Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 30 of 199
Found at i:9635545 original size:13 final size:15
Alignment explanation
Indices: 9635513--9635542 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9635503 TTTCTTAATA
*
9635513 ATTTTTTTTGTTTAT
1 ATTTCTTTTGTTTAT
9635528 ATTTCTTTTGTTTAT
1 ATTTCTTTTGTTTAT
9635543 TTCATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (15 bp):
ATTTCTTTTGTTTAT
Found at i:9642114 original size:5 final size:5
Alignment explanation
Indices: 9642104--9642129 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9642094 AAGCCATGCC
9642104 CCATA CCATA CCATA CCATA CCATA C
1 CCATA CCATA CCATA CCATA CCATA C
9642130 GTACTCTTTT
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:0.38, C:0.42, G:0.00, T:0.19
Consensus pattern (5 bp):
CCATA
Found at i:9643150 original size:29 final size:28
Alignment explanation
Indices: 9643080--9643150 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 28
9643070 ATTTTCTTTT
*
9643080 GTTACCCAATTATGAAAAGATACAAAATA
1 GTTA-CCAACTATGAAAAGATACAAAATA
* *
9643109 GTTAACCAGCTATGAAAAGATACAAAATG
1 GTT-ACCAACTATGAAAAGATACAAAATA
9643138 GTTACCTAACTAT
1 GTTACC-AACTAT
9643151 TCAATTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 32 0.89
30 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (28 bp):
GTTACCAACTATGAAAAGATACAAAATA
Found at i:9643612 original size:18 final size:18
Alignment explanation
Indices: 9643589--9643625 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9643579 ATAAAAATTA
* *
9643589 TATATATGATATTTATAT
1 TATATATAACATTTATAT
9643607 TATATATAACATTTATAT
1 TATATATAACATTTATAT
9643625 T
1 T
9643626 TGGATAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATATATAACATTTATAT
Found at i:9643966 original size:40 final size:40
Alignment explanation
Indices: 9643920--9644039 Score: 132
Period size: 40 Copynumber: 3.0 Consensus size: 40
9643910 ATAAAGCAGG
* *
9643920 AAAACGCTTCCTCAAGGAAACACTTTGTCCACGTGGACAA
1 AAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACAA
* ** * * *
9643960 AAAACGCTTCCCCATCGAAGCGCTTTGTCCACGTGAATAG
1 AAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACAA
**
9644000 AAAACGCTTCCTTGAGGAAGCGCTTTGTGTCCACGTGGAC
1 AAAACGCTTCCTCAAGGAAGCGC-TT-TGTCCACGTGGAC
9644040 CTTCCTTGAG
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
40 50 0.79
41 2 0.03
42 11 0.17
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
AAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACAA
Found at i:9644382 original size:97 final size:96
Alignment explanation
Indices: 9644129--9644453 Score: 422
Period size: 96 Copynumber: 3.3 Consensus size: 96
9644119 GCTTTTAGAT
* * * * *
9644129 TTTAGGG-TTTTAAGGAAAAATTTAAATAAATAAGGGTTTAGGGTTAGGATTTCTTAATTAAATT
1 TTTAGGGTTTTTAAGGAAAAA-TCAAATAAATTAGGGTTTA--G--A-G-TTACTTGAGTAAATT
*
9644193 AATTATAAATTTT-AAAAAATTAGATTAGAGTTTAGTG
59 AATTATAAATTTTAAAAAAATTAGATTAGGGTTTAGTG
* *
9644230 TTTATGGTTTTTAAGGAAAAAAAT-AAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
1 TTTAGGGTTTTTAAGG--AAAAATCAAATAAATTAGGGTTTAGAGTTACTTGAGTAAATTAATTA
9644294 TAAATTTTAAAAAAAATTAGATTAGGGTTTAGTG
64 TAAATTTT-AAAAAAATTAGATTAGGGTTTAGTG
* *
9644328 TTTAGGGTTTTTAAGGTAACATCAAATAAATTAGGGTTTAGAGTTACTTGAGTAAATTAATTATA
1 TTTAGGGTTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGAGTTACTTGAGTAAATTAATTATA
* * *
9644393 ATTTTTAAAAAAATTAGATTGGGGTTTAGTA
66 AATTTTAAAAAAATTAGATTAGGGTTTAGTG
9644424 TTTAGGGTTTTTAAGGAAAAATCAAATAAA
1 TTTAGGGTTTTTAAGGAAAAATCAAATAAA
9644454 ACTAGTTGTT
Statistics
Matches: 202, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
96 80 0.40
97 47 0.23
98 38 0.19
100 1 0.00
101 6 0.03
102 24 0.12
103 1 0.00
104 5 0.02
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (96 bp):
TTTAGGGTTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGAGTTACTTGAGTAAATTAATTATA
AATTTTAAAAAAATTAGATTAGGGTTTAGTG
Found at i:9645277 original size:40 final size:41
Alignment explanation
Indices: 9645219--9645303 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 41
9645209 AAAACCCTAA
* *
9645219 TTTTTCTGTCCATATGGACAAAGCGCGTCCTTGAGGAAGCG
1 TTTTTCTGTCCACATGGACAAAGCGCGTCCTTAAGGAAGCG
* *
9645260 TTTTT-TGTCCACGTGGACAAAGCGCTTCCTTAAGGAAGCG
1 TTTTTCTGTCCACATGGACAAAGCGCGTCCTTAAGGAAGCG
9645300 TTTT
1 TTTT
9645304 CCTGCTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.88
41 5 0.12
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (41 bp):
TTTTTCTGTCCACATGGACAAAGCGCGTCCTTAAGGAAGCG
Found at i:9648919 original size:14 final size:14
Alignment explanation
Indices: 9648900--9648929 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9648890 TCAAATCACC
9648900 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
9648914 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
9648928 GG
1 GG
9648930 CCTAAATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.13, G:0.47, T:0.33
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:9654045 original size:14 final size:14
Alignment explanation
Indices: 9654026--9654055 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9654016 TCAAATCACC
9654026 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
9654040 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
9654054 GG
1 GG
9654056 CCTAAATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.13, G:0.47, T:0.33
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:9658940 original size:20 final size:20
Alignment explanation
Indices: 9658915--9658953 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9658905 GGCTTGATGT
* *
9658915 CGGTGAAATGTTTTAGACTG
1 CGGTGAAATATTTCAGACTG
9658935 CGGTGAAATATTTCAGACT
1 CGGTGAAATATTTCAGACT
9658954 TTACATCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
CGGTGAAATATTTCAGACTG
Found at i:9670872 original size:22 final size:22
Alignment explanation
Indices: 9670838--9670881 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9670828 AAATAATAAG
*
9670838 AATAATAAGAATAAATA-TAAAA
1 AATAATAACAAT-AATAGTAAAA
*
9670860 AATAATGACAATAATAGTAAAA
1 AATAATAACAATAATAGTAAAA
9670882 GGGATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (22 bp):
AATAATAACAATAATAGTAAAA
Found at i:9672903 original size:45 final size:45
Alignment explanation
Indices: 9672630--9672963 Score: 222
Period size: 44 Copynumber: 7.5 Consensus size: 45
9672620 TACTTCATTA
** * * * *
9672630 CAACTTCAATGAGATAAGACT-TGTAACTTCAATCTGCTCCATTG
1 CAACTTCAGGGAGATAAGATTCTGTATCTTTAATCTGCTCCACTG
* * * *
9672674 CAACTTTAGGGAGATAAGATTTGTAACTTGTAGCTGTAATCTGTTCCACTG
1 CAACTTCAGGGAGATAAGA--T-T--C-TGTATCTTTAATCTGCTCCACTG
* * * * * *
9672725 CAGCTTTA-GGAAATAAGATT-TGTAACTTCAATCTACTCCACTG
1 CAACTTCAGGGAGATAAGATTCTGTATCTTTAATCTGCTCCACTG
* * * * * ** *
9672768 CAAATTTAGGGAGATAATATT-TATAACTCCAA--T-CTCCACTA
1 CAACTTCAGGGAGATAAGATTCTGTATCTTTAATCTGCTCCACTG
**
9672809 CAACTTCAGGGAGATAAGATT-TGTGGCTTTAATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATTCTGTATCTTTAATCTGCTCCACTG
* *
9672853 CAACTTCAGGGAGATAAGATTCAT-TATCTTCAATCTGCTCCATTG
1 CAACTTCAGGGAGATAAGATTC-TGTATCTTTAATCTGCTCCACTG
* * * *
9672898 TAACTTTAGGGAGATAAGA-TCTGTAGT-TTTAATTTGCTCTACTG
1 CAACTTCAGGGAGATAAGATTCTGTA-TCTTTAATCTGCTCCACTG
*
9672942 CAGCTTCAGGGAGATAAGATTC
1 CAACTTCAGGGAGATAAGATTC
9672964 ACCACAGTGA
Statistics
Matches: 229, Mismatches: 45, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
41 31 0.14
42 1 0.00
43 26 0.11
44 96 0.42
45 37 0.16
46 1 0.00
47 2 0.01
48 1 0.00
50 9 0.04
51 25 0.11
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (45 bp):
CAACTTCAGGGAGATAAGATTCTGTATCTTTAATCTGCTCCACTG
Found at i:9679238 original size:34 final size:35
Alignment explanation
Indices: 9679194--9679260 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
9679184 CAGTAAAATA
*
9679194 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
9679228 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
9679261 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:9680282 original size:20 final size:20
Alignment explanation
Indices: 9680249--9680296 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
9680239 AAGGCCTTGG
*
9680249 TGGCTGGTTGTCACAGTCCT
1 TGGCTGGCTGTCACAGTCCT
*
9680269 TGGTTGGCTGTCACAGTCCT
1 TGGCTGGCTGTCACAGTCCT
9680289 TGGCTGGC
1 TGGCTGGC
9680297 ATACAGTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.08, C:0.25, G:0.33, T:0.33
Consensus pattern (20 bp):
TGGCTGGCTGTCACAGTCCT
Found at i:9684279 original size:12 final size:12
Alignment explanation
Indices: 9684262--9684295 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
9684252 GTCACATATT
9684262 TACATATCATGA
1 TACATATCATGA
9684274 TACATATCATGA
1 TACATATCATGA
9684286 TACATATCAT
1 TACATATCAT
9684296 TCTCTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (12 bp):
TACATATCATGA
Found at i:9684761 original size:49 final size:48
Alignment explanation
Indices: 9684708--9684823 Score: 128
Period size: 48 Copynumber: 2.4 Consensus size: 48
9684698 AGATCATGTA
* * * * * *
9684708 AGCCATTAACAGGAAGCTTATTCGGGCTATATAACGGGAAGCT-CATAAG
1 AGCCATTAACGGGAAGCTCATGCGAGCCA-ATAACAGGAAGCTCCA-AAG
*
9684757 AGCCA-TAATCGGGAAGCTCATGCGAGCCAATAACAGGTAGCTCCAAAG
1 AGCCATTAA-CGGGAAGCTCATGCGAGCCAATAACAGGAAGCTCCAAAG
9684805 AGCCATTAACGGGAAGCTC
1 AGCCATTAACGGGAAGCTC
9684824 CGGATAGCCA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
48 32 0.56
49 25 0.44
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (48 bp):
AGCCATTAACGGGAAGCTCATGCGAGCCAATAACAGGAAGCTCCAAAG
Found at i:9684772 original size:24 final size:24
Alignment explanation
Indices: 9684738--9684929 Score: 92
Period size: 24 Copynumber: 7.9 Consensus size: 24
9684728 TTCGGGCTAT
9684738 ATAA-CGGGAAGCTCATAAGAGCC
1 ATAATCGGGAAGCTCATAAGAGCC
**
9684761 ATAATCGGGAAGCTCATGCGAGCC
1 ATAATCGGGAAGCTCATAAGAGCC
* *
9684785 AATAA-CAGGTAGCTCCA-AAGAGCC
1 -ATAATCGGGAAGCT-CATAAGAGCC
*** *
9684809 ATTAA-CGGGAAGCTCCGGATAGCC
1 A-TAATCGGGAAGCTCATAAGAGCC
* * *
9684833 ATATATCGGGGAGTTCA-AGCGAGCC
1 ATA-ATCGGGAAGCTCATA-AGAGCC
* *
9684858 AT-ATCAGGAAGCTC-TGGAGAGCC
1 ATAATCGGGAAGCTCAT-AAGAGCC
** *
9684881 ATTAATTAGGAAGCTCACAAAGAGCC
1 A-TAATCGGGAAGCTCA-TAAGAGCC
* *
9684907 ATATATCGGGACGCTTATAAGAG
1 ATA-ATCGGGAAGCTCATAAGAG
9684930 TTGTGGCGTG
Statistics
Matches: 124, Mismatches: 30, Indels: 28
0.68 0.16 0.15
Matches are distributed among these distances:
23 23 0.19
24 47 0.38
25 38 0.31
26 16 0.13
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (24 bp):
ATAATCGGGAAGCTCATAAGAGCC
Found at i:9684871 original size:72 final size:72
Alignment explanation
Indices: 9684739--9684917 Score: 180
Period size: 72 Copynumber: 2.4 Consensus size: 72
9684729 TCGGGCTATA
* * *
9684739 TAACGGGAAGCTCATAAGAGCCATAATCGGGAAGCTCATGCGAGCCAATAACAGGTAGCTCCAAA
1 TAACGGGAAGCTCAGAAGAGCCATAATCGGGAAGCTCAAGCGAGCCAATAACAGGAAGCTCCAAA
9684804 GAGCCAT
66 GAGCCAT
* * * * * * ***
9684811 TAACGGGAAGCTCCGGATAGCCATATATCGGGGAGTTCAAGCGAGCC-ATATCAGGAAGCTCTGG
1 TAACGGGAAGCTCAGAAGAGCCATA-ATCGGGAAGCTCAAGCGAGCCAATAACAGGAAGCTCCAA
9684875 AGAGCCAT
65 AGAGCCAT
** *
9684883 TAATTAGGAAGCTCACAAAGAGCCATATATCGGGA
1 TAA-CGGGAAGCTCA-GAAGAGCCATA-ATCGGGA
9684918 CGCTTATAAG
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
72 44 0.52
73 26 0.31
74 15 0.18
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (72 bp):
TAACGGGAAGCTCAGAAGAGCCATAATCGGGAAGCTCAAGCGAGCCAATAACAGGAAGCTCCAAA
GAGCCAT
Found at i:9687644 original size:33 final size:32
Alignment explanation
Indices: 9687602--9687748 Score: 98
Period size: 33 Copynumber: 4.4 Consensus size: 32
9687592 ATAACCTAGT
*
9687602 TATGGTCTTATCATCAGAATGTCATAGCCCAGC
1 TATGGTCTTA-CATCAAAATGTCATAGCCCAGC
* * * *
9687635 TATGGTCTTACATATAAACACTGTCATGGTCCAAC
1 TATGGTCTTACAT-CAAA-A-TGTCATAGCCCAGC
* * * * * *
9687670 CATGGTCTTACGTTCATAGTG-CTATAACCCAGT
1 TATGGTCTTAC-ATCAAAATGTC-ATAGCCCAGC
* * *
9687703 TATGGTTTTATCATCAAAATTTCATGGCCCAGC
1 TATGGTCTTA-CATCAAAATGTCATAGCCCAGC
9687736 TATGGTCTTACAT
1 TATGGTCTTACAT
9687749 ATAAACACTG
Statistics
Matches: 82, Mismatches: 25, Indels: 15
0.67 0.20 0.12
Matches are distributed among these distances:
32 7 0.09
33 48 0.59
34 3 0.04
35 23 0.28
36 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (32 bp):
TATGGTCTTACATCAAAATGTCATAGCCCAGC
Found at i:9687764 original size:101 final size:101
Alignment explanation
Indices: 9687576--9687821 Score: 393
Period size: 101 Copynumber: 2.4 Consensus size: 101
9687566 AATTTATCCT
* * * *
9687576 TTACATTCGTAGTGCCATAACCTAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAGCTATGGT
*
9687641 CTTACATATAAACACTGTCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
* * * *
9687677 TTACGTTCATAGTGCTATAACCCAGTTATGGTTTTATCATCAAAATTTCATGGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAGCTATGGT
*
9687742 CTTACATATAAACACTGCCATGGTTCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
9687778 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCCATCAA
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTAT-CATCAA
9687822 TTCATCCTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 126 0.95
102 6 0.05
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAGCTATGGT
CTTACATATAAACACTGCCATGGTCCAACCATGGTC
Found at i:9689807 original size:19 final size:19
Alignment explanation
Indices: 9689769--9689821 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
9689759 GGGTCTTTTT
9689769 ATGAAATTTAATGCATATG-
1 ATGAAA-TTAATGCATATGA
9689788 ATGAAATGTAATGC-TGATGA
1 ATGAAAT-TAATGCAT-ATGA
*
9689808 ATGGAATTAATGCA
1 ATGAAATTAATGCA
9689822 AAAAGAGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.07
19 21 0.72
20 6 0.21
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (19 bp):
ATGAAATTAATGCATATGA
Found at i:9691594 original size:21 final size:21
Alignment explanation
Indices: 9691568--9691613 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
9691558 AGATGTTGGA
9691568 GGCTCTAAAATAAGCTTTGTC
1 GGCTCTAAAATAAGCTTTGTC
*
9691589 GGCTCTAGAATAAGCTTTGTC
1 GGCTCTAAAATAAGCTTTGTC
9691610 GGCT
1 GGCT
9691614 TGGATCCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (21 bp):
GGCTCTAAAATAAGCTTTGTC
Found at i:9696697 original size:20 final size:19
Alignment explanation
Indices: 9696673--9696755 Score: 89
Period size: 19 Copynumber: 4.3 Consensus size: 19
9696663 AAAAAATATA
9696673 AAAAATTTATTAAATTTTAAT
1 AAAAA-TTATTAAATTTT-AT
9696694 AAAAA-TATTGAAATTTTAT
1 AAAAATTATT-AAATTTTAT
*
9696713 AAAAATTA-TAATTTTTTAT
1 AAAAATTATTAA-ATTTTAT
* *
9696732 AAAAATTGTAAAATTTTAT
1 AAAAATTATTAAATTTTAT
9696751 AAAAA
1 AAAAA
9696756 ATCATAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 36 0.67
20 11 0.20
21 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAATTATTAAATTTTAT
Found at i:9696746 original size:38 final size:40
Alignment explanation
Indices: 9696673--9696755 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 40
9696663 AAAAAATATA
*
9696673 AAAAATTTATTAAATTTTAATAAAAATATTGAAATTTTAT
1 AAAAATTTATTAAATTTTAATAAAAATATTAAAATTTTAT
* *
9696713 AAAAA-TTA-TAATTTTTTATAAAAAT-TGTAAAATTTTAT
1 AAAAATTTATTAAATTTTAATAAAAATAT-TAAAATTTTAT
9696751 AAAAA
1 AAAAA
9696756 ATCATAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 1 0.03
38 30 0.77
39 3 0.08
40 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (40 bp):
AAAAATTTATTAAATTTTAATAAAAATATTAAAATTTTAT
Found at i:9696763 original size:20 final size:20
Alignment explanation
Indices: 9696669--9696774 Score: 85
Period size: 19 Copynumber: 5.3 Consensus size: 20
9696659 CAATAAAAAA
*
9696669 TATAAAAAATTTATTAAATTT
1 TATAAAAAA-TTATAAAATTT
*
9696690 TA-ATAAAAA-TATTGAAATTT
1 TATA-AAAAATTA-TAAAATTT
**
9696710 TAT-AAAAATTATAATTTTT
1 TATAAAAAATTATAAAATTT
*
9696729 TAT-AAAAATTGTAAAATTT
1 TATAAAAAATTATAAAATTT
* **
9696748 TATAAAAAATCATAAAAAAT
1 TATAAAAAATTATAAAATTT
9696768 TATAAAA
1 TATAAAA
9696775 TGCATCAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
19 31 0.45
20 31 0.45
21 7 0.10
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
TATAAAAAATTATAAAATTT
Found at i:9697076 original size:20 final size:21
Alignment explanation
Indices: 9697051--9697098 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
9697041 ATATATTTTG
*
9697051 TATTTTTTTA-CGAT-TTTAAA
1 TATTTTTTTATCAATATTT-AA
9697071 TATTTTTTTATCAATATTTAA
1 TATTTTTTTATCAATATTTAA
9697092 TATTTTT
1 TATTTTT
9697099 CTATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 12 0.48
22 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTTTTTTATCAATATTTAA
Found at i:9697113 original size:18 final size:18
Alignment explanation
Indices: 9697092--9697126 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9697082 CAATATTTAA
*
9697092 TATTTTTCTATTTTTATT
1 TATTTTTATATTTTTATT
*
9697110 TATTTTTATTTTTTTAT
1 TATTTTTATATTTTTAT
9697127 CGTTTTTTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
TATTTTTATATTTTTATT
Found at i:9708760 original size:30 final size:30
Alignment explanation
Indices: 9708726--9708792 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
9708716 AATTAAAAAT
*
9708726 CAAAATCCTCCAAAAAAAAAATCCCTAAAC
1 CAAAATACTCCAAAAAAAAAATCCCTAAAC
* *
9708756 CAAAATACTCCCAAAATAAAATCCCTAAAC
1 CAAAATACTCCAAAAAAAAAATCCCTAAAC
*
9708786 CTAAATA
1 CAAAATA
9708793 GTATTAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.16
Consensus pattern (30 bp):
CAAAATACTCCAAAAAAAAAATCCCTAAAC
Found at i:9722026 original size:22 final size:22
Alignment explanation
Indices: 9722001--9722048 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
9721991 CCTAACTGAA
9722001 CTTGAAAGAAGAGCTAGAGAGC
1 CTTGAAAGAAGAGCTAGAGAGC
9722023 CTTGAAAGAAGAGCTAGAGAGC
1 CTTGAAAGAAGAGCTAGAGAGC
9722045 CTTG
1 CTTG
9722049 GTCGCTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.17
Consensus pattern (22 bp):
CTTGAAAGAAGAGCTAGAGAGC
Found at i:9722259 original size:4 final size:4
Alignment explanation
Indices: 9722250--9722278 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
9722240 ACTCCTTCTG
9722250 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
9722279 AAAGCTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:9722610 original size:226 final size:226
Alignment explanation
Indices: 9722216--9722667 Score: 759
Period size: 226 Copynumber: 2.0 Consensus size: 226
9722206 TGGGCTTTCA
* * * *
9722216 AGACTTGCAAGCCTTTAATGTAACACTCCTTCTGATACATACATACATACATACATACATACAAA
1 AGACTTGCAAGCCTTTAATGCAACACTCCTTCTCAAACATACATACACACATACATACATACAAA
*
9722281 AGCTATTAAATTTTATTGAAGCAAACAAAAAGGTTACAAACTTTAGTGAGAGAACCAAGGAACTA
66 AGCTATTAAATTTTATTGAAGCAAACAAAAAGGTTACAAACTTAAGTGAGAGAACCAAGGAACTA
9722346 CATGCACTAATAAAACAACTTTGATTAAGCCTAAATATGAAGTAATAAACCCCAAGGAGAATAAT
131 CATGCACTAATAAAACAACTTTGATTAAGCCTAAATATGAAGTAATAAACCCCAAGGAGAATAAT
9722411 CTATTTTGGCAAATCAATTTGGATTAAACCC
196 CTATTTTGGCAAATCAATTTGGATTAAACCC
**
9722442 AGACTTGCAAGCCTTTAATGCAACACTCCTTC-CAAAGCA-AGCATGGACACATACATACATACA
1 AGACTTGCAAGCCTTTAATGCAACACTCCTTCTCAAA-CATA-CATACACACATACATACATACA
*
9722505 AAAGCTATTAAATTTTATTGAAGCAAACAATAAGGTTACAAACTTAAGTG-GTAGAACCAAGGAA
64 AAAGCTATTAAATTTTATTGAAGCAAACAAAAAGGTTACAAACTTAAGTGAG-AGAACCAAGGAA
*
9722569 CTACATGCACTAATAAAACAAC-TTGTATTAAGCCTAAATATGAAGTAATAAACCCTAAGGAGAA
128 CTACATGCACTAATAAAACAACTTTG-ATTAAGCCTAAATATGAAGTAATAAACCCCAAGGAGAA
9722633 TAATCTATTTTGGCAAATCAATTTGGATTAAACCC
192 TAATCTATTTTGGCAAATCAATTTGGATTAAACCC
9722668 GGATATGAAC
Statistics
Matches: 213, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
225 7 0.03
226 206 0.97
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (226 bp):
AGACTTGCAAGCCTTTAATGCAACACTCCTTCTCAAACATACATACACACATACATACATACAAA
AGCTATTAAATTTTATTGAAGCAAACAAAAAGGTTACAAACTTAAGTGAGAGAACCAAGGAACTA
CATGCACTAATAAAACAACTTTGATTAAGCCTAAATATGAAGTAATAAACCCCAAGGAGAATAAT
CTATTTTGGCAAATCAATTTGGATTAAACCC
Found at i:9725537 original size:31 final size:31
Alignment explanation
Indices: 9725499--9725569 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
9725489 ATTAAGAAGT
* * *
9725499 GTATTTTAAGTGGTGTTAAAAAATAATAGGG
1 GTATTTTAAGTAGTATTAAAAAACAATAGGG
* *
9725530 GTATTTTAGGTAGTATTAAAAACCAATAGGG
1 GTATTTTAAGTAGTATTAAAAAACAATAGGG
* *
9725561 ATAGTTTAA
1 GTATTTTAA
9725570 ATATTAAAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (31 bp):
GTATTTTAAGTAGTATTAAAAAACAATAGGG
Found at i:9729277 original size:26 final size:26
Alignment explanation
Indices: 9729242--9729300 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
9729232 AAGCTTCGGG
*
9729242 GAGCCATTAATTAGGAAGCTCATAAA
1 GAGCCATTAATCAGGAAGCTCATAAA
* * *
9729268 GAGCCTTTAATCGGGAAGCTCATGAA
1 GAGCCATTAATCAGGAAGCTCATAAA
9729294 GAGCCAT
1 GAGCCAT
9729301 ATATCGGGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCATAAA
Found at i:9729306 original size:26 final size:25
Alignment explanation
Indices: 9729176--9729322 Score: 76
Period size: 26 Copynumber: 6.0 Consensus size: 25
9729166 ATTCGGGCTG
*
9729176 TATAAT-GGAAAGCTCATAAGAGCC
1 TATAATCGGGAAGCTCATAAGAGCC
** *
9729200 -ATAATC-GGAGAGCTCATGCGAGTC
1 TATAATCGGGA-AGCTCATAAGAGCC
***
9729224 -AT-ATCGGGAAGCTTC-GGGGAGCC
1 TATAATCGGGAAGC-TCATAAGAGCC
**
9729247 -ATTAATTAGGAAGCTCATAAAGAGCC
1 TA-TAATCGGGAAGCTCAT-AAGAGCC
*
9729273 TTTAATCGGGAAGCTCATGAAGAGCC
1 TATAATCGGGAAGCTCAT-AAGAGCC
* *
9729299 -ATATATCGGGATGCTTATAAGAGC
1 TATA-ATCGGGAAGCTCATAAGAGC
9729323 TGTGGTGTAT
Statistics
Matches: 94, Mismatches: 19, Indels: 19
0.71 0.14 0.14
Matches are distributed among these distances:
23 19 0.20
24 21 0.22
25 16 0.17
26 38 0.40
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (25 bp):
TATAATCGGGAAGCTCATAAGAGCC
Found at i:9729814 original size:5 final size:5
Alignment explanation
Indices: 9729799--9729830 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
9729789 AATTTAATAT
9729799 AATTC ATATTC AATTC AATTC AATTC AATTC A
1 AATTC A-ATTC AATTC AATTC AATTC AATTC A
9729831 CATCTTAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTC
Found at i:9740961 original size:21 final size:21
Alignment explanation
Indices: 9740928--9740969 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9740918 GAGTAGTGGG
*
9740928 AGCGGTAGCGGTAGTGAAAGT
1 AGCGGAAGCGGTAGTGAAAGT
* *
9740949 AGCGGAAGTGGTAGTGGAAGT
1 AGCGGAAGCGGTAGTGAAAGT
9740970 GGAAGTGAAA
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:0.29, C:0.07, G:0.45, T:0.19
Consensus pattern (21 bp):
AGCGGAAGCGGTAGTGAAAGT
Found at i:9740970 original size:27 final size:27
Alignment explanation
Indices: 9740905--9740975 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
9740895 TCGAGTAGTA
* * *
9740905 GTAGTGGAAGTGAGAGTAGTGGGAGCG
1 GTAGTGGAAGTGAAAGTAGCGGAAGCG
* * *
9740932 GTAGCGGTAGTGAAAGTAGCGGAAGTG
1 GTAGTGGAAGTGAAAGTAGCGGAAGCG
*
9740959 GTAGTGGAAGTGGAAGT
1 GTAGTGGAAGTGAAAGT
9740976 GAAAGCAGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.28, C:0.04, G:0.48, T:0.20
Consensus pattern (27 bp):
GTAGTGGAAGTGAAAGTAGCGGAAGCG
Found at i:9746870 original size:17 final size:18
Alignment explanation
Indices: 9746836--9746870 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9746826 GTTAGAGCCT
*
9746836 ATATGTTGTGTCTTTATG
1 ATATGTTCTGTCTTTATG
9746854 ATATGTTCTGT-TTTATG
1 ATATGTTCTGTCTTTATG
9746871 TCAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.17, C:0.06, G:0.20, T:0.57
Consensus pattern (18 bp):
ATATGTTCTGTCTTTATG
Found at i:9750746 original size:2 final size:2
Alignment explanation
Indices: 9750672--9750733 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
9750662 AAAAAAGGAA
* ** * * *
9750672 AT AT A- AT AT AT AT AT AT AT AT AT AT AA AT AT GC AC GT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9750713 A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
9750734 GAATAGGTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9750815 original size:3 final size:3
Alignment explanation
Indices: 9750800--9750874 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
9750790 AATAGTAACG
* ** * *
9750800 ATA ATA GTA ATA ATA ATA ACC ATA ATA ATA ATA GTA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
9750847 ATA TTTA A-A ATA ATA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
9750875 CATAAAATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 52 0.91
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9750931 original size:29 final size:29
Alignment explanation
Indices: 9750886--9750973 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
9750876 ATAAAATTGC
9750886 TAAAATAT-GGGCTAAATCGAAATAAAACA
1 TAAAATATAGGGCTAAATCGAAATAAAA-A
* * *
9750915 -AAAATATAGGGCGAAATTGAAAGAAAAA
1 TAAAATATAGGGCTAAATCGAAATAAAAA
* *
9750943 TAAAATAAAAGGGACTAAATCAAAATAAAAA
1 TAAAAT-ATAGGG-CTAAATCGAAATAAAAA
9750974 AAGAAACTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.17
29 21 0.45
30 5 0.11
31 13 0.28
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (29 bp):
TAAAATATAGGGCTAAATCGAAATAAAAA
Found at i:9759270 original size:21 final size:21
Alignment explanation
Indices: 9759246--9759311 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
9759236 ATATAAGTGC
* * *
9759246 TAAATGGAAACCCGTAAGGGT
1 TAAACGGAAACCCATAAGAGT
* * *
9759267 TAAACGGAAGCTCATAAGAGC
1 TAAACGGAAACCCATAAGAGT
9759288 TAAACGGAAACCCATAAGAGT
1 TAAACGGAAACCCATAAGAGT
9759309 TAA
1 TAA
9759312 TCTAAAGCTC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.17
Consensus pattern (21 bp):
TAAACGGAAACCCATAAGAGT
Found at i:9759297 original size:42 final size:42
Alignment explanation
Indices: 9759238--9759366 Score: 141
Period size: 42 Copynumber: 3.1 Consensus size: 42
9759228 AAAAAAGCAT
* * * *
9759238 ATAAGTGCTAAATGGAAACCCGTAAGGGTTAAACGGAAGCTC
1 ATAAGAGCTAAACGGAAACCCATAAGGGTTAAACGAAAGCTC
* * *
9759280 ATAAGAGCTAAACGGAAACCCATAAGAGTTAATCTAAAGCTC
1 ATAAGAGCTAAACGGAAACCCATAAGGGTTAAACGAAAGCTC
* ** * * *
9759322 AGAAGAGCTAAACTAAAACCCATTAGGGTTAAACTAAAACTC
1 ATAAGAGCTAAACGGAAACCCATAAGGGTTAAACGAAAGCTC
9759364 ATA
1 ATA
9759367 TGAGTTAACT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (42 bp):
ATAAGAGCTAAACGGAAACCCATAAGGGTTAAACGAAAGCTC
Found at i:9759327 original size:21 final size:21
Alignment explanation
Indices: 9759277--9759397 Score: 109
Period size: 21 Copynumber: 5.8 Consensus size: 21
9759267 TAAACGGAAG
* **
9759277 CTCATAAGAGCTAAACGGAAA
1 CTCATAAGAGTTAAACTAAAA
* * *
9759298 CCCATAAGAGTTAATCTAAAG
1 CTCATAAGAGTTAAACTAAAA
* *
9759319 CTCAGAAGAGCTAAACTAAAA
1 CTCATAAGAGTTAAACTAAAA
* * *
9759340 CCCATTAGGGTTAAACTAAAA
1 CTCATAAGAGTTAAACTAAAA
* *
9759361 CTCATATGAGTT-AACTAAAG
1 CTCATAAGAGTTAAACTAAAA
*
9759381 CTCATAAGAGCTAAACT
1 CTCATAAGAGTTAAACT
9759398 GAAAGCAAAC
Statistics
Matches: 76, Mismatches: 23, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
20 17 0.22
21 59 0.78
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (21 bp):
CTCATAAGAGTTAAACTAAAA
Found at i:9761744 original size:5 final size:5
Alignment explanation
Indices: 9761734--9761762 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9761724 TATACTTAAA
9761734 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
9761763 AATAAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:9764040 original size:2 final size:2
Alignment explanation
Indices: 9764033--9764058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9764023 TTATGAATTC
9764033 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9764059 TAAGCAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9767367 original size:2 final size:2
Alignment explanation
Indices: 9767360--9767386 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9767350 TATCCAATGT
9767360 TA 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 TA T
9767387 TCCCATTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9768483 original size:21 final size:21
Alignment explanation
Indices: 9768459--9768502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9768449 TAAACCGATT
9768459 TTTCTATT-TTATTTTCAACTC
1 TTTCTATTATTATTTTCAA-TC
*
9768480 TTTCTATTATTTTTTTCAATC
1 TTTCTATTATTATTTTCAATC
9768501 TT
1 TT
9768503 GTGAACAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTCTATTATTATTTTCAATC
Found at i:9770015 original size:18 final size:18
Alignment explanation
Indices: 9769992--9770080 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
9769982 CGTTTACGGT
*
9769992 ACTATTCACGTATACAAC
1 ACTATTCACGTATACAGC
*
9770010 ACTATTCACGTATACAGT
1 ACTATTCACGTATACAGC
*
9770028 ACTATTCACGTATACGGC
1 ACTATTCACGTATACAGC
* * *
9770046 ACTATTCACATATACGGT
1 ACTATTCACGTATACAGC
*
9770064 ACTGTTCACGTATACAG
1 ACTATTCACGTATACAG
9770081 TAGTTGGGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (18 bp):
ACTATTCACGTATACAGC
Found at i:9770037 original size:36 final size:36
Alignment explanation
Indices: 9769990--9770079 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 36
9769980 ACCGTTTACG
*
9769990 GTACTATTCACGTATACAACACTATTCACGTATACA
1 GTACTATTCACGTATACAACACTATTCACATATACA
** *
9770026 GTACTATTCACGTATACGGCACTATTCACATATACG
1 GTACTATTCACGTATACAACACTATTCACATATACA
*
9770062 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
9770080 GTAGTTGGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.31
Consensus pattern (36 bp):
GTACTATTCACGTATACAACACTATTCACATATACA
Found at i:9775240 original size:17 final size:17
Alignment explanation
Indices: 9775218--9775254 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
9775208 ATACATGACC
9775218 TTAATGACATGTTTAAG
1 TTAATGACATGTTTAAG
9775235 TTAATGACATGTTTAAG
1 TTAATGACATGTTTAAG
9775252 TTA
1 TTA
9775255 TGTTTGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.43
Consensus pattern (17 bp):
TTAATGACATGTTTAAG
Found at i:9778305 original size:30 final size:31
Alignment explanation
Indices: 9778244--9778306 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
9778234 TACAAAATGA
9778244 TCATTGAACTATTCAAAAGTTTTCATTTAAG
1 TCATTGAACTATTCAAAAGTTTTCATTTAAG
*
9778275 TCATTGAACTATTCAAAAGTTTT-TTTTAAG
1 TCATTGAACTATTCAAAAGTTTTCATTTAAG
9778305 TC
1 TC
9778307 CAATAACAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (31 bp):
TCATTGAACTATTCAAAAGTTTTCATTTAAG
Found at i:9782237 original size:27 final size:28
Alignment explanation
Indices: 9782194--9782254 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
9782184 TAATAAATTT
*
9782194 AATTT-TAATTCT-AAAAAAATCACGAC
1 AATTTATAATTCTAAAAAAAATCACAAC
* *
9782220 AATTTATAATTTTTAAAAAAATCACAAC
1 AATTTATAATTCTAAAAAAAATCACAAC
9782248 AATTTAT
1 AATTTAT
9782255 TCTTTTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 5 0.16
27 6 0.19
28 20 0.65
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (28 bp):
AATTTATAATTCTAAAAAAAATCACAAC
Found at i:9787521 original size:3 final size:3
Alignment explanation
Indices: 9787513--9787610 Score: 74
Period size: 3 Copynumber: 30.7 Consensus size: 3
9787503 TTTAGTCTCG
* * *
9787513 TTA TTA TTA TTA TTA TTA TTA TTA -AA CTAA GTA GTT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA
*
9787558 TTA TTA TTA TTGCA TTTA TTA TTA TTA CTTA CCTTA TTA TTA TCA TTA
1 TTA TTA TTA TT--A -TTA TTA TTA TTA -TTA --TTA TTA TTA TTA TTA
9787606 TTA TT
1 TTA TT
9787611 TACCCATTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
2 3 0.04
3 63 0.79
4 7 0.09
5 5 0.06
6 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:9804593 original size:7 final size:7
Alignment explanation
Indices: 9804548--9804572 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9804538 TTCAGATTTG
9804548 AAAAGAA
1 AAAAGAA
9804555 AAAAGAA
1 AAAAGAA
9804562 AAAAGAA
1 AAAAGAA
9804569 AAAA
1 AAAA
9804573 AATCAAAGTC
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:9804607 original size:30 final size:29
Alignment explanation
Indices: 9804555--9804631 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
9804545 TTGAAAAGAA
9804555 AAAAG-AAAAAAGAAAAAAAATCAAAGTC
1 AAAAGAAAAAAAGAAAAAAAATCAAAGTC
**
9804583 AAAAGAAAAAAAGAGAAATCAATCAAAGTC
1 AAAAGAAAAAAAGA-AAAAAAATCAAAGTC
* *
9804613 AAAATAAAAATATGAAAAA
1 AAAAGAAAAA-AAGAAAAA
9804632 GAGAAAAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.12
29 8 0.20
30 25 0.61
31 3 0.07
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.10
Consensus pattern (29 bp):
AAAAGAAAAAAAGAAAAAAAATCAAAGTC
Found at i:9804965 original size:13 final size:13
Alignment explanation
Indices: 9804941--9804974 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9804931 AGGATTTCAA
9804941 AAAAAATG-AAAT
1 AAAAAATGAAAAT
*
9804953 TAAAAATGAAAAT
1 AAAAAATGAAAAT
9804966 AAAAAATGA
1 AAAAAATGA
9804975 CGAAAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (13 bp):
AAAAAATGAAAAT
Found at i:9806358 original size:87 final size:87
Alignment explanation
Indices: 9806207--9806469 Score: 427
Period size: 87 Copynumber: 3.0 Consensus size: 87
9806197 GTGAAAATAA
*
9806207 AAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
9806272 ACGTTAACAGCGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
* *
9806294 AAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTTCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
9806359 GCATTAACAGCGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
** *
9806381 AAAACAAAGCCTTGCCTCCATTAGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCCTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* * *
9806446 GCGTCAACAGTGAAACAGATCG
66 GCGTTAACAGCGAAGCAGATCG
9806468 AA
1 AA
9806470 GATTACAAGT
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 162 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
GCGTTAACAGCGAAGCAGATCG
Found at i:9806680 original size:9 final size:9
Alignment explanation
Indices: 9806666--9806696 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9806656 GTTAAACGAA
9806666 TCGAGTTAT
1 TCGAGTTAT
*
9806675 TCGAGTTAA
1 TCGAGTTAT
9806684 TCGAGTTAT
1 TCGAGTTAT
9806693 TCGA
1 TCGA
9806697 ATCAACTCAA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:9806768 original size:9 final size:9
Alignment explanation
Indices: 9806751--9806787 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
9806741 TGAGTTTTCA
9806751 AATTCGAAT
1 AATTCGAAT
*
9806760 AACTCGAAT
1 AATTCGAAT
9806769 AATTCGAAT
1 AATTCGAAT
9806778 AATTCGAAT
1 AATTCGAAT
9806787 A
1 A
9806788 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:9820219 original size:2 final size:2
Alignment explanation
Indices: 9820212--9820242 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9820202 AAATCATACA
9820212 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9820243 ATTGACCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9824248 original size:21 final size:20
Alignment explanation
Indices: 9824219--9824259 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9824209 ATGAATTAAG
9824219 TTCAAATAAGAATTTATATTT
1 TTCAAATAA-AATTTATATTT
* *
9824240 TTCATATAATATTTATATTT
1 TTCAAATAAAATTTATATTT
9824260 GGTAAAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
TTCAAATAAAATTTATATTT
Found at i:9826033 original size:15 final size:16
Alignment explanation
Indices: 9826013--9826043 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9826003 TTAAAATATT
9826013 CATATAT-TATAAAAA
1 CATATATCTATAAAAA
9826028 CATATATCTATAAAAA
1 CATATATCTATAAAAA
9826044 AATGCATGGG
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:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (16 bp):
CATATATCTATAAAAA
Found at i:9826877 original size:11 final size:11
Alignment explanation
Indices: 9826861--9826892 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9826851 TTATTTATTT
9826861 ATAAAAAGAAA
1 ATAAAAAGAAA
9826872 ATAAAAAGAAA
1 ATAAAAAGAAA
9826883 A-AAAAAGAAA
1 ATAAAAAGAAA
9826893 TAACGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (11 bp):
ATAAAAAGAAA
Found at i:9827617 original size:50 final size:50
Alignment explanation
Indices: 9827559--9828104 Score: 375
Period size: 50 Copynumber: 10.9 Consensus size: 50
9827549 CACTCCACTA
9827559 CAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* * * * * * * **
9827609 CAATGTCAGGAAAACTAA-ATCCACCGTCGTAGTTTCAATCTATTCCATTG
1 CAATGTCAGG-GAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* *
9827659 CACTG-CTAGGAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
1 CAATGTC-AGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* *** * * * * ** *
9827709 CAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCACTG
1 CAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* * * *
9827759 CACTG-CTGAGGAAGTAAAATCCGCCGTTGTGGCTTTAATCTTTTTAATTG
1 CAATGTCAG-GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* *** * * * * ** *
9827809 CAATATCAGGGAAACCAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTG
1 CAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* * * *
9827859 CACTG-CTGAGGAAGTAAGATCCGCTGTTGTGGCTTTAATCTTTTTAATTG
1 CAATGTCAG-GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* *** * * ** *
9827909 CAATATCAGGGAAACCAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTG
1 CAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* * ** *
9827959 CACTG-CTGATCAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTTAATTG
1 CAATGTCAG-GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* *** * * * * ** *
9828009 CAATATCAGGGAAACCAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTG
1 CAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
* * *
9828059 CACTG-CTGAGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTA
1 CAATGTCAG-GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
9828105 CTTTTCAACC
Statistics
Matches: 353, Mismatches: 132, Indels: 22
0.70 0.26 0.04
Matches are distributed among these distances:
49 15 0.04
50 326 0.92
51 12 0.03
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (50 bp):
CAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTG
Found at i:9827718 original size:100 final size:100
Alignment explanation
Indices: 9827568--9828104 Score: 878
Period size: 100 Copynumber: 5.4 Consensus size: 100
9827558 ACAATGTCAG
* * * * *
9827568 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGAAAACTAAATCCAC
1 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGC
* * *
9827633 CGTCGTAGTTTCAATCTATTCCATTGCACTGCT-A
66 CGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
*
9827667 GGAAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCA
1 GG-AAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCG
9827732 CCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
65 CCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
* * *
9827768 GGAAGTAAAATCCGCCGTTGTGGCTTTAATCTTTTTAATTGCAATATCAGGGAAACCAGATTCGC
1 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGC
9827833 CGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
66 CGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
* *
9827868 GGAAGTAAGATCCGCTGTTGTGGCTTTAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGC
1 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGC
*
9827933 CGTTGTAGCTTCAATCTGTTCCACTGCACTGCTGA
66 CGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
** * *
9827968 TCAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTTAATTGCAATATCAGGGAAACCAGATTCGC
1 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGC
9828033 CGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
66 CGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
*
9828068 GGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTA
1 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
9828105 CTTTTCAACC
Statistics
Matches: 410, Mismatches: 26, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
99 2 0.00
100 405 0.99
101 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (100 bp):
GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGC
CGTCGTAGCTTCAATCTGTTCCACTGCACTGCTGA
Found at i:9831769 original size:17 final size:18
Alignment explanation
Indices: 9831741--9831791 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
9831731 TTATTTATTT
* *
9831741 AGAAAAACAAAATAAA-A
1 AGAAAAAAAAAAGAAATA
9831758 AGAAAAAAAAAAGAAATA
1 AGAAAAAAAAAAGAAATA
*
9831776 ACGAAAAGAAAAAGAA
1 A-GAAAAAAAAAAGAA
9831792 CAAAAATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.48
18 2 0.07
19 13 0.45
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (18 bp):
AGAAAAAAAAAAGAAATA
Found at i:9831788 original size:30 final size:28
Alignment explanation
Indices: 9831741--9831797 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
9831731 TTATTTATTT
*
9831741 AGAAAAACAAAATAAAAAGAAAAAAAAA
1 AGAAAAACAAAAGAAAAAGAAAAAAAAA
*
9831769 AGAAATAACGAAAAGAAAAAGAACAAAAA
1 AGAAA-AAC-AAAAGAAAAAGAAAAAAAA
9831798 TCCAATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 3 0.12
30 17 0.68
ACGTcount: A:0.81, C:0.05, G:0.11, T:0.04
Consensus pattern (28 bp):
AGAAAAACAAAAGAAAAAGAAAAAAAAA
Found at i:9839839 original size:21 final size:21
Alignment explanation
Indices: 9839797--9839839 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
9839787 ACATGTTAAT
* *
9839797 TTTATCTTATTACAGAGTATA
1 TTTATCATATTACAGAATATA
9839818 TTTATCATATTACA-AATCATA
1 TTTATCATATTACAGAAT-ATA
9839839 T
1 T
9839840 ATAGCATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTATCATATTACAGAATATA
Found at i:9841020 original size:16 final size:17
Alignment explanation
Indices: 9840993--9841025 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9840983 TTAAGTTTTC
*
9840993 AATTTAAATTTAGAGTT
1 AATTTAAATTTAAAGTT
9841010 AATTT-AATTTAAAGTT
1 AATTTAAATTTAAAGTT
9841026 TTCGATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTAAAGTT
Found at i:9844624 original size:16 final size:17
Alignment explanation
Indices: 9844603--9844637 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
9844593 TAAAAGTGAA
9844603 AAAAAAATACTTT-TTT
1 AAAAAAATACTTTATTT
*
9844619 AAAAAAATATTTTATTT
1 AAAAAAATACTTTATTT
9844636 AA
1 AA
9844638 TAATGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAAAATACTTTATTT
Found at i:9846827 original size:25 final size:25
Alignment explanation
Indices: 9846782--9846846 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
9846772 GTCATTAGGG
*
9846782 TTACCGATTC-CAGCTATTATGAGC
1 TTACCGATACTCAGCTATTATGAGC
9846806 TTACCGATACTCAGCTCA-TATGAGC
1 TTACCGATACTCAGCT-ATTATGAGC
*
9846831 TTACCGTTACTCAGCT
1 TTACCGATACTCAGCT
9846847 TGGAGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 9 0.24
25 27 0.73
26 1 0.03
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (25 bp):
TTACCGATACTCAGCTATTATGAGC
Found at i:9850083 original size:306 final size:306
Alignment explanation
Indices: 9849530--9850145 Score: 1205
Period size: 306 Copynumber: 2.0 Consensus size: 306
9849520 CTATGGTTTG
*
9849530 TTGTTAGAGAAGGGCAACCTTATGGTCGTAGAAATAAAGACGACAATGCTTTTAGTTCGCAGGGA
1 TTGTTAGAGAAGGGCAACATTATGGTCGTAGAAATAAAGACGACAATGCTTTTAGTTCGCAGGGA
*
9849595 TTAGATAAAGGAAAAGGCAAGCAGGTCCCAATAGGGGTGATTAATGTAACAATTGACACTAATGA
66 TTAGATAAAGGAAAAGGCAAGCAGGTCCCAATAGGGATGATTAATGTAACAATTGACACTAATGA
*
9849660 AGAATGTGCTAGATCCAATACTAAGAGGAAAGCTTATTTGCACAGCATGATGTCCATGATTACAT
131 AGAATGTGCTAGATCCAATACTAAGAGGAAAGCTTATCTGCACAGCATGATGTCCATGATTACAT
9849725 CAGCAAAGAAATCTCGATAGGTACAACTGTAGAAAGTTGGATTCTTAAATCATGATGAAACAAAT
196 CAGCAAAGAAATCTCGATAGGTACAACTGTAGAAAGTTGGATTCTTAAATCATGATGAAACAAAT
9849790 TTGAATGATCCAGATGGTAATTATTCATTAGTGGTTTCATCGATGA
261 TTGAATGATCCAGATGGTAATTATTCATTAGTGGTTTCATCGATGA
9849836 TTGTTAGAGAAGGGCAACATTATGGTCGTAGAAATAAAGACGACAATGCTTTTAGTTCGCAGGGA
1 TTGTTAGAGAAGGGCAACATTATGGTCGTAGAAATAAAGACGACAATGCTTTTAGTTCGCAGGGA
9849901 TTAGATAAAGGAAAAGGCAAGCAGGTCCCAATAGGGATGATTAATGTAACAATTGACACTAATGA
66 TTAGATAAAGGAAAAGGCAAGCAGGTCCCAATAGGGATGATTAATGTAACAATTGACACTAATGA
9849966 AGAATGTGCTAGATCCAATACTAAGAGGAAAGCTTATCTGCACAGCATGATGTCCATGATTACAT
131 AGAATGTGCTAGATCCAATACTAAGAGGAAAGCTTATCTGCACAGCATGATGTCCATGATTACAT
9850031 CAGCAAAGAAATCTCGATAGGTACAACTGTAGAAAGTTGGATTCTTAAATCATGATGAAACAAAT
196 CAGCAAAGAAATCTCGATAGGTACAACTGTAGAAAGTTGGATTCTTAAATCATGATGAAACAAAT
9850096 TTGAATGATCCAGATGGTAATTATTCATTAGTGGTTTCATCGATGA
261 TTGAATGATCCAGATGGTAATTATTCATTAGTGGTTTCATCGATGA
9850142 TTGT
1 TTGT
9850146 GGGGTTTGAG
Statistics
Matches: 307, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
306 307 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (306 bp):
TTGTTAGAGAAGGGCAACATTATGGTCGTAGAAATAAAGACGACAATGCTTTTAGTTCGCAGGGA
TTAGATAAAGGAAAAGGCAAGCAGGTCCCAATAGGGATGATTAATGTAACAATTGACACTAATGA
AGAATGTGCTAGATCCAATACTAAGAGGAAAGCTTATCTGCACAGCATGATGTCCATGATTACAT
CAGCAAAGAAATCTCGATAGGTACAACTGTAGAAAGTTGGATTCTTAAATCATGATGAAACAAAT
TTGAATGATCCAGATGGTAATTATTCATTAGTGGTTTCATCGATGA
Found at i:9855390 original size:5 final size:5
Alignment explanation
Indices: 9855319--9855402 Score: 62
Period size: 5 Copynumber: 16.8 Consensus size: 5
9855309 ACAAACCTAC
* * * * * *
9855319 CAGAA CAGGA CAGAG CAGAA CATG-A CAGAA TAGAA CAGAG CAGAG TAGAA
1 CAGAA CAGAA CAGAA CAGAA CA-GAA CAGAA CAGAA CAGAA CAGAA CAGAA
* * * *
9855369 TAGAA CAGAG CAAAA CAGAA CAGAA CATAA CAGA
1 CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGA
9855403 GTAGAGCAAA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
4 1 0.02
5 59 0.97
6 1 0.02
ACGTcount: A:0.54, C:0.17, G:0.24, T:0.06
Consensus pattern (5 bp):
CAGAA
Found at i:9855400 original size:15 final size:15
Alignment explanation
Indices: 9855370--9855422 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
9855360 AGAGTAGAAT
*
9855370 AGAACAGAGCAAAAC
1 AGAACAGAACAAAAC
*
9855385 AGAACAGAACATAAC
1 AGAACAGAACAAAAC
** *
9855400 AGAGTAGAGCAAAAC
1 AGAACAGAACAAAAC
*
9855415 TGAACAGA
1 AGAACAGA
9855423 GCTATGCAGA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.57, C:0.17, G:0.21, T:0.06
Consensus pattern (15 bp):
AGAACAGAACAAAAC
Found at i:9868670 original size:6 final size:6
Alignment explanation
Indices: 9868659--9868690 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
9868649 AAACAAATGA
9868659 AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AG
1 AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AG
9868691 ACTGAGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
AGTGAG
Found at i:9868697 original size:18 final size:18
Alignment explanation
Indices: 9868659--9868697 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9868649 AAACAAATGA
**
9868659 AGTGAGAGTGAGAGTGAG
1 AGTGAGAGTGAGAGACAG
*
9868677 AGTGAGAGTGAGAGACTG
1 AGTGAGAGTGAGAGACAG
9868695 AGT
1 AGT
9868698 AATGGAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.46, T:0.18
Consensus pattern (18 bp):
AGTGAGAGTGAGAGACAG
Found at i:9870786 original size:30 final size:30
Alignment explanation
Indices: 9870718--9870806 Score: 107
Period size: 25 Copynumber: 3.1 Consensus size: 30
9870708 TCCATATTTA
*
9870718 TGGAAAGTCAAAGATATGAGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
9870745 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* *
9870773 TGGAAATTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
9870804 TGG
1 TGG
9870807 CATAAGAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
25 20 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 20 0.38
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:9875440 original size:30 final size:30
Alignment explanation
Indices: 9875379--9875464 Score: 110
Period size: 25 Copynumber: 3.0 Consensus size: 30
9875369 ATATTTATGA
9875379 AAAGTCAAAGATATGGGTATC-AA-A-T--
1 AAAGTCAAAGATATGGGTATCAAATATTGG
9875404 AAAGTCAAAGATATGGGTATCAAATATTGG
1 AAAGTCAAAGATATGGGTATCAAATATTGG
* *
9875434 AAAGTCAAAGATATGGATATCGAGATATTGG
1 AAAGTCAAAGATATGGGTATC-AAATATTGG
9875465 CATAAGAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 20 0.38
31 8 0.15
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (30 bp):
AAAGTCAAAGATATGGGTATCAAATATTGG
Found at i:9880066 original size:229 final size:229
Alignment explanation
Indices: 9879665--9880350 Score: 1336
Period size: 229 Copynumber: 3.0 Consensus size: 229
9879655 TATATTAATT
*
9879665 TTTTTTAGTTTAAATAAAATATTATTGGTTTTTTTCCCGGATTAGTATATAACTCGGGTATACGA
1 TTTTTTAGTTTAAATAAAATATTATTAGTTTTTTTCCCGGATTAGTATATAACTCGGGTATACGA
* * *
9879730 AATACAGGGACTAATTGAGCCTATCTGACAGGCGCGACTAGTTGTGCCTAACTCAGATGCACGAA
66 AATACAGGGACTAATTGAGCCTATCTGACAGGTGCGACTAGTTGTGCCTAACTCAGAGGCGCGAA
9879795 TGGTGGACCCCACTGCTGCTTCATTTTTCCCCTATCTTATATAGTATGTTGATAGTCAATCAACT
131 TGGTGGACCCCACTGCTGCTTCATTTTTCCCCTATCTTATATAGTATGTTGATAGTCAATCAACT
9879860 ATATTCATTACATAAATATGAAATTATTTATATA
196 ATATTCATTACATAAATATGAAATTATTTATATA
9879894 TTTTTTAGTTTAAATAAAATATTATTAGTTTTTTTCCCGGATTAGTATATAACTCGGGTATACGA
1 TTTTTTAGTTTAAATAAAATATTATTAGTTTTTTTCCCGGATTAGTATATAACTCGGGTATACGA
9879959 AATACAGGGACTAATTGAGCCTATCTGACAGGTGCGACTAGTTGTGCCTAACTCAGAGGCGCGAA
66 AATACAGGGACTAATTGAGCCTATCTGACAGGTGCGACTAGTTGTGCCTAACTCAGAGGCGCGAA
9880024 TGGTGGACCCCACTGCTGCTTCATTTTTCCCCTATCTTATATAGTATGTTGATAGTCAATCAACT
131 TGGTGGACCCCACTGCTGCTTCATTTTTCCCCTATCTTATATAGTATGTTGATAGTCAATCAACT
9880089 ATATTCATTACATAAATATGAAATTATTTATATA
196 ATATTCATTACATAAATATGAAATTATTTATATA
9880123 TTTTTTAGTTTAAATAAAATATTATTAGTTTTTTTCCCGGATTAGTATATAACTCGGGTATACGA
1 TTTTTTAGTTTAAATAAAATATTATTAGTTTTTTTCCCGGATTAGTATATAACTCGGGTATACGA
9880188 AATACAGGGACTAATTGAGCCTATCTGACAGGTGCGACTAGTTGTGCCTAACTCAGAGGCGCGAA
66 AATACAGGGACTAATTGAGCCTATCTGACAGGTGCGACTAGTTGTGCCTAACTCAGAGGCGCGAA
9880253 TGGTGGACCCCACTGCTGCTTCATTTTTCCCCTATCTTATATAGTATGTTGATAGTCAATCAACT
131 TGGTGGACCCCACTGCTGCTTCATTTTTCCCCTATCTTATATAGTATGTTGATAGTCAATCAACT
9880318 ATATTCATTACATAAATATGAAATTATTTATAT
196 ATATTCATTACATAAATATGAAATTATTTATAT
9880351 TACAAAAATA
Statistics
Matches: 453, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 453 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (229 bp):
TTTTTTAGTTTAAATAAAATATTATTAGTTTTTTTCCCGGATTAGTATATAACTCGGGTATACGA
AATACAGGGACTAATTGAGCCTATCTGACAGGTGCGACTAGTTGTGCCTAACTCAGAGGCGCGAA
TGGTGGACCCCACTGCTGCTTCATTTTTCCCCTATCTTATATAGTATGTTGATAGTCAATCAACT
ATATTCATTACATAAATATGAAATTATTTATATA
Found at i:9884533 original size:56 final size:56
Alignment explanation
Indices: 9884460--9884572 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
9884450 CCAATTGCTC
* * * *
9884460 ATATCATATCACATTTTCATTTGTCAACTTTCTCTACTCCACCTCCTGTCCTACGT
1 ATATCACATCACATTTTCATTTGTCAACTTTCTCCACTCCACCACCTATCCTACGT
* *
9884516 ATATCACATCACTTTTTCATTTGTCAACTTTCTCCACTCCACCACCTATCCTCCGT
1 ATATCACATCACATTTTCATTTGTCAACTTTCTCCACTCCACCACCTATCCTACGT
9884572 A
1 A
9884573 CAACTTTGCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.22, C:0.35, G:0.04, T:0.39
Consensus pattern (56 bp):
ATATCACATCACATTTTCATTTGTCAACTTTCTCCACTCCACCACCTATCCTACGT
Found at i:9889113 original size:18 final size:18
Alignment explanation
Indices: 9889090--9889134 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
9889080 TTCAAAATCC
9889090 ACACATTTCACAC-ATTT
1 ACACATTTCACACAATTT
*
9889107 GACACATTTGACACAATTT
1 -ACACATTTCACACAATTT
*
9889126 TCACATTTC
1 ACACATTTC
9889135 TCAATTTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (18 bp):
ACACATTTCACACAATTT
Found at i:9894297 original size:66 final size:65
Alignment explanation
Indices: 9894189--9894312 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 65
9894179 CTATAGTTGA
* *
9894189 AGTTCGTCATATTTTCTGCTTGCCTCTGCTTCCCTCGCTGCTGCATCCGCTTTAAGTTGTAGCTA
1 AGTTCGTCATATTTTCT-CTTGCCTCTACTTCCCTCGATGCTGCATCCGCTTTAAGTTGTAGCTA
9894254 G
65 G
* * * **
9894255 AGTTCTTCATATTTTCT-TTGAGCCTCTACTTCTCTCGATGCTGCCTTTGCTTTAAGTT
1 AGTTCGTCATATTTTCTCTT--GCCTCTACTTCCCTCGATGCTGCATCCGCTTTAAGTT
9894313 AAGCAATTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
64 2 0.04
66 47 0.96
ACGTcount: A:0.13, C:0.27, G:0.17, T:0.44
Consensus pattern (65 bp):
AGTTCGTCATATTTTCTCTTGCCTCTACTTCCCTCGATGCTGCATCCGCTTTAAGTTGTAGCTAG
Found at i:9897517 original size:19 final size:19
Alignment explanation
Indices: 9897495--9897534 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9897485 TCAAAAACAC
9897495 ATCAAAATTTTAAAAATTT
1 ATCAAAATTTTAAAAATTT
* * *
9897514 ATCAACATTTTTAAACTTT
1 ATCAAAATTTTAAAAATTT
9897533 AT
1 AT
9897535 ATTAATACTC
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:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (19 bp):
ATCAAAATTTTAAAAATTT
Found at i:9898053 original size:21 final size:21
Alignment explanation
Indices: 9898029--9898096 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
9898019 ACTAAATATT
9898029 AACTTTTATTACAAAGAACTA
1 AACTTTTATTACAAAGAACTA
* * * * ** *
9898050 AACTTTAAGTCCTATCAAAT-
1 AACTTTTATTACAAAGAACTA
*
9898070 ATCTTTTATTACAAAGAACTA
1 AACTTTTATTACAAAGAACTA
9898091 AACTTT
1 AACTTT
9898097 AAGTCCTATC
Statistics
Matches: 30, Mismatches: 16, Indels: 2
0.62 0.33 0.04
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (21 bp):
AACTTTTATTACAAAGAACTA
Found at i:9898082 original size:41 final size:41
Alignment explanation
Indices: 9898031--9898115 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
9898021 TAAATATTAA
9898031 CTTTTATTACAAAGAACTAAACTTTAAGTCCTATCAAATAT
1 CTTTTATTACAAAGAACTAAACTTTAAGTCCTATCAAATAT
9898072 CTTTTATTACAAAGAACTAAACTTTAAGTCCTATCAAATAT
1 CTTTTATTACAAAGAACTAAACTTTAAGTCCTATCAAATAT
9898113 CTT
1 CTT
9898116 AATGCTGGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.38
Consensus pattern (41 bp):
CTTTTATTACAAAGAACTAAACTTTAAGTCCTATCAAATAT
Found at i:9904285 original size:43 final size:43
Alignment explanation
Indices: 9904224--9904332 Score: 148
Period size: 43 Copynumber: 2.5 Consensus size: 43
9904214 TCGATAACTA
*
9904224 TTTTCGTGTAAGACCACGTCTGGAACATTAGCATCGACTTGTG
1 TTTTCGTGTAAGACCACGTCTGGAACATTAGAATCGACTTGTG
* ** *
9904267 TTTTCGTGTAAGACCACGTCTGGGATGTTGGAATCGACTTGTG
1 TTTTCGTGTAAGACCACGTCTGGAACATTAGAATCGACTTGTG
*
9904310 TTTTTGTGTAAGACC-CTGTCTGG
1 TTTTCGTGTAAGACCAC-GTCTGG
9904333 GACAGTGGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (43 bp):
TTTTCGTGTAAGACCACGTCTGGAACATTAGAATCGACTTGTG
Found at i:9914267 original size:43 final size:43
Alignment explanation
Indices: 9914206--9914308 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 43
9914196 TTTCTGGTAA
* *
9914206 GTATTTTCATGTAAGACCACATCTGGGACGATGGCATCGGTTT
1 GTATTTTCGTGTAAGACCACATCTGGGACGATGGCATCGATTT
*
9914249 GTATTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTT
1 GTATTTTCGTGTAAGACCACATCTGGGACGATGGCATCGATTT
*
9914292 GTATTTTCGAGTAAGAC
1 GTATTTTCGTGTAAGAC
9914309 TCTGTCTGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
GTATTTTCGTGTAAGACCACATCTGGGACGATGGCATCGATTT
Found at i:9914316 original size:43 final size:43
Alignment explanation
Indices: 9914206--9914369 Score: 167
Period size: 43 Copynumber: 3.8 Consensus size: 43
9914196 TTTCTGGTAA
* *
9914206 GTATTTTC-ATGTAAGACCACATCTGGGACGATGGCATCGGTTT
1 GTATTTTCGA-GTAAGACCACGTCTGGGACGATGGCATCGATTT
*
9914249 GTATTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTT
1 GTATTTTCGAGTAAGACCACGTCTGGGACGATGGCATCGATTT
* * *
9914292 GTATTTTCGAGTAAGACTC-TGTCTGGGAC-AGTGGTATCGATTG
1 GTATTTTCGAGTAAGAC-CACGTCTGGGACGA-TGGCATCGATTT
* * *
9914335 GCGA-TTAC-ATGTAAGACCACGTCTGGGATGATGGC
1 G-TATTTTCGA-GTAAGACCACGTCTGGGACGATGGC
9914370 GTTGTATGAA
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
42 3 0.03
43 96 0.94
44 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (43 bp):
GTATTTTCGAGTAAGACCACGTCTGGGACGATGGCATCGATTT
Found at i:9918553 original size:15 final size:16
Alignment explanation
Indices: 9918533--9918565 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
9918523 TTTGACATAG
9918533 ATAATAATATATA-AA
1 ATAATAATATATATAA
9918548 ATAATAATATATATAA
1 ATAATAATATATATAA
9918564 AT
1 AT
9918566 TTAAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAATATATATAA
Found at i:9920049 original size:44 final size:44
Alignment explanation
Indices: 9920001--9920181 Score: 149
Period size: 44 Copynumber: 4.2 Consensus size: 44
9919991 CGTCAAAGGT
* *
9920001 ATAGGATTCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 ATAGGATTCATGATTTTAATCTGCTCCACTGCAACTTCAGAGAG
* * * *
9920045 ATAGGATTAAT-AGCTTCAGTCTGCTCCACTGCAACTTCAGAGAG
1 ATAGGATTCATGA-TTTTAATCTGCTCCACTGCAACTTCAGAGAG
* * * *
9920089 ATAAGA--C-TGGA-TGTGATCTGCTCTACTGCAACTTCAGAGAG
1 ATAGGATTCAT-GATTTTAATCTGCTCCACTGCAACTTCAGAGAG
** * * * *
9920130 ATAAAATAT-GTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 ATAGGAT-TCATGATTTTAATCTGCTCCACTGCAACTTCAGAGAG
9920174 ATAGGATT
1 ATAGGATT
9920182 GATTTCTTCT
Statistics
Matches: 108, Mismatches: 21, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
41 31 0.29
43 4 0.04
44 73 0.68
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
ATAGGATTCATGATTTTAATCTGCTCCACTGCAACTTCAGAGAG
Found at i:9920276 original size:128 final size:128
Alignment explanation
Indices: 9920014--9921043 Score: 1585
Period size: 128 Copynumber: 8.0 Consensus size: 128
9920004 GGATTCATCA
* ** ** * * **
9920014 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAGTCTGCTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* * * * *
9920079 CTTCAGAGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAAATATGTGG
66 CTT-AGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
*
9920143 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* * *
9920208 TTTAGGGAGATAAGACTTAATGCGATCTTCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
* *
9920271 ATTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
*
9920336 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
* * * * * * **
9920399 TTTCAATCCGCTCCACTACAGCTTTAGGGAGATAGGATT-GTTTTTTCTGTCTGCTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* * *
9920463 CTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
66 CTT-AGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
* *
9920527 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATATGATTGGTTTCTTTTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
*
9920592 CTTAGGGAGATAAGACTTGATGCGATTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
* * * *
9920655 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTATCTACTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
** *
9920720 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTATAACTCCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
9920783 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* * * *
9920848 CTTAGGGAGATAAAACTTGATGCTATCTGCTCTACTGTAACTTCAGAAAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
* * *
9920911 TTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTCCTTCTATCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
*
9920976 TTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
9921039 TTTTA
1 TTTTA
9921044 CTGATCTGTC
Statistics
Matches: 825, Mismatches: 74, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
127 24 0.03
128 719 0.87
129 82 0.10
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (128 bp):
TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
Found at i:9920412 original size:84 final size:83
Alignment explanation
Indices: 9920321--9920927 Score: 297
Period size: 84 Copynumber: 7.1 Consensus size: 83
9920311 GTTTCTTCTG
* *
9920321 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTGCAACTTCAGAGAG
9920386 ATAAGATCTGTGGTTTCAA
66 ATAAGA-CTGTGGTTTCAA
* * * * *
9920405 TCCGCTCCACTACAGCTTTAGGGAGATAGGA-TTGTTTTTTCTG-TCTGCTCCACTGCAACTTCA
1 TCTGCTCCACTACTGC-TTAGGGAGATAAGACTTG---ATGC-GATCTGCTCCACTGCAACTTCA
* * * *
9920468 GGGAGATAAGACTG-GATGT-GA
61 GAGAGATAAGACTGTGGTTTCAA
* * * * * *** *
9920489 TCTGCTCTACT-GTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCA
1 TCTGCTCCACTACT-GCTT-AGGGAGATAAGA-CT-T-GATGCGATCTGCTCCACTGCAACTTCA
* * **
9920553 GGGAGATATGA-T-TGGTTTCTTTTG
61 GAGAGATAAGACTGTGGTTTC---AA
* *
9920577 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATTTGCTCTACTGCAACTTCAGAGAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTGCAACTTCAGAGAG
*
9920642 ATAAGATCTGTGGTTTTAA
66 ATAAGA-CTGTGGTTTCAA
* ** * * * * * * **
9920661 TCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTAGTTTCTTCTATCTACTCCACTACTGCTT-A
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTT-G---ATGCGATCTGCTCCACTGCAACTTCA
* * * *
9920724 GGGAGATAAGACT-T-GATGCGA
61 GAGAGATAAGACTGTGGTTTCAA
* * * * * *** *
9920745 TCTGCTCTACTA-TAACTCCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCA
1 TCTGCTCCACTACT-GCT-TAGGGAGATAAGA-CT-T-GATGCGATCTGCTCCACTGCAACTTCA
* * **
9920809 GGGAGATAGGA-T-TGGTTTCTTCTG
61 GAGAGATAAGACTGTGG--T-TTCAA
* * * * *
9920833 TCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATGCTATCTGCTCTACTGTAACTTCAGAAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTGCAACTTCAGAGAG
*
9920898 ATAAGATCTGTGGTTTTAA
66 ATAAGA-CTGTGGTTTCAA
*
9920917 TCCGCTCCACT
1 TCTGCTCCACT
9920928 GCAACTTTAG
Statistics
Matches: 384, Mismatches: 99, Indels: 80
0.68 0.18 0.14
Matches are distributed among these distances:
83 2 0.01
84 172 0.45
85 76 0.20
86 13 0.03
87 74 0.19
88 45 0.12
89 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (83 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTGCAACTTCAGAGAG
ATAAGACTGTGGTTTCAA
Found at i:9920456 original size:43 final size:43
Alignment explanation
Indices: 9920020--9920990 Score: 216
Period size: 44 Copynumber: 22.7 Consensus size: 43
9920010 ATCATTTTAA
* * * *** *
9920020 TCTGCTCCACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATT-GTTTTTTCTG
* * * ** *
9920064 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTG---GATGTG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTGTTTTTTCTG
* * * * * **
9920104 ATCTGCTCTACTGCAACTTCAGAGAGATAAAATATGTGGTTTT-AA
1 -TCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGT-TTTTTCTG
* * * *
9920149 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTG-TTTTTTCTG
* ** * ** *
9920193 TCTGCTCCACTAC-TGTTTAGGGAGATAAGA--CTTAATGC-G
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTGTTTTTTCTG
* * * * ** **
9920232 ATCTTCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGATTT-AA
1 -TCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGT-TTTTTCTG
* * *
9920277 TCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATT-GTTTTTTCTG
* ** * *
9920321 TCTGCTCCACTACTGC-TTAGGGAGATAAGACTTG---ATGC-G
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTGTTTTTTCTG
* * * * ** **
9920360 ATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTCAA
1 -TCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGTTTTTTCTG
* * * *
9920405 TCCGCTCCACTACAGCTTTAGGGAGATAGGATTGTTTTTTCTG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTGTTTTTTCTG
* * ** *
9920448 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTG---GATGTG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTGTTTTTTCTG
* * * * * **
9920488 ATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTT-AA
1 -TCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGT-TTTTTCTG
* * *
9920533 TCCGCTCCACTGCAACTTCAGGGAGATATGATTGGTTTCTTT-TG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATT-GTTT-TTTCTG
* ** * *
9920577 TCTGCTCCACTACTGC-TTAGGGAGATAAGACTTG---ATGC-G
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTGTTTTTTCTG
* * * * * **
9920616 ATTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT-AA
1 -TCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGT-TTTTTCTG
* * * *
9920661 TCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATT-GTTTTTTCTG
* * ** * *
9920705 TCTACTCCACTACTGC-TTAGGGAGATAAGACTTG---ATGC-G
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTGTTTTTTCTG
* ** ** * * **
9920744 ATCTGCTCTACTATAACTCCAGAGAGATAAGATCTGTGGTTTT-AA
1 -TCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGT-TTTTTCTG
* * * *
9920789 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATT-GTTTTTTCTG
* ** * * * *
9920833 TCTGCTCCACTACTGC-TTAGGGAGATAAAACTTG---ATGCTA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTGTTTTTTCTG
* * * ** * **
9920873 TCTGCTCTACTGTAACTTCAGAAAGATAAGATCTGTGGTTTT-AA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGAT-TGT-TTTTTCTG
* * ** *
9920917 TCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTCCTTCTA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGATT-GTTTTTTCTG
* **
9920961 TCTGCTCCACTAC-TGTTTAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTTAGGGAGATAAGA
9920991 CTTGATGCGA
Statistics
Matches: 657, Mismatches: 205, Indels: 131
0.66 0.21 0.13
Matches are distributed among these distances:
39 4 0.01
40 74 0.11
41 123 0.19
42 4 0.01
43 135 0.21
44 310 0.47
45 5 0.01
46 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTTAGGGAGATAAGATTGTTTTTTCTG
Found at i:9921325 original size:24 final size:24
Alignment explanation
Indices: 9921291--9921348 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
9921281 CAGATTGGCC
9921291 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
* *
9921315 CTACTGTAATCTTCAAGGTTCAGT
1 CCACTGTAATCTTCAAGGTTCAAT
9921339 CCACTGTAAT
1 CCACTGTAAT
9921349 TTTGGGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTCAAT
Found at i:9922343 original size:25 final size:25
Alignment explanation
Indices: 9922286--9922335 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
9922276 ACCTTGGCCT
9922286 CTCCTTTTTCTTTTCTTTTATTTTC
1 CTCCTTTTTCTTTTCTTTTATTTTC
9922311 CTCCTTTTTCTTTTCATTTT-TTTTC
1 CTCCTTTTTCTTTTC-TTTTATTTTC
9922336 TTTTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (25 bp):
CTCCTTTTTCTTTTCTTTTATTTTC
Found at i:9924060 original size:23 final size:22
Alignment explanation
Indices: 9924017--9924060 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
9924007 TTTCAAGTCA
9924017 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
9924040 ATATTCATCATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
9924061 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:9924186 original size:23 final size:23
Alignment explanation
Indices: 9924159--9924278 Score: 195
Period size: 23 Copynumber: 5.2 Consensus size: 23
9924149 ATAAGTGCCA
9924159 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
9924182 AACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
9924205 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
9924228 CACTGAAAAGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
9924251 AACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
9924274 CACTG
1 CACTG
9924279 GTCAATAACA
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:9927038 original size:47 final size:49
Alignment explanation
Indices: 9926933--9927040 Score: 132
Period size: 47 Copynumber: 2.2 Consensus size: 49
9926923 TCCAACTATA
* * *
9926933 GTCTTACATGTAATCACATATCACATACCGATGCAATAGCCCAGCTATG
1 GTCTTACACGGAATCACATATCACATACCGATGCAATAGCCCAGATATG
* **
9926982 GTCTTACACGGAATCACATATCACA-A-TGATGTC-ATATTCCAGATATG
1 GTCTTACACGGAATCACATATCACATACCGATG-CAATAGCCCAGATATG
9927029 GTCTTACACGGA
1 GTCTTACACGGA
9927041 GATTTCATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 27 0.52
48 2 0.04
49 23 0.44
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (49 bp):
GTCTTACACGGAATCACATATCACATACCGATGCAATAGCCCAGATATG
Found at i:9928859 original size:31 final size:32
Alignment explanation
Indices: 9928823--9928887 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
9928813 CTTAGATAAT
9928823 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
9928854 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
9928886 TT
1 TT
9928888 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:9929490 original size:20 final size:19
Alignment explanation
Indices: 9929449--9929527 Score: 73
Period size: 20 Copynumber: 4.4 Consensus size: 19
9929439 AAAAAAAAAG
9929449 AAAAAAAGAGCAAAAACAGC
1 AAAAAAAGAGCAAAAAC-GC
9929469 AAAAAAAGAGCAAAAAGCGC
1 AAAAAAAGAGCAAAAA-CGC
9929489 ---AAAAGA--AAAAA-G-
1 AAAAAAAGAGCAAAAACGC
*
9929501 AAAAAAAAAGCAAAAAGCGC
1 AAAAAAAGAGCAAAAA-CGC
9929521 AAAAAAA
1 AAAAAAA
9929528 AAAGTTGCCT
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
13 1 0.02
15 10 0.20
17 11 0.22
19 1 0.02
20 25 0.51
21 1 0.02
ACGTcount: A:0.73, C:0.11, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAGCAAAAACGC
Found at i:9929515 original size:11 final size:11
Alignment explanation
Indices: 9929433--9929516 Score: 54
Period size: 11 Copynumber: 8.0 Consensus size: 11
9929423 TTCTTTAAAT
*
9929433 AAAAGAAAAAA
1 AAAAGCAAAAA
9929444 AAAAG-AAAAA
1 AAAAGCAAAAA
*
9929454 AAGAGC--AAA
1 AAAAGCAAAAA
*
9929463 AACAGCAAAAA
1 AAAAGCAAAAA
*
9929474 AAGAGC--AAA
1 AAAAGCAAAAA
**
9929483 AAGCGCAAAAGAA
1 AAAAGC-AAA-AA
9929496 AAAAG-AAAAA
1 AAAAGCAAAAA
9929506 AAAAGCAAAAA
1 AAAAGCAAAAA
9929517 GCGCAAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
9 16 0.27
10 16 0.27
11 21 0.36
12 1 0.02
13 5 0.08
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAGCAAAAA
Found at i:9932693 original size:31 final size:32
Alignment explanation
Indices: 9932657--9932720 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
9932647 TTAGATAATC
9932657 TTAAAGAG-TTTTATTAGGATTCAATTACTCT
1 TTAAAGAGTTTTTATTAGGATTCAATTACTCT
9932688 TTAAAGAGTTTTTATTAGGATTCAATTACTCT
1 TTAAAGAGTTTTTATTAGGATTCAATTACTCT
9932720 T
1 T
9932721 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (32 bp):
TTAAAGAGTTTTTATTAGGATTCAATTACTCT
Found at i:9933314 original size:20 final size:21
Alignment explanation
Indices: 9933291--9933332 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
9933281 GAAAAACAAC
9933291 AGCAAAAA-CAGCAAAA-AAAA
1 AGCAAAAAGC-GCAAAAGAAAA
9933311 AGCAAAAAGCGCAAAAGAAAA
1 AGCAAAAAGCGCAAAAGAAAA
9933332 A
1 A
9933333 AAGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (21 bp):
AGCAAAAAGCGCAAAAGAAAA
Found at i:9933345 original size:33 final size:33
Alignment explanation
Indices: 9933294--9933368 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 33
9933284 AAACAACAGC
*
9933294 AAAAACAGCAAAAAAAAAGCAAAAAGCGCAAAA
1 AAAAAAAGCAAAAAAAAAGCAAAAAGCGCAAAA
9933327 GAAAAAAAG-AAAAAAAAAGCAAAAAGCGCAAAA
1 -AAAAAAAGCAAAAAAAAAGCAAAAAGCGCAAAA
9933360 AAAGAAAAG
1 AAA-AAAAG
9933369 TTGCCTACCT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 3 0.08
33 29 0.74
34 7 0.18
ACGTcount: A:0.75, C:0.11, G:0.15, T:0.00
Consensus pattern (33 bp):
AAAAAAAGCAAAAAAAAAGCAAAAAGCGCAAAA
Found at i:9936536 original size:31 final size:32
Alignment explanation
Indices: 9936500--9936563 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
9936490 TTAGATAATC
9936500 TTAAAGAG-TTTTATTAGGATTCAATTACTCT
1 TTAAAGAGTTTTTATTAGGATTCAATTACTCT
9936531 TTAAAGAGTTTTTATTAGGATTCAATTACTCT
1 TTAAAGAGTTTTTATTAGGATTCAATTACTCT
9936563 T
1 T
9936564 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (32 bp):
TTAAAGAGTTTTTATTAGGATTCAATTACTCT
Found at i:9937189 original size:32 final size:32
Alignment explanation
Indices: 9937148--9937210 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
9937138 AAAAACAGCC
9937148 AAAAAAAGCAAAAACCGCAAAAGAAA-AAAAGA
1 AAAAAAAGCAAAAACCGCAAAA-AAAGAAAAGA
*
9937180 AAAAAAAGCAAAAAGCGCAAAAAAAGAAAAG
1 AAAAAAAGCAAAAACCGCAAAAAAAGAAAAG
9937211 TTGCCTACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.75, C:0.11, G:0.14, T:0.00
Consensus pattern (32 bp):
AAAAAAAGCAAAAACCGCAAAAAAAGAAAAGA
Found at i:9937190 original size:23 final size:23
Alignment explanation
Indices: 9937148--9937192 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9937138 AAAAACAGCC
* **
9937148 AAAAAAAGCAAAAACCGCAAAAG
1 AAAAAAAGAAAAAAAAGCAAAAG
9937171 AAAAAAAGAAAAAAAAGCAAAA
1 AAAAAAAGAAAAAAAAGCAAAA
9937193 AGCGCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAAGCAAAAG
Found at i:9937209 original size:8 final size:9
Alignment explanation
Indices: 9937128--9937209 Score: 57
Period size: 9 Copynumber: 9.4 Consensus size: 9
9937118 AGAAAAAGAA
9937128 AAAAAACAGC
1 AAAAAA-AGC
*
9937138 AAAAACAGCC
1 AAAAAAAG-C
9937148 AAAAAAAGC
1 AAAAAAAGC
**
9937157 AAAAACCGC
1 AAAAAAAGC
9937166 ---AAAAG-
1 AAAAAAAGC
*
9937171 AAAAAAAGA
1 AAAAAAAGC
9937180 AAAAAAAGC
1 AAAAAAAGC
**
9937189 AAAAAGCGC
1 AAAAAAAGC
9937198 AAAAAAAG-
1 AAAAAAAGC
9937206 AAAA
1 AAAA
9937210 GTTGCCTACC
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
6 3 0.05
8 9 0.16
9 31 0.55
10 13 0.23
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGC
Found at i:9940376 original size:31 final size:32
Alignment explanation
Indices: 9940340--9940404 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
9940330 CTTAGATAAT
9940340 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
*
9940371 TTTAAAGAGTTTTTTTTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
9940403 TT
1 TT
9940405 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:9941418 original size:23 final size:22
Alignment explanation
Indices: 9941375--9941418 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
9941365 TTTCAAGTCA
9941375 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
9941398 ATATTCATCATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
9941419 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:9941592 original size:23 final size:23
Alignment explanation
Indices: 9941517--9941591 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
9941507 ATAAGTGCCA
*
9941517 CACTGAAATCTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
9941540 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
9941563 CACTGATATGTAGCCAAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
9941586 CACTGA
1 CACTGA
9941592 TCAATAACAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:9945712 original size:19 final size:20
Alignment explanation
Indices: 9945688--9945734 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
9945678 TGTGAAAATC
*
9945688 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
9945707 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
9945727 -AATGCAAA
1 TAATGCAAA
9945735 AAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:9947945 original size:50 final size:51
Alignment explanation
Indices: 9947831--9947962 Score: 130
Period size: 50 Copynumber: 2.6 Consensus size: 51
9947821 GAATAAAATT
* *
9947831 ATAAAAA-CATAAAAAGATATATAAGTATGTATAGATATATGTACATTAAA
1 ATAAAAAGCATAAAAAGATATATAAGTATATATAGATATATGTACATGAAA
* * * * **
9947881 ATTATAAAGTATAAAAAAATATATAAGTATATAT-TA-ATATGTTTATGAAA
1 A-TAAAAAGCATAAAAAGATATATAAGTATATATAGATATATGTACATGAAA
*
9947931 ATAAAAATGCATAAATAGATATAT-A-TATATAT
1 ATAAAAA-GCATAAAAAGATATATAAGTATATAT
9947963 GTAAATAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
48 7 0.10
49 6 0.09
50 26 0.39
51 6 0.09
52 22 0.33
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.34
Consensus pattern (51 bp):
ATAAAAAGCATAAAAAGATATATAAGTATATATAGATATATGTACATGAAA
Found at i:9947956 original size:2 final size:2
Alignment explanation
Indices: 9947949--9948025 Score: 54
Period size: 2 Copynumber: 40.0 Consensus size: 2
9947939 GCATAAATAG
* * *
9947949 AT AT AT AT AT AT AT GT AA AT AA AT -T AT A- AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
9947988 AT AT AT AT A- AGT AT GT AT AT GT AC AT AT AT AT GT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
9948026 GAATTAAAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:9947980 original size:22 final size:22
Alignment explanation
Indices: 9947942--9948025 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
9947932 TAAAAATGCA
*
9947942 TAAATAGATATATATATATATG
1 TAAATAAATATATATATATATG
*
9947964 TAAATAAAT-TATA-ATATATA
1 TAAATAAATATATATATATATG
* *
9947984 TATAATATATATAAGTATGTATATG
1 TA-AATAAATAT-A-TATATATATG
* * *
9948009 TACATATATATGTATAT
1 TAAATAAATATATATAT
9948026 GAATTAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
20 8 0.16
21 10 0.20
22 13 0.27
23 1 0.02
24 10 0.20
25 7 0.14
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (22 bp):
TAAATAAATATATATATATATG
Found at i:9948204 original size:15 final size:16
Alignment explanation
Indices: 9948184--9948216 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
9948174 TTTGACATAG
9948184 ATAATAATATATA-AA
1 ATAATAATATATATAA
9948199 ATAATAATATATATAA
1 ATAATAATATATATAA
9948215 AT
1 AT
9948217 TTAAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAATATATATAA
Found at i:9948909 original size:11 final size:11
Alignment explanation
Indices: 9948885--9948920 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
9948875 AAACAAAAGT
9948885 AAAAAT-AA-A
1 AAAAATGAACA
9948894 AAAAATGAACA
1 AAAAATGAACA
9948905 AAAAATGAACA
1 AAAAATGAACA
9948916 AAAAA
1 AAAAA
9948921 AAGGTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.24
10 2 0.08
11 17 0.68
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.08
Consensus pattern (11 bp):
AAAAATGAACA
Found at i:9953328 original size:23 final size:21
Alignment explanation
Indices: 9953287--9953344 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
9953277 ATCTGCCGAC
*
9953287 ATTTTTATAATTTAATTTTTTT
1 ATTTTTAAAATTT-ATTTTTTT
9953309 ATTTTTAAAATATTATTTTTTT
1 ATTTTTAAAAT-TTATTTTTTT
*
9953331 ATTTTTCAAATTTA
1 ATTTTTAAAATTTA
9953345 AAAATTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 28 0.85
23 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTTAAAATTTATTTTTTT
Found at i:9953406 original size:13 final size:12
Alignment explanation
Indices: 9953371--9953408 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
9953361 TGGCATCATC
9953371 ATTAAA-TTTTT
1 ATTAAATTTTTT
9953382 ATTAAATTTTTT
1 ATTAAATTTTTT
9953394 ATTAAATTATTTT
1 ATTAAATT-TTTT
9953407 AT
1 AT
9953409 GCGATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 6 0.24
12 13 0.52
13 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTAAATTTTTT
Done.