Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 99 of 202
Found at i:30258871 original size:33 final size:34
Alignment explanation
Indices: 30258824--30258897 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
30258814 GTTAGGCATA
**
30258824 TGTATATATGCATTCAGCTATTCATG-TTTAAAG
1 TGTATATACACATTCAGCTATTCATGTTTTAAAG
* *
30258857 TGTATATACACATTCGGCTATTCATGTTTTAAAT
1 TGTATATACACATTCAGCTATTCATGTTTTAAAG
30258891 TGTATAT
1 TGTATAT
30258898 GCATTCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 23 0.64
34 13 0.36
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.45
Consensus pattern (34 bp):
TGTATATACACATTCAGCTATTCATGTTTTAAAG
Found at i:30262116 original size:16 final size:16
Alignment explanation
Indices: 30262074--30262119 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
30262064 ATCATCTCAT
* *
30262074 ATATATATATATATCAC
1 ATAT-TATAAATATTAC
30262091 A-ATTAT-AATATTAC
1 ATATTATAAATATTAC
30262105 ATATTATAAATATTA
1 ATATTATAAATATTA
30262120 TAAACAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 9 0.36
17 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAAATATTAC
Found at i:30263619 original size:21 final size:21
Alignment explanation
Indices: 30263595--30263637 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
30263585 TCTCACAATG
*
30263595 TAAACGTTCTTACAGTGTCAC
1 TAAACGTTCTTACAGTGCCAC
30263616 TAAACGTTCTTACAGTGCCAC
1 TAAACGTTCTTACAGTGCCAC
30263637 T
1 T
30263638 TATCATCAAT
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:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (21 bp):
TAAACGTTCTTACAGTGCCAC
Found at i:30265462 original size:13 final size:14
Alignment explanation
Indices: 30265429--30265469 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
30265419 AGCTCGATCG
*
30265429 TATTAATTTTTTTA
1 TATTAATTTTTTAA
*
30265443 TATTAATATTTTAA
1 TATTAATTTTTTAA
30265457 TA-TAATTTTTTAA
1 TATTAATTTTTTAA
30265470 AAAATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTAATTTTTTAA
Found at i:30266342 original size:6 final size:6
Alignment explanation
Indices: 30266321--30266356 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
30266311 ATCATGCATT
*
30266321 AAATTA TAATTAA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATT-A AAATTA AAATTA AAATTA AAATT
30266357 TCAATAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AAATTA
Found at i:30267029 original size:31 final size:30
Alignment explanation
Indices: 30266984--30267072 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
30266974 TTAACCCATT
*
30266984 ATTAACTTT-ATTTAATTACATCATATAATA
1 ATTAA-TTTAATTTAATTACATAATATAATA
* * **
30267014 TTTTAATTTAATTTAATCACATTTTATAATA
1 -ATTAATTTAATTTAATTACATAATATAATA
30267045 ATTAATTTAATTTAATTACCATAATATA
1 ATTAATTTAATTTAATTA-CATAATATA
30267073 CACCTCACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 19 0.40
31 29 0.60
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTAATTTAATTTAATTACATAATATAATA
Found at i:30267245 original size:5 final size:5
Alignment explanation
Indices: 30267235--30267273 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
30267225 CATATATACA
*
30267235 CATAT CATAT CATAT CATAT TATAT CATAT CATAT -ATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
30267274 AATAAAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (5 bp):
CATAT
Found at i:30272813 original size:24 final size:24
Alignment explanation
Indices: 30272786--30272835 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
30272776 ACATCTCTGT
30272786 CAGAAACAATTGTTTTAGGGATGC
1 CAGAAACAATTGTTTTAGGGATGC
30272810 CAGAAACAATTGTTTTAGGGATGC
1 CAGAAACAATTGTTTTAGGGATGC
30272834 CA
1 CA
30272836 TGAAGTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (24 bp):
CAGAAACAATTGTTTTAGGGATGC
Found at i:30279721 original size:30 final size:30
Alignment explanation
Indices: 30279683--30279958 Score: 176
Period size: 30 Copynumber: 9.3 Consensus size: 30
30279673 CCATTGACAG
30279683 TGAAAAGGGATAGCTTCAGCTATCGAAATAA
1 TGAAAAGGGATAGCTTCAGCTATCGAAAT-A
* * * *
30279714 T-AAAAGGGAT-G-GTGACGACCATCGAATTA
1 TGAAAAGGGATAGCTTCA-G-CTATCGAAATA
* * * *
30279743 TGAAAAGGGATAACTTCGGCTATTGAACTA
1 TGAAAAGGGATAGCTTCAGCTATCGAAATA
*
30279773 TGAAAAGGGATAGATTCAGCTATCGAAATA
1 TGAAAAGGGATAGCTTCAGCTATCGAAATA
* *
30279803 TGAAAAGGGATAGCTTTAGCTATCGAATTA
1 TGAAAAGGGATAGCTTCAGCTATCGAAATA
* * * * *
30279833 TGAAAAGGGAT-GGTGACAACCATC-AACTA
1 TGAAAAGGGATAGCT-TCAGCTATCGAAATA
* * * * *
30279862 TGAAAAAGGAT-G-GTGACGACAATCGAATTA
1 TGAAAAGGGATAGCTTCA-G-CTATCGAAATA
* **
30279892 TGAAAAGGAATAGCTTTGGCTATC-AAATTA
1 TGAAAAGGGATAGCTTCAGCTATCGAAA-TA
* *
30279922 TGAAAAGGGATACCTTC-GACTATCG-ATTA
1 TGAAAAGGGATAGCTTCAG-CTATCGAAATA
30279951 TGAAAAGG
1 TGAAAAGG
30279959 AATGGCGACG
Statistics
Matches: 188, Mismatches: 43, Indels: 30
0.72 0.16 0.11
Matches are distributed among these distances:
27 1 0.01
28 2 0.01
29 38 0.20
30 141 0.75
31 4 0.02
32 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (30 bp):
TGAAAAGGGATAGCTTCAGCTATCGAAATA
Found at i:30279765 original size:60 final size:59
Alignment explanation
Indices: 30279683--30279872 Score: 206
Period size: 60 Copynumber: 3.2 Consensus size: 59
30279673 CCATTGACAG
*
30279683 TGAAAAGGGATAGCTTCAGCTATCGAAATAAT-AAAAGGGATGGTGACGACCATCGAATTA
1 TGAAAAGGGATAGCTTCAGCTATCGAAAT-ATGAAAAGGGATGGTGAC-ACCATCGAAATA
* * * * * * *
30279743 TGAAAAGGGATAACTTCGGCTATTGAACTATGAAAAGGGATAGAT-TCAGCTATCGAAATA
1 TGAAAAGGGATAGCTTCAGCTATCGAAATATGAAAAGGGAT-GGTGACA-CCATCGAAATA
* * *
30279803 TGAAAAGGGATAGCTTTAGCTATCGAATTATGAAAAGGGATGGTGACAACCATC-AACTA
1 TGAAAAGGGATAGCTTCAGCTATCGAAATATGAAAAGGGATGGTGAC-ACCATCGAAATA
*
30279862 TGAAAAAGGAT
1 TGAAAAGGGAT
30279873 GGTGACGACA
Statistics
Matches: 107, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
59 19 0.18
60 85 0.79
61 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (59 bp):
TGAAAAGGGATAGCTTCAGCTATCGAAATATGAAAAGGGATGGTGACACCATCGAAATA
Found at i:30279873 original size:29 final size:30
Alignment explanation
Indices: 30279824--30279897 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
30279814 AGCTTTAGCT
* * *
30279824 ATCGAATTATGAAAAGGGATGGTGACAACC
1 ATCGAACTATGAAAAAGGATGGTGACAACA
*
30279854 ATC-AACTATGAAAAAGGATGGTGACGACA
1 ATCGAACTATGAAAAAGGATGGTGACAACA
*
30279883 ATCGAATTATGAAAA
1 ATCGAACTATGAAAA
30279898 GGAATAGCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (30 bp):
ATCGAACTATGAAAAAGGATGGTGACAACA
Found at i:30279898 original size:29 final size:30
Alignment explanation
Indices: 30279715--30280003 Score: 157
Period size: 30 Copynumber: 9.7 Consensus size: 30
30279705 TCGAAATAAT
30279715 AAAAGGGATGGTGACGACCATCGAATTATG
1 AAAAGGGATGGTGACGACCATCGAATTATG
** * * * * *
30279745 AAAAGGGATAACT-TCGGCTATTGAACTATG
1 AAAAGGGAT-GGTGACGACCATCGAATTATG
* * * *
30279775 AAAAGGGATAGAT-TC-AGCTATCGAAATATG
1 AAAAGGGAT-GGTGACGA-CCATCGAATTATG
* * *
30279805 AAAAGGGATAGCTTTA-G-CTATCGAATTATG
1 AAAAGGGAT-G-GTGACGACCATCGAATTATG
* *
30279835 AAAAGGGATGGTGACAACCATC-AACTATG
1 AAAAGGGATGGTGACGACCATCGAATTATG
* *
30279864 AAAAAGGATGGTGACGACAATCGAATTATG
1 AAAAGGGATGGTGACGACCATCGAATTATG
* * ** * * *
30279894 AAAAGGAATAGCT-TTGGCTATCAAATTATG
1 AAAAGGGAT-GGTGACGACCATCGAATTATG
** * *
30279924 AAAAGGGATACCT-TCGACTATCG-ATTATG
1 AAAAGGGAT-GGTGACGACCATCGAATTATG
* *
30279953 AAAAGGAATGGCGACGACCATC-AATTATG
1 AAAAGGGATGGTGACGACCATCGAATTATG
*
30279982 AAAATGGATGGTGACGACCATC
1 AAAAGGGATGGTGACGACCATC
30280004 TTGATACCAC
Statistics
Matches: 202, Mismatches: 46, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
28 2 0.01
29 72 0.36
30 124 0.61
31 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.23
Consensus pattern (30 bp):
AAAAGGGATGGTGACGACCATCGAATTATG
Found at i:30279917 original size:59 final size:58
Alignment explanation
Indices: 30279824--30279999 Score: 156
Period size: 59 Copynumber: 3.0 Consensus size: 58
30279814 AGCTTTAGCT
* * * * *
30279824 ATCGAATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAAGGATGGTGACGACA
1 ATCG-ATTATGAAAAGGAATAGCGACGACCATCAATTATGAAAAAGGATGGTGACGACA
*** * * * ** * *
30279883 ATCGAATTATGAAAAGGAATAGCTTTGGCTATCAAATTATGAAAAGGGATACCT-TCGACT
1 ATCG-ATTATGAAAAGGAATAGCGACGACCATC-AATTATGAAAAAGGAT-GGTGACGACA
* *
30279943 ATCGATTATGAAAAGGAATGGCGACGACCATCAATTATGAAAATGGATGGTGACGAC
1 ATCGATTATGAAAAGGAATAGCGACGACCATCAATTATGAAAAAGGATGGTGACGAC
30280000 CATCTTGATA
Statistics
Matches: 89, Mismatches: 25, Indels: 7
0.74 0.21 0.06
Matches are distributed among these distances:
57 1 0.01
58 19 0.21
59 46 0.52
60 22 0.25
61 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (58 bp):
ATCGATTATGAAAAGGAATAGCGACGACCATCAATTATGAAAAAGGATGGTGACGACA
Found at i:30279953 original size:89 final size:89
Alignment explanation
Indices: 30279794--30279985 Score: 228
Period size: 89 Copynumber: 2.2 Consensus size: 89
30279784 AGATTCAGCT
* * * **
30279794 ATCGAAATATGAAAAGGGATAGCTTTAGCTATCGAATTATGAAAAGGGATGGTGACAACCATCAA
1 ATCGAATTATGAAAAGGAATAGCTTTAGCTATCAAATTATGAAAAGGGATCCTGACAACCATCAA
*
30279859 CTATGAAAAAGG-ATGGTGACGACA
66 CTATG-AAAAGGAATGGCGACGACA
* * * * *
30279883 ATCGAATTATGAAAAGGAATAGCTTTGGCTATCAAATTATGAAAAGGGATACCT-TCGACTATCG
1 ATCGAATTATGAAAAGGAATAGCTTTAGCTATCAAATTATGAAAAGGGAT-CCTGACAACCATCA
* *
30279947 ATTATGAAAAGGAATGGCGACGACC
65 ACTATGAAAAGGAATGGCGACGACA
30279972 ATC-AATTATGAAAA
1 ATCGAATTATGAAAA
30279986 TGGATGGTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
88 17 0.19
89 70 0.80
90 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.23
Consensus pattern (89 bp):
ATCGAATTATGAAAAGGAATAGCTTTAGCTATCAAATTATGAAAAGGGATCCTGACAACCATCAA
CTATGAAAAGGAATGGCGACGACA
Found at i:30286217 original size:16 final size:16
Alignment explanation
Indices: 30286198--30286234 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
30286188 TGTTAATTTT
30286198 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
30286214 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
30286230 AATGT
1 AATGT
30286235 AGGGACTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.30
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:30287029 original size:36 final size:36
Alignment explanation
Indices: 30286950--30287036 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
30286940 AGTAAAAGAC
* **
30286950 TCTACTGATATACTGAATAAATCTCATGGAATGTTA
1 TCTACTGATATACTGAAGAAATCTCATGGAATGAAA
* * *
30286986 TCCACTGATATACTGAAGAAA-CTCAATTGAGTGAAA
1 TCTACTGATATACTGAAGAAATCTC-ATGGAATGAAA
30287022 TCTACTGATATACTG
1 TCTACTGATATACTG
30287037 GGTAAAGCTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 3 0.07
36 40 0.93
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (36 bp):
TCTACTGATATACTGAAGAAATCTCATGGAATGAAA
Found at i:30288243 original size:18 final size:18
Alignment explanation
Indices: 30288205--30288249 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
30288195 TGAATATTAC
30288205 TTGTAATTATGGAATTGAA
1 TTGT-ATTATGGAATTGAA
*
30288224 TTG-ATTATTGAATGTGAA
1 TTGTATTATGGAAT-TGAA
30288242 TTGTATTA
1 TTGTATTA
30288250 ACTGTTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 9 0.39
18 7 0.30
19 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (18 bp):
TTGTATTATGGAATTGAA
Found at i:30291941 original size:19 final size:19
Alignment explanation
Indices: 30291919--30291956 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30291909 TCAATCATTC
30291919 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
30291938 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
30291957 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:30293904 original size:21 final size:22
Alignment explanation
Indices: 30293880--30293923 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
30293870 GTAAGTTATC
30293880 ATGAAGAATT-T-ATAGAATTTT
1 ATGAAGAATTATCATAG-ATTTT
*
30293901 ATGATGAATTATCATAGATTTT
1 ATGAAGAATTATCATAGATTTT
30293923 A
1 A
30293924 AGCTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (22 bp):
ATGAAGAATTATCATAGATTTT
Found at i:30294605 original size:46 final size:46
Alignment explanation
Indices: 30294534--30294672 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
30294524 CATGGCAAAG
*
30294534 TGTGGAACA-TAGGTATGGTAATTCAGTAAAGAAAACCATACTGAGT
1 TGTGGAA-AGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
* *
30294580 TGTGGAATGTAGGTATGGTATTTCAGTAACGAAAACCATACTGAGT
1 TGTGGAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
* *
30294626 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGGAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
30294672 T
1 T
30294673 ATAGCATTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGGAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
Found at i:30297574 original size:27 final size:26
Alignment explanation
Indices: 30297544--30297596 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
30297534 TGGTTTCAGT
*
30297544 AAAATTATTT-TTAATTTAATTTTAATA
1 AAAATAATTTATTAATTT--TTTTAATA
30297571 AAAATAATTTAATTAATTTTTTTAAT
1 AAAATAATTT-ATTAATTTTTTTAAT
30297597 TTCTAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 16 0.70
29 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AAAATAATTTATTAATTTTTTTAATA
Found at i:30297842 original size:81 final size:85
Alignment explanation
Indices: 30297756--30297925 Score: 195
Period size: 91 Copynumber: 2.0 Consensus size: 85
30297746 GTGTAAAAAA
*
30297756 CCCTCAAAC-TTAAAAAAA-AATTAAGCCCCTA-TT-TTATTTCACCCAATTGGGTACTTGAACT
1 CCCTCAAACTTTAAAAAAACAACTAAGCCCCTACTTATTATTTCACCCAATTGGGTACTTGAACT
** *
30297817 TTCAAAATGTATCAAAAATG
66 GCCAAAATGCATCAAAAATG
* * *
30297837 CCCTCAAACTTTTTTTAAAAAAAGCAACTAATCCCCTACCTTATTTTTTCACTCAATTGGGTACT
1 CCCTCAAAC----TTTAAAAAAA-CAACTAAGCCCCTA-CTTATTATTTCACCCAATTGGGTACT
30297902 TGAACTGCCAAAATGCATCAAAAA
60 TGAACTGCCAAAATGCATCAAAAA
30297926 GGTTCTTTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
81 9 0.12
86 9 0.12
88 11 0.15
90 2 0.03
91 41 0.57
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (85 bp):
CCCTCAAACTTTAAAAAAACAACTAAGCCCCTACTTATTATTTCACCCAATTGGGTACTTGAACT
GCCAAAATGCATCAAAAATG
Found at i:30298103 original size:26 final size:26
Alignment explanation
Indices: 30298068--30298120 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
30298058 AAAGATTATA
**
30298068 AAAATTATTAAATTTTAATAAAAAAT
1 AAAATTATTAAAAATTAATAAAAAAT
*
30298094 AAAATTATTAAAAATTATTAAAAAAT
1 AAAATTATTAAAAATTAATAAAAAAT
30298120 A
1 A
30298121 TAAAAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AAAATTATTAAAAATTAATAAAAAAT
Found at i:30298107 original size:10 final size:10
Alignment explanation
Indices: 30298057--30298161 Score: 67
Period size: 10 Copynumber: 11.0 Consensus size: 10
30298047 TGAAAATCAA
*
30298057 TAAAGATTA-
1 TAAAAATTAT
30298066 TAAAAATTAT
1 TAAAAATTAT
** *
30298076 TAAATTTTAA
1 TAAAAATTAT
30298086 TAAAAA--A-
1 TAAAAATTAT
30298093 T-AAAATTAT
1 TAAAAATTAT
30298102 TAAAAATTAT
1 TAAAAATTAT
*
30298112 TAAAAAATAT
1 TAAAAATTAT
* *
30298122 AAAAAATTGT
1 TAAAAATTAT
* *
30298132 AAAAAATTGT
1 TAAAAATTAT
* *
30298142 AAAAAATTGT
1 TAAAAATTAT
*
30298152 AAAAAATTAT
1 TAAAAATTAT
30298162 AATAAATTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 2 0.03
9 9 0.11
10 64 0.80
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:30298126 original size:20 final size:20
Alignment explanation
Indices: 30298094--30298174 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
30298084 AATAAAAAAT
* *
30298094 AAAATTATTAAAAATTATTAA
1 AAAATTATAAAAAATT-GTAA
30298115 AAAA-TATAAAAAATTGTAA
1 AAAATTATAAAAAATTGTAA
*
30298134 AAAATTGTAAAAAATTGTAA
1 AAAATTATAAAAAATTGTAA
*
30298154 AAAATTATAATAAATTGTAA
1 AAAATTATAAAAAATTGTAA
30298174 A
1 A
30298175 TTTTTATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
19 7 0.13
20 43 0.80
21 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAATTATAAAAAATTGTAA
Found at i:30298127 original size:36 final size:36
Alignment explanation
Indices: 30298055--30298128 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
30298045 AATGAAAATC
***
30298055 AATAAAGATTATAAAAATTATTAAATTTTAATAAAA
1 AATAAAGATTATAAAAATTATTAAAAAATAATAAAA
30298091 AATAAA-ATTATTAAAAATTATTAAAAAAT-ATAAAA
1 AATAAAGATTA-TAAAAATTATTAAAAAATAATAAAA
30298126 AAT
1 AAT
30298129 TGTAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 13 0.38
36 21 0.62
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (36 bp):
AATAAAGATTATAAAAATTATTAAAAAATAATAAAA
Found at i:30298168 original size:10 final size:10
Alignment explanation
Indices: 30298094--30298174 Score: 92
Period size: 10 Copynumber: 8.1 Consensus size: 10
30298084 AATAAAAAAT
*
30298094 AAAATTATTA
1 AAAATTATAA
30298104 AAAATTATTAA
1 AAAATTA-TAA
30298115 AAAA-TATAA
1 AAAATTATAA
*
30298124 AAAATTGTAA
1 AAAATTATAA
*
30298134 AAAATTGTAA
1 AAAATTATAA
*
30298144 AAAATTGTAA
1 AAAATTATAA
30298154 AAAATTATAA
1 AAAATTATAA
* *
30298164 TAAATTGTAA
1 AAAATTATAA
30298174 A
1 A
30298175 TTTTTATTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
9 7 0.11
10 50 0.79
11 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (10 bp):
AAAATTATAA
Found at i:30298269 original size:19 final size:19
Alignment explanation
Indices: 30298247--30298302 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
30298237 TTATGAAGTC
30298247 GTAAGAAAATTATAAAAAT-
1 GTAA-AAAATTATAAAAATA
*
30298266 GTAAAGAAA-TATAAAATTA
1 GTAAA-AAATTATAAAAATA
*
30298285 GTAACAAATTATAAAAAT
1 GTAAAAAATTATAAAAAT
30298303 TATCGTACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (19 bp):
GTAAAAAATTATAAAAATA
Found at i:30298295 original size:11 final size:9
Alignment explanation
Indices: 30298252--30298305 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
30298242 AAGTCGTAAG
30298252 AAAATTATA
1 AAAATTATA
30298261 AAAATGTA-A
1 AAAAT-TATA
30298270 AGAAA-TAT-
1 A-AAATTATA
30298278 AAAATTAGTA
1 AAAATTA-TA
30298288 ACAAATTATA
1 A-AAATTATA
30298298 AAAATTAT
1 AAAATTAT
30298306 CGTACCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
7 3 0.08
8 5 0.13
9 15 0.39
10 9 0.24
11 6 0.16
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:30298362 original size:16 final size:15
Alignment explanation
Indices: 30298341--30298370 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30298331 TTTTCTATAT
30298341 TTTTTATTGATTTTTA
1 TTTTTATT-ATTTTTA
30298357 TTTTTATTATTTTT
1 TTTTTATTATTTTT
30298371 CACCACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTATTATTTTTA
Found at i:30298502 original size:20 final size:20
Alignment explanation
Indices: 30298477--30298538 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
30298467 TTAAAGGGTC
30298477 TTTTTTATGCA-TTTTATAAT
1 TTTTTTATG-ATTTTTATAAT
30298497 TTTTTTATGATTTTTATAA-
1 TTTTTTATGATTTTTATAAT
** *
30298516 AATTTTAT-ATTTTTACAAT
1 TTTTTTATGATTTTTATAAT
30298535 TTTT
1 TTTT
30298539 ATAAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.26
19 9 0.26
20 17 0.49
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTTTATGATTTTTATAAT
Found at i:30298545 original size:28 final size:27
Alignment explanation
Indices: 30298506--30298558 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
30298496 TTTTTTTATG
*
30298506 ATTTTTAT-AAAATTTTATATTTTTACA
1 ATTTTTATAAAAAATTTA-ATTTTTACA
30298533 ATTTTTATAAAAAAATTTAATTTTTA
1 ATTTTTAT-AAAAAATTTAATTTTTA
30298559 ATAAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 8 0.35
28 7 0.30
29 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTTTATAAAAAATTTAATTTTTACA
Found at i:30298556 original size:19 final size:19
Alignment explanation
Indices: 30298532--30298589 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 19
30298522 ATATTTTTAC
*
30298532 AATTTTTATAAAAAAATTT
1 AATTTTTATATAAAAATTT
**
30298551 AATTTTTA-ATAAATTTTT
1 AATTTTTATATAAAAATTT
*
30298569 AATTTTT-TATTAAAATTT
1 AATTTTTATATAAAAATTT
30298587 AAT
1 AAT
30298590 AATTTTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 24 0.75
19 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTTTATATAAAAATTT
Found at i:30298921 original size:89 final size:87
Alignment explanation
Indices: 30298742--30299011 Score: 353
Period size: 89 Copynumber: 3.0 Consensus size: 87
30298732 AAGGACATTG
* * * *
30298742 TTGATGCATTTTGACAGTCCAAGTACCCAATTGAGTGGAAAAAAAAAGCAGGGCCTTAATTGTTT
1 TTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGT-GAAAAAAAAAGCAGGGGCTTAA-TGTTT
* *
30298807 TTTCTGAAAAAGTTTGAGGGTCTTT
64 TTTTTGAAAAAATTTGAGGG-CTTT
30298832 TTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGAAAAAAAAAGCAGGGGCTTAATGATTTT
1 TTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGAAAAAAAAAGCAGGGGCTTAATG-TTTT
*
30298897 TTTTGAAAAAAATTGAGGGCCTTT
65 TTTTGAAAAAATTTGAGGG-CTTT
* * * *
30298921 TTGATGCATTTTGAAAGTTTAAGTACCCAATTAAGTGTAACAAAAAGC-GGGGACTTAATTTTTT
1 TTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGAAAAAAAAAGCAGGGG-CTTAA-TGTTT
*
30298985 TTTTTCAAAAAAGTTTGAGGGCTTT
64 TTTTTGAAAAAA-TTTGAGGGCTTT
30299010 TT
1 TT
30299012 ACACTATTAA
Statistics
Matches: 162, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
88 6 0.04
89 115 0.71
90 41 0.25
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.35
Consensus pattern (87 bp):
TTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGAAAAAAAAAGCAGGGGCTTAATGTTTTT
TTTGAAAAAATTTGAGGGCTTT
Found at i:30300283 original size:31 final size:31
Alignment explanation
Indices: 30300208--30300271 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
30300198 TCATTCAATT
30300208 TTTAAAATTTACATAATGATTATTAATATTA
1 TTTAAAATTTACATAATGATTATTAATATTA
*
30300239 TTTAAAATTTACATAATGATTATTTATATTA
1 TTTAAAATTTACATAATGATTATTAATATTA
30300270 TT
1 TT
30300272 GAATTCTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTAAAATTTACATAATGATTATTAATATTA
Found at i:30304029 original size:31 final size:31
Alignment explanation
Indices: 30303994--30304322 Score: 310
Period size: 31 Copynumber: 10.6 Consensus size: 31
30303984 CATTGTCAAA
**
30303994 TTGATTTGTATAGAGATATACATTTTCGAAT
1 TTGATTTGTATAGAGATATACATTGCCGAAT
* * * *
30304025 TTGATTTGTTTATAGATATACATTGCCCAAA
1 TTGATTTGTATAGAGATATACATTGCCGAAT
* * * * * *
30304056 TTAAATTGTTTATAGATATACATTGTCTAAT
1 TTGATTTGTATAGAGATATACATTGCCGAAT
* * *
30304087 TTGAATTGTTTATAGATATACATTGCCGAAT
1 TTGATTTGTATAGAGATATACATTGCCGAAT
*
30304118 TTGATTTGTATATG-GTTATACATTGCCGAAT
1 TTGATTTGTATA-GAGATATACATTGCCGAAT
* * *
30304149 TTGATTTGTATATG-GTTATACATTACCGATT
1 TTGATTTGTATA-GAGATATACATTGCCGAAT
* **
30304180 TTGATTTGTATATAGATATACATTGTTGAAT
1 TTGATTTGTATAGAGATATACATTGCCGAAT
* * *
30304211 TTGATTTATATATG-GTTATACATTACCGAAT
1 TTGATTTGTATA-GAGATATACATTGCCGAAT
* *
30304242 TTGATTTGTATATG-GATATTCATTGCCGGA-
1 TTGATTTGTATA-GAGATATACATTGCCGAAT
*
30304272 TTGATTTGTATATAGATATACATTGCCGAAT
1 TTGATTTGTATAGAGATATACATTGCCGAAT
*
30304303 TTGATTCGTATATG-GATATA
1 TTGATTTGTATA-GAGATATA
30304323 TATATTACCG
Statistics
Matches: 250, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
30 26 0.10
31 224 0.90
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (31 bp):
TTGATTTGTATAGAGATATACATTGCCGAAT
Found at i:30304075 original size:62 final size:62
Alignment explanation
Indices: 30303994--30304322 Score: 390
Period size: 62 Copynumber: 5.3 Consensus size: 62
30303984 CATTGTCAAA
* * * * *
30303994 TTGATTTGTATAGAGATATACATTTTCGAATTTGATTTGTTTATAGATATACATTGCCCAAA
1 TTGATTTGTATATAGATATACATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAAT
* * * * * *
30304056 TTAAATTGTTTATAGATATACATTGTCTAATTTGAATTGTTTATAGATATACATTGCCGAAT
1 TTGATTTGTATATAGATATACATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAAT
* * * * * * *
30304118 TTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGTATATGGTTATACATTACCGATT
1 TTGATTTGTATATAGATATACATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAAT
* * * * *
30304180 TTGATTTGTATATAGATATACATTGTTGAATTTGATTTATATATGGTTATACATTACCGAAT
1 TTGATTTGTATATAGATATACATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAAT
* * * *
30304242 TTGATTTGTATATGGATATTCATTGCCGGA-TTGATTTGTATATAGATATACATTGCCGAAT
1 TTGATTTGTATATAGATATACATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAAT
* *
30304303 TTGATTCGTATATGGATATA
1 TTGATTTGTATATAGATATA
30304323 TATATTACCG
Statistics
Matches: 228, Mismatches: 39, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
61 45 0.20
62 183 0.80
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (62 bp):
TTGATTTGTATATAGATATACATTGTCGAATTTGATTTGTATATAGATATACATTGCCGAAT
Found at i:30304122 original size:93 final size:93
Alignment explanation
Indices: 30303994--30304322 Score: 408
Period size: 93 Copynumber: 3.5 Consensus size: 93
30303984 CATTGTCAAA
* ** * * * * *
30303994 TTGATTTGTATAGAGATATACATTTTCGAATTTGATTTGTTTATAGATATACATTGCCCAAATTA
1 TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTTG
* * * * *
30304059 AATTGTTTATAGATATACATTGTCTAAT
66 ATTTGTATATGGATATACATTGCCGAAT
* * *
30304087 TTGAATTGTTTATAGATATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTG
1 TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTTG
* * *
30304152 ATTTGTATATGGTTATACATTACCGATT
66 ATTTGTATATGGATATACATTGCCGAAT
** * * *
30304180 TTGATTTGTATATAGATATACATTGTTGAATTTGATTTATATATGGTTATACATTACCGAATTTG
1 TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTTG
* *
30304245 ATTTGTATATGGATATTCATTGCCGGA-
66 ATTTGTATATGGATATACATTGCCGAAT
*
30304272 TTGATTTGTATATAGATATACATTGCCGAATTTGATTCGTATATGGATATA
1 TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATA
30304323 TATATTACCG
Statistics
Matches: 201, Mismatches: 35, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
92 46 0.23
93 155 0.77
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (93 bp):
TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTTG
ATTTGTATATGGATATACATTGCCGAAT
Found at i:30304576 original size:41 final size:40
Alignment explanation
Indices: 30304458--30304584 Score: 139
Period size: 43 Copynumber: 3.0 Consensus size: 40
30304448 TTCCGAGGTG
30304458 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGA-A
1 TGATTT-GTGTAAGACCATGTCTGGGACATTGGCATCGATA
** *
30304498 GTGAGAAAATGTGTAAGACCATGTCTGGGGCATTGGCATCGTATA
1 -T--G-ATTTGTGTAAGACCATGTCTGGGACATTGGCATCG-ATA
* * *
30304543 TGATTTGTATAAGACCCTGTCTGGGACAATGGCATCGATA
1 TGATTTGTGTAAGACCATGTCTGGGACATTGGCATCGATA
30304583 TG
1 TG
30304585 CGTTAACATG
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
40 5 0.07
41 30 0.42
42 1 0.01
43 31 0.43
44 4 0.06
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (40 bp):
TGATTTGTGTAAGACCATGTCTGGGACATTGGCATCGATA
Found at i:30314285 original size:33 final size:33
Alignment explanation
Indices: 30314248--30314559 Score: 188
Period size: 33 Copynumber: 8.8 Consensus size: 33
30314238 TCCTCCAAGG
30314248 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
30314281 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
*
30314323 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
30314350 GGTTGCTATGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
30314383 GGTTGGTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
30314425 GGTTGCTAAGTACTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
30314458 GGTTGCTAAGTGCTGATTCCACCG-TATCATTGAATGT
1 GGTTGCTAAGTGCTGATTCC-CCGAT-TCATTG---GT
* * *
30314495 GAAAGGGGTTGCTAAGTGCTGATTCCCTGAATCACTGGT
1 ------GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
30314534 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
30314560 AACGGATAAC
Statistics
Matches: 219, Mismatches: 23, Indels: 73
0.70 0.07 0.23
Matches are distributed among these distances:
27 21 0.10
28 2 0.01
31 2 0.01
32 2 0.01
33 78 0.36
34 18 0.08
35 2 0.01
36 2 0.01
37 8 0.04
38 6 0.03
39 5 0.02
40 1 0.00
41 5 0.02
42 47 0.21
43 20 0.09
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:30314393 original size:102 final size:102
Alignment explanation
Indices: 30314216--30314446 Score: 390
Period size: 102 Copynumber: 2.3 Consensus size: 102
30314206 ATTGAATATA
* *
30314216 AAGGGGGTTGCTAAGTGTTGATTCCTCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
30314281 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
*
30314318 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTATGTGCTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
30314383 GGTTGGTAAGTGCTGATCCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
* *
30314420 AAAGGGGTTGCTAAGTACTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
30314447 GATTCATTGG
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 121 1.00
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
Found at i:30314537 original size:76 final size:75
Alignment explanation
Indices: 30314346--30314557 Score: 334
Period size: 76 Copynumber: 2.8 Consensus size: 75
30314336 TGATTCCCCC
* * *
30314346 AAGGGGTTGCTATGTGCTGATTCCCCGATTCATTGGTGGTTGGTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
30314411 TTAAATGTGA
66 TTAAATGTGA
*
30314421 AAGGGGTTGCTAAGTACTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
30314486 ATTGAATGTGA
66 -TTAAATGTGA
* * * *
30314497 AAGGGGTTGCTAAGTGCTGATTCCCTGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
30314558 ATAACGGATA
Statistics
Matches: 126, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 61 0.48
76 65 0.52
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:30318000 original size:19 final size:19
Alignment explanation
Indices: 30317958--30318014 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
30317948 TGTAATGAAA
30317958 GAAAGAAAGAAAAAGA-AAT
1 GAAA-AAAGAAAAAGAGAAT
*
30317977 CAAAAAAGAAAAAGAGAAT
1 GAAAAAAGAAAAAGAGAAT
30317996 GAAAAAGAGCAAAAAGAGA
1 GAAAAA-AG-AAAAAGAGA
30318015 TTGAGAGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 11 0.33
19 11 0.33
20 2 0.06
21 9 0.27
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.04
Consensus pattern (19 bp):
GAAAAAAGAAAAAGAGAAT
Found at i:30329797 original size:19 final size:19
Alignment explanation
Indices: 30329770--30329809 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30329760 GTATTGAGAG
*
30329770 GAATTTGAGAGAGAATTGA
1 GAATGTGAGAGAGAATTGA
*
30329789 GAATGTGAGAGAGAGTTGA
1 GAATGTGAGAGAGAATTGA
30329808 GA
1 GA
30329810 TTGAATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.23
Consensus pattern (19 bp):
GAATGTGAGAGAGAATTGA
Found at i:30330463 original size:1 final size:1
Alignment explanation
Indices: 30330459--30330485 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
30330449 AGAACAGAGC
30330459 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
30330486 GAAAGAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30336859 original size:18 final size:18
Alignment explanation
Indices: 30336836--30336871 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30336826 TCAATCTAAA
30336836 GTGAAAGCAAGCAACCCT
1 GTGAAAGCAAGCAACCCT
30336854 GTGAAAGCAAGCAACCCT
1 GTGAAAGCAAGCAACCCT
30336872 AATCACAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (18 bp):
GTGAAAGCAAGCAACCCT
Found at i:30337648 original size:22 final size:22
Alignment explanation
Indices: 30337623--30337669 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
30337613 GAGCCGTGGA
30337623 GGACCGAAGATGGATCGGTGCC
1 GGACCGAAGATGGATCGGTGCC
* * *
30337645 GGACCGGAGGTGGATTGGTGCC
1 GGACCGAAGATGGATCGGTGCC
30337667 GGA
1 GGA
30337670 GGTGAATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.47, T:0.15
Consensus pattern (22 bp):
GGACCGAAGATGGATCGGTGCC
Found at i:30337802 original size:22 final size:22
Alignment explanation
Indices: 30337777--30337818 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
30337767 GTGGAGGGCC
*
30337777 GGAGGTGGATTGGTGCCGGACT
1 GGAGGTGGATCGGTGCCGGACT
30337799 GGAGGTGGATCGGTGCCGGA
1 GGAGGTGGATCGGTGCCGGA
30337819 GGTGAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.52, T:0.19
Consensus pattern (22 bp):
GGAGGTGGATCGGTGCCGGACT
Found at i:30338485 original size:18 final size:18
Alignment explanation
Indices: 30338462--30338501 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
30338452 ATTATTTTTG
30338462 AAAAATATATAAAAT-TAT
1 AAAAATAT-TAAAATATAT
*
30338480 AAAAATATTTAAATATAT
1 AAAAATATTAAAATATAT
30338498 AAAA
1 AAAA
30338502 GCCTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATATTAAAATATAT
Found at i:30338514 original size:2 final size:2
Alignment explanation
Indices: 30338505--30338551 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
30338495 TATAAAAGCC
30338505 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30338546 TA TA TA
1 TA TA TA
30338552 AGATTATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30338960 original size:16 final size:16
Alignment explanation
Indices: 30338927--30338956 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30338917 CGTATAAACT
30338927 TATAAAAAATATATAG
1 TATAAAAAATATATAG
30338943 TATAAAAAAT-TATA
1 TATAAAAAATATATA
30338957 AGTAGATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TATAAAAAATATATAG
Found at i:30341704 original size:35 final size:35
Alignment explanation
Indices: 30341658--30341783 Score: 180
Period size: 35 Copynumber: 3.6 Consensus size: 35
30341648 GTTGATATTC
*
30341658 TGATTTGCATGTTAAGCATGCTATTATTCTGATTT
1 TGATTCGCATGTTAAGCATGCTATTATTCTGATTT
*
30341693 TGATTCACATGTTAAGCATGCTATTATTCTGATTT
1 TGATTCGCATGTTAAGCATGCTATTATTCTGATTT
* ** *
30341728 TGATTTGCATGTTAAGCATGCTGCTATACTGATTT
1 TGATTCGCATGTTAAGCATGCTATTATTCTGATTT
* *
30341763 TGATTCGCATGTAAAGTATGC
1 TGATTCGCATGTTAAGCATGC
30341784 CTACTAAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 81 1.00
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (35 bp):
TGATTCGCATGTTAAGCATGCTATTATTCTGATTT
Found at i:30341969 original size:49 final size:49
Alignment explanation
Indices: 30341881--30341980 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 49
30341871 AGTATACCCG
* *
30341881 CAATATTCTGTATTTGGCAGCTTGACGACAATATATGGTGGCTTGACCA
1 CAATATTCTGTATCTGGCAGCTTGACGACAATATATGGTGACTTGACCA
* * * *
30341930 CAATATTCTGTATCTGGCAGCTTTACTG-CATTATCTGGTGACTTGTCCA
1 CAATATTCTGTATCTGGCAGCTTGAC-GACAATATATGGTGACTTGACCA
30341979 CA
1 CA
30341981 TAATTGGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
49 43 0.98
50 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (49 bp):
CAATATTCTGTATCTGGCAGCTTGACGACAATATATGGTGACTTGACCA
Found at i:30347579 original size:3 final size:3
Alignment explanation
Indices: 30347571--30347610 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
30347561 TGAATCTAAT
30347571 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
30347611 TAATAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:30347615 original size:3 final size:3
Alignment explanation
Indices: 30347609--30347684 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
30347599 CAACAACAAC
30347609 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30347657 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
30347685 GATAGATAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30347691 original size:4 final size:4
Alignment explanation
Indices: 30347682--30347761 Score: 160
Period size: 4 Copynumber: 20.0 Consensus size: 4
30347672 AATAATAATA
30347682 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
30347730 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
30347762 TGCTTTAAAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:30348345 original size:18 final size:18
Alignment explanation
Indices: 30348322--30348356 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30348312 AATTATTTTA
30348322 TTCTGTAGCAAACGTCGT
1 TTCTGTAGCAAACGTCGT
*
30348340 TTCTGTAGCAAAGGTCG
1 TTCTGTAGCAAACGTCG
30348357 ACGTTAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (18 bp):
TTCTGTAGCAAACGTCGT
Found at i:30352873 original size:25 final size:25
Alignment explanation
Indices: 30352809--30352874 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
30352799 GTGCTTGGAT
30352809 TGTAATTAAGTAATAAGTTAGTAGA
1 TGTAATTAAGTAATAAGTTAGTAGA
* *
30352834 TGTACATATCA--AATAAGTTAGTAGG
1 TGTA-AT-TAAGTAATAAGTTAGTAGA
30352859 TGTAATTAAGTAATAA
1 TGTAATTAAGTAATAA
30352875 TTAATTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 26 0.76
26 2 0.06
27 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (25 bp):
TGTAATTAAGTAATAAGTTAGTAGA
Found at i:30356444 original size:32 final size:30
Alignment explanation
Indices: 30356380--30356444 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
30356370 TTTTCTTTTC
* *
30356380 TTCTTTTTTCTTCTTATTTTTGAGTTAGTT
1 TTCTTTTTTCTTCTTATTTTTGAGTAAATT
* *
30356410 TTCTTTTTTTTTCTTTTTCTTTAGAGTAAATT
1 TTCTTTTTTCTTCTTATT-TTT-GAGTAAATT
30356442 TTC
1 TTC
30356445 ACTGTTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 16 0.55
31 3 0.10
32 10 0.34
ACGTcount: A:0.12, C:0.11, G:0.08, T:0.69
Consensus pattern (30 bp):
TTCTTTTTTCTTCTTATTTTTGAGTAAATT
Found at i:30361511 original size:19 final size:19
Alignment explanation
Indices: 30361487--30361524 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
30361477 CTTTGAATGG
30361487 AAAACTAATGAACTAGCAA
1 AAAACTAATGAACTAGCAA
30361506 AAAACTAATGAACTAGCAA
1 AAAACTAATGAACTAGCAA
30361525 GCAAAGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (19 bp):
AAAACTAATGAACTAGCAA
Found at i:30362909 original size:43 final size:43
Alignment explanation
Indices: 30362859--30363130 Score: 275
Period size: 43 Copynumber: 6.3 Consensus size: 43
30362849 CGCTTTTTTC
30362859 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCT
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCT
* * * *
30362902 ACGAACGCCGCTAAAGACTATGACCTTTAGCGGCGC-TTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCT
** * * * *
30362944 ACAATTGCCGCTAAAGACTAGGACCTTTAGTGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCT
* *
30362987 ACAAACACCGCTAAAGA-CAATGACCTTTAGCGACGCTTTT-CT
1 ACAAACGCCGCTAAAGACCAA-GACCTTTAGCGGCGCTTTTCCT
* * **
30363029 CACAAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTTAT
1 -ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCT
* * * * *
30363073 CACAAATGCCGCTATAGATCAA-ATCTTTAGCGGCGCTTCTCGC-
1 -ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTC-CT
*
30363116 AAAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
30363131 AACATAACCT
Statistics
Matches: 189, Mismatches: 34, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
42 50 0.26
43 118 0.62
44 21 0.11
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCT
Found at i:30363001 original size:85 final size:86
Alignment explanation
Indices: 30362849--30363130 Score: 300
Period size: 85 Copynumber: 3.3 Consensus size: 86
30362839 AATGTAGTGG
** * * *
30362849 CGCTTTTTTCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTACGAACGCCGCT
1 CGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACACCGCT
* *
30362914 AAAGACTATGACCTTTAGCGG
66 AAAGACAATGACCTTTAGCGA
** * * *
30362935 CGC-TTTCCCACAATTGCCGCTAAAGACTAGGACCTTTAGTGGCGCTTTTCCCACAAACACCGCT
1 CGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACACCGCT
30362999 AAAGACAATGACCTTTAGCGA
66 AAAGACAATGACCTTTAGCGA
* * * ** **
30363020 CGCTTTTCTCACAAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTTATCACAAATGCCGC
1 CGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCCCACAAACACCGC
* * *
30363085 TATAGATCAA--ATCTTTAGCGG
65 TAAAGA-CAATGACCTTTAGCGA
* * *
30363106 CGCTTCTCGCAAAAACGCCGCTAAA
1 CGCTTTTCCCACAAACGCCGCTAAA
30363131 AACATAACCT
Statistics
Matches: 164, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
85 73 0.45
86 69 0.42
87 19 0.12
88 3 0.02
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (86 bp):
CGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACACCGCT
AAAGACAATGACCTTTAGCGA
Found at i:30363141 original size:128 final size:127
Alignment explanation
Indices: 30362861--30363142 Score: 311
Period size: 128 Copynumber: 2.2 Consensus size: 127
30362851 CTTTTTTCAC
* * * *
30362861 AAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTCCTACGAACGCCGCTAAAGACTATGA
1 AAACGCCGCTAAA-AACATA-ACCTTTAGCGACGCTTTTCCTACAAACGCCGCTAAAGACCATGA
* * * * * *
30362925 CCTTTAGCGGCGCTTTCCCACAATTGCCGCTAAAGACTAGGACCTTTAGTGGCGCTTTTCCCAC
64 CCTTTAGCGGCGCTTTACCACAAATGCCGCTAAAGACTAGAACCTTTAGCGGCGCTTCTCCCAA
* * *
30362989 AAACACCGCTAAAGACAATGACCTTTAGCGACGCTTTT-CTCACAAACGCCGCTAAAGACCATGA
1 AAACGCCGCTAAAAAC-ATAACCTTTAGCGACGCTTTTCCT-ACAAACGCCGCTAAAGACCATGA
* * * * *
30363053 CTTTTAGCGGCGCTTTTTATCACAAATGCCGCTATAGA-TCA-AATCTTTAGCGGCGCTTCTCGC
64 CCTTTAGCGGCGC--TTTACCACAAATGCCGCTAAAGACT-AGAACCTTTAGCGGCGCTTCTCCC
30363116 AA
126 AA
30363118 AAACGCCGCTAAAAACATAACCTTT
1 AAACGCCGCTAAAAACATAACCTTT
30363143 TAAAAAAAAT
Statistics
Matches: 127, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
127 3 0.02
128 71 0.56
129 33 0.26
130 20 0.16
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (127 bp):
AAACGCCGCTAAAAACATAACCTTTAGCGACGCTTTTCCTACAAACGCCGCTAAAGACCATGACC
TTTAGCGGCGCTTTACCACAAATGCCGCTAAAGACTAGAACCTTTAGCGGCGCTTCTCCCAA
Found at i:30367397 original size:12 final size:13
Alignment explanation
Indices: 30367378--30367407 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
30367368 GATCGATTTT
30367378 GGGAAAAAGAAGG
1 GGGAAAAAGAAGG
30367391 GGGAAAAAGAAGG
1 GGGAAAAAGAAGG
30367404 GGGA
1 GGGA
30367408 TCGATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (13 bp):
GGGAAAAAGAAGG
Found at i:30367628 original size:41 final size:41
Alignment explanation
Indices: 30367508--30367670 Score: 127
Period size: 41 Copynumber: 4.0 Consensus size: 41
30367498 CCACTATTGA
* * *
30367508 CCTGAGCATTAGCGGCG-TTTCATTAAAAACGCCGCTAAAG-C
1 CCTGAGCATTAGTGGCGCTTT--TTAAAAACACCACTAAAGAC
* ** * ** *
30367549 CCCGAGTTTTAGTGGCGCTTTTTCAGAAACGTCGCTAAAGAC
1 CCTGAGCATTAGTGGCGCTTTTT-AAAAACACCACTAAAGAC
* *
30367591 CC-GATCATTAGTGGCGCTTTTTAAAAAGCACCTCTAAA-AC
1 CCTGAGCATTAGTGGCGCTTTTTAAAAA-CACCACTAAAGAC
* *
30367631 CCTGAGCATTAGCGGCGCTTCTTAAAAAACACCACTAAAG
1 CCTGAGCATTAGTGGCGCTT-TTTAAAAACACCACTAAAG
30367671 TTATGAAATA
Statistics
Matches: 98, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
40 10 0.10
41 75 0.77
42 13 0.13
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (41 bp):
CCTGAGCATTAGTGGCGCTTTTTAAAAACACCACTAAAGAC
Found at i:30367843 original size:40 final size:40
Alignment explanation
Indices: 30367708--30367846 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 40
30367698 TCGGCTTAGG
* * * *
30367708 TTTTTTGCGGCGCTTTTTGAAAATCGCCGCTAATGC-TAA
1 TTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTTAA
* *** * * *
30367747 TTTTTAGTGGCGTTTTCCAAAAAGCGTCGCTAATACTCAA
1 TTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTTAA
* * *
30367787 TCTTTAGTGGCATTTTTTTAAAAGCGCCGCTAATGCTTAA
1 TTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTTAA
30367827 TTTTTAGCGGCGTTTTTTTA
1 TTTTTAGCGGCGTTTTTTTA
30367847 TCCAAACGCC
Statistics
Matches: 78, Mismatches: 21, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
39 27 0.35
40 51 0.65
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTTAA
Found at i:30380942 original size:30 final size:30
Alignment explanation
Indices: 30380829--30380930 Score: 204
Period size: 30 Copynumber: 3.4 Consensus size: 30
30380819 TGAAAGAAAG
30380829 AGAAAATCAAGATTCACTTTCTTGTTTTCA
1 AGAAAATCAAGATTCACTTTCTTGTTTTCA
30380859 AGAAAATCAAGATTCACTTTCTTGTTTTCA
1 AGAAAATCAAGATTCACTTTCTTGTTTTCA
30380889 AGAAAATCAAGATTCACTTTCTTGTTTTCA
1 AGAAAATCAAGATTCACTTTCTTGTTTTCA
30380919 AGAAAATCAAGA
1 AGAAAATCAAGA
30380931 AACCGAATCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (30 bp):
AGAAAATCAAGATTCACTTTCTTGTTTTCA
Found at i:30380942 original size:60 final size:60
Alignment explanation
Indices: 30380829--30380942 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
30380819 TGAAAGAAAG
** **
30380829 AGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCAAGATTCACTTTCTTGTTTTCA
1 AGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCAAGAAACACAATCTTGTTTTCA
30380889 AGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCAAGAAAC-CGAATCTTG
1 AGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCAAGAAACAC-AATCTTG
30380943 GCCCAATCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (60 bp):
AGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAATCAAGAAACACAATCTTGTTTTCA
Found at i:30398902 original size:10 final size:10
Alignment explanation
Indices: 30398879--30398926 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
30398869 GAATCTGTCG
*
30398879 AAAATAAATT
1 AAAATTAATT
*
30398889 AAAATTAATC
1 AAAATTAATT
*
30398899 AAAATTTATTAT
1 AAAA-TTAAT-T
30398911 AAAATTAATT
1 AAAATTAATT
30398921 AAAATT
1 AAAATT
30398927 CAAAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 19 0.61
11 8 0.26
12 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTAATT
Found at i:30416218 original size:20 final size:20
Alignment explanation
Indices: 30416193--30416240 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
30416183 TTAACATAGT
30416193 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* * *
30416213 TCAGCTTATTCGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
30416233 TCAGCTCA
1 TCAGCTCA
30416241 ACCTTAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:30418177 original size:21 final size:20
Alignment explanation
Indices: 30418136--30418178 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
30418126 ACAAGAAACC
*
30418136 GAAAAAGAAAATGAGAGTGA
1 GAAAAAGAAAATGAAAGTGA
*
30418156 GAAAAAGAAAAATGAAATTGA
1 GAAAAAG-AAAATGAAAGTGA
30418177 GA
1 GA
30418179 TTGAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.12
Consensus pattern (20 bp):
GAAAAAGAAAATGAAAGTGA
Found at i:30418177 original size:27 final size:25
Alignment explanation
Indices: 30418136--30418187 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
30418126 ACAAGAAACC
30418136 GAAAAAGAAAATGAGAGTGAGAAAAA
1 GAAAAAGAAAATGAGAGTGA-AAAAA
* *
30418162 GAAAAATGAAATTGAGATTGAAAAAA
1 GAAAAA-GAAAATGAGAGTGAAAAAA
30418188 TAAGTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.13
Consensus pattern (25 bp):
GAAAAAGAAAATGAGAGTGAAAAAA
Found at i:30418221 original size:39 final size:37
Alignment explanation
Indices: 30418154--30418236 Score: 94
Period size: 39 Copynumber: 2.2 Consensus size: 37
30418144 AAATGAGAGT
** * *
30418154 GAGAAAAAGAAAAATGAAATTGAGATTGAAAAAATAA
1 GAGAAAAAGAAAAATGAAAAAGAAATTGAAAAAAGAA
* *
30418191 GTGAAAAAGATAAAATCGAAAAAGAAATTGAAGAAAGAA
1 GAGAAAAAGA-AAAAT-GAAAAAGAAATTGAAAAAAGAA
30418230 GAGAAAA
1 GAGAAAA
30418237 TGAGTTAGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
37 9 0.24
38 5 0.14
39 23 0.62
ACGTcount: A:0.65, C:0.01, G:0.20, T:0.13
Consensus pattern (37 bp):
GAGAAAAAGAAAAATGAAAAAGAAATTGAAAAAAGAA
Found at i:30419093 original size:33 final size:33
Alignment explanation
Indices: 30419056--30419127 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
30419046 TGATCGAGCC
* * *
30419056 AGGTAAAATCGAACTTTGTTTCCCTGCTCCAAA
1 AGGTAAAACCGAACATTATTTCCCTGCTCCAAA
* *
30419089 AGGTAAAACCGAACATTATTTTCCTGCTCCTAA
1 AGGTAAAACCGAACATTATTTCCCTGCTCCAAA
30419122 AGGTAA
1 AGGTAA
30419128 GCCTCCTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (33 bp):
AGGTAAAACCGAACATTATTTCCCTGCTCCAAA
Found at i:30420021 original size:20 final size:20
Alignment explanation
Indices: 30419996--30420039 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
30419986 CTTAGTTCAA
*
30419996 CTCATTCGAGCTCAAGTCAG
1 CTCATTCGAGCTCAACTCAG
30420016 CTCATTCGAGCTCAACTCAG
1 CTCATTCGAGCTCAACTCAG
30420036 CTCA
1 CTCA
30420040 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (20 bp):
CTCATTCGAGCTCAACTCAG
Found at i:30420760 original size:22 final size:21
Alignment explanation
Indices: 30420731--30420778 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
30420721 AAGCATGAAC
*
30420731 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
30420752 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
30420773 TGAACA
1 TGAACA
30420779 CATAGATGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:30428867 original size:2 final size:2
Alignment explanation
Indices: 30428860--30428889 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30428850 TTTATCCCTC
30428860 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
30428890 CGTGCAGCGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30429027 original size:8 final size:8
Alignment explanation
Indices: 30429014--30429042 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
30429004 TTATTTTTGG
30429014 ATTAAATT
1 ATTAAATT
30429022 ATTAAATT
1 ATTAAATT
30429030 ATTAAATT
1 ATTAAATT
30429038 -TTAAA
1 ATTAAA
30429043 GGTTACGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTAAATT
Found at i:30429136 original size:30 final size:30
Alignment explanation
Indices: 30429069--30429151 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
30429059 AAGTTTATGT
*
30429069 ATTTTTTTTATATTTAAAATTTAATCTCTA
1 ATTTTTTTTATATTTAAAATTTAAGCTCTA
*
30429099 ATTTTTTTTATTTTTAAGAATTT-AGCTC-A
1 ATTTTTTTTATATTTAA-AATTTAAGCTCTA
* *
30429128 TTTATTTTTTCATA-TAAAAATTTA
1 ATT-TTTTTT-ATATTTAAAATTTA
30429152 GGTTCAATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 8 0.18
30 29 0.66
31 7 0.16
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (30 bp):
ATTTTTTTTATATTTAAAATTTAAGCTCTA
Found at i:30430296 original size:125 final size:124
Alignment explanation
Indices: 30429895--30430293 Score: 645
Period size: 124 Copynumber: 3.2 Consensus size: 124
30429885 ACCCACGTTT
* *
30429895 ACGCGCTTTCGCTACAGTAGGTCCTGAAAAAACAATTTCGAGTTGACGTTTCTGAGCAAATAGTA
1 ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTA
30429960 TAAAATCGCTTCTAGCAGGATGTTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGG
66 TAAAATCGCTTCTAGCAGGATGTTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGG
30430019 ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTA
1 ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTA
* *
30430084 TAAAATCCCTTCCAGCAGGATGTTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGG
66 TAAAATCGCTTCTAGCAGGATGTTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGG
* * *
30430143 ACGCACTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGT
1 ACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT
* ** * * * *
30430208 ATACAATCGCTTCTAGCATAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGG
65 ATAAAATCGCTTCTAGCAGGATGTTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGG
* *
30430268 ACACGCTTTTGCTATAGTAGGTCCTG
1 ACGCGCTTTTGCTACAGTAGGTCCTG
30430294 GAAATTGAGA
Statistics
Matches: 255, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 145 0.57
125 110 0.43
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (124 bp):
ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTA
TAAAATCGCTTCTAGCAGGATGTTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGG
Found at i:30430565 original size:15 final size:16
Alignment explanation
Indices: 30430547--30430588 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
30430537 TTTTCCCACG
30430547 TTAGGTTTTTGGA-TT
1 TTAGGTTTTTGGATTT
* *
30430562 TTAGGGTTTAGGATTT
1 TTAGGTTTTTGGATTT
30430578 TTAGGGTTTTT
1 TTA-GGTTTTT
30430589 AGGGTTTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 11 0.52
16 5 0.24
17 5 0.24
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (16 bp):
TTAGGTTTTTGGATTT
Found at i:30430569 original size:16 final size:17
Alignment explanation
Indices: 30430550--30430588 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
30430540 TCCCACGTTA
30430550 GGTTTTTGGA-TTTTAG
1 GGTTTTTGGATTTTTAG
*
30430566 GG-TTTAGGATTTTTAG
1 GGTTTTTGGATTTTTAG
30430582 GGTTTTT
1 GGTTTTT
30430589 AGGGTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
15 6 0.32
16 10 0.53
17 3 0.16
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (17 bp):
GGTTTTTGGATTTTTAG
Found at i:30430582 original size:9 final size:9
Alignment explanation
Indices: 30430560--30430596 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
30430550 GGTTTTTGGA
30430560 TTTTAGGG-
1 TTTTAGGGT
*
30430568 -TTTAGGAT
1 TTTTAGGGT
30430576 TTTTAGGGT
1 TTTTAGGGT
30430585 TTTTAGGGT
1 TTTTAGGGT
30430594 TTT
1 TTT
30430597 GTAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.24
9 19 0.76
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:30430842 original size:125 final size:125
Alignment explanation
Indices: 30430620--30430913 Score: 426
Period size: 125 Copynumber: 2.4 Consensus size: 125
30430610 AACAAATAAG
* ** * * * *
30430620 TCGCGCCCACGTTTACGCGCTTTCGCTATAGTAGGTCTTGAAAAAAATAATTTCGAGTTGACGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTT
* * * *
30430685 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGTTGTTTGATAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTGAAA
* *
30430745 TCGCGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTT
30430810 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTGAAA
*** * *
30430870 TTTTGCCCTCGTGGACGTGCTTTTTCTACAGTAGGTCCTGGAAA
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAA
30430914 TTGAGAGGAA
Statistics
Matches: 149, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
125 149 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (125 bp):
TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTT
TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTGAAA
Found at i:30432171 original size:25 final size:25
Alignment explanation
Indices: 30432143--30432211 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
30432133 AAATATCTTT
30432143 TAAAATTAAATATTTTAATTAATAA
1 TAAAATTAAATATTTTAATTAATAA
* **
30432168 TAAAATTGAATATAATAATTAATAA
1 TAAAATTAAATATTTTAATTAATAA
**
30432193 TAATTTTAAATATGTTTAA
1 TAAAATTAAATAT-TTTAA
30432212 AAATATTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 32 0.91
26 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
TAAAATTAAATATTTTAATTAATAA
Found at i:30440250 original size:17 final size:17
Alignment explanation
Indices: 30440228--30440261 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30440218 ATTCTTATAA
30440228 AAATATCTTTTAAATAT
1 AAATATCTTTTAAATAT
* *
30440245 AAATATTTTTTATATAT
1 AAATATCTTTTAAATAT
30440262 TTAAACCACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATCTTTTAAATAT
Found at i:30443267 original size:17 final size:17
Alignment explanation
Indices: 30443242--30443274 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30443232 TATTACATTA
*
30443242 ATTATAAATTCTAAATT
1 ATTAAAAATTCTAAATT
30443259 ATTAAAAATTCTAAAT
1 ATTAAAAATTCTAAAT
30443275 AGCTTCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAAAATTCTAAATT
Found at i:30444136 original size:2 final size:2
Alignment explanation
Indices: 30444119--30444176 Score: 91
Period size: 2 Copynumber: 28.5 Consensus size: 2
30444109 TAGGAAAATC
30444119 AT AT AT CAT AT CAT 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
30444163 AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT A
30444177 AAAGAAGGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.02
2 48 0.91
3 4 0.08
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30446095 original size:22 final size:21
Alignment explanation
Indices: 30446063--30446105 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
30446053 TGTTGATATA
*
30446063 TTGATGAATTAGGCTT-GAAT
1 TTGATGAATTAAGCTTAGAAT
30446083 TTGATAGATATTAAGCTTAGAAT
1 TTGAT-GA-ATTAAGCTTAGAAT
30446106 ATGAAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 8 0.42
23 4 0.21
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (21 bp):
TTGATGAATTAAGCTTAGAAT
Found at i:30447590 original size:20 final size:20
Alignment explanation
Indices: 30447535--30447590 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
30447525 AGCTTATGCT
* * *
30447535 AAGTAAATAAAATGGAAAGT
1 AAGTAAATAGAATGGTAAGA
* *
30447555 AAGTAAATGGAGTGGTAAGA
1 AAGTAAATAGAATGGTAAGA
30447575 AAGTAAATAGAATGGT
1 AAGTAAATAGAATGGT
30447591 TCATAGTCTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.21
Consensus pattern (20 bp):
AAGTAAATAGAATGGTAAGA
Found at i:30461167 original size:20 final size:20
Alignment explanation
Indices: 30461141--30461247 Score: 85
Period size: 20 Copynumber: 5.5 Consensus size: 20
30461131 TTGTACTTCG
30461141 GTACCCCTGATTGCACTTAC
1 GTACCCCTGATTGCACTTAC
* * **
30461161 GTTCCCCT-ATTGTACTTTG
1 GTACCCCTGATTGCACTTAC
* *
30461180 GTACCCCTGATTACACTTAT
1 GTACCCCTGATTGCACTTAC
* *
30461200 GTGCCCCT-ATTGTACTT-C
1 GTACCCCTGATTGCACTTAC
* *
30461218 GATACCCCTAATTACACTTAC
1 G-TACCCCTGATTGCACTTAC
*
30461239 GTGCCCCTG
1 GTACCCCTG
30461248 TTGTACTTCG
Statistics
Matches: 65, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
18 1 0.02
19 28 0.43
20 34 0.52
21 2 0.03
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.35
Consensus pattern (20 bp):
GTACCCCTGATTGCACTTAC
Found at i:30461184 original size:39 final size:39
Alignment explanation
Indices: 30461131--30461257 Score: 191
Period size: 39 Copynumber: 3.3 Consensus size: 39
30461121 TAGATAATTG
* *
30461131 TTGTACTTCGGTACCCCTGATTGCACTTACGTTCCCCTA
1 TTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTA
* *
30461170 TTGTACTTTGGTACCCCTGATTACACTTATGTGCCCCTA
1 TTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTA
* * *
30461209 TTGTACTTCGATACCCCTAATTACACTTACGTGCCCCTG
1 TTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTA
30461248 TTGTACTTCG
1 TTGTACTTCG
30461258 ATACACACAA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.17, C:0.31, G:0.15, T:0.37
Consensus pattern (39 bp):
TTGTACTTCGGTACCCCTGATTACACTTACGTGCCCCTA
Found at i:30461275 original size:78 final size:77
Alignment explanation
Indices: 30461131--30461275 Score: 175
Period size: 78 Copynumber: 1.9 Consensus size: 77
30461121 TAGATAATTG
* * * * * * * *
30461131 TTGTACTTCGGTACCCCTGATTGCACTTACGTTCCCCTATTGTACTTTGGTACCCCTGATTACAC
1 TTGTACTTCGATACCCCTAATTACACTTACGTGCCCCTATTGTACTTCGATACCAC-GAATACAC
30461196 TTATGTGCCCCTA
65 TTATGTGCCCCTA
*
30461209 TTGTACTTCGATACCCCTAATTACACTTACGTGCCCCTGTTGTACTTCGATACACAC-AATAGCA
1 TTGTACTTCGATACCCCTAATTACACTTACGTGCCCCTATTGTACTTCGATAC-CACGAATA-CA
30461273 CTT
64 CTT
30461276 TCGTATCGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
77 3 0.05
78 51 0.91
79 2 0.04
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (77 bp):
TTGTACTTCGATACCCCTAATTACACTTACGTGCCCCTATTGTACTTCGATACCACGAATACACT
TATGTGCCCCTA
Found at i:30462865 original size:21 final size:21
Alignment explanation
Indices: 30462825--30462866 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30462815 CATGGCTAGT
* *
30462825 AAATGAAATGAAATTAGATTG
1 AAATAAAATGAAATGAGATTG
*
30462846 AAATAAAATGAAATGGGATTG
1 AAATAAAATGAAATGAGATTG
30462867 GTGATTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.26
Consensus pattern (21 bp):
AAATAAAATGAAATGAGATTG
Found at i:30464703 original size:16 final size:15
Alignment explanation
Indices: 30464677--30464706 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30464667 ATTAAATTAA
30464677 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
30464692 TTAACGTAAATGCAA
1 TTAAC-TAAATGCAA
30464707 ATGAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:30468711 original size:24 final size:23
Alignment explanation
Indices: 30468667--30468724 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
30468657 AAACTACCCA
30468667 AAAATAAAAACCAAAAATAAACT
1 AAAATAAAAACCAAAAATAAACT
*
30468690 AAAATGAAAAA-CAAGAATTAAACAT
1 AAAAT-AAAAACCAA-AAATAAAC-T
30468715 GAAAATAAAA
1 -AAAATAAAA
30468725 TAAAAGGTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.27
24 12 0.40
25 5 0.17
26 5 0.17
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (23 bp):
AAAATAAAAACCAAAAATAAACT
Found at i:30470972 original size:28 final size:28
Alignment explanation
Indices: 30470935--30471001 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
30470925 TAAGTACACA
30470935 CCACAAAGGCTTTCCTTTCA-GA-GTCTCG
1 CCACAAAGGCTTTCCTTT-ATGAGGT-TCG
*
30470963 CCACAAAGGC-ATCCTTTATGAGGTTCG
1 CCACAAAGGCTTTCCTTTATGAGGTTCG
*
30470990 CCACGAAGGCTT
1 CCACAAAGGCTT
30471002 ACCCTTCTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.03
27 20 0.61
28 12 0.36
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (28 bp):
CCACAAAGGCTTTCCTTTATGAGGTTCG
Found at i:30471037 original size:57 final size:57
Alignment explanation
Indices: 30470974--30471094 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
30470964 CACAAAGGCA
** * * *
30470974 TCCTTTATGAGGTTCGCCACGAAGGCTTACCCTTCTAGAGTTTTACCATAAATG-TTG
1 TCCTTTAACAGGTTCACCACAAAGGCTTACCCTTCTAGAGTTTTACCACAAA-GCTTG
* * * * *
30471031 TCCTTTAACAGGTTCACCATAAAGGCTTACCTTTTTGGAGTTTTGCCACAAAGCTTG
1 TCCTTTAACAGGTTCACCACAAAGGCTTACCCTTCTAGAGTTTTACCACAAAGCTTG
30471088 TCCTTTA
1 TCCTTTA
30471095 CTTGTTGTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 1 0.02
57 52 0.98
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (57 bp):
TCCTTTAACAGGTTCACCACAAAGGCTTACCCTTCTAGAGTTTTACCACAAAGCTTG
Found at i:30472526 original size:40 final size:40
Alignment explanation
Indices: 30472472--30472564 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 40
30472462 GGCTTTTGGA
30472472 TAAAAAACGCCGCTATAGAT-AGAGA-ATTAGCGGCGCTTTT
1 TAAAAAACGCCGCTATAGATCA-A-ACATTAGCGGCGCTTTT
*
30472512 TAAAAAAAGCCGCTATAGATCAAACATTAGCGGCGCTTTT
1 TAAAAAACGCCGCTATAGATCAAACATTAGCGGCGCTTTT
*
30472552 TGAAAAACGCCGC
1 TAAAAAACGCCGC
30472565 AAAAAATAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
39 1 0.02
40 46 0.96
41 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (40 bp):
TAAAAAACGCCGCTATAGATCAAACATTAGCGGCGCTTTT
Found at i:30473112 original size:24 final size:24
Alignment explanation
Indices: 30473082--30473131 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
30473072 TTTAAAAGAG
30473082 ATAGTATTAATTTTCAAATATTGA
1 ATAGTATTAATTTTCAAATATTGA
30473106 ATAGTATTAATTTTCAAATATTGA
1 ATAGTATTAATTTTCAAATATTGA
30473130 AT
1 AT
30473132 TAATTATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
ATAGTATTAATTTTCAAATATTGA
Found at i:30473162 original size:7 final size:7
Alignment explanation
Indices: 30473141--30473300 Score: 72
Period size: 7 Copynumber: 22.4 Consensus size: 7
30473131 TTAATTATCA
*
30473141 TTATAGT
1 TTATGGT
*
30473148 TTAGGGT
1 TTATGGT
30473155 TTATGGT
1 TTATGGT
* *
30473162 TGACGGT
1 TTATGGT
*
30473169 TTAAGGT
1 TTATGGT
*
30473176 TTAGGAGT
1 TTATG-GT
30473184 TACTAT--T
1 T--TATGGT
*
30473191 TTAAGGT
1 TTATGGT
*
30473198 TTATGGA
1 TTATGGT
30473205 TTATGGGT
1 TTAT-GGT
* *
30473213 TTAGGGA
1 TTATGGT
*
30473220 TTATGAT
1 TTATGGT
30473227 TTATGGT
1 TTATGGT
30473234 TTATGGT
1 TTATGGT
* *
30473241 TTAAGGG
1 TTATGGT
*
30473248 TTAGGGT
1 TTATGGT
*
30473255 TTAAGGGT
1 TT-ATGGT
*
30473263 TTAGGGT
1 TTATGGT
* *
30473270 TTAGGGG
1 TTATGGT
*
30473277 TTATGTT
1 TTATGGT
*
30473284 TTATGAT
1 TTATGGT
*
30473291 TTAAGGT
1 TTATGGT
30473298 TTA
1 TTA
30473301 AGGGATAGAA
Statistics
Matches: 116, Mismatches: 30, Indels: 14
0.73 0.19 0.09
Matches are distributed among these distances:
5 2 0.02
7 97 0.84
8 15 0.13
10 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (7 bp):
TTATGGT
Found at i:30473239 original size:29 final size:29
Alignment explanation
Indices: 30473209--30473306 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
30473199 TATGGATTAT
30473209 GGGTTT-AGGGATTATGATTTATGGTTTA
1 GGGTTTAAGGGATTATGATTTATGGTTTA
* * * *
30473237 TGGTTTAAGGG-TTAGGGTTTAAGGGTTTA
1 GGGTTTAAGGGATTATGATTT-ATGGTTTA
* * *
30473266 GGGTTT-AGGGGTTATGTTTTATGATTTA
1 GGGTTTAAGGGATTATGATTTATGGTTTA
*
30473294 AGGTTTAAGGGAT
1 GGGTTTAAGGGAT
30473307 AGAAATTAAG
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 27 0.49
29 28 0.51
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (29 bp):
GGGTTTAAGGGATTATGATTTATGGTTTA
Found at i:30473244 original size:50 final size:50
Alignment explanation
Indices: 30473190--30473306 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
30473180 GAGTTACTAT
* * * * *
30473190 TTTAAGGTTTATGGATTATGGGTTTAGGGATTATGATTTATGGTTTATGG
1 TTTAAGGTTTAGGGATTAAGGGTTTAGGGATTAGGAGTTATGGTTTATGA
* * * * *
30473240 TTTAAGGGTTAGGGTTTAAGGGTTTAGGGTTTAGGGGTTATGTTTTATGA
1 TTTAAGGTTTAGGGATTAAGGGTTTAGGGATTAGGAGTTATGGTTTATGA
30473290 TTTAAGGTTTAAGGGAT
1 TTTAAGGTTT-AGGGAT
30473307 AGAAATTAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 49 0.91
51 5 0.09
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.45
Consensus pattern (50 bp):
TTTAAGGTTTAGGGATTAAGGGTTTAGGGATTAGGAGTTATGGTTTATGA
Found at i:30473255 original size:14 final size:14
Alignment explanation
Indices: 30473238--30473329 Score: 67
Period size: 14 Copynumber: 6.4 Consensus size: 14
30473228 TATGGTTTAT
30473238 GGTTTAAGGGTTAG
1 GGTTTAAGGGTTAG
30473252 GGTTTAAGGGTTTAG
1 GGTTTAAGGG-TTAG
* *
30473267 GGTTTAGGGGTTAT
1 GGTTTAAGGGTTAG
* * ** *
30473281 GTTTTATGATTTAA
1 GGTTTAAGGGTTAG
*
30473295 GGTTTAAGGGATAG
1 GGTTTAAGGGTTAG
***
30473309 AAATTAAGGGTTTAG
1 GGTTTAAGGG-TTAG
30473324 GGTTTA
1 GGTTTA
30473330 GATTAATTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
14 37 0.66
15 19 0.34
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (14 bp):
GGTTTAAGGGTTAG
Found at i:30473266 original size:15 final size:15
Alignment explanation
Indices: 30473231--30473278 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
30473221 TATGATTTAT
*
30473231 GGTTTATGGTTTAAG
1 GGTTTAGGGTTTAAG
30473246 GG-TTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
*
30473260 GGTTTAGGGTTTAGG
1 GGTTTAGGGTTTAAG
30473275 GGTT
1 GGTT
30473279 ATGTTTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GGTTTAGGGTTTAAG
Found at i:30473272 original size:57 final size:57
Alignment explanation
Indices: 30473209--30473330 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 57
30473199 TATGGATTAT
* * * ***
30473209 GGGTTTAGGGATTATGATTTATGGTTTATGGTTTAAGGGTTAGGGTTTAAGGGTTTA
1 GGGTTTAGGGATTATGATTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
* *
30473266 GGGTTTAGGGGTTATGTTTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
1 GGGTTTAGGGATTATGATTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
30473323 GGGTTTAG
1 GGGTTTAG
30473331 ATTAATTAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (57 bp):
GGGTTTAGGGATTATGATTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
Found at i:30477034 original size:23 final size:22
Alignment explanation
Indices: 30476991--30477034 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
30476981 TTCTAAGTCG
30476991 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
30477014 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
30477035 TTAGTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:30477151 original size:45 final size:45
Alignment explanation
Indices: 30477087--30477172 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
30477077 CTCGATAGAT
30477087 TCAGCACATAGCAACCACCTTAT-TAATCAATGATGTCCGGTGGAA
1 TCAGCACATAGCAACCACCTT-TCTAATCAATGATGTCCGGTGGAA
* *
30477132 TCAGCACATATCAACCACCTTTCTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTTCTAATCAATGATGTCCGGT
30477173 TCACATAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTTCTAATCAATGATGTCCGGTGGAA
Found at i:30477236 original size:51 final size:50
Alignment explanation
Indices: 30477169--30477364 Score: 225
Period size: 51 Copynumber: 3.9 Consensus size: 50
30477159 CAATGATGTT
* *
30477169 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATC
* * * * * *
30477220 CGATACACGTAGTAGCCTGCACATAGTACCACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * * *
30477271 CGGTACGCATAGTAGCCTGCACATAATACTACACATGTGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
*
30477321 TGGTACACGTAGTAGCCCT-CACATAGTACTACACATGTGACCAT
1 CGGTACACGTAGTAG-CCTGCACATAGTACTACACATGTGACCAT
30477365 CACTTTCACT
Statistics
Matches: 119, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
49 2 0.02
50 37 0.31
51 78 0.66
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:30477384 original size:101 final size:99
Alignment explanation
Indices: 30477175--30477360 Score: 250
Period size: 102 Copynumber: 1.8 Consensus size: 99
30477165 TGTTCGGTTC
*
30477175 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAATACTACACATGTGACCA-TACCATCCGATACACGTAGTAGCCTGC
*
30477240 ACATAGTACCACACACGTGATCGAAACTATCCGGT
65 ACATAGTACCACACACGTGATCCAAACTATCCGGT
* * *
30477275 ACGCATAGTAGCCTGCACATAATACTACACATGTGACC-TATCATTCTGGTACACGTAGTAGCCC
1 A--CATAGTAGCCTGCACATAATACTACACATGTGACCATACCA-TCCGATACACGTAGTAG-CC
* *
30477339 T-CACATAGTACTACACATGTGA
62 TGCACATAGTACCACACACGTGA
30477361 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
100 5 0.07
101 34 0.45
102 37 0.49
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAATACTACACATGTGACCATACCATCCGATACACGTAGTAGCCTGCA
CATAGTACCACACACGTGATCCAAACTATCCGGT
Found at i:30481066 original size:43 final size:43
Alignment explanation
Indices: 30480994--30481201 Score: 215
Period size: 43 Copynumber: 4.8 Consensus size: 43
30480984 CACTAGTGGT
* * *
30480994 GTTTGTGATAAAAACGTCGTTAAATGTCATGTTCTTTAGCGGA
1 GTTTGTGATAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGA
* *
30481037 GTTTGTGATAAAAGCGTCACTAAAGGTCATGTTCTTTAGC-AA
1 GTTTGTGATAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGA
** ** **
30481079 TGTTTGTGATAAAAGCCCCGCTAAAGAACATGACCTTTAGCGGCA
1 -GTTTGTGATAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGG-A
* *
30481124 -TTTGTGATAAAAGCATCGCTAAAGGTCATGTTCTTTAGCGGC
1 GTTTGTGATAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGA
* * * *
30481166 GTTTATCGGT-AAAGTGCCGCTAAAGGTCATGTTCTT
1 GTTTGT-GATAAAAGCGTCGCTAAAGGTCATGTTCTT
30481202 CGGCGGCATT
Statistics
Matches: 135, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
42 1 0.01
43 131 0.97
44 2 0.01
45 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (43 bp):
GTTTGTGATAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGA
Found at i:30481809 original size:39 final size:39
Alignment explanation
Indices: 30481754--30481895 Score: 223
Period size: 39 Copynumber: 3.6 Consensus size: 39
30481744 TTCAAGTGCC
*
30481754 TATATGAGTATTGTGATATATGCTTGAATGTTATGTGAT
1 TATATGAGTATGGTGATATATGCTTGAATGTTATGTGAT
*
30481793 TATATGATTATGGTGATATATGCTTGAATGTTATGTGAT
1 TATATGAGTATGGTGATATATGCTTGAATGTTATGTGAT
*
30481832 TATATGAGTATGGTGATATATGCTTAAATGTTATGTGAT
1 TATATGAGTATGGTGATATATGCTTGAATGTTATGTGAT
* *
30481871 TATATGTGTAAT-GTGATATGTGCTT
1 TATATGAGT-ATGGTGATATATGCTT
30481896 AAAAGTGAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
39 94 0.98
40 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.46
Consensus pattern (39 bp):
TATATGAGTATGGTGATATATGCTTGAATGTTATGTGAT
Found at i:30483142 original size:53 final size:52
Alignment explanation
Indices: 30483028--30483156 Score: 186
Period size: 53 Copynumber: 2.5 Consensus size: 52
30483018 TCCTTAAAAT
* *
30483028 TTCCTATATGATGCCATAACCCACTAGTTATAGCTTACACAATATGGTCTTC
1 TTCCAATATGATGCCATAACCCACTAGTTACAGCTTACACAATATGGTCTTC
* * *
30483080 TTCCCATATGATGTCATAACCCACTAGTTACGGTCTTACACAATATGGTCTTC
1 TTCCAATATGATGCCATAACCCACTAGTTACAG-CTTACACAATATGGTCTTC
* *
30483133 TTTCAATATGAGGCCATAACCCAC
1 TTCCAATATGATGCCATAACCCAC
30483157 CAATTGTGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
52 29 0.43
53 39 0.57
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
TTCCAATATGATGCCATAACCCACTAGTTACAGCTTACACAATATGGTCTTC
Found at i:30483173 original size:53 final size:53
Alignment explanation
Indices: 30483028--30483181 Score: 148
Period size: 53 Copynumber: 2.9 Consensus size: 53
30483018 TCCTTAAAAT
* * * * ** *
30483028 TTCCTATATGATGCCATAACCCACTAGTTATAG-CTTACACAATATGGTCTTC
1 TTCCAATATGAGGCCATAACCCACCAATTACGGTCATACACAATATGGTCTTC
* * * * * *
30483080 TTCCCATATGATGTCATAACCCACTAGTTACGGTCTTACACAATATGGTCTTC
1 TTCCAATATGAGGCCATAACCCACCAATTACGGTCATACACAATATGGTCTTC
* ** *
30483133 TTTCAATATGAGGCCATAACCCACCAATTGTGGTCATACACGATATGGT
1 TTCCAATATGAGGCCATAACCCACCAATTACGGTCATACACAATATGGT
30483182 TTTTTAGCGC
Statistics
Matches: 87, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
52 29 0.33
53 58 0.67
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (53 bp):
TTCCAATATGAGGCCATAACCCACCAATTACGGTCATACACAATATGGTCTTC
Found at i:30489348 original size:20 final size:19
Alignment explanation
Indices: 30489323--30489373 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
30489313 AGGAGCAGTT
30489323 TTTCAATCGATTTATAAAAG
1 TTTCAATCGATTT-TAAAAG
*
30489343 TTTCAATCGA-GTTAAAAG
1 TTTCAATCGATTTTAAAAG
30489361 TTTCAATC-ATTTT
1 TTTCAATCGATTTT
30489374 TGAACTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 16 0.57
19 1 0.04
20 10 0.36
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (19 bp):
TTTCAATCGATTTTAAAAG
Found at i:30498795 original size:17 final size:18
Alignment explanation
Indices: 30498775--30498859 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 18
30498765 ATGATACATA
*
30498775 AAATATTTTAAA-AATTT
1 AAATATTATAAATAATTT
*
30498792 AAATATAATAAATAATTT
1 AAATATTATAAATAATTT
* *
30498810 -AATATTACTATAT-A-TG
1 AAATATTA-TAAATAATTT
30498826 AAATATT-TAAATAATTT
1 AAATATTATAAATAATTT
*
30498843 AATATAATGATAAATAA
1 AA-AT-ATTATAAATAA
30498860 ATTTTAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
15 4 0.08
16 2 0.04
17 26 0.50
18 11 0.21
19 2 0.04
20 7 0.13
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (18 bp):
AAATATTATAAATAATTT
Found at i:30498804 original size:26 final size:26
Alignment explanation
Indices: 30498745--30498811 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
30498735 AGTAATTAAT
*
30498745 ATAAATTATTTGAAAAATTAATGATAC
1 ATAAA-TATTTTAAAAATTAATGATAC
30498772 ATAAAATATTTTAAAAATTTAAAT-ATA-
1 AT-AAATATTTTAAAAA-TT-AATGATAC
*
30498799 ATAAATAATTTAA
1 ATAAATATTTTAA
30498812 TATTACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 10 0.29
27 14 0.40
28 8 0.23
29 3 0.09
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (26 bp):
ATAAATATTTTAAAAATTAATGATAC
Found at i:30507631 original size:15 final size:15
Alignment explanation
Indices: 30507611--30507640 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30507601 TATTAGTATC
*
30507611 TTTCCTAACTTAGAG
1 TTTCCTAAATTAGAG
30507626 TTTCCTAAATTAGAG
1 TTTCCTAAATTAGAG
30507641 AAATAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (15 bp):
TTTCCTAAATTAGAG
Found at i:30516212 original size:34 final size:34
Alignment explanation
Indices: 30516169--30516236 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
30516159 CGATGGCATT
*
30516169 CATAACTCATCGACGATTGCTATTCGCCAACTTA
1 CATAACTCATCGACAATTGCTATTCGCCAACTTA
*
30516203 CATAACTCATTGACAATTGCTATTCGCCAACTTA
1 CATAACTCATCGACAATTGCTATTCGCCAACTTA
30516237 GCACGACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (34 bp):
CATAACTCATCGACAATTGCTATTCGCCAACTTA
Found at i:30520075 original size:34 final size:34
Alignment explanation
Indices: 30520037--30520102 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
30520027 TAGTAAAATA
* *
30520037 TTTTCCGGAAAATGATTT-TTGGAAAATGATTTAC
1 TTTTCCAGAAAATGATTTACTGGAAAAT-ATTTAC
*
30520071 TTTTCTAGAAAATGATTTACTGGAAAATATTT
1 TTTTCCAGAAAATGATTTACTGGAAAATATTT
30520103 TCTGGTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 20 0.71
35 8 0.29
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTTCCAGAAAATGATTTACTGGAAAATATTTAC
Done.