Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold294
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: 984289
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.22
Warning! 328246 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:4650 original size:51 final size:50
Alignment explanation
Indices: 4569--4682 Score: 138
Period size: 51 Copynumber: 2.3 Consensus size: 50
4559 TGAACAGTAC
* * * * * *
4569 ATGTATCGAGACACTCTGTTTTTTATCCAGATGTATTGATACATTTTTTA
1 ATGTATCGATACACTCTGTTTGTTACCCAGATGTATCGATACATTATTCA
* *
4619 ATGTATCGATTCATTCTGGTTTGTTACCCAGATGTATCGATACATTATTCA
1 ATGTATCGATACACTCT-GTTTGTTACCCAGATGTATCGATACATTATTCA
*
4670 ATGTACCGATACA
1 ATGTATCGATACA
4683 TCTAGTTAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
50 14 0.26
51 39 0.74
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (50 bp):
ATGTATCGATACACTCTGTTTGTTACCCAGATGTATCGATACATTATTCA
Found at i:17612 original size:25 final size:25
Alignment explanation
Indices: 17583--17633 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
17573 AAACTTCACG
17583 TAAAGAACGAAAACCTGAAAACGCA
1 TAAAGAACGAAAACCTGAAAACGCA
*
17608 TAAAGGACGAAAACCTGAAAACGCA
1 TAAAGAACGAAAACCTGAAAACGCA
17633 T
1 T
17634 CATTCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.53, C:0.20, G:0.18, T:0.10
Consensus pattern (25 bp):
TAAAGAACGAAAACCTGAAAACGCA
Found at i:18933 original size:28 final size:28
Alignment explanation
Indices: 18893--19540 Score: 595
Period size: 28 Copynumber: 22.4 Consensus size: 28
18883 ATACGACCCT
* *
18893 TTTCAAAGTCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
18921 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
18949 TTTTAGAGTCCGCAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
18977 TCTT-AAAGCCCACAAGTCAGTGGTATCC
1 T-TTCAAAGCCCACAAGTCAGTGGCATCC
* * *
19005 TCTCAAAGCCCACAAGTTAGTGGTATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
19033 TCTCAAAGGCCACAAGTCAGTGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTC------AGTGGCATCC
** *
19067 TTTCAAAGTTCATAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
19094 TTTTCAAAGCCCACAAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
19123 TTCTCAAAGCCCATAAGTCAGTGGCA-CC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* * *
19151 TTTTCAAAGCCCACAAGTTAATGGCAACC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
19180 TTCTCAAAGCTCACAAGTCAATGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* *
19209 TTCTCAAAGCCCATAAGTTAGTGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
*
19238 TTTCAAAGCCCACACAAGTCAGTGGCAACC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCC
* *
19268 TCTCTCAAAGCCCACAAGTCGGTGGCAACCC
1 T-T-TCAAAGCCCACAAGTCAGTGGC-ATCC
* * *
19299 CTT-AAAGCCCACACAAGTCGGTGGCAACCTC
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ATC-C
* *
19330 TTTCAAAGCCCACAAGTCGGTGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
19358 TCTCTCAAAGCTCACAAGTTAGTGGCACCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
* * * *
19388 TTTTAAAGCTCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
19416 TTTCGAAGCCCACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
19444 TTTCGAAGCCCACAAGTTAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
19472 TTTCAAAGCCCACAAATCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
19500 TTTTAAAGCCCACAAGTCAGTGGTAATCC
1 TTTCAAAGCCCACAAGTCAGTGG-CATCC
19529 -TTCTAAAGCCCA
1 TTTC-AAAGCCCA
19541 TACAAATTGG
Statistics
Matches: 530, Mismatches: 63, Indels: 53
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.01
28 297 0.56
29 101 0.19
30 85 0.16
31 11 0.02
32 10 0.02
34 23 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:19067 original size:34 final size:34
Alignment explanation
Indices: 19020--19088 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
19010 AAGCCCACAA
*
19020 GTTAGTGGTATCCTCTCAAAGGCCACAAGTCAGT
1 GTTAGTGGCATCCTCTCAAAGGCCACAAGTCAGT
* ** *
19054 GTTAGTGGCATCCTTTCAAAGTTCATAAGTCAGT
1 GTTAGTGGCATCCTCTCAAAGGCCACAAGTCAGT
19088 G
1 G
19089 GCACCTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (34 bp):
GTTAGTGGCATCCTCTCAAAGGCCACAAGTCAGT
Found at i:19105 original size:90 final size:91
Alignment explanation
Indices: 18967--19540 Score: 342
Period size: 90 Copynumber: 6.5 Consensus size: 91
18957 TCCGCAAGTC
* * *
18967 AGTGGCATCCTCTTAAAGCCCACAAGTCAGTGGTATCCTCTCAAAGCCCACAAGTTAGTGGTATC
1 AGTGGCATCCTCTTAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAGTGGCATC
*
19032 C-TCTCAAAGGCCACAAGTCAGTGTT
66 CTTCTCAAAGCCCACAAGTCAGTGTT
** * *
19057 AGTGGCATCCT-TTCAAAGTTCATAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 AGTGGCATCCTCTT-AAAGCCCACAAGTCAGTGGCATCC-TCTCAAAGCCCACAAGTCAGTGGCA
*
19120 TCCTTCTCAAAGCCCATAAGTC------
64 TCCTTCTCAAAGCCCACAAGTCAGTGTT
* * * * * *
19142 AGTGGCA-CCTTTTCAAAGCCCACAAGTTAATGGCAACCTTCTCAAAGCTCACAAGTCAATGGCA
1 AGTGGCATCCTCTT-AAAGCCCACAAGTCAGTGGCATCC-TCTCAAAGCCCACAAGTCAGTGGCA
*
19206 TCCTTCTCAAAG-CC-C-A-T-A-AGTT
64 TCCTTCTCAAAGCCCACAAGTCAGTGTT
* *
19228 AGTGGCATCCT-TTCAAAGCCCACACAAGTCAGTGGCAACCTCTCTCAAAGCCCACAAGTCGGTG
1 AGTGGCATCCTCTT-AAAG-CC-CACAAGTCAGTGGC-ATC-CTCTCAAAGCCCACAAGTCAGTG
* * * * *
19292 GCAACC-CCTTAAAGCCCAC-A--CA-AGTC
61 GCATCCTTCTCAAAGCCCACAAGTCAGTGTT
* * * * * *
19318 GGTGGCAACCTCTTTCAAAGCCCACAAGTCGGTGGCAACCTCTCTCAAAGCTCACAAGTTAGTGG
1 AGTGGCATCCTC-TT-AAAGCCCACAAGTCAGTGGC-ATC-CTCTCAAAGCCCACAAGTCAGTGG
* * *
19383 CACCCTT-TTAAAGCTCAC-A---A--GTT
62 CATCCTTCTCAAAGCCCACAAGTCAGTGTT
* * * * * * * * *
19406 AGTGGCACCCT-TTCGAAGCCCACAAGTCAATGGCACCCTTTCGAAGCCCACAAGTTAATGGCAC
1 AGTGGCATCCTCTT-AAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAGTGGCAT
*
19470 CCTT-TCAAAGCCCACAA---A---TC
65 CCTTCTCAAAGCCCACAAGTCAGTGTT
* *
19490 AGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGTAATCCT-TCTAAAGCCCA
1 AGTGGCATCCTCTTAAAGCCCACAAGTCAGTGG-CATCCTCTC-AAAGCCCA
19541 TACAAATTGG
Statistics
Matches: 403, Mismatches: 56, Indels: 55
0.78 0.11 0.11
Matches are distributed among these distances:
82 1 0.00
83 1 0.00
84 69 0.17
85 46 0.11
86 71 0.18
87 5 0.01
88 29 0.07
89 33 0.08
90 123 0.31
91 18 0.04
92 7 0.02
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (91 bp):
AGTGGCATCCTCTTAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAGTGGCATC
CTTCTCAAAGCCCACAAGTCAGTGTT
Found at i:20686 original size:51 final size:50
Alignment explanation
Indices: 20605--20719 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 50
20595 TGAACAGTAC
* ** * *
20605 ATGTATCGATACATTCAGTTTTTTATCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCACTTTGATACCCAGATGTATCGATACATTATTCA
*
20655 ATGTATCGATAGATTCTACTTTGATACCCAGATGTATCGATACATTATTCA
1 ATGTATCGATACATTC-ACTTTGATACCCAGATGTATCGATACATTATTCA
20706 ATGTATCGATACAT
1 ATGTATCGATACAT
20720 CTAGTTAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 15 0.26
51 42 0.74
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (50 bp):
ATGTATCGATACATTCACTTTGATACCCAGATGTATCGATACATTATTCA
Found at i:21367 original size:13 final size:13
Alignment explanation
Indices: 21349--21374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21339 TACACAAAGT
21349 ATGTATCGATACA
1 ATGTATCGATACA
21362 ATGTATCGATACA
1 ATGTATCGATACA
21375 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21393 original size:34 final size:32
Alignment explanation
Indices: 21331--21395 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
21321 TAGCCAAACT
**
21331 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
21363 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
21396 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:25462 original size:15 final size:15
Alignment explanation
Indices: 25442--25472 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25432 TAAAAATGTC
*
25442 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
25457 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
25472 C
1 C
25473 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:27201 original size:13 final size:13
Alignment explanation
Indices: 27183--27207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27173 CATTTTTCTT
27183 TGTATCGATACAC
1 TGTATCGATACAC
27196 TGTATCGATACA
1 TGTATCGATACA
27208 GGGGGATTAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:27362 original size:20 final size:20
Alignment explanation
Indices: 27319--27364 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
27309 AAATCTTTTG
27319 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
27340 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
27360 CAAAA
1 CAAAA
27365 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:29777 original size:21 final size:20
Alignment explanation
Indices: 29731--29783 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
29721 GTAGCCAAAC
**
29731 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
29751 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACAC-AAAAAA
29771 TTGTATCGATACA
1 TTGTATCGATACA
29784 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:33586 original size:156 final size:155
Alignment explanation
Indices: 33417--34367 Score: 877
Period size: 157 Copynumber: 6.1 Consensus size: 155
33407 TACTTAGTCA
* * *
33417 TCCTAGAGAACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATATCTATCTTCGGCATA
1 TCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATA-CTACCTTCGGCATA
* * * *
33482 AAAGTAGACCCGATGATAACCTAGGACTTGGTTCTAAAAAAAATACGAAAATGCCTTTAAGGGAT
65 AAAGCAGACCCGATGACAACCTAGGACTTGGTTCTAAAAAAATTACGAAAATGCCTCTAAGGGAT
33547 ACTTTCGAATTAGAAGTGCCCGATAC
130 ACTTTCGAATTAGAAGTGCCCGATAC
* *
33573 TCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCTACCTTTGGCATA
1 TCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATA-CTACCTTCGGCATA
* * * * * * *
33638 AAAGC-GAACCTAGTGAAAACCTAGGACTAT-ATTCT-AAAAAATTATGAAAATACCT-TTAGAG
65 AAAGCAGACCCGA-TGACAACCTAGGACT-TGGTTCTAAAAAAATTACGAAAATGCCTCTAAG-G
* * * *
33699 GATACCTTCGACTTAGAAATGCCCAATAC
127 GATACTTTCGAATTAGAAGTGCCCGATAC
* * * * * * *
33728 CCCTAAAGGACTTAAAAA-GACTATAGACGGGATAAACCTATCCTAAATACTCATCTTCAGCATA
1 TCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATACT-ACCTTCGGCATA
** ** * * * * * *
33792 AAAGTGGACTTGGTAACAACCTAAGACTAGGTTCTGAAAAAAATTAAGAAAATGCCTCTAGGGGA
65 AAAGCAGACCCGATGACAACCTAGGACTTGGTTCT-AAAAAAATTACGAAAATGCCTCTAAGGGA
* *
33857 TACCTTCGAATTAGAAGTGCTCGATAC
129 TACTTTCGAATTAGAAGTGCCCGATAC
* * * *
33884 TCCTAAAGGACTTAAAAAAGATTATAGATGGGATGAACCTATCCTAAATACGCACCTTTGGCATA
1 TCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATAC-TACCTTCGGCATA
* * * * *
33949 AAAGCAAACCCGGTTACAACCTAGGACTTGATTCTGAAAAAAATTACGAAAATGCCTCTAATGGA
65 AAAGCAGACCCGATGACAACCTAGGACTTGGTTCT-AAAAAAATTACGAAAATGCCTCTAAGGGA
* *
34014 TAGC-TCCGATTTAGAAGTGCCCGATAC
129 TA-CTTTCGAATTAGAAGTGCCCGATAC
* * * ** **
34041 CCCTAAAAGACTTAAAAAGGATTATAAACAAGATGAACCTATCCTAAATACTCACCTTCAACATA
1 TCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATACT-ACCTTCGGCATA
* * * ** * * *
34106 AAAGCAGA-CCTATGACAACCTAGGAC-TCGATCTTGAAAAATTACAAAAATACCT-TTAGGAGA
65 AAAGCAGACCCGATGACAACCTAGGACTTGGTTCTAAAAAAATTACGAAAATGCCTCTAAGG-GA
* * *
34168 TATTTTCGACTTAGAAGTACCCGATAC
129 TACTTTCGAATTAGAAGTGCCCGATAC
* * ** * * * **
34195 CCCTAAAGAACTTAAAAAGGATTATA-AAAAGATGAACCTATCTTAAAGGCAC-ACCTTTGGTGT
1 TCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAA--TACTACCTTCGGCAT
* ** * **
34258 AAAAGCAGACCCGGTGGTAACCTAGGACTTGGTTCTAAAGAAATTAAAAAAATGCCTCTAAGGGA
64 AAAAGCAGACCCGATGACAACCTAGGACTTGGTTCTAAAAAAATTACGAAAATGCCTCTAAGGGA
* *
34323 TACTTTTGACA-TAGAAGTACCC-AGTA-
129 TACTTTCGA-ATTAGAAGTGCCCGA-TAC
*
34349 TCCCTAAAGGATTTAAAAA
1 T-CCTAAAGGACTTAAAAA
34368 CATGAGGGAA
Statistics
Matches: 648, Mismatches: 124, Indels: 47
0.79 0.15 0.06
Matches are distributed among these distances:
153 39 0.06
154 140 0.22
155 131 0.20
156 161 0.25
157 176 0.27
158 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (155 bp):
TCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATACTACCTTCGGCATAA
AAGCAGACCCGATGACAACCTAGGACTTGGTTCTAAAAAAATTACGAAAATGCCTCTAAGGGATA
CTTTCGAATTAGAAGTGCCCGATAC
Found at i:34147 original size:311 final size:308
Alignment explanation
Indices: 33426--34325 Score: 1013
Period size: 311 Copynumber: 2.9 Consensus size: 308
33416 ATCCTAGAGA
* *
33426 ACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATA-TCTATCTTCGGCATAAAAGTAGA
1 ACTTAAAAAGGATTATAGACGAGATGAACCTATCCTAAATACTC-ATCTTCAGCATAAAAGTAGA
* * * * ** * * *
33490 CCCGATGATAACCTAGGACTTGGTTCTAAAAAAAATACGAAAATGCCTTTAAGGGATACTTTCGA
65 -CCTATGACAACCTAGGAC-TAGATCTTGAAAAATTAAGAAAATGCCTTTAGGGGATACTTTCGA
33555 ATTAGAAGTGCCCGATACTCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAA
128 ATTAGAAGTGCCCGATACTCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAA
* ** *
33620 ATACCTACCTTTGGCATAAAAGCGAACCTAGTGAAAACCTAGGACTAT-ATTCT-AAAAAATTAT
193 ATACC-ACCTTTGGCATAAAAGCAAACCCGGTGAAAACCTAGGACT-TGATTCTAAAAAAATTAA
* * * *
33683 GAAAATACCTTTAGAGGATACCTTCGACTTAGAAATGCCCAATACCCCTAAAGG
256 GAAAATGCCTCTA-AGGATACCTCCGACTTAGAAATGCCCAATACCCCTAAAAG
* * * *
33737 ACTTAAAAA-GACTATAGACGGGATAAACCTATCCTAAATACTCATCTTCAGCATAAAAGTGGAC
1 ACTTAAAAAGGATTATAGACGAGATGAACCTATCCTAAATACTCATCTTCAGCATAAAAGTAGAC
* * * * * * *
33801 TTGGTAACAACCTAAGACTAGGT-TCTGAAAAAAATTAAGAAAATGCCTCTAGGGGATACCTTCG
66 CT-ATGACAACCTAGGACTAGATCT-TG--AAAAATTAAGAAAATGCCTTTAGGGGATACTTTCG
* *
33865 AATTAGAAGTGCTCGATACTCCTAAAGGACTTAAAAAAGATTATAGATGGGATGAACCTATCCTA
127 AATTAGAAGTGCCCGATACTCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTA
* *
33930 AATACGCACCTTTGGCATAAAAGCAAACCCGGTTACAACCTAGGACTTGATTCTGAAAAAAATTA
192 AATAC-CACCTTTGGCATAAAAGCAAACCCGGTGAAAACCTAGGACTTGATTCT-AAAAAAATTA
* * * * *
33995 CGAAAATGCCTCTAATGGATAGCTCCGATTTAGAAGTGCCCGATACCCCTAAAAG
255 AGAAAATGCCTCTAA-GGATACCTCCGACTTAGAAATGCCCAATACCCCTAAAAG
* * * * *
34050 ACTTAAAAAGGATTATAAACAAGATGAACCTATCCTAAATACTCACCTTCAACATAAAAGCAGAC
1 ACTTAAAAAGGATTATAGACGAGATGAACCTATCCTAAATACTCATCTTCAGCATAAAAGTAGAC
* * * * *
34115 CTATGACAACCTAGGACTCGATCTTGAAAAATTACA-AAAATACCTTTAGGAGATATTTTCGACT
66 CTATGACAACCTAGGACTAGATCTTGAAAAATTA-AGAAAATGCCTTTAGGGGATACTTTCGAAT
* * * *** * *
34179 TAGAAGTACCCGATACCCCTAAAGAACTTAAAAAGGATTATA-AAAAGATGAACCTATCTTAAAG
130 TAGAAGTGCCCGATACTCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAAT
* ** * ** * * *
34243 GCACACCTTTGGTGTAAAAGCAGACCCGGTGGTAACCTAGGACTTGGTTCTAAAGAAATTAAAAA
195 AC-CACCTTTGGCATAAAAGCAAACCCGGTGAAAACCTAGGACTTGATTCTAAAAAAATTAAGAA
34308 AATGCCTCTAAGGGATAC
259 AATGCCTCTAA-GGATAC
34326 TTTTGACATA
Statistics
Matches: 494, Mismatches: 82, Indels: 28
0.82 0.14 0.05
Matches are distributed among these distances:
308 1 0.00
309 31 0.06
310 116 0.23
311 216 0.44
312 3 0.01
313 79 0.16
314 48 0.10
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (308 bp):
ACTTAAAAAGGATTATAGACGAGATGAACCTATCCTAAATACTCATCTTCAGCATAAAAGTAGAC
CTATGACAACCTAGGACTAGATCTTGAAAAATTAAGAAAATGCCTTTAGGGGATACTTTCGAATT
AGAAGTGCCCGATACTCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATA
CCACCTTTGGCATAAAAGCAAACCCGGTGAAAACCTAGGACTTGATTCTAAAAAAATTAAGAAAA
TGCCTCTAAGGATACCTCCGACTTAGAAATGCCCAATACCCCTAAAAG
Found at i:36297 original size:165 final size:165
Alignment explanation
Indices: 36117--36562 Score: 423
Period size: 165 Copynumber: 2.7 Consensus size: 165
36107 GAAAATAGTG
* *
36117 AATTTTAA-GGAAAAAAAAGAAAACTCAAGAAAATAAATGAAAATTTTAAAAATGATTTATTGTG
1 AATTTTAATAGAAAAAAAAGAAAACTCATGAAAATAAATGAAAATTTTAAAAATGATTTA-TGTG
* * *
36181 AATTAAATGATAATATTTGATAAATTTTAAAAATT-TCAAACTAAGAAAAAACCCTT-AAAAACC
65 AATTAAATGATAATATTTGATGAATTTTAAAAATTAT-AAACCAAGAAAAAACCCTTCAAAAACA
* *
36244 TTTATGGAATAGAAAACTC-AATTTGTCGAAAATCAAG-G
129 TTTATGGAATAGAAAACTCGAATTT-T-AAAAAT-AAGAA
* * * * *
36282 AA-TTTAGA-AG-AAAAAATGAAACACTTATGAAAATAAATG-AATTTTTCAAAACTGATTCACT
1 AATTTTA-ATAGAAAAAAAAGAAA-ACTCATGAAAATAAATGAAAATTTT-AAAAATGATTTA-T
* * * *
36343 ATGAATTAAATGATGATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCCTTCGAAAA
62 GTGAATTAAATGATAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAAACCCTTCAAAAA
* ** *
36408 TATTTATGGCGTAGAAAACTCTGTATTTTAAAAATAAGAA
127 CATTTATGGAATAGAAAACTC-GAATTTTAAAAATAAGAA
*
36448 AATTTTAATA-AAAAATAAAAAAAACTCATG-AAATAAA--AAGAACTTTTAAAAACTGATTTGA
1 AATTTTAATAGAAAAA-AAAGAAAACTCATGAAAATAAATGAA-AA-TTTTAAAAA-TGATTT-A
* * ** **
36509 TGCGAATTAAATAATAATATTTGATGAATTTTAAATTTTATAAAATAAGAAAAA
61 TGTGAATTAAATGATAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAA
36563 TCCTCCCGAA
Statistics
Matches: 229, Mismatches: 35, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
164 20 0.09
165 86 0.38
166 42 0.18
167 71 0.31
168 10 0.04
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (165 bp):
AATTTTAATAGAAAAAAAAGAAAACTCATGAAAATAAATGAAAATTTTAAAAATGATTTATGTGA
ATTAAATGATAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAAACCCTTCAAAAACATT
TATGGAATAGAAAACTCGAATTTTAAAAATAAGAA
Found at i:40153 original size:13 final size:13
Alignment explanation
Indices: 40113--40165 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
40103 TCGTTACAAG
40113 CAATGTATCGATA
1 CAATGTATCGATA
40126 C-AT-T-TC-AT-
1 CAATGTATCGATA
40134 C-ATGTATCGATA
1 CAATGTATCGATA
40146 CAATGTATCGATA
1 CAATGTATCGATA
*
40159 CATTGTA
1 CAATGTA
40166 CCATGTATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 3 0.09
9 3 0.09
10 4 0.12
11 3 0.09
12 3 0.09
13 18 0.53
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:40153 original size:33 final size:33
Alignment explanation
Indices: 40113--40181 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
40103 TCGTTACAAG
* *
40113 CAATGTATCGATACATT-TCATCATGTATCGATA
1 CAATGTATCGATACATTGT-ACCATGTATCGAAA
40146 CAATGTATCGATACATTGTACCATGTATCGAAA
1 CAATGTATCGATACATTGTACCATGTATCGAAA
40179 CAA
1 CAA
40182 ATAGTGATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGAAA
Found at i:40254 original size:19 final size:19
Alignment explanation
Indices: 40210--40282 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
40200 CTGCCAGTTT
* **
40210 CATGTATCAATACAATTGTC
1 CATGTATCGATACAA-TGAA
40230 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
40249 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAATG-AA
* *
40269 GATGTATTGATACA
1 CATGTATCGATACA
40283 TGTGGGTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 18 0.39
20 28 0.61
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:41857 original size:33 final size:33
Alignment explanation
Indices: 41820--41886 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
41810 TTCAACGATC
41820 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
41853 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
41886 T
1 T
41887 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:41858 original size:13 final size:13
Alignment explanation
Indices: 41840--41864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41830 CATAAAATGT
41840 TGTATCGATACAA
1 TGTATCGATACAA
41853 TGTATCGATACA
1 TGTATCGATACA
41865 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:41948 original size:13 final size:13
Alignment explanation
Indices: 41930--41954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41920 ATTACTCACA
41930 TGTATCGATACAT
1 TGTATCGATACAT
41943 TGTATCGATACA
1 TGTATCGATACA
41955 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:52561 original size:20 final size:20
Alignment explanation
Indices: 52536--52588 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
52526 ATTACAAGCA
*
52536 ATGTATCGATACATT-TCATC
1 ATGTATCGATACATTGT-ACC
52556 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
*
52576 ATGTAGCGATACA
1 ATGTATCGATACA
52589 AATAGTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:52637 original size:13 final size:13
Alignment explanation
Indices: 52619--52645 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52609 TGCCAGTTTC
52619 ATGTATCGATACA
1 ATGTATCGATACA
52632 ATGTATCGATACA
1 ATGTATCGATACA
52645 A
1 A
52646 AGCAAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:53501 original size:23 final size:23
Alignment explanation
Indices: 53472--53552 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
53462 GCTATTTTCT
53472 TGCTTGTTTGCTTGTTGTCTTGC
1 TGCTTGTTTGCTTGTTGTCTTGC
*
53495 TGCTTGTTCGTGCTTGTTGTTTTGC
1 TGCTTGTT--TGCTTGTTGTCTTGC
* *
53520 TTG-TTGTTTGCTTGCTGTCTTAC
1 -TGCTTGTTTGCTTGTTGTCTTGC
*
53543 TACTTGTTTG
1 TGCTTGTTTG
53553 TGTTTGCTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.02
23 27 0.55
25 19 0.39
26 2 0.04
ACGTcount: A:0.02, C:0.16, G:0.25, T:0.57
Consensus pattern (23 bp):
TGCTTGTTTGCTTGTTGTCTTGC
Found at i:53512 original size:25 final size:23
Alignment explanation
Indices: 53472--53579 Score: 85
Period size: 25 Copynumber: 4.5 Consensus size: 23
53462 GCTATTTTCT
*
53472 TGCTTGTTTGCTTGTTGTCTTGC
1 TGCTTGTTTGCTTGCTGTCTTGC
* *
53495 TGCTTGTTCGTGCTTGTTGTTTTGC
1 TGCTTGTT--TGCTTGCTGTCTTGC
*
53520 TTG-TTGTTTGCTTGCTGTCTTAC
1 -TGCTTGTTTGCTTGCTGTCTTGC
* * *
53543 TACTTGTTTGTGTTTGCTGTTTTGC
1 TGCTTG-TT-TGCTTGCTGTCTTGC
53568 TTGC-TGTTTGCT
1 -TGCTTGTTTGCT
53580 GCTATTTTGC
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
22 1 0.01
23 26 0.38
24 4 0.06
25 33 0.49
26 4 0.06
ACGTcount: A:0.02, C:0.16, G:0.25, T:0.57
Consensus pattern (23 bp):
TGCTTGTTTGCTTGCTGTCTTGC
Found at i:53531 original size:48 final size:48
Alignment explanation
Indices: 53460--53579 Score: 152
Period size: 48 Copynumber: 2.5 Consensus size: 48
53450 TGTTTTTGTT
* * * *
53460 TTGCTATTTT-CTTGCTTGTTTGCTTGTTGTCTTGCTGCTTGTTCGTGC
1 TTGCTGTTTTGCTTG-TTGTTTGCTTGCTGTCTTACTACTTGTTCGTGC
* * *
53508 TTGTTGTTTTGCTTGTTGTTTGCTTGCTGTCTTACTACTTGTTTGTGT
1 TTGCTGTTTTGCTTGTTGTTTGCTTGCTGTCTTACTACTTGTTCGTGC
*
53556 TTGCTGTTTTGCTTGCTGTTTGCT
1 TTGCTGTTTTGCTTGTTGTTTGCT
53580 GCTATTTTGC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 58 0.94
49 4 0.06
ACGTcount: A:0.03, C:0.16, G:0.23, T:0.58
Consensus pattern (48 bp):
TTGCTGTTTTGCTTGTTGTTTGCTTGCTGTCTTACTACTTGTTCGTGC
Found at i:53573 original size:12 final size:12
Alignment explanation
Indices: 53460--53602 Score: 75
Period size: 12 Copynumber: 12.1 Consensus size: 12
53450 TGTTTTTGTT
*
53460 TTGCTATTTT-C
1 TTGCTGTTTTGC
53471 TTGCT-TGTTTGC
1 TTGCTGT-TTTGC
* *
53483 TTGTTGTCTTGC
1 TTGCTGTTTTGC
*
53495 -TGCTTGTTCGTGC
1 TTGC-TGTT-TTGC
*
53508 TTGTTGTTTTGC
1 TTGCTGTTTTGC
*
53520 TTGTTG-TTTGC
1 TTGCTGTTTTGC
* *
53531 TTGCTGTCTTAC
1 TTGCTGTTTTGC
* *
53543 -TACTTGTTTGTGT
1 TTGC-TGTTT-TGC
53556 TTGCTGTTTTGC
1 TTGCTGTTTTGC
53568 TTGCTG-TTTGC
1 TTGCTGTTTTGC
*
53579 -TGCTATTTTGC
1 TTGCTGTTTTGC
* *
53590 TGGCTGTGTTGC
1 TTGCTGTTTTGC
53602 T
1 T
53603 ATTGTTTTTG
Statistics
Matches: 100, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
10 5 0.05
11 32 0.32
12 45 0.45
13 14 0.14
14 4 0.04
ACGTcount: A:0.03, C:0.16, G:0.24, T:0.57
Consensus pattern (12 bp):
TTGCTGTTTTGC
Found at i:53582 original size:22 final size:23
Alignment explanation
Indices: 53557--53602 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
53547 TGTTTGTGTT
* *
53557 TGCTGTTTTGCTTGCTGT-TTGC
1 TGCTATTTTGCTGGCTGTGTTGC
53579 TGCTATTTTGCTGGCTGTGTTGC
1 TGCTATTTTGCTGGCTGTGTTGC
53602 T
1 T
53603 ATTGTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.02, C:0.17, G:0.28, T:0.52
Consensus pattern (23 bp):
TGCTATTTTGCTGGCTGTGTTGC
Found at i:54238 original size:10 final size:10
Alignment explanation
Indices: 54225--54259 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
54215 TAATATATTA
54225 TTATATTTTT
1 TTATATTTTT
*
54235 TTATTATTATT
1 TTA-TATTTTT
54246 TTATATTTTT
1 TTATATTTTT
54256 TTAT
1 TTAT
54260 TTAGTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATATTTTT
Found at i:54251 original size:21 final size:23
Alignment explanation
Indices: 54220--54275 Score: 89
Period size: 21 Copynumber: 2.5 Consensus size: 23
54210 TATTATAATA
54220 TATTATTATATTTTTTTA-TTA-T
1 TATT-TTATATTTTTTTATTTAGT
54242 TATTTTATATTTTTTTATTTAGT
1 TATTTTATATTTTTTTATTTAGT
54265 TATTTTATATT
1 TATTTTATATT
54276 AAATAAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.41
22 7 0.22
23 12 0.38
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTTTATATTTTTTTATTTAGT
Found at i:60434 original size:20 final size:20
Alignment explanation
Indices: 60388--60446 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
60378 CGATACACAT
*
60388 ATAAATGTTATTGATACAATTC
1 ATAAATG-TATTGATAC-ATCC
60410 A-AAATGTATTGATACATCC
1 ATAAATGTATTGATACATCC
* *
60429 ATAAATGAATCGATACAT
1 ATAAATGTATTGATACAT
60447 TGAGTTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.12
20 23 0.70
21 5 0.15
22 1 0.03
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (20 bp):
ATAAATGTATTGATACATCC
Found at i:61778 original size:20 final size:20
Alignment explanation
Indices: 61755--61827 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
61745 ACAATTCAAA
61755 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
61775 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
61796 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
61816 GTATCGATACAT
1 GTATCGATACAT
61828 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:61884 original size:13 final size:13
Alignment explanation
Indices: 61866--61891 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61856 TACAGAAAGT
61866 ATGTATCGATACA
1 ATGTATCGATACA
61879 ATGTATCGATACA
1 ATGTATCGATACA
61892 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:61889 original size:32 final size:33
Alignment explanation
Indices: 61848--61911 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
61838 TAGCCAAACT
* **
61848 TGTATCGATACAGAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
61880 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
61912 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:68068 original size:20 final size:21
Alignment explanation
Indices: 67989--68067 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
67979 AATGTCCAAA
*
67989 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
68009 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
68034 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
68054 TTGTATCGATACAT
1 ATGTATCGATACAT
68068 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:68072 original size:13 final size:13
Alignment explanation
Indices: 68054--68079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68044 ACATTTTTCT
68054 TTGTATCGATACA
1 TTGTATCGATACA
68067 TTGTATCGATACA
1 TTGTATCGATACA
68080 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:70554 original size:20 final size:20
Alignment explanation
Indices: 70531--70603 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
70521 ACAATTCAAA
70531 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
70551 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
70572 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
70592 GTATCGATACAT
1 GTATCGATACAT
70604 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:70660 original size:13 final size:13
Alignment explanation
Indices: 70642--70667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70632 TACAGAAAGT
70642 ATGTATCGATACA
1 ATGTATCGATACA
70655 ATGTATCGATACA
1 ATGTATCGATACA
70668 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:70665 original size:32 final size:33
Alignment explanation
Indices: 70624--70687 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
70614 TAGCCAAACT
* **
70624 TGTATCGATACAGAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
70656 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
70688 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:76358 original size:35 final size:35
Alignment explanation
Indices: 76310--76379 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
76300 GGTTTTCCAG
*
76310 ATTGTATCGATACAATGAATAATGTAT-AGATACAT
1 ATTGTATCAATACAATGAATAATGTATCA-ATACAT
* *
76345 ATTGTATCAATACAATTACTAATGTATCAATACAT
1 ATTGTATCAATACAATGAATAATGTATCAATACAT
76380 TCTCTATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (35 bp):
ATTGTATCAATACAATGAATAATGTATCAATACAT
Found at i:77791 original size:13 final size:13
Alignment explanation
Indices: 77773--77803 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
77763 GTTACAAGCT
77773 ATGTATCGATACA
1 ATGTATCGATACA
77786 ATGTATCGATACA
1 ATGTATCGATACA
*
77799 TTGTA
1 ATGTA
77804 CTATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:77888 original size:13 final size:13
Alignment explanation
Indices: 77870--77896 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
77860 CAATTTGTCC
77870 ATGTATCGATACA
1 ATGTATCGATACA
77883 ATGTATCGATACA
1 ATGTATCGATACA
77896 A
1 A
77897 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:86564 original size:13 final size:13
Alignment explanation
Indices: 86546--86609 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
86536 ACATTTCTTC
86546 ATGTATCGATACA
1 ATGTATCGATACA
86559 ATGTATCGATAC-
1 ATGTATCGATACA
*
86571 AT-T-TC--TTC-
1 ATGTATCGATACA
*
86579 ATGTATCGATATA
1 ATGTATCGATACA
86592 ATGTATCGATACA
1 ATGTATCGATACA
*
86605 TTGTA
1 ATGTA
86610 CCATGTATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
8 4 0.10
9 1 0.02
10 4 0.10
11 1 0.02
12 3 0.07
13 28 0.68
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:86564 original size:33 final size:33
Alignment explanation
Indices: 86526--86625 Score: 150
Period size: 33 Copynumber: 3.0 Consensus size: 33
86516 GTTACAAGCT
*
86526 ATGTATCAATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
*
86559 ATGTATCGATACATTTCTTCATGTATCGATATA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
86592 ATGTATCGATACATTGTAC--CATGTATCGATACA
1 ATGTATCGATACATT-T-CTTCATGTATCGATACA
86625 A
1 A
86626 ATATTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
33 60 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATTTCTTCATGTATCGATACA
Found at i:86584 original size:20 final size:20
Alignment explanation
Indices: 86526--86589 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
86516 GTTACAAGCT
*
86526 ATGTATCAATACATTTCTTC
1 ATGTATCGATACATTTCTTC
86546 ATGTATCGATACA-------
1 ATGTATCGATACATTTCTTC
86559 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
86579 ATGTATCGATA
1 ATGTATCGATA
86590 TAATGTATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 13 0.36
20 23 0.64
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTCTTC
Found at i:86699 original size:19 final size:19
Alignment explanation
Indices: 86675--86739 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
86665 ACAATTTGTC
86675 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
86694 CATGTATCGATAC-AT---
1 CATGTATCGATACAATGAA
86709 --TGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
86726 CATGTATCGATACA
1 CATGTATCGATACA
86740 TTGTATCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
14 2 0.05
18 2 0.05
19 25 0.62
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:86714 original size:13 final size:12
Alignment explanation
Indices: 86675--86752 Score: 68
Period size: 13 Copynumber: 7.2 Consensus size: 12
86665 ACAATTTGTC
86675 CATGTATCGATA
1 CATGTATCGATA
86687 CA---AT-GA-A
1 CATGTATCGATA
86694 CATGTATCGATA
1 CATGTATCGATA
86706 CATTGTATCGATA
1 CA-TGTATCGATA
86719 CA---AT-GA-A
1 CATGTATCGATA
86726 CATGTATCGATA
1 CATGTATCGATA
86738 CATTGTATCGATA
1 CA-TGTATCGATA
86751 CA
1 CA
86753 AAGCAGCATG
Statistics
Matches: 54, Mismatches: 0, Indels: 23
0.70 0.00 0.30
Matches are distributed among these distances:
7 6 0.11
8 4 0.07
9 4 0.07
10 4 0.07
11 4 0.07
12 8 0.15
13 24 0.44
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:86718 original size:32 final size:32
Alignment explanation
Indices: 86677--86773 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
86667 AATTTGTCCA
86677 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAATGAACATGTATCGATACAT
86709 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAATGAACATGTATCGATACAT
* *
86741 TGTATCGATACAAAGCAGCATGTATCGATACAT
1 TGTATCGATACAATG-AACATGTATCGATACAT
86774 CTGGGTGTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 46 0.74
33 16 0.26
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAATGAACATGTATCGATACAT
Found at i:88996 original size:20 final size:20
Alignment explanation
Indices: 88971--89036 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
88961 AACCCTCATT
88971 TGTATCAACACATAT-ATAAA
1 TGTATCAACACAT-TCATAAA
88991 TGTATCGATACA-ATTCA-AAA
1 TGTATC-A-ACACATTCATAAA
* *
89011 TGTATCAATACATTGATAAA
1 TGTATCAACACATTCATAAA
89031 TGTATC
1 TGTATC
89037 GATACATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.05
19 5 0.13
20 25 0.64
21 4 0.10
22 3 0.08
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (20 bp):
TGTATCAACACATTCATAAA
Found at i:89041 original size:20 final size:20
Alignment explanation
Indices: 88986--89046 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
88976 CAACACATAT
*
88986 ATAAATGTATCGATACAATTC
1 ATAAATGTATCGATAC-ATTG
*
89007 A-AAATGTATCAATACATTG
1 ATAAATGTATCGATACATTG
89026 ATAAATGTATCGATACATTG
1 ATAAATGTATCGATACATTG
89046 A
1 A
89047 GTCCAACGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.11
20 31 0.86
21 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (20 bp):
ATAAATGTATCGATACATTG
Found at i:89126 original size:82 final size:81
Alignment explanation
Indices: 88989--89185 Score: 272
Period size: 82 Copynumber: 2.4 Consensus size: 81
88979 CACATATATA
* *
88989 AATGTATCGATACAATTCAA--AATGTATCAATACATTGATAAATGTATCGATACATTGAGTCCA
1 AATGTATCGATAC-ATT-AAGTAATATATCAATACATCGATAAATGTATCGATACATTGAGTCCA
* *
89052 ACGGCTAGTTTTTTAAAGC
64 ACGGCTAG-TTTTAAAACC
* **
89071 AATGTATTGATACATTAAGTAATATATCAATACATCGATAAATGTATCGATACATTGAGTTTAAC
1 AATGTATCGATACATTAAGTAATATATCAATACATCGATAAATGTATCGATACATTGAGTCCAAC
89136 GGCTAGTTTTAAAACC
66 GGCTAGTTTTAAAACC
* *
89152 AATGTATCGATACATTAAGTAATAAATCGATACA
1 AATGTATCGATACATTAAGTAATATATCAATACA
89186 ATGACGCGAA
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
80 2 0.02
81 42 0.41
82 59 0.57
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (81 bp):
AATGTATCGATACATTAAGTAATATATCAATACATCGATAAATGTATCGATACATTGAGTCCAAC
GGCTAGTTTTAAAACC
Found at i:89616 original size:20 final size:20
Alignment explanation
Indices: 89591--89628 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
89581 CTTGAAACGA
89591 TAGATTTGTAAGGTTATACC
1 TAGATTTGTAAGGTTATACC
89611 TAGATTTGTAAGGTTATA
1 TAGATTTGTAAGGTTATA
89629 TCTTGGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (20 bp):
TAGATTTGTAAGGTTATACC
Found at i:94887 original size:78 final size:78
Alignment explanation
Indices: 94648--94955 Score: 302
Period size: 78 Copynumber: 3.9 Consensus size: 78
94638 ACGGGGCTAA
* * * * * **
94648 AGTATCCCCACTAAAATGGTGGGGCTGGAGTATCCCCTAAGATGAAAAAAATTCCATGTTTGGGA
1 AGTATCCCCTC-AAAATGATGGGGTTGGAGTATCCCTTGAGATG---AAAATTCGGTGTTTGGGA
94713 AATAAAAATAGGGTTGG
62 AATAAAAATAGGGTTGG
* * * * *
94730 AGTATCCCCTCAGAAATGGTGGGGTTGGTGTATCCCTTAAGATGAAAATTCGGTGTTTTAGG-AG
1 AGTATCCCCTCA-AAATGATGGGGTTGGAGTATCCCTTGAGATGAAAATTCGGTG-TTTGGGAAA
*
94794 TAAAAACAGGGTTGG
64 TAAAAATAGGGTTGG
* * * **
94809 AGTAT-CTCTCGAAAATGCT-GGGTTGGAATATCCCTTGAGATGAAAAATTTAGTGTTTGGGAAA
1 AGTATCCCCTC-AAAATGATGGGGTTGGAGTATCCCTTGAGATG-AAAATTCGGTGTTTGGGAAA
*
94872 TAAAAATAGGATTGG
64 TAAAAATAGGGTTGG
*
94887 AGTATCCCCTTAAAAATGATGGGGTTGGAGTAT--CTTCGAGATGAAAATTCGGTGTTTGGGAAA
1 AGTATCCCC-TCAAAATGATGGGGTTGGAGTATCCCTT-GAGATGAAAATTCGGTGTTTGGGAAA
*
94950 TGAAAA
64 TAAAAA
94956 CGGGGGTTGG
Statistics
Matches: 190, Mismatches: 27, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
77 25 0.13
78 64 0.34
79 45 0.24
80 17 0.09
81 1 0.01
82 38 0.20
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (78 bp):
AGTATCCCCTCAAAATGATGGGGTTGGAGTATCCCTTGAGATGAAAATTCGGTGTTTGGGAAATA
AAAATAGGGTTGG
Found at i:97435 original size:51 final size:52
Alignment explanation
Indices: 97336--97455 Score: 163
Period size: 51 Copynumber: 2.3 Consensus size: 52
97326 TGCATTGAAG
** * **
97336 AATGTATCGATATTTTTGGGTCAAAAACTTAAAATGTATTGATACAATGA-A
1 AATGTATCGATACATTTGGGTCAAAAACCTAAAATGTATCAATACAATGAGA
*
97387 AAGTGTATCGATACATTTGGGTC-AAAACCTAGAATGTATCAATACAATGAGA
1 AA-TGTATCGATACATTTGGGTCAAAAACCTAAAATGTATCAATACAATGAGA
97439 AATGTATCGATACATTT
1 AATGTATCGATACATTT
97456 TCCTTTGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 40 0.66
52 21 0.34
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (52 bp):
AATGTATCGATACATTTGGGTCAAAAACCTAAAATGTATCAATACAATGAGA
Found at i:97519 original size:20 final size:21
Alignment explanation
Indices: 97494--97544 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
97484 CATGGTCCTA
97494 TATCGATACAGTCACTTA-TG
1 TATCGATACAGTCACTTATTG
* *
97514 TATCGATACATTCATTTATTG
1 TATCGATACAGTCACTTATTG
*
97535 TATCAATACA
1 TATCGATACA
97545 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (21 bp):
TATCGATACAGTCACTTATTG
Found at i:100102 original size:13 final size:13
Alignment explanation
Indices: 100084--100109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100074 TACAGCAAGT
100084 ATGTATCGATACA
1 ATGTATCGATACA
100097 ATGTATCGATACA
1 ATGTATCGATACA
100110 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:102360 original size:21 final size:21
Alignment explanation
Indices: 102327--102371 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
102317 TTGCAAGTTG
*
102327 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
102349 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
102369 AAA
1 AAA
102372 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:106302 original size:13 final size:13
Alignment explanation
Indices: 106284--106309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106274 ACATTTTTCT
106284 TTGTATCGATACA
1 TTGTATCGATACA
106297 TTGTATCGATACA
1 TTGTATCGATACA
106310 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:108860 original size:13 final size:13
Alignment explanation
Indices: 108842--108868 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
108832 TACAGCAAGT
108842 ATGTATCGATACA
1 ATGTATCGATACA
108855 ATGTATCGATACA
1 ATGTATCGATACA
108868 A
1 A
108869 CAAAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:444098 original size:28 final size:28
Alignment explanation
Indices: 444044--444113 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
444034 AATAAAGCCA
** *
444044 GGGTTGGAGTATCCCCTCGGAAGTAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
* *
444072 GGGTTGGAGTATTCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
*
444100 AGGTTGGAGTATCC
1 GGGTTGGAGTATCC
444114 TCGATTGTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGAGGAAATAACG
Found at i:444236 original size:79 final size:79
Alignment explanation
Indices: 444153--444375 Score: 290
Period size: 79 Copynumber: 2.8 Consensus size: 79
444143 TAAAATCGGA
* *
444153 GTTGGAATATCTCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTCGAGTATCCCC
1 GTTGGAGTATCTCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
444218 TTGAAAATAACGGG
66 TTGAAAATAACGGG
** * * *
444232 GTTGGAGTAT-TCCCGATTGT-GAGAAATTAATATTTTAGAAATAAAGCCAGGGTTGGAGTATCC
1 GTTGGAGTATCT-CCGATTGTGGAG-AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
*
444295 CCTTGGAAATAACGGG
64 CCTTGAAAATAACGGG
* * * *
444311 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTT-GAAAATAAAATCGGAGTTGGAGTATCCC
1 GTTGGAGTATCTCCGATTGTGGAGAATTGGTGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCC
444375 C
65 C
444376 GATTATGGAA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
78 5 0.04
79 115 0.94
80 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (79 bp):
GTTGGAGTATCTCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
TTGAAAATAACGGG
Found at i:444374 original size:51 final size:51
Alignment explanation
Indices: 444311--444441 Score: 192
Period size: 51 Copynumber: 2.6 Consensus size: 51
444301 AAATAACGGG
* * *
444311 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAG-AAATAAAACCGGA
*
444362 GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGGA
* *
444413 GTTGGAGTACCCCCGATTATGAAAAATTA
1 GTTGGAGTATCCCCGATTATGGAAAATTA
444442 AGAAACTTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
51 72 0.99
52 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGGA
Found at i:446897 original size:19 final size:21
Alignment explanation
Indices: 446873--446924 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
446863 AGCGATACAC
**
446873 TGTATCGATACA-TTAC-TTA
1 TGTATCGATACATTTACAGAA
*
446892 TGTATCGTTACATTTACAGAA
1 TGTATCGATACATTTACAGAA
446913 TGTATCGATACA
1 TGTATCGATACA
446925 AATTATTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACAGAA
Found at i:449214 original size:87 final size:86
Alignment explanation
Indices: 449025--449292 Score: 318
Period size: 87 Copynumber: 3.2 Consensus size: 86
449015 TCATTTTGCG
*
449025 TTCCCCACCTCCTCCAGCTAATGTTCCAACACGGCCTTCCTCAAAGTCT----C-CACCACCAGC
1 TTCCCCACCTCCTCCAGCTAATGTTCCAACCCGGCCTTCCTCAAAGTCTCCACCTCACCACCAGC
449085 AAGATCTCCACCTGAAAGCGC
66 AAGATCTCCACCTGAAAGCGC
*
449106 TTCCCCTCCTCCTCCAGCTAATGTTCCAACCCGGCCTTCCTCAAAGTCTCCACCATCACCACCAG
1 TTCCCCACCTCCTCCAGCTAATGTTCCAACCCGGCCTTCCTCAAAGTCTCCACC-TCACCACCAG
*
449171 CAAGATCTCCATCTGAAAGCGC
65 CAAGATCTCCACCTGAAAGCGC
* * * *
449193 TTTCCCACCTCCTCCAGCTAATGCTT-CAATACTGG-CTT-CTGCAAAGTCTCCACCTTCACTAC
1 TTCCCCACCTCCTCCAGCTAATG-TTCCAA-CCCGGCCTTCCT-CAAAGTCTCCACC-TCACCAC
* * * *
449255 CAGCAACATCACCACCTAAAAGCTC
62 CAGCAAGATCTCCACCTGAAAGCGC
* *
449280 TTCCTCGCCTCCT
1 TTCCCCACCTCCT
449293 ATGCTTGCGC
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
81 47 0.29
85 1 0.01
86 2 0.01
87 106 0.66
88 5 0.03
ACGTcount: A:0.24, C:0.43, G:0.11, T:0.23
Consensus pattern (86 bp):
TTCCCCACCTCCTCCAGCTAATGTTCCAACCCGGCCTTCCTCAAAGTCTCCACCTCACCACCAGC
AAGATCTCCACCTGAAAGCGC
Found at i:462092 original size:2 final size:2
Alignment explanation
Indices: 462085--462136 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
462075 TTTTGTTGGG
462085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
462127 AT AT AT AT AT
1 AT AT AT AT AT
462137 TTGTTTTAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:462310 original size:3 final size:3
Alignment explanation
Indices: 462302--462337 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
462292 ACTAGGTTTT
*
462302 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
462338 CTAGGATGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:462487 original size:22 final size:21
Alignment explanation
Indices: 462448--462488 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
462438 ATTTTTTTAA
* *
462448 TTATTTAAAATTATAATATTT
1 TTATTTAAAATAAAAATATTT
462469 TTATTATAAAATAAAAATAT
1 TTATT-TAAAATAAAAATAT
462489 AAGCTAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTTAAAATAAAAATATTT
Found at i:463097 original size:15 final size:15
Alignment explanation
Indices: 463077--463108 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
463067 AATTTTATAC
463077 AATATATAATATGTT
1 AATATATAATATGTT
463092 AATATATAATATGTT
1 AATATATAATATGTT
463107 AA
1 AA
463109 GTATGATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (15 bp):
AATATATAATATGTT
Found at i:463243 original size:11 final size:11
Alignment explanation
Indices: 463207--463245 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
463197 CGATAATTTT
463207 TAAATACAATA
1 TAAATACAATA
*
463218 TAATTATATAATA
1 TAA--ATACAATA
463231 TAAATACAATA
1 TAAATACAATA
463242 TAAA
1 TAAA
463246 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 14 0.58
13 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATACAATA
Found at i:463274 original size:28 final size:28
Alignment explanation
Indices: 463227--463297 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
463217 ATAATTATAT
463227 AATATAAATACAATATAAAAA-AATTAAA
1 AATATAAATACAATATAAAAATAA-TAAA
*
463255 AATATAAA-ACGATATGAAAAATAATAAA
1 AATATAAATACAATAT-AAAAATAATAAA
*
463283 AACATAATATA-AATA
1 AATATAA-ATACAATA
463298 CGTAAACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 6 0.17
28 23 0.64
29 6 0.17
30 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (28 bp):
AATATAAATACAATATAAAAATAATAAA
Found at i:464129 original size:17 final size:17
Alignment explanation
Indices: 464103--464170 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
464093 TGTTATAAAA
* *
464103 TTTTTGTTTAGAATAAT
1 TTTTTATTTAAAATAAT
464120 TTTTTATTTAAAATAA-
1 TTTTTATTTAAAATAAT
* * *
464136 CTCTTATTCAAAA-AAT
1 TTTTTATTTAAAATAAT
*
464152 ATTTTT-TTTGAAATAAT
1 -TTTTTATTTAAAATAAT
464169 TT
1 TT
464171 GTATTCAGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
15 2 0.05
16 17 0.44
17 20 0.51
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTTTATTTAAAATAAT
Found at i:464958 original size:20 final size:21
Alignment explanation
Indices: 464921--464966 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
464911 TTCAACAATT
*
464921 TGTATCGATATAATAAGTGAA
1 TGTATCAATATAATAAGTGAA
464942 TGTATCAATAT-ATAAGTGAA
1 TGTATCAATATAATAAGTGAA
464962 TGTAT
1 TGTAT
464967 TGAAACATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (21 bp):
TGTATCAATATAATAAGTGAA
Found at i:466075 original size:21 final size:20
Alignment explanation
Indices: 466040--466084 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
466030 TCTAAACAGC
*
466040 CCATG-TTCATGCATTTTGAA
1 CCATGTTTCATACATTTT-AA
466060 CCATGTTTCATACATTTTAA
1 CCATGTTTCATACATTTTAA
466080 -CATGT
1 CCATGT
466085 CCAATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 11 0.48
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (20 bp):
CCATGTTTCATACATTTTAA
Found at i:468637 original size:16 final size:16
Alignment explanation
Indices: 468627--468697 Score: 51
Period size: 16 Copynumber: 4.5 Consensus size: 16
468617 TAGGTTTAGG
468627 TCATTTCAGGTTCAGA
1 TCATTTCAGGTTCAGA
* *
468643 TCATTTTAGATTC-GAA
1 TCATTTCAGGTTCAG-A
*
468659 TCATTT-AGTTTC-GAA
1 TCATTTCAGGTTCAG-A
*
468674 TCATTTTAGGTTCA-A
1 TCATTTCAGGTTCAGA
468689 GTCATTTCA
1 -TCATTTCA
468698 ATTTCAAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
15 16 0.35
16 30 0.65
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (16 bp):
TCATTTCAGGTTCAGA
Found at i:468671 original size:15 final size:15
Alignment explanation
Indices: 468642--468679 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
468632 TCAGGTTCAG
468642 ATCATTTTAGATTCGA
1 ATCA-TTTAGATTCGA
*
468658 ATCATTTAGTTTCGA
1 ATCATTTAGATTCGA
468673 ATCATTT
1 ATCATTT
468680 TAGGTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (15 bp):
ATCATTTAGATTCGA
Found at i:469422 original size:155 final size:153
Alignment explanation
Indices: 469188--469528 Score: 366
Period size: 155 Copynumber: 2.2 Consensus size: 153
469178 TTACATAGTA
* * * * * *
469188 TTTTTT-TGTCTTTTAAGGTTATTGGAATACTTTCACGTCGAAAGTATACTTTAAGGGCATTTTG
1 TTTTTTGTGTCCTTTAAGGTTATCGGGATAC-TTCACATCGAAACTATACTTCAAGGGCATTTTG
* * * ** **
469252 ATCATTTATTCAAAATCCAGTCTTAAGTGGTCA-TCGGGTCACTTTTATACCAAAGGTATTTGTT
65 ATAATTTATTCAAAATCAAGTCCTAAGTAATCACT-GGGTCACTTTTATACCAAAGGTATTCATT
* *
469316 TAGGATAGGTTCATCCTTTAATAATT
129 TAGGATAGGTTAAACCTTTAATAA-T
*
469342 TTTTTTGTGTCCTTTAAGGTTATCGGGATACTTCACATCGAAACTATA-TTCCAAGGGTATTTTG
1 TTTTTTGTGTCCTTTAAGGTTATCGGGATACTTCACATCGAAACTATACTT-CAAGGGCATTTTG
* * ** *
469406 GTAATTTTTTCTAAAATCAAGTCCTAAGTAATCACTGGGTTGCTTTTATGCCAAAGGTATTCATT
65 ATAATTTATTC-AAAATCAAGTCCTAAGTAATCACTGGGTCACTTTTATACCAAAGGTATTCATT
* *
469471 TAGGATAGGTTAAACCTTTTATGAT
129 TAGGATAGGTTAAACCTTTAATAAT
* * *
469496 CTTTTTGTGTCCTTT-AGAGTTACCGAGATACTT
1 TTTTTTGTGTCCTTTAAG-GTTATCGGGATACTT
469529 TTACGTCGGA
Statistics
Matches: 156, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
153 4 0.03
154 68 0.44
155 83 0.53
156 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (153 bp):
TTTTTTGTGTCCTTTAAGGTTATCGGGATACTTCACATCGAAACTATACTTCAAGGGCATTTTGA
TAATTTATTCAAAATCAAGTCCTAAGTAATCACTGGGTCACTTTTATACCAAAGGTATTCATTTA
GGATAGGTTAAACCTTTAATAAT
Found at i:469886 original size:152 final size:152
Alignment explanation
Indices: 469606--469889 Score: 351
Period size: 152 Copynumber: 1.9 Consensus size: 152
469596 TGGGTTGCTT
**
469606 TTATGTCAAAGGTAGACATTTAGGATATGGTTATCCTTTTATGATTTTTTCATGTCTTTTAAGGT
1 TTATGTCAAAGGTAGACATTTAGGATATGGTTATCCTTTTATGATCATTTCATGTCTTTTAAGGT
* * * * * * *
469671 TACTAAGATATTTTTAAGTCAAAGGCATAGCCTAGGCATTTAGGTAATTTTTCATAGAACCAAGT
66 TACCAAGATACTTTCAAGTCAAAAGCATAACCAAGGCATTTAGGTAATTTAT-ATAGAACCAAGT
469736 CTTAGGTAGTCACTGAGTCATTG
130 CTTAGGTAGTCACTGAGTCATTG
* * *
469759 TTATGTCAAAGGTATATATTTAGG-TA-GGTTCATCCTTTTATGATCATTTCATGTTTTTTAAGG
1 TTATGTCAAAGGTAGACATTTAGGATATGGTT-ATCCTTTTATGATCATTTCATGTCTTTTAAGG
* * * *
469822 TTACCGAGATACTTTCATA-TCAAAAGTATAACCAAAGGCATTTTGGTAACTTTAT-TAGAGCCA
65 TTACCAAGATACTTTCA-AGTCAAAAGCATAACC-AAGGCATTTAGGTAA-TTTATATAGAACCA
469885 AGTCT
127 AGTCT
469890 GATGTAGTTA
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
151 4 0.04
152 67 0.60
153 36 0.32
154 4 0.04
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.40
Consensus pattern (152 bp):
TTATGTCAAAGGTAGACATTTAGGATATGGTTATCCTTTTATGATCATTTCATGTCTTTTAAGGT
TACCAAGATACTTTCAAGTCAAAAGCATAACCAAGGCATTTAGGTAATTTATATAGAACCAAGTC
TTAGGTAGTCACTGAGTCATTG
Found at i:470008 original size:18 final size:17
Alignment explanation
Indices: 469979--470020 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
469969 TAATATATTC
469979 TTTAATATTTTTAATAAAA
1 TTTAA-ATTTTTAA-AAAA
469998 TTTAAATTTTTAAAAAA
1 TTTAAATTTTTAAAAAA
*
470015 TCTAAA
1 TTTAAA
470021 CAATGTCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 8 0.36
19 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATTTTTAAAAAA
Found at i:471970 original size:15 final size:15
Alignment explanation
Indices: 471950--471981 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
471940 AATAAGAAAC
471950 AAGAAAAAAAAAGAA
1 AAGAAAAAAAAAGAA
*
471965 AAGAAAAACAAAGAA
1 AAGAAAAAAAAAGAA
471980 AA
1 AA
471982 CATGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:474726 original size:112 final size:110
Alignment explanation
Indices: 474528--474966 Score: 549
Period size: 112 Copynumber: 3.9 Consensus size: 110
474518 ACTTGAAAAA
**
474528 ACATCAAATTTGTCTAATTTTTAAAGAAATTTGTGTTTTATACAACCTGATCCATGTT-TGCCTA
1 ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTGATCCAT-TTGTGCCTA
* * * * *
474592 GGAAAATAGGGCATATATCCTATTACTTTTGAAATTTATAAGCCAAC
65 GGAAAATGGGGCATGTATCCTATCAGTTTTGAAATTT-TAATCCAAC
* *
474639 AGCATCAAATTTATCT-ATCTTTTAAAGAAATTCATGTTTTATACAACCTGATCCATTTGTACCT
1 A-CATCAAATTTGTCTAAT-TTTTAAAGAAATTCATGTTTTATACAACCTGATCCATTTGTGCCT
*
474703 AGGAAAATGGGGCATGTATCCTATCAGTTTTGAAACTTTTAATCGAAC
64 AGGAAAATGGGGCATGTATCCTATCAGTTTTGAAA-TTTTAATCCAAC
* * *
474751 AACATCAAATTTGTCTGATTTCTAAAGAAATTCATGTTTTATACAACTTGATCCATTTGTGCCTA
1 -ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTGATCCATTTGTGCCTA
* * * * *
474816 GGAAAATGAGGCATGTATCCTAACAATTTTTAAATTTTTGATCCAAC
65 GGAAAATGGGGCATGTATCCTATCAGTTTTGAAA-TTTTAATCCAAC
* * * * * **
474863 TACATCAATTTTGTCTAATTTTCAAAGAAATTCATGATTTATACAATCTAATCCATGCGTGCCTA
1 -ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTGATCCATTTGTGCCTA
* *
474928 GAAAAATGGAGCATGTATCCTATCAGTTTTGAAATTTTA
65 GGAAAATGGGGCATGTATCCTATCAGTTTTGAAATTTTA
474967 CCAAAGTTTT
Statistics
Matches: 283, Mismatches: 39, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
111 9 0.03
112 268 0.95
113 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (110 bp):
ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTGATCCATTTGTGCCTAG
GAAAATGGGGCATGTATCCTATCAGTTTTGAAATTTTAATCCAAC
Found at i:475756 original size:73 final size:72
Alignment explanation
Indices: 475569--475857 Score: 222
Period size: 74 Copynumber: 3.9 Consensus size: 72
475559 TATCCTAATC
** * * * *
475569 ACCCTTAGTTGACTGATTTGGTTTTGCCCTAGTGAACTCTTTTTGACTTAGGTCTCATCCTATTC
1 ACCCTTAGTTGACT-ATTTTATTTTGCCCTGGTCAAC-CTTTTCGACTTAGGTCTCATCCTAATC
*
475634 A-TTTTTTT
64 ACCTTTTTT
* * * * *
475642 ACCTTTAGTTGATTATTGTAGTTT-CCCTTTGGTCAACCCTTTTCGACTTAAGTCTCATCCTAAT
1 ACCCTTAGTTGACTATTTTATTTTGCCC--TGGTCAA-CCTTTTCGACTTAGGTCTCATCCTAAT
*
475706 CACCCTTTTT
63 CACCTTTTTT
* * * * * *
475716 ACCCTTAGTTGACTATTCTTATTTTGTCCTGGTTAACCTTTTTCAATTTAGGTGTCATCCTAGTC
1 ACCCTTAGTTGACTATT-TTATTTTGCCCTGGTCAACC-TTTTCGACTTAGGTCTCATCCTAATC
475781 ACCTTTTTT
64 ACCTTTTTT
* * * * * * * * * *
475790 ACCCTTTGTTGGCTATTCTAGTTTTACCTTGGTCAACCCTTTCCGATTTAGGTTTCATTCTAGTC
1 ACCCTTAGTTGACTATTTTA-TTTTGCCCTGGTCAA-CCTTTTCGACTTAGGTCTCATCCTAATC
475855 ACC
64 ACC
475858 CTTAGTTAAC
Statistics
Matches: 171, Mismatches: 36, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
71 3 0.02
72 6 0.04
73 46 0.27
74 107 0.63
75 7 0.04
76 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (72 bp):
ACCCTTAGTTGACTATTTTATTTTGCCCTGGTCAACCTTTTCGACTTAGGTCTCATCCTAATCAC
CTTTTTT
Found at i:479518 original size:12 final size:11
Alignment explanation
Indices: 479487--479547 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
479477 AGTCTTCAAA
479487 TTTTC-TCTCT
1 TTTTCTTCTCT
479497 ATTTTCTTCTCT
1 -TTTTCTTCTCT
479509 TTTTCTT-TC-
1 TTTTCTTCTCT
479518 TTTTCTTTCTCT
1 TTTTC-TTCTCT
479530 TTTTCTCTCCTCT
1 TTTTCT-T-CTCT
479543 TTTTC
1 TTTTC
479548 AGCTGAACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.11
10 4 0.09
11 15 0.34
12 11 0.25
13 9 0.20
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTCTTCTCT
Found at i:479519 original size:15 final size:15
Alignment explanation
Indices: 479499--479537 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
479489 TTCTCTCTAT
*
479499 TTTCTTCTCTTTTTC
1 TTTCTTCTCTTTCTC
*
479514 TTTCTTTTCTTTCTC
1 TTTCTTCTCTTTCTC
479529 TTT-TTCTCT
1 TTTCTTCTCT
479538 CCTCTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTCTCTTTCTC
Found at i:479547 original size:21 final size:21
Alignment explanation
Indices: 479503--479547 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
479493 CTCTATTTTC
* *
479503 TTCTCTTTTTCTTTCTTTTCT
1 TTCTCTTTTTCTTCCTCTTCT
479524 TTCTCTTTTTCTCTCCTCTT-T
1 TTCTCTTTTTCT-TCCTCTTCT
479545 TTC
1 TTC
479548 AGCTGAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTCTTTTTCTTCCTCTTCT
Found at i:480518 original size:166 final size:163
Alignment explanation
Indices: 480042--480592 Score: 554
Period size: 167 Copynumber: 3.4 Consensus size: 163
480032 TGAAATAATT
* * * * * * *
480042 TGAA-TTTTGCAAAATTGATTTAATGTGAA-TATAATGACAATATTAGATAAATTTTAAAAATTT
1 TGAATTTTTG-AAAAATGATTTAATATGAATTA-AATAATAATATTTGATGAATTTTAAAAATTA
* * * * * **
480105 TAAATCGAGAAAAATCTCCCTGAAAATATTTATGG-GATAGAAAAC-TCGATTTTTTTAAAATAG
64 AAAACCAAGAAAAATCTCCC-GAAAACATTTATGGAG-CAGAAAACTTCG-TTTTTCAAAAATAG
* * * *
480168 GTAAATTTCAAAGAAAAAATAAAAAACTCATGAAAATAAA
126 GAAAATTTCAAGGAAAAAAT-AAAAA-TAATGAAAATGAA
* * * *
480208 TGAATTTTTTGACATA-GATTTAATATGAATTAAATAATAATATTTTATGAATTTCAAAAATTAA
1 TGAA-TTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAA
* * * * * *
480272 AAACCAAGAAAAATCATCTCGAAAAACATTTATGGAACAGAAAACTCCATTGTTTGGAAACA-A-
65 AAACCAAGAAAAATC-TCCCG-AAAACATTTATGGAGCAGAAAACTTCGTT-TTT-CAAAAATAG
*
480335 GAGAATTTCAAGGAAAAAATGAAAAATGAATGAAAATGAA
126 GAAAATTTCAAGGAAAAAAT-AAAAAT-AATGAAAATGAA
* *
480375 TGAATTTTTGAAAAATGATTTGATATGATTTAAATAATAATATTTGATGAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
*
480440 AAGCAAGAAAAATCTTCCCGAAAACATTTATGGAGCAGAAAACTTCGTTTTTCAAAAATAGGAAA
66 AACCAAGAAAAATC-TCCCGAAAACATTTATGGAGCAGAAAACTTCGTTTTTCAAAAATAGGAAA
*
480505 ATTTCAAGG----AA-AAAAATAA-AAAAATGAA
130 ATTTCAAGGAAAAAATAAAAATAATGAAAATGAA
*
480533 TGAATTTTT-AAAAATTGATTTAATATGAATTAAATAATAATATTTGGTGAATTTTAAAAA
1 TGAATTTTTGAAAAA-TGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAA
480593 AATTTGGATA
Statistics
Matches: 323, Mismatches: 48, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
157 5 0.02
158 59 0.18
159 2 0.01
160 6 0.02
162 2 0.01
164 4 0.01
165 4 0.01
166 102 0.32
167 126 0.39
168 10 0.03
169 3 0.01
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (163 bp):
TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
AACCAAGAAAAATCTCCCGAAAACATTTATGGAGCAGAAAACTTCGTTTTTCAAAAATAGGAAAA
TTTCAAGGAAAAAATAAAAATAATGAAAATGAA
Found at i:484979 original size:17 final size:16
Alignment explanation
Indices: 484938--485000 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
484928 GTTGCTTCGG
484938 TTTTG-TTTG-TTCTT
1 TTTTGTTTTGTTTCTT
484952 TTTGGTGTTTTGTTTCTGT
1 TTT--TGTTTTGTTTCT-T
* *
484971 TGTTT-TTTTCTTCCTT
1 T-TTTGTTTTGTTTCTT
484987 TTTTGTTTTGTTTC
1 TTTTGTTTTGTTTC
485001 AATTTTTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
14 3 0.08
15 3 0.08
16 11 0.29
17 12 0.32
18 5 0.13
19 2 0.05
20 2 0.05
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.75
Consensus pattern (16 bp):
TTTTGTTTTGTTTCTT
Found at i:485070 original size:31 final size:34
Alignment explanation
Indices: 485003--485092 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 34
484993 TTTGTTTCAA
*
485003 TTTTTCTTTCTTTTTTTTCGATTGCTACTTTGTTT
1 TTTTTCTTTCTTTTTTTTCGATTGCTA-TGTGTTT
*
485038 TTTTTCTTT-TTTTTATTTCGATT-CT-TGTTTTT
1 TTTTTCTTTCTTTTT-TTTCGATTGCTATGTGTTT
485070 TTCTTTCTATTGCTATTTTTTTC
1 TT-TTTCT-TT-CT-TTTTTTTC
485093 TATTTTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
32 7 0.15
33 5 0.11
34 9 0.19
35 17 0.36
36 5 0.11
37 4 0.09
ACGTcount: A:0.07, C:0.13, G:0.07, T:0.73
Consensus pattern (34 bp):
TTTTTCTTTCTTTTTTTTCGATTGCTATGTGTTT
Found at i:485089 original size:21 final size:19
Alignment explanation
Indices: 485044--485097 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
485034 GTTTTTTTTC
485044 TTTTTTTTATTTCGATTCT
1 TTTTTTTTATTTCGATTCT
* *
485063 TGTTTTTTTCTTTCTATTGCT
1 T-TTTTTTTATTTCGATT-CT
485084 ATTTTTTTCTATTT
1 -TTTTTTT-TATTT
485098 TTCTTTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 8 0.29
22 5 0.18
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.74
Consensus pattern (19 bp):
TTTTTTTTATTTCGATTCT
Found at i:485132 original size:22 final size:22
Alignment explanation
Indices: 485087--485133 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
485077 TATTGCTATT
* *
485087 TTTTTCTATTTTTCTTTCTTTA
1 TTTTTCTAGTTTTCTTTCTCTA
485109 TTTTTCTAGTTTTCTTGT-TCTA
1 TTTTTCTAGTTTTCTT-TCTCTA
485131 TTT
1 TTT
485134 CCATTGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTCTAGTTTTCTTTCTCTA
Found at i:485423 original size:30 final size:30
Alignment explanation
Indices: 485388--485454 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
485378 TTCCTTGCTG
* * *
485388 CTTGATTCATTTTTTTCTTCATTGTAGCAT
1 CTTGATTCATTTTTGTCTTCATTGCAACAT
485418 CTTGATTCATTTTTGTCTTCATTGCAACAT
1 CTTGATTCATTTTTGTCTTCATTGCAACAT
485448 CTTGATT
1 CTTGATT
485455 ACTTTAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.54
Consensus pattern (30 bp):
CTTGATTCATTTTTGTCTTCATTGCAACAT
Found at i:485541 original size:12 final size:12
Alignment explanation
Indices: 485526--485567 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
485516 ACTTTGCCGT
485526 TTGCTTTCTTCA
1 TTGCTTTCTTCA
485538 TTGCATTTGCTTCA
1 TTGC-TTT-CTTCA
*
485552 TTGTTTTCTTCA
1 TTGCTTTCTTCA
485564 TTGC
1 TTGC
485568 ACCTTAGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 12 0.46
13 6 0.23
14 8 0.31
ACGTcount: A:0.10, C:0.21, G:0.12, T:0.57
Consensus pattern (12 bp):
TTGCTTTCTTCA
Found at i:486627 original size:33 final size:33
Alignment explanation
Indices: 486582--486646 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
486572 TTTGGGAGAA
*
486582 TGTATCGATACAAT-TCTTCATGTATCGATACAT
1 TGTATCGATACAATGT-GTCATGTATCGATACAT
*
486615 TGTATCGGTACAATGTGTCATGTATCGATACA
1 TGTATCGATACAATGTGTCATGTATCGATACA
486647 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTGTCATGTATCGATACAT
Found at i:486741 original size:20 final size:19
Alignment explanation
Indices: 486697--486748 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
486687 ACATTTATGC
* * *
486697 ATGTATTAATACAATGATC
1 ATGTATTGATACAAAGATA
486716 ATGTATTGATACAAAGCATA
1 ATGTATTGATACAAAG-ATA
*
486736 ATGTATCGATACA
1 ATGTATTGATACA
486749 TCTGGATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
ATGTATTGATACAAAGATA
Found at i:487429 original size:34 final size:34
Alignment explanation
Indices: 487343--487414 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
487333 GGCTCGCTAA
*
487343 AAAATTTTCAAGATTTTCTCCCCCTTATTGTTAT
1 AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
487377 AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
1 AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
487411 AAAA
1 AAAA
487415 ATTCTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (34 bp):
AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
Found at i:489454 original size:13 final size:13
Alignment explanation
Indices: 489436--489461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
489426 ACAAAGAGCC
489436 ATGTATCGATACA
1 ATGTATCGATACA
489449 ATGTATCGATACA
1 ATGTATCGATACA
489462 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:489457 original size:33 final size:33
Alignment explanation
Indices: 489415--489481 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
489405 AAAATTTCCA
***
489415 AATGTATCGATACAAAGAGCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
489448 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
489481 A
1 A
489482 TTTCTTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:489525 original size:19 final size:18
Alignment explanation
Indices: 489501--489600 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
489491 CAGAAGCTAA
489501 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
489520 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
489535 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
489552 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
489567 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
489584 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
489601 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:489541 original size:13 final size:13
Alignment explanation
Indices: 489523--489579 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
489513 ACAATACTTA
489523 TGTATCGATACAT
1 TGTATCGATACAT
489536 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
489554 ATGTATCGATACAT
1 -TGTATCGATACAT
489568 TGTATCGATACA
1 TGTATCGATACA
489580 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:489545 original size:32 final size:32
Alignment explanation
Indices: 489504--489598 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
489494 AAGCTAATTA
*
489504 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
489536 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
489568 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
489599 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:489680 original size:21 final size:21
Alignment explanation
Indices: 489656--489712 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
489646 CATTTGTAGG
489656 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
489677 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
489698 ATGTATCGATACATT
1 ATGTATCGATACATT
489713 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:489734 original size:12 final size:12
Alignment explanation
Indices: 489717--489741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
489707 TACATTTGGA
489717 TAATTTTTTTTT
1 TAATTTTTTTTT
489729 TAATTTTTTTTT
1 TAATTTTTTTTT
489741 T
1 T
489742 TCAAACACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TAATTTTTTTTT
Found at i:490946 original size:13 final size:13
Alignment explanation
Indices: 490928--490954 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
490918 ACATGCTACT
490928 TTGTATCGATACA
1 TTGTATCGATACA
490941 TTGTATCGATACA
1 TTGTATCGATACA
490954 T
1 T
490955 GGACAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:497197 original size:13 final size:13
Alignment explanation
Indices: 497179--497207 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
497169 ACAACATTCC
497179 TTGTATCGATACA
1 TTGTATCGATACA
497192 TTGTATCGATACA
1 TTGTATCGATACA
497205 TTG
1 TTG
497208 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:499066 original size:18 final size:19
Alignment explanation
Indices: 499008--499058 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
498998 TAAATTTTTT
499008 ATATAAAAAGGGGGAGAAG
1 ATATAAAAAGGGGGAGAAG
499027 ATATAAAAAGGGGGAGAAG
1 ATATAAAAAGGGGGAGAAG
499046 ATATAAAAAGGGG
1 ATATAAAAAGGGG
499059 AAAAGATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.12
Consensus pattern (19 bp):
ATATAAAAAGGGGGAGAAG
Found at i:499109 original size:37 final size:37
Alignment explanation
Indices: 499062--499138 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
499052 AAAGGGGAAA
*
499062 AGATAATCGTTTAAGGGGGAGAATTTTTTTTAAGAGG
1 AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGAGG
*
499099 AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGGGG
1 AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGAGG
499136 AGA
1 AGA
499139 AAAATGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (37 bp):
AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGAGG
Found at i:499137 original size:18 final size:19
Alignment explanation
Indices: 499071--499139 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
499061 AAGATAATCG
*
499071 TTTAAGGGGGAGAATTTTT
1 TTTAAGGGGGAGAATATTT
* **
499090 TTTAA-GAGGAG-ATAATCG
1 TTTAAGGGGGAGAAT-ATTT
499108 TTTAAGGGGGAGAATATTT
1 TTTAAGGGGGAGAATATTT
499127 TTTAA-GGGGAGAA
1 TTTAAGGGGGAGAA
499140 AAATGAAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.05
18 19 0.47
19 17 0.43
20 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.32, T:0.33
Consensus pattern (19 bp):
TTTAAGGGGGAGAATATTT
Found at i:499697 original size:13 final size:13
Alignment explanation
Indices: 499679--499705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
499669 ACATGCTACT
499679 TTGTATCGATACA
1 TTGTATCGATACA
499692 TTGTATCGATACA
1 TTGTATCGATACA
499705 T
1 T
499706 GTTCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:499717 original size:19 final size:21
Alignment explanation
Indices: 499691--499746 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
499681 GTATCGATAC
**
499691 ATTGTATCGATACATGTTC-A
1 ATTGTATCGATACATGGACAA
499711 A-TGTATCGATACATGGACAA
1 ATTGTATCGATACATGGACAA
499731 ATTGTATCGATACATG
1 ATTGTATCGATACATG
499747 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 15 0.47
20 3 0.09
21 14 0.44
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (21 bp):
ATTGTATCGATACATGGACAA
Found at i:499738 original size:21 final size:20
Alignment explanation
Indices: 499691--499828 Score: 79
Period size: 20 Copynumber: 6.8 Consensus size: 20
499681 GTATCGATAC
**
499691 ATTGTATCGATACATGTTCA
1 ATTGTATCGATACATGGACA
499711 A-TGTATCGATACATGGACAA
1 ATTGTATCGATACATGGAC-A
499731 ATTGTATCGATACAT-GA-A
1 ATTGTATCGATACATGGACA
* * * *
499749 ATTGGCAGTAGCTACCCTAT-CACTA
1 ATT-GTA-TCGATA--C-ATGGAC-A
*
499774 TTTGTATCGATACATGGTACA
1 ATTGTATCGATACATGG-ACA
* *
499795 A-TGTATCGATACATGAAGA
1 ATTGTATCGATACATGGACA
*
499814 AATGTATCGATACAT
1 ATTGTATCGATACAT
499829 TGTATCGATA
Statistics
Matches: 92, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.04
19 20 0.22
20 38 0.41
21 15 0.16
22 3 0.03
23 7 0.08
24 2 0.02
25 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:499801 original size:20 final size:19
Alignment explanation
Indices: 499776--499861 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 19
499766 TATCACTATT
499776 TGTATCGATACATG-GTACAA
1 TGTATCGATACATGAG-A-AA
499796 TGTATCGATACATGAAGAAA
1 TGTATCGATACATG-AGAAA
499816 TGTATCGATACAT------
1 TGTATCGATACATGAGAAA
499829 TGTATCGATACATGAAGAAA
1 TGTATCGATACATG-AGAAA
*
499849 TGTATTGATACAT
1 TGTATCGATACAT
499862 AGCTTGTAAC
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
13 13 0.23
20 41 0.73
21 1 0.02
22 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
TGTATCGATACATGAGAAA
Found at i:499834 original size:13 final size:13
Alignment explanation
Indices: 499816--499841 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
499806 CATGAAGAAA
499816 TGTATCGATACAT
1 TGTATCGATACAT
499829 TGTATCGATACAT
1 TGTATCGATACAT
499842 GAAGAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:499838 original size:33 final size:33
Alignment explanation
Indices: 499791--499861 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
499781 CGATACATGG
*
499791 TACAATGTATCGATACATGAAGAAATGTATCGA
1 TACATTGTATCGATACATGAAGAAATGTATCGA
*
499824 TACATTGTATCGATACATGAAGAAATGTATTGA
1 TACATTGTATCGATACATGAAGAAATGTATCGA
499857 TACAT
1 TACAT
499862 AGCTTGTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (33 bp):
TACATTGTATCGATACATGAAGAAATGTATCGA
Found at i:501696 original size:13 final size:14
Alignment explanation
Indices: 501678--501707 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
501668 CATAAAGTGT
501678 TGTATCGATACA-A
1 TGTATCGATACATA
501691 TGTATCGATACATA
1 TGTATCGATACATA
501705 TGT
1 TGT
501708 TTTGTATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:501718 original size:32 final size:33
Alignment explanation
Indices: 501658--501726 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
501648 TTCAACGATT
501658 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *
501691 TGTATCGATACAT-ATGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
501723 TGTA
1 TGTA
501727 AGCTACTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 21 0.62
33 13 0.38
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:501782 original size:13 final size:13
Alignment explanation
Indices: 501764--501788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
501754 ATTACTCAAA
501764 TGTATCGATACAT
1 TGTATCGATACAT
501777 TGTATCGATACA
1 TGTATCGATACA
501789 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:501841 original size:52 final size:52
Alignment explanation
Indices: 501797--501927 Score: 244
Period size: 52 Copynumber: 2.5 Consensus size: 52
501787 CACTAATCTT
501797 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
* *
501849 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
501901 TGTATCGATACATGCAGGCAAATTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
501928 ATATTTTGAG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
Found at i:505513 original size:15 final size:15
Alignment explanation
Indices: 505489--505522 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
505479 TTGACTTGTG
505489 TTGTACCTTCGTGTA
1 TTGTACCTTCGTGTA
* *
505504 TTGTATCTTCGTGTG
1 TTGTACCTTCGTGTA
505519 TTGT
1 TTGT
505523 GACGAGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.53
Consensus pattern (15 bp):
TTGTACCTTCGTGTA
Found at i:506894 original size:20 final size:20
Alignment explanation
Indices: 506871--506923 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
506861 CAAAGCATAA
506871 TGTATCGATACATCTAGATG
1 TGTATCGATACATCTAGATG
506891 TGTATCGATACATCTAGATG
1 TGTATCGATACATCTAGATG
506911 TGTATCGATACAT
1 TGTATCGATACAT
506924 ATAAGGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATCTAGATG
Found at i:507045 original size:21 final size:22
Alignment explanation
Indices: 507009--507065 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
506999 TTATTTTTTG
*
507009 TAAAAACATTCGATTCA-AA-GC
1 TAAAAACATT-TATTCATAACGC
507030 TCAAAAACATTTATTCATAACGC
1 T-AAAAACATTTATTCATAACGC
507053 T-AAAACATTTATT
1 TAAAAACATTTATT
507066 GATATTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 18 0.56
22 11 0.34
23 3 0.09
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
TAAAAACATTTATTCATAACGC
Found at i:508754 original size:333 final size:334
Alignment explanation
Indices: 507765--509565 Score: 1670
Period size: 333 Copynumber: 5.4 Consensus size: 334
507755 CAACAGACAA
* * * ** *
507765 AAGGTGAA-AAAGTCTCTAAGGTCAAAGCCAACAGGCAGAC-TGAGGGTAAGAAAGTCTCCAAGG
1 AAGGT-AAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGA-GGTGAGGTAGTCTCCAGGG
* * * * ** *
507828 TCAAAGCCGACAGACAAACTTGA-GGTGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TA
64 TCAAAGCTG-CAGGCAGAC-TGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTG
* ** * * * * ** *
507891 AGGGTAAGAAAGTCTCCAAGGTCAAAGCCAATAGGTAGACTTGA-GGTAAGGTAGCCTCT-GAGG
127 A-GGTGAGGCAGTCTCTAGGGTCAAAGCCGATAGGCAGAC-TGAGGGTAAGAAAGTCTCTAGA-G
* ** * *
507954 TCAAAGCCGACAGGCAGACTAAAGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTAA
189 TCAAAACCGACAGGCAGACTTGAGGTGAAATAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TAA
* * * *
508019 -TGTGAGATAGTCTCTAGGATCAAAGCCGATAAGCAGACTTGAGGTGAGGCAGTCTCCAGGGTCA
253 GGGTAAGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTTGAGGTGAGGCAGTCTCCAGGGTCA
*
508083 AAGTCGCAGGCGGACTG
318 AAGTCGCAGGCAGACTG
* * * * ** * *
508100 AGGGTAAGAAAGTCTCCACCA-GTCAAAGCCAATAGGCAGACTTGAGGAGAGGCGGTTTCTAGGG
1 AAGGTAAGAAAGTCTCCA--AGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAGGG
* * *
508164 TCAAAGCCGATAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGG
64 TCAAAGCTG-CAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGA
* * * * ** * * *
508229 GGTGAGGTAGTCTCCAAGGTTAAAGTTGATAGGCAGACTAAGGGTAAGAAAGTCTCCAGGGGTCA
128 GGTGAGGCAGTCTCTAGGGTCAAAGCCGATAGGCAGACTGAGGGTAAGAAAGTCTCTA-GAGTCA
* * * * *
508294 AAGCCGACAGGCAGACTTGAGGTGAAATAGTCTCC-AGAGTCAAAACTGACAGGCAAACTTAGGG
192 AAACCGACAGGCAGACTTGAGGTGAAATAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTAAGGG
* * * * * ** * * * *
508358 TAAGAAAATCTCCAAGGTTAAAACTAACAAGCAAACTTGAGGTAAGGCAGTCTCCAAGGTCAAAG
256 TAAGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTTGAGGTGAGGCAGTCTCCAGGGTCAAAG
* * *
508423 CCGACAGGCAAACTA
321 TCG-CAGGCAGACTG
* * * * *
508438 AAGGTAGGAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACTTGATGTGAGGTAGTCTCCACGGTC
1 AAGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAGGGTC
* * * *
508503 AAAGCTGCAGGCAGACTGAGGGTAAGAAAGTCT-CAGGGTCAAAGCCGATAGGTAGACTTGAGAT
66 AAAGCTGCAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGT
* * * *
508567 GAGGCAGTCTCTAGGGT-AAAGTCGATAGGCAGACTGAGGGCAAGAAAATCTCTAGAGTTAAAAC
131 GAGGCAGTCTCTAGGGTCAAAGCCGATAGGCAGACTGAGGGTAAGAAAGTCTCTAGAGTCAAAAC
* * * * * * *
508631 CGACAGGCAAACTTGGGGTGAAACAGTCTCCAAAGTCAAAGCCAACAGGCAAACTAAGAGTAAGA
196 CGACAGGCAGACTTGAGGTGAAATAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGTAAGA
* * * * *
508696 AAGTCTCTAGGGTCAAAGTCGATAGGCAGAC-TGGGAGTGAGGTAGTTTCCAGGGTCAAAGTCGC
261 AAGTCTCTAGGGTCAAAGCCGATAAGCAGACTTGAG-GTGAGGCAGTCTCCAGGGTCAAAGTCGC
* *
508760 AGGTAGACTA
325 AGGCAGACTG
* * * * * *
508770 AAAGTAGAGAAAGTCTCC-AGGTCAAAGCCGATAGGTAAACTTGAGGTAAGGTAGTCTCTAGGGT
1 AAGGTA-AGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAGGGT
** * * *
508834 CAAAGCCACAGGCAGACTTAGGGTAAGAAAGTCTCC-AGCATCAAAGCCGACAGGCAGACTTGGG
65 CAAAGCTGCAGGCAGACTGAGGGTAAGAAAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTTGAG
* ** * * * * *
508898 GTGAGGCAATCTCTAAAGTCAAAGCCGACAGGAAGACTGAGGGGAAGAAAGTCTCAAGGGTCAAA
129 GTGAGGCAGTCTCTAGGGTCAAAGCCGATAGGCAGACTGAGGGTAAGAAAGTCTCTAGAGTCAAA
* * * ** *
508963 ATCAACAAGCAGACTT-AGGGTGAGGTAGTCTCCAAGGTCAAAGCCGACAAGCAGACTGAA-GGT
194 ACCGACAGGCAGACTTGA-GGTGAAATAGTCTCCAAGGTCAAAGCCGACAGGCAGACT-AAGGGT
* * * * *
509026 -AGAGAGTCTCCAGGGTCAAAGCCGATAAGCAGACTTGAGGTGAAGCAGTCTCCAGAGTCAAAGC
257 AAGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTTGAGGTGAGGCAGTCTCCAGGGTCAAAGT
*
509090 CGTAGGCAGACTG
322 CGCAGGCAGACTG
* * * * * *
509103 AGGGTAAGAAAGTCTCCAGGGTCAAACCCGACAGGCAGACTTGAGATGAGATAGTCT-GAGGGTC
1 AAGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAGGGTC
* * * *
509167 AAAGCTGACAGGCAGACTAAGGATAATAAAGTCTCCATGGTCAAAGCCGACAGGCAGACTT-AGG
66 AAAGCTG-CAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGA-G
*
509231 GTGAGGCAGTCTCCAGGGTCAAAGCCGACT-GGCAGACTGAGGGTAAGAAAGTCTCCTAGA-TCA
129 GTGAGGCAGTCTCTAGGGTCAAAGCCGA-TAGGCAGACTGAGGGTAAGAAAGTCT-CTAGAGTCA
* * * * * * *
509294 AAGCTGACAGGTAGACTTGAGGT-AAGGTAGTCTCCAGGGTCAAAGCTGACAGGCAGACTGAGGG
192 AAACCGACAGGCAGACTTGAGGTGAA-ATAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGG
* * * * * *
509358 TAAGAAAGTCTCCT-GGATCAAAACCGACAAGCAGACTTGAGGTAAGGCAGTCTCTAAGGTCAAA
256 TAAGAAAGTCT-CTAGGGTCAAAGCCGATAAGCAGACTTGAGGTGAGGCAGTCTCCAGGGTCAAA
* *
509422 GTTGATAGGCAGACTG
320 GTCG-CAGGCAGACTG
** * * * * * *
509438 AAGGTAAGAAAGTCTGTAAGGTTAAAGCCGACAAGCAAATTTGAGGTGA-GTAATCTCCAAGGTC
1 AAGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAGGGTC
** * * *
509502 AAAGCTAATAGGCAGACTGAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGATAAGCAGACTTGAG
66 AAAGCT-GCAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAG
509566 AAAGTTAAAA
Statistics
Matches: 1182, Mismatches: 247, Indels: 74
0.79 0.16 0.05
Matches are distributed among these distances:
332 110 0.09
333 389 0.33
334 183 0.15
335 169 0.14
336 153 0.13
337 153 0.13
338 25 0.02
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (334 bp):
AAGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAGGGTC
AAAGCTGCAGGCAGACTGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGT
GAGGCAGTCTCTAGGGTCAAAGCCGATAGGCAGACTGAGGGTAAGAAAGTCTCTAGAGTCAAAAC
CGACAGGCAGACTTGAGGTGAAATAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGTAAGA
AAGTCTCTAGGGTCAAAGCCGATAAGCAGACTTGAGGTGAGGCAGTCTCCAGGGTCAAAGTCGCA
GGCAGACTG
Done.