Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 157 of 373
Found at i:52263100 original size:13 final size:13
Alignment explanation
Indices: 52263084--52263116 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52263074 TTTAATTAAA
*
52263084 TTAGTTAATTAGT
1 TTAGATAATTAGT
52263097 TTAGATAATTAGT
1 TTAGATAATTAGT
52263110 TTA-ATAA
1 TTAGATAA
52263117 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:52268474 original size:5 final size:5
Alignment explanation
Indices: 52268448--52268540 Score: 68
Period size: 5 Copynumber: 17.8 Consensus size: 5
52268438 ATCCTCCTTT
52268448 TTTTA -TTTA TTCTTA TTTTTA TTTTA TTTTA TTTTA -TTTA TTTTTA
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
* *
52268494 TTTTTC TTTTGA TTTTTA TTTTCA TTTAAA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTT-A -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
52268541 GAAAGACATA
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
3 3 0.04
4 8 0.11
5 32 0.44
6 24 0.33
7 6 0.08
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:52268510 original size:7 final size:6
Alignment explanation
Indices: 52268453--52268520 Score: 66
Period size: 6 Copynumber: 11.2 Consensus size: 6
52268443 CCTTTTTTTA
* * *
52268453 TTTATT CTTATT TTTA-T TTTATT TTATTTT ATTTATT TTTATT TTTCTT
1 TTTATT TTTATT TTTATT TTTATT TT-TATT -TTTATT TTTATT TTTATT
* *
52268502 TTGATT TTTATT TTCATT T
1 TTTATT TTTATT TTTATT T
52268521 AAATTTTATT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
5 5 0.10
6 37 0.74
7 6 0.12
8 2 0.04
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:52268527 original size:18 final size:16
Alignment explanation
Indices: 52268447--52268521 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
52268437 AATCCTCCTT
* *
52268447 TTTTTATTTATTCTTA
1 TTTTCATTTATTTTTA
*
52268463 TTTTTATTT-TATTTTA
1 TTTTCATTTAT-TTTTA
52268479 TTTT-ATTTATTTTTA
1 TTTTCATTTATTTTTA
*
52268494 TTTTTCTTTTGATTTTTA
1 -TTTTCATTT-ATTTTTA
52268512 TTTTCATTTA
1 TTTTCATTTA
52268522 AATTTTATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
15 10 0.20
16 23 0.45
17 11 0.22
18 7 0.14
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTCATTTATTTTTA
Found at i:52277227 original size:13 final size:13
Alignment explanation
Indices: 52277205--52277237 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52277195 AAGGGTTTGT
52277205 TTAT-TAAACTAA
1 TTATCTAAACTAA
52277217 TTATCTAAACTAA
1 TTATCTAAACTAA
*
52277230 TTAACTAA
1 TTATCTAA
52277238 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:52288704 original size:47 final size:47
Alignment explanation
Indices: 52288646--52289020 Score: 563
Period size: 47 Copynumber: 8.0 Consensus size: 47
52288636 TTTAGGATTT
* *
52288646 AATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * *
52288693 AATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * *
52288740 AATGTGATTAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* *
52288787 AATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* *
52288834 TATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
*
52288881 AATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * *
52288928 AATGTGATGAACGTGAGCATGCATATGTGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * *
52288975 AATGT-AGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 AATGTGA-TGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
52289021 TAGTGTGAAA
Statistics
Matches: 296, Mismatches: 31, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 1 0.00
47 295 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
Found at i:52288868 original size:25 final size:25
Alignment explanation
Indices: 52288834--52288913 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
52288824 CCGAATGGCC
52288834 TATGTGATGAATGTGAACATGCATA
1 TATGTGATGAATGTGAACATGCATA
* * *
52288859 TATGTGATG-AGGCCG-A-ATGGC-CA
1 TATGTGATGAATG-TGAACAT-GCATA
*
52288882 -ATGTGATGAATGTGAGCATGCATA
1 TATGTGATGAATGTGAACATGCATA
52288906 TATGTGAT
1 TATGTGAT
52288914 AAGGCCGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 9 0.22
23 7 0.17
24 8 0.20
25 17 0.41
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (25 bp):
TATGTGATGAATGTGAACATGCATA
Found at i:52289028 original size:94 final size:94
Alignment explanation
Indices: 52288646--52289020 Score: 633
Period size: 94 Copynumber: 4.0 Consensus size: 94
52288636 TTTAGGATTT
52288646 AATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAC
1 AATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAC
*
52288711 ATGTATATATGTGATAAGGCCGAATGGCC
66 ATGCATATATGTGATAAGGCCGAATGGCC
*
52288740 AATGTGATTAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAC
1 AATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAC
52288805 ATGCATATATGTGATAAGGCCGAATGGCC
66 ATGCATATATGTGATAAGGCCGAATGGCC
* * * * * * *
52288834 TATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAGC
1 AATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAC
52288899 ATGCATATATGTGATAAGGCCGAATGGCC
66 ATGCATATATGTGATAAGGCCGAATGGCC
* *
52288928 AATGTGATGAACGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTAGTGAATATGAAC
1 AATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAC
* *
52288993 ATGCATATATGTGGTAAAGCCGAATGGC
66 ATGCATATATGTGATAAGGCCGAATGGC
52289021 TAGTGTGAAA
Statistics
Matches: 260, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 260 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (94 bp):
AATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAAC
ATGCATATATGTGATAAGGCCGAATGGCC
Found at i:52289241 original size:37 final size:37
Alignment explanation
Indices: 52289191--52289334 Score: 207
Period size: 37 Copynumber: 3.9 Consensus size: 37
52289181 ATTCCAGGTG
* * *
52289191 AGACCTGATGACTACGTGTGGAGAGTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTA
*
52289228 AGACCCGATGACTACGTGTAGAGATTTTGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTA
*
52289265 AGACCCGATGACTACGTGTGGAGCTTTTGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTA
* * * *
52289302 AGACCCGATAACTTCATGTGGAGATTTCGTCCG
1 AGACCCGATGACTACGTGTGGAGATTTTGTCCG
52289335 AGCTAAAGGT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTA
Found at i:52292718 original size:46 final size:46
Alignment explanation
Indices: 52292668--52292843 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
52292658 TGGTTGAGCA
*
52292668 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
52292714 TCCGAACTCGTTGAGTTGAGTCCAAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
52292761 TCCGAACGCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
52292807 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52292844 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 63 0.59
47 27 0.25
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:52292776 original size:93 final size:93
Alignment explanation
Indices: 52292665--52292835 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
52292655 GGATGGTTGA
* * *
52292665 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACGCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
52292730 TGAGTCCAAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
* *
52292758 GCATCCGAACGCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACGCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
52292823 TGAGTCCGAGTTC
66 TGAGTCCAAGTTC
52292836 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACGCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:52295789 original size:15 final size:15
Alignment explanation
Indices: 52295769--52295824 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
52295759 GTATCTTGGG
52295769 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
52295784 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
52295799 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
52295814 TTTCTTTATTC
1 TTTCTTTATTC
52295825 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52297807 original size:46 final size:46
Alignment explanation
Indices: 52297757--52297928 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
52297747 TGAGCATCCA
*
52297757 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
* * * *
52297803 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCCG
* * *
52297850 AACTCGTTGAGTTGAGTTCGAGTTCACTCATGGATGCGAACG-CCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-G
* * *
52297896 AGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52297929 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 55 0.54
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
Found at i:52297909 original size:93 final size:93
Alignment explanation
Indices: 52297750--52297921 Score: 265
Period size: 93 Copynumber: 1.8 Consensus size: 93
52297740 GGATGGTTGA
* * *
52297750 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCATTGAGT
52297815 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
52297843 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTCATGGATGCGAACG-CCTGAGCTCATTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCC-GAACTCATTGAG
52297907 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
52297922 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:52300955 original size:25 final size:24
Alignment explanation
Indices: 52300912--52300964 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
52300902 AAGTTCAAGC
52300912 GAGCCATATCAGAAAGCTCA-AGAA
1 GAGCCATATCAGAAAGCTCATA-AA
* *
52300936 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAGAAAGCTCATAAA
52300961 GAGC
1 GAGC
52300965 TGTGTTTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 19 0.76
26 1 0.04
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAGAAAGCTCATAAA
Found at i:52318927 original size:28 final size:27
Alignment explanation
Indices: 52318864--52319015 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
52318854 ATATTAAGTC
* * *
52318864 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
52318891 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
52318919 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
52318946 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
52318974 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
52319001 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52319016 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:52318948 original size:55 final size:55
Alignment explanation
Indices: 52318864--52319015 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
52318854 ATATTAAGTC
* * *
52318864 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
52318919 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
52318974 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
52319016 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:52326973 original size:28 final size:27
Alignment explanation
Indices: 52326910--52327061 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
52326900 ATATTAAGTC
* * *
52326910 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
52326937 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
52326965 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
52326992 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
52327020 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
52327047 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52327062 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:52326994 original size:55 final size:55
Alignment explanation
Indices: 52326910--52327061 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
52326900 ATATTAAGTC
* * *
52326910 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
52326965 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
52327020 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
52327062 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:52330101 original size:12 final size:12
Alignment explanation
Indices: 52330084--52330110 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52330074 GTTGTTGTTG
52330084 GTGCTTAGGCTT
1 GTGCTTAGGCTT
52330096 GTGCTTAGGCTT
1 GTGCTTAGGCTT
52330108 GTG
1 GTG
52330111 GTTGGACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.41
Consensus pattern (12 bp):
GTGCTTAGGCTT
Found at i:52331078 original size:30 final size:30
Alignment explanation
Indices: 52331044--52331140 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
52331034 AGCTCACTCC
52331044 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
52331074 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* *
52331104 CAGCTCAACCTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAA-CTTCAGCTCACGAGCTAAACCT
52331134 TAGCTCA
1 TAGCTCA
52331141 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 1 0.02
30 48 0.92
31 3 0.06
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:52332625 original size:28 final size:28
Alignment explanation
Indices: 52332593--52332654 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
52332583 TTCGTATCAA
52332593 TACCTTAGTTAACAAAATAACCATTATT
1 TACCTTAGTTAACAAAATAACCATTATT
52332621 TACCTTAGTTAACAAAATAACCATTATT
1 TACCTTAGTTAACAAAATAACCATTATT
52332649 TACCTT
1 TACCTT
52332655 GTGGCCGACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.37
Consensus pattern (28 bp):
TACCTTAGTTAACAAAATAACCATTATT
Found at i:52344795 original size:53 final size:53
Alignment explanation
Indices: 52344714--52344822 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
52344704 ACGAAGGAAC
* * *
52344714 AAAGTTTTTCATCCCATCTACTATGCAAGTCAAACTTTGATAGGAGCTCAACT
1 AAAGTTTTTCATCCCATCTACTACGCAAGTCAAACTCTGACAGGAGCTCAACT
*
52344767 AAAGTTTTTCATCCCATCTACTACGCAAGTCGAACTCTGACAGGAGCTCAACT
1 AAAGTTTTTCATCCCATCTACTACGCAAGTCAAACTCTGACAGGAGCTCAACT
52344820 AAA
1 AAA
52344823 TTATACAGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (53 bp):
AAAGTTTTTCATCCCATCTACTACGCAAGTCAAACTCTGACAGGAGCTCAACT
Found at i:52364781 original size:49 final size:49
Alignment explanation
Indices: 52364686--52364816 Score: 131
Period size: 49 Copynumber: 2.7 Consensus size: 49
52364676 GCACATCAAA
* * * * * *
52364686 GTCGATGCCATGTCCTAGATAGGTCTTACATTGACTTTCATATATCGAG-
1 GTCGATGCCATATCCCAGACAGGTCTTACACTGGCTCTCATATATCG-GT
* * * * *
52364735 G-CTGATGCCGTATCCTAGACAGGTTTTATACTGGCTCTCATCTATCGGT
1 GTC-GATGCCATATCCCAGACAGGTCTTACACTGGCTCTCATATATCGGT
52364784 GTCGATGCCATATCCCAGACAGGTCTTACACTG
1 GTCGATGCCATATCCCAGACAGGTCTTACACTG
52364817 ACACGCAGCA
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
48 2 0.03
49 63 0.95
50 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (49 bp):
GTCGATGCCATATCCCAGACAGGTCTTACACTGGCTCTCATATATCGGT
Found at i:52371598 original size:40 final size:40
Alignment explanation
Indices: 52371515--52371777 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
52371505 TTGAATGCTG
* * * * * *
52371515 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
52371555 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
52371595 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
52371635 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
52371675 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
52371715 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
52371754 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52371778 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:52371797 original size:79 final size:80
Alignment explanation
Indices: 52371554--52371812 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
52371544 AAGTGAATAT
* * * * * *
52371554 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
52371618 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
52371634 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
52371699 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
52371714 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
52371778 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
52371793 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
52371813 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:52379549 original size:40 final size:40
Alignment explanation
Indices: 52379466--52379728 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
52379456 TTGAATGCTG
* * * * * *
52379466 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
52379506 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
52379546 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
52379586 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
52379626 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
52379666 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
52379705 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52379729 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:52379748 original size:79 final size:80
Alignment explanation
Indices: 52379505--52379763 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
52379495 AAGTGAATAT
* * * * * *
52379505 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
52379569 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
52379585 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
52379650 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
52379665 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
52379729 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
52379744 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
52379764 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:52382489 original size:27 final size:27
Alignment explanation
Indices: 52382459--52382513 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
52382449 AAATAAATTT
52382459 TGGGTCTAATTGTCTTTAAATCCTTTC
1 TGGGTCTAATTGTCTTTAAATCCTTTC
52382486 TGGGTCTAATTGTCTTTAAATCCTTTC
1 TGGGTCTAATTGTCTTTAAATCCTTTC
52382513 T
1 T
52382514 CATTAGACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (27 bp):
TGGGTCTAATTGTCTTTAAATCCTTTC
Found at i:52403556 original size:46 final size:46
Alignment explanation
Indices: 52403483--52403654 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 46
52403473 TAGGGTTTAA
* * * * * *
52403483 TATTACTGTATTGTCAAGTCCATAACACATGCAAGAGCTTAGAACC
1 TATTCCTGTATTCTCGAGTCCACAACACATGCATGAGCTTGGAACC
** *
52403529 TAAACCTGTATTCTCGAGTCCGCAACACATGCATGAGCTTGGAACC
1 TATTCCTGTATTCTCGAGTCCACAACACATGCATGAGCTTGGAACC
* * *
52403575 TATTCCTGTATTCTCGAGTCCACAACATATGTATGAGCTTGGAACT
1 TATTCCTGTATTCTCGAGTCCACAACACATGCATGAGCTTGGAACC
*
52403621 TATTCTTGTATTCTCGAGTCAGCAACAACACATG
1 TATTCCTGTATTCTCGAGTC--C-ACAACACATG
52403655 TAGGAGCTCA
Statistics
Matches: 106, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
46 96 0.91
48 1 0.01
49 9 0.08
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (46 bp):
TATTCCTGTATTCTCGAGTCCACAACACATGCATGAGCTTGGAACC
Found at i:52406681 original size:18 final size:18
Alignment explanation
Indices: 52406658--52406696 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52406648 TTCAAGCACC
52406658 GTTTTTAA-TGATTTTTAT
1 GTTTTTAAGT-ATTTTTAT
*
52406676 GTTTTTAAGTTTTTTTAT
1 GTTTTTAAGTATTTTTAT
52406694 GTT
1 GTT
52406697 AATCTAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (18 bp):
GTTTTTAAGTATTTTTAT
Found at i:52407556 original size:68 final size:68
Alignment explanation
Indices: 52407419--52407572 Score: 191
Period size: 68 Copynumber: 2.3 Consensus size: 68
52407409 GCAGATTCTC
* * * *
52407419 CACAGCTTGTGTGAGCAACACCATGTAGCTTACATTCCAACCCATAACTCGTGTAAGGAGGCCCG
1 CACAGCTCGTGTGAGCAACACCATGTAGCTTACATTCCAACCCACAACTCGTGTAAGCAGGCCCA
52407484 TTT
66 TTT
* * * * * ***
52407487 CACAGCTCGTGTGAGCTACATCATGTAGCTTACATTTCGACCCACAACTCGTGTGAGCAGTTGCA
1 CACAGCTCGTGTGAGCAACACCATGTAGCTTACATTCCAACCCACAACTCGTGTAAGCAGGCCCA
52407552 TTT
66 TTT
*
52407555 CATAGCTCGTGTGAGCAA
1 CACAGCTCGTGTGAGCAA
52407573 TGATGTAAAG
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 72 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (68 bp):
CACAGCTCGTGTGAGCAACACCATGTAGCTTACATTCCAACCCACAACTCGTGTAAGCAGGCCCA
TTT
Found at i:52409342 original size:2 final size:2
Alignment explanation
Indices: 52409337--52409368 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52409327 TTTTTTATTG
52409337 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52409369 TTTTACTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:52413891 original size:28 final size:28
Alignment explanation
Indices: 52413860--52413919 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
52413850 ATAAAAGTTA
52413860 TTAAATTTTAATAAAAATATA-AAAATAT
1 TTAAATTTTAATAAAAAT-TAGAAAATAT
* *
52413888 TTAAATTTTATTAAAAATTAGAAAATTT
1 TTAAATTTTAATAAAAATTAGAAAATAT
52413916 TTAA
1 TTAA
52413920 TAATAATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
TTAAATTTTAATAAAAATTAGAAAATAT
Found at i:52414046 original size:20 final size:20
Alignment explanation
Indices: 52413986--52414046 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
52413976 TTATAAAGTC
* *
52413986 GTAAGAAAATTATAAAAAAT
1 GTAAAAAAATTATAAAAATT
* **
52414006 GTAAATAAA-TATAAATTTT
1 GTAAAAAAATTATAAAAATT
52414025 GTAAAAAAATTATAAAAATT
1 GTAAAAAAATTATAAAAATT
52414045 GT
1 GT
52414047 TGTACCAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAATT
Found at i:52414277 original size:21 final size:21
Alignment explanation
Indices: 52414253--52414319 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
52414243 TGTAAATGAT
*
52414253 TTTTATAAATTTTTTTTCTAA
1 TTTTATAAATTTTTTTTATAA
*
52414274 TTTTA-AATATTTTTTATTAAAA
1 TTTTATAA-ATTTTTT-TTATAA
*
52414296 TTTAAT-AATTTTTTTTATAA
1 TTTTATAAATTTTTTTTATAA
52414316 TTTT
1 TTTT
52414320 TATTGATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 10 0.26
21 19 0.50
22 9 0.24
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATAAATTTTTTTTATAA
Found at i:52414328 original size:22 final size:22
Alignment explanation
Indices: 52414251--52414330 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 22
52414241 ATTGTAAATG
*
52414251 ATTTTT-ATAAATTTTTTTTCTA
1 ATTTTTAAT-AATTTTTTTTATA
*
52414273 ATTTTAAAT-ATTTTTTATTA-A
1 ATTTTTAATAATTTTTT-TTATA
*
52414294 A-ATTTAATAATTTTTTTTATA
1 ATTTTTAATAATTTTTTTTATA
* *
52414315 ATTTTTATTGATTTTT
1 ATTTTTAATAATTTTT
52414331 ATTTTTTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 8 0.17
21 18 0.39
22 18 0.39
23 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
ATTTTTAATAATTTTTTTTATA
Found at i:52414747 original size:5 final size:5
Alignment explanation
Indices: 52414737--52414761 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52414727 CTTCGCGTTC
52414737 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
52414762 AGTTTACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:52416760 original size:90 final size:86
Alignment explanation
Indices: 52416590--52416810 Score: 228
Period size: 90 Copynumber: 2.5 Consensus size: 86
52416580 CAAATGATCT
* * * *
52416590 TTTTAATGCATATTTTAACAGTTCAAGTACCCAATTGAGTGAAAAAAATCAGGAGCTTAATTGCT
1 TTTTAATGCA-CTTTGAA-AGTTCAAGTACCCAATTGAGTAAAAAAAATCAAGAGCTTAATTGCT
* * *
52416655 TTTTTTGAAAAAGTTTGAGGGACT
64 TTATTAGAAAAAGTTTGAGGG-CC
* *
52416679 TTTTGATGCACTTTGAAAGTTCAAGTACTCAATTGAGTACTAAAAAAAAGT-AAGAGCTTAATTG
1 TTTTAATGCACTTTGAAAGTTCAAGTACCCAATTGAG---TAAAAAAAA-TCAAGAGCTTAATTG
*
52416743 CTTTATTAGAAATAGTTTGAGGGCC
62 CTTTATTAGAAAAAGTTTGAGGGCC
* * * * **
52416768 TTTTAATGTATTTTGAAAGTTAAAATGTCCAATTGAGTAAAAA
1 TTTTAATGCACTTTGAAAGTTCAAGTACCCAATTGAGTAAAAA
52416811 GAGTATGGAC
Statistics
Matches: 110, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
86 6 0.05
87 19 0.17
88 5 0.05
89 39 0.35
90 40 0.36
91 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (86 bp):
TTTTAATGCACTTTGAAAGTTCAAGTACCCAATTGAGTAAAAAAAATCAAGAGCTTAATTGCTTT
ATTAGAAAAAGTTTGAGGGCC
Found at i:52417318 original size:17 final size:18
Alignment explanation
Indices: 52417298--52417343 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
52417288 TTAATTCCAA
52417298 TATATATTTTTAAAT-TT
1 TATATATTTTTAAATATT
*
52417315 TATAT-TATTTAAATATT
1 TATATATTTTTAAATATT
52417332 TATATATTTTTA
1 TATATATTTTTA
52417344 CAAATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATATTTTTAAATATT
Found at i:52417850 original size:17 final size:19
Alignment explanation
Indices: 52417813--52417851 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
52417803 AATCTAGTAT
*
52417813 ATTATTTGTTTTTTATATA
1 ATTATTTGTTCTTTATATA
52417832 ATTATTT-TTCTTT-TATA
1 ATTATTTGTTCTTTATATA
52417849 ATT
1 ATT
52417852 TTTAACCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTATTTGTTCTTTATATA
Found at i:52425331 original size:40 final size:40
Alignment explanation
Indices: 52425268--52425456 Score: 299
Period size: 40 Copynumber: 4.8 Consensus size: 40
52425258 GAGCATTGGA
* * *
52425268 ATATATCC-GGCTAAGACCGGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52425307 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
52425347 ATATATCCGGGCTAAGACCCGAAAGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
52425387 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52425427 ATATGTCCGGGTTAAGACCCGAAGGCAATT
1 ATATATCCGGGCTAAGACCCGAAGGCAATT
52425457 GTTTGCGCTA
Statistics
Matches: 140, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 8 0.06
40 132 0.94
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:52427669 original size:2 final size:2
Alignment explanation
Indices: 52427659--52427687 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
52427649 TTTTTTATTG
52427659 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52427688 TTTTACTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:52432150 original size:28 final size:26
Alignment explanation
Indices: 52432080--52432156 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 26
52432070 AATAAAAATG
* *
52432080 ATAAAAGTCATAAAAGTTATTAAATTTA
1 ATAAAAAT-ATAAAAATT-TTAAATTTA
52432108 ATAAAAATATAAAAATATTTAAATTTTA
1 ATAAAAATATAAAAAT-TTTAAA-TTTA
*
52432136 TTAAAAAT-TAGAAAATTTTAA
1 ATAAAAATATA-AAAATTTTAA
52432157 TAATAATCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 19 0.44
28 24 0.56
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (26 bp):
ATAAAAATATAAAAATTTTAAATTTA
Found at i:52432284 original size:20 final size:20
Alignment explanation
Indices: 52432223--52432284 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
52432213 TTATAAAGTC
* *
52432223 GTAAGAAAATTATAAAAAAAT
1 GTAAAAAAATTAT-AAAAATT
* **
52432244 GTAAATAAA-TATAAATTTT
1 GTAAAAAAATTATAAAAATT
52432263 GTAAAAAAATTATAAAAATT
1 GTAAAAAAATTATAAAAATT
52432283 GT
1 GT
52432285 TGTACCAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 12 0.38
20 13 0.41
21 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAATT
Found at i:52432511 original size:20 final size:20
Alignment explanation
Indices: 52432488--52432553 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
52432478 TGTAAATGAT
*
52432488 TTTTATAAATTTTTTTCTAA
1 TTTTATAAATTTTTTTATAA
*
52432508 TTTTA-AATATTTTTATTAAAA
1 TTTTATAA-ATTTTT-TTATAA
*
52432529 TTTAAT-AATTTTTTTATAA
1 TTTTATAAATTTTTTTATAA
52432548 TTTTAT
1 TTTTAT
52432554 TGATTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 12 0.32
20 17 0.45
21 9 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATAAATTTTTTTATAA
Found at i:52432535 original size:19 final size:21
Alignment explanation
Indices: 52432495--52432564 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 21
52432485 GATTTTTATA
* *
52432495 AATTTTT-TTCTAATTTTAA-
1 AATTTTTATTATAAATTTAAT
52432514 ATATTTTTATTA-AAATTTAAT
1 A-ATTTTTATTATAAATTTAAT
* *
52432535 AATTTTT-TTATAATTTTATT
1 AATTTTTATTATAAATTTAAT
*
52432555 GATTTTTATT
1 AATTTTTATT
52432565 TTTATAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.10
20 32 0.78
21 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (21 bp):
AATTTTTATTATAAATTTAAT
Found at i:52435006 original size:89 final size:86
Alignment explanation
Indices: 52434814--52435033 Score: 230
Period size: 89 Copynumber: 2.5 Consensus size: 86
52434804 CAAATGATCT
* *
52434814 TTTTAATGCATATTTT-AACAGTTCAAGTACCCAATTGAGTGAAAAAAATCAGGAGCTTAATTGC
1 TTTTAATG--TATTTTGAA-AGTTCAAGTACCCAATTGAGTAAAAAAAATCAAGAGCTTAATTGC
* *
52434878 TTTTTTGAAAAAGTTTGAGGGACT
63 TTTTTAGAAAAAGTTTGAGGGACC
* * * *
52434902 TTTTGATGCACTTTGAAAGTTCAAGTACTCAATTGAGTACTAAAAAAAAGT-AAGAGCTTAATTG
1 TTTTAATGTATTTTGAAAGTTCAAGTACCCAATTGAG---TAAAAAAAA-TCAAGAGCTTAATTG
*
52434966 CTTTATTAGAAATAGTTTGAGGG-CC
62 CTTT-TTAGAAAAAGTTTGAGGGACC
* * **
52434991 TTTTAATGTATTTTGAAAGTTAAAATGTCCAATTGAGTAAAAA
1 TTTTAATGTATTTTGAAAGTTCAAGTACCCAATTGAGTAAAAA
52435034 GAGTATGGAC
Statistics
Matches: 109, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
86 29 0.27
87 2 0.02
88 7 0.06
89 54 0.50
90 17 0.16
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (86 bp):
TTTTAATGTATTTTGAAAGTTCAAGTACCCAATTGAGTAAAAAAAATCAAGAGCTTAATTGCTTT
TTAGAAAAAGTTTGAGGGACC
Found at i:52436072 original size:17 final size:19
Alignment explanation
Indices: 52436035--52436073 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
52436025 AATCTAGTAT
*
52436035 ATTATTTGTTTTTTATATA
1 ATTATTTGTTCTTTATATA
52436054 ATTATTT-TTCTTT-TATA
1 ATTATTTGTTCTTTATATA
52436071 ATT
1 ATT
52436074 TTTAACCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTATTTGTTCTTTATATA
Found at i:52443610 original size:40 final size:40
Alignment explanation
Indices: 52443546--52443733 Score: 304
Period size: 40 Copynumber: 4.7 Consensus size: 40
52443536 GAGCATTGGA
* * *
52443546 ATATATCCGGGCTAAGACCGGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52443586 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
52443626 ATATATCCGGGCTAAGACCCGAAAGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
52443666 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52443706 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
52443734 ATGTGTTTGC
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 139 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:52445997 original size:2 final size:2
Alignment explanation
Indices: 52445992--52446021 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52445982 TTTTTTATTG
52445992 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52446022 TTTTACTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:52450552 original size:28 final size:28
Alignment explanation
Indices: 52450507--52450566 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
52450497 ATAAAAGTTA
52450507 TTAAATTTTAATAAAAAATATA-AAAATAT
1 TTAAATTTTAATAAAAAAT-TAGAAAAT-T
*
52450536 TTAAATTTT-ATTAAAAATTAGAAAATT
1 TTAAATTTTAATAAAAAATTAGAAAATT
52450563 TTAA
1 TTAA
52450567 TAATAATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.24
28 13 0.45
29 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TTAAATTTTAATAAAAAATTAGAAAATT
Found at i:52450693 original size:20 final size:20
Alignment explanation
Indices: 52450632--52450693 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
52450622 TTATAAAGTC
* *
52450632 GTAAGAAAATTATAAAAAAAT
1 GTAAAAAAATTAT-AAAAATT
* **
52450653 GTAAATAAA-TATAAATTTT
1 GTAAAAAAATTATAAAAATT
52450672 GTAAAAAAATTATAAAAATT
1 GTAAAAAAATTATAAAAATT
52450692 GT
1 GT
52450694 TGTACCAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 12 0.38
20 13 0.41
21 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAATT
Found at i:52450922 original size:20 final size:19
Alignment explanation
Indices: 52450899--52450954 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
52450889 GTAAATGATT
**
52450899 TTTATAAATTTTTTTTCTAA
1 TTTA-AAATTTTTTTTAAAA
52450919 TTTAAATATTTTTTATTAAAA
1 TTTAAA-ATTTTTT-TTAAAA
52450940 TTTAATAATTTTTTT
1 TTTAA-AATTTTTTT
52450955 ATAATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 16 0.52
22 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAAAATTTTTTTTAAAA
Found at i:52450941 original size:21 final size:19
Alignment explanation
Indices: 52450917--52450961 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
52450907 TTTTTTTTCT
*
52450917 AATTTAAATATTTTTTATTAA
1 AATTT-AATAATTTTT-TTAA
*
52450938 AATTTAATAATTTTTTTAT
1 AATTTAATAATTTTTTTAA
52450957 AATTT
1 AATTT
52450962 TTATTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTAATAATTTTTTTAA
Found at i:52453955 original size:17 final size:18
Alignment explanation
Indices: 52453935--52453981 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
52453925 TTAATTCCAA
52453935 TATATATTTTTAAAT-TT
1 TATATATTTTTAAATATT
*
52453952 TATAT-TATTTAAAATATT
1 TATATAT-TTTTAAATATT
52453970 TATATATTTTTA
1 TATATATTTTTA
52453982 CAAATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 12 0.48
18 11 0.44
19 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATTTTTAAATATT
Found at i:52453977 original size:20 final size:19
Alignment explanation
Indices: 52453948--52453988 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
52453938 ATATTTTTAA
52453948 ATTTTATATTATTTA-AAAT
1 ATTTTATATT-TTTACAAAT
52453967 ATTTATATATTTTTACAAAT
1 ATTT-TATATTTTTACAAAT
52453987 AT
1 AT
52453989 AATGATATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTATATTTTTACAAAT
Found at i:52454486 original size:17 final size:19
Alignment explanation
Indices: 52454449--52454487 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
52454439 AATCTAGTAT
*
52454449 ATTATTTGTTTTTTATATA
1 ATTATTTGTTCTTTATATA
52454468 ATTATTT-TTCTTT-TATA
1 ATTATTTGTTCTTTATATA
52454485 ATT
1 ATT
52454488 TTTAACCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTATTTGTTCTTTATATA
Found at i:52462035 original size:40 final size:40
Alignment explanation
Indices: 52461971--52462158 Score: 304
Period size: 40 Copynumber: 4.7 Consensus size: 40
52461961 GAGCATTGGA
* * *
52461971 ATATATCCGGGCTAAGACCGGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52462011 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
52462051 ATATATCCGGGCTAAGACCCGAAAGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
52462091 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52462131 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
52462159 ATGTGTTTGC
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 139 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:52464421 original size:2 final size:2
Alignment explanation
Indices: 52464416--52464445 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52464406 TTTTTTATTG
52464416 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52464446 TTTTACTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:52468944 original size:27 final size:26
Alignment explanation
Indices: 52468914--52468970 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
52468904 ATAAAAGTTA
52468914 TTAAATTTAATAAAAATATAAAAATAT
1 TTAAATTTAATAAAAAT-TAAAAATAT
* * * *
52468941 TTAAATTTTATTAAAATTAGAAATTT
1 TTAAATTTAATAAAAATTAAAAATAT
52468967 TTAA
1 TTAA
52468971 TAATAATCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTAAATTTAATAAAAATTAAAAATAT
Found at i:52469095 original size:19 final size:19
Alignment explanation
Indices: 52469026--52469095 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
52469016 ATTATAAATT
* * *
52469026 TTATAAAGTCGTAAGAAAA
1 TTATAAAATTGTAAAAAAA
* *
52469045 TTATAAAAAATGTAAATAAA
1 TTAT-AAAATTGTAAAAAAA
*
52469065 -TATAAATTTTGTAAAAAAA
1 TTATAAA-ATTGTAAAAAAA
52469084 TTATAAAATTGT
1 TTATAAAATTGT
52469096 TGTACCAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
18 3 0.08
19 20 0.51
20 16 0.41
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.34
Consensus pattern (19 bp):
TTATAAAATTGTAAAAAAA
Found at i:52469328 original size:19 final size:19
Alignment explanation
Indices: 52469305--52469359 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
52469295 GATTTTTATA
52469305 AATTTTTTCTAATTTTAAAT
1 AATTTTTT-TAATTTTAAAT
*
52469325 -ATTTTTATTAAATTT-AAT
1 AATTTTT-TTAATTTTAAAT
52469343 AATTTTTTTATATTTTA
1 AATTTTTTTA-ATTTTA
52469360 TTGATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 22 0.76
20 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTTTTTAATTTTAAAT
Found at i:52469343 original size:18 final size:20
Alignment explanation
Indices: 52469325--52469371 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
52469315 AATTTTAAAT
52469325 ATTTTTATTA-AATTTAATA
1 ATTTTTATTATAATTTAATA
* * *
52469344 ATTTTT-TTATATTTTATTG
1 ATTTTTATTATAATTTAATA
52469363 ATTTTTATT
1 ATTTTTATT
52469372 TTTTATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 18 0.78
20 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTTTTATTATAATTTAATA
Found at i:52469384 original size:17 final size:17
Alignment explanation
Indices: 52469298--52469385 Score: 54
Period size: 17 Copynumber: 4.8 Consensus size: 17
52469288 TGTAAATGAT
*
52469298 TTTTATAAATTTTTTCTAA
1 TTTTAT-AATTTTTTAT-A
52469317 TTTTA-AATATTTTTATTAAA
1 TTTTATAAT-TTTTTA-T--A
*
52469337 TTTAATAATTTTTTTATA
1 TTTTATAA-TTTTTTATA
* *
52469355 TTTTATTGA-TTTTTATT
1 TTTTA-TAATTTTTTATA
52469372 TTTTATAATTTTTT
1 TTTTATAATTTTTT
52469386 TTGTAACGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
16 2 0.04
17 20 0.36
18 10 0.18
19 8 0.14
20 7 0.12
21 8 0.14
22 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (17 bp):
TTTTATAATTTTTTATA
Found at i:52471798 original size:89 final size:84
Alignment explanation
Indices: 52471608--52471825 Score: 233
Period size: 89 Copynumber: 2.5 Consensus size: 84
52471598 CAAATGATCT
* *
52471608 TTTTAATGCATATTTT-AACAGTTCAAGTACCCAATTGAGTGAAAAAAATCAGGAGCTTAATTGC
1 TTTTAATG--TATTTTGAA-AGTTCAAGTACCCAATTGAGTAAAAAAAATCAAGAGCTTAATTGC
*
52471672 TTTTTTGAAAAGTTTGAGGGAC
63 TTTTTAGAAAAGTTTGAGGGAC
* * * *
52471694 TTTTGATGCACTTTGAAAGTTCAAGTACTCAATTGAGTACTAAAAAAAAGT-AAGAGCTTAATTG
1 TTTTAATGTATTTTGAAAGTTCAAGTACCCAATTGAG---TAAAAAAAA-TCAAGAGCTTAATTG
*
52471758 CTTTATTAGAAATAGTTTGAGGGCC
62 CTTT-TTAGAAA-AGTTTGAGGGAC
* * **
52471783 TTTTAATGTATTTTGAAAGTTAAAATGTCCAATTGAGTAAAAA
1 TTTTAATGTATTTTGAAAGTTCAAGTACCCAATTGAGTAAAAA
52471826 GAGTATGGAC
Statistics
Matches: 109, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
84 23 0.21
85 2 0.02
86 13 0.12
87 24 0.22
88 7 0.06
89 40 0.37
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (84 bp):
TTTTAATGTATTTTGAAAGTTCAAGTACCCAATTGAGTAAAAAAAATCAAGAGCTTAATTGCTTT
TTAGAAAAGTTTGAGGGAC
Found at i:52472302 original size:23 final size:23
Alignment explanation
Indices: 52472276--52472320 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52472266 AATAAAAACA
*
52472276 TTAACTTATAATATA-ATTTTTAT
1 TTAA-TTACAATATATATTTTTAT
*
52472299 TTAATTCCAATATATATTTTTA
1 TTAATTACAATATATATTTTTA
52472321 AATTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATTACAATATATATTTTTAT
Found at i:52472329 original size:17 final size:18
Alignment explanation
Indices: 52472309--52472355 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
52472299 TTAATTCCAA
52472309 TATATATTTTTAAAT-TT
1 TATATATTTTTAAATATT
*
52472326 TATAT-TATTTAAAATATT
1 TATATAT-TTTTAAATATT
52472344 TATATATTTTTA
1 TATATATTTTTA
52472356 CAAATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 12 0.48
18 11 0.44
19 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATTTTTAAATATT
Found at i:52472351 original size:20 final size:19
Alignment explanation
Indices: 52472322--52472362 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
52472312 ATATTTTTAA
52472322 ATTTTATATTATTTA-AAAT
1 ATTTTATATT-TTTACAAAT
52472341 ATTTATATATTTTTACAAAT
1 ATTT-TATATTTTTACAAAT
52472361 AT
1 AT
52472363 AATGATATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTATATTTTTACAAAT
Found at i:52472860 original size:17 final size:19
Alignment explanation
Indices: 52472823--52472861 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
52472813 AATCTAGTAT
*
52472823 ATTATTTGTTTTTTATATA
1 ATTATTTGTTCTTTATATA
52472842 ATTATTT-TTCTTT-TATA
1 ATTATTTGTTCTTTATATA
52472859 ATT
1 ATT
52472862 TTAACCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTATTTGTTCTTTATATA
Found at i:52480391 original size:40 final size:40
Alignment explanation
Indices: 52480332--52480519 Score: 322
Period size: 40 Copynumber: 4.7 Consensus size: 40
52480322 GAGCATTGGA
* *
52480332 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52480372 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
52480412 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
52480452 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52480492 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
52480520 ATGTGTTTGC
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:52489029 original size:40 final size:40
Alignment explanation
Indices: 52488965--52489152 Score: 313
Period size: 40 Copynumber: 4.7 Consensus size: 40
52488955 GAGCATTGGA
* * *
52488965 ATATATCCGGGCTAAGACCGGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52489005 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
52489045 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
52489085 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
52489125 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
52489153 ATGTGTTTGC
Statistics
Matches: 141, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 141 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:52491701 original size:75 final size:75
Alignment explanation
Indices: 52491578--52491728 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
52491568 AAATGAAAAC
* * * *
52491578 TAAGATTATTCCCTTATTAATAGAGAAGACAAATGAAAATTTAGAAAAAGGAATTATATTCTTTC
1 TAAGATTATTCACTTATTAATAGAGAAGACAAATGAAAAGTTAGAAAAAGAAATTATATTATTTC
52491643 CAAAAGAATA
66 CAAAAGAATA
*
52491653 TAAGATTATTCACTTATTAATAGAGAAGTCAAATTG-AAAGTTAGAAAAAGAAATTATATTATTT
1 TAAGATTATTCACTTATTAATAGAGAAGACAAA-TGAAAAGTTAGAAAAAGAAATTATATTATTT
52491717 CCAAAAGAATA
65 CCAAAAGAATA
52491728 T
1 T
52491729 TAATTTCCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 68 0.97
76 2 0.03
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (75 bp):
TAAGATTATTCACTTATTAATAGAGAAGACAAATGAAAAGTTAGAAAAAGAAATTATATTATTTC
CAAAAGAATA
Found at i:52491952 original size:138 final size:138
Alignment explanation
Indices: 52491704--52492260 Score: 850
Period size: 138 Copynumber: 4.0 Consensus size: 138
52491694 TAGAAAAAGA
*
52491704 AATTATATT-ATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTA
1 AATTATATTCA-TTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTA
* *
52491768 ATAAAACTGTTTATATTAATAAATTCGGTAAAATATATACTATTAATATTTTGTATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
*
52491833 TTATATATT
130 TCATATATT
*
52491842 AATTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTGTATTTTGACCAAAATTAATTAA
1 AATTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
* *
52491907 TATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
52491972 CATATATT
131 CATATATT
* *
52491980 AATTATATTCTTTCCAAAA-AATATTAATTTCCACGTCTTTTATATTTTGA-CAGAAATTAATTA
1 AATTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCA-AAATTAATTA
* * *
52492043 ATATAATTGTTTATATTAATAAATTCGGTCAAATGTATATACAATTAATATTTTATATGAATCAA
65 ATATAACTGTTTATATTAATAAATTCGGT-AAA-ATATATACAATTAATATTTTGTATGAATCAA
52492108 ATTCATATATT
128 ATTCATATATT
* * * * *
52492119 AACTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTAACCGAAATTAATTAA
1 AATTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
* * * * *
52492184 TTTAATTGTTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTATAAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
52492249 CTTATATT
131 CATATATT
52492257 AATT
1 AATT
52492261 TTATCTATGT
Statistics
Matches: 385, Mismatches: 28, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
136 2 0.01
137 65 0.17
138 190 0.49
139 62 0.16
140 65 0.17
141 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:52492216 original size:277 final size:276
Alignment explanation
Indices: 52491704--52492260 Score: 900
Period size: 277 Copynumber: 2.0 Consensus size: 276
52491694 TAGAAAAAGA
* *
52491704 AATTATATTATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTCCACGTCTTTTATATTTTGACAGAAATTAATTAA
* *
52491769 TAAAACTGTTTATATTAATAAATTCGGTAAAATATATACTATTAATATTTTGTATGAATCAAATT
66 TAAAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAATT
* * * *
52491834 TATATATTAATTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTGTATTTTGACCAAAA
131 CATATATTAACTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTAACCAAAA
*
52491899 TTAATTAATATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGA
196 TTAATTAATATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATAA
52491964 ATCAAATTCATATATT
261 ATCAAATTCATATATT
*
52491980 AATTATATTCTTTCCAAAA-AATATTAATTTCCACGTCTTTTATATTTTGACAGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTCCACGTCTTTTATATTTTGACAGAAATTAATTAA
* * *
52492044 TATAATTGTTTATATTAATAAATTCGGTCAAATGTATATACAATTAATATTTTATATGAATCAAA
66 TAAAACTGTTTATATTAATAAATTCGGT-AAA-ATATATACAATTAATATTTTATATGAATCAAA
* * *
52492109 TTCATATATTAACTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTAACCGA
129 TTCATATATTAACTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTAACCAA
* * * *
52492174 AATTAATTAATTTAATTGTTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTAT
194 AATTAATTAATATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTAT
*
52492239 AAATCAAATTCTTATATT
259 AAATCAAATTCATATATT
52492257 AATT
1 AATT
52492261 TTATCTATGT
Statistics
Matches: 258, Mismatches: 21, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
275 69 0.27
276 21 0.08
277 168 0.65
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (276 bp):
AATTATATTATTTCCAAAAGAATATTAATTTCCACGTCTTTTATATTTTGACAGAAATTAATTAA
TAAAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAATT
CATATATTAACTATATTCATTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTAACCAAAA
TTAATTAATATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATAA
ATCAAATTCATATATT
Found at i:52493636 original size:26 final size:26
Alignment explanation
Indices: 52493607--52493657 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
52493597 AAGAAAAATT
* * *
52493607 AGAATGTTACAATTAAATTAAAAAAA
1 AGAATATTAAAATTAAAATAAAAAAA
52493633 AGAATATTAAAATTAAAATAAAAAA
1 AGAATATTAAAATTAAAATAAAAAA
52493658 TGGATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (26 bp):
AGAATATTAAAATTAAAATAAAAAAA
Found at i:52496982 original size:32 final size:32
Alignment explanation
Indices: 52496941--52497006 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
52496931 ATACCTAGGA
52496941 AAGAATCTGCTTAAATTCCATTTGTCACTACC
1 AAGAATCTGCTTAAATTCCATTTGTCACTACC
*
52496973 AAGAATCTGCTTAAATTTCATTTGTCACTACC
1 AAGAATCTGCTTAAATTCCATTTGTCACTACC
52497005 AA
1 AA
52497007 TCTAAATTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (32 bp):
AAGAATCTGCTTAAATTCCATTTGTCACTACC
Found at i:52499743 original size:28 final size:28
Alignment explanation
Indices: 52499667--52499745 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
52499657 TCGACTAAAT
52499667 ATGGCACTTAGTGTGCGAAATATTAAGA
1 ATGGCACTTAGTGTGCGAAATATTAAGA
* * *
52499695 ATGACACTTAGTGTGCCAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTAAGA
*
52499723 ATGGCACTTAGTGTGTGAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
52499746 CGAATGATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTAAGA
Found at i:52505665 original size:16 final size:15
Alignment explanation
Indices: 52505642--52505676 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
52505632 TACTTTAGCC
52505642 ATTTATTTTATTGCA
1 ATTTATTTTATTGCA
*
52505657 ATTTAATTTTATTTCA
1 ATTT-ATTTTATTGCA
52505673 ATTT
1 ATTT
52505677 TGTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTTATTTTATTGCA
Found at i:52514383 original size:18 final size:18
Alignment explanation
Indices: 52514360--52514406 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
52514350 TAAATTTTTA
*
52514360 TTTATTTTTATTTTTATC
1 TTTATTTTTATTTTTAAC
* *
52514378 TTTATTTATCTTTTTAAC
1 TTTATTTTTATTTTTAAC
52514396 -TTACTTTTTAT
1 TTTA-TTTTTAT
52514407 CCTATTTCTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTTTATTTTTAAC
Found at i:52516317 original size:21 final size:20
Alignment explanation
Indices: 52516293--52516331 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
52516283 ATAGGAGAGT
*
52516293 AAAAAGAGCGAGAAACGGGCC
1 AAAAAGAGAGA-AAACGGGCC
*
52516314 AAAAATAGAGAAAACGGG
1 AAAAAGAGAGAAAACGGG
52516332 TCAATGTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.13, G:0.31, T:0.03
Consensus pattern (20 bp):
AAAAAGAGAGAAAACGGGCC
Found at i:52517912 original size:39 final size:39
Alignment explanation
Indices: 52517858--52517935 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
52517848 ATAGAATTTC
52517858 TCGATTTAGCTATAAAGAGAAGTTGAGTTCGTGATTCAT
1 TCGATTTAGCTATAAAGAGAAGTTGAGTTCGTGATTCAT
52517897 TCGATTTAGCTATAAAGAGAAGTTGAGTTCGTGATTCAT
1 TCGATTTAGCTATAAAGAGAAGTTGAGTTCGTGATTCAT
52517936 CAGGCTGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (39 bp):
TCGATTTAGCTATAAAGAGAAGTTGAGTTCGTGATTCAT
Found at i:52519452 original size:28 final size:28
Alignment explanation
Indices: 52519406--52519515 Score: 118
Period size: 28 Copynumber: 4.0 Consensus size: 28
52519396 TTATGTAAAG
** * *
52519406 CACTTAGTGTGCGGGATA-TCAAATATGG
1 CACTTAGTGTGCGAAATATTCAGA-ATGA
* *
52519434 CACTTAGCGTGCGAAATATTGAGAATGA
1 CACTTAGTGTGCGAAATATTCAGAATGA
* *
52519462 CACTTAGTGTGCGAGATATTGAGAATGA
1 CACTTAGTGTGCGAAATATTCAGAATGA
52519490 CACTTAGTGTGCGAAATA-TC-GAATGA
1 CACTTAGTGTGCGAAATATTCAGAATGA
52519516 TTCAACAAGC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
26 6 0.08
27 1 0.01
28 61 0.86
29 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (28 bp):
CACTTAGTGTGCGAAATATTCAGAATGA
Found at i:52523175 original size:40 final size:40
Alignment explanation
Indices: 52523120--52523307 Score: 253
Period size: 40 Copynumber: 4.8 Consensus size: 40
52523110 GGATGATAAG
*
52523120 GAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTGACTATA-TCCGGGCTAAGTCCC
* *
52523160 GAAGGCATTTGTGCTA--GACTA-ATTCCGAGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTGACTATA-TCCGGGCTAAGTCCC
*
52523198 GAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCC
52523238 GAAGGCATTTGTGCGAGCT-ACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTCCC
*
52523278 GAAGGCATTTGAGCGAGT-AGCTATATCCGG
1 GAAGGCATTTGTGCGAGTGA-CTATATCCGG
52523308 TTAAATCCCA
Statistics
Matches: 138, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
38 36 0.26
39 2 0.01
40 98 0.71
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCC
Found at i:52523249 original size:78 final size:79
Alignment explanation
Indices: 52523120--52523307 Score: 267
Period size: 78 Copynumber: 2.4 Consensus size: 79
52523110 GGATGATAAG
* * *
52523120 GAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGACTA-AT
1 GAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-CTACAT
52523183 -TCCGAGCTAAGTCCC
64 ATCCGAGCTAAGTCCC
52523198 GAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATA
1 GAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTAC-ATA
*
52523263 TCCGGGCTAAGTCCC
65 TCCGAGCTAAGTCCC
*
52523278 GAAGGCATTTGAGCGAG-TAGCTATATCCGG
1 GAAGGCATTTGTGCGAGTTA-CTATATCCGG
52523308 TTAAATCCCA
Statistics
Matches: 100, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
77 3 0.03
78 52 0.52
79 5 0.05
80 40 0.40
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
GAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACATAT
CCGAGCTAAGTCCC
Found at i:52531086 original size:40 final size:40
Alignment explanation
Indices: 52531031--52531232 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
52531021 GGATGATAAG
* *
52531031 GAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTGACTATA-TCCGAGCTAAGTCCC
*
52531071 GAAGGCATTTGTGCTA--GACTA-ATTCCGAGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTGACTATA-TCCGAGCTAAGTCCC
*
52531109 GAAGGCATTTGTGCGAGTTACTATATCCGAGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTGACTATATCCGAGCTAAGTCCC
*
52531149 GAAGGCATTTGTGCGAGCT-ACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAG-TGACTATATCCGAGCTAAGTCCC
* * *
52531189 GAAGGCATTTGAGCGAGT-AGCTATATCCG-GTTAAATCCC
1 GAAGGCATTTGTGCGAGTGA-CTATATCCGAGCTAAGTCCC
52531228 GAAGG
1 GAAGG
52531233 TACTTGGTTT
Statistics
Matches: 150, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
38 36 0.24
39 15 0.10
40 97 0.65
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GAAGGCATTTGTGCGAGTGACTATATCCGAGCTAAGTCCC
Found at i:52531160 original size:78 final size:78
Alignment explanation
Indices: 52531031--52531232 Score: 259
Period size: 78 Copynumber: 2.6 Consensus size: 78
52531021 GGATGATAAG
* * *
52531031 GAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGACTA-AT
1 GAAGGCATTTGTGCGAGTTACTATA-TCC-GGCTAAGTCCCGAAGGCATTTGTGCGAG-CTACAT
52531094 -TCCGAGCTAAGTCCC
63 ATCCGAGCTAAGTCCC
52531109 GAAGGCATTTGTGCGAGTTACTATATCCGAGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATA
1 GAAGGCATTTGTGCGAGTTACTATATCCG-GCTAAGTCCCGAAGGCATTTGTGCGAGCTAC-ATA
*
52531174 TCCGGGCTAAGTCCC
64 TCCGAGCTAAGTCCC
* * *
52531189 GAAGGCATTTGAGCGAG-TAGCTATATCCGGTTAAATCCCGAAGG
1 GAAGGCATTTGTGCGAGTTA-CTATATCCGGCTAAGTCCCGAAGG
52531233 TACTTGGTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
77 4 0.04
78 50 0.45
79 18 0.16
80 39 0.35
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (78 bp):
GAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACATATC
CGAGCTAAGTCCC
Found at i:52535214 original size:64 final size:64
Alignment explanation
Indices: 52535133--52535316 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
52535123 AGACATTATG
* * *
52535133 ATGTAGCTAGGTCGCATGGGTGATACCATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACCATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * *
52535197 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACC-A-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
52535262 AA
63 AA
* * * *
52535264 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACCATGTGTACACCATGTAG-ACAAGAGAGC
52535317 CGAACTATAT
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
65 2 0.02
66 20 0.20
67 31 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACCATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:52535250 original size:67 final size:64
Alignment explanation
Indices: 52535109--52535262 Score: 182
Period size: 67 Copynumber: 2.3 Consensus size: 64
52535099 CATCATGTGT
* * * *
52535109 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACCATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCATGAGGACACCATG
52535174 TAG
62 TAG
* * *
52535177 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACC-A-TG-AGGACACCATGT
52535242 AG
63 AG
52535244 ACAAGAGAGCTACGAGATA
1 ACAAGAGAGCTACGAGATA
52535263 AACTGGCTAG
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
64 24 0.32
65 4 0.05
66 4 0.05
67 30 0.40
68 13 0.17
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.21
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACCATGAGGACACCATGTAG
Found at i:52538531 original size:19 final size:19
Alignment explanation
Indices: 52538500--52538549 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
52538490 CATTCGGAGG
52538500 AAGAAGAAA--AAA-TAAA
1 AAGAAGAAAGGAAATTAAA
**
52538516 AAGAAGAAAAGGAAATTAGG
1 AAGAAG-AAAGGAAATTAAA
52538536 AAGAAGAAAGGAAA
1 AAGAAGAAAGGAAA
52538550 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 3 0.11
19 11 0.39
20 8 0.29
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (19 bp):
AAGAAGAAAGGAAATTAAA
Found at i:52538541 original size:20 final size:21
Alignment explanation
Indices: 52538516--52538563 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
52538506 AAAAAATAAA
52538516 AAGAAGAAAAGG-AAATTAGG
1 AAGAAGAAAAGGAAAATTAGG
*
52538536 AAGAAG-AAAGGAAAATTGGG
1 AAGAAGAAAAGGAAAATTAGG
*
52538556 AAAAAGAA
1 AAGAAGAA
52538564 GGAAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.08
Consensus pattern (21 bp):
AAGAAGAAAAGGAAAATTAGG
Found at i:52538570 original size:20 final size:20
Alignment explanation
Indices: 52538523--52538569 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
52538513 AAAAAGAAGA
*
52538523 AAAGG-AAATTAGGAAGAAG
1 AAAGGAAAATTAGGAAAAAG
*
52538542 AAAGGAAAATTGGGAAAAAG
1 AAAGGAAAATTAGGAAAAAG
52538562 -AAGGAAAA
1 AAAGGAAAA
52538570 AAAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.09
Consensus pattern (20 bp):
AAAGGAAAATTAGGAAAAAG
Found at i:52545238 original size:37 final size:37
Alignment explanation
Indices: 52545185--52545324 Score: 226
Period size: 37 Copynumber: 3.8 Consensus size: 37
52545175 CGAATAGTCC
* *
52545185 CCACACGTAGTTATCGGGTCTTACCTGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
* *
52545222 CCACATGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
52545259 CCACACGTAGTCATCGGGTCTTACCCAGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
52545296 CCACACGTAGTCATCGGGTCTTACTCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
52545325 ATATATTTCC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 94 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:52545551 original size:48 final size:48
Alignment explanation
Indices: 52545497--52545948 Score: 823
Period size: 48 Copynumber: 9.4 Consensus size: 48
52545487 GCCGAATCAC
*
52545497 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCGCAT
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
52545545 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
52545593 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
*
52545641 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAC
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
*
52545689 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAC
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
*
52545737 TAGCCATTCGGCTTTACCACGCATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
52545785 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
**
52545833 TAGCCATTCGGCTTTACCAAATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
* * *
52545881 TAGTCATTCGGCTTTACTACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
52545929 TAGCCATTCGGCTTTACCAC
1 TAGCCATTCGGCTTTACCAC
52545949 ACACATATAT
Statistics
Matches: 392, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 392 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
Found at i:52550544 original size:35 final size:35
Alignment explanation
Indices: 52550505--52550577 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
52550495 GGTATGTGAT
52550505 ATATATATTATTTATGTGAGATTGATCTGACGAGA
1 ATATATATTATTTATGTGAGATTGATCTGACGAGA
52550540 ATATATATTATTTATGTGAGATTGATCTGACGAGA
1 ATATATATTATTTATGTGAGATTGATCTGACGAGA
52550575 ATA
1 ATA
52550578 AAGAATGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (35 bp):
ATATATATTATTTATGTGAGATTGATCTGACGAGA
Found at i:52552407 original size:40 final size:39
Alignment explanation
Indices: 52552336--52552451 Score: 106
Period size: 40 Copynumber: 2.9 Consensus size: 39
52552326 CATATAATTA
** **
52552336 TTTCCATATAACTGATTCATATAATTGTTTCGTTTATCTGT
1 TTTCC-TATAACTGATTCATATAATCATTTCGCATATCT-T
* *
52552377 TTTCCTATAACTGGTTTATATAATCATTTCGCATATCTT
1 TTTCCTATAACTGATTCATATAATCATTTCGCATATCTT
* ** * *
52552416 TTTCTATATAACCAATTCTTATAATCATTTCCCATA
1 TTTC-CTATAACTGATTCATATAATCATTTCGCATA
52552452 ACCAATTCAT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 5 0.08
40 51 0.84
41 5 0.08
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTCCTATAACTGATTCATATAATCATTTCGCATATCTT
Found at i:52552438 original size:13 final size:13
Alignment explanation
Indices: 52552417--52552468 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
52552407 GCATATCTTT
52552417 TTCTATATAACCAA
1 TTCT-TATAACCAA
* *
52552431 TTCTTATAATCAT
1 TTCTTATAACCAA
**
52552444 TTCCCATAACCAA
1 TTCTTATAACCAA
*
52552457 TTCATATAACCA
1 TTCTTATAACCA
52552469 TTTCGTATCG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (13 bp):
TTCTTATAACCAA
Found at i:52552453 original size:26 final size:26
Alignment explanation
Indices: 52552423--52552472 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
52552413 CTTTTTCTAT
* *
52552423 ATAACCAATTCTTATAATCATTTCCC
1 ATAACCAATTCATATAACCATTTCCC
52552449 ATAACCAATTCATATAACCATTTC
1 ATAACCAATTCATATAACCATTTC
52552473 GTATCGCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAACCAATTCATATAACCATTTCCC
Found at i:52555664 original size:18 final size:18
Alignment explanation
Indices: 52555641--52555678 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
52555631 ATATTCAGTC
52555641 TTAATGTAACATGGCTTT
1 TTAATGTAACATGGCTTT
52555659 TTAATGTAACATGGCTTT
1 TTAATGTAACATGGCTTT
52555677 TT
1 TT
52555679 GCCACTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (18 bp):
TTAATGTAACATGGCTTT
Found at i:52564678 original size:15 final size:15
Alignment explanation
Indices: 52564658--52564702 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
52564648 TATGATATTG
52564658 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
*
52564673 TATCTTGGATTTCTC
1 TATCTTGGATTTCTT
*
52564688 TATCTTGGACTTCTT
1 TATCTTGGATTTCTT
52564703 AACTCTGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.13, C:0.18, G:0.13, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:52568089 original size:150 final size:150
Alignment explanation
Indices: 52567818--52568121 Score: 545
Period size: 150 Copynumber: 2.0 Consensus size: 150
52567808 ACGGGTATTG
* * * *
52567818 ATATGTAATGGATGTGATGAAAGTCCCGAGAAGGGCATGTTAGGAGGTATGGTTATATGATATAC
1 ATATGGAATGAATGTGATGAAAGTCCCGAGAAGGGCATGTTAAGAGGTATGATTATATGATATAC
*
52567883 TACGATGAGCACAGGTATGTACGCTAAATTCATGAGTAATACTTTGGTGAATGATGACTTGTGAT
66 TACGATGAGCACAAGTATGTACGCTAAATTCATGAGTAATACTTTGGTGAATGATGACTTGTGAT
*
52567948 GAGGAAGCATCTGTATGTGT
131 GAGGAAGCATATGTATGTGT
*
52567968 ATATGGAATGAATGTGATGAAAGTCCTGAGAAGGGCATGTTAAGAGGTATGATTATATGATATAC
1 ATATGGAATGAATGTGATGAAAGTCCCGAGAAGGGCATGTTAAGAGGTATGATTATATGATATAC
52568033 TACGATGAGCACAAGTATGTACGCTAAATTCATGAGTAATACTTTGGTGAATGATGACTTGTGAT
66 TACGATGAGCACAAGTATGTACGCTAAATTCATGAGTAATACTTTGGTGAATGATGACTTGTGAT
52568098 GAGGAAGCATATGTATGTGT
131 GAGGAAGCATATGTATGTGT
52568118 ATAT
1 ATAT
52568122 ATATGATAAA
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 147 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (150 bp):
ATATGGAATGAATGTGATGAAAGTCCCGAGAAGGGCATGTTAAGAGGTATGATTATATGATATAC
TACGATGAGCACAAGTATGTACGCTAAATTCATGAGTAATACTTTGGTGAATGATGACTTGTGAT
GAGGAAGCATATGTATGTGT
Found at i:52569629 original size:21 final size:21
Alignment explanation
Indices: 52569603--52569645 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52569593 GTGAGGGTTT
*
52569603 ATAGTTGACTAAGGCTTGGAA
1 ATAGTTGACCAAGGCTTGGAA
52569624 ATAGTTGACCAAGGCTTGGAA
1 ATAGTTGACCAAGGCTTGGAA
52569645 A
1 A
52569646 ATACCCTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (21 bp):
ATAGTTGACCAAGGCTTGGAA
Found at i:52582445 original size:17 final size:16
Alignment explanation
Indices: 52582408--52582452 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
52582398 GGCATTATAT
*
52582408 TAAAATAAAAAAATAG
1 TAAAATAACAAAATAG
*
52582424 TAAAATAACAAAATGG
1 TAAAATAACAAAATAG
*
52582440 TGAAAAGAACAAA
1 T-AAAATAACAAA
52582453 GCTTGTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.69, C:0.04, G:0.11, T:0.16
Consensus pattern (16 bp):
TAAAATAACAAAATAG
Found at i:52584424 original size:78 final size:78
Alignment explanation
Indices: 52584279--52584434 Score: 224
Period size: 78 Copynumber: 2.0 Consensus size: 78
52584269 GCATGATATT
* * *
52584279 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAACATATCCGGACTTGAGGTCC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAACATATCCGGACCTAAAGTCC
52584344 GCAGGCTTCGTGC
66 GCAGGCTTCGTGC
* * * *
52584357 TGGAAACATATCCGGACTTGAGGTCTGCAGGCTACGTGCTGG-AATATATCTGGGCCTAAAGTCC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAACATATCCGGACCTAAAGT-C
*
52584421 CGCAGGCTTTGTGC
65 CGCAGGCTTCGTGC
52584435 CAGTAACTGG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 14 0.20
78 55 0.80
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (78 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAACATATCCGGACCTAAAGTCC
GCAGGCTTCGTGC
Found at i:52584428 original size:39 final size:39
Alignment explanation
Indices: 52584279--52584400 Score: 226
Period size: 39 Copynumber: 3.1 Consensus size: 39
52584269 GCATGATATT
52584279 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
*
52584318 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTTCGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
*
52584357 TGGAAACATATCCGGACTTGAGGTCTGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
52584396 TGGAA
1 TGGAA
52584401 TATATCTGGG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.22
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
Found at i:52596193 original size:23 final size:23
Alignment explanation
Indices: 52596166--52596211 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
52596156 GTTAACCATA
*
52596166 GTTTAATTGATGATAATGTCCCT
1 GTTTAATTGATGACAATGTCCCT
52596189 GTTTAATTGATGACAATGTCCCT
1 GTTTAATTGATGACAATGTCCCT
52596212 ACATTGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (23 bp):
GTTTAATTGATGACAATGTCCCT
Found at i:52600949 original size:19 final size:19
Alignment explanation
Indices: 52600915--52600953 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
52600905 GTTAGAATTA
*
52600915 TTATTCTTAGAAAATAGAAT
1 TTATACTTAGAAAATA-AAT
52600935 TTATACTTA-AAAATAAAT
1 TTATACTTAGAAAATAAAT
52600953 T
1 T
52600954 CTCACTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATACTTAGAAAATAAAT
Found at i:52608100 original size:48 final size:48
Alignment explanation
Indices: 52607992--52608320 Score: 281
Period size: 48 Copynumber: 6.9 Consensus size: 48
52607982 TAGGGTTATG
* * * * *
52607992 AGAGCTAGTGTAAGACCATGTCTGGGACATGACATCAGCCTCGATATG
1 AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATCGATATA
* * * * **
52608040 TGAGCCATTGTAAGACCATGTTTGGAACATGGCATCGGCATTTATATA
1 AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATCGATATA
* * * *
52608088 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATG
1 AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATCGATATA
* * * * *
52608136 TGGGCTAGTGTAAGACCATGTTTGGAACATGGCATTGGCACCGATATA
1 AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATCGATATA
* * * *
52608184 TGAGAGCTAGTCTAAGACCATGTCTGG-----GGCATTGGCCTCGACATA
1 --AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATCGATATA
* * * * * * *
52608229 GGGGCTAATGTAAGACCATGTTTGGAACATGGCATTGACACCGATATA
1 AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATCGATATA
* * *
52608277 TGAAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC
1 --AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATC
52608321 TTACCCTTTT
Statistics
Matches: 216, Mismatches: 56, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
43 20 0.09
45 15 0.07
48 128 0.59
50 53 0.25
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATCGATATA
Found at i:52608156 original size:96 final size:97
Alignment explanation
Indices: 52607992--52608317 Score: 425
Period size: 93 Copynumber: 3.4 Consensus size: 97
52607982 TAGGGTTATG
* * * * * *
52607992 AGAGCTAGTGTAAGACCATGTCTGGGACATGACATCAGCCTCGATATGTGAGCCATTGTAAGACC
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGGGCTAATGTAAGACC
* **
52608057 ATGTTTGGAACATGGCATCGGCA-TTTATATA
66 ATGTTTGGAACATGGCATTGGCACGATATATA
*
52608088 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGGGCTAGTGTAAGACC
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGGGCTAATGTAAGACC
*
52608153 ATGTTTGGAACATGGCATTGGCACCGATATATG
66 ATGTTTGGAACATGGCATTGGCA-CGATATATA
* *
52608186 AGAGCTAGTCTAAGACCATGTCT-GG----GGCATTGGCCTCGACATAG-GGGCTAATGTAAGAC
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACAT-GTGGGCTAATGTAAGAC
*
52608245 CATGTTTGGAACATGGCATTGACACCGATATATGA
65 CATGTTTGGAACATGGCATTGGCA-CGATATAT-A
*
52608280 A-AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
52608318 ATCTTACCCT
Statistics
Matches: 203, Mismatches: 18, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
93 81 0.40
94 4 0.02
96 81 0.40
97 2 0.01
98 35 0.17
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (97 bp):
AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGGGCTAATGTAAGACC
ATGTTTGGAACATGGCATTGGCACGATATATA
Found at i:52611794 original size:24 final size:24
Alignment explanation
Indices: 52611767--52611819 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
52611757 CGTGAAGTCA
52611767 TTGTCAATATTTTTGCATTGGATT
1 TTGTCAATATTTTTGCATTGGATT
**
52611791 TTGTCTGTATTTTTGCATTGGATT
1 TTGTCAATATTTTTGCATTGGATT
52611815 TTGTC
1 TTGTC
52611820 TGCATTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.09, G:0.19, T:0.57
Consensus pattern (24 bp):
TTGTCAATATTTTTGCATTGGATT
Found at i:52611820 original size:24 final size:24
Alignment explanation
Indices: 52611774--52611827 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
52611764 TCATTGTCAA
52611774 TATTTTTGCATTGGATTTTGTCTG
1 TATTTTTGCATTGGATTTTGTCTG
52611798 TATTTTTGCATTGGATTTTGTCTG
1 TATTTTTGCATTGGATTTTGTCTG
*
52611822 CATTTT
1 TATTTT
52611828 AGACTTGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.09, G:0.19, T:0.59
Consensus pattern (24 bp):
TATTTTTGCATTGGATTTTGTCTG
Found at i:52612154 original size:20 final size:19
Alignment explanation
Indices: 52612127--52612196 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
52612117 AATTAGAAAA
52612127 AAAATTCAAAATAATTTTC
1 AAAATTCAAAATAATTTTC
* * *
52612146 ATAAGTTCAAAACAATTTTT
1 A-AAATTCAAAATAATTTTC
*
52612166 AAAATTCAAAAT-ATTTATAA
1 AAAATTCAAAATAATTT-T-C
52612186 AAAATTCAAAA
1 AAAATTCAAAA
52612197 ATCATATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
18 4 0.10
19 11 0.26
20 27 0.64
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:52612367 original size:16 final size:16
Alignment explanation
Indices: 52612348--52612378 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52612338 TTGAAAAAGT
52612348 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
52612364 TTTCAAATTTATATG
1 TTTCAAATATATATG
52612379 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:52612493 original size:21 final size:20
Alignment explanation
Indices: 52612440--52612498 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
52612430 AATTTTTTTA
52612440 ATTTAACTCGAA--CAATTTC
1 ATTTAACTC-AACTCAATTTC
* *
52612459 ATTTAATTCGACTCGAATTTC
1 ATTTAACTCAACTC-AATTTC
*
52612480 ATTTCACTCAACTCAATTT
1 ATTTAACTCAACTCAATTT
52612499 GAAAAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 8 0.25
20 6 0.19
21 17 0.53
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTTAACTCAACTCAATTTC
Found at i:52615683 original size:291 final size:291
Alignment explanation
Indices: 52615159--52615732 Score: 1069
Period size: 291 Copynumber: 2.0 Consensus size: 291
52615149 GTACGCACCG
*
52615159 AGCAATGTATAATAAGAAACTCAATTTCTACAAAGGATTTCTAGAGTAATACTTTATAGAATAAT
1 AGCAATGTATAACAAGAAACTCAATTTCTACAAAGGATTTCTAGAGTAATACTTTATAGAATAAT
*
52615224 CTAATAATATTAGAAAATGAAGAAAGGAAAGAAAGAATATTAGAATTTGTTGGTGTATTTTCCAA
66 CTAATAATATTAGAAAATAAAGAAAGGAAAGAAAGAATATTAGAATTTGTTGGTGTATTTTCCAA
*
52615289 ATGAAATCTCATTCCTATTTATAGGAATTTTCATGTCTCTTCATATAGACATCTTTCAATAGGTG
131 ATGAAATCTCATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCTTTCAATAGGTG
52615354 TCTTTCTGAATAATAATGTCTTTAAAATAAACACATAATTATTCATTTAATATTATAACTATTTA
196 TCTTTCTGAATAATAATGTCTTTAAAATAAACACATAATTATTCATTTAATATTATAACTATTTA
52615419 AATAATATTATTTAAATAGTTATACGCATTA
261 AATAATATTATTTAAATAGTTATACGCATTA
52615450 AGCAATGTATAACAAGAAACTCAATTTCTACAAAGGATTTCT-GCAGTAATACTTTATAGAATAA
1 AGCAATGTATAACAAGAAACTCAATTTCTACAAAGGATTTCTAG-AGTAATACTTTATAGAATAA
* *
52615514 TCTAATAATATTAGAAAATAAAGGAAGGAAATAAAGAATATTAGAATTTGTTGGTGTATTTTCCA
65 TCTAATAATATTAGAAAATAAAGAAAGGAAAGAAAGAATATTAGAATTTGTTGGTGTATTTTCCA
*
52615579 AATGAAATCTCATTCCTATTTGTAGGAATTTTCATGTCTCTTCATAGAGACATCTTTCAATAGGT
130 AATGAAATCTCATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCTTTCAATAGGT
*
52615644 GTCTTTCTGAATAATAATGTCTTTAAAATAAACACATAATTATTTATTTAATATTATAACTATTT
195 GTCTTTCTGAATAATAATGTCTTTAAAATAAACACATAATTATTCATTTAATATTATAACTATTT
52615709 AAATAATATTATTTAAATAGTTAT
260 AAATAATATTATTTAAATAGTTAT
52615733 TATTCTTTTT
Statistics
Matches: 275, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
290 1 0.00
291 274 1.00
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (291 bp):
AGCAATGTATAACAAGAAACTCAATTTCTACAAAGGATTTCTAGAGTAATACTTTATAGAATAAT
CTAATAATATTAGAAAATAAAGAAAGGAAAGAAAGAATATTAGAATTTGTTGGTGTATTTTCCAA
ATGAAATCTCATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCTTTCAATAGGTG
TCTTTCTGAATAATAATGTCTTTAAAATAAACACATAATTATTCATTTAATATTATAACTATTTA
AATAATATTATTTAAATAGTTATACGCATTA
Found at i:52632495 original size:23 final size:21
Alignment explanation
Indices: 52632464--52632509 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
52632454 TCCTTATTCT
52632464 AATATACTAAAAGATAAAATAA
1 AATATACTAAAAGAT-AAATAA
* *
52632486 AATATTACTAGAATATAAATAA
1 AATA-TACTAAAAGATAAATAA
52632508 AA
1 AA
52632510 CTTATCTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (21 bp):
AATATACTAAAAGATAAATAA
Found at i:52636295 original size:19 final size:18
Alignment explanation
Indices: 52636273--52636312 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
52636263 TGAATAAAAC
*
52636273 TTATCTACCTAAATAAGAT
1 TTATCTACCCAAATAA-AT
52636292 TTATCTACCCAAATAAAT
1 TTATCTACCCAAATAAAT
52636310 TTA
1 TTA
52636313 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:52647766 original size:25 final size:25
Alignment explanation
Indices: 52647738--52647806 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
52647728 TTTTCTTTTC
*
52647738 TTTTCTTTTTCTTTTTTAAATTAGA
1 TTTTCTTTTTCTTTTTTAAAGTAGA
*
52647763 TTTTCTCTTTTC-TTTTTAGAGTAGA
1 TTTTCT-TTTTCTTTTTTAAAGTAGA
* *
52647788 TATTCTTTTTGTTGTTTTA
1 TTTTCTTTTTCTT-TTTTA
52647807 TATTTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.11
25 23 0.62
26 10 0.27
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.67
Consensus pattern (25 bp):
TTTTCTTTTTCTTTTTTAAAGTAGA
Found at i:52655857 original size:20 final size:20
Alignment explanation
Indices: 52655834--52655908 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
52655824 AACTTTGTTA
52655834 TCTGAGCTCATGAGTTGTGG
1 TCTGAGCTCATGAGTTGTGG
* *
52655854 TCTGAGCTCATGAAATATGTGA
1 TCTGAGCTCATG-AGT-TGTGG
* *
52655876 TCTAAACTCATGAGTTGTGG
1 TCTGAGCTCATGAGTTGTGG
* *
52655896 TATGAGTTCATGA
1 TCTGAGCTCATGA
52655909 TATATGTGAC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 25 0.58
21 4 0.09
22 14 0.33
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (20 bp):
TCTGAGCTCATGAGTTGTGG
Found at i:52666978 original size:11 final size:11
Alignment explanation
Indices: 52666964--52667008 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
52666954 AGATAAATAT
52666964 TATTTTATTAA
1 TATTTTATTAA
*
52666975 TATTTTAATAA
1 TATTTTATTAA
*
52666986 TATCTTTTATTAT
1 TA--TTTTATTAA
52666999 TATTTTATTA
1 TATTTTATTA
52667009 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 20 0.69
13 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Done.