Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 110 of 214
Found at i:33164590 original size:40 final size:40
Alignment explanation
Indices: 33164535--33164848 Score: 547
Period size: 40 Copynumber: 7.8 Consensus size: 40
33164525 GAGCATTTGA
33164535 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
33164575 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
33164615 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
33164655 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
33164695 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
33164735 ATATATCCGGGCTATGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
33164775 ATATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* ** * *
33164815 CTATGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
33164849 TTGTGGTAAT
Statistics
Matches: 261, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 261 1.00
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
Found at i:33167576 original size:19 final size:19
Alignment explanation
Indices: 33167552--33167618 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
33167542 ACAGTGTATA
33167552 TGGGCCCAAAACCCGCTAT
1 TGGGCCCAAAACCCGCTAT
* * *
33167571 TGGGCCAATAAGAACAG-TAT
1 TGGGCCCA-AA-ACCCGCTAT
* *
33167591 ATAGGCCCAAAACTCGCTAT
1 -TGGGCCCAAAACCCGCTAT
33167611 TGGGCCCA
1 TGGGCCCA
33167619 TGTGGGCCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 16 0.46
20 10 0.29
21 9 0.26
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.18
Consensus pattern (19 bp):
TGGGCCCAAAACCCGCTAT
Found at i:33167598 original size:40 final size:41
Alignment explanation
Indices: 33167531--33167616 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 41
33167521 AATATGATTA
* *
33167531 GGCCCATAAGAACAGTGTATATGGGCCCAAAACCCGCTATTG
1 GGCCAATAAGAACAG-GTATATAGGCCCAAAACCCGCTATTG
*
33167573 GGCCAATAAGAACA-GTATATAGGCCCAAAACTCGCTATTG
1 GGCCAATAAGAACAGGTATATAGGCCCAAAACCCGCTATTG
33167613 GGCC
1 GGCC
33167617 CATGTGGGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 28 0.68
42 13 0.32
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (41 bp):
GGCCAATAAGAACAGGTATATAGGCCCAAAACCCGCTATTG
Found at i:33171768 original size:13 final size:13
Alignment explanation
Indices: 33171750--33171774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33171740 ACAAATGATA
33171750 AAATTTTCACACG
1 AAATTTTCACACG
33171763 AAATTTTCACAC
1 AAATTTTCACAC
33171775 ATATAAATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:33186639 original size:29 final size:28
Alignment explanation
Indices: 33186585--33186922 Score: 207
Period size: 29 Copynumber: 11.8 Consensus size: 28
33186575 TATAAGTAAG
* * *
33186585 CCTTTGTGGCTATATC--TAAAAAGAAA
1 CCTTTGTGGCTATCTCTGTTAAATGAAA
* *
33186611 CCTTTGCGGCGATCTCTGTTAAATCGAAA
1 CCTTTGTGGCTATCTCTGTTAAAT-GAAA
* * * * * *
33186640 TCTTTGTGGTTATTTTTGTTAAAGGAAG
1 CCTTTGTGGCTATCTCTGTTAAATGAAA
* * * *
33186668 CCATTGTGG-TAATCTCTGTTCTAAGGAAG
1 CCTTTGTGGCT-ATCTCTGTT-AAATGAAA
* * *
33186697 CCTTTGTGGCTGTCTTTGTTAAATGAAT
1 CCTTTGTGGCTATCTCTGTTAAATGAAA
* * *
33186725 GCTTT-TGCAGCTATCCCTATTAAATGAAA
1 CCTTTGTG--GCTATCTCTGTTAAATGAAA
*
33186754 GCCTTTGTGGCTATCTCTATTAAATGAAA
1 -CCTTTGTGGCTATCTCTGTTAAATGAAA
* *
33186783 GCCTTTGTGGCTATCTCTATTAAATGAATG
1 -CCTTTGTGGCTATCTCTGTTAAATGAA-A
* *
33186813 CCTTTGTGGCGATCTCTGTTAAATGGAAT
1 CCTTTGTGGCTATCTCTGTTAAAT-GAAA
* * *
33186842 CCTTTGTGGCAATTTATGTTAAATGGAAA
1 CCTTTGTGGCTATCTCTGTTAAAT-GAAA
* * * * * * * *
33186871 TCTTTGTGGTTGTTTTTATTAAACAGATA
1 CCTTTGTGGCTATCTCTGTTAAA-TGAAA
*
33186900 CTTTTGTGGCTATCTCTGTTAAA
1 CCTTTGTGGCTATCTCTGTTAAA
33186923 AGGATGCCTT
Statistics
Matches: 244, Mismatches: 55, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
26 13 0.05
27 3 0.01
28 30 0.12
29 188 0.77
30 8 0.03
31 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (28 bp):
CCTTTGTGGCTATCTCTGTTAAATGAAA
Found at i:33186785 original size:87 final size:87
Alignment explanation
Indices: 33186582--33186966 Score: 279
Period size: 87 Copynumber: 4.5 Consensus size: 87
33186572 CCGTATAAGT
* * * * *
33186582 AAGCCTTTGTGGCTATATCTA--AAAAGAAA-CCTTTGCGGC-GATCTCTGTTAAATCGAAAT-C
1 AAGCCTTTGTGGCAATATCTATTAAATGAAAGCCTTTGTGGCTG-TCTTTATTAAAT-G-AATGC
* * *
33186642 -TTTGTGGTTATTTTTGTTAAA-GG
63 TTTTGTGGCTATCTCTGTTAAATGG
* * * * * * *
33186665 AAGCCATTGTGGTAATCTCTGTTCTAA-GGAAGCCTTTGTGGCTGTCTTTGTTAAATGAATGCTT
1 AAGCCTTTGTGGCAATATCTATT-AAATGAAAGCCTTTGTGGCTGTCTTTATTAAATGAATGCTT
** * * *
33186729 TTGCAGCTATCCCTATTAAATGA
65 TTGTGGCTATCTCTGTTAAATGG
* * * * *
33186752 AAGCCTTTGTGGCTATCTCTATTAAATGAAAGCCTTTGTGGCTATCTCTATTAAATGAATGCCTT
1 AAGCCTTTGTGGCAATATCTATTAAATGAAAGCCTTTGTGGCTGTCTTTATTAAATGAATGCTTT
*
33186817 TGTGGCGATCTCTGTTAAATGG
66 TGTGGCTATCTCTGTTAAATGG
* * * * * * * * *
33186839 AATCCTTTGTGGCAATTTATGTTAAATGGAAA-TCTTTGTGGTTGTTTTTATTAAA-CAGATACT
1 AAGCCTTTGTGGCAATATCTATTAAAT-GAAAGCCTTTGTGGCTGTCTTTATTAAATGA-ATGCT
*
33186902 TTTGTGGCTATCTCTGTTAAAAGG
64 TTTGTGGCTATCTCTGTTAAATGG
* * * *
33186926 ATGCCTTTGTGGCCATATCTATTAAAGGAATGCC-TTGTGGC
1 AAGCCTTTGTGGCAATATCTATTAAATGAAAGCCTTTGTGGC
33186967 AAACTTTGTT
Statistics
Matches: 232, Mismatches: 58, Indels: 21
0.75 0.19 0.07
Matches are distributed among these distances:
83 16 0.07
84 3 0.01
85 5 0.02
86 48 0.21
87 156 0.67
88 4 0.02
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (87 bp):
AAGCCTTTGTGGCAATATCTATTAAATGAAAGCCTTTGTGGCTGTCTTTATTAAATGAATGCTTT
TGTGGCTATCTCTGTTAAATGG
Found at i:33186934 original size:29 final size:29
Alignment explanation
Indices: 33186641--33186985 Score: 171
Period size: 29 Copynumber: 12.0 Consensus size: 29
33186631 AAATCGAAAT
* * * *
33186641 CTTTGTGGTTATTTTTGTT-AAAGGAAGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGC
* ** *
33186669 CATTGTGG-TAATCTCTGTTCTAAGGAAGC
1 CTTTGTGGCT-ATCTCTGTTAAAAGGATGC
* * * *
33186698 CTTTGTGGCTGTCTTTGTTAAATGAATGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGC
* ** * * * * *
33186727 TTTTGCAGCTATCCCTATTAAATGAAAGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGC
* * * *
33186756 CTTTGTGGCTATCTCTATTAAATGAAAGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGC
* * *
33186785 CTTTGTGGCTATCTCTATTAAATGAATGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGC
* *
33186814 CTTTGTGGCGATCTCTGTTAAATGGAAT-C
1 CTTTGTGGCTATCTCTGTTAAAAGG-ATGC
* * * * ***
33186843 CTTTGTGGCAATTTATGTTAAATGGAAAT
1 CTTTGTGGCTATCTCTGTTAAAAGGATGC
* * * * * *
33186872 CTTTGTGGTTGTTTTTATTAAACA-GATAC
1 CTTTGTGGCTATCTCTGTTAAA-AGGATGC
*
33186901 TTTTGTGGCTATCTCTGTTAAAAGGATGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGC
* * *
33186930 CTTTGTGGCCATATCTATT-AAAGGAATGC
1 CTTTGTGGCTATCTCTGTTAAAAGG-ATGC
* * *
33186959 C-TTGTGGCAAACTTTGTTAAAAGGATG
1 CTTTGTGGCTATCTCTGTTAAAAGGATG
33186986 ACTTCACGAT
Statistics
Matches: 251, Mismatches: 57, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
27 1 0.00
28 36 0.14
29 211 0.84
30 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (29 bp):
CTTTGTGGCTATCTCTGTTAAAAGGATGC
Found at i:33186949 original size:58 final size:57
Alignment explanation
Indices: 33186584--33186985 Score: 213
Period size: 58 Copynumber: 7.0 Consensus size: 57
33186574 GTATAAGTAA
* * * * * *
33186584 GCCTTTGTGGCTATATCTA--AAAAGAAACCTTTGCGGCGATCTCTGTTAAATCGAA
1 GCCTTTGTGGCTATCTCTATTAAAAGAAGCCTTTGTGGCTATCTCTGTTAAATGGAT
** * * * * * * * *
33186639 ATCTTTGTGGTTATTTTTGTTAAAGGAAGCCATTGTGG-TAATCTCTGTTCTAA-GGAA
1 GCCTTTGTGGCTATCTCTATTAAAAGAAGCCTTTGTGGCT-ATCTCTGTT-AAATGGAT
* * * * * ** * * * *
33186696 GCCTTTGTGGCTGTCTTTGTTAAATGAATGCTTTTGCAGCTATCCCTATTAAATGAAA
1 GCCTTTGTGGCTATCTCTATTAAAAGAA-GCCTTTGTGGCTATCTCTGTTAAATGGAT
* * *
33186754 GCCTTTGTGGCTATCTCTATTAAATGAAAGCCTTTGTGGCTATCTCTATTAAATGAAT
1 GCCTTTGTGGCTATCTCTATTAAAAG-AAGCCTTTGTGGCTATCTCTGTTAAATGGAT
* * * * * * * *
33186812 GCCTTTGTGGCGATCTCTGTTAAATGGAATCCTTTGTGGCAATTTATGTTAAATGGAA
1 GCCTTTGTGGCTATCTCTATTAAA-AGAAGCCTTTGTGGCTATCTCTGTTAAATGGAT
** * * * * * *
33186870 ATCTTTGTGGTTGTTTTTATTAAACAGATA-CTTTTGTGGCTATCTCTGTTAAAAGGAT
1 GCCTTTGTGGCTATCTCTATTAAA-AGA-AGCCTTTGTGGCTATCTCTGTTAAATGGAT
* * * * * * *
33186928 GCCTTTGTGGCCATATCTATTAAAGGAATGCC-TTGTGGCAAACTTTGTTAAAAGGAT
1 GCCTTTGTGGCTATCTCTATTAAAAGAA-GCCTTTGTGGCTATCTCTGTTAAATGGAT
33186985 G
1 G
33186986 ACTTCACGAT
Statistics
Matches: 262, Mismatches: 73, Indels: 22
0.73 0.20 0.06
Matches are distributed among these distances:
55 13 0.05
56 1 0.00
57 74 0.28
58 169 0.65
59 5 0.02
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (57 bp):
GCCTTTGTGGCTATCTCTATTAAAAGAAGCCTTTGTGGCTATCTCTGTTAAATGGAT
Found at i:33191706 original size:14 final size:14
Alignment explanation
Indices: 33191687--33191718 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
33191677 ATTTTCTATC
*
33191687 TTTCTTTTCTTTAA
1 TTTCTTTACTTTAA
33191701 TTTCTTTACTTTAA
1 TTTCTTTACTTTAA
33191715 TTTC
1 TTTC
33191719 ATTCTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCTTTACTTTAA
Found at i:33191863 original size:530 final size:528
Alignment explanation
Indices: 33190864--33191923 Score: 1877
Period size: 530 Copynumber: 2.0 Consensus size: 528
33190854 TGATGTGCAA
* *
33190864 AAAGGAAAACTGACTATGAGGGTGAATGACCAACAGGTTACATTCAACATATTCGATGCCTTGAA
1 AAAGGAAAACTGACTATGAGGGTGAATGACCAACAGGTTACATCCAACATATTCGATGCCCTGAA
33190929 ATGTGTTAATAGAGTGAAGATTGTCAGGCCATTGGTTTGGTAGAAACGACAGTGGAAGAAAAGTT
66 ATGTGTTAATAGAGTGAAGATTGTCAGGCCATTGGTTTGGTAGAAACGACAGTGGAAGAAAAGTT
*
33190994 TGAAAGATGTTTGCCTCAACAAAATCTTCTGTCTCCAAAAATCCATTTGAGTAGCAAATACTCAA
131 TGAAAGATGTTTGCCTCAACAAAATCTTCTGTCTCAAAAAATCCATTTGAGTAGCAAATACTCAA
33191059 CACATTCGGTCAGTTGCAGAAGCAACTTAATCTCTTTGAGACATAGCAATTCCAAATTGCTGCGG
196 CACATTCGGTCAGTTGCAGAAGCAACTTAATCTCTTTGAGACATAGCAATTCCAAATTGCTGCGG
* * *
33191124 AATTTGAAAAAACATAAAAAAATGTTTTCTATCTTTCTTTTGTTTAATTGCTTTACTTTAATTTC
261 AATTGGAAAAAACATAAAAAAATATTTTCTATCTTTCTTTTCTTTAATTGCTTTACTTTAATTTC
*
33191189 ATTCTTATTATTTTTATCTTTAATTACATAAAGTTATTTTAATTTTTGATTTATCGCCTTATTAA
326 ATTCTTATTATTTTTATCTTTAATTACATAAAGTTATTTTAATTTCTGATTTATCGCCTTATTAA
*
33191254 TGAGATCATGTAGTCTGATAAAGAAAGGGAGGATTTGCACCCAATGAAAAGGAGCTGTTATCGGA
391 TGAGATCATGTAGTCTGATAAAGAAAGGGAGGATTTGCACCCAATGAAAAGGAGCTATTATCGGA
* *
33191319 TGAAAATGAAGGGGACGAGGATGAAGCTAAAGTTGATGTGCCTGGACCTACCACACACACTGCCA
456 TGAAAATGAAGGGGACGAGGATGAAGCTAAAGCTAATGTGCCTGGACCTACCACACACACTGCCA
33191384 TTGAGGAG
521 TTGAGGAG
* * *
33191392 AAAGGAAAATTGACTATGAGGGTGAATGATCAACATGTTACATCCAACATATTCGATGCCCTGAA
1 AAAGGAAAACTGACTATGAGGGTGAATGACCAACAGGTTACATCCAACATATTCGATGCCCTGAA
*
33191457 ATGTGTTAATGAGAGTGAAGATTGTCAGGCCATTGGTTTGGTGGAAACGACAGTGGAAGAAAAGT
66 ATGTGTTAAT-AGAGTGAAGATTGTCAGGCCATTGGTTTGGTAGAAACGACAGTGGAAGAAAAGT
* * * *
33191522 TTGCAAGATGTTTGCCTCAACAGAATCTTTTGTCTCAAAAAATCCATTTTAGTAGCAAATACTCA
130 TTGAAAGATGTTTGCCTCAACAAAATCTTCTGTCTCAAAAAATCCATTTGAGTAGCAAATACTCA
* *
33191587 ACTCATTCTGTCAGTTGCAGAAGCAACTTAATCTCTTTGAGACATAGCAATTCCAAATTGCTGCG
195 ACACATTCGGTCAGTTGCAGAAGCAACTTAATCTCTTTGAGACATAGCAATTCCAAATTGCTGCG
*
33191652 GAATTGGAAAAAACATAAAAAAAATATTTTCTATCTTTCTTTTCTTTAATTTCTTTACTTTAATT
260 GAATTGGAAAAAACAT-AAAAAAATATTTTCTATCTTTCTTTTCTTTAATTGCTTTACTTTAATT
* *
33191717 TCATTCTTATTATTTTTATCTTTAATTACTTAAAGTTATTTTAATTTCTGATTTATCGCGTTATT
324 TCATTCTTATTATTTTTATCTTTAATTACATAAAGTTATTTTAATTTCTGATTTATCGCCTTATT
* *
33191782 AATGAGATCATGTAGTCTGATAAAGAAAGGGAGGATTTGCACCCAATGAGAAGGAGCTATTATTG
389 AATGAGATCATGTAGTCTGATAAAGAAAGGGAGGATTTGCACCCAATGAAAAGGAGCTATTATCG
33191847 GATGAAAATGAAGGGGACGAGGATGAAGCTAAAGCTAATGTGCCTGGACCTACCACACACACTGC
454 GATGAAAATGAAGGGGACGAGGATGAAGCTAAAGCTAATGTGCCTGGACCTACCACACACACTGC
33191912 CATTGAGGAG
519 CATTGAGGAG
33191922 AA
1 AA
33191924 GTAATAGAAA
Statistics
Matches: 505, Mismatches: 25, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
528 70 0.14
529 191 0.38
530 244 0.48
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (528 bp):
AAAGGAAAACTGACTATGAGGGTGAATGACCAACAGGTTACATCCAACATATTCGATGCCCTGAA
ATGTGTTAATAGAGTGAAGATTGTCAGGCCATTGGTTTGGTAGAAACGACAGTGGAAGAAAAGTT
TGAAAGATGTTTGCCTCAACAAAATCTTCTGTCTCAAAAAATCCATTTGAGTAGCAAATACTCAA
CACATTCGGTCAGTTGCAGAAGCAACTTAATCTCTTTGAGACATAGCAATTCCAAATTGCTGCGG
AATTGGAAAAAACATAAAAAAATATTTTCTATCTTTCTTTTCTTTAATTGCTTTACTTTAATTTC
ATTCTTATTATTTTTATCTTTAATTACATAAAGTTATTTTAATTTCTGATTTATCGCCTTATTAA
TGAGATCATGTAGTCTGATAAAGAAAGGGAGGATTTGCACCCAATGAAAAGGAGCTATTATCGGA
TGAAAATGAAGGGGACGAGGATGAAGCTAAAGCTAATGTGCCTGGACCTACCACACACACTGCCA
TTGAGGAG
Found at i:33196885 original size:27 final size:26
Alignment explanation
Indices: 33196844--33196899 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 26
33196834 CTCGCCATAT
33196844 CAATTGGCAAACCCCAGCTTGC-CAAAC
1 CAATTGGCAAACCCCAG-TT-CACAAAC
33196871 CAATTGG-AAACCCCCAGTTCACAAAC
1 CAATTGGCAAA-CCCCAGTTCACAAAC
33196897 CAA
1 CAA
33196900 CTGACGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 1 0.04
26 13 0.48
27 13 0.48
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.14
Consensus pattern (26 bp):
CAATTGGCAAACCCCAGTTCACAAAC
Found at i:33196899 original size:26 final size:27
Alignment explanation
Indices: 33196811--33196884 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
33196801 CCTTAGTTTT
* * * *
33196811 CCAAACCAACTGGCAAAACCTAGCTCG
1 CCAAACCAATTGGCAAACCCCAGCTTG
* *
33196838 CCATATCAATTGGCAAACCCCAGCTTG
1 CCAAACCAATTGGCAAACCCCAGCTTG
33196865 CCAAACCAATTGG-AAACCCC
1 CCAAACCAATTGGCAAACCCC
33196885 CAGTTCACAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 7 0.18
27 32 0.82
ACGTcount: A:0.35, C:0.36, G:0.14, T:0.15
Consensus pattern (27 bp):
CCAAACCAATTGGCAAACCCCAGCTTG
Found at i:33201506 original size:28 final size:28
Alignment explanation
Indices: 33201449--33201510 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
33201439 GTCATTAATT
* *
33201449 TGTCATAGTATGTTGCATATTTAAAACA
1 TGTCATAGTATATTACATATTTAAAACA
* **
33201477 TGTCTTAGTATATTACATATTTAATTCA
1 TGTCATAGTATATTACATATTTAAAACA
33201505 TGTCAT
1 TGTCAT
33201511 TGTTTGTCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (28 bp):
TGTCATAGTATATTACATATTTAAAACA
Found at i:33209081 original size:16 final size:18
Alignment explanation
Indices: 33209050--33209083 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
33209040 TGTTTTTAAG
33209050 TATTTATATGTAAAATTT
1 TATTTATATGTAAAATTT
33209068 TATTTA-AT-TAAAATTT
1 TATTTATATGTAAAATTT
33209084 AATACATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTATATGTAAAATTT
Found at i:33210088 original size:12 final size:12
Alignment explanation
Indices: 33210071--33210095 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33210061 ATAAATCATA
33210071 ATGTATATTAAT
1 ATGTATATTAAT
33210083 ATGTATATTAAT
1 ATGTATATTAAT
33210095 A
1 A
33210096 GAAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATGTATATTAAT
Found at i:33210440 original size:21 final size:21
Alignment explanation
Indices: 33210416--33210512 Score: 106
Period size: 21 Copynumber: 4.5 Consensus size: 21
33210406 CATTATTTCT
*
33210416 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTATCC
**
33210437 AATCTCACCGCTACAGTAATTAAT
1 AATCTCACCGCTACAGT-A-T-CC
*
33210461 AATCTCACCACTACAGTATCC
1 AATCTCACCGCTACAGTATCC
*
33210482 AATCTCACCGCTACAGTAAT-T
1 AATCTCACCGCTACAGT-ATCC
33210503 AATCTCACCG
1 AATCTCACCG
33210513 TCACTGCTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
21 42 0.66
22 4 0.06
23 2 0.03
24 16 0.25
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.27
Consensus pattern (21 bp):
AATCTCACCGCTACAGTATCC
Found at i:33210479 original size:45 final size:45
Alignment explanation
Indices: 33210415--33210505 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
33210405 CCATTATTTC
**
33210415 TAATCTCACTGCTACAGTATCCAATCTCACCGCTACAGTAATTAA
1 TAATCTCACCACTACAGTATCCAATCTCACCGCTACAGTAATTAA
33210460 TAATCTCACCACTACAGTATCCAATCTCACCGCTACAGTAATTAA
1 TAATCTCACCACTACAGTATCCAATCTCACCGCTACAGTAATTAA
33210505 T
1 T
33210506 CTCACCGTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.30, G:0.08, T:0.29
Consensus pattern (45 bp):
TAATCTCACCACTACAGTATCCAATCTCACCGCTACAGTAATTAA
Found at i:33211249 original size:45 final size:45
Alignment explanation
Indices: 33211185--33211520 Score: 352
Period size: 45 Copynumber: 7.5 Consensus size: 45
33211175 AGGAAATGAT
* * * * ** *
33211185 TAAGACTATAGTTGAAAGACACTATGGAATCA-AATTAGAAACGAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCACAATT-CTATCGAG
* * * *
33211230 TAAGACCATAACTGAAAGACGTTATGGCATCACGATTCTATCAAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCACAATTCTATCGAG
* * ** **
33211275 TAAGACTATAACTGAAAGACATTATGGCATCATGATTCTATTTAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCACAATTCTATCGAG
* * *
33211320 TAAGACCATAGCTGAAATACATTATGGCATCACGATTCTATTGAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCACAATTCTATCGAG
* * * *
33211365 TAAGACCATAACTGAAAGACGTTATGACATCA-AGATTCTATTGAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCACA-ATTCTATCGAG
*
33211410 TAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTATCGAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCACAATTCTATCGAG
* * * * *
33211455 TAAGACCATAGCTGAAAGACACTATGGCATCACAACTCAAACGAA
1 TAAGACCATAGCTGAAAGACATTATGGCATCACAATTCTATCGAG
* *
33211500 CAAGACCATAGTTGAAAGACA
1 TAAGACCATAGCTGAAAGACA
33211521 CAATGGCAAC
Statistics
Matches: 251, Mismatches: 37, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
45 247 0.98
46 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (45 bp):
TAAGACCATAGCTGAAAGACATTATGGCATCACAATTCTATCGAG
Found at i:33211345 original size:90 final size:90
Alignment explanation
Indices: 33211227--33211486 Score: 403
Period size: 90 Copynumber: 2.9 Consensus size: 90
33211217 AATTAGAAAC
* * *
33211227 GAGTAAGACCATAACTGAAAGACGTTATGGCATCACGATTCTATCAAGTAAGACTATAACTGAAA
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATAACTGAAA
*
33211292 GACATTATGGCATCATGATTCTATT
66 GACATTATGGCATCAAGATTCTATT
* * * *
33211317 TAGTAAGACCATAGCTGAAATACATTATGGCATCACGATTCTATTGAGTAAGACCATAACTGAAA
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATAACTGAAA
* *
33211382 GACGTTATGACATCAAGATTCTATT
66 GACATTATGGCATCAAGATTCTATT
* *
33211407 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTATCGAGTAAGACCATAGCTGAAA
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATAACTGAAA
*
33211472 GACACTATGGCATCA
66 GACATTATGGCATCA
33211487 CAACTCAAAC
Statistics
Matches: 151, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 151 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (90 bp):
GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATAACTGAAA
GACATTATGGCATCAAGATTCTATT
Found at i:33211505 original size:135 final size:135
Alignment explanation
Indices: 33211185--33211519 Score: 420
Period size: 135 Copynumber: 2.5 Consensus size: 135
33211175 AGGAAATGAT
* * * *
33211185 TAAGACTATAGTTGAAAGACACTATGGAATCA-AATTAGAAACGAGTAAGACCATAACTGAAAGA
1 TAAGACCATAGCTGAAAGACACTATGGCATCACAATT-CAAACGAGTAAGACCATAACTGAAAGA
* * * **
33211249 CGTTATGGCATCACGATTCTATCAAGTAAGACTATAACTGAAAGACATTATGGCATCATGATTCT
65 CGTTATGACATCAAGATTCTATCAAGTAAGACCATAACTGAAAGACATTATGGCATCACAATTCT
**
33211314 ATTTAG
130 ATCGAG
* * * * **
33211320 TAAGACCATAGCTGAAATACATTATGGCATCACGATTCTATTGAGTAAGACCATAACTGAAAGAC
1 TAAGACCATAGCTGAAAGACACTATGGCATCACAATTCAAACGAGTAAGACCATAACTGAAAGAC
** * *
33211385 GTTATGACATCAAGATTCTATTGAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTA
66 GTTATGACATCAAGATTCTATCAAGTAAGACCATAACTGAAAGACATTATGGCATCACAATTCTA
33211450 TCGAG
131 TCGAG
* ** **
33211455 TAAGACCATAGCTGAAAGACACTATGGCATCACAACTCAAACGAACAAGACCATAGTTGAAAGAC
1 TAAGACCATAGCTGAAAGACACTATGGCATCACAATTCAAACGAGTAAGACCATAACTGAAAGAC
33211520 ACAATGGCAA
Statistics
Matches: 167, Mismatches: 32, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
135 164 0.98
136 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (135 bp):
TAAGACCATAGCTGAAAGACACTATGGCATCACAATTCAAACGAGTAAGACCATAACTGAAAGAC
GTTATGACATCAAGATTCTATCAAGTAAGACCATAACTGAAAGACATTATGGCATCACAATTCTA
TCGAG
Found at i:33211563 original size:46 final size:46
Alignment explanation
Indices: 33211455--33211666 Score: 273
Period size: 46 Copynumber: 4.6 Consensus size: 46
33211445 TTCTATCGAG
* * * * ** *
33211455 TAAGACCATAGCTGAAAGACACTATGGCATCACAAC-TCAAACGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACTCAACAGAAAATGAA
* * *
33211500 CAAGACCATAGTTGAAAGACACAATGGCAACTCAACAGAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACTCAACAGAAAATGAA
* **
33211546 TAAGACCATGGTTGAAAGACACTATGGAAACTCAATGGAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACTCAACAGAAAATGAA
* *
33211592 TAAGACCATGGTTGAAAGACACTATGGAAACTCGACAGAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAACTCAACAGAAAATGAA
*
33211638 TAAGACCATGGTTGAAAGACACCATGGCA
1 TAAGACCATGGTTGAAAGACACTATGGCA
33211667 TCCTTCAACC
Statistics
Matches: 147, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 31 0.21
46 116 0.79
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGACACTATGGCAACTCAACAGAAAATGAA
Found at i:33221208 original size:21 final size:21
Alignment explanation
Indices: 33221184--33221272 Score: 55
Period size: 21 Copynumber: 4.4 Consensus size: 21
33221174 TCACTTTAAA
33221184 ATTAATTTAATATAATATAAT
1 ATTAATTTAATATAATATAAT
* * * *
33221205 ATTAA-TCAAGATGAATATTAG
1 ATTAATTTAATAT-AATATAAT
33221226 ATTAAATTTAATAT--TA-AAT
1 ATT-AATTTAATATAATATAAT
* *
33221245 ATT-A-TTAAAATAATAAAAT
1 ATTAATTTAATATAATATAAT
*
33221264 ATTTATTTA
1 ATTAATTTA
33221273 CAAGATAAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
16 6 0.12
17 1 0.02
18 2 0.04
19 10 0.20
20 8 0.16
21 17 0.33
22 2 0.04
23 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (21 bp):
ATTAATTTAATATAATATAAT
Found at i:33221330 original size:20 final size:18
Alignment explanation
Indices: 33221283--33221331 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
33221273 CAAGATAAAC
33221283 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
33221300 ATT-AATATAATCACTTTAAT
1 ATTAAAT-TAAT-A-TTTAAT
33221320 ATTAAATTAATA
1 ATTAAATTAATA
33221332 AAACACTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 6 0.22
19 2 0.07
20 13 0.48
21 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:33230699 original size:157 final size:157
Alignment explanation
Indices: 33230413--33230712 Score: 582
Period size: 157 Copynumber: 1.9 Consensus size: 157
33230403 ATCTCAATCC
*
33230413 GTGTATTATAAGTGCATAGATTTGGCTTTTATTTTTGACTTAGCTCAACTATGCTCACTGATTCC
1 GTGTATTATAAGTGCATAGATTTGGCTTTTATTTTTGACTTAGCTCAAATATGCTCACTGATTCC
33230478 GTGGTTCATCTCCATTTCAATGCTCATGCCTGCTGCATGATATGTAGTCTTGCATTTTCATATAT
66 GTGGTTCATCTCCATTTCAATGCTCATGCCTGCTGCATGATATGTAGTCTTGCATTTTCATATAT
*
33230543 GAATATGTTTTTTTTTTAAGGGAATAT
131 GAATATGTCTTTTTTTTAAGGGAATAT
33230570 GTGTATTATAAGTGCATAGATTTGGCTTTTATTTTTGACTTAGCTCAAATATGCTCACTGATTCC
1 GTGTATTATAAGTGCATAGATTTGGCTTTTATTTTTGACTTAGCTCAAATATGCTCACTGATTCC
33230635 GTGGTTCATCTCCATTTCAATGCTCATGCCTGCTGCATGATATGTAGTCTTGCATTTTCATATAT
66 GTGGTTCATCTCCATTTCAATGCTCATGCCTGCTGCATGATATGTAGTCTTGCATTTTCATATAT
33230700 GAATATGTCTTTT
131 GAATATGTCTTTT
33230713 ACATTGTTGT
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 141 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (157 bp):
GTGTATTATAAGTGCATAGATTTGGCTTTTATTTTTGACTTAGCTCAAATATGCTCACTGATTCC
GTGGTTCATCTCCATTTCAATGCTCATGCCTGCTGCATGATATGTAGTCTTGCATTTTCATATAT
GAATATGTCTTTTTTTTAAGGGAATAT
Found at i:33231118 original size:9 final size:9
Alignment explanation
Indices: 33231101--33231131 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
33231091 AATAAAAAAA
33231101 AAATATTTTT
1 AAAT-TTTTT
33231111 AAATTTTTT
1 AAATTTTTT
33231120 AAATTTTTT
1 AAATTTTTT
33231129 AAA
1 AAA
33231132 AAATTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AAATTTTTT
Found at i:33232589 original size:21 final size:21
Alignment explanation
Indices: 33232564--33232605 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
33232554 TTCCAATTGG
33232564 TAGCAACTAATAGATGTTCTA
1 TAGCAACTAATAGATGTTCTA
33232585 TAGCAACTAATAGATGTTCTA
1 TAGCAACTAATAGATGTTCTA
33232606 ACACCCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
TAGCAACTAATAGATGTTCTA
Found at i:33233703 original size:28 final size:28
Alignment explanation
Indices: 33233650--33233703 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
33233640 TTTCTTTGTC
* * *
33233650 TAAAATAATAAAACAACTTCTTTAAACA
1 TAAAATAATAAAAAAACTTATATAAACA
33233678 TAAAA-AATAACAAAAACTTATATAAA
1 TAAAATAATAA-AAAAACTTATATAAA
33233704 TAACATGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (28 bp):
TAAAATAATAAAAAAACTTATATAAACA
Found at i:33236146 original size:24 final size:24
Alignment explanation
Indices: 33236096--33236161 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
33236086 ATGCGAATAC
* *
33236096 ACATAAATGATTTTCATTGAACTT
1 ACATAAATGATCTTGATTGAACTT
*
33236120 ACATAAATGATCTTGATTG-ATTAT
1 ACATAAATGATCTTGATTGAACT-T
* *
33236144 ACATGAATAATCTTGATT
1 ACATAAATGATCTTGATT
33236162 AAATTCTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 2 0.06
24 34 0.94
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (24 bp):
ACATAAATGATCTTGATTGAACTT
Found at i:33259939 original size:20 final size:22
Alignment explanation
Indices: 33259897--33259939 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
33259887 AGCTTGTGTT
* *
33259897 AATATGGTGTTTTTATGCTTAA
1 AATATGGTGTTTTTAAGCGTAA
33259919 AATA-GGTGTTTTTAAG-GTAA
1 AATATGGTGTTTTTAAGCGTAA
33259939 A
1 A
33259940 CAATAAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (22 bp):
AATATGGTGTTTTTAAGCGTAA
Found at i:33259944 original size:22 final size:22
Alignment explanation
Indices: 33259897--33259944 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
33259887 AGCTTGTGTT
* *
33259897 AATATGGTGTTTTTATGCTTAA
1 AATATGGTGTTTTTAAGCTAAA
*
33259919 AATA-GGTGTTTTTAAGGTAAA
1 AATATGGTGTTTTTAAGCTAAA
33259940 CAATA
1 -AATA
33259945 AGGTATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (22 bp):
AATATGGTGTTTTTAAGCTAAA
Found at i:33272534 original size:14 final size:14
Alignment explanation
Indices: 33272515--33272541 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33272505 GAGGTCCAGT
33272515 TGAACTGAACCGAG
1 TGAACTGAACCGAG
33272529 TGAACTGAACCGA
1 TGAACTGAACCGA
33272542 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:33276889 original size:16 final size:17
Alignment explanation
Indices: 33276854--33276887 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33276844 CACATCTTTC
33276854 CTCTCTTCTCTCCATTTT
1 CTCTCTTCTCTCCA-TTT
*
33276872 CTCTCTTCTTTCCATT
1 CTCTCTTCTCTCCATT
33276888 CTAAAATTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.13
18 13 0.87
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (17 bp):
CTCTCTTCTCTCCATTT
Found at i:33277583 original size:35 final size:35
Alignment explanation
Indices: 33277554--33277624 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
33277544 TATTTCGATT
33277554 TAATAAGTATGTATGTGCAATAACATATTTGTCTA
1 TAATAAGTATGTATGTGCAATAACATATTTGTCTA
33277589 TAATAAGTATGTATGTGCAATAACATATTTGTCTA
1 TAATAAGTATGTATGTGCAATAACATATTTGTCTA
33277624 T
1 T
33277625 TAAGATTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (35 bp):
TAATAAGTATGTATGTGCAATAACATATTTGTCTA
Found at i:33279685 original size:50 final size:50
Alignment explanation
Indices: 33279570--33279762 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
33279560 GATAATAACA
* * * * ** *
33279570 TGCCAAAGTCATGTCCCAGACATGGTCTTACTTGAGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
33279621 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
33279671 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
33279721 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
33279763 TTACCAAAAT
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 96 0.76
51 31 0.24
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:33285401 original size:100 final size:100
Alignment explanation
Indices: 33285228--33285429 Score: 404
Period size: 100 Copynumber: 2.0 Consensus size: 100
33285218 GCCATTGTCG
33285228 TATATTTTTTCGGTTCACCATGCTACAAGATTTTCGAGCAATCTAGAGCTAAAATTCTTAAAATA
1 TATATTTTTTCGGTTCACCATGCTACAAGATTTTCGAGCAATCTAGAGCTAAAATTCTTAAAATA
33285293 CCCCTAAAACTCCTAGGCCCAATTTTGGGGTGTTA
66 CCCCTAAAACTCCTAGGCCCAATTTTGGGGTGTTA
33285328 TATATTTTTTCGGTTCACCATGCTACAAGATTTTCGAGCAATCTAGAGCTAAAATTCTTAAAATA
1 TATATTTTTTCGGTTCACCATGCTACAAGATTTTCGAGCAATCTAGAGCTAAAATTCTTAAAATA
33285393 CCCCTAAAACTCCTAGGCCCAATTTTGGGGTGTTA
66 CCCCTAAAACTCCTAGGCCCAATTTTGGGGTGTTA
33285428 TA
1 TA
33285430 GGATGTGTGG
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (100 bp):
TATATTTTTTCGGTTCACCATGCTACAAGATTTTCGAGCAATCTAGAGCTAAAATTCTTAAAATA
CCCCTAAAACTCCTAGGCCCAATTTTGGGGTGTTA
Found at i:33287635 original size:22 final size:22
Alignment explanation
Indices: 33287610--33287655 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
33287600 CAAACCGAAA
* *
33287610 CACCACTATACAACCACCATAG
1 CACCACCACACAACCACCATAG
*
33287632 CACCACCACACCACCACCATAG
1 CACCACCACACAACCACCATAG
33287654 CA
1 CA
33287656 TAACCATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.48, G:0.04, T:0.09
Consensus pattern (22 bp):
CACCACCACACAACCACCATAG
Found at i:33287636 original size:11 final size:11
Alignment explanation
Indices: 33287622--33287682 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
33287612 CCACTATACA
33287622 ACCACCATAGC
1 ACCACCATAGC
* *
33287633 ACCACCACACC
1 ACCACCATAGC
33287644 ACCACCATAGC
1 ACCACCATAGC
** *
33287655 ATAACCATATC
1 ACCACCATAGC
* *
33287666 ACCACCCTTGC
1 ACCACCATAGC
33287677 ACCACC
1 ACCACC
33287683 TCCACAGCTG
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.34, C:0.49, G:0.05, T:0.11
Consensus pattern (11 bp):
ACCACCATAGC
Found at i:33290247 original size:15 final size:16
Alignment explanation
Indices: 33290227--33290257 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33290217 GTCACATCTC
33290227 AAAAATT-GGGTTAGT
1 AAAAATTGGGGTTAGT
33290242 AAAAATTGGGGTTAGT
1 AAAAATTGGGGTTAGT
33290258 GAACCAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (16 bp):
AAAAATTGGGGTTAGT
Found at i:33290930 original size:11 final size:10
Alignment explanation
Indices: 33290912--33290961 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
33290902 AAAAATTGAA
33290912 ACACCACCAT
1 ACACCACCAT
33290922 ACAACCACCAT
1 AC-ACCACCAT
*
33290933 AGCACCACCAC
1 A-CACCACCAT
33290944 ACCACCACCAT
1 A-CACCACCAT
33290955 AGCACCA
1 A-CACCA
33290962 TCGTATCACC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 2 0.06
11 31 0.91
12 1 0.03
ACGTcount: A:0.40, C:0.50, G:0.04, T:0.06
Consensus pattern (10 bp):
ACACCACCAT
Found at i:33290974 original size:22 final size:22
Alignment explanation
Indices: 33290913--33290961 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
33290903 AAAATTGAAA
* *
33290913 CACCACCATACAACCACCATAG
1 CACCACCACACCACCACCATAG
33290935 CACCACCACACCACCACCATAG
1 CACCACCACACCACCACCATAG
33290957 CACCA
1 CACCA
33290962 TCGTATCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.51, G:0.04, T:0.06
Consensus pattern (22 bp):
CACCACCACACCACCACCATAG
Found at i:33295144 original size:48 final size:47
Alignment explanation
Indices: 33295069--33295159 Score: 137
Period size: 48 Copynumber: 1.9 Consensus size: 47
33295059 TTATCTACGA
* **
33295069 TTATGTGGTCGTTATTGGCAATCATGTGGTGGCTTGTCCACAATATC
1 TTATGTGGCCGTTATCAGCAATCATGTGGTGGCTTGTCCACAATATC
*
33295116 TTATGTGGCCGTTTATCAGCAATTATGTGGTGGCTTGTCCACAA
1 TTATGTGGCCG-TTATCAGCAATCATGTGGTGGCTTGTCCACAA
33295160 ATTGTGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 10 0.26
48 29 0.74
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (47 bp):
TTATGTGGCCGTTATCAGCAATCATGTGGTGGCTTGTCCACAATATC
Found at i:33296995 original size:49 final size:50
Alignment explanation
Indices: 33296942--33297171 Score: 246
Period size: 49 Copynumber: 4.8 Consensus size: 50
33296932 GGTGGAAGTA
* *
33296942 AGTGGCAATTTATCTACAAATCAGTGGTGGCTTGACCACAAAGTGTT-TC
1 AGTGGCAATTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTATC
* * * *
33296991 AGTGGCAGTATATCTGC--AT-ATTAGTGG-TT-T-CACAAAGTGTTATC
1 AGTGGCAATTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTATC
33297035 AGTGG-AAGTTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTT-TC
1 AGTGGCAA-TTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTATC
* * ** * * *
33297084 AATGGCAGTACATTTGCATATCAGTGGTGGCTTGTCCACAAAGTGTTATT
1 AGTGGCAATTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTATC
*
33297134 AGTGG-AAGTTTATCTGCAAATCAGTGGTGACTTGTCCA
1 AGTGGCAA-TTTATCTGCAAATCAGTGGTGGCTTGTCCA
33297172 TAAATTGAGT
Statistics
Matches: 146, Mismatches: 24, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
43 12 0.08
44 15 0.10
45 2 0.01
46 8 0.05
47 8 0.05
48 2 0.01
49 57 0.39
50 42 0.29
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (50 bp):
AGTGGCAATTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTATC
Found at i:33297161 original size:99 final size:93
Alignment explanation
Indices: 33296942--33297171 Score: 318
Period size: 93 Copynumber: 2.4 Consensus size: 93
33296932 GGTGGAAGTA
* * * *
33296942 AGTGGCAA-TTTATCTACAAATCAGTGGTGGCTTGACCACAAAGTGTTTCAGTGGCAGTATATCT
1 AGTGG-AAGTTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCAATGGCAGTACATCT
33297006 GCATATTAGTGGTTTCACAAAGTGTTATC
65 GCATATTAGTGGTTTCACAAAGTGTTATC
*
33297035 AGTGGAAGTTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCAATGGCAGTACATTTG
1 AGTGGAAGTTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCAATGGCAGTACATCTG
* *
33297100 CATATCAGTGGTGGCTTGTCCACAAAGTGTTATT
66 CATAT---TAGTGG-TT-T-CACAAAGTGTTATC
*
33297134 AGTGGAAGTTTATCTGCAAATCAGTGGTGACTTGTCCA
1 AGTGGAAGTTTATCTGCAAATCAGTGGTGGCTTGTCCA
33297172 TAAATTGAGT
Statistics
Matches: 122, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
92 2 0.02
93 62 0.51
96 5 0.04
97 2 0.02
98 1 0.01
99 50 0.41
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (93 bp):
AGTGGAAGTTTATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCAATGGCAGTACATCTG
CATATTAGTGGTTTCACAAAGTGTTATC
Found at i:33302697 original size:9 final size:9
Alignment explanation
Indices: 33302683--33302710 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
33302673 TGAGCTTTTG
33302683 AATTCGAAT
1 AATTCGAAT
33302692 AATTCGAAT
1 AATTCGAAT
33302701 AATTCGAAT
1 AATTCGAAT
33302710 A
1 A
33302711 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:33303874 original size:197 final size:199
Alignment explanation
Indices: 33303585--33303982 Score: 669
Period size: 197 Copynumber: 2.0 Consensus size: 199
33303575 GACAATGGTT
*
33303585 ACAAGGACCCAAAATTTTTTTTAAATTTAACTCGAACAAATATATTTGATTCGATTCGATTCGAT
1 ACAAGGACCCAAAATTTTTTTAAAATTTAACTCGAACAAATATA-TTGATTCGATTCGATTCGAT
33303650 TCGAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATAAAGTTAGGATGATAAAATGAG
65 TCGAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATAAAGTTAGGATGATAAAATGAG
* * *
33303715 ATTCAAAAACTCGATTAACTCAAAATTTTTCAATTCGATTTGATTCGATTCGATCGAATGCTCAC
130 ATTCAAAAACTCGATTAACTCAAAAATTTTCAATTCGATTCGATTCGATTCGATCGAATACTCAC
33303780 CCCTA
195 CCCTA
*
33303785 ACAATGACCCAAAATTACTTTTTAAAATTTAACTCGAAC-AA-ATA-T-ATTCGATTCGATTCGA
1 ACAAGGACCCAAAATT--TTTTTAAAATTTAACTCGAACAAATATATTGATTCGATTCGATTCGA
33303846 TTCGAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATAAAGTTAGGATGATAAAATGA
64 TTCGAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATAAAGTTAGGATGATAAAATGA
** *
33303911 GATTTGAAAACTCGATTAACTCAAAAATTTTCGATTCGATTCGATTCGATTCGATCGAATACTCA
129 GATTCAAAAACTCGATTAACTCAAAAATTTTCAATTCGATTCGATTCGATTCGATCGAATACTCA
33303976 CCCCTA
194 CCCCTA
33303982 A
1 A
33303983 TTGAATATAC
Statistics
Matches: 188, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
197 147 0.78
198 1 0.01
200 18 0.10
201 2 0.01
202 20 0.11
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (199 bp):
ACAAGGACCCAAAATTTTTTTAAAATTTAACTCGAACAAATATATTGATTCGATTCGATTCGATT
CGAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATAAAGTTAGGATGATAAAATGAGA
TTCAAAAACTCGATTAACTCAAAAATTTTCAATTCGATTCGATTCGATTCGATCGAATACTCACC
CCTA
Found at i:33303950 original size:5 final size:5
Alignment explanation
Indices: 33303940--33303965 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33303930 CTCAAAAATT
33303940 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
33303966 CGAATACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:33305765 original size:32 final size:32
Alignment explanation
Indices: 33305708--33305780 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
33305698 TTTTGATCAA
*
33305708 TTCAAGTACCAACTAGGTTCTTTTTGGACAAG
1 TTCAAGTACCAACTAGGTTCATTTTGGACAAG
* *
33305740 TTCAAGTACCAACTAGGTAT-ATTTTGTATAAG
1 TTCAAGTACCAACTAGGT-TCATTTTGGACAAG
*
33305772 TTTAAGTAC
1 TTCAAGTAC
33305781 TAATTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (32 bp):
TTCAAGTACCAACTAGGTTCATTTTGGACAAG
Found at i:33307099 original size:24 final size:23
Alignment explanation
Indices: 33307045--33307091 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
33307035 AAGAAGAGAC
33307045 TGAGTTTTTCTGAGCTGGGTTGT
1 TGAGTTTTTCTGAGCTGGGTTGT
33307068 TGAGTTTTTCTGAGCTGGGTTGT
1 TGAGTTTTTCTGAGCTGGGTTGT
33307091 T
1 T
33307092 CTTGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (23 bp):
TGAGTTTTTCTGAGCTGGGTTGT
Found at i:33315481 original size:13 final size:14
Alignment explanation
Indices: 33315464--33315507 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
33315454 TGTTTCAATT
33315464 TAATTTTAATAATA
1 TAATTTTAATAATA
*
33315478 -AATTTTAAAAATAA
1 TAATTTTAATAAT-A
33315492 TAATTTTAAATAATA
1 TAATTTT-AATAATA
33315507 T
1 T
33315508 TCTTCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
15 8 0.32
16 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATTTTAATAATA
Found at i:33315492 original size:16 final size:16
Alignment explanation
Indices: 33315470--33315506 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
33315460 AATTTAATTT
33315470 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
33315487 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
33315502 TAATA
1 TAATA
33315507 TTCTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:33315516 original size:29 final size:27
Alignment explanation
Indices: 33315464--33315519 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
33315454 TGTTTCAATT
33315464 TAATTTTAATAATAAATTTTAAAAATAA
1 TAATTTTAATAAT-AATTTTAAAAATAA
33315492 TAATTTTAAATAAT-ATTCTTCAAAAATA
1 TAATTTT-AATAATAATT-TT-AAAAATA
33315520 TTAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.12
28 9 0.36
29 13 0.52
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATTTTAATAATAATTTTAAAAATAA
Found at i:33317641 original size:18 final size:17
Alignment explanation
Indices: 33317620--33317657 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
33317610 TTTCCCTTCA
33317620 TTTTA-TTTATTTATTTAT
1 TTTTATTTTA-TTATTT-T
33317638 TTTTATTTTATTATTTT
1 TTTTATTTTATTATTTT
33317655 TTT
1 TTT
33317658 AATGCTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTTATTATTTT
Found at i:33319866 original size:21 final size:21
Alignment explanation
Indices: 33319842--33319883 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33319832 TTTATAGATG
* *
33319842 CCTTTGTTTTCTGTTGAAAAT
1 CCTTTATTCTCTGTTGAAAAT
*
33319863 CCTTTATTCTCTTTTGAAAAT
1 CCTTTATTCTCTGTTGAAAAT
33319884 AAACAATTTG
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:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (21 bp):
CCTTTATTCTCTGTTGAAAAT
Found at i:33321983 original size:101 final size:102
Alignment explanation
Indices: 33321863--33322047 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
33321853 AAAGTGATGG
* *
33321863 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACTGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTA-TCGAATGATAATGGTCACATGTGTAGT
33321926 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* *
33321964 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGAATGATAATGGTCACATGTGTAGTA
33322029 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
33322048 TGAACCGAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 7 0.09
101 37 0.47
102 34 0.44
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGAATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:33321985 original size:51 final size:51
Alignment explanation
Indices: 33321859--33322054 Score: 218
Period size: 51 Copynumber: 3.9 Consensus size: 51
33321849 AGTGAAAGTG
* * * *
33321859 ATGGTCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACTGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * *
33321908 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * * * *
33321959 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* *
33322011 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
33322055 AACATCATTG
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.31
51 79 0.65
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
Found at i:33322049 original size:26 final size:26
Alignment explanation
Indices: 33321969--33322049 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
33321959 TTCGATCACG
33321969 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
33321995 CGTGTA-T-CGAATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
33322020 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
33322046 TGTG
1 TGTG
33322050 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:33322102 original size:45 final size:45
Alignment explanation
Indices: 33322051--33322145 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
33322041 TACTATGTGA
* * *
33322051 ACCGAACATCATTGATTAGTAAAGTGGTTGCTATGTGTTGATTCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
*
33322096 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
33322141 ACCGA
1 ACCGA
33322146 GTATCTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAAGTGGTTGCTATGTGCTGAATCC
Found at i:33329322 original size:41 final size:41
Alignment explanation
Indices: 33329276--33329389 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
33329266 ATACTTAATT
*
33329276 ATACCCTTGAATTGCACATATGTGCCCCTGTTTGTACTTCG
1 ATACCCTTGAATTGCACATACGTGCCCCTGTTTGTACTTCG
*
33329317 ATACCCTTGAATTGCACATACGTGCCCCTATTTGTACTTCG
1 ATACCCTTGAATTGCACATACGTGCCCCTGTTTGTACTTCG
* * * *
33329358 GTACCCCT-AATTGCATATACGTGCCCATGTTT
1 ATACCCTTGAATTGCACATACGTGCCCCTGTTT
33329390 ACAGTCCAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
40 21 0.32
41 45 0.68
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (41 bp):
ATACCCTTGAATTGCACATACGTGCCCCTGTTTGTACTTCG
Found at i:33332690 original size:24 final size:24
Alignment explanation
Indices: 33332663--33332709 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
33332653 AAATGGAGTA
33332663 AGTTTATAGAATTTAGTGAGTTCC
1 AGTTTATAGAATTTAGTGAGTTCC
33332687 AGTTTATAGAATTTAGTGAGTTC
1 AGTTTATAGAATTTAGTGAGTTC
33332710 TAGAGGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (24 bp):
AGTTTATAGAATTTAGTGAGTTCC
Found at i:33351053 original size:12 final size:13
Alignment explanation
Indices: 33351029--33351057 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
33351019 GGGCTATAAC
33351029 TATTGCATTTATT
1 TATTGCATTTATT
33351042 TATTGC-TTTATT
1 TATTGCATTTATT
33351054 TATT
1 TATT
33351058 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:33366191 original size:50 final size:50
Alignment explanation
Indices: 33366132--33366277 Score: 175
Period size: 50 Copynumber: 2.8 Consensus size: 50
33366122 ATGGGAGTTT
* *
33366132 TCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
1 TCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
* * *
33366182 TCATCTCGGTGCCAACGCCATGTCCTAGACATGGTCTTACGTGGGACCTC
1 TCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
* *
33366232 TCATGATCTCAATGATGCCAATGTCATGTCCCAGACATGGTCTTAC
1 TC---ATCTC---GGTGCCAATGCCATGTCCCAGACATGGTCTTAC
33366278 ATGGGATCTC
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
50 47 0.58
53 5 0.06
56 29 0.36
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
Found at i:33368427 original size:18 final size:18
Alignment explanation
Indices: 33368404--33368441 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
33368394 TCGATAACGG
33368404 TACCCCACATAGTCTAAC
1 TACCCCACATAGTCTAAC
**
33368422 TACCCCATGTAGTCTAAC
1 TACCCCACATAGTCTAAC
33368440 TA
1 TA
33368442 TCTCTGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (18 bp):
TACCCCACATAGTCTAAC
Found at i:33373783 original size:50 final size:50
Alignment explanation
Indices: 33373705--33373821 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 50
33373695 ATGTCATATA
* * ** * *
33373705 CCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTC
1 CCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
* *
33373755 CCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 CCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
33373805 CCAGACATGGTCTTACA
1 CCAGACATGGTCTTACA
33373822 TAGGAACTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
CCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTC
Found at i:33375864 original size:15 final size:16
Alignment explanation
Indices: 33375844--33375873 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33375834 TGGTGCCTTA
33375844 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
33375859 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
33375874 AGCATGTTTG
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:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:33377453 original size:30 final size:30
Alignment explanation
Indices: 33377398--33377459 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
33377388 CACTAAGCAA
33377398 GTTTCATATACATGTATCATCCATTT-CAT
1 GTTTCATATACATGTATCATCCATTTCCAT
33377427 GTTTCAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTC-ATATA-CATGT-ATCATCCATTTCCAT
33377458 GT
1 GT
33377460 ATATACCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
GTTTCATATACATGTATCATCCATTTCCAT
Found at i:33383954 original size:18 final size:18
Alignment explanation
Indices: 33383931--33383966 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
33383921 AAAACTAATC
33383931 ATGTGTTCAATAAAACCA
1 ATGTGTTCAATAAAACCA
33383949 ATGTGTTCAATAAAACCA
1 ATGTGTTCAATAAAACCA
33383967 CGACAACCCT
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:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
ATGTGTTCAATAAAACCA
Found at i:33389686 original size:21 final size:21
Alignment explanation
Indices: 33389660--33389699 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33389650 AATCATCCTA
33389660 GGAAGGCAATTCCTAGCAATT
1 GGAAGGCAATTCCTAGCAATT
**
33389681 GGAAGGCCTTTCCTAGCAA
1 GGAAGGCAATTCCTAGCAA
33389700 CTAAAAGGAC
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:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
GGAAGGCAATTCCTAGCAATT
Found at i:33393341 original size:16 final size:15
Alignment explanation
Indices: 33393314--33393347 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
33393304 ATAACTAGTA
*
33393314 TATAATTATATTTAT
1 TATAATTATATTAAT
33393329 TATAATATATATTAAT
1 TATAAT-TATATTAAT
33393345 TAT
1 TAT
33393348 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:33396256 original size:15 final size:15
Alignment explanation
Indices: 33396238--33396271 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33396228 AATGCTCGAG
*
33396238 AAAAAAAA-CAAACA
1 AAAAAAAAGAAAACA
33396252 AAAAAAAAGAAAACA
1 AAAAAAAAGAAAACA
33396267 AAAAA
1 AAAAA
33396272 GAGAAGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAACA
Found at i:33397019 original size:10 final size:10
Alignment explanation
Indices: 33396962--33397018 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
33396952 GAACATGTTA
*
33396962 AATTTAAATT
1 AATTTTAATT
*
33396972 AATTTTATATAA
1 AATTTTA-AT-T
*
33396984 AATTTTCATT
1 AATTTTAATT
*
33396994 AATTTTGATT
1 AATTTTAATT
33397004 AATTTTAATT
1 AATTTTAATT
33397014 -ATTTT
1 AATTTT
33397019 TGATAGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 5 0.13
10 24 0.62
11 4 0.10
12 6 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
AATTTTAATT
Found at i:33397028 original size:20 final size:20
Alignment explanation
Indices: 33396962--33397022 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
33396952 GAACATGTTA
*
33396962 AATTTAAATTAATTTT-ATAT
1 AATTTTAATTAATTTTGAT-T
*
33396982 AAAATTTTCATTAATTTTGATT
1 --AATTTTAATTAATTTTGATT
*
33397004 AATTTTAATTATTTTTGAT
1 AATTTTAATTAATTTTGAT
33397023 AGATTTGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
22 15 0.44
23 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (20 bp):
AATTTTAATTAATTTTGATT
Found at i:33414230 original size:101 final size:101
Alignment explanation
Indices: 33414110--33414294 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 101
33414100 AAAGTGATGG
* *
33414110 TCACGTGTGTAGTACTATGTGCAGGCTAATACGTGTACCGGAAT-G-ATGGGTCGCATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGTGTACCGG-ATGGAAT-GGTCACATGTGTAGT
*
33414173 ACTATGTGCGGGCTACTATGCGTACCGAATAGCTTCGA
64 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
* *
33414211 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAAATGGTCACATGTGTAGTA
1 TCACATGTGTAGTACTATGTGCAGGCTAATACGTGTACCGGATGG-AATGGTCACATGTGTAGTA
33414276 CTATGTGCAGGCTACTATG
65 CTATGTGCAGGCTACTATG
33414295 TGAACTGAGT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
100 2 0.03
101 39 0.51
102 33 0.43
103 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCTAATACGTGTACCGGATGGAATGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
Found at i:33414231 original size:51 final size:48
Alignment explanation
Indices: 33414104--33414292 Score: 216
Period size: 51 Copynumber: 3.8 Consensus size: 48
33414094 AAAGTGAAAG
* *
33414104 TGATGGTCACGTGTGTAGTACTATGTGCAGGCTAATACGTGTACCGGAA
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAA
* * * *
33414153 TGATGGGTCGCATGTGTAGTACTATGTGCGGGCTACTATGCGTACCGAA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
* * * *
33414202 TAGCTTCGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGA
1 T-G-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
33414253 TGGAAATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 T-G--ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
33414293 TGTGAACTGA
Statistics
Matches: 117, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
49 8 0.07
50 36 0.31
51 72 0.62
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (48 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
Found at i:33414296 original size:26 final size:26
Alignment explanation
Indices: 33414215--33414296 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
33414205 CTTCGATCAC
33414215 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAGGCTACT
* * *
33414241 ACGTGTA-T-CGGATG-GAAATGG-TCAC-
1 ATGTGTAGTAC-TATGTG-CA-GGCT-ACT
33414266 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAGGCTACT
33414292 ATGTG
1 ATGTG
33414297 AACTGAGTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.39
26 21 0.51
27 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (26 bp):
ATGTGTAGTACTATGTGCAGGCTACT
Found at i:33425642 original size:17 final size:17
Alignment explanation
Indices: 33425620--33425654 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
33425610 CTCATGGTCC
33425620 CGTAAAGATGTATAAAA
1 CGTAAAGATGTATAAAA
33425637 CGTAAAGATGTATAAAA
1 CGTAAAGATGTATAAAA
33425654 C
1 C
33425655 TATTGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (17 bp):
CGTAAAGATGTATAAAA
Found at i:33429497 original size:19 final size:19
Alignment explanation
Indices: 33429460--33429499 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33429450 AATTGGTGAA
** *
33429460 ATTTGGTTTTGTTATTTTT
1 ATTTGGTTTCATTAGTTTT
33429479 ATTTGGTTTCATTAGTTTT
1 ATTTGGTTTCATTAGTTTT
33429498 AT
1 AT
33429500 CTAACTTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.68
Consensus pattern (19 bp):
ATTTGGTTTCATTAGTTTT
Found at i:33448667 original size:4 final size:4
Alignment explanation
Indices: 33448658--33448689 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
33448648 AGTTGTAAAG
33448658 TTAT TTAT TTAT TTAT TTAT TTAT TTACT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTA
33448690 ATTTTTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:33456115 original size:4 final size:4
Alignment explanation
Indices: 33456106--33456133 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33456096 AAGTTTTATT
33456106 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
33456134 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:33460232 original size:12 final size:11
Alignment explanation
Indices: 33460199--33460231 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
33460189 TAGTAGTTTC
33460199 TTCAAAAAAAA
1 TTCAAAAAAAA
33460210 TTCAAAAAAAA
1 TTCAAAAAAAA
33460221 TTCAAAAAAAA
1 TTCAAAAAAAA
33460232 AAATTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:33460296 original size:16 final size:16
Alignment explanation
Indices: 33460275--33460312 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
33460265 TATCAAGTTG
33460275 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
33460291 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
33460307 AAAAAA
1 AAAAAA
33460313 GAAGAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (16 bp):
AAAAAAAATTCGTGAA
Found at i:33477720 original size:18 final size:18
Alignment explanation
Indices: 33477691--33477735 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
33477681 TACTTTCTTT
33477691 TCTTTCTTCAATCTCACTC
1 TCTTT-TTCAATCTCACTC
* **
33477710 TCTTTTTCAATTTCTTTC
1 TCTTTTTCAATCTCACTC
33477728 TCTTTTTC
1 TCTTTTTC
33477736 TTCTTTTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTTTTCAATCTCACTC
Found at i:33477764 original size:27 final size:27
Alignment explanation
Indices: 33477689--33477764 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
33477679 CATACTTTCT
*
33477689 TTTCTTTCTTCAATCTCACTCTCTTTTTCAA
1 TTTCTTT-TTCAATCT--CT-TCTTTTGCAA
* ** *
33477720 TTTCTTTCTCTTTTTCTTCTTTTGCAA
1 TTTCTTTTTCAATCTCTTCTTTTGCAA
33477747 TTTCTTTTTCAATCTCTT
1 TTTCTTTTTCAATCTCTT
33477765 TTTCACTTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
27 23 0.64
28 2 0.06
30 4 0.11
31 7 0.19
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTCTTTTTCAATCTCTTCTTTTGCAA
Found at i:33479126 original size:21 final size:23
Alignment explanation
Indices: 33479081--33479127 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33479071 TCACCTGCAA
* *
33479081 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
33479104 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
33479125 TAA
1 TAA
33479128 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:33481185 original size:19 final size:18
Alignment explanation
Indices: 33481149--33481188 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33481139 TTTCCACTCG
*
33481149 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
33481167 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
33481186 TTT
1 TTT
33481189 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:33482264 original size:13 final size:13
Alignment explanation
Indices: 33482246--33482298 Score: 88
Period size: 13 Copynumber: 4.0 Consensus size: 13
33482236 CTAGCTCTCT
33482246 TTTTTTTTCACAA
1 TTTTTTTTCACAA
33482259 TTTTTTTTCACAA
1 TTTTTTTTCACAA
*
33482272 TTTTTTTTCAAAA
1 TTTTTTTTCACAA
33482285 TTTTTTTTTCACAA
1 -TTTTTTTTCACAA
33482299 CTTGATATCC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
13 25 0.68
14 12 0.32
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:33482289 original size:27 final size:26
Alignment explanation
Indices: 33482246--33482298 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
33482236 CTAGCTCTCT
*
33482246 TTTTTTTTCACAATTTTTTTTCACAA
1 TTTTTTTTCAAAATTTTTTTTCACAA
33482272 TTTTTTTTCAAAATTTTTTTTTCACAA
1 TTTTTTTTCAAAA-TTTTTTTTCACAA
33482299 CTTGATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTTTTCAAAATTTTTTTTCACAA
Found at i:33482354 original size:14 final size:14
Alignment explanation
Indices: 33482335--33482370 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33482325 ATGGAAACCA
33482335 AAATTTTTTTTTTG
1 AAATTTTTTTTTTG
33482349 AAATTTTTTTTTTG
1 AAATTTTTTTTTTG
33482363 -AATTTTTT
1 AAATTTTTT
33482371 CGAGAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (14 bp):
AAATTTTTTTTTTG
Found at i:33483403 original size:21 final size:23
Alignment explanation
Indices: 33483358--33483404 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33483348 TCACCTGCAA
* *
33483358 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
33483381 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
33483402 TAA
1 TAA
33483405 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:33487189 original size:50 final size:51
Alignment explanation
Indices: 33487064--33487196 Score: 148
Period size: 50 Copynumber: 2.6 Consensus size: 51
33487054 TGAACAAATG
* * *
33487064 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAAACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAA-GATGCAAACTTAAACTAACATGGA
** * * *
33487116 AGTTACATAATGCATGTCATTATTTAAGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAAGATGCAAACTTAAACTAACATGGA
33487166 AGTTACATAATGCATAACTTTA-TTAA-ATGCA
1 AGTTACATAATGCATAACTTTATTTAAGATGCA
33487197 GAACACACAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 5 0.07
49 4 0.06
50 29 0.42
51 10 0.14
52 21 0.30
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (51 bp):
AGTTACATAATGCATAACTTTATTTAAGATGCAAACTTAAACTAACATGGA
Found at i:33489604 original size:22 final size:22
Alignment explanation
Indices: 33489574--33489617 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33489564 TTTGGTATTT
33489574 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
33489596 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
33489618 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:33495523 original size:33 final size:32
Alignment explanation
Indices: 33495485--33495546 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
33495475 GATTACTCAC
33495485 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CA-ACTCTCTTTCTTT
* *
33495518 TTCACTTGATTTCTTTTCAAGTCTCTTTC
1 TTCACTCGATTTCTTTTCAACTCTCTTTC
33495547 AATTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 9 0.35
33 9 0.35
34 8 0.31
ACGTcount: A:0.13, C:0.26, G:0.06, T:0.55
Consensus pattern (32 bp):
TTCACTCGATTTCTTTTCAACTCTCTTTCTTT
Found at i:33495573 original size:21 final size:21
Alignment explanation
Indices: 33495544--33495599 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
33495534 TCAAGTCTCT
*
33495544 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
33495565 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
33495586 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
33495600 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:33495592 original size:14 final size:14
Alignment explanation
Indices: 33495543--33495599 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
33495533 TTCAAGTCTC
33495543 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
33495556 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
33495570 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
33495584 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
33495598 TT
1 TT
33495600 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:33495659 original size:18 final size:18
Alignment explanation
Indices: 33495561--33495699 Score: 88
Period size: 18 Copynumber: 7.7 Consensus size: 18
33495551 TCTTTTTTCG
33495561 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
33495580 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
33495600 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
33495618 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
33495636 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
33495654 CTTTTT-GTTTTC--TTT
1 CTTTTTCTTTTTCATTTT
** * *
33495669 CAATTTCTTTTTCAATCT
1 CTTTTTCTTTTTCATTTT
*
33495687 CTTTTTCCTTTTC
1 CTTTTTCTTTTTC
33495700 TTGCTCAATG
Statistics
Matches: 91, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
15 7 0.08
16 5 0.05
17 6 0.07
18 54 0.59
19 3 0.03
20 8 0.09
21 8 0.09
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:33495681 original size:6 final size:6
Alignment explanation
Indices: 33495561--33495668 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
33495551 TCTTTTTTCG
* * * **
33495561 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
33495612 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33495660 -GTTTT CTTT
1 CTTTTT CTTT
33495669 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:33495701 original size:12 final size:12
Alignment explanation
Indices: 33495563--33495701 Score: 83
Period size: 12 Copynumber: 11.6 Consensus size: 12
33495553 TTTTTTCGCT
33495563 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
33495576 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
33495590 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
33495601 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
33495615 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
33495625 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
33495638 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
33495650 TTTTCTTTTT-G
1 TTTTCTTTTTCA
33495661 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
33495671 ATTTCTTTTTCA
1 TTTTCTTTTTCA
* * *
33495683 ATCTCTTTTTCC
1 TTTTCTTTTTCA
33495695 TTTTCTT
1 TTTTCTT
33495702 GCTCAATGGA
Statistics
Matches: 100, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
9 3 0.03
10 4 0.04
11 10 0.10
12 59 0.59
13 12 0.12
14 9 0.09
15 3 0.03
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:33496724 original size:39 final size:37
Alignment explanation
Indices: 33496681--33496756 Score: 100
Period size: 40 Copynumber: 2.0 Consensus size: 37
33496671 GCAAGACTTT
*
33496681 TCACTT-TTTTTTCTTCTTTTTTTTAACTCGATTTTTTTG
1 TCACTTCTTTTTTCTTCCTTTTTTT---TCGATTTTTTTG
*
33496720 TCACTTCTTTTTTTTTCCTTTTTTTTCGATTTTTTTG
1 TCACTTCTTTTTTCTTCCTTTTTTTTCGATTTTTTTG
33496757 AATTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 12 0.35
39 6 0.18
40 16 0.47
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (37 bp):
TCACTTCTTTTTTCTTCCTTTTTTTTCGATTTTTTTG
Found at i:33496766 original size:10 final size:10
Alignment explanation
Indices: 33496739--33496771 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
33496729 TTTTTTTCCT
33496739 TTTTTTTCG-A
1 TTTTTTT-GAA
33496749 TTTTTTTGAA
1 TTTTTTTGAA
33496759 TTTTTTTGAA
1 TTTTTTTGAA
33496769 TTT
1 TTT
33496772 CTTCTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 1 0.05
10 21 0.95
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:33500254 original size:33 final size:33
Alignment explanation
Indices: 33500216--33500278 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33500206 GATTACTCAC
33500216 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
33500249 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
33500279 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:33500305 original size:21 final size:21
Alignment explanation
Indices: 33500276--33500331 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
33500266 CAAGCTCTCT
*
33500276 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
33500297 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
33500318 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
33500332 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:33500324 original size:14 final size:14
Alignment explanation
Indices: 33500275--33500331 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
33500265 TCAAGCTCTC
33500275 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
33500288 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
33500302 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
33500316 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
33500330 TT
1 TT
33500332 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:33500391 original size:18 final size:18
Alignment explanation
Indices: 33500293--33500396 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
33500283 TCTTTTTTCG
33500293 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
33500312 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
33500332 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
33500350 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
33500368 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
33500386 CTTTTTGTTTT
1 CTTTTTCTTTT
33500397 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:33500413 original size:6 final size:6
Alignment explanation
Indices: 33500293--33500400 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
33500283 TCTTTTTTCG
* * * **
33500293 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
33500344 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33500392 -GTTTT CTTT
1 CTTTTT CTTT
33500401 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:33500711 original size:33 final size:34
Alignment explanation
Indices: 33500656--33500730 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
33500646 AGATTTAAAC
* *
33500656 AAATTAATTAGTAGCACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
33500690 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
33500723 AATTTAAT
1 AAATTAAT
33500731 GAACTAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:33501739 original size:22 final size:22
Alignment explanation
Indices: 33501714--33501760 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
33501704 ATAACCACAG
33501714 AAACTGTTTAAGGCACGAACAT
1 AAACTGTTTAAGGCACGAACAT
33501736 AAACTGTTTAAGGCACGAACAT
1 AAACTGTTTAAGGCACGAACAT
33501758 AAA
1 AAA
33501761 TTTTCGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (22 bp):
AAACTGTTTAAGGCACGAACAT
Found at i:33504056 original size:12 final size:12
Alignment explanation
Indices: 33504036--33504083 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
33504026 TAGTAGTTTC
*
33504036 TTCAAAAAAAAT
1 TTCAAAAAAAAA
*
33504048 TTCAGAAAAAAA
1 TTCAAAAAAAAA
33504060 TTCAAAAAAAAAA
1 TTC-AAAAAAAAA
33504073 TTCAAAAAAAA
1 TTCAAAAAAAA
33504084 TTTGGTTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:33504068 original size:24 final size:24
Alignment explanation
Indices: 33504039--33504085 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
33504029 TAGTTTCTTC
*
33504039 AAAAAAAATTTCAGAAAAAAATTCA
1 AAAAAAAAATTCA-AAAAAAATTCA
33504064 AAAAAAAAATTCAAAAAAAATT
1 AAAAAAAAATTCAAAAAAAATT
33504086 TGGTTTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.19
Consensus pattern (24 bp):
AAAAAAAAATTCAAAAAAAATTCA
Found at i:33504146 original size:16 final size:17
Alignment explanation
Indices: 33504125--33504161 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
33504115 TATCAAGTTG
33504125 AAAAAAAA-TTCGTGAA
1 AAAAAAAATTTCGTGAA
33504141 AAAAAAAATTTTCGTGAA
1 AAAAAAAA-TTTCGTGAA
33504159 AAA
1 AAA
33504162 GAAGAAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (17 bp):
AAAAAAAATTTCGTGAA
Found at i:33511711 original size:22 final size:22
Alignment explanation
Indices: 33511683--33511726 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33511673 TTTTGAACCA
33511683 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33511705 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33511727 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33514584 original size:19 final size:18
Alignment explanation
Indices: 33514548--33514587 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33514538 TTTCCACTCG
*
33514548 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
33514566 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
33514585 TTT
1 TTT
33514588 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:33515684 original size:15 final size:14
Alignment explanation
Indices: 33515647--33515681 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
33515637 TAGCTTCTTC
*
33515647 TTTTTTTCACTAAT
1 TTTTTTTCACGAAT
33515661 TTTTTTTCACGAAT
1 TTTTTTTCACGAAT
33515675 TTTTTTT
1 TTTTTTT
33515682 TCAACTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTTTTCACGAAT
Found at i:33515739 original size:13 final size:13
Alignment explanation
Indices: 33515721--33515757 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
33515711 AATGGAAACC
**
33515721 AATTTTTTTTTTG
1 AATTTTTTTTTCA
33515734 AATTTTTTTTTCA
1 AATTTTTTTTTCA
33515747 AATTTTTTTTT
1 AATTTTTTTTT
33515758 GAAGAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (13 bp):
AATTTTTTTTTCA
Found at i:33515741 original size:12 final size:12
Alignment explanation
Indices: 33515724--33515760 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
33515714 GGAAACCAAT
33515724 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
33515736 TTTTTTTTTCAAA
1 TTTTTTTTT-GAA
33515749 TTTTTTTTTGAA
1 TTTTTTTTTGAA
33515761 GAAACTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:33521414 original size:23 final size:25
Alignment explanation
Indices: 33521362--33521415 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
33521352 ACAATCTATA
33521362 GAAAAATCAAAAGAAGAACAAGAT-
1 GAAAAATCAAAAGAAGAACAAGATG
* *
33521386 TAAAAAACTAAAA-AAGAA-AAGATG
1 GAAAAATC-AAAAGAAGAACAAGATG
33521410 GAAAAA
1 GAAAAA
33521416 AAAGAGAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 4 0.16
ACGTcount: A:0.70, C:0.06, G:0.15, T:0.09
Consensus pattern (25 bp):
GAAAAATCAAAAGAAGAACAAGATG
Found at i:33525104 original size:20 final size:19
Alignment explanation
Indices: 33525081--33525145 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
33525071 AAGCTCAAAC
33525081 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
33525101 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
33525121 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
33525141 GAGCT
1 GAGCT
33525146 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:33527596 original size:30 final size:29
Alignment explanation
Indices: 33527560--33527625 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
33527550 GACTTTTCAC
*
33527560 TTTTTTTTAACTTGATTTTTTTGGTCACTT
1 TTTTTTTTAACTCGATTTTTTT-GTCACTT
** *
33527590 TTTTTTTTTGCTCGATTTTTTTTTCACTT
1 TTTTTTTTAACTCGATTTTTTTGTCACTT
33527619 TTTTTTT
1 TTTTTTT
33527626 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.09, C:0.11, G:0.08, T:0.73
Consensus pattern (29 bp):
TTTTTTTTAACTCGATTTTTTTGTCACTT
Found at i:33527608 original size:17 final size:17
Alignment explanation
Indices: 33527575--33527613 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
33527565 TTTAACTTGA
*
33527575 TTTTTTTGGTCACTTTT
1 TTTTTTTGCTCACTTTT
33527592 TTTTTTTGCTCGA-TTTT
1 TTTTTTTGCTC-ACTTTT
33527609 TTTTT
1 TTTTT
33527614 CACTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.74
Consensus pattern (17 bp):
TTTTTTTGCTCACTTTT
Found at i:33527620 original size:12 final size:12
Alignment explanation
Indices: 33527604--33527642 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
33527594 TTTTTGCTCG
33527604 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
33527616 CTTTTTTTTTGA
1 ATTTTTTTTTCA
33527628 ATTTTTTTTTTCA
1 A-TTTTTTTTTCA
33527641 AT
1 AT
33527643 CAAATTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:33527663 original size:13 final size:13
Alignment explanation
Indices: 33527617--33527666 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
33527607 TTTTTTTCAC
33527617 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
33527630 TTTTTTTTTCAAT
1 TTTTTTTTTGAAT
33527643 CAAATTTTTTTTTGAAT
1 ----TTTTTTTTTGAAT
33527660 TTTTTTT
1 TTTTTTT
33527667 GATTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 19 0.61
17 12 0.39
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:33529312 original size:20 final size:19
Alignment explanation
Indices: 33529289--33529353 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
33529279 AAGCTCAAAC
33529289 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
33529309 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
33529329 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
33529349 GAGCT
1 GAGCT
33529354 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Done.