Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 151 of 322
Found at i:49535749 original size:31 final size:31
Alignment explanation
Indices: 49535714--49535893 Score: 245
Period size: 31 Copynumber: 5.8 Consensus size: 31
49535704 CTTGTCACTT
*
49535714 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
49535745 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
49535776 GTAGCCGGAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
49535807 GTAGCCGGAA-CTGCCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* *
49535838 GTAGCAGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
***
49535869 GTAGCTTCAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
49535894 TGTCATTTGT
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
30 3 0.02
31 127 0.96
32 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:49535873 original size:93 final size:93
Alignment explanation
Indices: 49535714--49535893 Score: 281
Period size: 93 Copynumber: 1.9 Consensus size: 93
49535704 CTTGTCACTT
* *
49535714 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCGGAGCTACCATTTTTCACTGATCAGGTA
1 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCATTTTTCACTGATCAGGTA
*
49535779 GCCGGAGCTACCACTTTTCACTGATCAA
66 GCCGCAGCTACCACTTTTCACTGATCAA
* *
49535807 GTAGCCGGAA-CTGCCACTTTTCACTGATCAGGTAGCAGAAGCTACCATTTTTCACTGATCAGGT
1 GTAGCC-GAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCATTTTTCACTGATCAGGT
**
49535871 AGCTTCAGCTACCACTTTTCACT
65 AGCCGCAGCTACCACTTTTCACT
49535894 TGTCATTTGT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 76 0.96
94 3 0.04
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (93 bp):
GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCATTTTTCACTGATCAGGTA
GCCGCAGCTACCACTTTTCACTGATCAA
Found at i:49535975 original size:50 final size:51
Alignment explanation
Indices: 49535877--49535997 Score: 192
Period size: 50 Copynumber: 2.4 Consensus size: 51
49535867 AGGTAGCTTC
* *
49535877 AGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCGA
1 AGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCGA
*
49535928 AGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGTGTAGCCGA
1 AGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGTGTAGCCGA
49535978 AGCTATCACTTATCACTTGT
1 AGCTATCACTTATCACTTGT
49535998 TACCATGGTC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
50 45 0.69
51 20 0.31
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (51 bp):
AGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCCGA
Found at i:49542099 original size:62 final size:62
Alignment explanation
Indices: 49542033--49542158 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
49542023 GATTCTAGAA
*
49542033 AAGGAAAAAGAAAAGTATGTTGTCTGATATGCACAAATACTTTTTCTTACAAGTTTATATAT
1 AAGGAAAAAGAAAAGTATGTTGTCTGATATGCACAAATACTTTTTCTTACAAGTCTATATAT
*
49542095 AAGGAAAATGAAAAGTATGTTGTCTGATATGCACAAATACTTTTTCTTACAAGTCTATATAT
1 AAGGAAAAAGAAAAGTATGTTGTCTGATATGCACAAATACTTTTTCTTACAAGTCTATATAT
49542157 AA
1 AA
49542159 TTATATCTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (62 bp):
AAGGAAAAAGAAAAGTATGTTGTCTGATATGCACAAATACTTTTTCTTACAAGTCTATATAT
Found at i:49542426 original size:23 final size:23
Alignment explanation
Indices: 49542400--49542444 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
49542390 GACATGAAAT
* *
49542400 ATATCAATTTAAATTATAATAAA
1 ATATAAATATAAATTATAATAAA
* *
49542423 ATATAAATATAATTTATTATAA
1 ATATAAATATAAATTATAATAA
49542445 CTCATTATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATAAATATAAATTATAATAAA
Found at i:49542692 original size:18 final size:18
Alignment explanation
Indices: 49542666--49542706 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
49542656 GATCACGAAG
*
49542666 CATTATCGAACAAAAACA
1 CATTTTCGAACAAAAACA
**
49542684 CATTTTCGAACAACCACA
1 CATTTTCGAACAAAAACA
49542702 CATTT
1 CATTT
49542707 ATACAAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (18 bp):
CATTTTCGAACAAAAACA
Found at i:49544359 original size:56 final size:56
Alignment explanation
Indices: 49544268--49544379 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 56
49544258 TTTTACATGT
* *
49544268 AATCACAAATCGATGCCACTGTCCCAAACAGGGTCTTACTCGCACACATATATCGA
1 AATCACAAATCGATGCCAATGTACCAAACAGGGTCTTACTCGCACACATATATCGA
* **
49544324 AATCACATATCGATGCCAATGTATTAAAC-GTGGTCTTACTCGCACACATATATCGA
1 AATCACAAATCGATGCCAATGTACCAAACAG-GGTCTTACTCGCACACATATATCGA
49544380 TGCCATGGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
55 1 0.02
56 49 0.98
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (56 bp):
AATCACAAATCGATGCCAATGTACCAAACAGGGTCTTACTCGCACACATATATCGA
Found at i:49549319 original size:69 final size:70
Alignment explanation
Indices: 49549239--49549402 Score: 204
Period size: 69 Copynumber: 2.4 Consensus size: 70
49549229 TCCTCATTGA
* * * * **
49549239 AATACCATACCTAAATTTTACAACTCAGTATGGGAAATGCTATTCCTACGTTTCTTAACTCAGTA
1 AATACCATACCTAAATTTCACAACTCAGTATGGGAAATACCATACCTACGTTTCACAACTCAGTA
49549304 T-GAT
66 TGGAT
** **
49549308 AATACCATACCTACGTTTCACAACTCAGTATGGTTAATACCATACCTACGTTTCACAACTCAGTA
1 AATACCATACCTAAATTTCACAACTCAGTATGGGAAATACCATACCTACGTTTCACAACTCAGTA
49549373 TGGAT
66 TGGAT
* **
49549378 GATACCATACCTACGTTTCACAACT
1 AATACCATACCTAAATTTCACAACT
49549403 TTGCAATGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 56 0.67
70 27 0.33
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (70 bp):
AATACCATACCTAAATTTCACAACTCAGTATGGGAAATACCATACCTACGTTTCACAACTCAGTA
TGGAT
Found at i:49549420 original size:35 final size:35
Alignment explanation
Indices: 49549239--49549402 Score: 215
Period size: 35 Copynumber: 4.7 Consensus size: 35
49549229 TCCTCATTGA
** *
49549239 AATACCATACCTAAATTTTACAACTCAGTATGGGA-
1 AATACCATACCTACGTTTCACAACTCAGTAT-GGAT
* * * **
49549274 AATGCTATTCCTACGTTTCTTAACTCAGTAT-GAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
*
49549308 AATACCATACCTACGTTTCACAACTCAGTATGGTT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
49549343 AATACCATACCTACGTTTCACAACTCAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
*
49549378 GATACCATACCTACGTTTCACAACT
1 AATACCATACCTACGTTTCACAACT
49549403 TTGCAATGGA
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
33 2 0.02
34 26 0.23
35 83 0.75
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGAT
Found at i:49550498 original size:21 final size:21
Alignment explanation
Indices: 49550474--49550515 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
49550464 TTTTTTATTT
49550474 AATTGACT-AACCAAACGTTAA
1 AATT-ACTCAACCAAACGTTAA
* *
49550495 AATTTCTCAACCAAACTTTAA
1 AATTACTCAACCAAACGTTAA
49550516 TACTAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (21 bp):
AATTACTCAACCAAACGTTAA
Found at i:49550649 original size:8 final size:8
Alignment explanation
Indices: 49550627--49550656 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
49550617 AAATTCTTTT
49550627 AATTCACC
1 AATTCACC
49550635 AAATTCACC
1 -AATTCACC
49550644 AATTCACC
1 AATTCACC
49550652 AATTC
1 AATTC
49550657 TTTTAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (8 bp):
AATTCACC
Found at i:49552292 original size:30 final size:31
Alignment explanation
Indices: 49552256--49552322 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
49552246 AAACCAAATT
* *
49552256 CATATATTCAACAT-GATA-TTTATATACTTA
1 CATATATTCAA-ATCGATACATCATATACTTA
49552286 CATATA-TCAAATCGATACATCATATACTTA
1 CATATATTCAAATCGATACATCATATACTTA
*
49552316 GATATAT
1 CATATAT
49552323 AAGTGCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 2 0.06
29 8 0.26
30 21 0.68
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (31 bp):
CATATATTCAAATCGATACATCATATACTTA
Found at i:49555500 original size:3 final size:3
Alignment explanation
Indices: 49555492--49555516 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49555482 AGTAAAGTAT
49555492 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
49555517 GTGGAGACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:49560095 original size:23 final size:24
Alignment explanation
Indices: 49560039--49560096 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
49560029 AATTTGTTAG
* *
49560039 ATATTTATAAATATTTTTATATAC
1 ATATTAATAAATATTTTTATATAA
*
49560063 ATA-TATTAAATATTTTTCA-A-AA
1 ATATTAATAAATATTTTT-ATATAA
49560085 ATATTAATAAAT
1 ATATTAATAAAT
49560097 TTGAAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 4 0.14
23 20 0.71
24 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTAATAAATATTTTTATATAA
Found at i:49562475 original size:96 final size:95
Alignment explanation
Indices: 49562299--49562493 Score: 300
Period size: 96 Copynumber: 2.0 Consensus size: 95
49562289 AAGGCCCAAA
49562299 CTCTAAAAAATCCAAAAATTAGAACTTTACCCTAGACCCAAAACTGAAAACAAGCCTTCAGAACA
1 CTCTAAAAAATCCAAAAATTAGAACTTTACCCTAGACCCAAAACTGAAAACAAGCCTTCAGAACA
** * * *
49562364 CAAGTTTTATTAATAGCTTTCTTCATCACT
66 CAAGCATTATCAATAGCTTACATCATCACT
* *
49562394 CTCTAAAAAAATTCAAAAATTAGAACTTTACCCTAGACCCAAAACTGAAAACAAGCGTTCAGAAC
1 CTCT-AAAAAATCCAAAAATTAGAACTTTACCCTAGACCCAAAACTGAAAACAAGCCTTCAGAAC
* *
49562459 ACAGGCATTATCAATAGCTTACATCATCATT
65 ACAAGCATTATCAATAGCTTACATCATCACT
49562490 CTCT
1 CTCT
49562494 TCCATTTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 4 0.04
96 86 0.96
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (95 bp):
CTCTAAAAAATCCAAAAATTAGAACTTTACCCTAGACCCAAAACTGAAAACAAGCCTTCAGAACA
CAAGCATTATCAATAGCTTACATCATCACT
Found at i:49571911 original size:21 final size:21
Alignment explanation
Indices: 49571887--49571931 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
49571877 TATATTATAT
49571887 TTAT-ATTAATTATATTAACTA
1 TTATGATTAATT-TATTAACTA
* *
49571908 TTATGGTTAATTTATTAATTA
1 TTATGATTAATTTATTAACTA
49571929 TTA
1 TTA
49571932 AGAAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
TTATGATTAATTTATTAACTA
Found at i:49580090 original size:18 final size:18
Alignment explanation
Indices: 49580069--49580106 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
49580059 TATTTTAAAA
49580069 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAG-ATTTT
49580087 TATAAATATTTAGATTTT
1 TATAAATATTTAGATTTT
49580105 TA
1 TA
49580107 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TATAAATATTTAGATTTT
Found at i:49583514 original size:39 final size:39
Alignment explanation
Indices: 49583459--49583574 Score: 169
Period size: 39 Copynumber: 3.0 Consensus size: 39
49583449 TTCAGTGATG
49583459 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * *
49583498 TATATCCGGACCTAAGGTCCACAGGCTATGTGCTAGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
49583537 TATAACCGGACTTAAGGTCTGTAGGCTACGTGCTGGAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAA
49583575 ATATGTCTGG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:49583600 original size:78 final size:77
Alignment explanation
Indices: 49583459--49583602 Score: 182
Period size: 78 Copynumber: 1.8 Consensus size: 77
49583449 TTCAGTGATG
* * * *
49583459 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACCTAAGGTCCACAGGC
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGA-CTAAAGTCCACAGGC
49583524 TATGTGCTAGAAT
65 TATGTGCTAGAAT
* * * *
49583537 TATAACCGGACTTAAGGTCTGTAGGCTACGTGCTGGAAATATGTCTGGGA-TAAAGTCCTACAGG
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATC-CGGACTAAAGTCC-ACAGG
49583601 CT
64 CT
49583603 TCGAGCTGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
77 7 0.12
78 46 0.82
79 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (77 bp):
TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGTCCACAGGCT
ATGTGCTAGAAT
Found at i:49583796 original size:63 final size:63
Alignment explanation
Indices: 49583717--49584062 Score: 683
Period size: 63 Copynumber: 5.5 Consensus size: 63
49583707 TACGATATTG
*
49583717 AATGTTCGCAGTAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49583780 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49583843 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49583906 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49583969 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49584032 AATGTTCGCAATAAACCATCATTGAGTAAGT
1 AATGTTCGCAATAAACCATCATTGAGTAAGT
49584063 CAATGACCTA
Statistics
Matches: 282, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 282 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (63 bp):
AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
Found at i:49584268 original size:43 final size:43
Alignment explanation
Indices: 49584220--49584306 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
49584210 TAAGTCTGTT
49584220 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
1 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
49584263 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
1 TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
49584306 T
1 T
49584307 GCTTAAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (43 bp):
TAAATGAATGTTTCAATTTTCGATAAGTCTTAATTGTTTGTGA
Found at i:49591552 original size:39 final size:39
Alignment explanation
Indices: 49591497--49591622 Score: 162
Period size: 39 Copynumber: 3.2 Consensus size: 39
49591487 TTCAGTGATG
*
49591497 TATATCCGGACTTAAGGTCCGCAGGTTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
49591536 TATATCCGGACCTAAGGTCCGTAGGCTATATGCTAGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
49591575 TATAACCGGACTTAAGGTCTGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
49591614 TATGTCCGG
1 TATATCCGG
49591623 GATAAAGTCC
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:49591639 original size:78 final size:77
Alignment explanation
Indices: 49591497--49591640 Score: 182
Period size: 78 Copynumber: 1.8 Consensus size: 77
49591487 TTCAGTGATG
* * * * * *
49591497 TATATCCGGACTTAAGGTCCGCAGGTTATGTGCTGGAATTATATCCGGACCTAAGGTCCGTAGGC
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGA-CTAAAGTCCATAGGC
49591562 TATATGCTAGAAT
65 TATATGCTAGAAT
* *
49591575 TATAACCGGACTTAAGGTCTGCAGGCTACGTGCTGGAAATATGTCCGGGA-TAAAGTCCCATAGG
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCC-GGACTAAAGT-CCATAGG
49591639 CT
64 CT
49591641 TCGAGCTGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
77 5 0.09
78 48 0.86
79 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (77 bp):
TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTAAAGTCCATAGGCT
ATATGCTAGAAT
Found at i:49591834 original size:63 final size:63
Alignment explanation
Indices: 49591755--49592129 Score: 741
Period size: 63 Copynumber: 6.0 Consensus size: 63
49591745 TACGATATTG
*
49591755 AATGTTCGCAGTAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49591818 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49591881 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49591944 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49592007 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
49592070 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTA
1 AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTA
49592130 TTACTTACAC
Statistics
Matches: 311, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 311 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (63 bp):
AATGTTCGCAATAAACCATCATTGAGTAAGTACTATACATTTAAGATGTTCAGGTACGTACTC
Found at i:49594225 original size:22 final size:24
Alignment explanation
Indices: 49594200--49594256 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
49594190 GATACTTTTC
49594200 TTTTTTTTTCTTTC-T-TCCTAAA
1 TTTTTTTTTCTTTCTTCTCCTAAA
*
49594222 TTTTTTTGTTC-TTCTTCTCCTATA
1 TTTTTTT-TTCTTTCTTCTCCTAAA
*
49594246 TTTTGTTTTCT
1 TTTTTTTTTCT
49594257 CAATCAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 10 0.34
23 7 0.24
24 12 0.41
ACGTcount: A:0.09, C:0.18, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTTTTTCTTTCTTCTCCTAAA
Found at i:49597087 original size:21 final size:22
Alignment explanation
Indices: 49597061--49597102 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
49597051 GACAAAAAAT
*
49597061 ATGTTTTTTT-TTGTTTTTTTA
1 ATGTTTTTTTCTTGTTGTTTTA
49597082 ATGTTTTTTTCTTGTTGTTTT
1 ATGTTTTTTTCTTGTTGTTTT
49597103 CTCCCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.07, C:0.02, G:0.12, T:0.79
Consensus pattern (22 bp):
ATGTTTTTTTCTTGTTGTTTTA
Found at i:49597355 original size:11 final size:11
Alignment explanation
Indices: 49597339--49597369 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
49597329 TATATATATT
49597339 TAAAAATTATA
1 TAAAAATTATA
*
49597350 TAAAAATAATA
1 TAAAAATTATA
49597361 TAAAAATTA
1 TAAAAATTA
49597370 ATACTGCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:49598440 original size:48 final size:47
Alignment explanation
Indices: 49598360--49598472 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 47
49598350 TGCTTTTTTT
* *
49598360 ACAATGCACT-GAAAATAATGCACTAAACCTATCTCAATGTTCGAAA
1 ACAATGCACTGGAAAATAATACACTAAACCTATCTAAATGTTCGAAA
* * * *
49598406 ATAATGCACTGGAAAAATAATACATTGAAGCTATCTAAATGTTCGAAA
1 ACAATGCACTGG-AAAATAATACACTAAACCTATCTAAATGTTCGAAA
*
49598454 ACAATGCACT-GTAAATAAT
1 ACAATGCACTGGAAAATAAT
49598473 GATTAAAACT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
46 16 0.28
47 2 0.04
48 39 0.68
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (47 bp):
ACAATGCACTGGAAAATAATACACTAAACCTATCTAAATGTTCGAAA
Found at i:49600592 original size:33 final size:33
Alignment explanation
Indices: 49600555--49600695 Score: 90
Period size: 33 Copynumber: 4.2 Consensus size: 33
49600545 GCCCAACCAC
* * *
49600555 GGTCTTACATTC-GTTGTGCCATAACCCTGTTAT
1 GGTCTTACATTCAG-AGTGCCATAACCCAGCTAT
*
49600588 GGTCTTATCA-TCAGAGTGCCATAGCCCAGCTAT
1 GGTCTTA-CATTCAGAGTGCCATAACCCAGCTAT
* * * *** * *
49600621 GGTCTTACATGTAAACATTGCCATGGTCCAACCAT
1 GGTCTTACAT-T-CAGAGTGCCATAACCCAGCTAT
* *
49600656 GGTCTTACATTC-GTAGTGCCACAACCCAGTTAT
1 GGTCTTACATTCAG-AGTGCCATAACCCAGCTAT
49600689 GGTCTTA
1 GGTCTTA
49600696 TCCGTCAATT
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
32 2 0.02
33 49 0.60
34 5 0.06
35 25 0.31
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (33 bp):
GGTCTTACATTCAGAGTGCCATAACCCAGCTAT
Found at i:49606508 original size:15 final size:15
Alignment explanation
Indices: 49606488--49606516 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49606478 GTATTGTTGT
49606488 TTGATAACACGATGA
1 TTGATAACACGATGA
49606503 TTGATAACACGATG
1 TTGATAACACGATG
49606517 TGTGAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (15 bp):
TTGATAACACGATGA
Found at i:49609013 original size:19 final size:19
Alignment explanation
Indices: 49608954--49609013 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
49608944 AATCCTTTAA
*
49608954 AAATTAACAAAATACTATT
1 AAATTAACAAATTACTATT
*
49608973 AAGA-TAATC-ACTTACATATT
1 AA-ATTAA-CAAATTAC-TATT
49608993 AAATTAACAAATTACTATT
1 AAATTAACAAATTACTATT
49609012 AA
1 AA
49609014 GATAAGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATTAACAAATTACTATT
Found at i:49610243 original size:16 final size:16
Alignment explanation
Indices: 49610222--49610286 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
49610212 TTCGTTGTAT
49610222 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
49610238 TGGAATAGAAGTGTAA
1 TGGAATAGAGGCGTAA
49610254 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
49610270 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
49610286 T
1 T
49610287 AGCAATTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.40, C:0.05, G:0.34, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:49610263 original size:32 final size:32
Alignment explanation
Indices: 49610217--49610278 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
49610207 TTTGGTTCGT
*
49610217 TGTATTGGAATAGAGGCGTAATGGAATAGAAG
1 TGTAATGGAATAGAGGCGTAATGGAATAGAAG
49610249 TGTAATGGAATAGAGGCGTAATGGAATAGA
1 TGTAATGGAATAGAGGCGTAATGGAATAGA
49610279 GACGTAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.34, T:0.24
Consensus pattern (32 bp):
TGTAATGGAATAGAGGCGTAATGGAATAGAAG
Found at i:49610330 original size:45 final size:44
Alignment explanation
Indices: 49610266--49610362 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
49610256 GAATAGAGGC
49610266 GTAATGGAATAGAGACGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* * *
49610311 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAAT
*
49610355 GGAATGGA
1 GTAATGGA
49610363 GGTGTAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.51
45 22 0.47
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:49610536 original size:16 final size:16
Alignment explanation
Indices: 49610499--49610540 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
49610489 TTAATCATAT
*
49610499 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
49610515 TT-AAATATATTATAA
1 TTAAAATATATTATAA
49610530 TTAAAATATAT
1 TTAAAATATAT
49610541 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:49610547 original size:14 final size:15
Alignment explanation
Indices: 49610508--49610549 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
49610498 TTTAAACATA
*
49610508 ATTATTATTAAATAT
1 ATTATAATTAAATAT
49610523 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
49610537 A-TATAATTTAATA
1 ATTATAATTAAATA
49610550 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:49610600 original size:59 final size:58
Alignment explanation
Indices: 49610532--49610644 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 58
49610522 TATTATAATT
*
49610532 AAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACNGATA
1 AAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTAC-GATA
*
49610591 AAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAC
1 AAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTAC
49610645 TAAAATCATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (58 bp):
AAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACGATA
Found at i:49610686 original size:23 final size:21
Alignment explanation
Indices: 49610642--49610682 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
49610632 TATATGAATT
49610642 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATATAA
49610663 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
49610683 TAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:49618155 original size:25 final size:25
Alignment explanation
Indices: 49618102--49618156 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
49618092 AACCCCAAAG
*
49618102 TTTTAATCATTTTTAATTTTAATCC
1 TTTTAATCATTTTTAATTTTAATCA
* *
49618127 TTTTATAT-ATTTTTAATTTTATTTA
1 TTTTA-ATCATTTTTAATTTTAATCA
49618152 TTTTA
1 TTTTA
49618157 GATACCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTAATCATTTTTAATTTTAATCA
Found at i:49618245 original size:5 final size:5
Alignment explanation
Indices: 49618221--49618326 Score: 58
Period size: 5 Copynumber: 21.0 Consensus size: 5
49618211 TATTTCCAAG
* * * *
49618221 TATA- TATAT TACTTT TATAT TATAT TA-ACA TATAT TATTT TATAT TTTAT
1 TATAT TATAT TA-TAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT
* * * * *
49618271 TAAAT GT-TAT ATATAT TATAT TATTT TATGT TTTAA TATA- TATAT ATATAT
1 TATAT -TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
49618322 TATAT
1 TATAT
49618327 ATTAGGATAT
Statistics
Matches: 77, Mismatches: 17, Indels: 15
0.71 0.16 0.14
Matches are distributed among these distances:
4 9 0.12
5 54 0.70
6 14 0.18
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:49618261 original size:25 final size:26
Alignment explanation
Indices: 49618224--49618273 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
49618214 TTCCAAGTAT
49618224 ATATATTACTTTTATATTATATTAAC
1 ATATATTACTTTTATATTATATTAAC
*
49618250 ATATATTA-TTTTATATTTTATTAA
1 ATATATTACTTTTATATTATATTAA
49618274 ATGTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATATTACTTTTATATTATATTAAC
Found at i:49618327 original size:7 final size:7
Alignment explanation
Indices: 49618280--49618402 Score: 55
Period size: 7 Copynumber: 17.7 Consensus size: 7
49618270 TTAAATGTTA
49618280 TATATAT
1 TATATAT
49618287 TATATTAT
1 TATA-TAT
* *
49618295 TTTATGT
1 TATATAT
*
49618302 T-T-TAA
1 TATATAT
49618307 TATATAT
1 TATATAT
49618314 ATATATAT
1 -TATATAT
49618322 TATATAT
1 TATATAT
*
49618329 TAGGATAT
1 TA-TATAT
49618337 T-TCATAT
1 TAT-ATAT
49618344 T-T-TAT
1 TATATAT
49618349 TATATAT
1 TATATAT
49618356 TAT-TA-
1 TATATAT
49618361 TATATAAT
1 TATAT-AT
* *
49618369 TTTGAAATT
1 TAT-ATA-T
*
49618378 TATAAAT
1 TATATAT
49618385 TAT-TAT
1 TATATAT
*
49618391 TAAATAT
1 TATATAT
49618398 TATAT
1 TATAT
49618403 TTTTATTCTT
Statistics
Matches: 89, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
5 9 0.10
6 10 0.11
7 42 0.47
8 24 0.27
9 4 0.04
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:49618353 original size:10 final size:10
Alignment explanation
Indices: 49618250--49618365 Score: 55
Period size: 10 Copynumber: 11.6 Consensus size: 10
49618240 TTATATTAAC
49618250 ATATATTATT
1 ATATATTATT
*
49618260 TTATATT-TT
1 ATATATTATT
* *
49618269 AT-TAAATGTT
1 ATAT-ATTATT
49618279 ATATA-TATT
1 ATATATTATT
49618288 ATATTATT-TT
1 ATA-TATTATT
* * *
49618298 ATGTTTTAAT
1 ATATATTATT
49618308 ATATA-TATAT
1 ATATATTAT-T
49618318 ATATTATATATT
1 ATA-TAT-TATT
* *
49618330 AGGATATT-TC
1 A-TATATTATT
*
49618340 ATATTTTATT
1 ATATATTATT
49618350 ATATATTATT
1 ATATATTATT
49618360 ATATAT
1 ATATAT
49618366 AATTTTGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
8 1 0.01
9 20 0.26
10 43 0.55
11 5 0.06
12 5 0.06
13 4 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (10 bp):
ATATATTATT
Found at i:49618467 original size:27 final size:28
Alignment explanation
Indices: 49618428--49618504 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
49618418 TAAACTTCAT
*
49618428 TTTATAATCTATATTATTACTTTATT-C
1 TTTATAATATATATTATTACTTTATTAC
* *
49618455 TTTATAATATATATTCTATTATTTTATTAT
1 TTTATAATATATA-T-TATTACTTTATTAC
*
49618485 TTTATATATATCTATTATTA
1 TTTATA-ATATATATTATTA
49618505 TGCATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 12 0.29
28 1 0.02
29 16 0.38
30 7 0.17
31 6 0.14
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTATAATATATATTATTACTTTATTAC
Found at i:49622404 original size:16 final size:16
Alignment explanation
Indices: 49622366--49622404 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
49622356 TCCAAAAAAA
*
49622366 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
49622382 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
49622398 AATAACT
1 AAAAACT
49622405 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:49622656 original size:30 final size:30
Alignment explanation
Indices: 49622566--49622664 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
49622556 TAGGTACAAG
49622566 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * *
49622596 AGGTAGTGAAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
49622626 TGTTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
49622656 TGGTGGTGG
1 TGGTGGTGG
49622665 CAAAGGCTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.18, C:0.06, G:0.47, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:49623554 original size:16 final size:16
Alignment explanation
Indices: 49623533--49623566 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
49623523 TTAATTTTTG
*
49623533 AAAAATATAAATTGAA
1 AAAAATAGAAATTGAA
49623549 AAAAATAGAAATTGAA
1 AAAAATAGAAATTGAA
49623565 AA
1 AA
49623567 TACCTTAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAATAGAAATTGAA
Found at i:49623608 original size:89 final size:89
Alignment explanation
Indices: 49623459--49623817 Score: 486
Period size: 89 Copynumber: 4.0 Consensus size: 89
49623449 ACTTAATTTG
** * * * * * *
49623459 AAAACAGATTTTGAAAATACTTC-GACATGTGCCCCGAGGCTCAACTCATCTCTCACAATATGAA
1 AAAACAGAAATTGAAAATACCTCAG-CATGT--CCTGAGGCTAAACTCACCTCTCGCAATATGAG
*
49623523 TTAATTTTTGAAAAATATAAATTGAAA
63 TTGATTTTTGAAAAATATAAATTGAAA
* * * *
49623550 AAAATAGAAATTGAAAATACCTTAGCGTGTCCTGAGGCTAAACTCACATCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
49623615 ATTTTTGAAAAATATAAATTGAAA
66 ATTTTTGAAAAATATAAATTGAAA
49623639 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
49623704 ATTTTTGAAAAATATAAATTGAAA
66 ATTTTTGAAAAATATAAATTGAAA
* * * * *
49623728 AAAACAGAACTTGAAAAGCACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTT
1 AAAACAGAAATTGAAAA-TACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTT
* * *
49623793 GATTTTTGACAAACAGAAATTGAAA
65 GATTTTTGAAAAATATAAATTGAAA
49623818 TTACCTCAGC
Statistics
Matches: 241, Mismatches: 25, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
89 153 0.63
90 65 0.27
91 22 0.09
92 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (89 bp):
AAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAAATATAAATTGAAA
Found at i:49623973 original size:72 final size:73
Alignment explanation
Indices: 49623729--49624174 Score: 668
Period size: 73 Copynumber: 6.1 Consensus size: 73
49623719 AAATTGAAAA
* ** * *
49623729 AAACAGAACTTGAAAAGCACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTG
1 AAACAGAAATTG-AAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
49623794 ATTTTTGAC
65 ATTTTTGAC
49623803 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
49623867 TGTTTTGAA
66 T-TTTTGAC
*
49623876 AAACATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG-AATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
49623940 TTTTTGAC
66 TTTTTGAC
* * *
49623948 AAACAGAAATTGAAATTACATCAGCGTGACCTGAGGCTCAACTTACCTCTCGCAATATGAGTTG-
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
49624012 TGTTTTGAC
66 T-TTTTGAC
*
49624021 AAACAAAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG-AATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
49624085 TTTTTGAC
66 TTTTTGAC
* * * **
49624093 AAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
49624158 ATTTTGA-
66 TTTTTGAC
*
49624165 AAATAGAAAT
1 AAACAGAAAT
49624175 AAAAACATCA
Statistics
Matches: 342, Mismatches: 24, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
72 140 0.41
73 191 0.56
74 11 0.03
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (73 bp):
AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAC
Found at i:49624011 original size:145 final size:145
Alignment explanation
Indices: 49623747--49624167 Score: 716
Period size: 145 Copynumber: 2.9 Consensus size: 145
49623737 CTTGAAAAGC
*
49623747 ACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGACAAACAGAAA
1 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG-AATATGAGTTGATTTTTGACAAACAGAAA
*
49623812 TTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAA
65 TTGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAA
*
49623877 AACATAAATTGAAATT
130 AACAAAAATTGAAATT
49623893 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGAATATGAGTTGATTTTTGACAAACAGAAAT
1 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGAATATGAGTTGATTTTTGACAAACAGAAAT
* * *
49623958 TGAAATTACATCAGCGTGACCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGTGTTTTGACAA
66 TGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAAA
49624023 ACAAAAATTGAAATT
131 ACAAAAATTGAAATT
49624038 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGAATATGAGTTGATTTTTGACAAACAGAAAT
1 ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGAATATGAGTTGATTTTTGACAAACAGAAAT
* * * ** **
49624103 TGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
66 TGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAAA
49624168 TAGAAATAAA
Statistics
Matches: 259, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
145 225 0.87
146 34 0.13
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (145 bp):
ACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGAATATGAGTTGATTTTTGACAAACAGAAAT
TGAAATTACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTGTTTTGAAAA
ACAAAAATTGAAATT
Found at i:49630433 original size:13 final size:13
Alignment explanation
Indices: 49630400--49630425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49630390 GAGGTGCATA
49630400 CTTCTCTTTCGTT
1 CTTCTCTTTCGTT
49630413 CTTCTCTTTCGTT
1 CTTCTCTTTCGTT
49630426 GGTTTCTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
CTTCTCTTTCGTT
Found at i:49636163 original size:25 final size:23
Alignment explanation
Indices: 49636111--49636165 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
49636101 TATAAATAGT
49636111 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
49636134 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
49636159 AATAGTG
1 AATAGTG
49636166 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:49636297 original size:27 final size:27
Alignment explanation
Indices: 49636239--49636359 Score: 97
Period size: 27 Copynumber: 4.5 Consensus size: 27
49636229 AAATATGTAC
* * *
49636239 ATAATATAGTGTAAAA-A-ATACATAC
1 ATAATATAATATAAAATATATACATAA
49636264 ATAATATAAT-TAAAATATATACATAA
1 ATAATATAATATAAAATATATACATAA
* * * *
49636290 GATAATAT-GTAGAAAAAATATATATAA
1 -ATAATATAATATAAAATATATACATAA
*
49636317 ATAATATAGTATTAAAGATATATACATAAA
1 ATAATATAATA-TAAA-ATATATACAT-AA
*
49636347 ATAGTATAATATA
1 ATAATATAATATA
49636360 TATACGTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
24 5 0.06
25 10 0.13
26 15 0.19
27 23 0.30
28 3 0.04
29 10 0.13
30 11 0.14
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (27 bp):
ATAATATAATATAAAATATATACATAA
Found at i:49636339 original size:29 final size:28
Alignment explanation
Indices: 49636239--49636346 Score: 104
Period size: 27 Copynumber: 4.0 Consensus size: 28
49636229 AAATATGTAC
* *
49636239 ATAATATAGT-GTAAAA-A-ATACATAC
1 ATAATATAGTATTAAAATATATACATAA
49636264 ATAATATA--ATTAAAATATATACATAA
1 ATAATATAGTATTAAAATATATACATAA
* * *
49636290 GATAATAT-GTA-GAAAAAATATATATAA
1 -ATAATATAGTATTAAAATATATACATAA
49636317 ATAATATAGTATTAAAGATATATACATAA
1 ATAATATAGTATTAAA-ATATATACATAA
49636346 A
1 A
49636347 ATAGTATAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
24 5 0.08
25 9 0.14
26 14 0.21
27 23 0.35
28 4 0.06
29 11 0.17
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (28 bp):
ATAATATAGTATTAAAATATATACATAA
Found at i:49636345 original size:25 final size:25
Alignment explanation
Indices: 49636231--49636442 Score: 95
Period size: 25 Copynumber: 8.6 Consensus size: 25
49636221 ATATAAAAAA
* * * *
49636231 ATATGTACATAATATAGTGTAAAAA
1 ATATATACATAATATAGTATTAAAG
*
49636256 ATACATACATAATATA--ATTAAA-
1 ATATATACATAATATAGTATTAAAG
** *
49636278 ATATATACATAAGATAATATGTAGAAAAAAT
1 ATATATACAT-A-AT-ATA-GT--ATTAAAG
*
49636309 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
49636334 ATATATACATAAAATAGTA-T-AAT
1 ATATATACATAATATAGTATTAAAG
* * *
49636357 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
49636381 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* *
49636403 AATATATATATATATAATAATATTAAA-
1 -ATATATACATA-AT-ATAGTATTAAAG
*
49636430 AAATATA-ATAATA
1 ATATATACATAATA
49636443 ACAAAAAAAA
Statistics
Matches: 143, Mismatches: 27, Indels: 36
0.69 0.13 0.17
Matches are distributed among these distances:
21 1 0.01
22 11 0.08
23 38 0.27
24 15 0.10
25 43 0.30
26 9 0.06
27 3 0.02
28 7 0.05
29 2 0.01
30 5 0.03
31 9 0.06
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:49636414 original size:28 final size:28
Alignment explanation
Indices: 49636382--49636436 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
49636372 AGAATTTAGA
*
49636382 ATATACCTAAT-ATATTAAAAGAATATAT
1 ATATACATAATAATATTAAAA-AATATAT
*
49636410 ATATATATAATAATATTAAAAAATATA
1 ATATACATAATAATATTAAAAAATATA
49636437 ATAATAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (28 bp):
ATATACATAATAATATTAAAAAATATAT
Found at i:49636448 original size:18 final size:18
Alignment explanation
Indices: 49636414--49636450 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49636404 ATATATATAT
**
49636414 ATATAATAATATTAAAAA
1 ATATAATAATAACAAAAA
49636432 ATATAATAATAACAAAAA
1 ATATAATAATAACAAAAA
49636450 A
1 A
49636451 AAGAGGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
ATATAATAATAACAAAAA
Found at i:49636968 original size:30 final size:30
Alignment explanation
Indices: 49636922--49637020 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 30
49636912 TAGGTACAAG
*
49636922 TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * **
49636952 AGGTAGTGGAGCAAGTGTGGCTAGTAAAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
49636982 TGTTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
49637012 TGGTGGTGG
1 TGGTGGTGG
49637021 CAAAGGCTAG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.20, C:0.05, G:0.46, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:49637959 original size:17 final size:17
Alignment explanation
Indices: 49637932--49637975 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
49637922 AATTAAACAT
* * *
49637932 TAAATTAATATATGTTA
1 TAAAATAATATATATCA
*
49637949 TAATATAATATATATCA
1 TAAAATAATATATATCA
49637966 TAAAATAATA
1 TAAAATAATA
49637976 ATAAGCCATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAAATAATATATATCA
Found at i:49639110 original size:56 final size:56
Alignment explanation
Indices: 49639019--49639170 Score: 180
Period size: 56 Copynumber: 2.7 Consensus size: 56
49639009 GAATATGTGG
* * *
49639019 CATCTATATGTGACTT-TGATATATGTGTGCAAGTAAGACCACGTTTAATACGTTGA
1 CATCGATATGTGA-TTCTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
* * * * *
49639075 CATTGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCATGTTTCATACATTGG
1 CATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
* * * *
49639131 CATCGATATGTGATTCTGATTTGTGTTTACGAGTAAGACC
1 CATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACC
49639171 CTGTCTGGGA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
55 2 0.02
56 79 0.98
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (56 bp):
CATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
Found at i:49646560 original size:33 final size:33
Alignment explanation
Indices: 49646522--49646658 Score: 136
Period size: 33 Copynumber: 4.4 Consensus size: 33
49646512 TTAATATTAA
49646522 ATTAAATTAATATTTA-ATTTAATATTAAATCTT
1 ATTAAATTAATA-TTAGATTTAATATTAAATCTT
49646555 ATTAAATTAATA--AGATATTAA-ATTTAATATCTT
1 ATTAAATTAATATTAGAT-TTAATA-TTAA-ATCTT
*
49646588 ATTAATTTAATA--AGATTTAATATT-AA----
1 ATTAAATTAATATTAGATTTAATATTAAATCTT
49646614 ATTAAATTAATATTTA-ATTTAATATTAAATCTT
1 ATTAAATTAATA-TTAGATTTAATATTAAATCTT
49646647 ATTAAATTAATA
1 ATTAAATTAATA
49646659 AGATATTAAA
Statistics
Matches: 89, Mismatches: 2, Indels: 26
0.76 0.02 0.22
Matches are distributed among these distances:
26 11 0.12
28 10 0.11
29 3 0.03
30 2 0.02
31 4 0.04
32 14 0.16
33 45 0.51
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (33 bp):
ATTAAATTAATATTAGATTTAATATTAAATCTT
Found at i:49646625 original size:59 final size:60
Alignment explanation
Indices: 49646555--49646667 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
49646545 ATTAAATCTT
*
49646555 ATTAAATTAATAAGAT-ATTAAAT-TTAATATCTTATTAATTTAATAAGAT-TTAATATTAA
1 ATTAAATTAAT-AGATAATTAAATATTAA-ATCTTATTAAATTAATAAGATATTAATATTAA
** *
49646614 ATTAAATTAATATTTAATTTAATATTAAATCTTATTAAATTAATAAGATATTAA
1 ATTAAATTAATAGATAATTAAATATTAAATCTTATTAAATTAATAAGATATTAA
49646668 ATTTAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 2 0.04
59 37 0.79
60 8 0.17
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (60 bp):
ATTAAATTAATAGATAATTAAATATTAAATCTTATTAAATTAATAAGATATTAATATTAA
Found at i:49649780 original size:10 final size:10
Alignment explanation
Indices: 49649765--49649790 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
49649755 TTCGATCGAG
49649765 TCGAGTCGGA
1 TCGAGTCGGA
49649775 TCGAGTCGGA
1 TCGAGTCGGA
49649785 TCGAGT
1 TCGAGT
49649791 TAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (10 bp):
TCGAGTCGGA
Found at i:49650644 original size:31 final size:31
Alignment explanation
Indices: 49650591--49650651 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
49650581 TATGGATATT
* *
49650591 TTTTTATTTTAGTTACTTAACTATTCAAAAG
1 TTTTTATTTAAGTTACTTAACTATTAAAAAG
*
49650622 TTTTTATTTAATTTA-TTAAACTATTAAAAA
1 TTTTTATTTAAGTTACTT-AACTATTAAAAA
49650652 ATCAATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTTTATTTAAGTTACTTAACTATTAAAAAG
Found at i:49652768 original size:33 final size:34
Alignment explanation
Indices: 49652726--49652791 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
49652716 GTATTATTTT
49652726 AATTACTTATTAT-ATTTTTTTAAGGTTAACTCA
1 AATTACTTATTATAATTTTTTTAAGGTTAACTCA
49652759 AATTACTTATTATAAATTTTTTTAAGGTTAACT
1 AATTACTTATTAT-AATTTTTTTAAGGTTAACT
49652792 TAACACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 13 0.42
35 18 0.58
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (34 bp):
AATTACTTATTATAATTTTTTTAAGGTTAACTCA
Found at i:49653277 original size:29 final size:30
Alignment explanation
Indices: 49653232--49653321 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
49653222 TTGTAAGTAT
*
49653232 TGTTCTAGGAAAAATAATTTTGACAAGATAG
1 TGTTCT-GAAAAAATAATTTTGACAAGATAG
* ***
49653263 -GTTCTGAAAAAATAAATTTGATGTGAT-G
1 TGTTCTGAAAAAATAATTTTGACAAGATAG
* *
49653291 TGTTTTGAAAAAAAATATTTTGACAAGATAG
1 TGTTCTGAAAAAATA-ATTTTGACAAGATAG
49653322 ATTTTTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
28 1 0.02
29 29 0.64
30 14 0.31
31 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.34
Consensus pattern (30 bp):
TGTTCTGAAAAAATAATTTTGACAAGATAG
Found at i:49653455 original size:59 final size:59
Alignment explanation
Indices: 49653362--49653565 Score: 336
Period size: 59 Copynumber: 3.4 Consensus size: 59
49653352 CATAGTCAAT
* **
49653362 AATATATTTGTACAAAAGTATTCAAAAGAACTTCTATTTTATTAAATGAGGCAATATTAA
1 AATA-ATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
* *
49653422 AATAATTTGTACAAAATTATTCAAAAGAACTTCTATTGTATTAAATGAAACAATATTAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
* *
49653481 AATAATTTGTACAAAAATATTTAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
49653540 AATAATTTGTACAAAAATATTCAAAA
1 AATAATTTGTACAAAAATATTCAAAA
49653566 ATAAAACAAT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 131 0.97
60 4 0.03
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (59 bp):
AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
Found at i:49657302 original size:25 final size:27
Alignment explanation
Indices: 49657274--49657330 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
49657264 CTAATTATCA
49657274 CATAAG-GA-CCTCCACTTTAATATTT
1 CATAAGCGATCCTCCACTTTAATATTT
*
49657299 CAT-AGCTATTTCCTCCACTTTAATATTT
1 CATAAGCGA--TCCTCCACTTTAATATTT
49657327 CATA
1 CATA
49657331 GCTATTAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.08
25 4 0.15
28 20 0.77
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (27 bp):
CATAAGCGATCCTCCACTTTAATATTT
Found at i:49657313 original size:28 final size:28
Alignment explanation
Indices: 49657282--49657336 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
49657272 CACATAAGGA
49657282 CCTCCACTTTAATATTTCATAGCTATTT
1 CCTCCACTTTAATATTTCATAGCTATTT
49657310 CCTCCACTTTAATATTTCATAGCTATT
1 CCTCCACTTTAATATTTCATAGCTATT
49657337 AGACACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.45
Consensus pattern (28 bp):
CCTCCACTTTAATATTTCATAGCTATTT
Found at i:49662258 original size:28 final size:29
Alignment explanation
Indices: 49662194--49662258 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
49662184 TTCACATTTA
* *
49662194 TTTCACAATTTAACCCCTCAATTTACACT
1 TTTCTCAATTTAACCCCTCAATTGACACT
* * *
49662223 TTTCTCAATTTAA-TCCTTAATTGACATT
1 TTTCTCAATTTAACCCCTCAATTGACACT
*
49662251 TTTGTCAA
1 TTTCTCAA
49662259 AAATCACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTCTCAATTTAACCCCTCAATTGACACT
Found at i:49672731 original size:28 final size:29
Alignment explanation
Indices: 49672666--49672731 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
49672656 ACAGCCCATA
* *
49672666 TTTTCACAATTTAACCTCTCAATTTACAC
1 TTTTCTCAATTTAACCTCTCAATTGACAC
*
49672695 TTTTCTCAATTTAATCCT-T-AATTGACAT
1 TTTTCTCAATTTAA-CCTCTCAATTGACAC
*
49672723 TTTTGTCAA
1 TTTTCTCAA
49672732 AAATCACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 15 0.47
29 14 0.44
30 3 0.09
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTTCTCAATTTAACCTCTCAATTGACAC
Found at i:49682612 original size:27 final size:27
Alignment explanation
Indices: 49682580--49682720 Score: 164
Period size: 27 Copynumber: 5.2 Consensus size: 27
49682570 AGGAAGCGTC
* *
49682580 CTGGTGGTTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
49682607 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
49682633 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
* *
49682661 CTGGTGGCTCTGTCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
49682688 TTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
49682715 CTGGTG
1 CTGGTG
49682721 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
26 11 0.11
27 82 0.85
28 4 0.04
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:49682730 original size:54 final size:54
Alignment explanation
Indices: 49682577--49682738 Score: 231
Period size: 54 Copynumber: 3.0 Consensus size: 54
49682567 TGGAGGAAGC
* *
49682577 GTCCTGGTGGTTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
49682631 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
** * *
49682685 GTTTTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACT-TCGTCACA-ATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTCT-GTCACATATATCT
49682738 G
1 G
49682739 GCAGCTTCGC
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
53 14 0.14
54 86 0.86
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCT
Found at i:49682731 original size:27 final size:27
Alignment explanation
Indices: 49682593--49682738 Score: 149
Period size: 27 Copynumber: 5.4 Consensus size: 27
49682583 GTGGTTATGC
*
49682593 CACAATTATCTG-ATCTGGTGGCTCTGC
1 CACAA-TATCTGTATCTGGTGGCTCTGT
* * *
49682620 CACATATATCTGT-CCTGGTGGCTATGC
1 CACA-ATATCTGTATCTGGTGGCTCTGT
49682647 CACAATTATCTG-ATCTGGTGGCTCTGT
1 CACAA-TATCTGTATCTGGTGGCTCTGT
* *
49682674 CACATATATCTGT-TTTGGTGGCTCTGC
1 CACA-ATATCTGTATCTGGTGGCTCTGT
*
49682701 CACAATATCTGTATCTGGTGACT-TCGT
1 CACAATATCTGTATCTGGTGGCTCT-GT
49682728 CACAATATCTG
1 CACAATATCTG
49682739 GCAGCTTCGC
Statistics
Matches: 101, Mismatches: 10, Indels: 16
0.80 0.08 0.13
Matches are distributed among these distances:
26 10 0.10
27 89 0.88
28 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
CACAATATCTGTATCTGGTGGCTCTGT
Found at i:49684705 original size:49 final size:49
Alignment explanation
Indices: 49684644--49684744 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
49684634 TTGTCAAAAG
* *
49684644 TCACTTTACAAATGTTGTTTATCTAACAACAAGCATACATTTTCTATTA
1 TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
49684693 TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
1 TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
49684742 TCA
1 TCA
49684745 AACATCAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (49 bp):
TCACTTTACAAATGTTGTTTACCTAACAACAAGCATACATTTTCTATCA
Found at i:49686339 original size:16 final size:17
Alignment explanation
Indices: 49686313--49686348 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
49686303 TATCCAATTA
49686313 TTTTGAATTTTTTGATG
1 TTTTGAATTTTTTGATG
*
49686330 TTTT-AATTTTTTGGTG
1 TTTTGAATTTTTTGATG
49686346 TTT
1 TTT
49686349 CTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (17 bp):
TTTTGAATTTTTTGATG
Found at i:49691445 original size:27 final size:27
Alignment explanation
Indices: 49691414--49691467 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
49691404 AACAGAAAGG
49691414 CTAAAACTAACTAATCATGAAGAAGTT
1 CTAAAACTAACTAATCATGAAGAAGTT
49691441 CTAAAACTAACTAATCATGAAGAAGTT
1 CTAAAACTAACTAATCATGAAGAAGTT
49691468 AAATATAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (27 bp):
CTAAAACTAACTAATCATGAAGAAGTT
Found at i:49692898 original size:15 final size:15
Alignment explanation
Indices: 49692878--49692907 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49692868 AAAATTTGAT
*
49692878 TCGAGTTGAATTAAA
1 TCGAGTTAAATTAAA
49692893 TCGAGTTAAATTAAA
1 TCGAGTTAAATTAAA
49692908 ATAATTGAAC
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:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (15 bp):
TCGAGTTAAATTAAA
Found at i:49693736 original size:17 final size:17
Alignment explanation
Indices: 49693710--49693744 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
49693700 CCTAATTGTA
49693710 AAAAACTAAAAATATAT
1 AAAAACTAAAAATATAT
* *
49693727 AAAAATTAAAATTATAT
1 AAAAACTAAAAATATAT
49693744 A
1 A
49693745 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAACTAAAAATATAT
Found at i:49694232 original size:16 final size:16
Alignment explanation
Indices: 49694211--49694245 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
49694201 TATTAGCAAT
49694211 AATCTCCAAAATAAAA
1 AATCTCCAAAATAAAA
49694227 AATCTCCAAAATAAAA
1 AATCTCCAAAATAAAA
49694243 AAT
1 AAT
49694246 GCTAAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (16 bp):
AATCTCCAAAATAAAA
Found at i:49697487 original size:20 final size:20
Alignment explanation
Indices: 49697462--49697505 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
49697452 AAGGACTAAA
* *
49697462 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
49697482 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
49697502 ATGA
1 ATGA
49697506 TTACATTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:49701183 original size:22 final size:22
Alignment explanation
Indices: 49701158--49701211 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
49701148 TATAAGTAAA
*
49701158 TATTATTTTATTATT-AAATTGT
1 TATTATATTA-TATTAAAATTGT
*
49701180 TATTATATTATATTAAAATTTT
1 TATTATATTATATTAAAATTGT
49701202 TATTATATTA
1 TATTATATTA
49701212 ATATAAGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTATATTATATTAAAATTGT
Found at i:49701306 original size:13 final size:13
Alignment explanation
Indices: 49701288--49701312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49701278 AAAGAGTCAG
49701288 ATATTAATATATA
1 ATATTAATATATA
49701301 ATATTAATATAT
1 ATATTAATATAT
49701313 GGAAAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTAATATATA
Found at i:49701511 original size:15 final size:13
Alignment explanation
Indices: 49701464--49701503 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
49701454 AAATGGAATT
49701464 GAAACGAAAAGAGA
1 GAAAC-AAAAGAGA
49701478 GAAACAAAAGAGA
1 GAAACAAAAGAGA
49701491 GAAACAAAAGAGA
1 GAAACAAAAGAGA
49701504 AAGAAACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (13 bp):
GAAACAAAAGAGA
Found at i:49702503 original size:37 final size:38
Alignment explanation
Indices: 49702387--49702503 Score: 110
Period size: 37 Copynumber: 3.0 Consensus size: 38
49702377 TGTTCATGGA
* *
49702387 TACTTCGACCTTGAGTCGATGAGACACTAGGAGTCATACTGT
1 TACTTCG-GCTTGAGTCGATGAGACACTAGGTGTCA-AC--T
* * * * **
49702429 TACTTCGGATAGATTCGATGAGGCACTAGGTACCAACT
1 TACTTCGGCTTGAGTCGATGAGACACTAGGTGTCAACT
*
49702467 TACTTCGGCTTG-GTCGATGAGACACTGGGTGTCAACT
1 TACTTCGGCTTGAGTCGATGAGACACTAGGTGTCAACT
49702504 ATTGCTTCGA
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
37 20 0.33
38 11 0.18
40 2 0.03
41 20 0.33
42 7 0.12
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (38 bp):
TACTTCGGCTTGAGTCGATGAGACACTAGGTGTCAACT
Found at i:49703913 original size:25 final size:25
Alignment explanation
Indices: 49703884--49703935 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
49703874 ATGGTAAAAG
** *
49703884 GTTATTGCTTTTTGATTAACTTGAT
1 GTTATTGCCATTTGATGAACTTGAT
*
49703909 GTTATTGCCATTTGATGAATTTGAT
1 GTTATTGCCATTTGATGAACTTGAT
49703934 GT
1 GT
49703936 GATCTTGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (25 bp):
GTTATTGCCATTTGATGAACTTGAT
Found at i:49707665 original size:38 final size:38
Alignment explanation
Indices: 49707623--49707699 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
49707613 TTATCAAGGT
*
49707623 ATGAAAATAGGCCATAGATTTATCATGCTTGAAATTAG
1 ATGAAAATAGGCCATAGATTTATCATGCTCGAAATTAG
* *
49707661 ATGAAAATAGGCCATGGATTTATTATGCTCGAAATTAG
1 ATGAAAATAGGCCATAGATTTATCATGCTCGAAATTAG
49707699 A
1 A
49707700 AATTTATAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (38 bp):
ATGAAAATAGGCCATAGATTTATCATGCTCGAAATTAG
Found at i:49717828 original size:15 final size:14
Alignment explanation
Indices: 49717804--49717834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
49717794 GGAGAAATTA
49717804 TTTTTAATATTATT
1 TTTTTAATATTATT
49717818 TTTTTATATATTATT
1 TTTTTA-ATATTATT
49717833 TT
1 TT
49717835 ATGTGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTAATATTATT
Found at i:49719016 original size:48 final size:47
Alignment explanation
Indices: 49718964--49719351 Score: 292
Period size: 48 Copynumber: 7.9 Consensus size: 47
49718954 GTGTGCTAGT
*
49718964 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATT-ATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG--CGCATTGATGAGA
* *
49719012 GCTAGTGTAAGACCATGTTTGAGACATGGCATCG-GCATTGA-GACAAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTGATG---AGA
49719060 GCTAGTGTAAGACCATGTCTGGGACATGGCATCCAGACATGGCATTGGCATTGAGACTAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCAT-C-G-C---GCATT-G-A-T--G---AGA
* * * *
49719121 GCTAGTGTAAGACCATGTCTGTGACATGGCATCG-GCCTCGACATGTGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTG--ATGAGA
* * * *
49719169 GCCAGTGTAAGACCATGTTTGGGACATGGCATTG-GCATTGAGATAAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATT--GATGAGA
** *
49719217 GCTAGTGTAAGACCATGTCTAGTTA-ATGGCATCG-GCATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCT-GGGACATGGCATCGCGCATT--GATGAGA
* *
49719265 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG-GCCTCGACATGTA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTG--ATG-AGA
*
49719313 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG-GCATT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATT
49719352 TTACCCTATT
Statistics
Matches: 282, Mismatches: 33, Indels: 50
0.77 0.09 0.14
Matches are distributed among these distances:
45 5 0.02
46 2 0.01
47 2 0.01
48 213 0.76
49 4 0.01
50 2 0.01
51 1 0.00
53 2 0.01
54 5 0.02
55 5 0.02
56 1 0.00
57 1 0.00
59 1 0.00
60 1 0.00
61 37 0.13
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCGCATTGATGAGA
Found at i:49719128 original size:61 final size:61
Alignment explanation
Indices: 49719033--49719153 Score: 215
Period size: 61 Copynumber: 2.0 Consensus size: 61
49719023 ACCATGTTTG
49719033 AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCC
1 AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCC
* * *
49719094 AGACATGGCATTGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATC
1 AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
49719154 GGCCTCGACA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (61 bp):
AGACATGGCATCGGCATTGAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCC
Found at i:49719272 original size:96 final size:95
Alignment explanation
Indices: 49719095--49719351 Score: 329
Period size: 96 Copynumber: 2.7 Consensus size: 95
49719085 ATGGCATCCA
* *
49719095 GACATGGCATTGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCCTC
1 GACATGGCATTGGCATTGAGA-TAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCATT
* * *
49719160 GACATGTGAGCCAGTGTAAGACCATGTTTGG
65 GACACGAGAGCCAGTGTAAGACCATGTCTGG
*
49719191 GACATGGCATTGGCATTGAGATAAGAGCTAGTGTAAGACCATGTCTAGTTA-ATGGCATCGGCAT
1 GACATGGCATTGGCATTGAGAT-AGAGCTAGTGTAAGACCATGTCT-GTGACATGGCATCGGCAT
* *
49719255 TGAGACGAGAGCTAGTGTAAGACCATGTCTGG
64 TGACACGAGAGCCAGTGTAAGACCATGTCTGG
* * * * * *
49719287 GACATGGCATCGGCCTCGACAT-GTAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 GACATGGCATTGGCATTGAGATAG--AGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCAT
49719351 T
64 T
49719352 TTACCCTATT
Statistics
Matches: 141, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
94 1 0.01
95 3 0.02
96 134 0.95
97 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
GACATGGCATTGGCATTGAGATAGAGCTAGTGTAAGACCATGTCTGTGACATGGCATCGGCATTG
ACACGAGAGCCAGTGTAAGACCATGTCTGG
Found at i:49730384 original size:94 final size:93
Alignment explanation
Indices: 49730223--49730393 Score: 209
Period size: 94 Copynumber: 1.8 Consensus size: 93
49730213 ATACTGACGC
* ** * *
49730223 CATGTCCCAGACACGTCTTACACTGGCTTGTATATCGCGAGGGATTTGCATGTCCCAAACATGTC
1 CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCGCGAGGGA-TCGCATGTCCCAAACATATC
49730288 TTACACTAGCTCTCGTCTCAATGCTGATG
65 TTACACTAGCTCTCGTCTCAATGCTGATG
* * * *
49730317 CATGTCCCAGACAAGTCTTATACTGGCTTAAATATCTCGAGGCCGA-CGCATGTCCGAGACATAT
1 CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCGCGAGG--GATCGCATGTCCCAAACATAT
* *
49730381 CTTATACTGGCTC
64 CTTACACTAGCTC
49730394 CTATACTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
94 62 0.97
96 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (93 bp):
CATGTCCCAGACAAGTCTTACACTGGCTTAAATATCGCGAGGGATCGCATGTCCCAAACATATCT
TACACTAGCTCTCGTCTCAATGCTGATG
Found at i:49730430 original size:46 final size:48
Alignment explanation
Indices: 49730269--49730430 Score: 127
Period size: 46 Copynumber: 3.5 Consensus size: 48
49730259 GCGAGGGATT
* * * * *
49730269 TGCATGTCCCAAACATGTCTTACACTAGCTC---TCGTCTCAATGCTGA
1 TGCATGTCCCAGACATGTCTTATACTGGCTCAAAT-ATCTCGATGCTGA
* * * *
49730315 TGCATGTCCCAGACAAGTCTTATACTGGCTTAAATATCTCGAGGCCGA
1 TGCATGTCCCAGACATGTCTTATACTGGCTCAAATATCTCGATGCTGA
* * * ** *
49730363 CGCATGTCCGAGACATATCTTATACTGGCTCCTATA-CT-GTTGCTGA
1 TGCATGTCCCAGACATGTCTTATACTGGCTCAAATATCTCGATGCTGA
* *
49730409 TGCATGTCCTAGCCATGTCTTA
1 TGCATGTCCCAGACATGTCTTA
49730431 CACTAGCACA
Statistics
Matches: 90, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
46 49 0.54
47 2 0.02
48 38 0.42
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (48 bp):
TGCATGTCCCAGACATGTCTTATACTGGCTCAAATATCTCGATGCTGA
Found at i:49736707 original size:21 final size:20
Alignment explanation
Indices: 49736678--49736716 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
49736668 TCCTGTAACA
49736678 GGGCACATGCCCGTGTGGAT
1 GGGCACATGCCCGTGTGGAT
49736698 GGGCAACATGCCCGTGTGG
1 GGGC-ACATGCCCGTGTGG
49736717 TCATTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (20 bp):
GGGCACATGCCCGTGTGGAT
Found at i:49738009 original size:48 final size:48
Alignment explanation
Indices: 49737952--49738120 Score: 191
Period size: 48 Copynumber: 3.6 Consensus size: 48
49737942 AAGCTGACGC
* **
49737952 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAGG-TCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCT-GATG
* * *
49738000 CATGTCCCAGACATGTCTTATACTGGCTTAAATATCTCGAGGCTGACG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCTGATG
* * * *** *
49738048 CATGTCCCAGACTTGTCTTACACTGGATCCCATA-CT-GTGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCTGATG
49738094 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
49738121 ACACACCTCA
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
46 32 0.31
47 2 0.02
48 68 0.66
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTCGAGGCTGATG
Found at i:49739641 original size:28 final size:27
Alignment explanation
Indices: 49739600--49739698 Score: 74
Period size: 28 Copynumber: 3.6 Consensus size: 27
49739590 AATGTGGCAG
* *
49739600 AAAAAGATAAAAAAAATTTAAATTAAT
1 AAAAATATTAAAAAAATTTAAATTAAT
* **
49739627 AAAAATTATT-AAAAAATATAGAAAAATAT
1 AAAAA-TATTAAAAAAATTTA-AATTA-AT
* * * *
49739656 AAAAATATTAAAAATATTAAAAATTTAG
1 AAAAATATTAAAAAAATT-TAAATTAAT
49739684 AAAAATATTAAAAAA
1 AAAAATATTAAAAAA
49739699 TAAAATATAT
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
27 14 0.26
28 24 0.44
29 15 0.28
30 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAAATATTAAAAAAATTTAAATTAAT
Found at i:49739641 original size:37 final size:37
Alignment explanation
Indices: 49739600--49739713 Score: 103
Period size: 36 Copynumber: 3.1 Consensus size: 37
49739590 AATGTGGCAG
* *
49739600 AAAAAGATA-AAAAAAAT-TTAAATTAATAAAAATTATT
1 AAAAA-ATATAAAAAAATATAAAAATAATAAAAA-TATT
* *
49739637 AAAAAATATAGAAAAATATAAAAATATTAAAAATATT
1 AAAAAATATAAAAAAATATAAAAATAATAAAAATATT
* * *
49739674 -AAAAATTTAGAAAAATATTAAAA-AAT-AAAATATAT
1 AAAAAATATAAAAAAATATAAAAATAATAAAAATAT-T
49739709 AAAAA
1 AAAAA
49739714 TGTAGAAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
34 7 0.11
35 3 0.05
36 28 0.42
37 16 0.24
38 12 0.18
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (37 bp):
AAAAAATATAAAAAAATATAAAAATAATAAAAATATT
Found at i:49739651 original size:9 final size:8
Alignment explanation
Indices: 49739638--49739714 Score: 66
Period size: 9 Copynumber: 8.8 Consensus size: 8
49739628 AAAATTATTA
49739638 AAAAATAT
1 AAAAATAT
49739646 AGAAAAATAT
1 --AAAAATAT
49739656 AAAAATATT
1 AAAAATA-T
49739665 AAAAATATT
1 AAAAATA-T
*
49739674 AAAAATTTAG
1 AAAAA--TAT
49739684 AAAAATATT
1 AAAAATA-T
49739693 AAAAA-AT
1 AAAAATAT
49739700 AAAATATAT
1 AAAA-ATAT
49739709 AAAAAT
1 AAAAAT
49739715 GTAGAAAGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
7 5 0.08
8 13 0.22
9 26 0.44
10 13 0.22
11 2 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:49739685 original size:36 final size:35
Alignment explanation
Indices: 49739611--49739755 Score: 125
Period size: 37 Copynumber: 4.0 Consensus size: 35
49739601 AAAAGATAAA
*
49739611 AAAAAT-TTAAATTAATAAAAATTATTAAAAAATATAG
1 AAAAATATTAAA-AAATAAAAA-TATT-AAAAATATAG
*
49739648 AAAAATA-TAAAAATATTAAAAATATTAAAAATTTAG
1 AAAAATATTAAAAA-A-TAAAAATATTAAAAATATAG
*
49739684 AAAAATATTAAAAAAT-AAAATATATAAAAATGTAG
1 AAAAATATTAAAAAATAAAAATAT-TAAAAATATAG
** * *
49739719 AAAGTTCATTAACAATATAAAAAAATTTAAAAATATA
1 AAAAAT-ATTAA-AAAATAAAAATA-TTAAAAATATA
49739756 AATTTATACG
Statistics
Matches: 91, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
34 7 0.08
35 15 0.16
36 23 0.25
37 25 0.27
38 20 0.22
39 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (35 bp):
AAAAATATTAAAAAATAAAAATATTAAAAATATAG
Found at i:49739687 original size:10 final size:10
Alignment explanation
Indices: 49739626--49739700 Score: 81
Period size: 10 Copynumber: 7.9 Consensus size: 10
49739616 TTTAAATTAA
*
49739626 TAAAAATTAT
1 TAAAAAATAT
49739636 TAAAAAATA-
1 TAAAAAATAT
49739645 TAGAAAAATA-
1 TA-AAAAATAT
49739655 T-AAAAATAT
1 TAAAAAATAT
49739664 T-AAAAATAT
1 TAAAAAATAT
49739673 T-AAAAAT-T
1 TAAAAAATAT
49739681 TAGAAAAATAT
1 TA-AAAAATAT
49739692 TAAAAAATA
1 TAAAAAATA
49739701 AAATATATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
8 9 0.15
9 18 0.31
10 29 0.49
11 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:49739713 original size:10 final size:10
Alignment explanation
Indices: 49739625--49739714 Score: 74
Period size: 10 Copynumber: 9.8 Consensus size: 10
49739615 ATTTAAATTA
49739625 ATAAAAAT-T
1 ATAAAAATAT
49739634 ATTAAAAA-AT
1 A-TAAAAATAT
49739644 ATAGAAAA-AT
1 ATA-AAAATAT
49739654 ATAAAAATAT
1 ATAAAAATAT
49739664 -TAAAAATAT
1 ATAAAAATAT
*
49739673 -TAAAAATTT
1 ATAAAAATAT
*
49739682 AGAAAAATAT
1 ATAAAAATAT
49739692 -T-AAAA-A-
1 ATAAAAATAT
49739698 AT-AAAATAT
1 ATAAAAATAT
49739707 ATAAAAAT
1 ATAAAAAT
49739715 GTAGAAAGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
7 6 0.09
8 5 0.07
9 26 0.38
10 31 0.46
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:49739756 original size:18 final size:18
Alignment explanation
Indices: 49739609--49739757 Score: 81
Period size: 18 Copynumber: 8.2 Consensus size: 18
49739599 GAAAAAGATA
49739609 AAAAAAATTTAAATTAATA-
1 AAAAAAATTTAAA--AATAT
** *
49739628 AAAATTATTAAAAAATAT
1 AAAAAAATTTAAAAATAT
* *
49739646 AGAAAAATATAAAAATAT
1 AAAAAAATTTAAAAATAT
* *
49739664 -TAAAAATATTAAAAATTT
1 AAAAAAAT-TTAAAAATAT
*
49739682 AGAAAAATATTAAAAA-AT
1 AAAAAAAT-TTAAAAATAT
* * *
49739700 -AAAATATATAAAAATGT
1 AAAAAAATTTAAAAATAT
* ** *
49739717 AGAAAGTTCATTAACAATAT
1 AAAAAAAT--TTAAAAATAT
49739737 AAAAAAATTTAAAAATAT
1 AAAAAAATTTAAAAATAT
49739755 AAA
1 AAA
49739758 TTTATACGAT
Statistics
Matches: 96, Mismatches: 27, Indels: 15
0.70 0.20 0.11
Matches are distributed among these distances:
16 6 0.06
17 16 0.17
18 38 0.40
19 24 0.25
20 12 0.12
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAAAATTTAAAAATAT
Found at i:49739885 original size:11 final size:12
Alignment explanation
Indices: 49739862--49739893 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
49739852 ACATAGGGAA
49739862 ATATAAAAA-TT
1 ATATAAAAATTT
49739873 AT-TAAAAATTT
1 ATATAAAAATTT
49739884 ATATAAAAAT
1 ATATAAAAAT
49739894 ATAGAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.32
11 6 0.32
12 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAAAAATTT
Found at i:49739943 original size:10 final size:10
Alignment explanation
Indices: 49739930--49739962 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
49739920 TAAATTATGG
49739930 AAAATATTAAA
1 AAAAT-TTAAA
49739941 AAAATTTAAA
1 AAAATTTAAA
49739951 AAAATTTAAA
1 AAAATTTAAA
49739961 AA
1 AA
49739963 GTTATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:49740101 original size:19 final size:18
Alignment explanation
Indices: 49740041--49740100 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
49740031 TTTTTAGTAA
49740041 ATTTTT-ATAATTTTTAT
1 ATTTTTAATAATTTTTAT
*
49740058 ACTTTTAATAATTTATTAT
1 ATTTTTAATAATTT-TTAT
*
49740077 ATTTTTAATAACTTTTAT
1 ATTTTTAATAATTTTTAT
49740095 ATTTTT
1 ATTTTT
49740101 TTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.13
18 17 0.45
19 16 0.42
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTAATAATTTTTAT
Found at i:49740176 original size:9 final size:9
Alignment explanation
Indices: 49740040--49740100 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
49740030 GTTTTTAGTA
49740040 AATTTTTAT
1 AATTTTTAT
49740049 AATTTTTAT
1 AATTTTTAT
* *
49740058 ACTTTTAAT
1 AATTTTTAT
49740067 AATTTATTAT
1 AATTT-TTAT
49740077 -ATTTTTAAT
1 AATTTTT-AT
*
49740086 AACTTTTAT
1 AATTTTTAT
49740095 -ATTTTT
1 AATTTTT
49740101 TTTCTAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
8 7 0.16
9 28 0.65
10 8 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:49744349 original size:3 final size:3
Alignment explanation
Indices: 49744341--49744369 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
49744331 TTGAATTATG
49744341 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49744370 TGTAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:49752570 original size:41 final size:41
Alignment explanation
Indices: 49752521--49752706 Score: 203
Period size: 41 Copynumber: 4.5 Consensus size: 41
49752511 AAATGTAAAC
** *
49752521 AGGGGCATGTATATGTTATTCAAGGGTACCGAAGTACAAAT
1 AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
* * * *
49752562 AGGTGCATGTATATGCAATTTAAGGGTACAAAAGTACAAAC
1 AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
* * *
49752603 AGGGGCATGTATGTGCAATACAGGGGTACCAAAGTACAAAT
1 AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
* * * *
49752644 AGGGGCACGTATGTGCAATTTAAGGGTACTGAAA-TACAAAT
1 AGGGGCATGTATATGCAATTCAAGGGTAC-CAAAGTACAAAT
** *
49752685 AGGGGCACATATGTGCAATTCA
1 AGGGGCATGTATATGCAATTCA
49752707 GGCTATAATT
Statistics
Matches: 123, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
41 120 0.98
42 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (41 bp):
AGGGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAAT
Found at i:49752661 original size:82 final size:82
Alignment explanation
Indices: 49752517--49752708 Score: 251
Period size: 82 Copynumber: 2.3 Consensus size: 82
49752507 ATCGAAATGT
* ** * * * *
49752517 AAACAGGGGCATGTATATGTTATTCAAGGGTACCGAAGTACAAATAGGTGCATGTATATGCAATT
1 AAACAGGGGCATGTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATATGCAATT
49752582 TAAGGGTAC-AAAAGTAC
66 TAAGGGTACTAAAA-TAC
* *
49752599 AAACAGGGGCATGTATGTGCAATACAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATT
1 AAACAGGGGCATGTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATATGCAATT
*
49752664 TAAGGGTACTGAAATAC
66 TAAGGGTACTAAAATAC
* **
49752681 AAATAGGGGCACATATGTGCAATTCAGG
1 AAACAGGGGCATGTATGTGCAATTCAGG
49752709 CTATAATTAA
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
82 92 0.97
83 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.23
Consensus pattern (82 bp):
AAACAGGGGCATGTATGTGCAATTCAGGGGTACCAAAGTACAAATAGGGGCACGTATATGCAATT
TAAGGGTACTAAAATAC
Found at i:49763924 original size:20 final size:20
Alignment explanation
Indices: 49763882--49763928 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
49763872 TAGAGACATA
* *
49763882 GGCGTGTCCCAAGCCATATG
1 GGCGTGTCCCAAGCCACACG
*
49763902 GGCGTGTCCCAAGCCGCACG
1 GGCGTGTCCCAAGCCACACG
49763922 GGCGTGT
1 GGCGTGT
49763929 GACCCCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17
Consensus pattern (20 bp):
GGCGTGTCCCAAGCCACACG
Found at i:49767248 original size:12 final size:12
Alignment explanation
Indices: 49767231--49767260 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49767221 AATATTATAC
49767231 ATATATATGCAT
1 ATATATATGCAT
49767243 ATATATATGCAT
1 ATATATATGCAT
*
49767255 ACATAT
1 ATATAT
49767261 GTGTGATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (12 bp):
ATATATATGCAT
Found at i:49770394 original size:16 final size:16
Alignment explanation
Indices: 49770363--49770407 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
49770353 AAATATCGTA
49770363 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
49770377 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
49770393 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
49770408 CTTGATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:49770405 original size:17 final size:16
Alignment explanation
Indices: 49770361--49770407 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
49770351 ATAAATATCG
49770361 TAAATTAATTT-T-AAT
1 TAAA-TAATTTCTCAAT
*
49770376 TAATTAATTTCTCAAT
1 TAAATAATTTCTCAAT
49770392 TAAATAATTTTCTCAA
1 TAAATAA-TTTCTCAA
49770408 CTTGATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 9 0.33
17 8 0.30
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATAATTTCTCAAT
Found at i:49779854 original size:47 final size:47
Alignment explanation
Indices: 49779535--49780004 Score: 293
Period size: 47 Copynumber: 10.0 Consensus size: 47
49779525 TAATATACGA
49779535 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
* ** * *
49779582 GTATCAG-CCACATT-ATGA-GA--GCCAGTGTAAGACCATGTCCGGGACAT
1 G--GC-GTCGGCATTGA-GACGAGTGCTAGTGTAAGA-CATGTCTGGGACAT
49779629 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
* ** * *
49779676 GTATCAG-CCACATT-ATGA-GA--GCCAGTGTAAGACCATGTCCGGGACAT
1 G--GC-GTCGGCATTGA-GACGAGTGCTAGTGTAAGA-CATGTCTGGGACAT
49779723 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
* ** * *
49779770 GTATCAG-CCACATT-ATGA-GA--GCCAGTGTAAGACCATGTCCGGGACAT
1 G--GC-GTCGGCATTGA-GACGAGTGCTAGTGTAAGA-CATGTCTGGGACAT
49779817 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
* ** * * * * * *
49779864 -GCATTAGCCTCGAGATGTA-AGCTAGTGTAAAACATGTATGGGACAT
1 GGCGTCGGCATTGAGACG-AGTGCTAGTGTAAGACATGTCTGGGACAT
* * * *
49779910 -GCTTCGGC-TACGAGATGA-TAG-TCAGAGTAAGACCATGTCTGGGACAT
1 GGCGTCGGCAT-TGAGACGAGT-GCT-AGTGTAAGA-CATGTCTGGGACAT
* * * *
49779957 GGCATC-GAATTGAGA-TATGAGCTAGTGTAAGACCATGTCTGGGACAT
1 GGCGTCGGCATTGAGACGA-GTGCTAGTGTAAGA-CATGTCTGGGACAT
49780004 G
1 G
49780005 ACATCATCAC
Statistics
Matches: 331, Mismatches: 52, Indels: 80
0.71 0.11 0.17
Matches are distributed among these distances:
44 3 0.01
45 27 0.08
46 98 0.30
47 128 0.39
48 48 0.15
49 24 0.07
50 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (47 bp):
GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACAT
Found at i:49779893 original size:94 final size:94
Alignment explanation
Indices: 49779535--49779864 Score: 660
Period size: 94 Copynumber: 3.5 Consensus size: 94
49779525 TAATATACGA
49779535 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
49779600 GAGCCAGTGTAAGACCATGTCCGGGACAT
66 GAGCCAGTGTAAGACCATGTCCGGGACAT
49779629 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
49779694 GAGCCAGTGTAAGACCATGTCCGGGACAT
66 GAGCCAGTGTAAGACCATGTCCGGGACAT
49779723 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
49779788 GAGCCAGTGTAAGACCATGTCCGGGACAT
66 GAGCCAGTGTAAGACCATGTCCGGGACAT
49779817 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATG
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATG
49779865 CATTAGCCTC
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 236 1.00
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (94 bp):
GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
GAGCCAGTGTAAGACCATGTCCGGGACAT
Found at i:49779893 original size:188 final size:187
Alignment explanation
Indices: 49779535--49779910 Score: 639
Period size: 188 Copynumber: 2.0 Consensus size: 187
49779525 TAATATACGA
49779535 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
49779600 GAGCCAGTGTAAGACCATGTCCGGGACATGGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACAT
66 GAGCCAGTGTAAGACCATGTCCGGGACATGGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACAT
* * * *
49779665 GTCTGGGACATGTATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTCCGGGACAT
131 GTCTGGGACATGCATCAGCCACATGATGAGAGCCAGTGTAA-AACATGTACGGGACAT
49779723 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
1 GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
49779788 GAGCCAGTGTAAGACCATGTCCGGGACATGGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACAT
66 GAGCCAGTGTAAGACCATGTCCGGGACATGGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACAT
* * * *
49779853 GTCTGGGACATGCATTAGCCTCGA-GATGTA-AGCTAGTGTAAAACATGTATGGGACAT
131 GTCTGGGACATGCATCAGCCAC-ATGATG-AGAGCCAGTGTAAAACATGTACGGGACAT
49779910 G
1 G
49779911 CTTCGGCTAC
Statistics
Matches: 178, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
187 14 0.08
188 162 0.91
189 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (187 bp):
GGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGA
GAGCCAGTGTAAGACCATGTCCGGGACATGGCGTCGGCATTGAGACGAGTGCTAGTGTAAGACAT
GTCTGGGACATGCATCAGCCACATGATGAGAGCCAGTGTAAAACATGTACGGGACAT
Found at i:49779940 original size:140 final size:140
Alignment explanation
Indices: 49779744--49780004 Score: 341
Period size: 140 Copynumber: 1.9 Consensus size: 140
49779734 TGAGACGAGT
* * * *
49779744 GCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAAACATGTATGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGTC
* * *
49779809 CGGGACATGGCGTCGGCATTGAGACGA-GTGCTAGTGTAAGA-CATGTCTGGGACATGCATTAGC
66 CGGGACATGGCATC-GAATTGAGA-GATGAGCTAGTGTAAGACCATGTCTGGGACATGCATTAGC
49779872 CTCGAGATGTAA
129 CTCGAGATGTAA
* * * *
49779884 GCTAGTGTAAAACATGTATGGGACATGCT-TCGGCTACGA-GATGATAGTCAGAGTAAGACCATG
1 GCTAGTGTAAAACATGTATGGGACATG-TATCAGCCAC-ATGATGAGAGCCAGAGTAAGACCATG
* *
49779947 TCTGGGACATGGCATCGAATTGAGATATGAGCTAGTGTAAGACCATGTCTGGGACATG
64 TCCGGGACATGGCATCGAATTGAGAGATGAGCTAGTGTAAGACCATGTCTGGGACATG
49780005 ACATCATCAC
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
138 1 0.01
139 21 0.20
140 80 0.77
141 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (140 bp):
GCTAGTGTAAAACATGTATGGGACATGTATCAGCCACATGATGAGAGCCAGAGTAAGACCATGTC
CGGGACATGGCATCGAATTGAGAGATGAGCTAGTGTAAGACCATGTCTGGGACATGCATTAGCCT
CGAGATGTAA
Found at i:49780759 original size:41 final size:41
Alignment explanation
Indices: 49780712--49780820 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 41
49780702 CACGGGTAGA
*
49780712 CACACGGGCATGTGTCTAGGCCGTGTGTGACACAC-AGCCAGG
1 CACACGGGC-TGTGTC-AGGCCGTGTGAGACACACGAGCCAGG
* * ** *
49780754 -TCACGGGC-GTGTCGAGGCCGTGAGAGGGACACGGGCCAGG
1 CACACGGGCTGTGTC-AGGCCGTGTGAGACACACGAGCCAGG
49780794 CACACGGGCGTGTGTCAGGCCGTGTGA
1 CACACGGGC-TGTGTCAGGCCGTGTGA
49780821 AAACCACTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
39 19 0.35
40 6 0.11
41 14 0.26
42 10 0.19
43 5 0.09
ACGTcount: A:0.18, C:0.27, G:0.40, T:0.15
Consensus pattern (41 bp):
CACACGGGCTGTGTCAGGCCGTGTGAGACACACGAGCCAGG
Found at i:49785599 original size:18 final size:18
Alignment explanation
Indices: 49785576--49785617 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
49785566 AGGTATTTTT
*
49785576 GAAAGTTTCTCTGCGGAG
1 GAAAGTTTCTCCGCGGAG
*
49785594 GAAAGTTTCTCCGTGGAG
1 GAAAGTTTCTCCGCGGAG
49785612 GAAAGT
1 GAAAGT
49785618 CCTCAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.26
Consensus pattern (18 bp):
GAAAGTTTCTCCGCGGAG
Found at i:49787259 original size:46 final size:47
Alignment explanation
Indices: 49787201--49787370 Score: 158
Period size: 46 Copynumber: 3.6 Consensus size: 47
49787191 TCACTTGTGT
*
49787201 GAGCTAGTGTAAGACATGTCTGGGACATGTATCAGCCACATT-ATGA-
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGA-GAC
* * *
49787247 GAGCCAGTGTAAGACCATGTCCGGGACATGGCATC-G--GCATTGAGAC
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACATTGAGAC
* *
49787293 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-C-C-TCGAGAT
1 GA--GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAGAC
*
49787339 GTATGCTAGTGTAATACATGTCTGGGACATGC
1 G-A-GCTAGTGTAAGACATGTCTGGGACATGC
49787371 TTCGGCTACG
Statistics
Matches: 106, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
45 6 0.06
46 55 0.52
47 30 0.28
48 15 0.14
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAGAC
Done.