Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 117 of 136
Found at i:39675757 original size:269 final size:269
Alignment explanation
Indices: 39675273--39675810 Score: 925
Period size: 269 Copynumber: 2.0 Consensus size: 269
39675263 TCCAAACTTC
*
39675273 AGCTACTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTTCGTAATTCCT
1 AGCTACTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTTCGCAATTCCT
* *
39675338 TTATTAGATCCTGTCGAACAGTAGGTGCCGGTACTGTAGCAAAAGTAATTTCCGCAACACACTAA
66 TTATTAGAGCCCGTCGAACAGTAGGTGCCGGTACTGTAGCAAAAGTAATTTCCGCAACACACTAA
*
39675403 AGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTTGCTCAAC
131 AGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTCGCTCAAC
*
39675468 ATTAGGTTGTTAAGCACTAGCTAGGTTAACATTCAGCGTTACTGATTCAGTTTCCTCACAATCCT
196 ATTAGGTTGTTAAGCACTAGCTAGGTTAACACTCAGCGTTACTGATTCAGTTTCCTCACAATCCT
*
39675533 CAGTATAAT
261 CACTATAAT
* *
39675542 AGCTGCTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTC-TCTGCAATTTC
1 AGCTACTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTTC-GCAATTCC
* * *
39675606 TTTATTAGAGCCCGTCGAACAGTAGGTGTCGGTACTGTAGCAGAAGTAATTTTCGCAACACACTA
65 TTTATTAGAGCCCGTCGAACAGTAGGTGCCGGTACTGTAGCAAAAGTAATTTCCGCAACACACTA
* *
39675671 AAGAGCATCAGCGATAGCTCGAAGTAAATTTGAATCACCTACTCCCTCATTATTAGCTCGCTCAA
130 AAGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTCGCTCAA
* *
39675736 CATTAGGTTGTTGAGCACTAGCTAGGTTAACACTCAGCGTTACTGATTCAGTTTCCTTACAATCC
195 CATTAGGTTGTTAAGCACTAGCTAGGTTAACACTCAGCGTTACTGATTCAGTTTCCTCACAATCC
39675801 TCACTATAAT
260 TCACTATAAT
39675811 CATCGCTAGA
Statistics
Matches: 253, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
268 2 0.01
269 251 0.99
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (269 bp):
AGCTACTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTTCGCAATTCCT
TTATTAGAGCCCGTCGAACAGTAGGTGCCGGTACTGTAGCAAAAGTAATTTCCGCAACACACTAA
AGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTCGCTCAAC
ATTAGGTTGTTAAGCACTAGCTAGGTTAACACTCAGCGTTACTGATTCAGTTTCCTCACAATCCT
CACTATAAT
Found at i:39678712 original size:19 final size:18
Alignment explanation
Indices: 39678678--39678726 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
39678668 ATCCATATCA
*
39678678 CATTTCATCATTTCATATT
1 CATTTC-TCATCTCATATT
39678697 CCATTTCTCATCTCATATT
1 -CATTTCTCATCTCATATT
39678716 CATTTCTCATC
1 CATTTCTCATC
39678727 ATTGTCATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 11 0.39
19 11 0.39
20 6 0.21
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
CATTTCTCATCTCATATT
Found at i:39678712 original size:27 final size:27
Alignment explanation
Indices: 39678658--39678712 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
39678648 ATATATGAAT
*
39678658 TCATTTCAATATCCATATCACATTTCA
1 TCATTTCAATATCCATATCACATCTCA
* *
39678685 TCATTTC-ATATTCCATTTCTCATCTCA
1 TCATTTCAATA-TCCATATCACATCTCA
39678712 T
1 T
39678713 ATTCATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (27 bp):
TCATTTCAATATCCATATCACATCTCA
Found at i:39681756 original size:3 final size:3
Alignment explanation
Indices: 39681748--39681784 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39681738 TTCATTTTAT
39681748 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39681785 AAGAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39682564 original size:13 final size:14
Alignment explanation
Indices: 39682546--39682579 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39682536 ATAATAAATA
39682546 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
39682559 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
39682573 TAATTTT
1 TATTTTT
39682580 AAAATACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:39682571 original size:14 final size:13
Alignment explanation
Indices: 39682546--39682579 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
39682536 ATAATAAATA
39682546 TATTTTTTATTTT
1 TATTTTTTATTTT
39682559 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
39682573 TAATTTT
1 T-ATTTT
39682580 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:39682626 original size:19 final size:21
Alignment explanation
Indices: 39682604--39682643 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
39682594 ATATATTTTT
39682604 TATTTTTT-TATTT-TTAAAA
1 TATTTTTTGTATTTATTAAAA
39682623 TATTTTTTGTATTTATTAAAA
1 TATTTTTTGTATTTATTAAAA
39682644 ATCGGGCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TATTTTTTGTATTTATTAAAA
Found at i:39689671 original size:15 final size:15
Alignment explanation
Indices: 39689646--39689680 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
39689636 GACTCTATTT
*
39689646 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
39689660 TAATTAATATTAAGA
1 TAATTAATATTAAGA
39689675 TAATTA
1 TAATTA
39689681 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:39693041 original size:46 final size:46
Alignment explanation
Indices: 39692974--39693066 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
39692964 TGAGTTAGGT
39692974 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
1 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
39693020 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
1 TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
39693066 T
1 T
39693067 GATACAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (46 bp):
TATCTCTGCTTGTATCTCTTTCTATTAATACAAAAGTAGTATAATA
Found at i:39694283 original size:22 final size:23
Alignment explanation
Indices: 39694241--39694289 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
39694231 TCAAATTAAT
39694241 ATATTAATATATGAATATATGA-
1 ATATTAATATATGAATATATGAC
* *
39694263 ATATT-ATATTTGGATATTATGAC
1 ATATTAATATATGAATA-TATGAC
39694286 ATAT
1 ATAT
39694290 AAACTAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 10 0.43
23 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (23 bp):
ATATTAATATATGAATATATGAC
Found at i:39694571 original size:55 final size:54
Alignment explanation
Indices: 39694512--39694622 Score: 134
Period size: 55 Copynumber: 2.0 Consensus size: 54
39694502 TATATTATGA
* *
39694512 TTTTAGTAAATTCATA-TAAGAATAATTATATTAAGAATCTTATTAAATTATATAT
1 TTTTAGTAAATT-ATATTAAGAATAATTATATTAA-AATATGATTAAATTATATAT
* * * *
39694567 TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAAATTATTTAT
1 TTTTAGTAAATTATA-TTAAGAATAATTATATTAAAATATGATTAAATTATATAT
39694622 T
1 T
39694623 ATTTTTATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
54 3 0.06
55 29 0.60
56 16 0.33
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (54 bp):
TTTTAGTAAATTATATTAAGAATAATTATATTAAAATATGATTAAATTATATAT
Found at i:39694803 original size:44 final size:45
Alignment explanation
Indices: 39694740--39694833 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 45
39694730 TATTACAATA
39694740 TCATTCCATTCAACCAAACACA-AGAA-TACCATTACAGTTCTATT
1 TCATTCCATTCAACCAAACA-ATAGAATTACCATTACAGTTCTATT
* *
39694784 TCATTCCATTCAACCAAACAATTGAATTACTATTACAGTTCTATT
1 TCATTCCATTCAACCAAACAATAGAATTACCATTACAGTTCTATT
*
39694829 CCATT
1 TCATT
39694834 ACACCTCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (45 bp):
TCATTCCATTCAACCAAACAATAGAATTACCATTACAGTTCTATT
Found at i:39694836 original size:16 final size:16
Alignment explanation
Indices: 39694815--39694886 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
39694805 TTGAATTACT
*
39694815 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
39694831 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
*
39694847 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
39694863 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
39694879 ATTACAGC
1 ATTACAGC
39694887 GAACCAAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:39699739 original size:199 final size:201
Alignment explanation
Indices: 39699399--39699798 Score: 759
Period size: 199 Copynumber: 2.0 Consensus size: 201
39699389 TTTAAATGGT
39699399 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
1 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
*
39699464 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAGTAAAATGAA
66 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
39699529 AACTATAATGTTTTAAGTTCAAACCAATGTGT-A-TTTTTTTTTATAAAGAAGATATAAAAAGAT
131 AACTATAATGTTTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
39699592 GAACTC
196 GAACTC
*
39699598 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAATA
1 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
39699663 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
66 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
*
39699728 AACTATAATGTTTTAAGTTCAAATCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
131 AACTATAATGTTTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
39699793 GAACTC
196 GAACTC
39699799 TCTCAAAATA
Statistics
Matches: 196, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
199 159 0.81
200 1 0.01
201 36 0.18
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (201 bp):
GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
AACTATAATGTTTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
GAACTC
Found at i:39700119 original size:26 final size:27
Alignment explanation
Indices: 39700078--39700130 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
39700068 TGAAAATAGA
* *
39700078 AAAAATACAATTGGAAAAA-TAGGAAG
1 AAAAATAAAATAGGAAAAAGTAGGAAG
39700104 AAAAATAAAATAGGAAAAAGTAGGAAG
1 AAAAATAAAATAGGAAAAAGTAGGAAG
39700131 TTATATGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.13
Consensus pattern (27 bp):
AAAAATAAAATAGGAAAAAGTAGGAAG
Found at i:39701945 original size:62 final size:64
Alignment explanation
Indices: 39701848--39701973 Score: 211
Period size: 62 Copynumber: 2.0 Consensus size: 64
39701838 AATTTCCTAG
**
39701848 AATTCTTAACGATTAGAAGATATTTGCGTATGGTGTACCAATTAATAAGCTTAA-G-GTGTTAT
1 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGAGTGTTAT
*
39701910 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATGAGCTTAATGAGTGTTAT
1 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGAGTGTTAT
39701974 GTTAAATGTC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 51 0.86
63 1 0.02
64 7 0.12
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (64 bp):
AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGAGTGTTAT
Found at i:39704335 original size:23 final size:23
Alignment explanation
Indices: 39704304--39704349 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39704294 TTATTAACAT
* *
39704304 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATATTCGATTAA
*
39704327 TGTTTGTGAACATATTCGATTAA
1 TGTTCGTGAACATATTCGATTAA
39704350 GTTAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATATTCGATTAA
Found at i:39706842 original size:20 final size:20
Alignment explanation
Indices: 39706819--39706856 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39706809 AATTAATATT
*
39706819 TAAAATTATAAAAAAAATCA
1 TAAAAGTATAAAAAAAATCA
*
39706839 TAAAAGTATTAAAAAAAT
1 TAAAAGTATAAAAAAAAT
39706857 ATTTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
TAAAAGTATAAAAAAAATCA
Found at i:39706864 original size:22 final size:22
Alignment explanation
Indices: 39706813--39706873 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
39706803 ATTAATAATT
*
39706813 AATA-TTTAAAATTA-TAAAAA
1 AATATTTTAAAAATATTAAAAA
** *
39706833 AA-ATCATAAAAGTATTAAAAA
1 AATATTTTAAAAATATTAAAAA
39706854 AATATTTTAAAAATATTAAA
1 AATATTTTAAAAATATTAAA
39706874 CATATTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.03
20 9 0.28
21 8 0.25
22 14 0.44
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATATTTTAAAAATATTAAAAA
Found at i:39708167 original size:21 final size:21
Alignment explanation
Indices: 39708140--39708193 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
39708130 TATTAAATCA
39708140 TTATAATATTTTAC-ATTTTT
1 TTATAATATTTTACAATTTTT
39708160 TTAATAAT-TGTTTACAATTTTT
1 TT-ATAATAT-TTTACAATTTTT
39708182 TTATAA-ATTTTA
1 TTATAATATTTTA
39708194 TAGCTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 7 0.23
21 15 0.50
22 8 0.27
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATAATATTTTACAATTTTT
Found at i:39711777 original size:15 final size:15
Alignment explanation
Indices: 39711759--39711790 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39711749 CATTTCACTA
*
39711759 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
39711774 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
39711789 TT
1 TT
39711791 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:39730938 original size:35 final size:35
Alignment explanation
Indices: 39730872--39730959 Score: 117
Period size: 35 Copynumber: 2.5 Consensus size: 35
39730862 GTACACGGTT
* *
39730872 AACCATCCAGCACACCAG-ATGCTCAAGTGAGCCA
1 AACCAACCAACACACCAGAATGCTCAAGTGAGCCA
* *
39730906 GACCAACCAACACACCAGAATGCTCGTA-TGAGCCA
1 AACCAACCAACACACCAGAATGCTC-AAGTGAGCCA
39730941 AACCAACCAACACACCAGA
1 AACCAACCAACACACCAGA
39730960 GTACACTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
34 15 0.32
35 31 0.66
36 1 0.02
ACGTcount: A:0.40, C:0.36, G:0.15, T:0.09
Consensus pattern (35 bp):
AACCAACCAACACACCAGAATGCTCAAGTGAGCCA
Found at i:39734605 original size:13 final size:13
Alignment explanation
Indices: 39734587--39734612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39734577 CCCATGTGAA
39734587 CTTAGTAAAAGGT
1 CTTAGTAAAAGGT
39734600 CTTAGTAAAAGGT
1 CTTAGTAAAAGGT
39734613 TAGAGTACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
CTTAGTAAAAGGT
Found at i:39741623 original size:22 final size:22
Alignment explanation
Indices: 39741595--39741650 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
39741585 CTGGAGTTCG
39741595 CAGAGAATGTCAATACTAGGGA
1 CAGAGAATGTCAATACTAGGGA
* * *
39741617 CAGAGAATGTCAGTACTGGGGG
1 CAGAGAATGTCAATACTAGGGA
*
39741639 CAGCGAA-GTCAA
1 CAGAGAATGTCAA
39741651 GAAAAAATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (22 bp):
CAGAGAATGTCAATACTAGGGA
Found at i:39744684 original size:23 final size:23
Alignment explanation
Indices: 39744574--39744688 Score: 140
Period size: 23 Copynumber: 4.9 Consensus size: 23
39744564 CGTCATTGGA
*
39744574 AAAGGATGAATTGACAGAAATGT
1 AAAGGATGAATTGACGGAAATGT
*
39744597 AAAGGATGAATTGACGAAAAATGT
1 AAAGGATGAATTGACG-GAAATGT
* * * *
39744621 AAAGGAGGAACTGATGAAAATGT
1 AAAGGATGAATTGACGGAAATGT
*
39744644 AAAGGATGAATTGACGGTAATGT
1 AAAGGATGAATTGACGGAAATGT
*
39744667 AAAGGATGAATTGGCGGTAAAT
1 AAAGGATGAATTGACGG-AAAT
39744689 TATCTGAGTA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
23 56 0.72
24 22 0.28
ACGTcount: A:0.45, C:0.04, G:0.29, T:0.22
Consensus pattern (23 bp):
AAAGGATGAATTGACGGAAATGT
Found at i:39752160 original size:23 final size:23
Alignment explanation
Indices: 39752130--39752233 Score: 111
Period size: 23 Copynumber: 4.4 Consensus size: 23
39752120 ATTGGGAAAT
39752130 GATGAATTGACGAAAATGTAAAG
1 GATGAATTGACGAAAATGTAAAG
*
39752153 GATGAATTGACGAAAAATGTAAAT
1 GATGAATTGACG-AAAATGTAAAG
* * **
39752177 GAGGAACTGGTGGAAAATGTAAAG
1 GATGAA-TTGACGAAAATGTAAAG
* *
39752201 GATGAATCGAC-AGTAATGTAAAG
1 GATGAATTGACGA-AAATGTAAAG
39752224 GATGAATTGA
1 GATGAATTGA
39752234 AGGCAAATTG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.02
23 32 0.48
24 30 0.45
25 3 0.05
ACGTcount: A:0.45, C:0.05, G:0.28, T:0.22
Consensus pattern (23 bp):
GATGAATTGACGAAAATGTAAAG
Found at i:39752174 original size:24 final size:24
Alignment explanation
Indices: 39752130--39752233 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
39752120 ATTGGGAAAT
39752130 GATGAATTGACG-AAAATGTAAAG
1 GATGAATTGACGAAAAATGTAAAG
*
39752153 GATGAATTGACGAAAAATGTAAAT
1 GATGAATTGACGAAAAATGTAAAG
* * ** *
39752177 GAGGAACTGGTGGAAAATGTAAAG
1 GATGAATTGACGAAAAATGTAAAG
* **
39752201 GATGAATCGAC-AGTAATGTAAAG
1 GATGAATTGACGAAAAATGTAAAG
39752224 GATGAATTGA
1 GATGAATTGA
39752234 AGGCAAATTG
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
23 30 0.47
24 34 0.53
ACGTcount: A:0.45, C:0.05, G:0.28, T:0.22
Consensus pattern (24 bp):
GATGAATTGACGAAAAATGTAAAG
Found at i:39753679 original size:29 final size:29
Alignment explanation
Indices: 39753637--39753693 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
39753627 GTTATGGGTG
*
39753637 TAAAGTCTGGTAATGCTTCGTAAAGTCTA
1 TAAAATCTGGTAATGCTTCGTAAAGTCTA
39753666 TAAAATCTGGTAATGCTTCGTAAAGTCT
1 TAAAATCTGGTAATGCTTCGTAAAGTCT
39753694 GTAATGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (29 bp):
TAAAATCTGGTAATGCTTCGTAAAGTCTA
Found at i:39763628 original size:91 final size:89
Alignment explanation
Indices: 39763520--39763693 Score: 258
Period size: 91 Copynumber: 1.9 Consensus size: 89
39763510 TATCCATGAG
* * * *
39763520 TTACTGGTAGCTTTTATCTGCAAACCCATTGTGTATTCACAACTACTGGTAGCATATTAACTTGC
1 TTACTGGCAACTTTTATCTGCAAACCCATTGTGTATTCACAACTA-TGGCAGCATATTAACCTGC
* *
39763585 AAACACTAGTGGTTTATCCACAATTT
65 -AACACTAGTGATTCATCCACAATTT
* *
39763611 TTACTGGCAACTTTTATCTGCAAACCCGTTGTGTATTCACAACTATTGCAGCATATTAACCTGCA
1 TTACTGGCAACTTTTATCTGCAAACCCATTGTGTATTCACAACTATGGCAGCATATTAACCTGCA
39763676 ACACTAGTGATTCATCCA
66 ACACTAGTGATTCATCCA
39763694 TGAACTAGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 17 0.23
90 16 0.21
91 42 0.56
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (89 bp):
TTACTGGCAACTTTTATCTGCAAACCCATTGTGTATTCACAACTATGGCAGCATATTAACCTGCA
ACACTAGTGATTCATCCACAATTT
Found at i:39769257 original size:25 final size:25
Alignment explanation
Indices: 39769221--39769378 Score: 101
Period size: 25 Copynumber: 6.4 Consensus size: 25
39769211 GCTCTCTCTC
*
39769221 GAGCCATATAACAGGAAGCTCATAT
1 GAGCCATATAACAGGAAGCTCATAA
* * * **
39769246 GAGCCATGTAACGGGAAGCTTATCC
1 GAGCCATATAACAGGAAGCTCATAA
* ** *
39769271 GGGCTGTATAACGGGAAGCTCATAA
1 GAGCCATATAACAGGAAGCTCATAA
* **
39769296 GAGCCATA-ATCAGGAAGCTCATGG
1 GAGCCATATAACAGGAAGCTCATAA
*
39769320 GAGCCA-ATAACAGGTAGCTC-TGAA
1 GAGCCATATAACAGGAAGCTCAT-AA
* *
39769344 GAGTCAT-TAATTAGGAAGCTCCA-AA
1 GAGCCATATAA-CAGGAAGCT-CATAA
*
39769369 TAGCCATATA
1 GAGCCATATA
39769379 CCGGGAAGTT
Statistics
Matches: 98, Mismatches: 28, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
23 2 0.02
24 36 0.37
25 57 0.58
26 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATAA
Found at i:39769315 original size:24 final size:24
Alignment explanation
Indices: 39769284--39769497 Score: 82
Period size: 25 Copynumber: 8.7 Consensus size: 24
39769274 CTGTATAACG
39769284 GGAAGCTCATAAGAGCCATAATCA
1 GGAAGCTCATAAGAGCCATAATCA
**
39769308 GGAAGCTCATGGGAGCCAATAA-CA
1 GGAAGCTCATAAGAGCC-ATAATCA
* * *
39769332 GGTAGCTC-TGAAGAGTCATTAATTA
1 GGAAGCTCAT-AAGAGCCA-TAATCA
* * *
39769357 GGAAGCTCCA-AATAGCCATATACCG
1 GGAAGCT-CATAAGAGCCATA-ATCA
* * *
39769382 GGAAGTTCA-AGCGAGCCAT-ATCG
1 GGAAGCTCATA-AGAGCCATAATCA
* ** *
39769405 GGAAACTTC-GGAGAGCCATTAATCT
1 GGAAGC-TCATAAGAGCCA-TAATCA
* * *
39769430 GGAAGCTCACAAAGGGCCTTTAATCA
1 GGAAGCTCA-TAAGAGCC-ATAATCA
* *
39769456 GGAAGCTCACGAAGAGCCATATATCG
1 GGAAGCTCA-TAAGAGCCATA-ATCA
39769482 GGACA-CTCATAAGAGC
1 GGA-AGCTCATAAGAGC
39769498 TGTTATGTGT
Statistics
Matches: 140, Mismatches: 33, Indels: 33
0.68 0.16 0.16
Matches are distributed among these distances:
23 15 0.11
24 41 0.29
25 46 0.33
26 37 0.26
27 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:39770491 original size:5 final size:5
Alignment explanation
Indices: 39770481--39770509 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
39770471 TATATGATGA
39770481 TATTT TATTT TATTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATT
39770510 ATTTATCATC
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):
TATTT
Found at i:39771963 original size:6 final size:6
Alignment explanation
Indices: 39771952--39771982 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
39771942 TCATTCTTTC
39771952 CCATTT CCATTT CCATTT CCATTT CCATTT C
1 CCATTT CCATTT CCATTT CCATTT CCATTT C
39771983 GAAGATCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.48
Consensus pattern (6 bp):
CCATTT
Found at i:39777054 original size:25 final size:25
Alignment explanation
Indices: 39777023--39777141 Score: 109
Period size: 25 Copynumber: 4.8 Consensus size: 25
39777013 GCTCTCTCTT
*
39777023 GAGCCATATAACAGGAAGCTCATAT
1 GAGCCATATAACAGGAAGCTCATAC
* * *
39777048 GAGCCATGTAACAGGAAGCTTATCC
1 GAGCCATATAACAGGAAGCTCATAC
* ** *
39777073 GGGCTGTATAACGGGAAGCTCAT-C
1 GAGCCATATAACAGGAAGCTCATAC
* *
39777097 AGAGCCATA-ATCAGGAAGCTCATGC
1 -GAGCCATATAACAGGAAGCTCATAC
*
39777122 GAGCCA-ATAACAGGTAGCTC
1 GAGCCATATAACAGGAAGCTC
39777142 CGGATAGCCA
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 29 0.39
25 44 0.59
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATAC
Found at i:39777151 original size:48 final size:47
Alignment explanation
Indices: 39777097--39777215 Score: 130
Period size: 48 Copynumber: 2.5 Consensus size: 47
39777087 GAAGCTCATC
* * *
39777097 AGAGCCATAATCAGGAAGCTCATGCGAGCCAATAACAGGTAGCTCCGG
1 AGAGCCATAATCAGGAAGCTCAAGCGAGCC-ATAACAGGAAGCTCCGA
* * * * *
39777145 ATAGCCATATATCGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGA
1 AGAGCCATA-ATCAGGAAGCTCAAGCGAGCCATAACAGGAAGCTCCGA
*
39777193 AGAGCCATTAATCAGTAAGCTCA
1 AGAGCCA-TAATCAGGAAGCTCA
39777216 GAAAGAGCCT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
48 37 0.65
49 20 0.35
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.18
Consensus pattern (47 bp):
AGAGCCATAATCAGGAAGCTCAAGCGAGCCATAACAGGAAGCTCCGA
Found at i:39777258 original size:26 final size:26
Alignment explanation
Indices: 39777147--39777267 Score: 92
Period size: 26 Copynumber: 4.8 Consensus size: 26
39777137 AGCTCCGGAT
* **
39777147 AGCCATATATCGGGAAGTTCA-AGCG
1 AGCCATATATCGGGAAGCTCACAAAG
*
39777172 AGCC--ATATCGGGAAGCTC-CGAAG
1 AGCCATATATCGGGAAGCTCACAAAG
* * *
39777195 AGCCAT-TAATCAGTAAGCTCAGAAAG
1 AGCCATAT-ATCGGGAAGCTCACAAAG
* *
39777221 AGCC-TTTAATCGAGAAGCTCACAAAG
1 AGCCATAT-ATCGGGAAGCTCACAAAG
*
39777247 AGCCATATATCGGGACGCTCA
1 AGCCATATATCGGGAAGCTCA
39777268 TAAGAGTTGC
Statistics
Matches: 74, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
23 18 0.24
24 1 0.01
25 15 0.20
26 38 0.51
27 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
AGCCATATATCGGGAAGCTCACAAAG
Found at i:39785323 original size:27 final size:28
Alignment explanation
Indices: 39785269--39785333 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 28
39785259 ATAAAAAATA
39785269 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
39785297 ACCAAAATATTATAA-TTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
39785324 ACCAAAATAT
1 ACCAAAATAT
39785334 ACCAAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:39785416 original size:27 final size:27
Alignment explanation
Indices: 39785386--39785437 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39785376 CACCCTGGTC
* *
39785386 GTGCCAAGGTGATTGGCAGCACCAAAG
1 GTGCCAAAGTCATTGGCAGCACCAAAG
**
39785413 GTGCCAAAGTCATTGGTGGCACCAA
1 GTGCCAAAGTCATTGGCAGCACCAA
39785438 TGTTATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (27 bp):
GTGCCAAAGTCATTGGCAGCACCAAAG
Found at i:39785487 original size:4 final size:4
Alignment explanation
Indices: 39785478--39785594 Score: 61
Period size: 4 Copynumber: 29.0 Consensus size: 4
39785468 GAATGAGAGG
* * *
39785478 GAAA GAAA GAAA GAAA GGAAT GAGAG GAAA GAAA GAAAA GGAAA G-GA
1 GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA G-AAA -GAAA GAAA
39785525 GAAGA GAAA -AAA -AAA GAAA G-AA G-AA GAAGA TGAAA GGAGAA GAAA
1 GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA -GA-AA GAAA
*
39785570 -AAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
39785595 AGGAAAGGAG
Statistics
Matches: 91, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
3 21 0.23
4 42 0.46
5 22 0.24
6 6 0.07
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:39785498 original size:27 final size:28
Alignment explanation
Indices: 39785468--39785524 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
39785458 GTGGGGGGGA
39785468 GAATGAGAGGGAAAGAAAG-AAA-GAAAG
1 GAATGAGA-GGAAAGAAAGAAAAGGAAAG
39785495 GAATGAGAGGAAAGAAAGAAAAGGAAAG
1 GAATGAGAGGAAAGAAAGAAAAGGAAAG
39785523 GA
1 GA
39785525 GAAGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 10 0.36
27 11 0.39
28 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.04
Consensus pattern (28 bp):
GAATGAGAGGAAAGAAAGAAAAGGAAAG
Found at i:39785512 original size:26 final size:26
Alignment explanation
Indices: 39785468--39785594 Score: 89
Period size: 28 Copynumber: 4.7 Consensus size: 26
39785458 GTGGGGGGGA
39785468 GAATGAGAGGGAAAGAAAGAAAGAAAG
1 GAATGAGA-GGAAAGAAAGAAAGAAAG
39785495 GAATGAGAGGAAAGAAAGAAAAGGAAAG
1 GAATGAGAGGAAAGAAAG-AAA-GAAAG
* * *
39785523 GAGAAGAGA-AAAAAAAAGAAAGAAGAAG
1 GA-ATGAGAGGAAAGAAAGAAAG-A-AAG
* *
39785551 AAGATGAAAGGAGAAGAAA-AAAGAAA-
1 GA-ATGAGAGGA-AAGAAAGAAAGAAAG
**
39785577 GAAAAAGAAGGAAAGAAA
1 GAATGAG-AGGAAAGAAA
39785595 AGGAAAGGAG
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
25 8 0.10
26 16 0.20
27 17 0.21
28 24 0.30
29 10 0.12
30 5 0.06
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.02
Consensus pattern (26 bp):
GAATGAGAGGAAAGAAAGAAAGAAAG
Found at i:39785532 original size:22 final size:21
Alignment explanation
Indices: 39785481--39785612 Score: 84
Period size: 22 Copynumber: 6.4 Consensus size: 21
39785471 TGAGAGGGAA
*
39785481 AGAAAGAAAG-AAAGGAATGAG
1 AGAAAGAAAGAAAAGGAAAG-G
39785502 AGGAAAGAAAGAAAAGGAAAGG
1 A-GAAAGAAAGAAAAGGAAAGG
* * *
39785524 AGAAGAGAAAAAAAAAGAAAGA
1 AGAA-AGAAAGAAAAGGAAAGG
*
39785546 AG-AAG-AAGATGAAAGG--AGA
1 AGAAAGAAAGA--AAAGGAAAGG
*
39785565 AGAAA-AAAG-AAA-GAAA-A
1 AGAAAGAAAGAAAAGGAAAGG
*
39785582 AGAAGGAAAGAAAAGGAAAGG
1 AGAAAGAAAGAAAAGGAAAGG
39785603 AGAAGAGAAA
1 AGAA-AGAAA
39785613 TGATTAAATG
Statistics
Matches: 88, Mismatches: 9, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
16 1 0.01
17 8 0.09
18 5 0.06
19 11 0.12
20 11 0.12
21 13 0.15
22 31 0.35
23 8 0.09
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (21 bp):
AGAAAGAAAGAAAAGGAAAGG
Found at i:39785544 original size:36 final size:36
Alignment explanation
Indices: 39785504--39785612 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 36
39785494 GGAATGAGAG
39785504 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
1 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
*
39785540 GAAAG-AAGAAGAAGATGAAAGGAGAAGAAAAAAGAAAGAAAAA
1 GAAAGAAAGAA-AAG--GAAAGGAGAAG-----AGAAAAAAAAA
*
39785583 GAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAA
39785613 TGATTAAATG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
35 5 0.08
36 13 0.21
38 11 0.18
41 11 0.18
43 17 0.27
44 5 0.08
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (36 bp):
GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
Found at i:39785551 original size:10 final size:10
Alignment explanation
Indices: 39785506--39785608 Score: 58
Period size: 10 Copynumber: 10.4 Consensus size: 10
39785496 AATGAGAGGA
39785506 AAGAAAGAA-
1 AAGAAAGAAG
*
39785515 AAGGAAAGGAG
1 AA-GAAAGAAG
39785526 AAGAGAA-AA-
1 AAGA-AAGAAG
39785535 AA-AAAGAAAG
1 AAGAAAG-AAG
39785545 AAG-AAGAAG
1 AAGAAAGAAG
* *
39785554 ATGAAAGGAG
1 AAGAAAGAAG
*
39785564 AAGAAAAAAG
1 AAGAAAGAAG
39785574 AAAGAAA-AAG
1 -AAGAAAGAAG
39785584 AAGGAAAGAA-
1 AA-GAAAGAAG
*
39785594 AAGGAAAGGAG
1 AA-GAAAGAAG
39785605 AAGA
1 AAGA
39785609 GAAATGATTA
Statistics
Matches: 74, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
7 2 0.03
8 1 0.01
9 13 0.18
10 44 0.59
11 14 0.19
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:39785562 original size:43 final size:41
Alignment explanation
Indices: 39785508--39785612 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 41
39785498 TGAGAGGAAA
39785508 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAG--AAAGAA-
1 GAAA-AAAAGGAAAGGAGAAGAGAAAAAAAAAGAAAAAGAAG
* * * *
39785547 GAAGAAGATGAAAGGAGAAGA-AAAAAGAAAGAAAAAGAAG
1 GAAAAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAAAAGAAG
39785587 GAAAGAAAAGGAAAGGAGAAGAGAAA
1 GAAA-AAAAGGAAAGGAGAAGAGAAA
39785613 TGATTAAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
37 9 0.17
38 15 0.28
39 9 0.17
40 3 0.06
41 15 0.28
42 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (41 bp):
GAAAAAAAGGAAAGGAGAAGAGAAAAAAAAAGAAAAAGAAG
Found at i:39789736 original size:3 final size:3
Alignment explanation
Indices: 39789728--39789753 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39789718 TCTTAATACT
39789728 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
39789754 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:39789758 original size:3 final size:3
Alignment explanation
Indices: 39789752--39789780 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39789742 CAACAACAAC
39789752 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39789781 CTAAAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39793518 original size:44 final size:44
Alignment explanation
Indices: 39793468--39793557 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
39793458 TGATAGTTAA
39793468 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
1 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
39793512 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
1 ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
39793556 AT
1 AT
39793558 TAACCCATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (44 bp):
ATCCATCTTTAGTTCTATAGTACAATGACAAATATAAATTGCAT
Found at i:39796135 original size:26 final size:26
Alignment explanation
Indices: 39796085--39796132 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 26
39796075 TAATGAAAGG
39796085 AAAAGAAAAAAAGAAGAATAAAACAT
1 AAAAGAAAAAAAGAAGAATAAAACAT
39796111 AAAAG---AAAAGAAGAATAAAACA
1 AAAAGAAAAAAAGAAGAATAAAACA
39796133 ACAACAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 17 0.77
26 5 0.23
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAAAGAAGAATAAAACAT
Found at i:39801148 original size:4 final size:4
Alignment explanation
Indices: 39801139--39801163 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39801129 TAATGGACAT
39801139 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
39801164 CATCAAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:39803204 original size:16 final size:16
Alignment explanation
Indices: 39803183--39803213 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39803173 CACCTAAGAC
39803183 ACACCTCAACCTTATA
1 ACACCTCAACCTTATA
*
39803199 ACACCTCAATCTTAT
1 ACACCTCAACCTTAT
39803214 CTGGATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
ACACCTCAACCTTATA
Found at i:39803819 original size:21 final size:21
Alignment explanation
Indices: 39803793--39803842 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
39803783 GTTTCCACAT
39803793 GCCCATGTCACTTACCCAGAC
1 GCCCATGTCACTTACCCAGAC
39803814 GCCCATGTCACTTACCCAGAC
1 GCCCATGTCACTTACCCAGAC
39803835 GCCCATGT
1 GCCCATGT
39803843 GCAACCCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20
Consensus pattern (21 bp):
GCCCATGTCACTTACCCAGAC
Found at i:39804852 original size:41 final size:41
Alignment explanation
Indices: 39804795--39804877 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
39804785 ATAGTGCCTC
39804795 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
1 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
39804836 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
1 AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
39804877 A
1 A
39804878 TCTACTCCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (41 bp):
AGACAACCCATTGAGTGGAGACTCATGCTCTACACTCTCTT
Found at i:39805154 original size:21 final size:21
Alignment explanation
Indices: 39805115--39805170 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
39805105 AAATCAAGCA
*
39805115 ATTCATTTACCAA-TTCCCAT
1 ATTCAATTACCAATTTCCCAT
39805135 ATTCAATTACCAATTTCCCAT
1 ATTCAATTACCAATTTCCCAT
39805156 ATTCAATTACCAATT
1 ATTCAATTACCAATT
39805171 GTAACACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 12 0.35
21 22 0.65
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTCAATTACCAATTTCCCAT
Found at i:39805310 original size:20 final size:20
Alignment explanation
Indices: 39805285--39805324 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39805275 CGTAAAATGA
*
39805285 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
39805305 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
39805325 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:39805314 original size:34 final size:35
Alignment explanation
Indices: 39805270--39805336 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39805260 CAGTAAAATA
*
39805270 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
39805304 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
39805337 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:39805340 original size:14 final size:15
Alignment explanation
Indices: 39805264--39805340 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
39805254 GATTGCCAGT
* *
39805264 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
39805278 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
39805292 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
39805312 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
39805327 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
39805341 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:39806688 original size:12 final size:12
Alignment explanation
Indices: 39806671--39806695 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39806661 CTTTGATTCG
39806671 TTCTAAATCATT
1 TTCTAAATCATT
39806683 TTCTAAATCATT
1 TTCTAAATCATT
39806695 T
1 T
39806696 GATTGAAAAT
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCTAAATCATT
Found at i:39807177 original size:17 final size:21
Alignment explanation
Indices: 39807137--39807182 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
39807127 ATTATTTTAA
39807137 AATTATTTTTCGATCTAAATT
1 AATTATTTTTCGATCTAAATT
39807158 AATTATTTTTC-A-CT-AA-T
1 AATTATTTTTCGATCTAAATT
39807175 AATTATTT
1 AATTATTT
39807183 AATTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 2 0.08
19 2 0.08
20 1 0.04
21 11 0.44
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTATTTTTCGATCTAAATT
Found at i:39811932 original size:138 final size:139
Alignment explanation
Indices: 39811684--39811958 Score: 419
Period size: 138 Copynumber: 2.0 Consensus size: 139
39811674 GGAGAACAAT
* * * * * *
39811684 AGGCTATAAGTGGATTTTTAAGCTACAAAAGAATGGTGATGGGACTATACCCAGATATAAGGCCA
1 AGGCTAGAAGTGGATTTTTAAGCTAAAAAAGAATGATGATGGAAATATACCCAGATACAAGGCCA
*
39811749 AACTAGTGGTCAAAGGGTATCTCCAAGAAATTGGTATTGATTTCCAAGAAACTTTTAG-CCTCTG
66 AACTAGTGGTCAAAGGGTATCTCCAAGAAACTGGTATTGATTTCCAAGAAACTTTTAGTCCTCTG
39811813 GTCAAACGA
131 GTCAAACGA
* * * *
39811822 AGGCTAGAAGTGGATTTTTAATCTAAAAAAGAATGATGATGGAAATATAGCTATATACAAGGCCA
1 AGGCTAGAAGTGGATTTTTAAGCTAAAAAAGAATGATGATGGAAATATACCCAGATACAAGGCCA
*
39811887 AACT-GATGGTCAAAGGGTATCTCCAAGAAGCTGGTATTGATTTCCAAGAAACTTTTAGTCCTCT
66 AACTAG-TGGTCAAAGGGTATCTCCAAGAAACTGGTATTGATTTCCAAGAAACTTTTAGTCCTCT
39811951 GGTCAAAC
130 GGTCAAAC
39811959 CAGCTACTAT
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
137 1 0.01
138 109 0.89
139 13 0.11
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (139 bp):
AGGCTAGAAGTGGATTTTTAAGCTAAAAAAGAATGATGATGGAAATATACCCAGATACAAGGCCA
AACTAGTGGTCAAAGGGTATCTCCAAGAAACTGGTATTGATTTCCAAGAAACTTTTAGTCCTCTG
GTCAAACGA
Found at i:39813213 original size:55 final size:55
Alignment explanation
Indices: 39813129--39813237 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
39813119 ACCAAACCTC
*
39813129 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACTTTGGTGTTGTTAGCAAGTA
1 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGTA
39813184 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGT
1 TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGT
39813238 CACTAGGAGG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (55 bp):
TATCAGCACCTTTTTTCAACAAGTTTAGGTTCAACCTTGGTGTTGTTAGCAAGTA
Found at i:39815032 original size:20 final size:20
Alignment explanation
Indices: 39815007--39815053 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
39814997 GATTGAGTTT
*
39815007 TTTTTTTTCTCAAAAGAGTA
1 TTTTTTTTCTCAAAAGAGAA
39815027 TTTTTTTTCTCAAAAGAGAA
1 TTTTTTTTCTCAAAAGAGAA
39815047 TTTTTTT
1 TTTTTTT
39815054 CTGGTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTTTTTCTCAAAAGAGAA
Found at i:39820016 original size:45 final size:45
Alignment explanation
Indices: 39819952--39820042 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
39819942 CTATCTCGAG
39819952 TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
1 TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
*
39819997 TTTCCAAGATATTTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
1 TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
39820042 T
1 T
39820043 AATTGTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (45 bp):
TTTCCAAGATATCTACCTTCTTATTCTTCTTTTTTTGCTTGTTTA
Found at i:39831697 original size:18 final size:19
Alignment explanation
Indices: 39831676--39831716 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
39831666 TATATAATTT
*
39831676 ATAAAAAAAATTTAA-TAA
1 ATAAAAAAAATTAAATTAA
*
39831694 ATAAAAAATATTAAATTAA
1 ATAAAAAAAATTAAATTAA
39831713 ATAA
1 ATAA
39831717 TATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAAAAAAATTAAATTAA
Found at i:39832144 original size:9 final size:9
Alignment explanation
Indices: 39832130--39832160 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39832120 TTTGGTTAAA
39832130 AATTAACCG
1 AATTAACCG
39832139 AATTAACCG
1 AATTAACCG
*
39832148 AATTAACTG
1 AATTAACCG
39832157 AATT
1 AATT
39832161 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:39834770 original size:16 final size:17
Alignment explanation
Indices: 39834745--39834778 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39834735 ATCATTTTCT
*
39834745 TTTAATTATAT-AATTA
1 TTTAAATATATCAATTA
39834761 TTTAAATATATCAATTA
1 TTTAAATATATCAATTA
39834778 T
1 T
39834779 AAATTAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATATATCAATTA
Found at i:39860180 original size:17 final size:17
Alignment explanation
Indices: 39860158--39860190 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39860148 TTATTCTATT
39860158 TAATTA-ATTTTACTAAA
1 TAATTATATTTT-CTAAA
39860175 TAATTATATTTTCTAA
1 TAATTATATTTTCTAA
39860191 TGTTGCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTATATTTTCTAAA
Found at i:39866442 original size:15 final size:17
Alignment explanation
Indices: 39866412--39866443 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
39866402 AAATATTTAT
39866412 ACAATTATTATATAATA
1 ACAATTATTATATAATA
39866429 ACAA-TATT-TATAATA
1 ACAATTATTATATAATA
39866444 TATTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ACAATTATTATATAATA
Found at i:39870575 original size:2 final size:2
Alignment explanation
Indices: 39870568--39870620 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
39870558 AGCAGAAAGC
39870568 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
39870610 CA CA CT CT CT C
1 CT CT CT CT CT C
39870621 ACAGTTTCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.04, C:0.51, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:39872182 original size:20 final size:20
Alignment explanation
Indices: 39872154--39872255 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
39872144 AGATGTTAAT
*
39872154 ATTTCTAATGCAAAACCAAA
1 ATTTCTAATGCAAAACAAAA
* *
39872174 ATTTGTAAT-CAATACAAAA
1 ATTTCTAATGCAAAACAAAA
*
39872193 ATTTCTAATGCAATATC-AAA
1 ATTTCTAATGCAA-AACAAAA
* * * *
39872213 ATATC-AATGCTATATAAAA
1 ATTTCTAATGCAAAACAAAA
* * *
39872232 ATCTCTAATGCAATACCAAA
1 ATTTCTAATGCAAAACAAAA
39872252 ATTT
1 ATTT
39872256 TTAAGAATAT
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
19 29 0.47
20 32 0.52
21 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTTCTAATGCAAAACAAAA
Found at i:39872195 original size:19 final size:21
Alignment explanation
Indices: 39872154--39872252 Score: 93
Period size: 19 Copynumber: 5.0 Consensus size: 21
39872144 AGATGTTAAT
* *
39872154 ATTTCTAATGCAA-AACCAAA
1 ATTTCTAATGCAATATCAAAA
*
39872174 ATTTGTAAT-CAATA-CAAAA
1 ATTTCTAATGCAATATCAAAA
39872193 ATTTCTAATGCAATATC-AAA
1 ATTTCTAATGCAATATCAAAA
* *
39872213 ATATC-AATGCTATAT-AAAA
1 ATTTCTAATGCAATATCAAAA
* *
39872232 ATCTCTAATGCAATACCAAAA
1 ATTTCTAATGCAATATCAAAA
39872253 TTTTTAAGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
19 31 0.48
20 29 0.45
21 5 0.08
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.29
Consensus pattern (21 bp):
ATTTCTAATGCAATATCAAAA
Found at i:39872197 original size:39 final size:39
Alignment explanation
Indices: 39872154--39872255 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 39
39872144 AGATGTTAAT
* *
39872154 ATTTCTAATGCAAAACCAAAATTTGTAAT-CAATACAAAA
1 ATTTCTAATGCAATACCAAAATTT-CAATGCAATACAAAA
* * * *
39872193 ATTTCTAATGCAATATCAAAATATCAATGCTATATAAAA
1 ATTTCTAATGCAATACCAAAATTTCAATGCAATACAAAA
*
39872232 ATCTCTAATGCAATACCAAAATTT
1 ATTTCTAATGCAATACCAAAATTT
39872256 TTAAGAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 3 0.06
39 50 0.94
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (39 bp):
ATTTCTAATGCAATACCAAAATTTCAATGCAATACAAAA
Found at i:39874443 original size:21 final size:21
Alignment explanation
Indices: 39874419--39874493 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 21
39874409 AAAGAAATTG
39874419 AAAAATCATTTTAAAAAATTC-
1 AAAAAT-ATTTTAAAAAATTCT
*
39874440 -AAAATATTTATAAAAAAATCT
1 AAAAATATTT-TAAAAAATTCT
39874461 AAAATTTATATTTTTAAAAAATTCT
1 AAAA---ATA-TTTTAAAAAATTCT
39874486 AAAAATAT
1 AAAAATAT
39874494 ATAAAGAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
19 4 0.09
20 14 0.31
21 1 0.02
22 6 0.13
25 17 0.38
26 3 0.07
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATATTTTAAAAAATTCT
Found at i:39874467 original size:19 final size:20
Alignment explanation
Indices: 39874420--39874470 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
39874410 AAGAAATTGA
*
39874420 AAAATCATTT-TAAAAAATTC
1 AAAAT-ATTTATAAAAAAATC
39874440 AAAATATTTATAAAAAAATC
1 AAAATATTTATAAAAAAATC
*
39874460 TAAA-ATTTATA
1 AAAATATTTATA
39874471 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATATTTATAAAAAAATC
Found at i:39885849 original size:25 final size:23
Alignment explanation
Indices: 39885821--39885891 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
39885811 CCAATATATA
39885821 GCTCTTCGAAGCTTCCCGATAACTG
1 GCTCTTCG-AGCTTCCCGATAA-TG
* *
39885846 GCTCTTATGGGCTTCCCGATTAATG
1 GCTCTT-CGAGCTTCCCGA-TAATG
* *
39885871 GCTCTCCGGAGCTTCCAGATA
1 GCTCTTC-GAGCTTCCCGATA
39885892 TTGACTCCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
24 2 0.05
25 31 0.84
26 4 0.11
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.30
Consensus pattern (23 bp):
GCTCTTCGAGCTTCCCGATAATG
Found at i:39887139 original size:73 final size:73
Alignment explanation
Indices: 39887034--39887208 Score: 332
Period size: 73 Copynumber: 2.4 Consensus size: 73
39887024 CACGGCCTGA
* *
39887034 CACACGGGCATGTGGCTTGGCCGTGTGACACCTGTACCTTATTTATGCAAGTCAGTATGTTCACA
1 CACACGGACGTGTGGCTTGGCCGTGTGACACCTGTACCTTATTTATGCAAGTCAGTATGTTCACA
39887099 CAACCTAG
66 CAACCTAG
39887107 CACACGGACGTGTGGCTTGGCCGTGTGACACCTGTACCTTATTTATGCAAGTCAGTATGTTCACA
1 CACACGGACGTGTGGCTTGGCCGTGTGACACCTGTACCTTATTTATGCAAGTCAGTATGTTCACA
39887172 CAACCTAG
66 CAACCTAG
39887180 CACACGGACGTGTGGCTTGGCCGTGTGAC
1 CACACGGACGTGTGGCTTGGCCGTGTGAC
39887209 CCAAGTCAGA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 100 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (73 bp):
CACACGGACGTGTGGCTTGGCCGTGTGACACCTGTACCTTATTTATGCAAGTCAGTATGTTCACA
CAACCTAG
Found at i:39890275 original size:14 final size:15
Alignment explanation
Indices: 39890258--39890290 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39890248 TCTTTCCATT
39890258 TCTTTCT-TCTTCCC
1 TCTTTCTCTCTTCCC
39890272 TCTTTCTCTCTTCCC
1 TCTTTCTCTCTTCCC
39890287 -CTTT
1 TCTTT
39890291 ATTATATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TCTTTCTCTCTTCCC
Found at i:39893233 original size:45 final size:45
Alignment explanation
Indices: 39893183--39893273 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
39893173 GAAGGAAACT
*
39893183 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTGGGTAATTA
1 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
39893228 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
1 AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
39893273 A
1 A
39893274 TCCTTCTAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (45 bp):
AAATACTTAGGATTTTCTAATTTGGAGGGGTTAATTAGGTAATTA
Found at i:39905355 original size:21 final size:21
Alignment explanation
Indices: 39905329--39905371 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39905319 TGATGCCAAG
*
39905329 TCCATCTACTTAGATTTTCCC
1 TCCATCTACTTAGAATTTCCC
39905350 TCCATCTACTTAGAATTTCCC
1 TCCATCTACTTAGAATTTCCC
39905371 T
1 T
39905372 TACTACACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.42
Consensus pattern (21 bp):
TCCATCTACTTAGAATTTCCC
Found at i:39913126 original size:12 final size:12
Alignment explanation
Indices: 39913109--39913134 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39913099 TTAGGTTTCC
39913109 AAAAATGGAAAT
1 AAAAATGGAAAT
39913121 AAAAATGGAAAT
1 AAAAATGGAAAT
39913133 AA
1 AA
39913135 TCCATTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAAATGGAAAT
Found at i:39913780 original size:30 final size:30
Alignment explanation
Indices: 39913744--39913812 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
39913734 TATTTCTATT
*
39913744 AAGAAGAGAGAATTTTCATTTTCACCCTAA
1 AAGAAGAGAGAATTTTCATTTTCACCCCAA
**
39913774 AAGAAGAGAGAATTTTTGTTTTCACCCCAA
1 AAGAAGAGAGAATTTTCATTTTCACCCCAA
*
39913804 AAGGAGAGA
1 AAGAAGAGA
39913813 AAACTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (30 bp):
AAGAAGAGAGAATTTTCATTTTCACCCCAA
Found at i:39919892 original size:26 final size:26
Alignment explanation
Indices: 39919862--39919924 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
39919852 ATGAAATTTC
*
39919862 TCAAAATTTTACCAAGGGTAAAATCA
1 TCAAAATTTTAACAAGGGTAAAATCA
* ** **
39919888 TCAAATTTTTAACGGGGGTAAAATTG
1 TCAAAATTTTAACAAGGGTAAAATCA
39919914 TCAAAATTTTA
1 TCAAAATTTTA
39919925 TTAGAGGTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTAACAAGGGTAAAATCA
Found at i:39933739 original size:29 final size:30
Alignment explanation
Indices: 39933689--39933749 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
39933679 AAGTTTTCGT
*
39933689 TTTGGTCACTTAACTAAACAAA-TTTACAA
1 TTTGGTCACTAAACTAAACAAAGTTTACAA
** *
39933718 TTTGGTCACTAAACTATTCAAAGTTTTCAA
1 TTTGGTCACTAAACTAAACAAAGTTTACAA
39933748 TT
1 TT
39933750 AAGCCGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (30 bp):
TTTGGTCACTAAACTAAACAAAGTTTACAA
Found at i:39934223 original size:14 final size:14
Alignment explanation
Indices: 39934200--39934231 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39934190 GACGATTCTC
*
39934200 AAAAGTAAAAGAAA
1 AAAAGAAAAAGAAA
39934214 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
39934228 AAAA
1 AAAA
39934232 AAATTTGTTA
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:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:39954108 original size:19 final size:19
Alignment explanation
Indices: 39954065--39954101 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39954055 AATTGAGGAT
39954065 TAGAAACGAGATTAGAATG
1 TAGAAACGAGATTAGAATG
*
39954084 TAGAAATGAGATTAGAAT
1 TAGAAACGAGATTAGAAT
39954102 TTTGAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (19 bp):
TAGAAACGAGATTAGAATG
Found at i:39956349 original size:6 final size:6
Alignment explanation
Indices: 39956341--39956370 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
39956331 GTAGACGTGT
*
39956341 GAATGT GAATGC GAATGC GAATGC GAATGC
1 GAATGC GAATGC GAATGC GAATGC GAATGC
39956371 TCAAGGGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (6 bp):
GAATGC
Found at i:39985104 original size:28 final size:30
Alignment explanation
Indices: 39985050--39985105 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
39985040 ATTTTTCCAT
* *
39985050 TGATGAATCTATGTGATTTTAGATGTTAAA
1 TGATGAATCTATGAGATATTAGATGTTAAA
*
39985080 TGATGAAT-T-TGAGATATTAGTTGTTA
1 TGATGAATCTATGAGATATTAGATGTTA
39985106 TTTAAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 1 0.04
30 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (30 bp):
TGATGAATCTATGAGATATTAGATGTTAAA
Found at i:39985794 original size:75 final size:74
Alignment explanation
Indices: 39985609--39985828 Score: 224
Period size: 75 Copynumber: 2.9 Consensus size: 74
39985599 ATGCAGTGAT
* * * *
39985609 TTTGGGCTATGTGCCTTGTAGGCTTTGTACCGGTGATTTTGGGATATGTGCCTAGCAGGCTTTGT
1 TTTGGGCTATGTGCCTAG-AAGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
**
39985674 GCCGATGTTA
65 GCCGATCATA
* * * * *
39985684 TTTGGGCTATGTGCTTAGTAGAATTTGTGCTGGTGATTTTGGGCTATGTGCCTAGCAGGGTTTGT
1 TTTGGGCTATGTGCCTAGAAG-CTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGT
** *
39985749 GTTGGTCATA
65 GCCGATCATA
* * * * * *
39985759 TTTGGGCTTTGTGCCTAGCAAGCTTTATGCCGGTGATATTCGAGCTCTGTGCCTAGTAGGCTTTG
1 TTTGGGCTATGTGCCTAG-AAGCTTTGTGCCGGTGAT-TTTGGGCTATGTGCCTAGCAGGCTTTG
39985824 TGCCG
64 TGCCG
39985829 GTGATATTCG
Statistics
Matches: 115, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
74 1 0.01
75 87 0.76
76 27 0.23
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.39
Consensus pattern (74 bp):
TTTGGGCTATGTGCCTAGAAGCTTTGTGCCGGTGATTTTGGGCTATGTGCCTAGCAGGCTTTGTG
CCGATCATA
Found at i:39985844 original size:38 final size:38
Alignment explanation
Indices: 39985604--39985836 Score: 247
Period size: 38 Copynumber: 6.2 Consensus size: 38
39985594 TAGAAATGCA
* * *
39985604 GTGAT-TTTGGGCTATGTGCCTTGTAGGCTTTGTACCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
*
39985641 GTGAT-TTTGGGATATGTGCCTAGCAGGCTTTGTGCCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* * * * ** *
39985678 ATGTTATTTGGGCTATGTGCTTAGTAGAATTTGTGCTG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* **
39985716 GTGAT-TTTGGGCTATGTGCCTAGCAGGGTTTGTGTTG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* * * *
39985753 GTCATATTTGGGCTTTGTGCCTAGCAAGCTTTATGCCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
* * * *
39985791 GTGATATTCGAGCTCTGTGCCTAGTAGGCTTTGTGCCG
1 GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
39985829 GTGATATT
1 GTGATATT
39985837 CGAGCTCTAT
Statistics
Matches: 161, Mismatches: 33, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
37 67 0.42
38 94 0.58
ACGTcount: A:0.14, C:0.15, G:0.32, T:0.39
Consensus pattern (38 bp):
GTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCCG
Found at i:39985861 original size:38 final size:38
Alignment explanation
Indices: 39985770--39985864 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
39985760 TTGGGCTTTG
* *
39985770 TGCCTAGCAAGCTTTATGCCGGTGATATTCGAGCTCTG
1 TGCCTAGCAAGCTTTGTGCCGGTGATATTCGAGCTCTA
* *
39985808 TGCCTAGTAGGCTTTGTGCCGGTGATATTCGAGCTCTA
1 TGCCTAGCAAGCTTTGTGCCGGTGATATTCGAGCTCTA
* *
39985846 TGGCTAGCAACCTTTGTGC
1 TGCCTAGCAAGCTTTGTGC
39985865 AAGTGTATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (38 bp):
TGCCTAGCAAGCTTTGTGCCGGTGATATTCGAGCTCTA
Found at i:39985947 original size:41 final size:41
Alignment explanation
Indices: 39985867--39985963 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 41
39985857 CTTTGTGCAA
* * * *
39985867 GTGTATTATATCAGGCTTTGTGCTTAGTTGGCTTTGTGCCG
1 GTGTATTATATCAGGCTTCGAGCTTAGTAGGCTTCGTGCCG
* * * *
39985908 GTGTGTTATATCAGGCTTCGAGCTTGGTAGTCTTCGTGCCA
1 GTGTATTATATCAGGCTTCGAGCTTAGTAGGCTTCGTGCCG
* *
39985949 ATGTATTGTATCAGG
1 GTGTATTATATCAGG
39985964 TAAGTTGTAC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.40
Consensus pattern (41 bp):
GTGTATTATATCAGGCTTCGAGCTTAGTAGGCTTCGTGCCG
Found at i:39993314 original size:41 final size:41
Alignment explanation
Indices: 39993234--39993356 Score: 117
Period size: 41 Copynumber: 3.0 Consensus size: 41
39993224 GATATTAAAC
* * * *
39993234 CAAGCTCTATGCCTAGCAGGCTTTGTGCTTG-TGACTTATAT
1 CAAGCTCTGTGCCTAGCAGGCTTCGTGC-CGATGATTTATAT
*
39993275 CAAGCTCTGTGCCTAGCAGGCTTCATGCCGATGATTTATAT
1 CAAGCTCTGTGCCTAGCAGGCTTCGTGCCGATGATTTATAT
* * * *
39993316 CAGGCT-TAGTACCTAACAGGCTTCGTTCC-AGTGATTTATAT
1 CAAGCTCT-GTGCCTAGCAGGCTTCGTGCCGA-TGATTTATAT
39993357 TAGAATTTGT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.04
41 66 0.96
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (41 bp):
CAAGCTCTGTGCCTAGCAGGCTTCGTGCCGATGATTTATAT
Found at i:39999210 original size:41 final size:41
Alignment explanation
Indices: 39999144--39999238 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
39999134 GAGATAATAA
* * * **
39999144 ATCAAGCTCTGTACCTAGTAGGCTTCGTGCCGGTGATTTAT
1 ATCAGGCTCTGTACCTAGCAAGCTTCGTGCCAATGATTTAT
*
39999185 ATCAGGCTCTGTGCCTAGCAAGCTTCGTGCCAATGATTTAT
1 ATCAGGCTCTGTACCTAGCAAGCTTCGTGCCAATGATTTAT
*
39999226 ATCAGGCTTTGTA
1 ATCAGGCTCTGTA
39999239 GAAAGCTTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (41 bp):
ATCAGGCTCTGTACCTAGCAAGCTTCGTGCCAATGATTTAT
Found at i:39999259 original size:37 final size:40
Alignment explanation
Indices: 39999165--39999264 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 40
39999155 TACCTAGTAG
* *
39999165 GCTTCGTGCCGGTGATTTATATCAGGCTCTGTGCCTAGCAA
1 GCTTCGTGCCAGTGATTTATATCAGGCTCTGTG-CTAGAAA
*
39999206 GCTTCGTGCCAATGATTTATATCAGGCT-T-TG-TAGAAA
1 GCTTCGTGCCAGTGATTTATATCAGGCTCTGTGCTAGAAA
* *
39999243 GCTTGGTGTCAGTGATTTATAT
1 GCTTCGTGCCAGTGATTTATAT
39999265 TAGCAAGCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 24 0.45
39 2 0.04
40 1 0.02
41 26 0.49
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
GCTTCGTGCCAGTGATTTATATCAGGCTCTGTGCTAGAAA
Found at i:40004130 original size:21 final size:22
Alignment explanation
Indices: 40004101--40004158 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
40004091 TGTAGGGGTA
* *
40004101 CACACGCCCATGTGAA-GGAGG
1 CACATGCCCGTGTGAAGGGAGG
*
40004122 CACATGCCCGGGTGAAGGGAGG
1 CACATGCCCGTGTGAAGGGAGG
*
40004144 CACATGGCCGTGTGA
1 CACATGCCCGTGTGA
40004159 CTATGACACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.24, C:0.26, G:0.38, T:0.12
Consensus pattern (22 bp):
CACATGCCCGTGTGAAGGGAGG
Found at i:40006215 original size:12 final size:12
Alignment explanation
Indices: 40006187--40006222 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
40006177 GCAAATGAAT
*
40006187 CATTTCTCATTTT
1 CATTTC-CATTTC
40006200 CATTTCCATTTC
1 CATTTCCATTTC
40006212 CATTTCCATTT
1 CATTTCCATTT
40006223 TGAGAAAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTTCCATTTC
Found at i:40006221 original size:18 final size:19
Alignment explanation
Indices: 40006187--40006222 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40006177 GCAAATGAAT
*
40006187 CATTTCTCATTTTCATTTC
1 CATTTCTCATTTCCATTTC
40006206 CATTTC-CATTTCCATTT
1 CATTTCTCATTTCCATTT
40006223 TGAGAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (19 bp):
CATTTCTCATTTCCATTTC
Found at i:40008323 original size:20 final size:21
Alignment explanation
Indices: 40008298--40008343 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
40008288 ATTGAATTTA
40008298 TTTTATCTTTT-TTTATAT-AT
1 TTTTAT-TTTTATTTATATGAT
*
40008318 TTTTATTTTTATTTGTATGAT
1 TTTTATTTTTATTTATATGAT
40008339 TTTTA
1 TTTTA
40008344 ATAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 7 0.30
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTATTTTTATTTATATGAT
Found at i:40008661 original size:29 final size:29
Alignment explanation
Indices: 40008628--40008718 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 29
40008618 GAAACTGTTG
*
40008628 AATTATCTTTTCTTTATCAATGTTGTTAA
1 AATTATCTTCTCTTTATCAATGTTGTTAA
* *
40008657 AATTAT-TATGTGTTTGA--AACTGTTG----
1 AATTATCT-TCTCTTT-ATCAA-TGTTGTTAA
40008682 AATTATCTTCTCTTTATCAATGTTGTTAA
1 AATTATCTTCTCTTTATCAATGTTGTTAA
40008711 AATTATCT
1 AATTATCT
40008719 CCTTATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 20
0.67 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 16 0.33
26 3 0.06
28 3 0.06
29 24 0.50
30 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (29 bp):
AATTATCTTCTCTTTATCAATGTTGTTAA
Found at i:40008674 original size:54 final size:54
Alignment explanation
Indices: 40008610--40008716 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
40008600 ACACTTTCTC
*
40008610 ATGTGTTTGAAACTGTTGAATTATCTTTTCTTTATCAATGTTGTTAAAATTATT
1 ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTATT
40008664 ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTAT
1 ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTAT
40008717 CTCCTTATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.50
Consensus pattern (54 bp):
ATGTGTTTGAAACTGTTGAATTATCTTCTCTTTATCAATGTTGTTAAAATTATT
Found at i:40015126 original size:25 final size:25
Alignment explanation
Indices: 40015098--40015150 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
40015088 CTCAACTAAA
40015098 TAATCCAACTCGAAATATAAAATTT
1 TAATCCAACTCGAAATATAAAATTT
40015123 TAATCCAACTCGAAATATAAAATTT
1 TAATCCAACTCGAAATATAAAATTT
40015148 TAA
1 TAA
40015151 AAATTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (25 bp):
TAATCCAACTCGAAATATAAAATTT
Found at i:40022750 original size:15 final size:15
Alignment explanation
Indices: 40022730--40022764 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
40022720 CTTTCAAAGT
40022730 ACATATCAATTTCAC
1 ACATATCAATTTCAC
40022745 ACATATCAATTTCAC
1 ACATATCAATTTCAC
40022760 ACATA
1 ACATA
40022765 CTTGAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (15 bp):
ACATATCAATTTCAC
Found at i:40029972 original size:5 final size:5
Alignment explanation
Indices: 40029962--40029995 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
40029952 AGGTATTTGT
40029962 TTTTC TTTTC TTTTC TTTTC TTTT- TATTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTT
40029996 TTGGACCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:40036883 original size:15 final size:16
Alignment explanation
Indices: 40036863--40036895 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40036853 ATTCGATCTC
40036863 AAAAAAAAAGAA-AAG
1 AAAAAAAAAGAAGAAG
*
40036878 AAAAAAGAAGAAGAAG
1 AAAAAAAAAGAAGAAG
40036894 AA
1 AA
40036896 GCAAAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAGAAG
Found at i:40036953 original size:40 final size:40
Alignment explanation
Indices: 40036891--40036994 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 40
40036881 AAAGAAGAAG
* * *
40036891 AAGAAGCAAAA-ACAAAAGCAAAAT-CAAGATCAAAACAAAA
1 AAGAAGAAAAAGA-AAAAGCAAAATAAAAAATCAAAA-AAAA
* *
40036931 AAGAAGAAAAAGAAAAATCAAAATAAAAAATCAAAATAAA
1 AAGAAGAAAAAGAAAAAGCAAAATAAAAAATCAAAAAAAA
*
40036971 ATGAGAGAAAAAGAAAGAAG-AAAA
1 AAGA-AGAAAAAGAAA-AAGCAAAA
40036995 GAAGAAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
40 26 0.49
41 25 0.47
42 2 0.04
ACGTcount: A:0.73, C:0.08, G:0.12, T:0.07
Consensus pattern (40 bp):
AAGAAGAAAAAGAAAAAGCAAAATAAAAAATCAAAAAAAA
Found at i:40036958 original size:12 final size:12
Alignment explanation
Indices: 40036938--40036971 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
40036928 AAAAAGAAGA
*
40036938 AAAAGAAAAATC
1 AAAATAAAAATC
40036950 AAAATAAAAAATC
1 AAAAT-AAAAATC
40036963 AAAATAAAA
1 AAAATAAAA
40036972 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:40036959 original size:13 final size:13
Alignment explanation
Indices: 40036943--40036971 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40036933 GAAGAAAAAG
40036943 AAAAATCAAAATA
1 AAAAATCAAAATA
40036956 AAAAATCAAAATA
1 AAAAATCAAAATA
40036969 AAA
1 AAA
40036972 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:40037885 original size:7 final size:7
Alignment explanation
Indices: 40037869--40037922 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 7
40037859 CTTTGAGTAA
*
40037869 AAAAACG
1 AAAAATG
40037876 AAAAATG
1 AAAAATG
40037883 AAAAAATG
1 -AAAAATG
40037891 -AAAATG
1 AAAAATG
*
40037897 GAAAATG
1 AAAAATG
40037904 AAAAA-G
1 AAAAATG
*
40037910 AAAAGT-
1 AAAAATG
40037916 AAAAATG
1 AAAAATG
40037923 GAGAGGCTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 16 0.41
7 16 0.41
8 7 0.18
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (7 bp):
AAAAATG
Found at i:40039267 original size:44 final size:44
Alignment explanation
Indices: 40039214--40039467 Score: 172
Period size: 44 Copynumber: 5.5 Consensus size: 44
40039204 CGAAGCCAAA
* *
40039214 AATCTTATCTCCTTGAGATTACAGCGGATCAGATTGAAGCTAGT
1 AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
* * ** *
40039258 AATCCTATCTCCCTGAGATTACAGTGGAGT-GGATT-AAAATAAAT
1 AATCCTATCTCCCTGAGATTACAGCGGA-TCAGATTGAAGCT-AGT
* * * * * * * *
40039302 GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGATTGAAACCAGA
1 AATCCTATCTCCCTGAGA-TTAC--------AG--CGGATCAGATTGAAGCTAGT
* * * *
40039356 AATCTTATCTCCCTGAAATTACAGCGAAGCAGATTGAAGCTAGT
1 AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
* *
40039400 AATCCTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAAT
1 AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
*
40039444 AATCCTATCTCCCTAAGATTACAG
1 AATCCTATCTCCCTGAGATTACAG
40039468 TGGAACGGAT
Statistics
Matches: 164, Mismatches: 30, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
43 5 0.03
44 124 0.76
45 1 0.01
46 2 0.01
52 2 0.01
53 1 0.01
54 23 0.14
55 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCCTGAGATTACAGCGGATCAGATTGAAGCTAGT
Found at i:40039670 original size:50 final size:50
Alignment explanation
Indices: 40039605--40040389 Score: 492
Period size: 50 Copynumber: 15.7 Consensus size: 50
40039595 GTAGTGGAAC
* * * *
40039605 AGATTAAATCCACAACGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * * * * * ** *
40039655 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *
40039705 AGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *** ** * * * ** ** *
40039755 AGATTAAAGCTACAGTAGCAAATCTTACCTCCCAGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *
40039805 AGATTAAAGCCACAACGGTGAATCTT-GTCTCCCTGACATTGCAGTTGAAA
1 AGATTAAAGCCACAACGGTGAATCTTACT-TCCCTGACATTGCAGTTAAAA
* * ** * * * * **
40039855 AGACTAAAGCCACAGC-GACAAGTGTTACTTCCCTGGCAATGCAGTGAAGC
1 AGATTAAAGCCACAACGGTGAA-TCTTACTTCCCTGACATTGCAGTTAAAA
* * * *
40039905 AGATTAAAGCCACAACGGTAAATCTTGCTTTCCTGACATTTCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * * * * * * * **
40039955 GGATTAAAGTCACAACGATGAATCTCACTCTCTCAGCCAGTACAG-TAGAGC
1 AGATTAAAGCCACAACGGTGAATCTTACT-TCCCTGACATTGCAGTTA-AAA
* * * *
40040006 ATATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGCT-AAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-TTCCCTGACATTGCAGTTAAAA
* * * * * * * ** *
40040055 AGAATTAAAGCTACAACAGCGAATCTTACTTCTCAGGCAGTGCAGTGGAAC
1 AG-ATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * *
40040106 AGGTTAAAGCCACAACGGTGAATCTT-GTCTCCCTAACATTGCAGTTGAAA
1 AGATTAAAGCCACAACGGTGAATCTTACT-TCCCTGACATTGCAGTTAAAA
* * * * * * * * **
40040156 AGACTAAAGCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAGC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
* *
40040206 AGATTAAAGCCACAACGGTAAATCTTGCTTTCCC-GACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-TTCCCTGACATTGCAGTTAAAA
* * ** * * * *
40040256 GGATTAAAGTCACAACGACGAATCTCAC-TCTCTAAGACAGTGCAG-TAGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCT--GACATTGCAGTTA-AAA
* *
40040307 AGATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-TTCCCTGACATTGCAGTTAAAA
* * *
40040357 GGATTAAAGCTACAACAGTGAATCTTACTTCCC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCC
40040390 AGGCAGTGCA
Statistics
Matches: 536, Mismatches: 178, Indels: 43
0.71 0.24 0.06
Matches are distributed among these distances:
48 3 0.01
49 15 0.03
50 431 0.80
51 83 0.15
52 1 0.00
53 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAAA
Found at i:40039752 original size:100 final size:100
Alignment explanation
Indices: 40039597--40040422 Score: 908
Period size: 100 Copynumber: 8.2 Consensus size: 100
40039587 CAAACGATGT
* * *
40039597 AGTGGAACAGATTAAATCCACAACGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAGATTAA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTAA
40039662 AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
66 AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
*
40039697 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTAA
** * *
40039762 AGCTACAGTAGCAAATCTTACCTCCCAGGCGGTGC
66 AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* *
40039797 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTG-TCTCCCTGACATTGCAGTTGAAAAGACTA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCT-TCCCTGACATTGCAGTTAAAAAGATTA
* * * *
40039861 AAGC--C-ACAGCGACAAGTGTTACTTCCCTGGCAATGC
65 AAGCTACAACAGCG--AA-TCTTACCTCCCAGGCAGTGC
* * * *
40039897 AGT-GAAGCAGATTAAAGCCACAACGGTAAATCTTGCTTTCCTGACATTTCAGTTAAAAGGATTA
1 AGTGGAA-CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTA
* * * * *
40039961 AAG-TCACAAC-GATGAATCTCACTCTCTCAGCCAGTAC
65 AAGCT-ACAACAG-CGAATCTTAC-CTCCCAGGCAGTGC
* * * * *
40039998 AGTAGAGCATATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGCT-AAAAGAATT
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC-TTCCCTGACATTGCAGTTAAAAAG-ATT
* *
40040061 AAAGCTACAACAGCGAATCTTACTTCTCAGGCAGTGC
64 AAAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* * * *
40040098 AGTGGAACAGGTTAAAGCCACAACGGTGAATCTTG-TCTCCCTAACATTGCAGTTGAAAAGACTA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCT-TCCCTGACATTGCAGTTAAAAAGATTA
* * * * * *
40040162 AAGCCACAGCAGCGAATGTTACTTCCCTGGCAATGC
65 AAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* *
40040198 AGT-GAAGCAGATTAAAGCCACAACGGTAAATCTTGCTTTCCC-GACATTGCAGTTAAAAGGATT
1 AGTGGAA-CAGATTAAAGCCACAACGGTGAATCTTGC-TTCCCTGACATTGCAGTTAAAAAGATT
* ** *
40040261 AAAG-TCACAAC-GACGAATCTCACTCTCTAAGACAGTGC
64 AAAGCT-ACAACAG-CGAATCTTAC-CTCCCAGGCAGTGC
* * *
40040299 AGTAGAACAGATTAAAGCCACATCGGTGAATCTTGCTTTCCC-GACATTGCAGTTAAAAGGATTA
1 AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGC-TTCCCTGACATTGCAGTTAAAAAGATTA
* *
40040363 AAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGC
65 AAGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
* * *
40040399 AGTGGAACAAATTGAAGCTACAAC
1 AGTGGAACAGATTAAAGCCACAAC
40040423 AACAAATCTC
Statistics
Matches: 607, Mismatches: 90, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
97 3 0.00
98 2 0.00
99 13 0.02
100 409 0.67
101 161 0.27
102 16 0.03
103 3 0.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (100 bp):
AGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGATTAA
AGCTACAACAGCGAATCTTACCTCCCAGGCAGTGC
Found at i:40040147 original size:301 final size:301
Alignment explanation
Indices: 40039604--40040422 Score: 1238
Period size: 301 Copynumber: 2.7 Consensus size: 301
40039594 TGTAGTGGAA
* * * * *
40039604 CAGATTAAATCCACAACGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAGATTAAAG-CTAC
1 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTC-AC
* * * * *
40039668 AAC-AGCGAATCTTAC-CTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTT
65 AACGA-CGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTT
* ** * * *
40039731 GC-CTCCCTGACATTGCAGTTAAAA-AGATTAAAGCTACAGTAGCAAATCTTACCTCCCAGGCGG
129 GCTTTCCC-GACATTGCAGTTAAAAGA-ATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAG
*
40039794 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTGACATTGCAGTTGAAAAGAC
192 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGAC
40039859 TAAAGCCACAGC-GAC-AAGTGTTACTTCCCTGGCAATGCAGTGAAG
257 TAAAGCCACAGCAG-CGAA-TGTTACTTCCCTGGCAATGCAGTGAAG
* *
40039904 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCTGACATTTCAGTTAAAAGGATTAAAGTCACA
1 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
* * * * *
40039969 ACGATGAATCTCACTCTCTCAGCCAGTACAGTAGAGCATATTAAAGCCACATCGGTGAATCTTGC
66 ACGACGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
* *
40040034 TTTCCCGACATTGCAGCTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCTCAGGCAGTGCA
131 TTTCCCGACATTGCAGTTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCA
*
40040099 GTGGAACAGGTTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGACTAAA
196 GTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGACTAAA
40040164 GCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAG
261 GCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAG
40040205 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
1 CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
*
40040270 ACGACGAATCTCACTCTCTAAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
66 ACGACGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
* *
40040335 TTTCCCGACATTGCAGTTAAAAGGATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCA
131 TTTCCCGACATTGCAGTTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCA
* * *
40040400 GTGGAACAAATTGAAGCTACAAC
196 GTGGAACAGATTAAAGCCACAAC
40040423 AACAAATCTC
Statistics
Matches: 470, Mismatches: 42, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
300 66 0.14
301 396 0.84
302 8 0.02
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (301 bp):
CAGATTAAAGCCACAACGGTAAATCTTGCTTTCCCGACATTGCAGTTAAAAGGATTAAAGTCACA
ACGACGAATCTCACTCTCTCAGACAGTGCAGTAGAACAGATTAAAGCCACATCGGTGAATCTTGC
TTTCCCGACATTGCAGTTAAAAGAATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCA
GTGGAACAGATTAAAGCCACAACGGTGAATCTTGTCTCCCTAACATTGCAGTTGAAAAGACTAAA
GCCACAGCAGCGAATGTTACTTCCCTGGCAATGCAGTGAAG
Found at i:40063252 original size:16 final size:15
Alignment explanation
Indices: 40063219--40063256 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
40063209 GGATTTTAAA
40063219 TTTTTAAAAATAGTT
1 TTTTTAAAAATAGTT
40063234 TTTTTAAAATATA-TAT
1 TTTTTAAAA-ATAGT-T
40063250 TTTTTAA
1 TTTTTAA
40063257 TTTTTAGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTAAAAATAGTT
Found at i:40063332 original size:61 final size:61
Alignment explanation
Indices: 40063267--40063501 Score: 185
Period size: 61 Copynumber: 3.9 Consensus size: 61
40063257 TTTTTAGTGG
* * *
40063267 TAGAACTAAATTGATAGATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAAT
1 TAGAAATAAAGTGATAAATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAAT
** * * * * ***** * * **
40063328 TAGAAATAAAGTGATAAAAATAGT--TTTTTAAAATATATATTT-TTTAA-TTTTTAGT-GG
1 TAGAAATAAAGTGATAAATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTA-TAAT
* * *
40063385 TAGAACTAAATTGATAGATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAAT
1 TAGAAATAAAGTGATAAATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAAT
** ** *
40063446 TAGAAATAAAGTGATAAATTTT-TAAACATTGAGGGTGAAATTTGTTAAATTTTTTA
1 TAGAAATAAAGTGATAAATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTA
40063502 GATTTAGGAT
Statistics
Matches: 124, Mismatches: 44, Indels: 13
0.69 0.24 0.07
Matches are distributed among these distances:
57 24 0.19
58 5 0.04
59 18 0.15
60 34 0.27
61 43 0.35
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (61 bp):
TAGAAATAAAGTGATAAATTTTGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAAT
Found at i:40063432 original size:118 final size:119
Alignment explanation
Indices: 40063223--40063463 Score: 475
Period size: 118 Copynumber: 2.0 Consensus size: 119
40063213 TTTAAATTTT
40063223 TAAAAATAGTTTTTTTAAAATATATATTTTTTAATTTTTAGTGGTAGAACTAAATTGATAGATTT
1 TAAAAATAGTTTTTTTAAAATATATATTTTTTAATTTTTAGTGGTAGAACTAAATTGATAGATTT
40063288 TGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAATTAGAAATAAAGTGA
66 TGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAATTAGAAATAAAGTGA
40063342 TAAAAATAG-TTTTTTAAAATATATATTTTTTAATTTTTAGTGGTAGAACTAAATTGATAGATTT
1 TAAAAATAGTTTTTTTAAAATATATATTTTTTAATTTTTAGTGGTAGAACTAAATTGATAGATTT
40063406 TGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAATTAGAAATAAAGTGA
66 TGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAATTAGAAATAAAGTGA
40063460 TAAA
1 TAAA
40063464 TTTTTAAACA
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 113 0.93
119 9 0.07
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (119 bp):
TAAAAATAGTTTTTTTAAAATATATATTTTTTAATTTTTAGTGGTAGAACTAAATTGATAGATTT
TGTAAATGTTGAGGGCCAAATTTATTAAATTTTTTATAATTAGAAATAAAGTGA
Found at i:40066115 original size:17 final size:18
Alignment explanation
Indices: 40066080--40066133 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 18
40066070 GTTATTGTTG
*
40066080 TTTATTATATTACTAATTTT
1 TTTATTAT-TTA-TAATATT
40066100 TTTA-T-TTTAT-ATATT
1 TTTATTATTTATAATATT
40066115 TTTATTATTTATAATATT
1 TTTATTATTTATAATATT
40066133 T
1 T
40066134 ATCACGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 8 0.27
16 2 0.07
17 8 0.27
18 7 0.23
19 1 0.03
20 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATTTATAATATT
Found at i:40066354 original size:21 final size:20
Alignment explanation
Indices: 40066324--40066368 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
40066314 AAGAAAAGGA
40066324 AAATTAATTACATTA-TTTT
1 AAATTAATTACATTAGTTTT
*
40066343 GAAATTATATTACTTTAGTTTT
1 -AAATTA-ATTACATTAGTTTT
40066365 AAAT
1 AAAT
40066369 GGGAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 12 0.55
22 4 0.18
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
AAATTAATTACATTAGTTTT
Found at i:40075692 original size:21 final size:21
Alignment explanation
Indices: 40075659--40075710 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
40075649 AGAAAATGGC
*
40075659 AGCAACAAAATGGTTGAAAAAT
1 AGCAAC-AAATGGGTGAAAAAT
*
40075681 AGCAACAAATGGGTGGAAAAT
1 AGCAACAAATGGGTGAAAAAT
* *
40075702 GGCAGCAAA
1 AGCAACAAA
40075711 GAGGGCCGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.13
Consensus pattern (21 bp):
AGCAACAAATGGGTGAAAAAT
Found at i:40075699 original size:22 final size:22
Alignment explanation
Indices: 40075659--40075700 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40075649 AGAAAATGGC
*
40075659 AGCAACAAAATGGTTGAAAAAT
1 AGCAACAAAATGGTGGAAAAAT
40075681 AGCAAC-AAATGGGTGGAAAA
1 AGCAACAAAAT-GGTGGAAAA
40075701 TGGCAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.10, G:0.24, T:0.14
Consensus pattern (22 bp):
AGCAACAAAATGGTGGAAAAAT
Found at i:40075967 original size:20 final size:21
Alignment explanation
Indices: 40075926--40075967 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40075916 AAAAAGTAAT
*
40075926 AAAGTGAAGAGAAAACGGAAA
1 AAAGTGAAAAGAAAACGGAAA
*
40075947 AAAGTGAAAAGAATA-GGAAA
1 AAAGTGAAAAGAAAACGGAAA
40075967 A
1 A
40075968 GAAAACAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.64, C:0.02, G:0.26, T:0.07
Consensus pattern (21 bp):
AAAGTGAAAAGAAAACGGAAA
Done.