
1 TTTTCTTTT
22390551 GAAGGAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:22391332 original size:19 final size:20
Alignment explanation
Indices: 22391299--22391337 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
22391289 GGTATAATAC
22391299 TTAAAAAAATCTTTAAATTAT
1 TTAAAAAAA-CTTTAAATTAT
22391320 TTAAAAAAA-TTTAAATTA
1 TTAAAAAAACTTTAAATTA
22391338 ATTTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAAAACTTTAAATTAT
Found at i:22398998 original size:18 final size:20
Alignment explanation
Indices: 22398960--22399000 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
22398950 AGAAAGGAAG
*
22398960 AAGAGACGAATACATTTAAA
1 AAGAAACGAATACATTTAAA
22398980 AAGAAACGAA-ACA-TTAAA
1 AAGAAACGAATACATTTAAA
22398998 AAG
1 AAG
22399001 TCACTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (20 bp):
AAGAAACGAATACATTTAAA
Found at i:22398999 original size:19 final size:20
Alignment explanation
Indices: 22398960--22398999 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
22398950 AGAAAGGAAG
* *
22398960 AAGAGACGAATACATTTAAA
1 AAGAAACGAATACATTAAAA
22398980 AAGAAACGAA-ACATTAAAA
1 AAGAAACGAATACATTAAAA
22398999 A
1 A
22399000 GTCACTAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (20 bp):
AAGAAACGAATACATTAAAA
Found at i:22400432 original size:10 final size:10
Alignment explanation
Indices: 22400417--22400450 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
22400407 AGAATGAATA
22400417 TATATATATT
1 TATATATATT
*
22400427 TATATATATG
1 TATATATATT
22400437 TATATATATT
1 TATATATATT
22400447 TATA
1 TATA
22400451 GCTGCTAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
TATATATATT
Found at i:22410253 original size:2 final size:2
Alignment explanation
Indices: 22410246--22410299 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
22410236 TGGCATGATG
22410246 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
22410288 TC TC TC TC TC TC
1 TC TC TC TC TC TC
22410300 AGAGCTGGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:22412259 original size:2 final size:2
Alignment explanation
Indices: 22412252--22412284 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22412242 CCTACCATTC
22412252 AT 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 AT A
22412285 ATTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22412334 original size:168 final size:168
Alignment explanation
Indices: 22412140--22412479 Score: 646
Period size: 168 Copynumber: 2.0 Consensus size: 168
22412130 AAGATTGAGT
22412140 CACATTTATGGGATTTTAATTGGGTGGCATAAACATAACCGTGAGAATGTTCTCATTATTTGGGA
1 CACATTTATGGGATTTTAATTGGGTGGCATAAACATAACCGTGAGAATGTTCTCATTATTTGGGA
22412205 AAAGTTGTTATTTTTGTTATCTTAATTTACCCTTAACCCTACCATTC-ATATATATATATATATA
66 AAAGTTGTTATTTTTGTTATCTTAATTTACCCTTAACCCTACCATTCAATATATATATATATATA
22412269 TATATATATATATATAATTTTTTTTTCATTATTTGATA
131 TATATATATATATATAATTTTTTTTTCATTATTTGATA
22412307 NCACATTTATGGGATTTTAATTGGGTGGCATAAACATAACCGTGAGAATGTTCTCATTATTTGGG
1 -CACATTTATGGGATTTTAATTGGGTGGCATAAACATAACCGTGAGAATGTTCTCATTATTTGGG
22412372 AAAAGTTGTTATTTTTGTTATCTTAATTTACCCTTAACCCTACCATTCATATATATATATATATA
65 AAAAGTTGTTATTTTTGTTATCTTAATTTACCCTTAACCCTACCATTCA-ATATATATATATATA
22412437 TATATATATATATATATAATTTTTTTTTCATTATTTGCATA
129 TATATATATATATATATAATTTTTTTTTCATTATTTG-ATA
22412478 CA
1 CA
22412480 TAATTATTAC
Statistics
Matches: 169, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
168 112 0.66
170 54 0.32
171 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (168 bp):
CACATTTATGGGATTTTAATTGGGTGGCATAAACATAACCGTGAGAATGTTCTCATTATTTGGGA
AAAGTTGTTATTTTTGTTATCTTAATTTACCCTTAACCCTACCATTCAATATATATATATATATA
TATATATATATATATAATTTTTTTTTCATTATTTGATA
Found at i:22412427 original size:2 final size:2
Alignment explanation
Indices: 22412420--22412454 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22412410 CCTACCATTC
22412420 AT AT 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 AT AT A
22412455 ATTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22417964 original size:3 final size:3
Alignment explanation
Indices: 22417956--22417989 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
22417946 TCTAGTAGCC
22417956 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
22417990 GTTCATAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:22427954 original size:51 final size:51
Alignment explanation
Indices: 22427897--22428016 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
22427887 TGTAAGATTA
22427897 CAATGCAATCACATTACAGCAAA-GAGATATAATGCGATTACAATCCAAAA-
1 CAATGCAATCACATTACAGCAAAGGA-ATATAATGCGATTACAATCCAAAAT
* *
22427947 CTAATGCAATCACATTACAGCAAAGGAATATAATGCGATTGCAATTCAAAAT
1 C-AATGCAATCACATTACAGCAAAGGAATATAATGCGATTACAATCCAAAAT
22427999 CAATGCAATCACATTACA
1 CAATGCAATCACATTACA
22428017 TTGCACTTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
50 1 0.02
51 61 0.94
52 3 0.05
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.23
Consensus pattern (51 bp):
CAATGCAATCACATTACAGCAAAGGAATATAATGCGATTACAATCCAAAAT
Found at i:22428115 original size:15 final size:15
Alignment explanation
Indices: 22428095--22428136 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
22428085 TGATGTTATA
22428095 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
* *
22428110 ATTAAAATATAATAT
1 ATTAAAATAAAAAAT
*
22428125 A-TAATATAAAAA
1 ATTAAAATAAAAA
22428137 TCAAAAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:22428149 original size:33 final size:33
Alignment explanation
Indices: 22428091--22428169 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 33
22428081 TTTGTGATGT
22428091 TATAAT-T-AAAATAAAAAATATTAAAATATAATA
1 TATAATATAAAAATAAAAAATATTAAAATA-AA-A
*
22428124 TATAATATAAAAATCAAAAA-A-TAAAATAAAA
1 TATAATATAAAAATAAAAAATATTAAAATAAAA
*
22428155 TAAAATATCAAAAAT
1 TATAATAT-AAAAAT
22428170 TAAATTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 8 0.20
32 8 0.20
33 13 0.32
34 2 0.05
35 10 0.24
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (33 bp):
TATAATATAAAAATAAAAAATATTAAAATAAAA
Found at i:22428157 original size:24 final size:25
Alignment explanation
Indices: 22428105--22428173 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
22428095 ATTAAAATAA
* * *
22428105 AAAATATTAAAATATAATATATAATAT
1 AAAATATCAAAAAATAA-A-ATAAAAT
22428132 AAAA-ATCAAAAAATAAAATAAAAT
1 AAAATATCAAAAAATAAAATAAAAT
*
22428156 AAAATATCAAAAATTAAA
1 AAAATATCAAAAAATAAA
22428174 TTTATATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 10 0.27
25 13 0.35
26 10 0.27
27 4 0.11
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAATATCAAAAAATAAAATAAAAT
Found at i:22428182 original size:25 final size:24
Alignment explanation
Indices: 22428125--22428182 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
22428115 AATATAATAT
22428125 ATAATATAAAAATCAAAAAATAAA
1 ATAATATAAAAATCAAAAAATAAA
* *
22428149 ATAAAATAAAATATCAAAAATTAAA
1 ATAATATAAAA-ATCAAAAAATAAA
* *
22428174 TTTATATAA
1 ATAATATAA
22428183 TATAGGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAATATAAAAATCAAAAAATAAA
Found at i:22428239 original size:33 final size:33
Alignment explanation
Indices: 22428202--22428282 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
22428192 AAGAAATTAC
* *
22428202 AATAAAATATATAATACAAAAAATTAT-ATTAAA
1 AATAAAA-ATAAAATACAAAAAATTATAATAAAA
* * * *
22428235 AATAAAAATACAATATATAAGATTATAATAAAA
1 AATAAAAATAAAATACAAAAAATTATAATAAAA
22428268 AATAAAAATAAAATA
1 AATAAAAATAAAATA
22428283 TATGATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 15 0.37
33 26 0.63
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (33 bp):
AATAAAAATAAAATACAAAAAATTATAATAAAA
Found at i:22428244 original size:27 final size:28
Alignment explanation
Indices: 22428205--22428298 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 28
22428195 AAATTACAAT
*
22428205 AAAATATATAATACAAA-AAATTATATTA
1 AAAATA-AAAATACAAATAAATTATATTA
*
22428233 AAAATAAAAATACAATATATAAGATTATAATAA
1 AAAATAAAAATAC-A-A-ATAA-ATTAT-ATTA
* *
22428266 AAAATAAAAATA-AAATATATGATATTA
1 AAAATAAAAATACAAATAAATTATATTA
22428293 AAAATA
1 AAAATA
22428299 TATTTAAGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
27 15 0.27
28 11 0.20
29 4 0.07
30 2 0.04
31 3 0.05
32 5 0.09
33 15 0.27
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
AAAATAAAAATACAAATAAATTATATTA
Found at i:22428267 original size:32 final size:33
Alignment explanation
Indices: 22428224--22428285 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
22428214 AATACAAAAA
* *
22428224 ATTAT-ATTAAAAATAAAAATACAATATATAAG
1 ATTATAATAAAAAATAAAAATAAAATATATAAG
22428256 ATTATAATAAAAAATAAAAATAAAATATAT
1 ATTATAATAAAAAATAAAAATAAAATATAT
22428286 GATATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (33 bp):
ATTATAATAAAAAATAAAAATAAAATATATAAG
Found at i:22428339 original size:14 final size:17
Alignment explanation
Indices: 22428316--22428354 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
22428306 GAGATGATAT
22428316 TATA-TAAAAAT-TAA-
1 TATATTAAAAATATAAG
22428330 TA-ATTAAAAATATAAG
1 TATATTAAAAATATAAG
22428346 TATATTAAA
1 TATATTAAA
22428355 CTTACGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 9 0.43
15 3 0.14
16 2 0.10
17 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TATATTAAAAATATAAG
Found at i:22428532 original size:15 final size:15
Alignment explanation
Indices: 22428503--22428543 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
22428493 ATTTTTCTTA
* *
22428503 CAATCATATTGCTTG
1 CAATCACATTACTTG
*
22428518 TAATCACATTACTTG
1 CAATCACATTACTTG
22428533 CAATCACATTA
1 CAATCACATTA
22428544 TCTATAATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (15 bp):
CAATCACATTACTTG
Found at i:22429038 original size:70 final size:70
Alignment explanation
Indices: 22428925--22429114 Score: 326
Period size: 70 Copynumber: 2.7 Consensus size: 70
22428915 TTCCCATATT
* * *
22428925 CACTAACAATATCTCATGTATAAGGAAAATATCATTTAACATATACTATAATAACACACTCAATT
1 CACTAACAATTTCTCATATATAAGAAAAATATCATTTAACATATACTATAATAACACACTCAATT
22428990 ATAAC
66 ATAAC
22428995 CACTAACAATTTCTCATATATAAGAAAAATATCATTTAACATATACTATAATAACACACTCAATT
1 CACTAACAATTTCTCATATATAAGAAAAATATCATTTAACATATACTATAATAACACACTCAATT
22429060 ATAAC
66 ATAAC
* * *
22429065 CATTAACAATTTATCATATATAAGAAAAATATCATTTAACATGTACTATA
1 CACTAACAATTTCTCATATATAAGAAAAATATCATTTAACATATACTATA
22429115 CTAATTTCGT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 114 1.00
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (70 bp):
CACTAACAATTTCTCATATATAAGAAAAATATCATTTAACATATACTATAATAACACACTCAATT
ATAAC
Found at i:22430940 original size:27 final size:26
Alignment explanation
Indices: 22430849--22430929 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 26
22430839 ATGTTATAGA
* * *
22430849 TTAAATTATATATAAAATATTAATAT
1 TTAAACTAAATATAAATTATTAATAT
*
22430875 TTAAA-T---TATCAATTATTAATAT
1 TTAAACTAAATATAAATTATTAATAT
*
22430897 TTTAACTAAATTATAAATTATTAATAT
1 TTAAACTAAA-TATAAATTATTAATAT
22430924 TTAAAC
1 TTAAAC
22430930 AATAAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
22 18 0.40
23 1 0.02
25 1 0.02
26 5 0.11
27 20 0.44
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAAACTAAATATAAATTATTAATAT
Found at i:22431127 original size:227 final size:216
Alignment explanation
Indices: 22430862--22431349 Score: 606
Period size: 227 Copynumber: 2.2 Consensus size: 216
22430852 AATTATATAT
22430862 AAAATATTAATATTTAAATTATCAATTATTAATATTTT-AACTAAATTATAAATTATTAATATTT
1 AAAATATTAATATTTAAATTATCAATTATTAATATTTTAAAC-AAATTATAAATTATTAATATTT
* *
22430926 AAACAATAAAATAAACTAAAAAATAGATAATCATATATTATAAT-AAAAGTTTGAGCATTTAATT
65 AAA-AAT---A-AAA-T--AAAATAGATAATCACATATTATAATAAAAAGTTTAAGCATTTAATT
*
22430990 ATATATTACAAAAAATAATATTTTAAATTTAAATTTAATTAAAATTATTAATATTTTAATCATAA
122 ATATATTACAAAAAATAATA-TTTAAA--T---TTTAATTAAAATTATTAATATTTTAATAATAA
* * *
22431055 TAATTTTTCAATTATAAAT-AAATACTAATA-TTTA
181 TAATATTTAAAATATAAATAAAATACTAATATTTTA
* * *
22431089 AAAATGTTAATATTTAAATTGTCAATTATTAATATTTTAAACAAATTATAATTTATTAATATTTA
1 AAAATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTA
* ** *
22431154 AAAATAAAATAAAATAGATAATCACATATTATAATAAAAATTTTAAGTTTTTAATTATATATTAT
66 AAAATAAAATAAAATAGATAATCACATATTATAATAAAAAGTTTAAGCATTTAATTATATATTAC
*
22431219 AAAAATTAATATTTAAATTTTAATTAAAATTATTAATATTTTAATAATAATAATATTTAAAATAT
131 AAAAAATAATATTTAAATTTTAATTAAAATTATTAATATTTTAATAATAATAATATTTAAAATAT
*
22431284 AAATAAAATATTAATATTTTA
196 AAATAAAATACTAATATTTTA
* * * *
22431305 ATAATAATAATATTTAAAATATAAATAAAATATTAATATTTTAAA
1 AAAATATTAATATTT-AAAT-T--ATCAATTATTAATATTTTAAA
22431350 TATCATTGAT
Statistics
Matches: 232, Mismatches: 21, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
214 47 0.20
215 10 0.04
216 16 0.07
217 5 0.02
218 1 0.00
219 30 0.13
220 52 0.22
221 1 0.00
222 3 0.01
223 1 0.00
226 3 0.01
227 60 0.26
228 3 0.01
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (216 bp):
AAAATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTA
AAAATAAAATAAAATAGATAATCACATATTATAATAAAAAGTTTAAGCATTTAATTATATATTAC
AAAAAATAATATTTAAATTTTAATTAAAATTATTAATATTTTAATAATAATAATATTTAAAATAT
AAATAAAATACTAATATTTTA
Found at i:22431269 original size:27 final size:27
Alignment explanation
Indices: 22431181--22431269 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
22431171 ATAATCACAT
*
22431181 ATTATAATAAAAATT-TTAAGT-TTTTA
1 ATTATAATTAAAATTATTAA-TATTTTA
* *
22431207 ATTATATATTATAAA-AATTAATATTTAA
1 ATTATA-ATTA-AAATTATTAATATTTTA
*
22431235 ATTTTAATTAAAATTATTAATATTTTA
1 ATTATAATTAAAATTATTAATATTTTA
*
22431262 ATAATAAT
1 ATTATAAT
22431270 AATATTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
26 9 0.18
27 25 0.50
28 16 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTATAATTAAAATTATTAATATTTTA
Found at i:22431272 original size:17 final size:16
Alignment explanation
Indices: 22431242--22431349 Score: 78
Period size: 17 Copynumber: 7.3 Consensus size: 16
22431232 TAAATTTTAA
*
22431242 TTAAAATTATTAATATT
1 TTAAAA-TAATAATATT
22431259 TTAATAATAATAATA-T
1 TTAA-AATAATAATATT
22431275 TTAAAAT-ATAA-A--
1 TTAAAATAATAATATT
*
22431287 -TAAAATATTAATATT
1 TTAAAATAATAATATT
22431302 TTAATAATAATAATA-T
1 TTAA-AATAATAATATT
22431318 TTAAAAT-ATAA-A--
1 TTAAAATAATAATATT
*
22431330 -TAAAATATTAATATT
1 TTAAAATAATAATATT
22431345 TTAAA
1 TTAAA
22431350 TATCATTGAT
Statistics
Matches: 75, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
11 12 0.16
12 6 0.08
13 4 0.05
14 8 0.11
15 6 0.08
16 17 0.23
17 20 0.27
18 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATAATAATATT
Found at i:22431308 original size:43 final size:43
Alignment explanation
Indices: 22431225--22431348 Score: 212
Period size: 43 Copynumber: 2.9 Consensus size: 43
22431215 TTATAAAAAT
* * *
22431225 TAATATTTAAATTTTAATTAAAATTATTAATATTTTAATAATAA
1 TAATATTTAAAATATAAATAAAA-TATTAATATTTTAATAATAA
22431269 TAATATTTAAAATATAAATAAAATATTAATATTTTAATAATAA
1 TAATATTTAAAATATAAATAAAATATTAATATTTTAATAATAA
22431312 TAATATTTAAAATATAAATAAAATATTAATATTTTAA
1 TAATATTTAAAATATAAATAAAATATTAATATTTTAA
22431349 ATATCATTGA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 57 0.74
44 20 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (43 bp):
TAATATTTAAAATATAAATAAAATATTAATATTTTAATAATAA
Found at i:22431402 original size:37 final size:38
Alignment explanation
Indices: 22431288--22431404 Score: 98
Period size: 43 Copynumber: 3.0 Consensus size: 38
22431278 AAATATAAAT
*
22431288 AAAATATTAATATTTTAATA-ATAATAAT-ATTTAAAATATAAA
1 AAAATATTAATATTTTAA-AGATAAT--TGA--TAAAAT-TATA
* * *
22431330 TAAAATATTAATATTTTAAATATCATTGATTAAATTATA
1 -AAAATATTAATATTTTAAAGATAATTGATAAAATTATA
22431369 AAAATATTAATATTTTAAAGA-AATT-ATAAAAATTAT
1 AAAATATTAATATTTTAAAGATAATTGAT-AAAATTAT
22431405 TAANAATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
36 2 0.03
37 10 0.15
38 20 0.31
39 3 0.05
40 5 0.08
41 1 0.02
42 2 0.03
43 22 0.34
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (38 bp):
AAAATATTAATATTTTAAAGATAATTGATAAAATTATA
Found at i:22431435 original size:21 final size:21
Alignment explanation
Indices: 22431390--22431444 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
22431380 ATTTTAAAGA
*
22431390 AATT-ATAA-AAATTATTAAN
1 AATTAATAATAAATTATTAAT
22431409 AATTAATAATAAATTATTAAT
1 AATTAATAATAAATTATTAAT
* *
22431430 ATTTAAAAATTAAAT
1 AATTAATAA-TAAAT
22431445 AGAAGATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 17 0.57
22 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTAATAATAAATTATTAAT
Found at i:22439599 original size:3 final size:3
Alignment explanation
Indices: 22439585--22439625 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
22439575 ACTTCTCAAA
*
22439585 AAG AAT AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
22439626 AAAGCTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:22443431 original size:44 final size:45
Alignment explanation
Indices: 22443362--22443450 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 45
22443352 TTTTAATACT
*
22443362 TTATGTTGAATACCTTTTGTAGGCAAAGAATGTGATTAATATAAC
1 TTATGTTGAATACCTTTTGTAGGCAAAGAATGTAATTAATATAAC
22443407 TTATGTTGAATA-CTTTTGTAGGCAAAGAATGTAATTAATATAAC
1 TTATGTTGAATACCTTTTGTAGGCAAAGAATGTAATTAATATAAC
22443451 AAGGGAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 31 0.72
45 12 0.28
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (45 bp):
TTATGTTGAATACCTTTTGTAGGCAAAGAATGTAATTAATATAAC
Found at i:22447329 original size:40 final size:40
Alignment explanation
Indices: 22447285--22447365 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
22447275 AACTTTACTT
* * *
22447285 AAAAATCATGCATTAATCATTAAATCAAATGTTTGAATTC
1 AAAAATCATACATTAATAATTAAATCAAATGCTTGAATTC
* *
22447325 AAAAATTATACATTAATAATTAAATCAAATGCTTGATTTC
1 AAAAATCATACATTAATAATTAAATCAAATGCTTGAATTC
22447365 A
1 A
22447366 TTTTAATTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (40 bp):
AAAAATCATACATTAATAATTAAATCAAATGCTTGAATTC
Found at i:22448797 original size:38 final size:38
Alignment explanation
Indices: 22448746--22448824 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
22448736 TGAGCAAGAT
22448746 TAATCATCTTCAAATACTCCAATACAACTCCTGTGCGG
1 TAATCATCTTCAAATACTCCAATACAACTCCTGTGCGG
22448784 TAATCATCTTCAAATACTCCAATACAACTCCTGTGCGG
1 TAATCATCTTCAAATACTCCAATACAACTCCTGTGCGG
22448822 TAA
1 TAA
22448825 GTGTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (38 bp):
TAATCATCTTCAAATACTCCAATACAACTCCTGTGCGG
Found at i:22457780 original size:20 final size:20
Alignment explanation
Indices: 22457743--22457782 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
22457733 CATAATATCT
**
22457743 AAAAAATATTTTAATTATTA
1 AAAAAATAAATTAATTATTA
*
22457763 AAAAAATAAATTATTTATTA
1 AAAAAATAAATTAATTATTA
22457783 TATTCAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAAATAAATTAATTATTA
Found at i:22457854 original size:13 final size:13
Alignment explanation
Indices: 22457824--22457859 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
22457814 TAAAATATAT
22457824 TATTA-TAATTAA
1 TATTATTAATTAA
22457836 TA--ATTAATTAA
1 TATTATTAATTAA
22457847 TATTATTAATTAA
1 TATTATTAATTAA
22457860 AATATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.43
12 2 0.10
13 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTATTAATTAA
Found at i:22458863 original size:23 final size:23
Alignment explanation
Indices: 22458837--22458889 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
22458827 ATATTTTAAC
22458837 ATTAAAAAT-TAT-AGAATACTAAT
1 ATTAAAAATGTATAAGAA-A-TAAT
*
22458860 ATTAGAAATGTATAAGAAATAAT
1 ATTAAAAATGTATAAGAAATAAT
22458883 A-TAAAAA
1 ATTAAAAA
22458890 CAGTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 13 0.50
24 4 0.15
25 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (23 bp):
ATTAAAAATGTATAAGAAATAAT
Found at i:22469851 original size:4 final size:4
Alignment explanation
Indices: 22469844--22469874 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
22469834 ACAAACAAAC
22469844 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
22469875 AGGAACCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:22488868 original size:92 final size:92
Alignment explanation
Indices: 22488724--22488891 Score: 255
Period size: 92 Copynumber: 1.8 Consensus size: 92
22488714 TGATTGACAA
* * * * *
22488724 CAATGTCTTTTGATTTAGATTTTTAAGACTAGCATTCATCCTAAAATTAATTGATAATAGATGGA
1 CAATGTCTTTTGATTTAGATTCTTAAGACGAGCATCCATCCTAAAACTAATTGATAATAGATAGA
* *
22488789 GAAGTCTTTGTAACTAATGAATGACGT
66 AAAATCTTTGTAACTAATGAATGACGT
* *
22488816 CAATGTCTTTTGATTTGGATTCTTAATACGAGCATCCATCCTAAAACTAATTGATAATAGATAGA
1 CAATGTCTTTTGATTTAGATTCTTAAGACGAGCATCCATCCTAAAACTAATTGATAATAGATAGA
22488881 AAAATCTTTGT
66 AAAATCTTTGT
22488892 TATATTTATA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 67 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (92 bp):
CAATGTCTTTTGATTTAGATTCTTAAGACGAGCATCCATCCTAAAACTAATTGATAATAGATAGA
AAAATCTTTGTAACTAATGAATGACGT
Found at i:22498830 original size:18 final size:18
Alignment explanation
Indices: 22498809--22498844 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22498799 ATAAAAGAAT
*
22498809 AAAAAGGAAGAGAAAGAG
1 AAAAAGAAAGAGAAAGAG
*
22498827 AAAAAGAAAGAGAGAGAG
1 AAAAAGAAAGAGAAAGAG
22498845 TAAGAGGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAGAAAGAG
Found at i:22505690 original size:25 final size:25
Alignment explanation
Indices: 22505631--22505693 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
22505621 GTTTTATTTC
* *
22505631 TAAAATATTT-TAACATTAATTTTA
1 TAAAAAATTTATAAAATTAATTTTA
22505655 TAAAAAA--TATAAAATTATATTTTA
1 TAAAAAATTTATAAAATTA-ATTTTA
22505679 -AAAAAATTTATAAAA
1 TAAAAAATTTATAAAA
22505694 AATCGAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 13 0.39
24 12 0.36
25 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAAAAATTTATAAAATTAATTTTA
Found at i:22516433 original size:27 final size:28
Alignment explanation
Indices: 22516391--22516448 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
22516381 TATTGTTTAT
* * **
22516391 TTTATTTTTAAATATTAGTAATGTATAA
1 TTTATTTTAAAATATTAATAATCAATAA
22516419 TTTA-TTTAAAATATTAATAATCAATAA
1 TTTATTTTAAAATATTAATAATCAATAA
22516446 TTT
1 TTT
22516449 CAATATTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (28 bp):
TTTATTTTAAAATATTAATAATCAATAA
Found at i:22516899 original size:14 final size:14
Alignment explanation
Indices: 22516880--22516907 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22516870 GCTATTTCTC
22516880 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
22516894 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
22516908 GACTTGCAGA
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTTCTTTTTTT
Found at i:22522059 original size:2 final size:2
Alignment explanation
Indices: 22522052--22522121 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
22522042 TTTTGAATAA
22522052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22522094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22522122 CTCTTTACAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22526653 original size:23 final size:23
Alignment explanation
Indices: 22526627--22526680 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
22526617 TAGTAATGCT
22526627 TATATATAA-ATTAA-ATATATGTA
1 TATATATAATATTAATATA-AT-TA
*
22526650 TATATATAATATTTATATAATTA
1 TATATATAATATTAATATAATTA
22526673 TATATATA
1 TATATATA
22526681 TTCATAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 19 0.68
24 6 0.21
25 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TATATATAATATTAATATAATTA
Found at i:22526690 original size:23 final size:21
Alignment explanation
Indices: 22526626--22526697 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 21
22526616 ATAGTAATGC
*
22526626 TTATATATAAATTA-AATATA
1 TTATATATATATTATAATATA
* *
22526646 TGTATATATATAATATTTATATAA
1 T-TATATATATATTA-TAATAT-A
*
22526670 TTATATATATATTCATAATATT
1 TTATATATATATT-ATAATATA
22526692 TTATAT
1 TTATAT
22526698 TACGAAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 11 0.27
22 6 0.15
23 20 0.49
24 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TTATATATATATTATAATATA
Found at i:22531376 original size:78 final size:80
Alignment explanation
Indices: 22531207--22531415 Score: 280
Period size: 78 Copynumber: 2.6 Consensus size: 80
22531197 AAGATGTTAA
** *
22531207 ATTTACATATTGGCGCCATTATACCTTCATGTATAATAGGAATGCCACATGCCGCACACTTATCA
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATG-CGCACACTTATCA
*
22531272 CGTGAACCTTGATGGT
65 CATGAACCTTGATGGT
* *
22531288 ATTTACATATTGGCATTATTATACCTTAATGTATAATAGGAATGCCACATG-TC-CACTTATCAC
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGCGCACACTTATCAC
*
22531351 ATGGACC-TGTATGGT
66 ATGAACCTTG-ATGGT
** * *
22531366 ATTTGTATATTGGTATCATTACACCTTAATGTATAATAGGAATGCCACAT
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACAT
22531416 ACCCATGCCT
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
77 2 0.02
78 65 0.57
79 1 0.01
81 47 0.41
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (80 bp):
ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGCGCACACTTATCAC
ATGAACCTTGATGGT
Found at i:22533414 original size:22 final size:22
Alignment explanation
Indices: 22533386--22533440 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
22533376 ATATGAAAAG
* *
22533386 ATTTTAATTAATTTTAAAATCA
1 ATTTTAATTAATGTTAAAATAA
** *
22533408 ATTTTAATTGCTGTTAAATTAA
1 ATTTTAATTAATGTTAAAATAA
22533430 ATTTTAATTAA
1 ATTTTAATTAA
22533441 GTTGAATTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTTAATTAATGTTAAAATAA
Found at i:22539724 original size:30 final size:33
Alignment explanation
Indices: 22539659--22539727 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 33
22539649 TTTAAGGAAT
*
22539659 ATAAATTAGCATGGCTATTTGGTTGAAAAGGAAA
1 ATAAATTAGCATGCCTATTTGGTTGAAAA-GAAA
22539693 ATAAATTAGCATGCCTATTTGG-T-AAAA-AAA
1 ATAAATTAGCATGCCTATTTGGTTGAAAAGAAA
22539723 ATAAA
1 ATAAA
22539728 GAGGAGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.24
32 4 0.12
33 1 0.03
34 21 0.62
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (33 bp):
ATAAATTAGCATGCCTATTTGGTTGAAAAGAAA
Found at i:22541700 original size:77 final size:77
Alignment explanation
Indices: 22541562--22541705 Score: 180
Period size: 77 Copynumber: 1.9 Consensus size: 77
22541552 TTAATTTTTT
* * * * * *
22541562 TCTTGAGTTTTCATTAATTTCTGATAATTTAATCGGTAAAAATAAAAGGTGAAAAGCAATAAGCA
1 TCTTGAGTTTTAATTAAATTCTAATAATTTAATCCGTAAAAATAAAAGGTAAAAAACAATAAGCA
22541627 ATAAGAATCTTG
66 ATAAGAATCTTG
* * * * * *
22541639 TCTTGTGTTTTAATTAAATTCTAATCATTTTATCCTTAAAAATAAAAGGTAAAAAATAATAATCA
1 TCTTGAGTTTTAATTAAATTCTAATAATTTAATCCGTAAAAATAAAAGGTAAAAAACAATAAGCA
22541704 AT
66 AT
22541706 TGTGTAAGCG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
77 55 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (77 bp):
TCTTGAGTTTTAATTAAATTCTAATAATTTAATCCGTAAAAATAAAAGGTAAAAAACAATAAGCA
ATAAGAATCTTG
Found at i:22542607 original size:13 final size:14
Alignment explanation
Indices: 22542582--22542623 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
22542572 TTTATTATAT
22542582 ATTATAAAA-ATTA
1 ATTATAAAATATTA
22542595 ATTA-AAAATATTA
1 ATTATAAAATATTA
22542608 ATTATAATAATATTA
1 ATTATAA-AATATTA
22542623 A
1 A
22542624 AAATTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.15
13 12 0.46
14 2 0.08
15 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTATAAAATATTA
Found at i:22542640 original size:24 final size:24
Alignment explanation
Indices: 22542595--22542640 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
22542585 ATAAAAATTA
* *
22542595 ATTAAAAATATTAATTATAATAAT
1 ATTAAAAATATTAAATAAAATAAT
22542619 ATTAAAAAT-TGTAAATAAAATA
1 ATTAAAAATAT-TAAATAAAATA
22542641 TTAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTAAAAATATTAAATAAAATAAT
Found at i:22542684 original size:20 final size:21
Alignment explanation
Indices: 22542631--22542686 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
22542621 TAAAAATTGT
*
22542631 AAATAAAATATTAATATTTTA
1 AAATAAAATATTAATATTATA
*
22542652 AAAT-TAATGATTAA-ATTATA
1 AAATAAAAT-ATTAATATTATA
22542672 AAATAAAATATTAAT
1 AAATAAAATATTAAT
22542687 TTTTTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATAAAATATTAATATTATA
Found at i:22542752 original size:41 final size:41
Alignment explanation
Indices: 22542633--22542754 Score: 121
Period size: 41 Copynumber: 3.0 Consensus size: 41
22542623 AAAATTGTAA
* *
22542633 ATAAAATATTAATATTTTAAAATTAATGATTAAATTATAAA-
1 ATAAAATATTAATATTTTAAAATAAATTA-TAAATTATAAAT
* *
22542674 ATAAAATATTAATTTTTTGAAAAT--ATTA-ATATT-TAAATT
1 ATAAAATATTAATATTTT-AAAATAAATTATAAATTATAAA-T
* *
22542713 ATCAATTATTAATATTTT-AAATAAATTATAAATTATAAAT
1 ATAAAATATTAATATTTTAAAATAAATTATAAATTATAAAT
22542753 AT
1 AT
22542755 TTAAAAAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
37 8 0.12
38 4 0.06
39 19 0.28
40 10 0.15
41 21 0.31
42 5 0.07
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (41 bp):
ATAAAATATTAATATTTTAAAATAAATTATAAATTATAAAT
Found at i:22551224 original size:97 final size:97
Alignment explanation
Indices: 22551100--22551385 Score: 500
Period size: 97 Copynumber: 2.9 Consensus size: 97
22551090 CTGATCCATC
* *
22551100 TAAAAAAGATGTTTGCGATTAACTAAAATTCCTTTGTTGAAGAAGAAGGAATAAGAAGAATCCAA
1 TAAAAAAGATATTTGTGATTAACTAAAATTCCTTTGTTGAAGAAGAAGGAATAAGAAGAATCCAA
* *
22551165 CTTACAGGAGTCTTAAGGTACAGATATCATCT
66 CTTACAGGAGTCTTAAGGTAGAGATATCACCT
** *
22551197 TAAAATGGATATTTGTGATTAACTAAAATTCCTTCGTTGAAGAAGAAGGAATAAGAAGAATCCAA
1 TAAAAAAGATATTTGTGATTAACTAAAATTCCTTTGTTGAAGAAGAAGGAATAAGAAGAATCCAA
22551262 CTTACAGGAGTCTTAAGGTAGAGATATCACCT
66 CTTACAGGAGTCTTAAGGTAGAGATATCACCT
*
22551294 TAAAAAAGATATTTATGATTAACTAAAATTCCTTTGTTGAAGAAGAAGGAATAAGAAGAATCCAA
1 TAAAAAAGATATTTGTGATTAACTAAAATTCCTTTGTTGAAGAAGAAGGAATAAGAAGAATCCAA
22551359 CTTACAGGAGTCTTAAGGTAGAGATAT
66 CTTACAGGAGTCTTAAGGTAGAGATAT
22551386 GTCCTATCTC
Statistics
Matches: 178, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 178 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (97 bp):
TAAAAAAGATATTTGTGATTAACTAAAATTCCTTTGTTGAAGAAGAAGGAATAAGAAGAATCCAA
CTTACAGGAGTCTTAAGGTAGAGATATCACCT
Found at i:22552780 original size:48 final size:48
Alignment explanation
Indices: 22552702--22552802 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 48
22552692 TAGAAGGAAG
*
22552702 GAAGCAGAGGCAGAGGAGAGTGACTAAGATGCGGATAGCGCTTAGTTT
1 GAAGCAGAGGCAGAGGAGAGTGAATAAGATGCGGATAGCGCTTAGTTT
*
22552750 GAAGCAGAGGCAGAGGAGAGTGAATGAGATGCGGATAGCGCTTAGTTT
1 GAAGCAGAGGCAGAGGAGAGTGAATAAGATGCGGATAGCGCTTAGTTT
22552798 GAAGC
1 GAAGC
22552803 GTAGCGGCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.32, C:0.12, G:0.39, T:0.18
Consensus pattern (48 bp):
GAAGCAGAGGCAGAGGAGAGTGAATAAGATGCGGATAGCGCTTAGTTT
Found at i:22553376 original size:15 final size:15
Alignment explanation
Indices: 22553356--22553394 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
22553346 TTGATTATTT
*
22553356 AAAAAAAGAAAGAAA
1 AAAAAAAGAAACAAA
*
22553371 AAAAAAAGCAACAAA
1 AAAAAAAGAAACAAA
*
22553386 GAAAAAAGA
1 AAAAAAAGA
22553395 CTAATTATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAACAAA
Found at i:22572348 original size:87 final size:91
Alignment explanation
Indices: 22572245--22572439 Score: 222
Period size: 93 Copynumber: 2.2 Consensus size: 91
22572235 TTAAAGTAAG
* *
22572245 ATTTGGATAAAAATATTAGGA-TCGAATAGTAA-TCATCT-CCCATTAAATAAAA-T-AAAAT-T
1 ATTTGGATAAAAATATTA-AATTCGAAAAGTAATTC-TCTCCCCATTAAATAAAATTAAAAATAT
* *
22572304 TATGATAACATTAAACTTTTGAGATTTA
64 TATGATAACATTAAACTTATAAGATTTA
* * * *
22572332 ATTTGGATATAAATATTAAATTTGAAAAGTAATTCTCTCCCCGTTATATAAAATTAAAAATAAAT
1 ATTTGGATAAAAATATTAAATTCGAAAAGTAATTCTCTCCCCATTAAATAAAATTAAAAAT--AT
* *
22572397 TATGATAATATTAAACTTATAAGATTTG
64 TATGATAACATTAAACTTATAAGATTTA
22572425 ATTTGGATAAAAATA
1 ATTTGGATAAAAATA
22572440 AAGTAATCTT
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
86 1 0.01
87 29 0.33
88 14 0.16
89 1 0.01
90 5 0.06
93 39 0.44
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.37
Consensus pattern (91 bp):
ATTTGGATAAAAATATTAAATTCGAAAAGTAATTCTCTCCCCATTAAATAAAATTAAAAATATTA
TGATAACATTAAACTTATAAGATTTA
Found at i:22577921 original size:21 final size:21
Alignment explanation
Indices: 22577895--22577948 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
22577885 TTTCAATTTT
*
22577895 TAATTTTTAT-TATTATATATA
1 TAATTTTTATATATAATATA-A
*
22577916 TAATTTGATATATATAATATAA
1 TAATTT-TTATATATAATATAA
*
22577938 TTATTTTTATA
1 TAATTTTTATA
22577949 ATTTGATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 10 0.37
22 9 0.33
23 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TAATTTTTATATATAATATAA
Found at i:22581234 original size:55 final size:53
Alignment explanation
Indices: 22581143--22581322 Score: 207
Period size: 55 Copynumber: 3.3 Consensus size: 53
22581133 GTTAGAGTTA
* * *
22581143 TTTTAACGTGTCACGGCTATTCCTGACGTGTTGTGGGTTAACTAGTTTTTTGGG
1 TTTTAGCGTGTCACGGCTATTCCTGGCGTGTCGTGGGTTAACT-GTTTTTTGGG
* *
22581197 TTGTTAGCGTGTCACGGCTATTCCTGGCGTGTCGTGGGTTAACTGAATTTATGGG
1 TT-TTAGCGTGTCACGGCTATTCCTGGCGTGTCGTGGGTTAACTG-TTTTTTGGG
* * * * * *
22581252 TTTTTGACGTGTCACGGTTGTTCCTGGCATGTCGTGGGTTAATTGGTTTTTTGAGT
1 TTTTAG-CGTGTCACGGCTATTCCTGGCGTGTCGTGGGTTAACT-GTTTTTTG-GG
22581308 TTTTAGCGTGTCACG
1 TTTTAGCGTGTCACG
22581323 ACTGTTGGTG
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
54 6 0.06
55 94 0.88
56 7 0.07
ACGTcount: A:0.13, C:0.15, G:0.30, T:0.42
Consensus pattern (53 bp):
TTTTAGCGTGTCACGGCTATTCCTGGCGTGTCGTGGGTTAACTGTTTTTTGGG
Found at i:22581410 original size:31 final size:31
Alignment explanation
Indices: 22581375--22581449 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
22581365 CACGACAATG
*
22581375 ATGCATGGCGTGTCACGACATTTGAC-TTGAT
1 ATGCATGGCGTGTCACAACATTTGACGTT-AT
* *
22581406 ATGCATGGCGTGTTACAACATTTTACGTTAT
1 ATGCATGGCGTGTCACAACATTTGACGTTAT
22581437 ATGCATGGCGTGT
1 ATGCATGGCGTGT
22581450 AGCAACACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (31 bp):
ATGCATGGCGTGTCACAACATTTGACGTTAT
Found at i:22586570 original size:16 final size:16
Alignment explanation
Indices: 22586549--22586582 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22586539 TCATTTTTTA
22586549 TTATTTAATTATATTT
1 TTATTTAATTATATTT
* *
22586565 TTATTTTATTTTATTT
1 TTATTTAATTATATTT
22586581 TT
1 TT
22586583 TTATTATATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTAATTATATTT
Found at i:22586574 original size:11 final size:11
Alignment explanation
Indices: 22586544--22586607 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 11
22586534 TTTTGTCATT
22586544 TTTTATTATTTAA
1 TTTTATT-TTT-A
*
22586557 TTATATTTTTA
1 TTTTATTTTTA
22586568 TTTTA-TTTTA
1 TTTTATTTTTA
22586578 TTTT-TTTATTA
1 TTTTATTT-TTA
*
22586589 -TATATTTTCTA
1 TTTTATTTT-TA
22586600 TTTTATTT
1 TTTTATTT
22586608 CTAATTATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 14 0.33
11 13 0.31
12 9 0.21
13 6 0.14
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:22586578 original size:18 final size:19
Alignment explanation
Indices: 22586557--22586627 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 19
22586547 TATTATTTAA
22586557 TTATATTTTTATTT-TATT
1 TTATATTTTTATTTATATT
*
22586575 TTATTTTTTTATTATATATT
1 TTATATTTTTATT-TATATT
* *
22586595 TTCTA-TTTTATTTCTAATT
1 TTATATTTTTATTTAT-ATT
22586614 ATTATTATTTTTAT
1 -TTA-TATTTTTAT
22586628 ACCTTACATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 14 0.33
19 11 0.26
20 9 0.21
21 2 0.05
22 6 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATATTTTTATTTATATT
Found at i:22586619 original size:32 final size:31
Alignment explanation
Indices: 22586522--22586621 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 31
22586512 TGCTAATGCA
* *
22586522 ATTATCTATTTTT-TTTGTCATTTTTTATTATT
1 ATTATATATTTTTATTT-T-ATTTTATATTATT
* * *
22586554 -TAATTATATTTTTATTTTATTTTATTTTTTT
1 ATTA-TATATTTTTATTTTATTTTATATTATT
22586585 ATTATATATTTTCTATTTTATTTCTA-ATTATT
1 ATTATATATTTT-TATTTTATTT-TATATTATT
22586617 ATTAT
1 ATTAT
22586622 TTTTATACCT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
31 20 0.36
32 30 0.55
33 5 0.09
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (31 bp):
ATTATATATTTTTATTTTATTTTATATTATT
Found at i:22586625 original size:29 final size:28
Alignment explanation
Indices: 22586552--22586625 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 28
22586542 TTTTTTATTA
*
22586552 TTTAATTA-TATT-TTTATTTTATTTTAT
1 TTTAATTATTATTATTT-TTCTATTTTAT
*
22586579 TTT-TTTATTA-TATATTTTCTATTTTAT
1 TTTAATTATTATTAT-TTTTCTATTTTAT
22586606 TTCTAATTATTATTATTTTT
1 TT-TAATTATTATTATTTTT
22586626 ATACCTTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
26 4 0.11
27 18 0.47
28 3 0.08
29 10 0.26
30 3 0.08
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTAATTATTATTATTTTTCTATTTTAT
Found at i:22586769 original size:19 final size:19
Alignment explanation
Indices: 22586733--22586774 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
22586723 GTTGTCTTAG
22586733 ATTTTATTATTATTTATTT
1 ATTTTATTATTATTTATTT
*
22586752 ATTTT-TTATTTTTCTATTT
1 ATTTTATTATTATT-TATTT
22586771 ATTT
1 ATTT
22586775 AATGTCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTATTATTATTTATTT
Found at i:22586857 original size:3 final size:3
Alignment explanation
Indices: 22586849--22586925 Score: 68
Period size: 3 Copynumber: 25.0 Consensus size: 3
22586839 ATATATTCGA
*
22586849 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT CATC ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
* * *
22586893 TTT ATCT ATT GTT ATTT ATTT ATT ATT TTT ATT
1 ATT AT-T ATT ATT A-TT A-TT ATT ATT ATT ATT
22586926 GAGTAATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.06
3 47 0.76
4 11 0.18
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:22589081 original size:25 final size:23
Alignment explanation
Indices: 22589043--22589098 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
22589033 TTACCAAGGT
*
22589043 TTTTTTTTTTTTTTGGTTTGTTTGG
1 TTTTTTTTTGTTTTGGTTT-TTT-G
*
22589068 TTTTTTTTTGTTTTTGTTTTTTG
1 TTTTTTTTTGTTTTGGTTTTTTG
22589091 TTTTTTTT
1 TTTTTTTT
22589099 AAATGAGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.31
24 3 0.10
25 17 0.59
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTGTTTTGGTTTTTTG
Done.