Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 167 of 208
Found at i:53770862 original size:14 final size:14
Alignment explanation
Indices: 53770843--53770870 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53770833 TGTGGATTGA
53770843 TTAAAATATATTTT
1 TTAAAATATATTTT
53770857 TTAAAATATATTTT
1 TTAAAATATATTTT
53770871 AAATTGAAGG
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:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAAATATATTTT
Found at i:53776342 original size:22 final size:22
Alignment explanation
Indices: 53776317--53776362 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53776307 ATAATTTATT
*
53776317 TTAAATTAGTAT-TTTATTTTTA
1 TTAAATTA-TATGTTTATTGTTA
53776339 TTAAATTATATGTTTATTGTTA
1 TTAAATTATATGTTTATTGTTA
53776361 TT
1 TT
53776363 TGAAAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TTAAATTATATGTTTATTGTTA
Found at i:53779561 original size:13 final size:13
Alignment explanation
Indices: 53779509--53779559 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
53779499 TTTAAATCAA
53779509 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
53779522 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
53779535 ACTTTTCCACAGT
1 ACTTTTCAAAAGC
53779548 ACTTTTCAAAAG
1 ACTTTTCAAAAG
53779560 TATTGCCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:53780309 original size:29 final size:30
Alignment explanation
Indices: 53780265--53780328 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
53780255 ATTTGGGCCT
* * *
53780265 AATTGTTTCTTTTTAATGGTATAGGGACTA
1 AATTGTTTCTATTTAATGATAAAGGGACTA
*
53780295 AATTGTTTC-ATTTAATGATAAATGGACTA
1 AATTGTTTCTATTTAATGATAAAGGGACTA
53780324 AATTG
1 AATTG
53780329 ATACAATCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (30 bp):
AATTGTTTCTATTTAATGATAAAGGGACTA
Found at i:53802564 original size:47 final size:47
Alignment explanation
Indices: 53802490--53802586 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
53802480 AACAGTAGGT
53802490 TAACCTAAACTTAACCTACTACCACTAACACACATAGTAACTTGTGC
1 TAACCTAAACTTAACCTACTACCACTAACACACATAGTAACTTGTGC
*
53802537 TAACGTAAACTTAACCTACTACCACTAACACACATAGTAACTTGTGC
1 TAACCTAAACTTAACCTACTACCACTAACACACATAGTAACTTGTGC
53802584 TAA
1 TAA
53802587 TTAACTTGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.26
Consensus pattern (47 bp):
TAACCTAAACTTAACCTACTACCACTAACACACATAGTAACTTGTGC
Found at i:53804296 original size:18 final size:19
Alignment explanation
Indices: 53804260--53804297 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53804250 AGACTCCAGG
*
53804260 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
*
53804279 TCTGATT-TCTTCAGTCAT
1 TCTGATTCTCTTCAATCAT
53804297 T
1 T
53804298 GCCTACTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:53807882 original size:13 final size:13
Alignment explanation
Indices: 53807864--53807911 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
53807854 AGTTCTTCAA
53807864 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
53807877 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
53807890 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
53807903 TGCTTTTGA
1 TGCTTTTGA
53807912 GGAATGCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:53807901 original size:26 final size:27
Alignment explanation
Indices: 53807862--53807928 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
53807852 CCAGTTCTTC
*
53807862 AATGCTTTTG-AAAAGTGCTTTTGA-A
1 AATGCTGTTGAAAAAGTGCTTTTGAGA
*
53807887 AAGTGCTG-TGAAAAAGTGCTTTTGAGG
1 AA-TGCTGTTGAAAAAGTGCTTTTGAGA
53807914 AATGCTGTTGAAAAA
1 AATGCTGTTGAAAAA
53807929 TTTGAGTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 4 0.11
26 23 0.64
27 9 0.25
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.33
Consensus pattern (27 bp):
AATGCTGTTGAAAAAGTGCTTTTGAGA
Found at i:53810416 original size:17 final size:17
Alignment explanation
Indices: 53810396--53810437 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
53810386 TATATGCATG
53810396 AAATATAAAACATTATA
1 AAATATAAAACATTATA
53810413 AAATAT-AAACATTATA
1 AAATATAAAACATTATA
53810429 AAATATAAA
1 AAATATAAA
53810438 TGTATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATATAAAACATTATA
Found at i:53810583 original size:3 final size:3
Alignment explanation
Indices: 53810575--53810617 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
53810565 ATGTATAGGT
53810575 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53810618 ACTTGATTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53812127 original size:50 final size:50
Alignment explanation
Indices: 53812047--53812618 Score: 396
Period size: 50 Copynumber: 11.4 Consensus size: 50
53812037 GGATTAATTT
* * * * * * *
53812047 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCATCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
** * ** * *
53812097 CTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* ** * * * *
53812147 CTTCAATCTTTTAAATTGCAATGTCAGGAAAACTAGATCCGTCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * ** * * *
53812197 CTTCAATCTATTCCATTGCACTG-CTAAGGAAGTAAGATCCACCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * * *
53812247 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGTCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * * ** * * * *
53812297 CTTCAATCTGTTCCACTACACTG-CTAAGGAAGTAAGATCCACCATTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * *
53812347 CTTCAATCTTTTTGATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * ** * *
53812397 CTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * * *
53812447 CTTCAATCTTTTTGATTGCAATATCAGGGAAACCACATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * ** * *
53812497 CTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * *
53812547 CTTCAATCTTTTTGATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
*
53812597 CTTCAATCTGTTCCACTGCACT
1 CTTCAATCTGTTCCATTGCACT
53812619 ACTAAGGAAG
Statistics
Matches: 376, Mismatches: 138, Indels: 16
0.71 0.26 0.03
Matches are distributed among these distances:
49 4 0.01
50 368 0.98
51 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
Found at i:53812228 original size:100 final size:100
Alignment explanation
Indices: 53812063--53812635 Score: 923
Period size: 100 Copynumber: 5.7 Consensus size: 100
53812053 TTTGTTCAAC
* * * * * *
53812063 TGCAATGTCGGGGAAACCAGATCCGCCATCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGA
**
53812127 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * * * *
53812163 TGCAATGTCAGGAAAACTAGATCCGTCGTCGTAGCTTCAATCTATTCCATTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
53812228 GTAAGATCCACCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* *
53812263 TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTCAATCTGTTCCACTACACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
53812328 GTAAGATCCACCATTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
53812363 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
53812428 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
*
53812463 TGCAATATCAGGGAAACCACATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
53812528 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
*
53812563 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTACTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
53812628 GTTAAGAT
66 G-TAAGAT
53812636 TACTGGCTTC
Statistics
Matches: 444, Mismatches: 27, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
100 437 0.98
101 7 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
Found at i:53812876 original size:47 final size:45
Alignment explanation
Indices: 53812818--53813286 Score: 216
Period size: 44 Copynumber: 10.4 Consensus size: 45
53812808 AAATCTGCCA
* *
53812818 TCTTCGATCTACTTCAAGCCAATACATGAAGACAAGATCTGTTTTT
1 TCTTCGATCTACTTC-AGCCAATACATGAAGACAAGATCTGTTATC
*** *
53812864 TCCTTCGATCTACTTC-GCCACCAGTATGGGAAGGCAAGATCTGTTATC
1 T-CTTCGATCTACTTCAGCCA--A-TACATGAAGACAAGATCTGTTATC
* *
53812912 TC-T-GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-T-
1 TCTTCGATCTACTTCA-GCCAATACATGAAGACAAGATCTGTTATC
** *** *
53812954 TCTTCGATCTGTTTC-GCCACCAGTATGGGAAGACAAGATCTATTATC
1 TCTTCGATCTACTTCAGCCA--A-TACATGAAGACAAGATCTGTTATC
* * *
53813001 T-TT-GATCTACTTCACACCAGTACATGAAGACAAGCTCTGCTT-TC
1 TCTTCGATCTACTTCA-GCCAATACATGAAGACAAGATCTG-TTATC
* *** *
53813045 T-TT-GATCTGCTTC-GCCACCAGTATGGGAAGGCAAGATCTG-TA--
1 TCTTCGATCTACTTCAGCCA--A-TACATGAAGACAAGATCTGTTATC
* * * * * *
53813087 TATTCGATCCACTTTACTA-CCAATATAGGAAGACAGGATCTGGTATC
1 TCTTCGATCTAC-TT-C-AGCCAATACATGAAGACAAGATCTGTTATC
*
53813134 T-TT-GATCTACTTCACGCCAGTACATGAAGACAAGATCTGTT-T-
1 TCTTCGATCTACTTCA-GCCAATACATGAAGACAAGATCTGTTATC
* * *
53813176 TCTTCGATCTACTTCA-CCACTAGTATGGGAAGGCAAGATCTAG-TATC
1 TCTTCGATCTACTTCAGCCAATA-CAT--GAAGACAAGATCT-GTTATC
* *
53813223 TC-T-GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TT
1 TCTTCGATCTACTTCA-GCCAATACATGAAGACAAGATCTG-TTATC
*
53813267 TCCTTCGATCTGCTTC-GCCA
1 T-CTTCGATCTACTTCAGCCA
53813287 CCAGTATGGG
Statistics
Matches: 321, Mismatches: 56, Indels: 93
0.68 0.12 0.20
Matches are distributed among these distances:
42 17 0.05
43 12 0.04
44 120 0.37
45 95 0.30
46 14 0.04
47 44 0.14
48 19 0.06
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCAGCCAATACATGAAGACAAGATCTGTTATC
Found at i:53812992 original size:89 final size:89
Alignment explanation
Indices: 53812823--53813085 Score: 400
Period size: 89 Copynumber: 2.9 Consensus size: 89
53812813 TGCCATCTTC
* * * *
53812823 GATCTACTTCAAGCCAATACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCACCAG
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTG--CTTT-CTTCGATCTGCTTCGCCACCAG
53812888 TATGGGAAGGCAAGATCTGTTATCTCT
63 TATGGGAAGGCAAGATCTGTTATCTCT
*
53812915 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTAT
* * *
53812980 GGGAAGACAAGATCTATTATCTTT
66 GGGAAGGCAAGATCTGTTATCTCT
* * *
53813004 GATCTACTTCACACCAGTACATGAAGACAAGCTCTGCTTTCTTTGATCTGCTTCGCCACCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTAT
53813069 GGGAAGGCAAGATCTGT
66 GGGAAGGCAAGATCTGT
53813086 ATATTCGATC
Statistics
Matches: 157, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
89 120 0.76
90 3 0.02
92 34 0.22
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTAT
GGGAAGGCAAGATCTGTTATCTCT
Found at i:53813118 original size:133 final size:134
Alignment explanation
Indices: 53812972--53813221 Score: 385
Period size: 133 Copynumber: 1.9 Consensus size: 134
53812962 CTGTTTCGCC
* * * *
53812972 ACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGCT
1 ACCAATATAGGAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGAT
* * *
53813037 CTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCT-GTATATTCGATCCACTT
66 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTATATTCGATCCACTT
53813101 TACT
131 TACT
* * *
53813105 ACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGAT
1 ACCAATATAGGAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGAT
* *
53813170 CTGTTTTCTTCGATCTACTTCACCACTAGTATGGGAAGGCAAGATCTAGTAT
66 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTAT
53813222 CTCTGATCTA
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
133 100 0.96
134 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (134 bp):
ACCAATATAGGAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGAT
CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTATATTCGATCCACTT
TACT
Found at i:53813119 original size:89 final size:88
Alignment explanation
Indices: 53812820--53813192 Score: 383
Period size: 89 Copynumber: 4.2 Consensus size: 88
53812810 ATCTGCCATC
* * *
53812820 TTCGATCTACTTCA-AGCCAATACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGCCA
1 TTCGATCTACTTCACA-CCAGTACATGAAGACAAGATCTG--CTTT-CTTTGATCTACTTCGCCA
53812884 CCAGTATGGGAAGGCAAGATCTGT-TA
62 CCAGTATGGGAAGGCAAGATCTGTATA
* * **
53812910 TCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACC
1 T-TC-GATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACC
* * *
53812975 AGTATGGGAAGACAAGATCTATTATC
64 AGTATGGGAAGGCAAGATCT-GTATA
* * *
53813001 TTTGATCTACTTCACACCAGTACATGAAGACAAGCTCTGCTTTCTTTGATCTGCTTCGCCACCAG
1 TTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAG
53813066 TATGGGAAGGCAAGATCTGTATA
66 TATGGGAAGGCAAGATCTGTATA
* * * * * * * * * *
53813089 TTCGATCCACTTTACTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTC-ACGCCA
1 TTCGATCTACTTCAC-ACCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCA
*** * * *
53813153 GTACATGAAGACAAGATCTGTTTTC
65 GTATGGGAAGGCAAGATCTG-TATA
53813178 TTCGATCTACTTCAC
1 TTCGATCTACTTCAC
53813193 CACTAGTATG
Statistics
Matches: 239, Mismatches: 37, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
88 35 0.15
89 161 0.67
90 6 0.03
91 4 0.02
92 33 0.14
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (88 bp):
TTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAG
TATGGGAAGGCAAGATCTGTATA
Found at i:53813207 original size:89 final size:89
Alignment explanation
Indices: 53812982--53813448 Score: 429
Period size: 89 Copynumber: 5.2 Consensus size: 89
53812972 ACCAGTATGG
* * *** * * *
53812982 GAAGACAAGATCTATTATCTTTGATCTACTTCA-CACCAGTACATGAAGACAAGCTCT-GCTTTC
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAG-TATC
* * * ***
53813045 TTTGATCTGCTTCGCCACCAGTATGG
65 TTTGATCTACTTC-ACGCCAGTACAT
* * * * * * * * * *
53813071 GAAGGCAAGATCTG-TATATTCGATCCACTTTACTACCAATATAGGAAGACAGGATCTGGTATCT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTATCT
53813135 TTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
* *
53813159 GAAGACAAGATCTGTTTTCTTCGATCTACTTCACCACTAGTATGGGAAGGCAAGATCTAGTATCT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTATCT
*
53813224 CTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
* * * *
53813248 GAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGTAAGATCTAGTA
1 GAAGACAAGATCTG--TTAT-CTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTA
*
53813313 TCTCTGATCTACTTCACGCCAGTACAT
63 TCTTTGATCTACTTCACGCCAGTACAT
* * * * * * * *
53813340 AAAGACAAGATTTGCTCTCTTTGATCTATTTCGCCACCAGTATGGGAAGGCAAGATCT-GCATCT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTATCT
* * * * * * *
53813404 TTGATCCATTTCGCTCCAGCATAG
66 TTGATCTACTTCACGCCAGTACAT
*
53813428 GAAGACAGGATCTGTTATCTT
1 GAAGACAAGATCTGTTATCTT
53813449 TCAACCTGCT
Statistics
Matches: 314, Mismatches: 58, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
88 71 0.23
89 157 0.50
90 3 0.01
91 4 0.01
92 79 0.25
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
GAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTAGTATCT
TTGATCTACTTCACGCCAGTACAT
Found at i:53813252 original size:133 final size:133
Alignment explanation
Indices: 53812981--53813261 Score: 377
Period size: 133 Copynumber: 2.1 Consensus size: 133
53812971 CACCAGTATG
** *
53812981 GGAAGACAAGATCTATTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGCTCTGCTTTCT
1 GGAAGACAAGATCTGGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
* * * *
53813046 TTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTATATTCGATCCACTTTACTACCAAT
66 TCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTGTATATTCGATCCACTTCACTACCAAT
*
53813111 ATA
131 ACA
* * *
53813114 GGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GGAAGACAAGATCTGGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
* * * *
53813179 TCGATCTACTTCACCACTAGTATGGGAAGGCAAGATCTAGTAT-CTCTGATCTACTTCAC-GCCA
66 TCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCT-GTATATTC-GATCCACTTCACTACCA
*
53813242 GTACA
129 ATACA
*
53813247 TGAAGACAAGATCTG
1 GGAAGACAAGATCTG
53813262 CTTTTTCCTT
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
133 114 0.89
134 14 0.11
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (133 bp):
GGAAGACAAGATCTGGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
TCGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTGTATATTCGATCCACTTCACTACCAAT
ACA
Found at i:53813253 original size:222 final size:225
Alignment explanation
Indices: 53812883--53813313 Score: 670
Period size: 222 Copynumber: 1.9 Consensus size: 225
53812873 CTACTTCGCC
* * * *
53812883 ACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGAT
1 ACCAATATAGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGAT
** * * *
53812948 CTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTACTT
66 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTT
* *
53813013 CACACCAGTACATGAAGACAAGCTCTGC-TTT-CTTTGATCTGCTTCGCCACCAGTATGGGAAGG
131 CACACCAGTACATGAAGACAAGATCTGCTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGG
53813076 CAAGATCT-GTATATTCGATCCACTTTACT
196 CAAGATCTAGTATATTCGATCCACTTTACT
* *
53813105 ACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGAT
1 ACCAATATAGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGAT
* * *
53813170 CTGTTTTCTTCGATCTACTTCACCACTAGTATGGGAAGGCAAGATCTAGTATCTCTGATCTACTT
66 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTT
*
53813235 CACGCCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAG
131 CACACCAGTACATGAAGACAAGATCTGC-TTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAG
*
53813300 GTAAGATCTAGTAT
195 GCAAGATCTAGTAT
53813314 CTCTGATCTA
Statistics
Matches: 187, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
222 142 0.76
224 3 0.02
225 38 0.20
226 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (225 bp):
ACCAATATAGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGAT
CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTT
CACACCAGTACATGAAGACAAGATCTGCTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGG
CAAGATCTAGTATATTCGATCCACTTTACT
Found at i:53813392 original size:314 final size:312
Alignment explanation
Indices: 53812817--53813449 Score: 959
Period size: 314 Copynumber: 2.0 Consensus size: 312
53812807 AAAATCTGCC
* *
53812817 ATCTTCGATCTACTTCAAGCCAATACATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGC
1 ATCTTTGATCTACTTCAAGCCAATACATGAAGACAAGATCTG-TTTTTCCTTCGATCTACTTCAC
53812882 CACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
65 CACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
* * *
53812947 TCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTACT
130 TCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACT
* * * *
53813012 TCACACCAGTACATGAAGACAAGCTCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGC
195 TCACACCAGTACATAAAGACAAGATCTGCTCTCTTTGATCTACTTCGCCACCAGTATGGGAAGGC
* *
53813077 AAGATCTGTATATTCGATCCACTTT-ACTACCAATATAGGAAGACAGGATCTGGT
260 AAGATCTGCATATTCGATCCA-TTTCACT-CCAACATAGGAAGACAGGATCTGGT
* *
53813131 ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TTTT-CTTCGATCTACTTCACC
1 ATCTTTGATCTACTTCAAGCCAATACATGAAGACAAGATCTGTTTTTCCTTCGATCTACTTCACC
*
53813194 ACTAGTATGGGAAGGCAAGATCTAG-TATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
66 ACCAGTATGGGAAGGCAAGATCT-GTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
**
53813258 TCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGTAAGATCTAGTATCTCTGATCT
130 TCTGC--TTT-CTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCT
* * *
53813323 ACTTCACGCCAGTACATAAAGACAAGATTTGCTCTCTTTGATCTATTTCGCCACCAGTATGGGAA
192 ACTTCACACCAGTACATAAAGACAAGATCTGCTCTCTTTGATCTACTTCGCCACCAGTATGGGAA
* * * * *
53813388 GGCAAGATCTGCATCTTTGATCCATTTCGCTCCAGCATAGGAAGACAGGATCTGTT
257 GGCAAGATCTGCATATTCGATCCATTTCACTCCAACATAGGAAGACAGGATCTGGT
53813444 ATCTTT
1 ATCTTT
53813450 CAACCTGCTC
Statistics
Matches: 290, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
311 82 0.28
312 5 0.02
313 34 0.12
314 169 0.58
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (312 bp):
ATCTTTGATCTACTTCAAGCCAATACATGAAGACAAGATCTGTTTTTCCTTCGATCTACTTCACC
ACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGAT
CTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTT
CACACCAGTACATAAAGACAAGATCTGCTCTCTTTGATCTACTTCGCCACCAGTATGGGAAGGCA
AGATCTGCATATTCGATCCATTTCACTCCAACATAGGAAGACAGGATCTGGT
Found at i:53813405 original size:44 final size:44
Alignment explanation
Indices: 53812870--53813449 Score: 389
Period size: 44 Copynumber: 13.0 Consensus size: 44
53812860 TTTTTCCTTC
* * *
53812870 GATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * * * * *
53812915 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
** * *
53812959 GATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTATTATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
* * * * *
53813004 GATCTACTTC-ACACCAGTACATGAAGACAAGCTCTGCTTTCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * * * *
53813048 GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTATATTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTATCTTT
* ** * * *
53813092 GATCCACTTTACTACCAATATAGGAAGACAGGATCTGGTATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
* * * * * *
53813137 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTTTCTTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * * * *
53813181 GATCTACTTCACCACTAGTATGGGAAGGCAAGATCTAGTATCTCT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
* * * * * *
53813226 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTTTCCTTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG---TAT-CTTT
* * ** *
53813273 GATCTGCTTCGCCACCAGTATGGGAAGGTAAGATCTAGTATCTCT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
* * * ** * *
53813318 GATCTACTTC-ACGCCAGTACATAAAGACAAGATTTGCTCTCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * * *
53813362 GATCTATTTCGCCACCAGTATGGGAAGGCAAGATCTGCATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTATCTTT
* * * * *
53813406 GATCCATTTCG-CTCCAGCATAGGAAGACAGGATCTGTTATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
53813450 CAACCTGCTC
Statistics
Matches: 396, Mismatches: 122, Indels: 35
0.72 0.22 0.06
Matches are distributed among these distances:
43 23 0.06
44 200 0.51
45 138 0.35
46 5 0.01
47 11 0.03
48 18 0.05
49 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTATCTTT
Found at i:53819780 original size:3 final size:3
Alignment explanation
Indices: 53819772--53819837 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
53819762 ATGTATAGGT
53819772 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53819820 ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
53819838 GTAAATAGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53829139 original size:8 final size:8
Alignment explanation
Indices: 53829126--53829150 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53829116 AAGTTTTTCA
53829126 AAAACCCT
1 AAAACCCT
53829134 AAAACCCT
1 AAAACCCT
53829142 AAAACCCT
1 AAAACCCT
53829150 A
1 A
53829151 GGTCTCGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAACCCT
Found at i:53830588 original size:20 final size:19
Alignment explanation
Indices: 53830549--53830591 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
53830539 GCATAACATT
53830549 TTTATTTTTATTTTATTGA
1 TTTATTTTTATTTTATTGA
53830568 TTTATTTATT-TTTTCATTGA
1 TTTATTT-TTATTTT-ATTGA
53830588 TTTA
1 TTTA
53830592 CTTGCTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTATTTTTATTTTATTGA
Found at i:53842367 original size:177 final size:176
Alignment explanation
Indices: 53841994--53842375 Score: 428
Period size: 177 Copynumber: 2.2 Consensus size: 176
53841984 GTCACCGTAC
* * * *** ** *
53841994 CAAATCTTATCTCCCTAAAGTTGCAGTGGATTGGATTGAAGCTACAAATCTTATCTTCCTAAAGT
1 CAAATCATATCTCCCTGAAGTTACAGTGGAGCAGATAAAAGCTACAAATCTTATCTCCCTAAAGT
* * * * * * *
53842059 TGCAGTGGAGTAGATTAAAGCCACAAATTTCATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGC
66 TACAGCGGAGCAGATTAAAGACACAAATGTCATCTCCCTGAAGTTACAGTGGAACAAATTGAAGC
*
53842124 CACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCA
131 CACAAATCTTATCTCCCTAAAGTTGCAGTGAAGCAGATTAAAACCA
* *
53842170 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAAGCTACAAATCTTATCTCCCTAAAGT
1 CAAATCATATCTCCCTGAAGTTACAGTGGAGCAGATAAAAGCTACAAATCTTATCTCCCTAAAGT
* * * * *
53842235 TACAGCGGAGCAGATTGAGGATATCGAATCGT-ATCTCCCT-AGAGTTATAGTGGAACAAATTGA
66 TACAGCGGAGCAGATTAAAGACA-CAAAT-GTCATCTCCCTGA-AGTTACAGTGGAACAAATTGA
* * * * * *
53842298 AGCTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCGA
128 AGCCACAAATCTTATCTCCCTAAAGTTGCAGTGAAGCAGATTAAAACCA
*
53842347 CAAATCATATAC-CTCTGAAGTTACAGTGG
1 CAAATCATAT-CTCCCTGAAGTTACAGTGG
53842376 GTTGGATTAA
Statistics
Matches: 173, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
176 75 0.43
177 96 0.55
178 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (176 bp):
CAAATCATATCTCCCTGAAGTTACAGTGGAGCAGATAAAAGCTACAAATCTTATCTCCCTAAAGT
TACAGCGGAGCAGATTAAAGACACAAATGTCATCTCCCTGAAGTTACAGTGGAACAAATTGAAGC
CACAAATCTTATCTCCCTAAAGTTGCAGTGAAGCAGATTAAAACCA
Found at i:53842368 original size:133 final size:130
Alignment explanation
Indices: 53842028--53842372 Score: 388
Period size: 133 Copynumber: 2.6 Consensus size: 130
53842018 AGTGGATTGG
* * *
53842028 ATTGAAGCTACAAATCTTATCTTCCTAAAGTTGCAGTGGAGTAGATTAAAGCCACAAATTTCATC
1 ATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAA--TCATA
* * * *
53842093 TCCCTGAAGTTACAGTGGAGCAGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGAAGC
64 TCCCTGAAGTTACAGCGGAGCAGATTGAAGACACAAATCGTATCTCCCTGAAGTTACAGTGAAGC
*
53842158 AG
129 AA
* * * * * * *
53842160 ATTAAAACCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAAGCTACAAATCTTATC
1 ATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATC--ATA
* * * * *
53842225 TCCCTAAAGTTACAGCGGAGCAGATTGAGGATATCGAATCGTATCTCCCT-AGAGTTATAGTGGA
64 TCCCTGAAGTTACAGCGGAGCAGATTGAAGACA-CAAATCGTATCTCCCTGA-AGTTACAGT-GA
53842289 A-CAA
126 AGCAA
* * *
53842293 ATTGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCGACAAATCATATA
1 ATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCATAT-
53842358 CCTCTGAAGTTACAG
65 CC-CTGAAGTTACAG
53842373 TGGGTTGGAT
Statistics
Matches: 178, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
130 2 0.01
131 3 0.02
132 84 0.47
133 86 0.48
134 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (130 bp):
ATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCATATC
CCTGAAGTTACAGCGGAGCAGATTGAAGACACAAATCGTATCTCCCTGAAGTTACAGTGAAGCAA
Found at i:53842469 original size:44 final size:44
Alignment explanation
Indices: 53841994--53842462 Score: 424
Period size: 44 Copynumber: 10.5 Consensus size: 44
53841984 GTCACCGTAC
* ***
53841994 CAAATCTTATCTCCCTAAAGTTGCAGTGGATTGGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
53842038 CAAATCTTATCTTCCTAAAGTTGCAGTGGAGTAGATTAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* *
53842082 CAAAT-TTCATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCA
1 CAAATCTT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
53842126 CAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
**
53842170 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
53842214 CAAATCTTATCTCCCTAAAGTTACAGCGGAGCAGATTGAGGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * ** * *
53842258 TCGAATCGTATCTCCCT-AGAGTTATAGTGGAACAAATTGAAGCTA
1 -CAAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTGAAGCTA
* * *
53842303 CAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * ** * *
53842347 CAAATCATATAC-CTCTGAAGTTACAGTGG-GTTGGATTAAATCTA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCTA
* *
53842391 CCATAGCGAGTTTTATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGCTA
1 -CA-A---A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * *
53842441 CGAATCTCATCTCTCTGAAGTT
1 CAAATCTTATCTCCCTGAAGTT
53842463 TTAGTGGGTT
Statistics
Matches: 347, Mismatches: 63, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.01
44 270 0.78
45 41 0.12
46 1 0.00
48 1 0.00
49 3 0.01
50 27 0.08
51 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
Found at i:53842661 original size:14 final size:13
Alignment explanation
Indices: 53842624--53842670 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
53842614 TCGTCTGATG
53842624 AAAAACCAAAAAT
1 AAAAACCAAAAAT
*
53842637 AAATAAACAAAATAT
1 AAA-AACCAAAA-AT
53842652 AAAAACCAAAAAAT
1 AAAAACC-AAAAAT
53842666 AAAAA
1 AAAAA
53842671 AGTCCATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 3 0.10
14 17 0.59
15 9 0.31
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAACCAAAAAT
Found at i:53842972 original size:22 final size:24
Alignment explanation
Indices: 53842944--53843001 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
53842934 AGAAATAAAG
*
53842944 ATAG-AAACAT-GAAGCAAAAATA
1 ATAGAAAACATAGAAGCAAAAAAA
*
53842966 ATAGAAAAGATAGAAGCAAAAAAA
1 ATAGAAAACATAGAAGCAAAAAAA
53842990 ATAAAGAAAACA
1 AT--AGAAAACA
53843002 CAAAAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.14
23 5 0.17
24 13 0.45
26 7 0.24
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (24 bp):
ATAGAAAACATAGAAGCAAAAAAA
Found at i:53843011 original size:26 final size:27
Alignment explanation
Indices: 53842959--53843011 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
53842949 AACATGAAGC
* * * *
53842959 AAAAATAATAGAAAAGATAGAAGCAAA
1 AAAAATAATAGAAAACACAAAAACAAA
53842986 AAAAATAA-AGAAAACACAAAAACAAA
1 AAAAATAATAGAAAACACAAAAACAAA
53843012 CATGAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.75, C:0.08, G:0.09, T:0.08
Consensus pattern (27 bp):
AAAAATAATAGAAAACACAAAAACAAA
Found at i:53846059 original size:40 final size:40
Alignment explanation
Indices: 53845991--53846120 Score: 188
Period size: 40 Copynumber: 3.2 Consensus size: 40
53845981 AGCGGCACTT
*
53845991 TTAGCGGCGTTTGGAGCAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGCGTTT-AAGCAAAAGCGCCGCTAAAGAGTGAGCA
*
53846032 TTAGCGGCGTTTAAGTAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGCGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
* * * *
53846072 TTAGTGGTGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCG
1 TTAGCGGCGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
*
53846112 TTAGTGGCG
1 TTAGCGGCG
53846121 GTTATAAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 70 0.85
41 12 0.15
ACGTcount: A:0.29, C:0.16, G:0.34, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
Found at i:53846333 original size:112 final size:112
Alignment explanation
Indices: 53846071--53846998 Score: 1488
Period size: 112 Copynumber: 8.3 Consensus size: 112
53846061 AAGAGTGAGC
* ** * * * ** *
53846071 ATTAGTGGTGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCGTTAGTGGCGGTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
53846136 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGA
66 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTT-GGGGGGGA
* * *
53846184 CTTAGTGGCATTTATTGTAAGGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
53846249 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
66 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
* *
53846296 ATTAGTGGCATTTATT-TCAAAGCGCCGCTAAAGAGTGAACATTAGCAGTGTTTATAAAAAACGC
1 ATTAGTGGCGTTTATTGT-AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGC
* *
53846360 CGCAAATAATACACCCAAACAGTGCTG-TTTGTGGCCTTTGGGGGGGGA
65 CGCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTT-GGGGGGGA
53846408 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
53846473 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
66 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
53846520 ATTAGTGGCGTTTATT-TCAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGC
1 ATTAGTGGCGTTTATTGT-AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGC
*
53846584 CGCAAATAATACACCCAAACGGTGTCGTTTTGTGGCCTTTGGGGGGGA
65 CGCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
* * *
53846632 ATTAGTCGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAACGTTTATAAAAAACGTC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
* * *
53846697 GCAAATAATACACCCAGATGGTGCCGTTTTATGGCCTTTGGGGGGGA
66 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
53846744 ATTAGTGGCGTTTATT-TCAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTAT-AAAAACGC
1 ATTAGTGGCGTTTATTGT-AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGC
53846807 CGCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
65 CGCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
*
53846855 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAGGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
* * **
53846920 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCTTTTTTCGGGGGA
66 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGC-CTTTGGGGGGGA
*
53846968 CTTAGTGGCGTTTATTGTAAAGCGCCGCTAA
1 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAA
53846999 TCTAAGTGTT
Statistics
Matches: 761, Mismatches: 44, Indels: 20
0.92 0.05 0.02
Matches are distributed among these distances:
111 119 0.16
112 498 0.65
113 144 0.19
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (112 bp):
ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
Found at i:53848833 original size:82 final size:83
Alignment explanation
Indices: 53848709--53848903 Score: 284
Period size: 82 Copynumber: 2.3 Consensus size: 83
53848699 TAAACTTTTG
** * * *
53848709 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAATGGTGTCATTTCTG
1 GTGGCGTTTTTACCAAAAAGCCACAAA-AATACAATTCCAGACCACGAAAACGGTGTCATTTCTG
53848774 TTCACAGCTGTAAGATTTA
65 TTCACAGCTGTAAGATTTA
* * *
53848793 GTGGCATTTTTA-TAAAAAGCCACAAAAATACAATTCCAGACCACGAAAACGGTGTCGTTTCTGT
1 GTGGCGTTTTTACCAAAAAGCCACAAAAATACAATTCCAGACCACGAAAACGGTGTCATTTCTGT
*
53848857 TCACAGCTGTAATATTTA
66 TCACAGCTGTAAGATTTA
53848875 GTGGCGTTTTTACCAAAAACGCCACAAAA
1 GTGGCGTTTTTACCAAAAA-GCCACAAAA
53848904 CGGTGTTAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
82 63 0.63
83 17 0.17
84 20 0.20
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (83 bp):
GTGGCGTTTTTACCAAAAAGCCACAAAAATACAATTCCAGACCACGAAAACGGTGTCATTTCTGT
TCACAGCTGTAAGATTTA
Found at i:53849158 original size:33 final size:33
Alignment explanation
Indices: 53849116--53849181 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
53849106 CGTTTGGTCT
53849116 ATAAACGCCGCAAAGGTGTTTTAAAATTTTTTC
1 ATAAACGCCGCAAAGGTGTTTTAAAATTTTTTC
53849149 ATAAACGCCGCAAAGGTGTTTTAAAATTTTTTC
1 ATAAACGCCGCAAAGGTGTTTTAAAATTTTTTC
53849182 TCAACGATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
ATAAACGCCGCAAAGGTGTTTTAAAATTTTTTC
Found at i:53850159 original size:11 final size:11
Alignment explanation
Indices: 53850139--53850178 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
53850129 GAATATCTCA
53850139 AACT-ATGGGT
1 AACTAATGGGT
53850149 AACTAATGGGT
1 AACTAATGGGT
53850160 AACTAATGGGT
1 AACTAATGGGT
53850171 AACTAATG
1 AACTAATG
53850179 TATTATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:53851587 original size:40 final size:40
Alignment explanation
Indices: 53851531--53851751 Score: 202
Period size: 40 Copynumber: 5.7 Consensus size: 40
53851521 AATACATTAC
*
53851531 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
53851571 TTACTAAAATACATTACTTAC-ATAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTA-AAATTTGTTTAAATTTA
*
53851611 TTTCTAAAATACATTACTTACTAAAA------TAAA-TTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
* * *
53851644 CTTACTAAAAT---TT-GTT--T-AAATTTATAACTAAAATACATTA
1 -TTACTAAAATACATTACTTACTAAAATTTGT---TTAAAT---TTA
*
53851684 CTTAGTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 -TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
53851725 TTACTAAAATACATTACTTACTAAAAT
1 TTACTAAAATACATTACTTACTAAAAT
53851752 ACATTACTTA
Statistics
Matches: 148, Mismatches: 10, Indels: 46
0.73 0.05 0.23
Matches are distributed among these distances:
27 3 0.02
28 1 0.01
30 2 0.01
31 2 0.01
33 3 0.02
34 13 0.09
36 3 0.02
39 1 0.01
40 99 0.67
41 4 0.03
43 2 0.01
44 7 0.05
46 1 0.01
47 7 0.05
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:53851632 original size:57 final size:57
Alignment explanation
Indices: 53851571--53851812 Score: 387
Period size: 57 Copynumber: 4.2 Consensus size: 57
53851561 TTTAAATTTA
*
53851571 TTACTAAAATACATTACTTAC-ATAAATTTGTTTAAATTTATTTCTAAAATACATTAC
1 TTACTAAAATACATTACTTACTA-AAATTTGTTTAAATTTATTACTAAAATACATTAC
* *
53851628 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATAACTAAAATACATTAC
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTAC
*
53851685 TTAGTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTAC
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTAC
*
53851742 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAATTACTTAAATACATTAC
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAA--T-TT-ATTACTAAAATACATTAC
53851803 TTACTAAAAT
1 TTACTAAAAT
53851813 TTGTTTAAAT
Statistics
Matches: 172, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
57 141 0.82
58 1 0.01
59 1 0.01
60 2 0.01
61 27 0.16
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (57 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTAC
Found at i:53851632 original size:97 final size:97
Alignment explanation
Indices: 53851505--53851687 Score: 348
Period size: 97 Copynumber: 1.9 Consensus size: 97
53851495 CGATTGAATG
53851505 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTT
*
53851570 ATTACTAAAATACATTACTTACATAAATTTGT
66 ATAACTAAAATACATTACTTACATAAATTTGT
*
53851602 TTAAATTTATTTCTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTT
53851667 ATAACTAAAATACATTACTTA
66 ATAACTAAAATACATTACTTA
53851688 GTAAAATACA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (97 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTT
ATAACTAAAATACATTACTTACATAAATTTGT
Found at i:53851796 original size:44 final size:44
Alignment explanation
Indices: 53851737--53851828 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
53851727 ACTAAAATAC
*
53851737 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
*
53851781 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
53851825 ATTA
1 ATTA
53851829 CTTAAATATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (44 bp):
ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:53851803 original size:13 final size:13
Alignment explanation
Indices: 53851785--53851866 Score: 69
Period size: 13 Copynumber: 6.3 Consensus size: 13
53851775 AAATTTATTA
*
53851785 ATTACTTAAATAC
1 ATTACTTAAATAT
*
53851798 ATTACTTACTAAAAT
1 ATTACTTA--AATAT
** *
53851813 -TTGTTTAAATTT
1 ATTACTTAAATAT
53851825 ATTACTTAAATAT
1 ATTACTTAAATAT
* *
53851838 GTTACTTAAATTT
1 ATTACTTAAATAT
53851851 ATTACTTAAATA-
1 ATTACTTAAATAT
53851863 ATTA
1 ATTA
53851867 TAAATAAGAT
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
12 7 0.13
13 38 0.72
14 5 0.09
15 3 0.06
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:53852091 original size:73 final size:73
Alignment explanation
Indices: 53852008--53852229 Score: 428
Period size: 73 Copynumber: 3.1 Consensus size: 73
53851998 TAAAATAAAA
*
53852008 TATAAAAAAATATGTGGAATATTAAAATTAACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
53852073 TTAATAAT
66 TTAATAAT
53852081 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
53852146 TTAATAAT
66 TTAATAAT
53852154 TAT-AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
53852218 TTAATAAT
66 TTAATAAT
53852226 TATA
1 TATA
53852230 TTAGTAATGT
Statistics
Matches: 147, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
72 72 0.49
73 75 0.51
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (73 bp):
TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
TTAATAAT
Found at i:53852202 original size:72 final size:72
Alignment explanation
Indices: 53852012--53852229 Score: 418
Period size: 72 Copynumber: 3.0 Consensus size: 72
53852002 ATAAAATATA
*
53852012 AAAAAATATGTGGAATATTAAAATTAACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
1 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
53852077 TAATTAT
66 TAATTAT
53852084 AAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTA
1 -AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTA
53852149 ATAATTAT
65 ATAATTAT
53852157 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
1 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
53852222 TAATTAT
66 TAATTAT
53852229 A
1 A
53852230 TTAGTAATGT
Statistics
Matches: 144, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
72 73 0.51
73 71 0.49
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (72 bp):
AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
TAATTAT
Found at i:53852308 original size:18 final size:18
Alignment explanation
Indices: 53852285--53852363 Score: 78
Period size: 18 Copynumber: 4.4 Consensus size: 18
53852275 AATAACTTAC
53852285 AACTTACATAATACATTT
1 AACTTACATAATACATTT
53852303 AACTTACATAACTTACA--T
1 AACTTACATAA--TACATTT
*
53852321 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
53852338 AACTTACATAATACATTT
1 AACTTACATAATACATTT
53852356 AACTTACA
1 AACTTACA
53852364 ACTTACCTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
16 7 0.14
17 2 0.04
18 22 0.44
19 11 0.22
20 5 0.10
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:53852327 original size:34 final size:35
Alignment explanation
Indices: 53852276--53852523 Score: 91
Period size: 33 Copynumber: 7.0 Consensus size: 35
53852266 ATAATACATA
* *
53852276 ATAACTTACAACTTACATAAT-ACATT-TAACTTAC
1 ATAACTTACAACATACATAATAAC-TTACAACTTAC
53852310 ATAACTTACATA-ATACATAATAACTTACAACTTACATAATAC
1 ATAACTTACA-ACATACATAATAACTTAC-A---AC-T--TAC
* * *
53852352 ATTTAACTTACAACTTACCTAAT-ACATT-TAACTTAC
1 A--TAACTTACAACATACATAATAAC-TTACAACTTAC
53852388 --AACTTAC-ACAATACATAATAACTTACAACTTAC
1 ATAACTTACAAC-ATACATAATAACTTACAACTTAC
* * * *
53852421 AT-A-GTACATA-ATA-ACTTACAACTTACATA-ATAC
1 ATAACTTACA-ACATACA-TAATAACTTACA-ACTTAC
* *
53852454 ATTTAACTTACAACTTACATAAT-ACATT-TAACTTAC
1 A--TAACTTACAACATACATAATAAC-TTACAACTTAC
53852490 --AACTTACATA-ATACATAATAACTTACAACTTAC
1 ATAACTTACA-ACATACATAATAACTTACAACTTAC
53852523 A
1 A
53852524 CAATACATTT
Statistics
Matches: 159, Mismatches: 20, Indels: 70
0.64 0.08 0.28
Matches are distributed among these distances:
31 2 0.01
32 35 0.22
33 39 0.25
34 22 0.14
35 6 0.04
36 12 0.08
37 10 0.06
38 2 0.01
39 4 0.03
40 1 0.01
42 5 0.03
43 3 0.02
44 18 0.11
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (35 bp):
ATAACTTACAACATACATAATAACTTACAACTTAC
Found at i:53852410 original size:51 final size:51
Alignment explanation
Indices: 53852266--53852702 Score: 684
Period size: 51 Copynumber: 8.5 Consensus size: 51
53852256 ATTTTATTAA
53852266 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACATAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTAC--AACTTAC
53852319 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
* * * *
53852370 CTAATACAT-TTAACTTACAACTTACACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACAT-TTAACTTACAACTTAC
*
53852421 ATAGTACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
* *
53852472 ATAATACAT-TTAACTTACAACTTACATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACAT-TTAACTTACAACTTAC
* * *
53852523 ACAATACAT-TTAACTTACAACTTACATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACAT-TTAACTTACAACTTAC
*
53852574 ATAATACAT-TTAACTTACAACTTACATAATACATTTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
*
53852624 ATAATACATAATAACTTACAACTTACACAATACATTTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
*
53852675 ATAATACATAATAACGTACAACTTACAT
1 ATAATACATAATAACTTACAACTTACAT
53852703 TTAACTTACA
Statistics
Matches: 361, Mismatches: 19, Indels: 10
0.93 0.05 0.03
Matches are distributed among these distances:
50 71 0.20
51 223 0.62
52 23 0.06
53 44 0.12
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.33
Consensus pattern (51 bp):
ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
Found at i:53852421 original size:76 final size:77
Alignment explanation
Indices: 53852266--53852702 Score: 720
Period size: 76 Copynumber: 5.7 Consensus size: 77
53852256 ATTTTATTAA
53852266 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACATAACTTACATAATACATAAT
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTAC--AACTTACATAATACATAAT
53852331 AACTTACAACTTAC
64 AACTTACAACTTAC
* * *
53852345 ATAATACAT-TTAACTTACAACTTACCTAATACATTTAACTTACAACTTACACAATACATAATAA
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAA
53852409 CTTACAACTTAC
66 CTTACAACTTAC
* *
53852421 ATAGTACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACAT-TTAA
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAA
53852485 CTTACAACTTAC
66 CTTACAACTTAC
*
53852497 ATAATACATAATAACTTACAACTTACACAATACATTTAACTTACAACTTACATAATACATAATAA
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAA
53852562 CTTACAACTTAC
66 CTTACAACTTAC
*
53852574 ATAATACAT-TTAACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAA
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAA
53852638 CTTACAACTTAC
66 CTTACAACTTAC
* * * *
53852650 ACAATACAT-TTAACTTACAACTTACATAATACATAATAACGTACAACTTACAT
1 ATAATACATAATAACTTACAACTTACATAATACAT-TTAACTTACAACTTACAT
53852703 TTAACTTACA
Statistics
Matches: 339, Mismatches: 16, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
76 211 0.62
77 87 0.26
78 32 0.09
79 9 0.03
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.33
Consensus pattern (77 bp):
ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAA
CTTACAACTTAC
Found at i:53852605 original size:127 final size:128
Alignment explanation
Indices: 53852268--53852702 Score: 743
Period size: 127 Copynumber: 3.4 Consensus size: 128
53852258 TTTATTAAAT
* *
53852268 AATACATAATAACTTACAACTTACATAATACAT-TTAACTTACATAACTTACATAATACATAATA
1 AATACATAATAACTTACAACTTACATAATACATAATAACTTAC--AACTTACATAATACAT-TTA
* *
53852332 ACTTACAACTTACATAATACATTTAACTTACAACTTACCTAATACAT-TTAACTTACAACTTACA
63 ACTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACA
53852396 C
128 C
*
53852397 AATACATAATAACTTACAACTTACATAGTACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
53852462 TACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAC
66 TACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAC
*
53852525 AATACAT-TTAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
53852589 TACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAC
66 TACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAC
* *
53852652 AATACAT-TTAACTTACAACTTACATAATACATAATAACGTACAACTTACAT
1 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACAT
53852703 TTAACTTACA
Statistics
Matches: 296, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
127 216 0.73
128 40 0.14
129 32 0.11
130 8 0.03
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.33
Consensus pattern (128 bp):
AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
TACAACTTACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAC
Found at i:53852710 original size:11 final size:10
Alignment explanation
Indices: 53852694--53852747 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
53852684 AATAACGTAC
53852694 AACTTACATTT
1 AACTTACA-TT
53852705 AACTTACA-T
1 AACTTACATT
53852714 AA--TACATTT
1 AACTTACA-TT
53852723 AACTTACA-T
1 AACTTACATT
53852732 AACTTACA-T
1 AACTTACATT
53852741 AACTTAC
1 AACTTAC
53852748 CATTGTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:53858252 original size:21 final size:21
Alignment explanation
Indices: 53858197--53858267 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
53858187 CTACAACTTA
* *
53858197 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
53858218 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * * *
53858239 AAGCGGAGGTTGCAACGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
53858260 AAGCAGAG
1 AAGCAGAG
53858268 CAGAGCAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.32, C:0.17, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:53858644 original size:42 final size:42
Alignment explanation
Indices: 53858590--53858922 Score: 270
Period size: 42 Copynumber: 7.9 Consensus size: 42
53858580 GTTTTTGTAT
* * *
53858590 AAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTATAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATAA
* * * * *
53858632 AAAAATGCCACTAAAAAACATGTTCTTTAGCGGCGCTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATAA
* * * * *
53858674 AAAAATGCCGCTAAAGAACACGTTCTTTAGAGGCGCTTAGAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTA-TAA
* * **
53858717 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCC
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATAA
** * * **
53858759 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATAA
** * * * * * **
53858801 CTAAGCGCCGCTAAAGAACGTGATCTTTAACGGCGTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATAA
* * * * * **
53858843 ACAAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATAA
** * *
53858885 CTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT
53858923 TTGTTTGTAA
Statistics
Matches: 252, Mismatches: 38, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 217 0.86
43 35 0.14
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTATAA
Found at i:53858923 original size:42 final size:42
Alignment explanation
Indices: 53858722--53858924 Score: 311
Period size: 42 Copynumber: 4.8 Consensus size: 42
53858712 AGAAAAAAAA
*
53858722 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTCCTTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-TAAG
*
53858764 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
53858806 CGCCGCTAAAGAACGTGATCTTTAACGGCGTTTTTTTAC-AAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-CTAAG
* *
53858848 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
*
53858890 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
53858925 GTTTGTAAAC
Statistics
Matches: 150, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
41 1 0.01
42 142 0.95
43 7 0.05
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:53859402 original size:20 final size:19
Alignment explanation
Indices: 53859377--53859427 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
53859367 AGCAATGAAT
*
53859377 CTGTTCACCAAGAGATATAA
1 CTGTTCA-CAAGAGATACAA
53859397 CTGTTCA-AA-AGATACAA
1 CTGTTCACAAGAGATACAA
53859414 CTGTTCATCAAGAG
1 CTGTTCA-CAAGAG
53859428 TCAGAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 2 0.07
20 9 0.33
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (19 bp):
CTGTTCACAAGAGATACAA
Found at i:53859801 original size:31 final size:29
Alignment explanation
Indices: 53859729--53859802 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
53859719 ACCTTAGGTT
*
53859729 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* ***
53859758 ACATTTTTGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
53859789 ACATTTTAGTCACT
1 ACATTTTAGTCACT
53859803 GAGCTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 1 0.03
31 17 0.46
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:53862839 original size:15 final size:15
Alignment explanation
Indices: 53862816--53862848 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53862806 TTTTTATGCC
53862816 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
53862831 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
53862846 ATT
1 ATT
53862849 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:53874804 original size:44 final size:41
Alignment explanation
Indices: 53874745--53875802 Score: 413
Period size: 44 Copynumber: 24.7 Consensus size: 41
53874735 GATCTCATCT
53874745 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGA-TAAG-AAGCA
*
53874789 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGA-T-AAGA-AGCA
* * * *
53874834 AATCTTATCTCCCTGAAGTTGTAGTGGAGCATATTA-AAGCCGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGATAAGAAG-C-A
* * *
53874877 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AAACA
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGA-TAAGAAGCA
* * * * *
53874920 CAGATCTTATCTCTTTGAAGTTGCAG-AGAGCAGAT-CGCATCTA
1 -AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGATAAGAAGC-A
*
53874963 A-TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTA-AAGCTGA
1 AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGATAAGAAGC--A
* * ** *
53875005 TAAT-TCTAT-TCCCTGAAGTTGTAGTGGAGTGGATTAA-AATC-
1 -AGTCT-TATCT-CCTGAAGTTGCAGTGGAGCAGA-TAAGAAGCA
* * * * * *
53875046 AGATCTTATCTCTCTGAAGTTACAG-AGAGCAGAT-CGCATCT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGATAAGAAGCA
53875087 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGA-TAAG-AAGCA
* *
53875131 AGTCTTATCCTTCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGA-T-AAGA-AGCA
* *
53875176 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTA-AAGCCGA
1 AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGATAAGAAG-C-A
* * *
53875219 TAATCCTAT-TCGCTGAAGTTGCAGTGGAGCAGATTAA-AAACA
1 -AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGA-TAAGAAGCA
* * * * * *
53875261 CAGATCTTATCCCTCTGAAGTTACAG-AGAGCAGAT-CGCATCTA
1 -AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGATAAGAAGC-A
*
53875304 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AAGCCGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGATAAGAAG-C-A
* * * ** *
53875346 TAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAA-AATC-
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGA-TAAGAAGCA
* * * * * *
53875388 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCATATCA-CATCT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGATAAGAAGCA
53875429 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGA-TAAG-AAGCA
* *
53875473 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGAA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGA-T-AAGA-AGCA
* *
53875518 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AAGCCGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGATAAGAAG-C-A
* * * * *
53875561 TAATCCTATCTACCTGAAGTTACAGTGGAGCGGATTAA-AATCA
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGA-TAAGAAGCA
* * * * *
53875604 CAGATCTTATTTCTCTGAAGTTGCAG-AGAGCAGAT-CGCATCTA
1 -AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGATAAGAAGC-A
* * * *
53875647 A-TATCATCTCCCTGAAGCTGCAGTGGAGCAGATTA-AAGTCGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGATAAGAAG-C-A
* * * * * *
53875689 TAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAA-AACCTT
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGA-TAAGAAGC-A
** * * * *
53875733 AGATCTTATCTCTCTGAAGTTGCA-AAGAGCAGAT-CGCATCT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGATAAGAAGCA
53875774 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAG
53875803 TAGACCCCAG
Statistics
Matches: 785, Mismatches: 140, Indels: 181
0.71 0.13 0.16
Matches are distributed among these distances:
39 1 0.00
40 123 0.16
41 74 0.09
42 61 0.08
43 102 0.13
44 304 0.39
45 114 0.15
46 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (41 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGATAAGAAGCA
Found at i:53874982 original size:84 final size:86
Alignment explanation
Indices: 53874747--53875802 Score: 604
Period size: 84 Copynumber: 12.3 Consensus size: 86
53874737 TCTCATCTAG
* * *
53874747 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAGTCTTATC-CTCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-CATCTAA-TCTTATCTCT-CTGAAGTTG
* * ** *
53874810 CAGT-GAGGCAGACTGAAGATGGCAAA
62 CAGTGGA-GCAGA-TTAAAATCACAGA
* * *** * *
53874836 TCTTATCTCCCTGAAGTTGTAGTGGAGCATATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGCATCTAATCTTATCTCTCTGAAGTTGCA
*
53874901 GTGGAGCAGATTAAAAACACAGA
64 GTGGAGCAGATTAAAATCACAGA
** * *
53874924 TCTTATCTCTTTGAAGTTGCAG-AGAGCAGA-TCGCATCTAATCTTATCTCTCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAGT
* * *
53874987 GGAGCAGATTAAAGCTGATA-A
66 GGAGCAGATTAAA-ATCACAGA
* ** ** *
53875008 T-TCTAT-TCCCTGAAGTTGTAGTGGAGTGGATTAAAATC-AGATCTTATCTCTCTGAAGTTACA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTA-ATCTTATCTCTCTGAAGTTGCA
* *** *
53875070 G-AGAGCAGA-TCGCATC-TAG-
64 GTGGAGCAGATTAAAATCACAGA
* * * *
53875089 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAGTCTTATC-CTTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-CATCTAA-TCTTATCTC-TCTGAAGTTG
* * ** *
53875152 CAGT-GAGGCAGACTGAAGATGGCAAA
62 CAGTGGA-GCAGA-TTAAAATCACAGA
* *** * *
53875178 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTAT-TCGCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGCATCTAATCTTATCTCTCTGAAGTTGCA
*
53875242 GTGGAGCAGATTAAAAACACAGA
64 GTGGAGCAGATTAAAATCACAGA
* * * *
53875265 TCTTATC-CCTCTGAAGTTACAG-AGAGCAGA-TCGCATCTAATCTTATCTCCCTGAAGTTGCAG
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAG
** *
53875327 TGGAGCAGATTAAAGCCGATA-A
65 TGGAGCAGATTAAAATC-ACAGA
* * ** **
53875349 TCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATC-AGATCTTATCTCTCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTA-ATCTTATCTCTCTGAAGTTGCAG
* * * * *
53875413 -AGAGCATA-TCACATC-TAG-
65 TGGAGCAGATTAAAATCACAGA
* * *
53875431 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAGTCTTATC-CTCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-CATCTAA-TCTTATCTCT-CTGAAGTTG
* * * *
53875494 CAGT-GAGGCAGACTGAAGATGGA-AAA
62 CAGTGGA-GCAGA-TTAAAAT-CACAGA
*** * *
53875520 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTAC-CTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGCATCTAATCTTATCT-CTCTGAAGTTGC
*
53875584 AGTGGAGCGGATTAAAATCACAGA
63 AGTGGAGCAGATTAAAATCACAGA
* * * * * * * *
53875608 TCTTATTTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAATATCATCTCCCTGAAGCTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAGT
* *
53875671 GGAGCAGATTAAAGTCGATA-A
66 GGAGCAGATTAAAATC-ACAGA
* * * ** *
53875692 TCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATC-TA-ATCTTATCTCTCTGAAGTTGCA
** *** *
53875757 -AAGAGCAGA-TCGCATC-TAG-
64 GTGGAGCAGATTAAAATCACAGA
53875776 TCTTATCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
53875803 TAGACCCCAG
Statistics
Matches: 747, Mismatches: 159, Indels: 127
0.72 0.15 0.12
Matches are distributed among these distances:
81 6 0.01
82 51 0.07
83 34 0.05
84 238 0.32
85 63 0.08
86 43 0.06
87 52 0.07
88 94 0.13
89 148 0.20
90 17 0.02
91 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (86 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAGT
GGAGCAGATTAAAATCACAGA
Found at i:53875093 original size:125 final size:127
Alignment explanation
Indices: 53874750--53875119 Score: 430
Period size: 125 Copynumber: 2.9 Consensus size: 127
53874740 CATCTAGTCT
* * *
53874750 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-AG-TCTTATC-CTCCTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AAACACAGATCTTATCTCT-CTGAAGTTACA
* * * * *
53874812 GTGAGGCAGA-CTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCATATTAAAGCCG
63 GAGA-GCAGATC-G--CAT--CTAATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCCG
53874876 ATAATCC
121 ATAATCC
* *
53874883 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTTTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTACAGAG
* *
53874948 AGCAGATCGCATCTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAATTC
66 AGCAGATCGCATCTAATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCC
* ** *
53875011 TAT-TCCCTGAAGTTGTAGTGGAGTGGATT-AAAA-TCAGATCTTATCTCTCTGAAGTTACAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTACAGAG
*
53875073 AGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGA
66 AGCAGATCGCATCTAATCTTATCTCC-TGAAGTTGCAGTGGAGCAGA
53875120 CTAAGTAAGC
Statistics
Matches: 214, Mismatches: 17, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
124 1 0.00
125 70 0.33
126 4 0.02
127 24 0.11
128 47 0.22
130 2 0.01
131 4 0.02
132 8 0.04
133 52 0.24
134 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTACAGAG
AGCAGATCGCATCTAATCTTATCTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCC
Found at i:53875237 original size:214 final size:211
Alignment explanation
Indices: 53874877--53875340 Score: 636
Period size: 216 Copynumber: 2.2 Consensus size: 211
53874867 TTAAAGCCGA
* *
53874877 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTTTGAAGTT
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAACACAGATCTTATCTCTTTGAAGTT
* *
53874942 GCAGAGAGCAGATCGCATCTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATA
66 GCAGAGAGCAGATCGCATCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
* * ** * *
53875007 ATTCTATTCCCTGAAGTTGTAGTGGAGTGGATT-AAAA-TCAGATCTTATCTCTCTGAAGTTACA
131 ATCCTATTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCCCTCTGAAGTTACA
53875070 GAGAGCAGATCGCATC
196 GAGAGCAGATCGCATC
* * *
53875086 TAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-AG-TCTTATC-CTTCTGAA
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAACACAGATCTTATCTCTT-TGAA
* *
53875148 GTTGCAGTGAGGCAGA-CTGAAGATGGCAAATCTTATCTC-CTTGAAGTTGCAGTGGAGCAGATT
63 GTTGCAGAGA-GCAGATC-G--CAT--CAAATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATT
*
53875211 AAAGCCGATAATCCTATTCGCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCCCTC
121 AAAGCCGATAATCCTATTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCCCTC
53875276 TGAAGTTACAGAGAGCAGATCGCATC
186 TGAAGTTACAGAGAGCAGATCGCATC
*
53875302 TAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAA
53875341 GCCGATAATC
Statistics
Matches: 224, Mismatches: 19, Indels: 19
0.85 0.07 0.07
Matches are distributed among these distances:
208 3 0.01
209 55 0.25
210 8 0.04
211 4 0.02
212 2 0.01
213 1 0.00
214 72 0.32
215 4 0.02
216 75 0.33
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (211 bp):
TAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAACACAGATCTTATCTCTTTGAAGTT
GCAGAGAGCAGATCGCATCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
ATCCTATTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCCCTCTGAAGTTACA
GAGAGCAGATCGCATC
Found at i:53875340 original size:127 final size:126
Alignment explanation
Indices: 53875092--53875461 Score: 456
Period size: 126 Copynumber: 2.9 Consensus size: 126
53875082 CATCTAGTCT
* * * * * *
53875092 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-AGTCTTATCCTTCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AAACAGA-TCTTATCCCTCTGAAGTTACAGA
* * * *
53875156 GAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
63 GA-GCAGA-T-CACAT--CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
53875221 ATCC
123 ATCC
*
53875225 TAT-TCGCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCCCTCTGAAGTTACAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAA-ACAGATCTTATCCCTCTGAAGTTACAGAG
*
53875289 AGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCC
64 AGCAGATCACATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCC
* ** * * *
53875352 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACAGATCTTATCCCTCTGAAGTTACAGAGAG
* *
53875417 CATATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
66 CAGATCACATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
53875462 CTAAGTAAGC
Statistics
Matches: 211, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
126 70 0.33
127 56 0.27
128 22 0.10
129 2 0.01
130 1 0.00
131 7 0.03
132 47 0.22
133 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (126 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACAGATCTTATCCCTCTGAAGTTACAGAGAG
CAGATCACATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCC
Found at i:53875365 original size:342 final size:342
Alignment explanation
Indices: 53874734--53875807 Score: 1819
Period size: 342 Copynumber: 3.1 Consensus size: 342
53874724 AGCAGATTGA
*
53874734 AGATCTCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
*
53874799 TCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGC
66 TCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
*
53874864 ATATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
131 AGATTAAAGCCGATAATCCTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
* *
53874929 TCTCTTTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAG
195 TCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* *
53874994 ATTAAAGCTGATAATTCTAT-TCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTC
260 ATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTC
*
53875058 TCTGAAGTTACAGAGAGC
325 TCTGAAGTTGCAGAGAGC
*
53875076 AGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
* *
53875141 TTCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGC
66 TCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
53875206 AGATTAAAGCCGATAATCCTAT-TCGCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
131 AGATTAAAGCCGATAATCCTATCTC-CTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
* *
53875270 TCCCTCTGAAGTTACAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
195 TCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
53875335 ATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTC
260 ATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTC
53875400 TCTGAAGTTGCAGAGAGC
325 TCTGAAGTTGCAGAGAGC
* *
53875418 ATATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
*
53875483 TCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
66 TCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* * *
53875548 AGATTAAAGCCGATAATCCTATCTACCTGAAGTTACAGTGGAGCGGATTAAAATCACAGATCTTA
131 AGATTAAAGCCGATAATCCTATCT-CCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
* * * *
53875613 TTTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATATCATCTCCCTGAAGCTGCAGTGGAGCAG
195 TCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* * * * *
53875678 ATTAAAGTCGATAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCTTAGATCTTATC
260 ATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAA--TCAGATCTTATC
*
53875743 TCTCTGAAGTTGCAAAGAGC
323 TCTCTGAAGTTGCAGAGAGC
*
53875763 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
53875808 CCCAGAAATA
Statistics
Matches: 689, Mismatches: 37, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
340 1 0.00
341 119 0.17
342 353 0.51
343 143 0.21
344 1 0.00
345 72 0.10
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (342 bp):
AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
TCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
AGATTAAAGCCGATAATCCTATCTCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTAT
CTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
TTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTCT
CTGAAGTTGCAGAGAGC
Found at i:53875694 original size:128 final size:128
Alignment explanation
Indices: 53875524--53875802 Score: 441
Period size: 128 Copynumber: 2.2 Consensus size: 128
53875514 GGAAAATCTT
*
53875524 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTACAGTGG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTACAGTAG
* * *
53875589 AGCGGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATATC
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCATCTAATATC
* * * *
53875652 ATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGTCGATAATCCTATCTCCCTGAAGTTGCAGTAG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTACAGTAG
** * * *
53875717 AGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCATCTAGTCTT
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCATCTAATATC
53875780 ATCTCCCTGAAGTTGCAGTGGAG
1 ATCTCCCTGAAGTTGCAGTGGAG
53875803 TAGACCCCAG
Statistics
Matches: 137, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 137 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (128 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTACAGTAG
AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCATCTAATATC
Found at i:53875766 original size:215 final size:215
Alignment explanation
Indices: 53875303--53875756 Score: 603
Period size: 217 Copynumber: 2.1 Consensus size: 215
53875293 GATCGCATCT
* *
53875303 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTA
* * * * *
53875368 TAGTGGAGTGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAGAGCATATCACATCTAGTC
66 CAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAATA
* * * *
53875433 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGT
131 TCATCTCCCTGAAGCTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGT
* **
53875498 GAGGCAGACTGAAGATGGAA
196 GAGGCAGACTGAAAACCGAA
53875518 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTA
* *
53875583 CAGTGGAGCGGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAA
66 CAGTGGAGCGGATTAAAAT--CAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAA
* *
53875648 TATCATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGT-CG-ATAATCCTAT-CTCCCTGAAGTT
129 TATCATCTCCCTGAAGCTGCAGTGGAGCAGACT-AAGTAAGCA-AATCCTATCCT-CCTGAAGTT
* * **
53875710 GCAGT-AGAGCGGA-TTAAAACCTTA
191 GCAGTGAG-GCAGACTGAAAACCGAA
* *
53875734 GATCTTATCTCTCTGAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
53875757 AAGAGCAGAT
Statistics
Matches: 209, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
215 80 0.38
216 31 0.15
217 94 0.45
218 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (215 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTACCTGAAGTTA
CAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAATA
TCATCTCCCTGAAGCTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGT
GAGGCAGACTGAAAACCGAA
Found at i:53877946 original size:15 final size:15
Alignment explanation
Indices: 53877923--53877953 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53877913 TTTTTATGCC
53877923 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
53877938 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
53877953 A
1 A
53877954 GTAGCATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:53881770 original size:23 final size:21
Alignment explanation
Indices: 53881744--53881799 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
53881734 TAAAAAATAT
53881744 ATTAACTAAAATTTTATATAAAA
1 ATTAA-TAAAATTTTA-ATAAAA
*
53881767 ATTAAATAAAATTTTAATTAAA
1 ATT-AATAAAATTTTAATAAAA
53881789 A-TAATAAAATT
1 ATTAATAAAATT
53881800 AAAGGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 1 0.03
22 6 0.19
23 13 0.42
24 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAATAAAATTTTAATAAAA
Found at i:53884884 original size:38 final size:37
Alignment explanation
Indices: 53884825--53884929 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 37
53884815 CATTTTTAAG
**
53884825 AATAT-AAAGAATATATATAAGTATGTATATGATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAAAT-TAGA
* * *
53884862 AATATGCATAAATATATGTAAGTATATA-AAAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAAATTA-GA
*
53884900 AATATGAAAAATATATTTAAGTATGTATAA
1 AATATGAAAAATATATATAAGTATGTATAA
53884930 GTACGTATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
36 2 0.04
37 26 0.47
38 25 0.45
39 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (37 bp):
AATATGAAAAATATATATAAGTATGTATAAAATTAGA
Found at i:53885310 original size:20 final size:20
Alignment explanation
Indices: 53885280--53885346 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
53885270 ACAACAGTAT
*
53885280 ATATAATATAATATTAGAAAA
1 ATAT-ATATAATAATAGAAAA
* *
53885301 ATATATATAATAGT-GTAAA
1 ATATATATAATAATAGAAAA
53885320 ATATA-ACTAATAATA-ATAAA
1 ATATATA-TAATAATAGA-AAA
53885340 ATATATA
1 ATATATA
53885347 CAATGATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 15 0.39
20 17 0.45
21 5 0.13
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (20 bp):
ATATATATAATAATAGAAAA
Found at i:53885322 original size:19 final size:21
Alignment explanation
Indices: 53885316--53885357 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
53885306 TATAATAGTG
53885316 TAAAATATA-ACTAATAATAA
1 TAAAATATATACTAATAATAA
*
53885336 TAAAATATATAC-AATGATAA
1 TAAAATATATACTAATAATAA
53885356 TA
1 TA
53885358 TATATAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAATATATACTAATAATAA
Found at i:53885401 original size:15 final size:14
Alignment explanation
Indices: 53885277--53885411 Score: 78
Period size: 13 Copynumber: 10.1 Consensus size: 14
53885267 TAAACAACAG
53885277 TATATATAATATAA
1 TATATATAATATAA
*
53885291 TAT-TAGAA-A-AA
1 TATATATAATATAA
*
53885302 TATATAT-A-ATAG
1 TATATATAATATAA
*
53885314 TGTA-A-AATATAA
1 TATATATAATATAA
*
53885326 CTA-ATAATAATAAAA
1 -TATAT-ATAATATAA
*
53885341 TATATACAATGATAA
1 TATATATAAT-ATAA
53885356 TATATATAA-A-AGA
1 TATATATAATATA-A
*
53885369 TATATGTATATATAA
1 TATATATA-ATATAA
53885384 T-TATATAATATAA
1 TATATATAATATAA
*
53885397 TAT-TAAAATATAA
1 TATATATAATATAA
53885410 TA
1 TA
53885412 ATACGACAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 31
0.68 0.09 0.23
Matches are distributed among these distances:
11 9 0.10
12 12 0.13
13 32 0.34
14 17 0.18
15 22 0.24
16 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (14 bp):
TATATATAATATAA
Found at i:53885628 original size:3 final size:3
Alignment explanation
Indices: 53885613--53885648 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
53885603 AAACATAAAC
* *
53885613 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53885649 CATTGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:53885780 original size:3 final size:3
Alignment explanation
Indices: 53885749--53885816 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
53885739 ATACACGTAC
* * * *
53885749 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
53885796 ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
53885817 CAAGGATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:53886295 original size:11 final size:12
Alignment explanation
Indices: 53886281--53886315 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
53886271 AGAAAAAAAA
53886281 AAGAGAG-AGGG
1 AAGAGAGAAGGG
53886292 AAGAGAGAAGGG
1 AAGAGAGAAGGG
53886304 -AGAGAGAAGGG
1 AAGAGAGAAGGG
53886315 A
1 A
53886316 GGGGGGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:53888339 original size:22 final size:22
Alignment explanation
Indices: 53888309--53888351 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53888299 ACAGCAGAAC
* *
53888309 AGGTTTTTAGCGGCGGTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
53888331 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
53888352 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.30, T:0.47
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:53888621 original size:42 final size:42
Alignment explanation
Indices: 53888445--53888813 Score: 484
Period size: 42 Copynumber: 8.9 Consensus size: 42
53888435 TTACATAAAG
53888445 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT--AAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
* *
53888485 AAACGCCACTAAAGATAATGTTCTTTAGCGGCGCTTAG-AAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
* *
53888526 AAA-GCCCCTAAAGATCATGTTCTTTAGCGGCGCTT-TAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
* *
53888566 AAACGCCCCTAAAGATCATGTTCTTTAGCAGCGCTTAGAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
*
53888608 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
*
53888650 AAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
* * *
53888692 AAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTGGAAGA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAGAAAA
* * * ****
53888735 AAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTCTTCAA
1 AAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGAAAA
53888777 AAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 AAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
53888814 TTTCACAAAC
Statistics
Matches: 293, Mismatches: 28, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
40 70 0.24
41 38 0.13
42 150 0.51
43 35 0.12
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
Found at i:53889287 original size:21 final size:21
Alignment explanation
Indices: 53889261--53889305 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
53889251 TCTCTCGCTA
*
53889261 CTTCTCTCGCTGCGGCCTCTG
1 CTTCTCTCGCTGCAGCCTCTG
*
53889282 CTTCTCTCGCTGTAGCCTCTG
1 CTTCTCTCGCTGCAGCCTCTG
53889303 CTT
1 CTT
53889306 TAAGTTGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.40, G:0.20, T:0.38
Consensus pattern (21 bp):
CTTCTCTCGCTGCAGCCTCTG
Found at i:53894844 original size:9 final size:9
Alignment explanation
Indices: 53894809--53894941 Score: 173
Period size: 9 Copynumber: 15.0 Consensus size: 9
53894799 TTAAACAATA
53894809 ATGTAAGTT
1 ATGTAAGTT
*
53894818 A-GGAAGGTT
1 ATGTAA-GTT
53894827 ATGT-A-TT
1 ATGTAAGTT
53894834 ATGTAAGTT
1 ATGTAAGTT
53894843 ATGTAAGTT
1 ATGTAAGTT
53894852 ATGTAAGTT
1 ATGTAAGTT
* *
53894861 ATTTAATTT
1 ATGTAAGTT
53894870 ATGTAAGTT
1 ATGTAAGTT
*
53894879 ATGTAAGAT
1 ATGTAAGTT
*
53894888 ATGTAAGAT
1 ATGTAAGTT
53894897 ATGTAAGTT
1 ATGTAAGTT
* *
53894906 ATTTAATTT
1 ATGTAAGTT
53894915 ATGTAAGTT
1 ATGTAAGTT
53894924 ATGTAAGTT
1 ATGTAAGTT
53894933 ATGTAAGTT
1 ATGTAAGTT
53894942 TATATAAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.06
8 4 0.04
9 97 0.90
10 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:53894979 original size:38 final size:39
Alignment explanation
Indices: 53894918--53895018 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
53894908 TTAATTTATG
53894918 TAAGTTATGTAAGTTATGTAAGTTTATA-TAAAAAAAATTA
1 TAAGTTATGT-A-TTATGTAAGTTTATATTAAAAAAAATTA
**
53894958 TAAGTTATGTATTATGTAAGTTTATATTAAAAAATTTTA
1 TAAGTTATGTATTATGTAAGTTTATATTAAAAAAAATTA
53894997 TAAGTTATGTATTATGTAAGTT
1 TAAGTTATGTATTATGTAAGTT
53895019 AAAAGTAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
38 15 0.26
39 33 0.57
40 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.46
Consensus pattern (39 bp):
TAAGTTATGTATTATGTAAGTTTATATTAAAAAAAATTA
Found at i:53895024 original size:23 final size:23
Alignment explanation
Indices: 53894998--53895041 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
53894988 AAAATTTTAT
*
53894998 AAGTTATGTATTATGTAAGTTAA
1 AAGTAATGTATTATGTAAGTTAA
53895021 AAGTAATGTATTATGTAAGTT
1 AAGTAATGTATTATGTAAGTT
53895042 TACATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
AAGTAATGTATTATGTAAGTTAA
Found at i:53895041 original size:39 final size:39
Alignment explanation
Indices: 53894913--53895026 Score: 115
Period size: 39 Copynumber: 2.9 Consensus size: 39
53894903 GTTATTTAAT
* * *
53894913 TTATGTAAGTTATGTAAGTTATGTAAGTTTATA-TAAAAAA
1 TTATATAAGTTATGT-A-TTATGTAAGTTAAAAGTAAAAAA
* * * *
53894953 -AATTATAAGTTATGTATTATGTAAGTTTATATTAAAAAA
1 TTA-TATAAGTTATGTATTATGTAAGTTAAAAGTAAAAAA
*
53894992 TTTTATAAGTTATGTATTATGTAAGTTAAAAGTAA
1 TTATATAAGTTATGTATTATGTAAGTTAAAAGTAA
53895027 TGTATTATGT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
38 15 0.23
39 38 0.59
40 11 0.17
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (39 bp):
TTATATAAGTTATGTATTATGTAAGTTAAAAGTAAAAAA
Found at i:53895127 original size:27 final size:27
Alignment explanation
Indices: 53895085--53895160 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
53895075 GTAATAATTT
*
53895085 TAAGT-AACATACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
53895111 TAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
*
53895138 TAAGTAAACTTGCTTAAATTTTA
1 TAAGTAAACTTACTTAAATTTTA
53895161 GTAAGTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 5 0.11
27 42 0.89
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (27 bp):
TAAGTAAACTTACTTAAATTTTACATA
Found at i:53895146 original size:90 final size:90
Alignment explanation
Indices: 53895040--53895351 Score: 563
Period size: 90 Copynumber: 3.5 Consensus size: 90
53895030 ATTATGTAAG
* *
53895040 TTTACATATATGTAAACTTCCTTAAATTTTAGTAAGTAATAATTTTAAGTAACATACTTAAATTT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATAATTTTAAGTAACATACTTAAATTT
53895105 TACATATAAGTAAACTTACTTAAAT
66 TACATATAAGTAAACTTACTTAAAT
*
53895130 TTTACATATAAGTAAACTTGCTTAAATTTTAGTAAGTAATAATTTTAAGTAACATACTTAAATTT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATAATTTTAAGTAACATACTTAAATTT
53895195 TACATATAAGTAAACTTACTTAAAT
66 TACATATAAGTAAACTTACTTAAAT
*
53895220 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAAT-GTATTTAAGTAACATACTTAAATT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATAAT-TTTAAGTAACATACTTAAATT
*
53895284 TTAGATATAAGTAAACTTACTTAAAT
65 TTACATATAAGTAAACTTACTTAAAT
53895310 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATAA
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATAA
53895352 CATACTTAAA
Statistics
Matches: 214, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
89 1 0.00
90 213 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (90 bp):
TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATAATTTTAAGTAACATACTTAAATTT
TACATATAAGTAAACTTACTTAAAT
Found at i:53895217 original size:27 final size:27
Alignment explanation
Indices: 53895175--53895250 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
53895165 GTAATAATTT
*
53895175 TAAGT-AACATACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
53895201 TAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
53895228 TAAGTAAACTTACTTAAATTTTA
1 TAAGTAAACTTACTTAAATTTTA
53895251 GTAAGTAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 5 0.10
27 43 0.90
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (27 bp):
TAAGTAAACTTACTTAAATTTTACATA
Found at i:53895307 original size:27 final size:27
Alignment explanation
Indices: 53895265--53895385 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
53895255 GTAATGTATT
* *
53895265 TAAGT-AACATACTTAAATTTTAGATA
1 TAAGTAAACTTACTTAAATTTTACATA
53895291 TAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
*
53895318 TAAGTAAACTTACTTAAATTTT--A-G
1 TAAGTAAACTTACTTAAATTTTACATA
*
53895342 TAAGTAATAACATACTTAAATTTTACATA
1 TAAGT-A-AACTTACTTAAATTTTACATA
53895371 TAAGTAAACTTACTT
1 TAAGTAAACTTACTT
53895386 GTTTAAGTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
24 5 0.06
25 2 0.02
26 20 0.24
27 49 0.59
28 2 0.02
29 5 0.06
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.40
Consensus pattern (27 bp):
TAAGTAAACTTACTTAAATTTTACATA
Found at i:53895360 original size:53 final size:54
Alignment explanation
Indices: 53895265--53895385 Score: 178
Period size: 53 Copynumber: 2.3 Consensus size: 54
53895255 GTAATGTATT
* *
53895265 TAAGT-AACATACTTAAATTTTAGATATAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTAGATATAAGTAAACATACTTAAATTTTACATA
53895318 TAAGTAAACTTACTTAAATTTTAG---TAAGTAATAACATACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTAGATATAAGT-A-AACATACTTAAATTTTACATA
53895371 TAAGTAAACTTACTT
1 TAAGTAAACTTACTT
53895386 GTTTAAGTTA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
51 5 0.08
52 1 0.02
53 40 0.63
54 17 0.27
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.40
Consensus pattern (54 bp):
TAAGTAAACTTACTTAAATTTTAGATATAAGTAAACATACTTAAATTTTACATA
Found at i:53895416 original size:13 final size:13
Alignment explanation
Indices: 53895398--53895449 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
53895388 TTAAGTTATG
*
53895398 TAAGTAATGTATT
1 TAAGTAATATATT
*
53895411 TAAGTAACATATT
1 TAAGTAATATATT
* *
53895424 TGAGTAATAAATT
1 TAAGTAATATATT
53895437 TAA-TATATATATT
1 TAAGTA-ATATATT
53895450 AGTAATAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
12 2 0.06
13 29 0.94
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:53897553 original size:19 final size:19
Alignment explanation
Indices: 53897529--53897570 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53897519 GGTCGGGTTT
*
53897529 GGGGAGCTGTTAGGGATTA
1 GGGGAGATGTTAGGGATTA
* *
53897548 GGGGAGATTTTAGGGATTT
1 GGGGAGATGTTAGGGATTA
53897567 GGGG
1 GGGG
53897571 GGAGAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.29
Consensus pattern (19 bp):
GGGGAGATGTTAGGGATTA
Found at i:53898094 original size:73 final size:73
Alignment explanation
Indices: 53898010--53898395 Score: 245
Period size: 73 Copynumber: 5.3 Consensus size: 73
53898000 GCATGTTAAG
*
53898010 CAAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGC
1 CAAA-CGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAAATCAAGCTTGTGGC
*
53898075 ATTTCCAAA
65 GTTTCCAAA
* * * *** *** **
53898084 CAAACACCACT-AATACCATTGA-CAAAACGACAACATTTCGATAAACA--TAAATACAATTTTG
1 CAAACGCCACTAAATA-TA-AGATC-AAACGATGTCATTTC-CCCAACATTTAAAT-CAAGCTTG
**
53898145 TGGCG-TTCCATG
61 TGGCGTTTCCAAA
* * * *
53898157 TAAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTGAACTCAAGCTTGTTGC
1 CAAA-CGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAAATCAAGCTTGTGGC
53898222 GTTTCCAAA
65 GTTTCCAAA
* * *** **** **
53898231 CAAACGCCACT-AATACCATTGA-CAAAACGACAACATTTTGATAAACA--TAAATACAATTTTG
1 CAAACGCCACTAAATA-TA-AGATC-AAACGATGTCA-TTTCCCCAACATTTAAAT-CAAGCTTG
* **
53898292 CGGCGTTT-CATG
61 TGGCGTTTCCAAA
* * * *
53898304 TAAAGCGCCACTAAATATAAGATCAAACAATGTCGTTTCCCCAACATTTAATTCAAGCTTGTGGC
1 CAAA-CGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAAATCAAGCTTGTGGC
53898369 GTTTCCAAA
65 GTTTCCAAA
53898378 CAAACGCCACTAAA-ATAA
1 CAAACGCCACTAAATATAA
53898396 AACATATAAA
Statistics
Matches: 221, Mismatches: 69, Indels: 46
0.66 0.21 0.14
Matches are distributed among these distances:
72 23 0.10
73 92 0.42
74 87 0.39
75 19 0.09
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (73 bp):
CAAACGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAAATCAAGCTTGTGGCG
TTTCCAAA
Found at i:53898146 original size:74 final size:74
Alignment explanation
Indices: 53898068--53898300 Score: 208
Period size: 74 Copynumber: 3.2 Consensus size: 74
53898058 TAACTCAAGC
* *
53898068 TTGTGGCATTTCCAAACAAACACCACTAATACCATTGACAAAACGACAACATTTCGATAAACATA
1 TTGTGGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATA
53898133 AATACAATT
66 AATACAATT
*** * * *** ***
53898142 TTGTGGCG-TTCCATGTAAAGCGCCACTAA-A-TATAAGATC-AAACGATGTCATTTC-CCCAAC
1 TTGTGGCGTTTCCAAACAAA-CGCCACTAATACCAT-TGA-CAAAACGACAACATTTCGATAAAC
* **
53898202 ATTGAACT-CAAGC
63 A-T-AAATACAATT
* *
53898215 TTGTTGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTTGATAAACATA
1 TTGTGGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATA
53898280 AATACAATT
66 AATACAATT
*
53898289 TTGCGGCGTTTC
1 TTGTGGCGTTTC
53898301 ATGTAAAGCG
Statistics
Matches: 114, Mismatches: 34, Indels: 22
0.67 0.20 0.13
Matches are distributed among these distances:
72 6 0.05
73 47 0.41
74 55 0.48
75 6 0.05
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (74 bp):
TTGTGGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATA
AATACAATT
Found at i:53898166 original size:147 final size:147
Alignment explanation
Indices: 53898011--53898390 Score: 670
Period size: 147 Copynumber: 2.6 Consensus size: 147
53898001 CATGTTAAGC
*
53898011 AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGCA
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGCG
*
53898076 TTTCCAAACAAACACCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAT
66 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAT
*
53898141 TTTGTGGCGTTCCATGT
131 TTTGCGGCGTTCCATGT
* *
53898158 AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTGAACTCAAGCTTGTTGCG
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGCG
*
53898223 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTTGATAAACATAAATACAAT
66 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAT
*
53898288 TTTGCGGCGTTTCATGT
131 TTTGCGGCGTTCCATGT
* * *
53898305 AAAGCGCCACTAAATATAAGATCAAACAATGTCGTTTCCCCAACATTTAATTCAAGCTTGTGGCG
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGCG
53898370 TTTCCAAACAAACGCCACTAA
66 TTTCCAAACAAACGCCACTAA
53898391 AATAAAACAT
Statistics
Matches: 221, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 221 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (147 bp):
AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGCG
TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAT
TTTGCGGCGTTCCATGT
Found at i:53899164 original size:23 final size:25
Alignment explanation
Indices: 53899136--53899189 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
53899126 GTACTAAACA
53899136 TTAAACCT-TAAACCC-TAAACCC-C
1 TTAAACCTAT-AACCCTTAAACCCTC
*
53899159 TTAAA-CTATAGCCCTTAAACCCTC
1 TTAAACCTATAACCCTTAAACCCTC
53899183 TTAAACC
1 TTAAACC
53899190 CCAAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 6 0.23
23 13 0.50
24 6 0.23
25 1 0.04
ACGTcount: A:0.37, C:0.35, G:0.02, T:0.26
Consensus pattern (25 bp):
TTAAACCTATAACCCTTAAACCCTC
Found at i:53905380 original size:18 final size:19
Alignment explanation
Indices: 53905357--53905392 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53905347 ATTAAATAAC
53905357 GATAAAT-ATAATGTAAAA
1 GATAAATAATAATGTAAAA
*
53905375 GATAAATAATAATTTAAA
1 GATAAATAATAATGTAAA
53905393 CTTAAACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (19 bp):
GATAAATAATAATGTAAAA
Found at i:53910405 original size:32 final size:32
Alignment explanation
Indices: 53910351--53910426 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
53910341 CATTATAAAT
* * *
53910351 TTATAAATTCATTACTTGAATTTAATAACTTA
1 TTATTAATTAATTAATTGAATTTAATAACTTA
* *
53910383 TTATTAATTAATTAATTTAATTTGATAACTTA
1 TTATTAATTAATTAATTGAATTTAATAACTTA
*
53910415 -TATTGATTAATT
1 TTATTAATTAATT
53910427 GAACTTGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (32 bp):
TTATTAATTAATTAATTGAATTTAATAACTTA
Found at i:53913789 original size:42 final size:36
Alignment explanation
Indices: 53913741--53913824 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 36
53913731 TTTTTTCATT
53913741 ATTTTTCCTTTTTCTCTCATTTTCATTTTGACCTTGATTTTG
1 ATTTTTCCTTTTTCT-TC-TTTTCATTTT----TTGATTTTG
* *
53913783 ATTTTTCTTTTTTCTTCTTTTTATTTTTTGATTTTG
1 ATTTTTCCTTTTTCTTCTTTTCATTTTTTGATTTTG
53913819 ATTTTT
1 ATTTTT
53913825 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 15 0.38
40 9 0.22
41 2 0.05
42 14 0.35
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.70
Consensus pattern (36 bp):
ATTTTTCCTTTTTCTTCTTTTCATTTTTTGATTTTG
Found at i:53913812 original size:30 final size:30
Alignment explanation
Indices: 53913778--53913841 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
53913768 TTGACCTTGA
** **
53913778 TTTTGATTTTTCTTTTTTCTTCTTTTTATT
1 TTTTGATTTTGATTTTTGATTCTTTTTATT
*
53913808 TTTTGATTTTGATTTTTGATTTTTTTTATT
1 TTTTGATTTTGATTTTTGATTCTTTTTATT
53913838 TTTT
1 TTTT
53913842 TGGGCTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.09, C:0.05, G:0.06, T:0.80
Consensus pattern (30 bp):
TTTTGATTTTGATTTTTGATTCTTTTTATT
Found at i:53917439 original size:13 final size:13
Alignment explanation
Indices: 53917421--53917445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53917411 AAAAGATCGT
53917421 AAATTTTCAAATC
1 AAATTTTCAAATC
53917434 AAATTTTCAAAT
1 AAATTTTCAAAT
53917446 TTCGATAATA
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTTTCAAATC
Found at i:53921847 original size:24 final size:23
Alignment explanation
Indices: 53921815--53921861 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
53921805 GTGCAATCTT
53921815 AGATATGATATATGCAATCTTAGA
1 AGATATGAT-TATGCAATCTTAGA
* * *
53921839 AGATGTGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
53921862 GATTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:53922291 original size:23 final size:23
Alignment explanation
Indices: 53922246--53922292 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
53922236 GTTATTTTAG
* *
53922246 TTTTATTATTATTAAATTAATTA
1 TTTTAATATTATTAAACTAATTA
53922269 TTTTAATATTATTAATACT-ATTA
1 TTTTAATATTATTAA-ACTAATTA
53922292 T
1 T
53922293 GTGGCATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAATATTATTAAACTAATTA
Found at i:53922421 original size:23 final size:23
Alignment explanation
Indices: 53922384--53922427 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
53922374 TATATATATA
*
53922384 TATATATATAGTATACGTATGCT
1 TATATATATAGTATACATATGCT
**
53922407 TATATATATCTTATACATATG
1 TATATATATAGTATACATATG
53922428 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (23 bp):
TATATATATAGTATACATATGCT
Found at i:53926662 original size:24 final size:22
Alignment explanation
Indices: 53926562--53926667 Score: 81
Period size: 24 Copynumber: 4.5 Consensus size: 22
53926552 AAATTTATTG
53926562 TATATTATTATTTTAATTTTATA
1 TATATTATT-TTTTAATTTTATA
*
53926585 TGTATTATTTTTCTAAGCTTTTCATGCA
1 TATATTATTTTT-TAA--TTTT-AT--A
*
53926613 T-TATT-TTTTTTAAATTTATTA
1 TATATTATTTTTTAATTTTA-TA
*
53926634 AATATTATTATTTTAATTTTCATA
1 TATATTATT-TTTTAATTTT-ATA
53926658 TATATTATTT
1 TATATTATTT
53926668 CATATGTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 22
0.71 0.05 0.23
Matches are distributed among these distances:
21 1 0.01
22 8 0.12
23 18 0.27
24 19 0.28
25 8 0.12
26 7 0.10
27 4 0.06
28 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (22 bp):
TATATTATTTTTTAATTTTATA
Found at i:53926887 original size:2 final size:2
Alignment explanation
Indices: 53926880--53926906 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53926870 ATTTCATTAT
53926880 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 T
53926907 TATCTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53937826 original size:114 final size:114
Alignment explanation
Indices: 53937614--53938105 Score: 533
Period size: 113 Copynumber: 4.3 Consensus size: 114
53937604 CAAAAGATCA
* * * * * * * *
53937614 GCATTAGCAGTGTTTATG-AGAGAAATGCCGCAATAGTTCAAGCATTAGCGGCGCTTTTCCAAAA
1 GCATTAGCGGTGCTTATGCA-A-AAACGCCGCTATAGGTCAAGAATTAGCAGCGCTTTTCTAAAA
* *
53937678 ACGCCG-TAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCCTAGTG
64 ACGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * * *
53937728 GCATTAGTGGTGCTTATGCAAAAACACCGTTATAGGTCAAGCATTAGCAGCGCTTTTCTAAAAAT
1 GCATTAGCGGTGCTTATGCAAAAACGCCGCTATAGGTCAAGAATTAGCAGCGCTTTTCTAAAAAC
* *
53937793 GCCGCAAAAAATGTTAATCAAAATGCATTGTTCTATCTTGAGCTTAGTG
66 GCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * * *
53937842 GAATTAGCGACT-TTTATGC-AAAATGCCGCTATAGGTCAAGAATTAGCAGCGGTTTTCTAAAAA
1 GCATTAGCG-GTGCTTATGCAAAAACGCCGCTATAGGTCAAGAATTAGCAGCGCTTTTCTAAAAA
* * * * *
53937905 TGCCGCAAAAAATGTTAATCAAAGCACATTGTTCTATCTTGAGCTTAATG
65 CGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * * * *
53937955 GCATTAGCGGTGGTGCTTATGCAAAAACGTCACTATAGATCGAGAATTAGCGGCGCTTTTATAAA
1 GCATTAGC---GGTGCTTATGCAAAAACGCCGCTATAGGTCAAGAATTAGCAGCGCTTTTCTAAA
** * *
53938020 AACATCGCAAAAAATGTTGATCAAAACGCACCGTTCTATCTTGAGCTTAGTG
63 AACGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * *
53938072 GTATTAGCGGCGCTTATGCAAAAGCGCTGCTATA
1 GCATTAGCGGTGCTTATGCAAAAACGCCGCTATA
53938106 TATATGTCGA
Statistics
Matches: 316, Mismatches: 54, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
113 132 0.42
114 90 0.28
115 3 0.01
116 7 0.02
117 84 0.27
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (114 bp):
GCATTAGCGGTGCTTATGCAAAAACGCCGCTATAGGTCAAGAATTAGCAGCGCTTTTCTAAAAAC
GCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
Found at i:53938091 original size:230 final size:226
Alignment explanation
Indices: 53937636--53938094 Score: 585
Period size: 230 Copynumber: 2.0 Consensus size: 226
53937626 TTTATGAGAG
* * * *
53937636 AAATGCCGCAATAGTTCAAGCATTAGCGGCGCTTTTCCAAAAACGCCGTAAAAATGTTAATCAAA
1 AAATGCCGCAATAGGTCAAGAATTAGCAGCGCTTTTCCAAAAACGCCGAAAAAATGTTAATCAAA
* * ** *
53937701 ACGCATCGTTCTATCTTGAGCCTAGTGGCATTAGTGGTGCTTATGCAAAAACACCGTTATAGGTC
66 ACACATCGTTCTATCTTGAGCCTAATGGCATTAGTGGTGCTTATGCAAAAACACCACTATAGATC
* * ** * **
53937766 AAGCATTAGCAGCGCTTTTCTAAAAATGCCGCAAAAAATGTTAATCAAAATGCATTGTTCTATCT
131 AAGAATTAGCAGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCGTTCTATCT
**
53937831 TGAGCTTAGTGGAATTAGCGACTTTTATGCA
196 TGAGCTTAGTGGAATTAGCGACGCTTATGCA
* * * *
53937862 AAATGCCGCTATAGGTCAAGAATTAGCAGCGGTTTTCTAAAAATGCCGCAAAAAATGTTAATCAA
1 AAATGCCGCAATAGGTCAAGAATTAGCAGCGCTTTTCCAAAAACGCCG-AAAAAATGTTAATCAA
* * * **
53937927 AGCACATTGTTCTATCTTGAGCTTAATGGCATTAGCGGTGGTGCTTATGCAAAAACGTCACTATA
65 AACACATCGTTCTATCTTGAGCCTAATGGCATTA---GTGGTGCTTATGCAAAAACACCACTATA
* * * *
53937992 GATCGAGAATTAGCGGCGCTTTTATAAAAACATCGCAAAAAATGTTGATCAAAACGCACCGTTCT
127 GATCAAGAATTAGCAGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCGTTCT
* *
53938057 ATCTTGAGCTTAGTGGTATTAGCGGCGCTTATGCA
192 ATCTTGAGCTTAGTGGAATTAGCGACGCTTATGCA
53938092 AAA
1 AAA
53938095 GCGCTGCTAT
Statistics
Matches: 196, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
226 41 0.21
227 44 0.22
230 111 0.57
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (226 bp):
AAATGCCGCAATAGGTCAAGAATTAGCAGCGCTTTTCCAAAAACGCCGAAAAAATGTTAATCAAA
ACACATCGTTCTATCTTGAGCCTAATGGCATTAGTGGTGCTTATGCAAAAACACCACTATAGATC
AAGAATTAGCAGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCGTTCTATCT
TGAGCTTAGTGGAATTAGCGACGCTTATGCA
Found at i:53938353 original size:7 final size:7
Alignment explanation
Indices: 53938343--53938372 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
53938333 TTGGGTTAGG
53938343 GGTTTAA
1 GGTTTAA
*
53938350 GGTTTAG
1 GGTTTAA
53938357 GGTTTAA
1 GGTTTAA
53938364 GGTTTAA
1 GGTTTAA
53938371 GG
1 GG
53938373 ATACTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (7 bp):
GGTTTAA
Found at i:53938355 original size:27 final size:27
Alignment explanation
Indices: 53938305--53938361 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
53938295 TGTTTATTAT
* *
53938305 TTTGGGTTAAGGGTTTATGTTTTAGAG
1 TTTGGGTTAAGGGTTTAAGGTTTAGAG
* *
53938332 TTTGGGTTAGGGGTTTAAGGTTTAGGG
1 TTTGGGTTAAGGGTTTAAGGTTTAGAG
53938359 TTT
1 TTT
53938362 AAGGTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (27 bp):
TTTGGGTTAAGGGTTTAAGGTTTAGAG
Found at i:53938548 original size:14 final size:14
Alignment explanation
Indices: 53938517--53938602 Score: 77
Period size: 14 Copynumber: 6.1 Consensus size: 14
53938507 TTCCCAAAGA
*
53938517 TATGGTTTA-GGAT
1 TATGGTTTAGGGTT
53938530 TATGGTTTAGGGTT
1 TATGGTTTAGGGTT
*
53938544 TATGGTTTAGAGTT
1 TATGGTTTAGGGTT
*
53938558 TAGGGTTT-GGGTTT
1 TATGGTTTAGGG-TT
** * *
53938572 TATAATTTAAGATT
1 TATGGTTTAGGGTT
53938586 TATGGTTTAAGGGTT
1 TATGGTTT-AGGGTT
53938601 TA
1 TA
53938603 GAGAATATTG
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
13 11 0.20
14 38 0.68
15 7 0.12
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:53938569 original size:27 final size:27
Alignment explanation
Indices: 53938517--53938571 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
53938507 TTCCCAAAGA
*
53938517 TATGGTTTAGGATTATGGTTTAGGGTT
1 TATGGTTTAGGATTAGGGTTTAGGGTT
*
53938544 TATGGTTTAGAGTTTAGGGTTT-GGGTT
1 TATGGTTTAG-GATTAGGGTTTAGGGTT
53938571 T
1 T
53938572 TATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (27 bp):
TATGGTTTAGGATTAGGGTTTAGGGTT
Found at i:53938571 original size:6 final size:7
Alignment explanation
Indices: 53938520--53938571 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
53938510 CCAAAGATAT
53938520 GGTTTA-
1 GGTTTAG
* *
53938526 GGATTAT
1 GGTTTAG
53938533 GGTTTAG
1 GGTTTAG
*
53938540 GGTTTAT
1 GGTTTAG
53938547 GGTTTAG
1 GGTTTAG
*
53938554 AGTTTAG
1 GGTTTAG
53938561 GGTTT-G
1 GGTTTAG
53938567 GGTTT
1 GGTTT
53938572 TATAATTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 11 0.29
7 27 0.71
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:53938733 original size:7 final size:7
Alignment explanation
Indices: 53938723--53938755 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
53938713 TGGGTTTAAT
53938723 GTTTAGG
1 GTTTAGG
53938730 GTTTAGG
1 GTTTAGG
*
53938737 GTTTAGA
1 GTTTAGG
53938744 GTTTAGG
1 GTTTAGG
53938751 GTTTA
1 GTTTA
53938756 ATCTTGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:53938738 original size:21 final size:21
Alignment explanation
Indices: 53938714--53938755 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53938704 GGTGGTCTAT
53938714 GGGTTTA-ATGTTTAGGGTTTA
1 GGGTTTAGA-GTTTAGGGTTTA
53938735 GGGTTTAGAGTTTAGGGTTTA
1 GGGTTTAGAGTTTAGGGTTTA
53938756 ATCTTGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (21 bp):
GGGTTTAGAGTTTAGGGTTTA
Found at i:53938792 original size:15 final size:15
Alignment explanation
Indices: 53938772--53938801 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53938762 GATTTTTTAG
*
53938772 AATATAAATCTAAAT
1 AATATAAATATAAAT
53938787 AATATAAATATAAAT
1 AATATAAATATAAAT
53938802 TATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:53939054 original size:21 final size:20
Alignment explanation
Indices: 53939014--53939051 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
53939004 AATATATTGA
53939014 TGTATTTATTTTTTAAAATG
1 TGTATTTATTTTTTAAAATG
53939034 TGTATTTATTTTTTAAAA
1 TGTATTTATTTTTTAAAA
53939052 ATGCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
TGTATTTATTTTTTAAAATG
Found at i:53939729 original size:17 final size:19
Alignment explanation
Indices: 53939708--53939752 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
53939698 AAATTTTCCC
* *
53939708 CATTTCCCCCAATTCC-AA
1 CATTTCCCCAAATCCCTAA
53939726 -ATTTCCCCAAATCCCTAA
1 CATTTCCCCAAATCCCTAA
53939744 CATTTCCCC
1 CATTTCCCC
53939753 TAACCCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.27, C:0.44, G:0.00, T:0.29
Consensus pattern (19 bp):
CATTTCCCCAAATCCCTAA
Found at i:53941019 original size:27 final size:26
Alignment explanation
Indices: 53940989--53941040 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
53940979 ATTTGAGCTT
*
53940989 GTTA-ATTTGCAATAATTTGTATTTAAA
1 GTTATATTTGAAAT-ATTT-TATTTAAA
*
53941016 GTTATATTTTAAATATTTTATTTAA
1 GTTATATTTGAAATATTTTATTTAA
53941041 TTTTAATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (26 bp):
GTTATATTTGAAATATTTTATTTAAA
Found at i:53941135 original size:9 final size:9
Alignment explanation
Indices: 53941121--53941191 Score: 70
Period size: 9 Copynumber: 7.6 Consensus size: 9
53941111 GTTCAAATTT
53941121 CATAACTTA
1 CATAACTTA
53941130 CATAACTTA
1 CATAACTTA
*
53941139 CATAATTTAAA
1 CATAACTT--A
* * *
53941150 GATCAAATTT
1 CAT-AACTTA
53941160 CATAACTTA
1 CATAACTTA
*
53941169 CATAATTTA
1 CATAACTTA
53941178 CATAACTTA
1 CATAACTTA
53941187 CATAA
1 CATAA
53941192 TTTAGAGATC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
9 41 0.82
10 2 0.04
11 3 0.06
12 4 0.08
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:53941141 original size:39 final size:39
Alignment explanation
Indices: 53941098--53941182 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
53941088 TCAAATTTAC
*
53941098 TACATAATTTAAAGTTCAAATTTCATAACTTACATAACT
1 TACATAATTTAAAGATCAAATTTCATAACTTACATAACT
*
53941137 TACATAATTTAAAGATCAAATTTCATAACTTACATAATT
1 TACATAATTTAAAGATCAAATTTCATAACTTACATAACT
53941176 TACATAA
1 TACATAA
53941183 CTTACATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (39 bp):
TACATAATTTAAAGATCAAATTTCATAACTTACATAACT
Found at i:53941179 original size:48 final size:48
Alignment explanation
Indices: 53941121--53941214 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
53941111 GTTCAAATTT
53941121 CATAACTTACATAACTTACATAATTTAAAGATCAAATTTCATAACTTA
1 CATAACTTACATAACTTACATAATTTAAAGATCAAATTTCATAACTTA
* *
53941169 CATAATTTACATAACTTACATAATTTAGAGATCAAATTTCATAACT
1 CATAACTTACATAACTTACATAATTTAAAGATCAAATTTCATAACT
53941215 ATTTATGAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (48 bp):
CATAACTTACATAACTTACATAATTTAAAGATCAAATTTCATAACTTA
Found at i:53941247 original size:17 final size:19
Alignment explanation
Indices: 53941225--53941264 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53941215 ATTTATGAAC
53941225 GAAGATA-TTACG-ATTAT
1 GAAGATATTTACGAATTAT
*
53941242 GAAGATATTTATGAATTAT
1 GAAGATATTTACGAATTAT
53941261 GAAG
1 GAAG
53941265 TAGTAAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (19 bp):
GAAGATATTTACGAATTAT
Found at i:53942564 original size:13 final size:14
Alignment explanation
Indices: 53942548--53942576 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53942538 TTGTAAATAT
53942548 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
53942561 TTATAATGGTTTAA
1 TTATAATGGTTTAA
53942575 TT
1 TT
53942577 CTTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:53943395 original size:86 final size:86
Alignment explanation
Indices: 53943303--53943523 Score: 194
Period size: 86 Copynumber: 2.6 Consensus size: 86
53943293 AAAAAACACC
* * *
53943303 GCTAAAGACCACGAACTATAGCGGTGTTTTCAAAAAAAGCGTCGC-AAAGTGCCATGA-TTTATA
1 GCTAAAGACCACGAACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAAG-GCAATGACTTT-TA
53943366 GCGGCGTTTTATAAAAAAGTGCT
64 GCGGCGTTTTATAAAAAAGTGCT
* ** * * * * * *
53943389 GCTAAAGATCTTGAATTTTCGCGGCGTTTTCTACAAAAGCGCCGCTAAAGGCAATTACTTTTAGC
1 GCTAAAGACCACGAACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAAGGCAATGACTTTTAGC
** * *
53943454 GGCGTTTTATAAATTAGCGCC
66 GGCGTTTTATAAAAAAGTGCT
* * * * * * * *
53943475 GCTAAAGGCCAAGACCTTTAGCGGCATTTTCTATAAAAGCGCCACTAAA
1 GCTAAAGACCACGAACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAA
53943524 AGTCATGATC
Statistics
Matches: 107, Mismatches: 26, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
86 100 0.93
87 7 0.07
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (86 bp):
GCTAAAGACCACGAACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAAGGCAATGACTTTTAGC
GGCGTTTTATAAAAAAGTGCT
Found at i:53943456 original size:43 final size:42
Alignment explanation
Indices: 53943321--53943523 Score: 142
Period size: 43 Copynumber: 4.7 Consensus size: 42
53943311 CCACGAACTA
* * * *
53943321 TAGCGGTGTTTTCAAAAAAAGCGTCGC-AAAGTGCCATGA-TTT
1 TAGCGGCGTTTTC-TAAAAAGCGCCGCTAAAG-GCCAAGACTTT
* * * ** ** *
53943363 ATAGCGGCGTTTTATAAAAAAGTGCTGCTAAAGATCTTGAATTT
1 -TAGCGGCGTTTTCT-AAAAAGCGCCGCTAAAGGCCAAGACTTT
* *
53943407 TCGCGGCGTTTTCTACAAAAGCGCCGCTAAAGG-CAATTACTTT
1 TAGCGGCGTTTTCTA-AAAAGCGCCGCTAAAGGCCAA-GACTTT
* * *
53943450 TAGCGGCGTTTTATAAATTAGCGCCGCTAAAGGCCAAGACCTT
1 TAGCGGCGTTTTCTAAA-AAGCGCCGCTAAAGGCCAAGACTTT
* *
53943493 TAGCGGCATTTTCTATAAAAGCGCCACTAAA
1 TAGCGGCGTTTTCTA-AAAAGCGCCGCTAAA
53943524 AGTCATGATC
Statistics
Matches: 125, Mismatches: 27, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
42 4 0.03
43 109 0.87
44 12 0.10
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTTCTAAAAAGCGCCGCTAAAGGCCAAGACTTT
Found at i:53944083 original size:31 final size:32
Alignment explanation
Indices: 53944021--53944085 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
53944011 AATAAAATAT
53944021 TTAAAATATATATTTTTATAATTAAATTTAAA
1 TTAAAATATATATTTTTATAATTAAATTTAAA
* *
53944053 TTAAAA-ATATTTTTTTATTATTTAAA-TTAAA
1 TTAAAATATATATTTTTA-TAATTAAATTTAAA
53944084 TT
1 TT
53944086 TGAATCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TTAAAATATATATTTTTATAATTAAATTTAAA
Done.