Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 41 of 136
Found at i:13448831 original size:25 final size:25
Alignment explanation
Indices: 13448750--13448832 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
13448740 ACGAGCTATA
13448750 AATCGGTAAGCTCATACGAGTTGAG
1 AATCGGTAAGCTCATACGAGTTGAG
* * *
13448775 AATCAGTAAGCTC-TCACGAGCT-AT
1 AATCGGTAAGCTCAT-ACGAGTTGAG
*
13448799 AATCGGTAAGCTCATATGAGTTGAG
1 AATCGGTAAGCTCATACGAGTTGAG
13448824 AATCGGTAA
1 AATCGGTAA
13448833 TCCCTGATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 19 0.40
25 29 0.60
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (25 bp):
AATCGGTAAGCTCATACGAGTTGAG
Found at i:13452690 original size:17 final size:17
Alignment explanation
Indices: 13452665--13452697 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13452655 TGAGAGAAAG
*
13452665 TAAATAACAAAAATAAT
1 TAAACAACAAAAATAAT
13452682 TAAACAACAAAAATAA
1 TAAACAACAAAAATAA
13452698 ACAAACAACT
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:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAACAACAAAAATAAT
Found at i:13452703 original size:17 final size:17
Alignment explanation
Indices: 13452670--13452706 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13452660 GAAAGTAAAT
**
13452670 AACAAAAATAATTAAAC
1 AACAAAAATAAACAAAC
13452687 AACAAAAATAAACAAAC
1 AACAAAAATAAACAAAC
13452704 AAC
1 AAC
13452707 TAAACGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.16, G:0.00, T:0.11
Consensus pattern (17 bp):
AACAAAAATAAACAAAC
Found at i:13462855 original size:24 final size:24
Alignment explanation
Indices: 13462828--13462879 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13462818 TTAGTAAGTC
*
13462828 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13462852 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13462876 AAAT
1 AAAT
13462880 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13467729 original size:78 final size:78
Alignment explanation
Indices: 13467656--13467961 Score: 443
Period size: 80 Copynumber: 3.9 Consensus size: 78
13467646 AAAGTTTATT
* * *
13467656 TATTTAAATTGCAAAAAAAAA-TCATAAAATTGATAAATAAAATGGCAAAAAAGTCATTACATAA
1 TATTTAAATTGCAAAAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAA
13467720 ATACAAAGTTGAC
66 ATACAAAGTTGAC
* * *
13467733 TATTTAAATTGAAAAAAAAAACCCATAAAATTGATGAATAAAATGACAAAAAATTCATTTCATAA
1 TATTTAAATTGCAAAAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAA
13467798 ATACAAAGTTGAC
66 ATACAAAGTTGAC
* * *
13467811 TATTTAAATTCCAAAAAAAAAAACCCATAAAATTGATAAATAAAATGATAACAAATTCATTACAT
1 TATTTAAATTGC--AAAAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACAT
**
13467876 AAATATGAAGTTGAC
64 AAATACAAAGTTGAC
* *
13467891 TATTTAAATTTCAAAAACAGTAAACCCATAAAATTGATAAACAAAATGACAAAAAATTCATTACA
1 TATTTAAATTGCAAAAA-A--AAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACA
13467956 TAAATA
63 TAAATA
13467962 TGAAGTTATT
Statistics
Matches: 205, Mismatches: 18, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
77 20 0.10
78 66 0.32
79 1 0.00
80 71 0.35
81 47 0.23
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (78 bp):
TATTTAAATTGCAAAAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAA
ATACAAAGTTGAC
Found at i:13467857 original size:158 final size:158
Alignment explanation
Indices: 13467656--13467961 Score: 447
Period size: 158 Copynumber: 1.9 Consensus size: 158
13467646 AAAGTTTATT
* * *
13467656 TATTTAAATTGCAAAAAAAAATCATAAAATTGATAAATAAAATGGCAAAAAAGTCATTACATAAA
1 TATTTAAATTCCAAAAAAAAACCATAAAATTGATAAATAAAATGACAAAAAAGTCATTACATAAA
* * *
13467721 TACAAAGTTGACTATTTAAA-TTGAAAAA-A-AAAACCCATAAAATTGATGAATAAAATGACAAA
66 TACAAAGTTGACTATTTAAATTTCAAAAACAGAAAACCCATAAAATTGATAAACAAAATGACAAA
*
13467783 AAATTCATTTCATAAATACAAAGTTGAC
131 AAATTCATTACATAAATACAAAGTTGAC
* * *
13467811 TATTTAAATTCCAAAAAAAAAAACCCATAAAATTGATAAATAAAATGATAACAAATTCATTACAT
1 TATTTAAATTCC--AAAAAAAAA-CCATAAAATTGATAAATAAAATGACAAAAAAGTCATTACAT
** *
13467876 AAATATGAAGTTGACTATTTAAATTTCAAAAACAGTAAACCCATAAAATTGATAAACAAAATGAC
63 AAATACAAAGTTGACTATTTAAATTTCAAAAACAGAAAACCCATAAAATTGATAAACAAAATGAC
13467941 AAAAAATTCATTACATAAATA
128 AAAAAATTCATTACATAAATA
13467962 TGAAGTTATT
Statistics
Matches: 132, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
155 11 0.08
157 9 0.07
158 57 0.43
159 7 0.05
160 1 0.01
161 47 0.36
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (158 bp):
TATTTAAATTCCAAAAAAAAACCATAAAATTGATAAATAAAATGACAAAAAAGTCATTACATAAA
TACAAAGTTGACTATTTAAATTTCAAAAACAGAAAACCCATAAAATTGATAAACAAAATGACAAA
AAATTCATTACATAAATACAAAGTTGAC
Found at i:13477034 original size:40 final size:39
Alignment explanation
Indices: 13476990--13477114 Score: 117
Period size: 40 Copynumber: 3.2 Consensus size: 39
13476980 GGCGTTTGGA
*
13476990 TAAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTT
1 TAAAAAAATGCCGCTAAAAAT-AAGCATTAGCGGCGCTTT
* * * * *
13477030 TAAAAAAATGCCACTAAAGATTGAGTATTAGCGGAGCTTT
1 TAAAAAAATGCCGCTAAA-AATAAGCATTAGCGGCGCTTT
*** * *
13477070 TTGGAAAATG-CGCTAAAAATTAGCATTAGCGGCGTTTT
1 TAAAAAAATGCCGCTAAAAATAAGCATTAGCGGCGCTTT
*
13477108 TCAAAAA
1 TAAAAAA
13477115 GCACCGCAAA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
38 20 0.30
39 6 0.09
40 38 0.58
41 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (39 bp):
TAAAAAAATGCCGCTAAAAATAAGCATTAGCGGCGCTTT
Found at i:13477262 original size:40 final size:40
Alignment explanation
Indices: 13477177--13477366 Score: 236
Period size: 41 Copynumber: 4.7 Consensus size: 40
13477167 TAAGTGGTGT
* * *
13477177 TTTTTAAAAAACGCCGCTAATGCTCAGGGTTTTAGTGACG
1 TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGGCG
*
13477217 TTTTTTAAAAAGCGCCACTAATGCTCAGGGTTTTAGCGGCG
1 -TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGGCG
*
13477258 TTTTTGAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGGCG
1 TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGGCG
* * ** * * *
13477298 TTTCTGAAAAAGCGCTGCTAACACTCGGGGCTTTAGCGGTG
1 TTT-TTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGGCG
*
13477339 TTGTTAAAGAAGCGCCGCTAATGCTCAG
1 TTTTTAAA-AAGCGCCGCTAATGCTCAG
13477367 TTCAATAGTG
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 45 0.35
41 82 0.65
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGGCG
Found at i:13477312 original size:81 final size:81
Alignment explanation
Indices: 13477177--13477366 Score: 245
Period size: 81 Copynumber: 2.3 Consensus size: 81
13477167 TAAGTGGTGT
* * * * **
13477177 TTTTTAAAAAACGCCGCTAATGCTCAGGGTTTTAGTGACGTTTTTTAAAAAGCGCCACTAATGCT
1 TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGACGTTTCTGAAAAAGCGCCACTAACACT
*
13477242 CAGGGTTTTAGCGGCG
66 CAGGGCTTTAGCGGCG
* * **
13477258 TTTTTGAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGGCGTTTCTGAAAAAGCGCTGCTAACACT
1 TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGACGTTTCTGAAAAAGCGCCACTAACACT
* *
13477323 CGGGGCTTTAGCGGTG
66 CAGGGCTTTAGCGGCG
*
13477339 TTGTTAAAGAAGCGCCGCTAATGCTCAG
1 TTTTTAAA-AAGCGCCGCTAATGCTCAG
13477367 TTCAATAGTG
Statistics
Matches: 93, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
81 74 0.80
82 19 0.20
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (81 bp):
TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCGACGTTTCTGAAAAAGCGCCACTAACACT
CAGGGCTTTAGCGGCG
Found at i:13479930 original size:12 final size:13
Alignment explanation
Indices: 13479913--13479943 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
13479903 AGGAAGCATT
13479913 AGACCAGGTAA-G
1 AGACCAGGTAATG
13479925 AGACCAGGTAATG
1 AGACCAGGTAATG
13479938 AGACCA
1 AGACCA
13479944 TGGTCTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.19, G:0.29, T:0.10
Consensus pattern (13 bp):
AGACCAGGTAATG
Found at i:13481156 original size:43 final size:44
Alignment explanation
Indices: 13481098--13481262 Score: 219
Period size: 43 Copynumber: 3.8 Consensus size: 44
13481088 TTTTTGCGAG
* * * *
13481098 AAGCGCCGCTAAAGGT-TTGATCTATAGTGGCGTTTGTGATAAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
* * *
13481141 AAGCACCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTGAT-AA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
* *
13481184 AAGCGCCGCTAAAGGTCATGGTCTTCAGCGGCGTTTGTGA-GAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
*
13481227 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
13481263 ATTTCTAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
43 89 0.82
44 19 0.18
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
Found at i:13481182 original size:44 final size:44
Alignment explanation
Indices: 13481098--13481284 Score: 202
Period size: 43 Copynumber: 4.3 Consensus size: 44
13481088 TTTTTGCGAG
* * * * *
13481098 AAGCGCCGCTAAAGGT-TTGATCTATAGTGGCGTTTGTGATAAA
1 AAGCACCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
* *
13481141 AAGCACCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTGAT-AA
1 AAGCACCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
* * *
13481184 AAGCGCCGCTAAAGGTCATGGTCTTCAGCGGCGTTTGTGA-GAA
1 AAGCACCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
* * * **
13481227 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTATTTCTAAA
1 AAGCACCGCTAAAGGTCATGGTCTTTAGCGGCGTTT-GTGATAAA
13481272 AA-CACCGCTAAAG
1 AAGCACCGCTAAAG
13481285 TTAGTGACGC
Statistics
Matches: 123, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
43 89 0.72
44 30 0.24
45 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (44 bp):
AAGCACCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGATAAA
Found at i:13481229 original size:86 final size:86
Alignment explanation
Indices: 13481066--13481262 Score: 238
Period size: 86 Copynumber: 2.3 Consensus size: 86
13481056 AATTTTTTTA
* * * * * *
13481066 AAAGGTTATGTT-TTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGGTTTGATCTATAGTGGCG
1 AAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTATGATCTATAGCGGCG
13481130 TTTGTGATAAAAAGCACCGCT
66 TTTGTGATAAAAAGCACCGCT
* * *
13481151 AAAGGTCATGTTCTTTAGCGACGTTTGTGATAAAAGCGCCGCTAAAGGTCATGGTCT-TCAGCGG
1 AAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGT-ATGATCTAT-AGCGG
* *
13481215 CGTTTGTGA-GAAAAGCGCCGCT
64 CGTTTGTGATAAAAAGCACCGCT
* *
13481237 AAAGGTCTTGGTCTTTAGCGGCGTTT
1 AAAGGTCATGTTCTTTAGCGGCGTTT
13481263 ATTTCTAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
85 11 0.12
86 66 0.69
87 18 0.19
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (86 bp):
AAAGGTCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTATGATCTATAGCGGCG
TTTGTGATAAAAAGCACCGCT
Found at i:13481332 original size:27 final size:27
Alignment explanation
Indices: 13481302--13481361 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
13481292 CGCTGTCATT
13481302 AGCGCCGTTTTTTACTGCGCTTCTCAA
1 AGCGCCGTTTTTTACTGCGCTTCTCAA
13481329 AGCGCCGTTTTTTACTGCGCTTCTCAA
1 AGCGCCGTTTTTTACTGCGCTTCTCAA
13481356 AGCGCC
1 AGCGCC
13481362 ACTAATACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.20, T:0.33
Consensus pattern (27 bp):
AGCGCCGTTTTTTACTGCGCTTCTCAA
Found at i:13481411 original size:22 final size:22
Alignment explanation
Indices: 13481383--13481425 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13481373 TAGCGGCGCT
* *
13481383 AAAAAGCTCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
13481405 AAAAAGCGCTGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
13481426 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:13487702 original size:19 final size:19
Alignment explanation
Indices: 13487677--13487716 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
13487667 TTTTATATAT
*
13487677 ATTTTTAATTAAT-TTTAA
1 ATTTTTTATTAATATTTAA
*
13487695 ATTTTTTATTATTATTTAA
1 ATTTTTTATTAATATTTAA
13487714 ATT
1 ATT
13487717 GAATTCCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTATTAATATTTAA
Found at i:13492621 original size:22 final size:24
Alignment explanation
Indices: 13492578--13492621 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
13492568 GATCCTTCCA
*
13492578 CCCTTAAAATATTTTCACTATTGG
1 CCCTTAAAATATTTCCACTATTGG
*
13492602 CCCTTCAAAT-TTTCCA-TATT
1 CCCTTAAAATATTTCCACTATT
13492622 TACACTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 5 0.28
24 9 0.50
ACGTcount: A:0.27, C:0.25, G:0.05, T:0.43
Consensus pattern (24 bp):
CCCTTAAAATATTTCCACTATTGG
Found at i:13493390 original size:7 final size:7
Alignment explanation
Indices: 13493382--13493425 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
13493372 TTAAGCGATG
*
13493382 TGGGATG
1 TGGGATA
*
13493389 TGTGATA
1 TGGGATA
13493396 TGGGATA
1 TGGGATA
13493403 TGGGATA
1 TGGGATA
13493410 TGGGATA
1 TGGGATA
13493417 TGGGTATA
1 TGGG-ATA
13493425 T
1 T
13493426 ATAGACTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
7 29 0.88
8 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.41, T:0.34
Consensus pattern (7 bp):
TGGGATA
Found at i:13495879 original size:21 final size:21
Alignment explanation
Indices: 13495850--13495889 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13495840 CATTTAAAAT
* *
13495850 ATCACTATTATTTATTATTTA
1 ATCAATATTATTAATTATTTA
13495871 ATCAATATTATTAATTATT
1 ATCAATATTATTAATTATT
13495890 ATCAAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATCAATATTATTAATTATTTA
Found at i:13500742 original size:23 final size:23
Alignment explanation
Indices: 13500716--13500814 Score: 105
Period size: 23 Copynumber: 4.3 Consensus size: 23
13500706 AATGTTATTG
13500716 ATCAGTGGTAGTTAC-GACTACAT
1 ATCAGTGGTAGTTACAG-CTACAT
13500739 ATCAGTGGTAGCTT-CAGCTACAT
1 ATCAGTGGTAG-TTACAGCTACAT
* * * *
13500762 TTTAGTGGTAGCTAC-GACTACGT
1 ATCAGTGGTAGTTACAG-CTACAT
*
13500785 ATCAGTGGTAGTTTCAGCTACAT
1 ATCAGTGGTAGTTACAGCTACAT
13500808 ATCAGTG
1 ATCAGTG
13500815 TGGCACTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.03
23 56 0.90
24 4 0.06
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGTTACAGCTACAT
Found at i:13500788 original size:46 final size:46
Alignment explanation
Indices: 13500719--13500807 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
13500709 GTTATTGATC
*
13500719 AGTGGTAGTTACGACTACATATCAGTGGTAGCTTCAGCTACATTTT
1 AGTGGTAGCTACGACTACATATCAGTGGTAGCTTCAGCTACATTTT
* *
13500765 AGTGGTAGCTACGACTACGTATCAGTGGTAGTTTCAGCTACAT
1 AGTGGTAGCTACGACTACATATCAGTGGTAGCTTCAGCTACAT
13500808 ATCAGTGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (46 bp):
AGTGGTAGCTACGACTACATATCAGTGGTAGCTTCAGCTACATTTT
Found at i:13506714 original size:14 final size:15
Alignment explanation
Indices: 13506697--13506725 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13506687 ACTTATCAAT
13506697 TTATAT-TTGAATTA
1 TTATATGTTGAATTA
13506711 TTATATGTTGAATTA
1 TTATATGTTGAATTA
13506726 AACATTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
TTATATGTTGAATTA
Found at i:13511519 original size:3 final size:3
Alignment explanation
Indices: 13511511--13511539 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13511501 ATTAAATATG
13511511 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
13511540 AATTCAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13533222 original size:15 final size:15
Alignment explanation
Indices: 13533187--13533228 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
13533177 TAACAATCCA
* *
13533187 AGTTCAAGAAAGCCTG
1 AGTTCAA-AAAACCCG
13533203 AGTTCAAAAAACCCG
1 AGTTCAAAAAACCCG
13533218 AGTTCAAAAAA
1 AGTTCAAAAAA
13533229 GTCCGAGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.17
Consensus pattern (15 bp):
AGTTCAAAAAACCCG
Found at i:13533234 original size:16 final size:15
Alignment explanation
Indices: 13533187--13533236 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
13533177 TAACAATCCA
*
13533187 AGTTCAAGAAAGCCTG
1 AGTTCAAAAAAGCC-G
*
13533203 AGTTCAAAAAACCCG
1 AGTTCAAAAAAGCCG
13533218 AGTTCAAAAAAGTCCG
1 AGTTCAAAAAAG-CCG
13533234 AGT
1 AGT
13533237 CTATAAGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (15 bp):
AGTTCAAAAAAGCCG
Found at i:13533612 original size:2 final size:2
Alignment explanation
Indices: 13533605--13533629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13533595 AGAATGAGTT
13533605 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13533630 TTAGGTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13535160 original size:17 final size:18
Alignment explanation
Indices: 13535138--13535184 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
13535128 TCATTAATGC
13535138 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
13535155 ATATATTATATACTATATG
1 ATATA-TATAAACTATATA
13535174 ATATGATATAA
1 ATAT-ATATAA
13535185 CATTGAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 9 0.38
20 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:13538313 original size:25 final size:25
Alignment explanation
Indices: 13538280--13538348 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
13538270 CCGATATTGG
13538280 CTCACATGAGCTTCCCGTTACATGA
1 CTCACATGAGCTTCCCGTTACATGA
* * *
13538305 CTCACATGAGCTTCCGGTTATATGG
1 CTCACATGAGCTTCCCGTTACATGA
** *
13538330 CTCGGAAGAGCTTCCCGTT
1 CTCACATGAGCTTCCCGTT
13538349 TATGTGCTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (25 bp):
CTCACATGAGCTTCCCGTTACATGA
Found at i:13538365 original size:25 final size:25
Alignment explanation
Indices: 13538263--13538372 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
13538253 TTGCTCTCCG
* * **
13538263 GAGCTACCCGATAT-TGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCGGAT
* * **
13538287 GAGCTTCCCGTTACATGACTCACAT
1 GAGCTTCCCGTTATATGGCTCGGAT
* *
13538312 GAGCTTCCGGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATATGGCTCGGAT
**
13538337 GAGCTTCCCGTT-TATGTGCTCTTAT
1 GAGCTTCCCGTTATATG-GCTCGGAT
13538362 GAGCATTCCCG
1 GAGC-TTCCCG
13538373 AATATGAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 15 0.22
25 48 0.70
26 6 0.09
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGGAT
Found at i:13540197 original size:24 final size:24
Alignment explanation
Indices: 13540161--13540208 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13540151 GACACACCAC
* *
13540161 AGCTCGCAAGAGCATCCCGTTATT
1 AGCTCCCAAGAGCATCCCGATATT
* *
13540185 AGCTCCCATGAGCATTCCGATATT
1 AGCTCCCAAGAGCATCCCGATATT
13540209 GGCTTTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (24 bp):
AGCTCCCAAGAGCATCCCGATATT
Found at i:13540401 original size:24 final size:24
Alignment explanation
Indices: 13540329--13540408 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
13540319 CTTATAAGTG
13540329 TCCCGATATATGGCTCACACGAGCT
1 TCCCGATAT-TGGCTCACACGAGCT
* *
13540354 TCCTGATTAATT-GCTCTC-CGGAGCT
1 TCCCGA-T-ATTGGCTCACAC-GAGCT
* *
13540379 ACCCGATATTGGCTCACATGAGCT
1 TCCCGATATTGGCTCACACGAGCT
13540403 TCCCGA
1 TCCCGA
13540409 ATATGAATTG
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
23 3 0.07
24 17 0.40
25 19 0.44
26 2 0.05
27 2 0.05
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (24 bp):
TCCCGATATTGGCTCACACGAGCT
Found at i:13548274 original size:8 final size:8
Alignment explanation
Indices: 13548261--13548306 Score: 65
Period size: 8 Copynumber: 5.4 Consensus size: 8
13548251 AGTAAAACGA
13548261 AAATAAAG
1 AAATAAAG
13548269 AAATAAAG
1 AAATAAAG
13548277 AAATAAAG
1 AAATAAAG
13548285 AAATAAAG
1 AAATAAAG
13548293 TAAAAATAAAG
1 ---AAATAAAG
13548304 AAA
1 AAA
13548307 GAATGGAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 27 0.77
11 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (8 bp):
AAATAAAG
Found at i:13549784 original size:31 final size:29
Alignment explanation
Indices: 13549749--13549843 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 29
13549739 ACGTTTTAGC
13549749 CACTTACGTTAACATGTTATAACATTTTAAT
1 CACTTACGTTAA-ATGTT-TAACATTTTAAT
*
13549780 CACTTATGTTTGAAATG-TT-ACATTTTAAT
1 CACTTACG-TT-AAATGTTTAACATTTTAAT
* * * *
13549809 TACTTACATTAATATGTTGTATCATTTTAGT
1 CACTTACGTTAA-ATGTT-TAACATTTTAAT
13549840 CACT
1 CACT
13549844 ATGCTGTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.04
28 5 0.10
29 16 0.31
30 2 0.04
31 19 0.37
32 5 0.10
33 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (29 bp):
CACTTACGTTAAATGTTTAACATTTTAAT
Found at i:13549808 original size:29 final size:29
Alignment explanation
Indices: 13549726--13549814 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
13549716 CACTTTTGTT
* **
13549726 TGTTTGAAATGTTACGTTTTAGCCACTTA
1 TGTTTGAAATGTTACATTTTAATCACTTA
*
13549755 CG-TT-AACATGTTATAACATTTTAATCACTTA
1 TGTTTGAA-ATG-T-T-ACATTTTAATCACTTA
*
13549786 TGTTTGAAATGTTACATTTTAATTACTTA
1 TGTTTGAAATGTTACATTTTAATCACTTA
13549815 CATTAATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.04
28 5 0.10
29 17 0.35
30 2 0.04
31 15 0.31
32 5 0.10
33 2 0.04
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (29 bp):
TGTTTGAAATGTTACATTTTAATCACTTA
Found at i:13549814 original size:60 final size:60
Alignment explanation
Indices: 13549726--13549843 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
13549716 CACTTTTGTT
* * *
13549726 TGTTTGAAATGTTACGTTTTAGCCACTTACGTTAACATGTTATAACATTTTAATCACTTA
1 TGTTTGAAATGTTACATTTTAACCACTTACATTAACATGTTATAACATTTTAATCACTTA
** * * * *
13549786 TGTTTGAAATGTTACATTTTAATTACTTACATTAATATGTTGTATCATTTTAGTCACT
1 TGTTTGAAATGTTACATTTTAACCACTTACATTAACATGTTATAACATTTTAATCACT
13549844 ATGCTGTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.47
Consensus pattern (60 bp):
TGTTTGAAATGTTACATTTTAACCACTTACATTAACATGTTATAACATTTTAATCACTTA
Found at i:13550441 original size:14 final size:14
Alignment explanation
Indices: 13550396--13550443 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
13550386 AATTAAATAG
13550396 TAAACAAAATTATTA
1 TAAA-AAAATTATTA
* **
13550411 TAAAAAATTTAAAA
1 TAAAAAAATTATTA
13550425 TAAAAAAATTATTA
1 TAAAAAAATTATTA
13550439 TAAAA
1 TAAAA
13550444 TTAAGGGGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAAAATTATTA
Found at i:13550447 original size:25 final size:29
Alignment explanation
Indices: 13550371--13550447 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 29
13550361 TGTAAAACTG
13550371 AATTAATTGATAATAAATTAAATAGTAAACAA
1 AATT-ATT-ATAA-AAATTAAATAGTAAACAA
13550403 AATTATTATAAAAAATTTAAA-A-TAAA-AA
1 AATTATTAT-AAAAA-TTAAATAGTAAACAA
13550431 AATTATTAT-AAAATTAA
1 AATTATTATAAAAATTAA
13550448 GGGGGAAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
25 4 0.09
26 4 0.09
28 11 0.26
29 4 0.09
30 6 0.14
31 10 0.23
32 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (29 bp):
AATTATTATAAAAATTAAATAGTAAACAA
Found at i:13553604 original size:19 final size:17
Alignment explanation
Indices: 13553580--13553643 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 17
13553570 CCTATTAATC
13553580 AAAATTTACAATAATTTCT
1 AAAATTT-CAA-AATTTCT
13553599 AAAATTTCTAAAATTTCT
1 AAAATTTC-AAAATTTCT
*
13553617 AAAATTTTTTAAAATTTCT
1 AAAA--TTTCAAAATTTCT
13553636 AAAATTTC
1 AAAATTTC
13553644 GACATGGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.08
18 12 0.30
19 22 0.55
20 3 0.08
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTTCAAAATTTCT
Found at i:13553606 original size:9 final size:9
Alignment explanation
Indices: 13553592--13553643 Score: 86
Period size: 9 Copynumber: 5.7 Consensus size: 9
13553582 AATTTACAAT
13553592 AATTTCTAA
1 AATTTCTAA
13553601 AATTTCTAA
1 AATTTCTAA
13553610 AATTTCTAA
1 AATTTCTAA
*
13553619 AATTTTTTAA
1 AA-TTTCTAA
13553629 AATTTCTAA
1 AATTTCTAA
13553638 AATTTC
1 AATTTC
13553644 GACATGGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
9 32 0.80
10 8 0.20
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTTCTAA
Found at i:13554236 original size:76 final size:76
Alignment explanation
Indices: 13554102--13554245 Score: 182
Period size: 76 Copynumber: 1.9 Consensus size: 76
13554092 ATATATTTAA
* * * *
13554102 TAAATATTTAAGAGTCCAATTTACGGGAATAGAGTCTCAGGAATGTACTTTCCAACACCCCTGAC
1 TAAATATTTAAGAGTCCAATTTACAGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTAAC
13554167 TATTTGGTCGT
66 TATTTGGTCGT
* * * ***
13554178 TAAATATTTACGAGTCTAATTTACAGGAACGGAGTCTC-GAGAATGCACTTTTTGACACCCCTAA
1 TAAATATTTAAGAGTCCAATTTACAGGAACAGAGTCTCAG-GAATGCACTTTCCAACACCCCTAA
13554242 CTAT
65 CTAT
13554246 CGAGTCGTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 1 0.02
76 56 0.98
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (76 bp):
TAAATATTTAAGAGTCCAATTTACAGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTAAC
TATTTGGTCGT
Found at i:13559539 original size:5 final size:5
Alignment explanation
Indices: 13559525--13559571 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
13559515 ACACACATAT
* * *
13559525 ATTCA TTTCA ATTCA ATTCA ATTCA A-TCA ACTTTA AATCA ATTCA AT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA A-TTCA ATTCA ATTCA AT
13559572 AATCAAAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
5 27 0.79
6 3 0.09
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:13561535 original size:24 final size:26
Alignment explanation
Indices: 13561501--13561552 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
13561491 GATTCCAGTC
13561501 AAAAACTCTAAA-TTTAAAAATATTA
1 AAAAACTCTAAATTTTAAAAATATTA
*
13561526 AAAAAC-CTAAATTTTAAAAATTTTA
1 AAAAACTCTAAATTTTAAAAATATTA
13561551 AA
1 AA
13561553 CCTAGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAACTCTAAATTTTAAAAATATTA
Found at i:13566539 original size:24 final size:24
Alignment explanation
Indices: 13566512--13566563 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
13566502 AATCAAAGTC
*
13566512 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
13566536 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
13566560 AAAT
1 AAAT
13566564 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:13573919 original size:22 final size:24
Alignment explanation
Indices: 13573848--13573914 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 24
13573838 TGTTATTTAT
13573848 TTATTTATTTTAAACCTATTTCTCATATA
1 TTATTTATTTTAAA--TATTT-T-AT-TA
13573877 TTATTTATTTTAAATTATTTTATTA
1 TTATTTATTTTAAA-TATTTTATTA
13573902 TTATTTATTTTAA
1 TTATTTATTTTAA
13573915 GTTTTCCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 15 0.41
26 2 0.05
27 1 0.03
28 5 0.14
29 14 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTTATTTTAAATATTTTATTA
Found at i:13574031 original size:26 final size:26
Alignment explanation
Indices: 13573848--13574249 Score: 241
Period size: 26 Copynumber: 15.2 Consensus size: 26
13573838 TGTTATTTAT
* *
13573848 TTATTTATTTTAAACCTATTTCTCATATA
1 TTATTTATTTTAAA-TTGTTT-T-ATATA
*
13573877 TTATTTATTTTAAATTATTTTAT-TA
1 TTATTTATTTTAAATTGTTTTATATA
* ** *
13573902 TTATTTATTTTAAGTT-TTCCACATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * * * *
13573927 TAATGTATTTTAAACTATTTCAAACTA
1 TTATTTATTTTAAATTGTTTTATA-TA
**
13573954 TTATCCATTTTAAATT-TTTTATATA
1 TTATTTATTTTAAATTGTTTTATATA
* **
13573979 TTATTTATTTTTAAACTGTCATATATA
1 TTATTTA-TTTTAAATTGTTTTATATA
*
13574006 TTATTTATTTTGAATTGTTTTTTATATA
1 TTATTTATTTTAAATTG--TTTTATATA
* *
13574034 TATCATTTATTTTTTTAAAAACT-TTTTAGTACA
1 T-T-ATTTA---TTTT--AAATTGTTTTA-TATA
* *
13574067 TTATTTATTTTAAACTTCTTTTTACATA
1 TTATTTATTTTAAA-TT-GTTTTATATA
*
13574095 TTATTTATTTTAAA--CTTTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* *
13574118 -TA-TTATTTTAAATTGTCTTATATG
1 TTATTTATTTTAAATTGTTTTATATA
* * *
13574142 TTATTTATTTTAAATTGCTTTGTCTA
1 TTATTTATTTTAAATTGTTTTATATA
* *
13574168 TTATTTATTTTAATTTGTTTTACATA
1 TTATTTATTTTAAATTGTTTTATATA
* *
13574194 TTAGTTACTTTAAATTG-TTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * *
13574218 CTATTTACTTCAAATTGTTCTATATA
1 TTATTTATTTTAAATTGTTTTATATA
13574244 TTATTT
1 TTATTT
13574250 TGTTTCGTTT
Statistics
Matches: 292, Mismatches: 56, Indels: 53
0.73 0.14 0.13
Matches are distributed among these distances:
21 10 0.03
22 2 0.01
23 6 0.02
24 27 0.09
25 45 0.15
26 92 0.32
27 30 0.10
28 33 0.11
29 20 0.07
30 5 0.02
31 5 0.02
32 6 0.02
33 8 0.03
35 3 0.01
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTTTTATATA
Found at i:13574077 original size:28 final size:27
Alignment explanation
Indices: 13574040--13574125 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 27
13574030 TATATATCAT
*
13574040 TTATTT-TTTTAAAAACTTTTTAGTACA
1 TTATTTATTTTAAAAACTTTTTA-TATA
** *
13574067 TTATTTATTTTAAACTTCTTTTTACATA
1 TTATTTATTTTAAA-AACTTTTTATATA
13574095 TTATTTATTTT--AAACTTTTTATATA
1 TTATTTATTTTAAAAACTTTTTATATA
13574120 TTATTT
1 TTATTT
13574126 TAAATTGTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
25 16 0.32
26 1 0.02
27 6 0.12
28 20 0.40
29 7 0.14
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (27 bp):
TTATTTATTTTAAAAACTTTTTATATA
Found at i:13574232 original size:24 final size:23
Alignment explanation
Indices: 13574198--13574245 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
13574188 TACATATTAG
* *
13574198 TTACTTTAAATTGTTTTATACTAT
1 TTACTTCAAATTGTTCTATA-TAT
13574222 TTACTTCAAATTGTTCTATATAT
1 TTACTTCAAATTGTTCTATATAT
13574245 T
1 T
13574246 ATTTTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (23 bp):
TTACTTCAAATTGTTCTATATAT
Found at i:13584042 original size:19 final size:20
Alignment explanation
Indices: 13584000--13584035 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
13583990 GTTTTCAAAT
13584000 AATT-ATAAAAATATATTAA
1 AATTAATAAAAATATATTAA
13584019 AATTAATAAAAAT-TATT
1 AATTAATAAAAATATATT
13584036 CGAATTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAATAAAAATATATTAA
Found at i:13587126 original size:168 final size:169
Alignment explanation
Indices: 13586883--13587219 Score: 667
Period size: 168 Copynumber: 2.0 Consensus size: 169
13586873 CATTTTTTAA
13586883 TGTTTACATTATTATATAGATTTAATATTTTATATGTTATAAAGTACATAATATATAAAAATAAA
1 TGTTTACATTATTATATAGATTTAATATTTTATATGTTATAAAGTACATAATATATAAAAATAAA
13586948 TAAAATAAAACATTAATAACTTAAAAACGAGTTGGATTGATTAAACGATTTTAATTCATTTTTTT
66 TAAAATAAAACATTAATAACTTAAAAACGAGTTGGATTGATTAAACGATTTTAATTCATTTTTTT
13587013 GTCTAAATTTATTTTTTAAATCAAACTTTCTTAAATTCC
131 GTCTAAATTTATTTTTTAAATCAAACTTTCTTAAATTCC
13587052 TGTTTACATT-TTATATAGATTTAATATTTTATATGTTATAAAGTACATAATATATAAAAATAAA
1 TGTTTACATTATTATATAGATTTAATATTTTATATGTTATAAAGTACATAATATATAAAAATAAA
13587116 TAAAATAAAACATTAATAACTTAAAAACGAGTTGGATTGATTAAACGATTTTAATTCATTTTTTT
66 TAAAATAAAACATTAATAACTTAAAAACGAGTTGGATTGATTAAACGATTTTAATTCATTTTTTT
13587181 GTCTAAATTTATTTTTTAAATCAAACTTTCTTAAATTCC
131 GTCTAAATTTATTTTTTAAATCAAACTTTCTTAAATTCC
13587220 AAACGTAACC
Statistics
Matches: 168, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
168 158 0.94
169 10 0.06
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (169 bp):
TGTTTACATTATTATATAGATTTAATATTTTATATGTTATAAAGTACATAATATATAAAAATAAA
TAAAATAAAACATTAATAACTTAAAAACGAGTTGGATTGATTAAACGATTTTAATTCATTTTTTT
GTCTAAATTTATTTTTTAAATCAAACTTTCTTAAATTCC
Found at i:13589426 original size:31 final size:31
Alignment explanation
Indices: 13589388--13589450 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
13589378 AAGGACACTG
*
13589388 AATACATTGTAATAAGGATCGGATTTTTTTT
1 AATACATTGTAATAAGGATCCGATTTTTTTT
13589419 AATACATTGTAATAAGGATCCGATTTTTTTT
1 AATACATTGTAATAAGGATCCGATTTTTTTT
13589450 A
1 A
13589451 CAAGAAATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (31 bp):
AATACATTGTAATAAGGATCCGATTTTTTTT
Found at i:13602197 original size:44 final size:44
Alignment explanation
Indices: 13602119--13602546 Score: 280
Period size: 44 Copynumber: 9.9 Consensus size: 44
13602109 AAAAATGGCA
* *
13602119 AATCTTATCTTCCTGAAGTTGCAGCAGAGCAGATTAAAGCCGAC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* * * * *
13602163 AATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACC-TC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* * *
13602206 AGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-T--CG-C-ATC
1 A-ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGA-C
* * * **
13602246 TAGTCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGTA-
1 -AATCTTATCTCCCTGAAGTTGCAGTAGA-GCAGATTAAAG-CCG-AC
* **
13602292 AATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTAAAGCCGAC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* ** * *
13602336 AATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACC-TC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* ** *
13602379 AGATCTTATCTCTCTGAAGTTATAG-AGAGCAGA-T--CG-C-ATC
1 A-ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGA-C
* * * ** *
13602419 TAGTCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGC
1 -AATCTTATCTCCCTGAAGTTGCAGTAGA-GCAGATTAAAGCCGAC
**
13602464 AAATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTAAAGCCGAC
1 -AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* * *
13602509 AAT-TCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAA
1 AATCT-TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAA
13602547 ATCTTAGATC
Statistics
Matches: 294, Mismatches: 64, Indels: 52
0.72 0.16 0.13
Matches are distributed among these distances:
39 2 0.01
40 43 0.15
41 12 0.04
42 4 0.01
43 18 0.06
44 144 0.49
45 66 0.22
46 4 0.01
48 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
Found at i:13602373 original size:173 final size:173
Alignment explanation
Indices: 13602085--13602600 Score: 863
Period size: 173 Copynumber: 3.0 Consensus size: 173
13602075 GTCTTATCCT
* * *
13602085 CCTGAAGTTGCAGTGGGGCAGACTAAAAATGGCAAATCTTATCTTCCTGAAGTTGCAGCAGAGCA
1 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
*
13602150 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCTCAGATCTTAT
66 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
13602215 CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
131 CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
*
13602258 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGTAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
1 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
* *
13602323 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTCAGATCTTAT
66 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
*
13602388 CTCTCTGAAGTTATAGAGAGCAGATCGCATCTAGTCTTATTTC
131 CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
*
13602431 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGCGGAGCA
1 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
* * * * *
13602496 GATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAATCTTAGATCTTAT
66 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
* * *
13602561 CTTTCTGAAATTGCAGAGAGCAGATCGCGA-CTAGTCTTAT
131 CTCTCTGAAGTTGTAGAGAGCAGATCGC-ATCTAGTCTTAT
13602601 CTCCTTAAAG
Statistics
Matches: 322, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
173 321 1.00
174 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (173 bp):
CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
Found at i:13602518 original size:129 final size:128
Alignment explanation
Indices: 13602294--13602528 Score: 280
Period size: 129 Copynumber: 1.8 Consensus size: 128
13602284 AGATGGTAAA
* *
13602294 TCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTAAAGACGACAATCCTATCTCCCTGAAGTTGCA
* ** * *
13602359 GTAGAGTGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTATAGAGAGCAGATCGCATCTAG
66 GCAGAGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTATAGAGAGCAGATCGCATCTAG
* * * *
13602422 TCTTAT-TTCCCTGAAGTTGCAG-TGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
1 TCTTATCTT-CCTGAAGTTGCAGCGGA-GCAGACTAAAGACGAC-AATCCTATCTCCCTGAAGTT
* *
13602485 GCAGCGGAGCAGATTAAAGCCGACA-AT-TCTATCTCCCTGAAGTT
63 GCAGCAGAGCAGATTAAAACC-ACAGATCT-TATCTCCCTGAAGTT
13602529 GCAATGGAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
127 4 0.04
128 32 0.36
129 51 0.57
130 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (128 bp):
TCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTAAAGACGACAATCCTATCTCCCTGAAGTTGCA
GCAGAGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTATAGAGAGCAGATCGCATCTAG
Found at i:13602562 original size:44 final size:44
Alignment explanation
Indices: 13602076--13602585 Score: 242
Period size: 44 Copynumber: 11.7 Consensus size: 44
13602066 ACAGATCGAG
* * *** *
13602076 TCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTAAAAATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAATCTTAGA
* ** * ** *
13602121 TCTTATCTTCCTGAAGTTGCAGCAGAGCAGATT-AAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTA-GA
* * * *
13602165 TCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* * * ***
13602209 TCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCGCATC-TAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* * ** *
13602249 TCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTAAA-ATCTTAGA
* * * ** *
13602294 TCTTATCTTCCTGAAGTTGCAGCGGAGCAGATT-AAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTA-GA
* * ** * *
13602338 TCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* ** * ***
13602382 TCTTATCTCTCTGAAGTTATAG-AGAGCAGA-TCGCATC-TAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* * *** *
13602422 TCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTAAA-ATCTTAGA
* * ** *
13602467 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGATT-AAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTA-GA
* *
13602511 T-TCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAATCTTAGA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
** * *
13602555 TCTTATCTTTCTGAAATTGCAG-AGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
13602586 CGCGACTAGT
Statistics
Matches: 347, Mismatches: 95, Indels: 48
0.71 0.19 0.10
Matches are distributed among these distances:
40 41 0.12
41 14 0.04
42 8 0.02
43 32 0.09
44 153 0.44
45 95 0.27
46 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
Found at i:13602891 original size:45 final size:43
Alignment explanation
Indices: 13602772--13602891 Score: 102
Period size: 45 Copynumber: 2.7 Consensus size: 43
13602762 AGATTGTAAG
* ** *
13602772 TCTTATTTCCCTGAAGTTGCAGTGGAATAGACTAGTGAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAGTG-AACAAA
* * *
13602816 TCTTATACT-CTTGAAGTGGCAGT-GAGGCAGACTGAAGATG-GCAAA
1 TCTTAT-CTCCCTGAAGTTGCAGTGGA-GCAGACT--AG-TGAACAAA
13602861 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
13602892 TTAAAGCCGA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
43 2 0.03
44 25 0.42
45 27 0.45
46 4 0.07
47 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAGTGAACAAA
Found at i:13602937 original size:44 final size:44
Alignment explanation
Indices: 13602859--13602942 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
13602849 GAAGATGGCA
* * * *
13602859 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGCCGAT
* * *
13602903 AATCTTATCTCCTTAAAGTTACAATGAAGTAGATTGAAGC
1 AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGC
13602943 ACTAATTCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGCCGAT
Found at i:13609345 original size:18 final size:17
Alignment explanation
Indices: 13609317--13609351 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13609307 ATTATTAAGA
*
13609317 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13609334 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13609352 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13609608 original size:16 final size:16
Alignment explanation
Indices: 13609587--13609622 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
13609577 GATTTGCTAT
*
13609587 TACACCTCTAATCCAA
1 TACACCTCTAAACCAA
13609603 TACACCTCTAAACCAA
1 TACACCTCTAAACCAA
13609619 TACA
1 TACA
13609623 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (16 bp):
TACACCTCTAAACCAA
Found at i:13615295 original size:6 final size:6
Alignment explanation
Indices: 13615284--13615314 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
13615274 AATTATGAAC
13615284 AATTAA AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA AATTAA A
13615315 CATAAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:13624864 original size:43 final size:42
Alignment explanation
Indices: 13624795--13624881 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 42
13624785 AAGCGTTGCA
* * *
13624795 AAAGATCATGTTCTGTAGCAACGTTTGTAGTAAAAGCGCCACT
1 AAAGATCATGTTCTATAGCAACGTTTGTAGGAAAA-CACCACT
***
13624838 AAAGATCATGTTCTATAGCGGTGTTTGTAGGAAAACACCACT
1 AAAGATCATGTTCTATAGCAACGTTTGTAGGAAAACACCACT
13624880 AA
1 AA
13624882 CATTAACAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
42 8 0.21
43 30 0.79
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (42 bp):
AAAGATCATGTTCTATAGCAACGTTTGTAGGAAAACACCACT
Found at i:13629070 original size:25 final size:25
Alignment explanation
Indices: 13629040--13629094 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
13629030 GGATGGGAAA
*
13629040 GAAAAAAATAAGTTAGGGAATTGGG
1 GAAAAAAATAAGTTAGAGAATTGGG
* *
13629065 GAAAAAACTAAGTTAGAGATTTGGG
1 GAAAAAAATAAGTTAGAGAATTGGG
13629090 GAAAA
1 GAAAA
13629095 TGATTTTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.29, T:0.20
Consensus pattern (25 bp):
GAAAAAAATAAGTTAGAGAATTGGG
Found at i:13629318 original size:83 final size:83
Alignment explanation
Indices: 13629171--13629331 Score: 191
Period size: 83 Copynumber: 1.9 Consensus size: 83
13629161 ATATTCGCGA
* * * *
13629171 CGTTTATGAGAAAAACACTACTATCGTTTTTAACCTTTTGCGGTATTTATGCAAAAACGTCACTA
1 CGTTTATGAGAAAAACACTACTATCGTTATTAACCTTTAGCGGCATTTATGCAAAAACGCCACTA
13629236 TTGT-TTTACCTTTTGCAG
66 TT-TCTTTACCTTTTGCAG
* * * * * **
13629254 CGTTTATGCGAAAAATACTGCTATTGTTATTATACCTTTAGCGGCGTTTA-GGGAAAACGCCACT
1 CGTTTATGAGAAAAACACTACTATCGTTATTA-ACCTTTAGCGGCATTTATGCAAAAACGCCACT
13629318 ATTTCTTTACCTTT
65 ATTTCTTTACCTTT
13629332 CACGGCGCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 1 0.02
83 50 0.77
84 14 0.22
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (83 bp):
CGTTTATGAGAAAAACACTACTATCGTTATTAACCTTTAGCGGCATTTATGCAAAAACGCCACTA
TTTCTTTACCTTTTGCAG
Found at i:13632742 original size:12 final size:12
Alignment explanation
Indices: 13632727--13632777 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
13632717 TAAAAGTAAC
13632727 CAAAAATAAAAA
1 CAAAAATAAAAA
*
13632739 CAAAAATAAACA
1 CAAAAATAAAAA
* *
13632751 TAAAAATGAAAA
1 CAAAAATAAAAA
* *
13632763 GAAAAA-GAAAA
1 CAAAAATAAAAA
13632774 CAAA
1 CAAA
13632778 TAAACTCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 8 0.24
12 25 0.76
ACGTcount: A:0.78, C:0.08, G:0.06, T:0.08
Consensus pattern (12 bp):
CAAAAATAAAAA
Found at i:13634237 original size:19 final size:19
Alignment explanation
Indices: 13634184--13634238 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
13634174 AAGCAAATTA
* *
13634184 AATAAAATAAG-AAATGAT
1 AATAAAAGAAGTAAATAAT
**
13634202 AAGCAAAGAGAGT-AATAAT
1 AATAAAAGA-AGTAAATAAT
13634221 AATAAAAGAAGTAAATAA
1 AATAAAAGAAGTAAATAA
13634239 AAAATAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.18
Consensus pattern (19 bp):
AATAAAAGAAGTAAATAAT
Found at i:13634256 original size:16 final size:16
Alignment explanation
Indices: 13634237--13634267 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13634227 AGAAGTAAAT
*
13634237 AAAAAATAAATAAAAG
1 AAAAAATAAAGAAAAG
13634253 AAAAAATAAAGAAAA
1 AAAAAATAAAGAAAA
13634268 AAGGGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAGAAAAG
Found at i:13640657 original size:22 final size:25
Alignment explanation
Indices: 13640631--13640685 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
13640621 TTATAAATTC
13640631 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
13640653 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
13640678 AATTTAAA
1 AATTTAAA
13640686 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.31
24 4 0.15
25 10 0.38
26 1 0.04
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:13647036 original size:4 final size:4
Alignment explanation
Indices: 13647027--13647059 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
13647017 TATTATTAAA
*
13647027 TTAT TTAT TTAT TTAT TTAT TTGT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
13647060 ATCATTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:13653198 original size:45 final size:45
Alignment explanation
Indices: 13653046--13653314 Score: 181
Period size: 44 Copynumber: 6.1 Consensus size: 45
13653036 CATCATGATG
* * * ** *
13653046 AATCTTATCTCCCTAAAGTTGTAGTGGAACAGATTAAAGCCA-CT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATAGCA
* * ** ** *
13653090 AATCTTA-CCCCCTTGAAGTTGTAGTGGGGCAGGTTGAAA-TTA-CA
1 AATCTTATCTCCC-TGAAGTTGCAGTGGAACAGACT-AAAGATAGCA
* * *
13653134 AGTCTTATCTCCTTAAAGTTGCAGTGGAACAGACTAAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATAGCA
* * ** *
13653179 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATAGCA
* * * * * **
13653223 AGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGACAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATAGCA
* ** * *
13653268 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATAGCA
13653312 AAT
1 AAT
13653315 TATTGCGGAT
Statistics
Matches: 173, Mismatches: 46, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
43 7 0.04
44 92 0.53
45 74 0.43
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAGATAGCA
Found at i:13653229 original size:89 final size:89
Alignment explanation
Indices: 13653048--13653295 Score: 286
Period size: 89 Copynumber: 2.8 Consensus size: 89
13653038 TCATGATGAA
* * * * *
13653048 TCTTATCTCCCTAAAGTTGTAGTGGAACAGATTAAAGCCA-CTAATCTTA-CCCCCTTGAAGTTG
1 TCTTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGACAGCAAATCTTATCTCCC-TGAAGTTG
* *
13653111 TAGTGGGGCAGGTTGAAATTACAAG
65 CAGTGGAGCAGGTTGAAATTACAAG
* * *
13653136 TCTTATCTCCTTAAAGTTGCAGTGGAACAGACTAAAGATAGCAAACCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGACAGCAAATCTTATCTCCCTGAAGTTGC
13653201 AGTGGAGCAGGTTGAAGA-TACAAG
66 AGTGGAGCAGGTTGAA-ATTACAAG
* * * * ** * **
13653225 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGACAGTGAATCTTATTTCCCTGGCGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGACAGCAAATCTTATCTCCCTGAAGTTGC
13653290 AGTGGA
66 AGTGGA
13653296 ACAGATTAAA
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
88 35 0.26
89 95 0.70
90 5 0.04
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (89 bp):
TCTTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGACAGCAAATCTTATCTCCCTGAAGTTGC
AGTGGAGCAGGTTGAAATTACAAG
Found at i:13653440 original size:143 final size:143
Alignment explanation
Indices: 13653182--13653781 Score: 717
Period size: 143 Copynumber: 4.2 Consensus size: 143
13653172 GATAGCAAAC
* * ** * *
13653182 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* *
13653247 TAGAGCAGACTGAAGACAGTGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
66 CAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
*
13653312 AATTATTGCGGAT
131 AATTATTGCAGAT
* * * * *
13653325 CTTATCTTCCCGAAGTTGTAGTAGAGCAGATTGAAGCCACCAGTCTTATCTCTCTGAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* * *
13653390 CAGAGCAAACTAAAGACAGCGAATCTTATTTCCCTAGCGTTGCAGTGGAACAGATTAAAGCTACA
66 CAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
** *
13653455 AA-TGGTGGAGAAT
131 AATTATTGCAG-AT
* * * *
13653468 CTTATCTTCCTAAAGTTACAGTGGAGCAGGTTGAAGCCACCAGCCTTATCTCTCTGAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* * * * * * * *
13653533 CGGAGCAGACTGAATATAGCGAACCTTATTTCTCTGGTGTTGCAGTGGAATAAATTAAAGCTACA
66 CAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
13653598 AATTA-TGACAGAT
131 AATTATTG-CAGAT
* * * *
13653611 CTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAACCTCATCTCCCTAAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* * ** * * * *
13653676 CAGAGCAGACTGAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAATAGATTGACGCTA-T
66 CAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
*
13653740 AA--ACTGCAGAT
131 AATTATTGCAGAT
*
13653751 CTTAT-TTCTCTGAAGTTGCAGTAGAGCAGAT
1 CTTATCTTC-CTGAAGTTGCAGTGGAGCAGAT
13653782 CATATTAAAC
Statistics
Matches: 393, Mismatches: 59, Indels: 13
0.85 0.13 0.03
Matches are distributed among these distances:
139 3 0.01
140 31 0.08
141 2 0.01
142 6 0.02
143 348 0.89
144 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (143 bp):
CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
CAGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
AATTATTGCAGAT
Found at i:13653897 original size:45 final size:45
Alignment explanation
Indices: 13653832--13653997 Score: 165
Period size: 45 Copynumber: 3.7 Consensus size: 45
13653822 TCGAAGTTAT
* *
13653832 AAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGACAGC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
* * * * *
13653877 TAGTCTTATCTCCCTCAAGTTGCAGTGAAGCAGACTGAAGATAAC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
* * * * * *
13653922 AAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAG-CCAC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
* * *
13653966 AAATCTAATCTCCCTGAA-TATGTAGTGGAGCA
1 AAGTCTTATCTCCCTGAAGT-TGCAGTGGAGCA
13653998 AATTGTAGAT
Statistics
Matches: 100, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
43 1 0.01
44 28 0.28
45 71 0.71
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (45 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
Found at i:13657702 original size:19 final size:18
Alignment explanation
Indices: 13657674--13657713 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
13657664 NNNNNNNNNN
* *
13657674 TATATTTTTAATAATTTT
1 TATATTTTTAAAAATGTT
13657692 TATAGTTTTTAAAAATGTT
1 TATA-TTTTTAAAAATGTT
13657711 TAT
1 TAT
13657714 TAAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATTTTTAAAAATGTT
Found at i:13659191 original size:9 final size:9
Alignment explanation
Indices: 13659174--13659204 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13659164 TCGAGTTGAT
13659174 TCGAATAAC
1 TCGAATAAC
*
13659183 TCGATTAAC
1 TCGAATAAC
13659192 TCGAATAAC
1 TCGAATAAC
13659201 TCGA
1 TCGA
13659205 TTCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:13662703 original size:6 final size:6
Alignment explanation
Indices: 13662692--13662716 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13662682 AGTTTTCTTC
13662692 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
13662717 CCTAGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:13665222 original size:92 final size:92
Alignment explanation
Indices: 13665060--13665236 Score: 275
Period size: 92 Copynumber: 1.9 Consensus size: 92
13665050 AAGCAGGTAG
* *
13665060 AAAAGATAGAGAGGATTGAGAATAGGAGAGAATAAAGAAGGAAGTTGTATTAACCAAAATTGATA
1 AAAAGATAGAGAGGATTGAGAAGAGGAGAGAATAAAGAAGGAAATTGTATTAACCAAAATTGATA
* *
13665125 GTTGTTTCCTCTCTCAACAGTAGAGAA
66 ATTGTTTCCCCTCTCAACAGTAGAGAA
* * *
13665152 AAAAGATATA-AGGAATTGAGAAGAGGATAGAATAATGAAGGAAATTGTATTAACCAAAATTGAT
1 AAAAGATAGAGAGG-ATTGAGAAGAGGAGAGAATAAAGAAGGAAATTGTATTAACCAAAATTGAT
13665216 AATTGTTTCCCCTCTCAACAG
65 AATTGTTTCCCCTCTCAACAG
13665237 CAGGTTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 3 0.04
92 74 0.96
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (92 bp):
AAAAGATAGAGAGGATTGAGAAGAGGAGAGAATAAAGAAGGAAATTGTATTAACCAAAATTGATA
ATTGTTTCCCCTCTCAACAGTAGAGAA
Found at i:13667848 original size:24 final size:24
Alignment explanation
Indices: 13667784--13667848 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
13667774 ATTCTTTGTC
13667784 ATTTGTCCTTTTTTTAAAGTTTTTT
1 ATTTGTCCTTTTTTT-AAGTTTTTT
*
13667809 ATTTAT--TTACTTTTTAAGTTTTTT
1 ATTTGTCCTT--TTTTTAAGTTTTTT
*
13667833 ATTTGTCCTTTATTTA
1 ATTTGTCCTTTTTTTA
13667849 TTTTACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 2 0.06
24 19 0.58
25 10 0.30
26 2 0.06
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (24 bp):
ATTTGTCCTTTTTTTAAGTTTTTT
Found at i:13667852 original size:22 final size:21
Alignment explanation
Indices: 13667827--13667872 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
13667817 ACTTTTTAAG
13667827 TTTT-TTATTTGTCCTTTATTTA
1 TTTTATTATTTGT--TTTATTTA
13667849 TTTTACTTATTTGTTTTATTTA
1 TTTTA-TTATTTGTTTTATTTA
13667871 TT
1 TT
13667873 GGTTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTATTATTTGTTTTATTTA
Found at i:13671340 original size:30 final size:30
Alignment explanation
Indices: 13671304--13671406 Score: 154
Period size: 30 Copynumber: 3.4 Consensus size: 30
13671294 CCTATGGCCA
*
13671304 GGTGATATGAACTTGAATCGCCCATGTCTG
1 GGTGATATGAACTCGAATCGCCCATGTCTG
* *
13671334 GGTGATATGAACTCAAATCGCCCATGTCCG
1 GGTGATATGAACTCGAATCGCCCATGTCTG
*
13671364 GGTGATATGAACTCGTA-CTGCCCATGTCTG
1 GGTGATATGAACTCGAATC-GCCCATGTCTG
13671394 GGTGATATGAACT
1 GGTGATATGAACT
13671407 GCTCTGCGAC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 1 0.02
30 65 0.98
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (30 bp):
GGTGATATGAACTCGAATCGCCCATGTCTG
Found at i:13671368 original size:60 final size:60
Alignment explanation
Indices: 13671270--13671406 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 60
13671260 TGGTTGTTGC
* * * *
13671270 TCTGGGTGAAATAAACTCAAACCGCCTATGGCCAGGTGATATGAACTTGAA-TCGCCCATG
1 TCTGGGTGATATGAACTCAAACCGCCCATGGCCAGGTGATATGAACTCGAACT-GCCCATG
* * * *
13671330 TCTGGGTGATATGAACTCAAATCGCCCATGTCCGGGTGATATGAACTCGTACTGCCCATG
1 TCTGGGTGATATGAACTCAAACCGCCCATGGCCAGGTGATATGAACTCGAACTGCCCATG
13671390 TCTGGGTGATATGAACT
1 TCTGGGTGATATGAACT
13671407 GCTCTGCGAC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 67 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (60 bp):
TCTGGGTGATATGAACTCAAACCGCCCATGGCCAGGTGATATGAACTCGAACTGCCCATG
Found at i:13674045 original size:21 final size:21
Alignment explanation
Indices: 13674019--13674072 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
13674009 TGACCAGTTA
13674019 TAATATATATTTTTAATTTTC
1 TAATATATATTTTTAATTTTC
* * *
13674040 TAATATAAATTTTTACTTTTT
1 TAATATATATTTTTAATTTTC
13674061 TAATATATATTT
1 TAATATATATTT
13674073 AAAAAAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATATATATTTTTAATTTTC
Found at i:13674152 original size:22 final size:22
Alignment explanation
Indices: 13674118--13674159 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
13674108 TTNATTTAAA
13674118 TTAAAAAATATATT-TAAAATT
1 TTAAAAAATATATTATAAAATT
13674139 TTAAAAAATAATATTATAAAA
1 TTAAAAAAT-ATATTATAAAA
13674160 CCTTTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAAAAATATATTATAAAATT
Found at i:13674280 original size:24 final size:24
Alignment explanation
Indices: 13674226--13674286 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
13674216 TAAATAAAGG
*
13674226 AAAAATAAAAAAACTTAAAAAGTAA
1 AAAAAT-AAAAAACTTAAAAAGAAA
* *
13674251 ATAAATAAAAAACTTAAAACGAAA
1 AAAAATAAAAAACTTAAAAAGAAA
*
13674275 AAAAATGAAAAA
1 AAAAATAAAAAA
13674287 GGACAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (24 bp):
AAAAATAAAAAACTTAAAAAGAAA
Found at i:13679397 original size:35 final size:34
Alignment explanation
Indices: 13679356--13679421 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
13679346 ATGTATATAT
*
13679356 ATGTATATGTTATAATAATAAATAA-AATGAATCTA
1 ATGTATATATTATAAT-AT-AATAATAATGAATCTA
13679391 ATGTATATATTATAATATAATAATAATGAAT
1 ATGTATATATTATAATATAATAATAATGAAT
13679422 GAAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 9 0.31
35 15 0.52
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.39
Consensus pattern (34 bp):
ATGTATATATTATAATATAATAATAATGAATCTA
Found at i:13680903 original size:19 final size:20
Alignment explanation
Indices: 13680874--13680917 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
13680864 CAAAGATTAA
13680874 AAATG-AATATGAGA-TGA-G
1 AAATGAAATATGA-ATTGATG
13680892 AAATGAAATATGAATTGATG
1 AAATGAAATATGAATTGATG
13680912 AAATGA
1 AAATGA
13680918 GATGTGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (20 bp):
AAATGAAATATGAATTGATG
Found at i:13690709 original size:19 final size:19
Alignment explanation
Indices: 13690685--13690726 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13690675 ATATATACAA
13690685 AATAAAATAATAATAAAAT
1 AATAAAATAATAATAAAAT
* * *
13690704 AATAAAATATTAGTAAACT
1 AATAAAATAATAATAAAAT
13690723 AATA
1 AATA
13690727 TTTATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AATAAAATAATAATAAAAT
Found at i:13696672 original size:102 final size:102
Alignment explanation
Indices: 13696496--13696694 Score: 346
Period size: 102 Copynumber: 2.0 Consensus size: 102
13696486 NNAATGTGAA
*
13696496 AGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
*
13696561 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
* *
13696598 AGGGGTTTCTAAGTGTTGATTCCCCGAA-TCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AGGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
13696662 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTC
65 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTC
13696695 TCCAACTCAT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 90 0.98
103 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:13698152 original size:45 final size:47
Alignment explanation
Indices: 13698101--13698211 Score: 163
Period size: 49 Copynumber: 2.4 Consensus size: 47
13698091 TCCATATAGA
* *
13698101 ATTACACTTCTTTTATTT-TATT-TTAGAATAAGGTTTTTCAACCTT
1 ATTACACTTCTTCTATTTATATTATTAGAATAAGGTATTTCAACCTT
*
13698146 ATTACACTTCATCTATTTGATATTAATTAGAATAAGGTATTTCAACCTT
1 ATTACACTTCTTCTATTT-ATATT-ATTAGAATAAGGTATTTCAACCTT
13698195 ATTACACTTCTTCTATT
1 ATTACACTTCTTCTATT
13698212 AGAATATGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
45 16 0.28
47 4 0.07
49 38 0.66
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (47 bp):
ATTACACTTCTTCTATTTATATTATTAGAATAAGGTATTTCAACCTT
Found at i:13703274 original size:100 final size:100
Alignment explanation
Indices: 13703085--13703272 Score: 301
Period size: 100 Copynumber: 1.9 Consensus size: 100
13703075 AAAAAACCAT
13703085 ATAGTACACTAGTGGCGCCATTCTATATGGCTAACCAAATAAAATATTATTTCTTTAAAAATTTA
1 ATAGTACACTAGTGGCGCCATTCTATATGGCTAACCAAATAAAATATTATTTCTTTAAAAATTTA
13703150 AAATAAAAAATAACACATTTAAAAATATATTATAC
66 AAATAAAAAATAACACATTTAAAAATATATTATAC
* * *
13703185 ATAGTATACTGGTGGCGCCATTCTATATGGCTCTACCAAATAAAATA-TATTT-TTTAAAAATTT
1 ATAGTACACTAGTGGCGCCATTCTATATGGCT-AACCAAATAAAATATTATTTCTTTAAAAATTT
* *
13703248 TAAATTAAAAA-AACACATTTAAAAA
65 AAAATAAAAAATAACACATTTAAAAA
13703273 AACCCTAATA
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
98 14 0.17
99 20 0.24
100 35 0.43
101 13 0.16
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.34
Consensus pattern (100 bp):
ATAGTACACTAGTGGCGCCATTCTATATGGCTAACCAAATAAAATATTATTTCTTTAAAAATTTA
AAATAAAAAATAACACATTTAAAAATATATTATAC
Found at i:13704530 original size:15 final size:16
Alignment explanation
Indices: 13704510--13704539 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13704500 CTTTAAAAAT
13704510 TATTAAAAT-ATAAAC
1 TATTAAAATAATAAAC
13704525 TATTAAAATAATAAA
1 TATTAAAATAATAAA
13704540 ATTGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TATTAAAATAATAAAC
Found at i:13706767 original size:28 final size:25
Alignment explanation
Indices: 13706687--13706853 Score: 69
Period size: 28 Copynumber: 6.5 Consensus size: 25
13706677 AAAGGTTGAT
13706687 AATTTAAATG-AAATGAGAA-AAAAA
1 AATTTAAATGAAAATGA-AAGAAAAA
*** * *
13706711 AATTTGTTTG-AAATGAAATGGTACAA
1 AATTTAAATGAAAATGAAA--GAAAAA
13706737 AATTTAAATGAAAATTGAAAGAAAGATA
1 AATTTAAATGAAAA-TGAAAGAAA-A-A
* *
13706765 AATTTAAAT-TAAATG--AGTAAAA
1 AATTTAAATGAAAATGAAAGAAAAA
* * *
13706787 ATTTTCATTG-AAATGAAATGAGAAAA
1 AATTTAAATGAAAATGAAA-GA-AAAA
* * *
13706813 AAATTAAATTAAATTTGAAAGAAAGATA
1 AATTTAAATGAAA-ATGAAAGAAA-A-A
13706841 AATTTAAATGAAA
1 AATTTAAATGAAA
13706854 TGAGAGGCAC
Statistics
Matches: 103, Mismatches: 24, Indels: 28
0.66 0.15 0.18
Matches are distributed among these distances:
22 12 0.12
23 3 0.03
24 18 0.17
25 1 0.01
26 25 0.24
27 12 0.12
28 32 0.31
ACGTcount: A:0.57, C:0.01, G:0.13, T:0.29
Consensus pattern (25 bp):
AATTTAAATGAAAATGAAAGAAAAA
Found at i:13706820 original size:76 final size:76
Alignment explanation
Indices: 13706687--13706898 Score: 230
Period size: 76 Copynumber: 2.8 Consensus size: 76
13706677 AAAGGTTGAT
* * ** * *
13706687 AATTTAAATGAAATGAGAAAAAAAAATTTGTTTGAAATGAAATG-GTACAAAATTTAAATGAAAA
1 AATTTAAATGAAATGAG--AGAAAATTTTAATTGAAATGAAATGAG-AAAAAAATTAAATGAAAA
13706751 TTGAAAGAAAGATA
63 TTGAAAGAAAGATA
* * * *
13706765 AATTTAAATTAAATGAGTA-AAAATTTTCATTGAAATGAAATGAGAAAAAAATTAAATTAAATTT
1 AATTTAAATGAAATGAG-AGAAAATTTTAATTGAAATGAAATGAGAAAAAAATTAAATGAAAATT
13706829 GAAAGAAAGATA
65 GAAAGAAAGATA
** * * * *
13706841 AATTTAAATGAAATGAGAGGCACTTTTAATTTAAATAAAATGAGAAAAAAATTTAATG
1 AATTTAAATGAAATGAGAGAAAATTTTAATTGAAATGAAATGAGAAAAAAATTAAATG
13706899 GAAAGATAGA
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
75 1 0.01
76 95 0.83
77 2 0.02
78 16 0.14
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (76 bp):
AATTTAAATGAAATGAGAGAAAATTTTAATTGAAATGAAATGAGAAAAAAATTAAATGAAAATTG
AAAGAAAGATA
Found at i:13706895 original size:27 final size:27
Alignment explanation
Indices: 13706686--13706897 Score: 81
Period size: 27 Copynumber: 8.1 Consensus size: 27
13706676 GAAAGGTTGA
13706686 TAATTTAAATGAAATGAGAAAAAAAAATT
1 TAATTTAAATGAAATGAG--AAAAAAATT
* * *
13706715 T-GTTTGAAATGAAATG-GTACAAAATT
1 TAATTT-AAATGAAATGAGAAAAAAATT
* * * *
13706741 TAA-ATGAA--AATTGA-AAGAAAGA-T
1 TAATTTAAATGAAATGAGAA-AAAAATT
* * * *
13706764 AAATTTAAATTAAATGAGTAAAAATTT
1 TAATTTAAATGAAATGAGAAAAAAATT
* *
13706791 TCATTGAAATGAAATGAGAAAAAAA-T
1 TAATTTAAATGAAATGAGAAAAAAATT
* * *
13706817 TAAATTAAAT---TTGA-AAGAAAGA-T
1 TAATTTAAATGAAATGAGAA-AAAAATT
* *** **
13706840 AAATTTAAATGAAATGAGAGGCACTTT
1 TAATTTAAATGAAATGAGAAAAAAATT
*
13706867 TAATTTAAATAAAATGAGAAAAAAATT
1 TAATTTAAATGAAATGAGAAAAAAATT
13706894 TAAT
1 TAAT
13706898 GGAAAGATAG
Statistics
Matches: 125, Mismatches: 43, Indels: 32
0.62 0.22 0.16
Matches are distributed among these distances:
22 2 0.02
23 24 0.19
24 6 0.05
25 2 0.02
26 29 0.23
27 47 0.38
28 4 0.03
29 11 0.09
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (27 bp):
TAATTTAAATGAAATGAGAAAAAAATT
Found at i:13707001 original size:48 final size:47
Alignment explanation
Indices: 13706867--13707063 Score: 162
Period size: 48 Copynumber: 4.3 Consensus size: 47
13706857 GAGGCACTTT
* * *
13706867 TAATTTAAATAAAATGAG--AAAA--AAATTT-AATGGAAAGATAGA
1 TAATTTAAATGAAATGAGAAAAAATTAAATTTAAATTGAAAAATAGA
* * ***
13706909 TAATTTAAAAGAAATGACAAAAAAAATTAAATTTGCGTTGAAAAATAGA
1 TAATTTAAATGAAATG--AGAAAAAATTAAATTTAAATTGAAAAATAGA
* *
13706958 AAATTTAAATGAAATGAGGAAAAAATTAAATTTAAATTTAAAAATA-A
1 TAATTTAAATGAAATGA-GAAAAAATTAAATTTAAATTGAAAAATAGA
* * * *
13707005 T-A--TATATGAATTGAGAAAAAAATAAATTTAAATTGAAAAA-ATA
1 TAATTTAAATGAAATGAGAAAAAATTAAATTTAAATTGAAAAATAGA
*
13707048 TAATTTAAGTGAAATG
1 TAATTTAAATGAAATG
13707064 GAATTGAAAT
Statistics
Matches: 121, Mismatches: 22, Indels: 20
0.74 0.13 0.12
Matches are distributed among these distances:
42 15 0.12
43 26 0.21
44 12 0.10
46 13 0.11
47 2 0.02
48 29 0.24
49 24 0.20
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.29
Consensus pattern (47 bp):
TAATTTAAATGAAATGAGAAAAAATTAAATTTAAATTGAAAAATAGA
Found at i:13707023 original size:22 final size:22
Alignment explanation
Indices: 13706976--13707047 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 22
13706966 ATGAAATGAG
*
13706976 GAAAAAAT--TAAATTTAAATT
1 GAAAAAATAATAAATATAAATT
* * *
13706996 -TAAAAATAATATATATGAATT
1 GAAAAAATAATAAATATAAATT
*
13707017 GAGAAAAA-AATAAATTTAAATT
1 GA-AAAAATAATAAATATAAATT
13707039 GAAAAAATA
1 GAAAAAATA
13707048 TAATTTAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 6 0.15
21 14 0.36
22 14 0.36
23 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (22 bp):
GAAAAAATAATAAATATAAATT
Found at i:13707060 original size:19 final size:19
Alignment explanation
Indices: 13707021--13707061 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13707011 TGAATTGAGA
*
13707021 AAAAAATAAATTTAAATTG
1 AAAAAATAAATTTAAAGTG
13707040 AAAAAATATAATTT-AAGTG
1 AAAAAATA-AATTTAAAGTG
13707059 AAA
1 AAA
13707062 TGGAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTTAAAGTG
Found at i:13707080 original size:12 final size:12
Alignment explanation
Indices: 13707057--13707086 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13707047 ATAATTTAAG
13707057 TGAAAT-GGAAT
1 TGAAATGGGAAT
13707068 TGAAATGGGAAT
1 TGAAATGGGAAT
13707080 TGAAATG
1 TGAAATG
13707087 AAATTGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAATGGGAAT
Found at i:13707090 original size:5 final size:5
Alignment explanation
Indices: 13707057--13707135 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
13707047 ATAATTTAAG
* * * *
13707057 TGAAA TGGAAT TGAAA TGGGAAT TGAAA TGAAA TTGGAA TGAAA TAAAA
1 TGAAA T-GAAA TGAAA T--GAAA TGAAA TGAAA -TGAAA TGAAA TGAAA
* *
13707106 TTAAAA TGAAA TGAAAA TGAAA AGAAA TGA
1 -TGAAA TGAAA TG-AAA TGAAA TGAAA TGA
13707136 CTAATCTGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 36 0.62
6 18 0.31
7 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.23
Consensus pattern (5 bp):
TGAAA
Found at i:13707098 original size:11 final size:11
Alignment explanation
Indices: 13707057--13707133 Score: 66
Period size: 11 Copynumber: 7.0 Consensus size: 11
13707047 ATAATTTAAG
*
13707057 TGAAATGGAAT
1 TGAAATGAAAT
*
13707068 TGAAATGGGAAT
1 TGAAAT-GAAAT
13707080 TGAAATGAAAT
1 TGAAATGAAAT
*
13707091 TGGAATGAAA-
1 TGAAATGAAAT
* * *
13707101 TAAAATTAAAA
1 TGAAATGAAAT
*
13707112 TGAAATGAAAA
1 TGAAATGAAAT
*
13707123 TGAAAAGAAAT
1 TGAAATGAAAT
13707134 GACTAATCTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
10 7 0.13
11 37 0.67
12 11 0.20
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (11 bp):
TGAAATGAAAT
Found at i:13707101 original size:16 final size:16
Alignment explanation
Indices: 13707057--13707135 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
13707047 ATAATTTAAG
*
13707057 TGAAATGGAATTGAAAT
1 TGAAAT-GAAATGAAAT
* *
13707074 GGGAATTGAAATGAAAT
1 -TGAAATGAAATGAAAT
* *
13707091 TGGAATGAAATAAAAT
1 TGAAATGAAATGAAAT
* *
13707107 TAAAATGAAATGAAAA
1 TGAAATGAAATGAAAT
*
13707123 TGAAAAGAAATGA
1 TGAAATGAAATGA
13707136 CTAATCTGCA
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
16 35 0.73
17 9 0.19
18 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.23
Consensus pattern (16 bp):
TGAAATGAAATGAAAT
Found at i:13709300 original size:49 final size:53
Alignment explanation
Indices: 13709220--13709318 Score: 143
Period size: 50 Copynumber: 1.9 Consensus size: 53
13709210 AGGTCAGCAT
* *
13709220 AAAAAAAAATTAATTTATTTTTATACTTGGT-GTGGCTATTGACAGGCCAACAC
1 AAAAAAAAATTAA-TTATCTTTATACTTGGTGGTGGCCATTGACAGGCCAACAC
13709273 AAAAAAAAATTAA-T-TCTTT-TACTTGGTGGTGGCCATTGACAGGCCA
1 AAAAAAAAATTAATTATCTTTATACTTGGTGGTGGCCATTGACAGGCCA
13709319 GCATCAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
49 8 0.19
50 21 0.49
51 1 0.02
53 13 0.30
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (53 bp):
AAAAAAAAATTAATTATCTTTATACTTGGTGGTGGCCATTGACAGGCCAACAC
Found at i:13712461 original size:32 final size:32
Alignment explanation
Indices: 13712424--13712490 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
13712414 TATATTTATA
13712424 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
1 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
13712456 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
1 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
13712488 TAA
1 TAA
13712491 AAAATTTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (32 bp):
TAATTTGATTTATTCTTTTATTGAAAGTAAAT
Found at i:13712597 original size:22 final size:23
Alignment explanation
Indices: 13712548--13712597 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
13712538 TAAGCTCTCA
*
13712548 TAAATTTTTAAAAAATTATAAAT
1 TAAATTGTTAAAAAATTATAAAT
13712571 T-AATTGTT-AAAAATT-TAGAAT
1 TAAATTGTTAAAAAATTATA-AAT
13712592 TAAATT
1 TAAATT
13712598 TTTTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 11 0.46
22 10 0.42
23 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAATTGTTAAAAAATTATAAAT
Found at i:13712750 original size:20 final size:19
Alignment explanation
Indices: 13712716--13712768 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
13712706 ATAAAAAAAT
* *
13712716 TAATTTTTGTAATTTGTTTA
1 TAATTTTTATAATTT-TTAA
*
13712736 TAATTTTTATGATTTTTAA
1 TAATTTTTATAATTTTTAA
13712755 T-ATTTTTA-AATTTT
1 TAATTTTTATAATTTT
13712769 AAAAGTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 4 0.14
20 13 0.45
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (19 bp):
TAATTTTTATAATTTTTAA
Found at i:13713334 original size:31 final size:31
Alignment explanation
Indices: 13713299--13713362 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
13713289 CCACGTAAAA
*
13713299 ATATATGGTACACTATTTTTAGAAAAAGTAT
1 ATATATGGTACACTATTTTTAGAAAAAATAT
13713330 ATATATGGTACACTATTTTTAGAAAAAATAT
1 ATATATGGTACACTATTTTTAGAAAAAATAT
13713361 AT
1 AT
13713363 GATAATTTTT
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:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (31 bp):
ATATATGGTACACTATTTTTAGAAAAAATAT
Found at i:13717306 original size:3 final size:3
Alignment explanation
Indices: 13717298--13717333 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
13717288 AATTGAAACA
13717298 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
13717334 CGTCAATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13725766 original size:3 final size:3
Alignment explanation
Indices: 13725758--13725783 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13725748 CCATGTACAT
13725758 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
13725784 GTCTCTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:13725886 original size:22 final size:22
Alignment explanation
Indices: 13725858--13725934 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
13725848 TTTCTTTTAA
13725858 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
13725880 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
13725904 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
13725926 TTAGGAGAT
1 TTAGGAGAT
13725935 AATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 20 0.49
24 11 0.27
25 1 0.02
26 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:13725907 original size:46 final size:46
Alignment explanation
Indices: 13725853--13725947 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
13725843 TCTCTTTTCT
13725853 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
13725899 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
13725945 TTT
1 TTT
13725948 CTATATTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:13729165 original size:44 final size:44
Alignment explanation
Indices: 13729116--13729343 Score: 271
Period size: 44 Copynumber: 5.2 Consensus size: 44
13729106 TCGACCTACA
* * * * *
13729116 GCAACTTCAGAGG-CATAGGATTCATCATTTTAATCCGCTCCACT
1 GCAACTTCAG-GGAGATAGGATTCGTAACTTTAATCTGCTCCACT
*
13729160 GCAACTTCAGGGAGATAGGATTTGTAACTTTAATCTGCTCCACT
1 GCAACTTCAGGGAGATAGGATTCGTAACTTTAATCTGCTCCACT
* * * * * *
13729204 GCAACTTTAGGGAGATAAGATTCACTATCTTCAATCTACTCCACT
1 GCAACTTCAGGGAGATAGGATTC-GTAACTTTAATCTGCTCCACT
* * *
13729249 GCAACTTCAGGGAGATAAGACTT-GTAACTTCAATCCGCTCCACT
1 GCAACTTCAGGGAGATAGGA-TTCGTAACTTTAATCTGCTCCACT
*
13729293 GCAACTTCAGGGAGATAGGATTTGTAACTTTAATCTGCTCCACT
1 GCAACTTCAGGGAGATAGGATTCGTAACTTTAATCTGCTCCACT
13729337 GCAACTT
1 GCAACTT
13729344 GGATCTACTC
Statistics
Matches: 159, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.03
44 117 0.74
45 36 0.23
46 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
GCAACTTCAGGGAGATAGGATTCGTAACTTTAATCTGCTCCACT
Found at i:13729274 original size:89 final size:88
Alignment explanation
Indices: 13728962--13729343 Score: 316
Period size: 89 Copynumber: 4.3 Consensus size: 88
13728952 TAATTTATAG
* * * * * *
13728962 CTTCAACCTGTTCCACTGTAACTTCAGGG-GAATAAGA-TTCACTATCTTTAGTCTGCTCCACTG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAG-ATAAGACTT--GTAACTTTAATCTGCTCCACTG
*
13729025 CAACTTTAGGGAGATAAGACTT-C-A-
63 CAACTTCAGGGAGATAAGA-TTACTAT
* *
13729049 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAAACTTGCTATGGCAGATTTAAT-TCGAC-C
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TA----A-CTTTAATCT-G-CTC
* * * *
13729112 TACAGCAACTTCAGAGG-CATAGGATT-C-AT
58 CACTGCAACTTCAG-GGAGATAAGATTACTAT
* * * *
13729141 CATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAACTTTAATCTGCTCCACTGC
1 C--TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGC
*
13729206 AACTTTAGGGAGATAAGATTCACTAT
64 AACTTCAGGGAGATAAGATT-ACTAT
* * *
13729232 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCCGCTCCACTGCAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAA
* ** *
13729297 CTTCAGGGAGATAGGATTTGTAA
66 CTTCAGGGAGATAAGATTACTAT
*
13729320 CTTTAATCTGCTCCACTGCAACTT
1 CTTCAATCTGCTCCACTGCAACTT
13729344 GGATCTACTC
Statistics
Matches: 237, Mismatches: 38, Indels: 39
0.75 0.12 0.12
Matches are distributed among these distances:
87 36 0.15
88 53 0.22
89 75 0.32
90 1 0.00
91 8 0.03
92 24 0.10
93 5 0.02
94 35 0.15
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (88 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAA
CTTCAGGGAGATAAGATTACTAT
Found at i:13729343 original size:21 final size:21
Alignment explanation
Indices: 13729318--13729366 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13729308 TAGGATTTGT
*
13729318 AACTTTAATCTGCTCCACTGC
1 AACTTTAATCTACTCCACTGC
** *
13729339 AACTTGGATCTACTCTACTGC
1 AACTTTAATCTACTCCACTGC
13729360 AACTTTA
1 AACTTTA
13729367 GAGAGATAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (21 bp):
AACTTTAATCTACTCCACTGC
Found at i:13745908 original size:20 final size:19
Alignment explanation
Indices: 13745885--13746091 Score: 85
Period size: 20 Copynumber: 10.4 Consensus size: 19
13745875 ATGCACATTA
13745885 GTGCCCCTGTTTGCACTTT
1 GTGCCCCTGTTTGCACTTT
* ***
13745904 GGTGCCCTTAAATGCACATTT
1 -GTGCCCCTGTTTGCAC-TTT
****
13745925 GTGCCCCTGAACACACATTT
1 GTGCCCCTGTTTGCAC-TTT
*
13745945 GTGCCCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
* * *
13745964 GGTACCCCTGTATACACTTT
1 -GTGCCCCTGTTTGCACTTT
* *
13745984 AGTGTCCCTGCTTGCACGTTT
1 -GTGCCCCTGTTTGCAC-TTT
* * **
13746005 GTGCTCCTGTTCGCACTACG
1 GTGCCCCTGTTTGCACT-TT
* * * * *
13746025 GTGCCCTTGTATACAATTCG
1 GTGCCCCTGTTTGCACTT-T
13746045 GTGTCCCC-GTTTGCACGTTT
1 GTG-CCCCTGTTTGCAC-TTT
*
13746065 GTG-CCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
13746083 AGTGCCCCT
1 -GTGCCCCT
13746092 ATTCTGTATA
Statistics
Matches: 137, Mismatches: 40, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
18 6 0.04
19 14 0.10
20 106 0.77
21 11 0.08
ACGTcount: A:0.13, C:0.31, G:0.21, T:0.35
Consensus pattern (19 bp):
GTGCCCCTGTTTGCACTTT
Found at i:13745949 original size:40 final size:40
Alignment explanation
Indices: 13745873--13745950 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
13745863 AGTGTTCCTG
****
13745873 AAATGCACATTAGTGCCCCTGTTTGCACTTTGGTGCCCTT
1 AAATGCACATTAGTGCCCCTGAACACACTTTGGTGCCCTT
*
13745913 AAATGCACATTTGTGCCCCTGAACACACATTT-GTGCCC
1 AAATGCACATTAGTGCCCCTGAACACAC-TTTGGTGCCC
13745951 CTGTTCGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 29 0.91
41 3 0.09
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (40 bp):
AAATGCACATTAGTGCCCCTGAACACACTTTGGTGCCCTT
Found at i:13745993 original size:60 final size:60
Alignment explanation
Indices: 13745878--13746039 Score: 164
Period size: 60 Copynumber: 2.7 Consensus size: 60
13745868 TCCTGAAATG
* * ** *
13745878 CACATTAGTGCCCCTGTTTGCACTTTGGTGCCCTTAAATGCACATTTGTGCCCCTGAACA
1 CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACACATTTGTGCCCCTGAACA
* * * ****
13745938 CACATTTGTGCCCCTGTTCGCACTTTGGTACCCCTGTATACAC-TTTAGTGTCCCTGCTTG
1 CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACACATTT-GTGCCCCTGAACA
* * **
13745998 CACGTTTGTGCTCCTGTTCGCACTACGGTGCCCTTGTATACA
1 CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACA
13746040 ATTCGGTGTC
Statistics
Matches: 83, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 3 0.04
60 80 0.96
ACGTcount: A:0.16, C:0.31, G:0.19, T:0.34
Consensus pattern (60 bp):
CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACACATTTGTGCCCCTGAACA
Found at i:13746049 original size:60 final size:59
Alignment explanation
Indices: 13745942--13746080 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 59
13745932 TGAACACACA
** * * *
13745942 TTTGTGCCCCTGTTCGCACTTTGGTACCCCTGTATACACTTTAGTGTCCCTGCTTGCACG
1 TTTGTG-CCCTGTTCGCACTACGGTACCCCTGTATACAATTCAGTGTCCCCGCTTGCACG
* * * *
13746002 TTTGTGCTCCTGTTCGCACTACGGTGCCCTTGTATACAATTCGGTGTCCCCGTTTGCACG
1 TTTGTGC-CCTGTTCGCACTACGGTACCCCTGTATACAATTCAGTGTCCCCGCTTGCACG
13746062 TTTGTGCCCTGTTCGCACT
1 TTTGTGCCCTGTTCGCACT
13746081 TTAGTGCCCC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 13 0.19
60 56 0.81
ACGTcount: A:0.11, C:0.31, G:0.22, T:0.37
Consensus pattern (59 bp):
TTTGTGCCCTGTTCGCACTACGGTACCCCTGTATACAATTCAGTGTCCCCGCTTGCACG
Found at i:13748145 original size:44 final size:42
Alignment explanation
Indices: 13748076--13748170 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 42
13748066 TGTGACATCG
* * * *
13748076 TGTAAGACCACGTCTTGGACGTTGGCCTCGATTTGAGATTTGCA
1 TGTAAGACCACGTCTTGGACATTGGCCTC-ATATAAGA-TTACA
* *
13748120 TGTAAGACCATGTC-TGAGACATTGGCGTCATATAAGATTACA
1 TGTAAGACCACGTCTTG-GACATTGGCCTCATATAAGATTACA
13748162 TGTAAGACC
1 TGTAAGACC
13748171 CTGTTTGGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 13 0.30
43 8 0.18
44 23 0.52
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTAAGACCACGTCTTGGACATTGGCCTCATATAAGATTACA
Found at i:13753369 original size:8 final size:8
Alignment explanation
Indices: 13753356--13753380 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
13753346 TTTTTAATGA
13753356 TATTTTAT
1 TATTTTAT
13753364 TATTTTAT
1 TATTTTAT
13753372 TATTTTAT
1 TATTTTAT
13753380 T
1 T
13753381 TAGCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:13758426 original size:7 final size:7
Alignment explanation
Indices: 13758414--13758438 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13758404 TAATAAATTA
13758414 GTTTAGG
1 GTTTAGG
13758421 GTTTAGG
1 GTTTAGG
13758428 GTTTAGG
1 GTTTAGG
13758435 GTTT
1 GTTT
13758439 TTAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:13758736 original size:126 final size:126
Alignment explanation
Indices: 13758511--13758796 Score: 412
Period size: 126 Copynumber: 2.3 Consensus size: 126
13758501 TAATTTAAAG
* * * * * *
13758511 AAGCTCCGACATGAACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGACGTTT
* * *
13758576 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGTAGAAGTACTGAAAA
66 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* * *
13758637 AAGCTCCCACGTGGACGCTCTTTTGTTACAGTAGCTCCTAAAAAAATAATTTTGAGTAGACGTTT
1 AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGACGTTT
13758702 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* * * *
13758763 AATCTTCCACTTGGAC-ATGCTTTTGCTACAGTAG
1 AAGCTCCCACATGGACGCT-CTTTTGCTACAGTAG
13758797 TTGAACGTTA
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
125 1 0.01
126 141 0.99
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (126 bp):
AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGACGTTT
CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:13759207 original size:21 final size:21
Alignment explanation
Indices: 13759162--13759209 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
13759152 TTTGTCCAGT
* * * *
13759162 CTCCGGCGGGGGTTGTGGTTG
1 CTCCGGCGGGGATTCTAGTTC
13759183 CTCCGGCGGGGATTCTAGTTC
1 CTCCGGCGGGGATTCTAGTTC
13759204 CTCCGG
1 CTCCGG
13759210 TATGGTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.27, G:0.42, T:0.27
Consensus pattern (21 bp):
CTCCGGCGGGGATTCTAGTTC
Done.